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1.	Beal, Jacob, et al. (author) Robust estimation of bacterial cell count from optical density 2020 In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1 Journal article (peer-reviewed)abstract Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
2.	2019 Journal article (peer-reviewed)
3.	Abelev, Betty, et al. (author) Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV 2013 In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41 Journal article (peer-reviewed)abstract Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
4.	Abelev, Betty, et al. (author) Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV 2012 In: Journal of High Energy Physics. - 1029-8479. ; :11 Journal article (peer-reviewed)abstract The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
5.	Abazajian, Kevork, et al. (author) CMB-S4 : Forecasting Constraints on Primordial Gravitational Waves 2022 In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 926:1 Journal article (peer-reviewed)abstract CMB-S4—the next-generation ground-based cosmic microwave background (CMB) experiment—is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the universe. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semianalytic projection tool, targeted explicitly toward optimizing constraints on the tensor-to-scalar ratio, r, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2–3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments, given a desired scientific goal. To form a closed-loop process, we couple this semianalytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for r > 0.003 at greater than 5σ, or in the absence of a detection, of reaching an upper limit of r < 0.001 at 95% CL.
6.	Abelev, Betty, et al. (author) Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC 2012 In: Journal of High Energy Physics. - 1029-8479. ; :7 Journal article (peer-reviewed)abstract We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
7.	Jansen, Willemijn J, et al. (author) Prevalence Estimates of Amyloid Abnormality Across the Alzheimer Disease Clinical Spectrum. 2022 In: JAMA neurology. - : American Medical Association (AMA). - 2168-6157 .- 2168-6149. ; 79:3, s. 228-243 Journal article (peer-reviewed)abstract One characteristic histopathological event in Alzheimer disease (AD) is cerebral amyloid aggregation, which can be detected by biomarkers in cerebrospinal fluid (CSF) and on positron emission tomography (PET) scans. Prevalence estimates of amyloid pathology are important for health care planning and clinical trial design.To estimate the prevalence of amyloid abnormality in persons with normal cognition, subjective cognitive decline, mild cognitive impairment, or clinical AD dementia and to examine the potential implications of cutoff methods, biomarker modality (CSF or PET), age, sex, APOE genotype, educational level, geographical region, and dementia severity for these estimates.This cross-sectional, individual-participant pooled study included participants from 85 Amyloid Biomarker Study cohorts. Data collection was performed from January 1, 2013, to December 31, 2020. Participants had normal cognition, subjective cognitive decline, mild cognitive impairment, or clinical AD dementia. Normal cognition and subjective cognitive decline were defined by normal scores on cognitive tests, with the presence of cognitive complaints defining subjective cognitive decline. Mild cognitive impairment and clinical AD dementia were diagnosed according to published criteria.Alzheimer disease biomarkers detected on PET or in CSF.Amyloid measurements were dichotomized as normal or abnormal using cohort-provided cutoffs for CSF or PET or by visual reading for PET. Adjusted data-driven cutoffs for abnormal amyloid were calculated using gaussian mixture modeling. Prevalence of amyloid abnormality was estimated according to age, sex, cognitive status, biomarker modality, APOE carrier status, educational level, geographical location, and dementia severity using generalized estimating equations.Among the 19097 participants (mean [SD] age, 69.1 [9.8] years; 10148 women [53.1%]) included, 10139 (53.1%) underwent an amyloid PET scan and 8958 (46.9%) had an amyloid CSF measurement. Using cohort-provided cutoffs, amyloid abnormality prevalences were similar to 2015 estimates for individuals without dementia and were similar across PET- and CSF-based estimates (24%; 95% CI, 21%-28%) in participants with normal cognition, 27% (95% CI, 21%-33%) in participants with subjective cognitive decline, and 51% (95% CI, 46%-56%) in participants with mild cognitive impairment, whereas for clinical AD dementia the estimates were higher for PET than CSF (87% vs 79%; mean difference, 8%; 95% CI, 0%-16%; P=.04). Gaussian mixture modeling-based cutoffs for amyloid measures on PET scans were similar to cohort-provided cutoffs and were not adjusted. Adjusted CSF cutoffs resulted in a 10% higher amyloid abnormality prevalence than PET-based estimates in persons with normal cognition (mean difference, 9%; 95% CI, 3%-15%; P=.004), subjective cognitive decline (9%; 95% CI, 3%-15%; P=.005), and mild cognitive impairment (10%; 95% CI, 3%-17%; P=.004), whereas the estimates were comparable in persons with clinical AD dementia (mean difference, 4%; 95% CI, -2% to 9%; P=.18).This study found that CSF-based estimates using adjusted data-driven cutoffs were up to 10% higher than PET-based estimates in people without dementia, whereas the results were similar among people with dementia. This finding suggests that preclinical and prodromal AD may be more prevalent than previously estimated, which has important implications for clinical trial recruitment strategies and health care planning policies.
8.	Zichi, Julien, et al. (author) NbxTi1-xN low timing jitter single-photon detectors with unity internal detection efficiency at 1550 nm Other publication (other academic/artistic)abstract The requirements in quantum optics experiments for high single photon detectionefficiency, low timing jitter, low dark count rate and short dead time have been fulfilled withthe development of superconducting nanowire single photon detectors. Although they offer adetection efficiency above 90%, achieving a high time resolution in devices made ofamorphous materials is a challenge, particularly at temperatures above 0.8 K. Devices madefrom niobium nitride and niobium titanium nitride allow to reach the best timing jitter, but inturn have stronger requirements in terms of film quality to achieve a high efficiency. Here wetake advantage of the flexibility of reactive co-sputter deposition to tailor the composition ofNbxTi1-xN superconducting films, and show that a Nb fraction of x = 0.62 allows for thefabrication of detectors from films as thick as 9 nm and covering an active area of 20 μm,with a wide detection saturation plateau at telecom wavelengths and in particular at 1550 nm.This is a signature of an internal detection efficiency saturation, achieved while maintainingthe high time resolution associated with NbTiN and operation at 2.5K. With our optimizedrecipe, we reliably fabricated detectors with high critical current densities reaching asaturation plateau at 1550 nm with 80% system detection efficiency, and with a FWHMtiming jitter as low as 19.47 ps.
9.	Abercrombie, Daniel, et al. (author) Dark Matter benchmark models for early LHC Run-2 Searches : Report of the ATLAS/CMS Dark Matter Forum 2020 In: Physics of the Dark Universe. - : Elsevier BV. - 2212-6864. ; 27 Journal article (peer-reviewed)abstract This document is the final report of the ATLAS-CMS Dark Matter Forum, a forum organized by the ATLAS and CMS collaborations with the participation of experts on theories of Dark Matter, to select a minimal basis set of dark matter simplified models that should support the design of the early LHC Run-2 searches. A prioritized, compact set of benchmark models is proposed, accompanied by studies of the parameter space of these models and a repository of generator implementations. This report also addresses how to apply the Effective Field Theory formalism for collider searches and present the results of such interpretations.
10.	Chang, Jin, et al. (author) Efficient mid-infrared single-photon detection using superconducting NbTiN nanowires with high time resolution in a Gifford-McMahon cryocooler 2022 In: Photonics Research. - : Optica Publishing Group. - 2327-9125. ; 10:4, s. 1063-1070 Journal article (peer-reviewed)abstract Shortly after their inception, superconducting nanowire single-photon detectors (SNSPDs) became the leading quantum light detection technology. With the capability of detecting single-photons with near-unity efficiency, high time resolution, low dark count rate, and fast recovery time, SNSPDs outperform conventional single-photon detection techniques. However, detecting lower energy single photons (<0.8 eV) with high efficiency and low timing jitter has remained a challenge. To achieve unity internal efficiency at mid-infrared wavelengths, previous works used amorphous superconducting materials with low energy gaps at the expense of reduced time resolution (close to a nanosecond), and by operating them in complex milliKelvin (mK) dilution refrigerators. In this work, we provide an alternative approach with SNSPDs fabricated from 5 to 9.5 nm thick NbTiN superconducting films and devices operated in conventional Gifford-McMahon cryocoolers. By optimizing the superconducting film deposition process, film thickness, and nanowire design, our fiber-coupled devices achieved >70% system detection efficiency (SDE) at 2 mu m and sub-15 ps timing jitter. Furthermore, detectors from the same batch demonstrated unity internal detection efficiency at 3 mu m and 80% internal efficiency at 4 mu m, paving the road for an efficient mid-infrared single-photon detection technology with unparalleled time resolution and without mK cooling requirements. We also systematically studied the dark count rates (DCRs) of our detectors coupled to different types of mid-infrared optical fibers and blackbody radiation filters. This offers insight into the trade-off between bandwidth and DCRs for mid-infrared SNSPDs. To conclude, this paper significantly extends the working wavelength range for SNSPDs made from polycrystalline NbTiN to 1.5-4 mu m, and we expect quantum optics experiments and applications in the mid-infrared range to benefit from this far-reaching technology. Published by Chinese Laser Press under the terms of the Creative Commons Attribution 4.0 License.
11.	Chang, Jin, et al. (author) Multimode-fiber-coupled superconducting nanowire single-photon detectors with high detection efficiency and time resolution 2019 In: Applied Optics. - : Optical Society of America. - 1559-128X .- 2155-3165. ; 58:36, s. 9803-9807 Journal article (peer-reviewed)abstract In the past decade, superconducting nanowire single-photon detectors (SNSPDs) have gradually become an indispensable part of any demanding quantum optics experiment. Until now, most SNSPDs have been coupled to single-mode fibers. SNSPDs coupled to multimode fibers have shown promising efficiencies but have yet to achieve high time resolution. For a number of applications ranging from quantum nano-photonics to bio-optics, high efficiency and high time resolution are desired at the same time. In this paper, we demonstrate the role of polarization on the efficiency of multimode-fiber-coupled detectors and fabricated high-performance 20 mu m, 25 mu m, and 50 mu m diameter detectors targeted for visible, near-infrared, and telecom wavelengths. A custom-built setup was used to simulate realistic experiments with randomized modes in the fiber. We achieved over 80% system efficiency and <20 ps timing jitter for 20 mu m SNSPDs. Also, we realized 70% system efficiency and <20 ps timing jitter for 50 mu m SNSPDs. The high-efficiency multimode-fiber-coupled SNSPDs with unparalleled time resolution will benefit various quantum optics experiments and applications in the future.
12.	Chang, Lantian, et al. (author) Chip based common-path optical coherence tomography system with an on-chip microlens and multi-reference suppression algorithm 2016 In: Optics Express. - : Optical Society of America. - 1094-4087. ; 24:12, s. 12635-12650 Journal article (peer-reviewed)abstract We demonstrate an integrated optical probe including an on-chip microlens for a common-path swept-source optical coherence tomography system. This common-path design uses the end facet of the silicon oxynitride waveguide as the reference plane, thus eliminating the need of a space-consuming and dispersive on-chip loop reference arm, thereby obviating the need for dispersion compensation. The on-chip micro-ball lens eliminates the need of external optical elements for coupling the light between the chip and the sample. The use of this lens leads to a signal enhancement up to 37 dB compared to the chip without a lens. The light source, the common-path arm and the detector are connected by a symmetric Y junction having a wavelength independent splitting ratio (50/50) over a much larger bandwidth than can be obtained with a directional coupler. The signal-to-noise ratio of the system was measured to be 71 dB with 2.6 mW of power on a mirror sample at a distance of 0.3 mm from the waveguide end facet. Cross-sectional OCT images of a layered optical phantom sample are demonstrated with our system. A method, based on an extended Fourier-domain OCT model, for suppressing ghost images caused by additional parasitic reference planes is experimentally demonstrated.
13.	Chang, Lantian, et al. (author) Waveguide-coupled micro-ball lens array suitable for mass fabrication 2015 In: Optics Express. - : Optica Publishing Group. - 1094-4087. ; 23:17, s. 22414-22423 Journal article (peer-reviewed)abstract We demonstrate a fabrication procedure for the direct integration of micro-ball lenses on planar integrated optical channel waveguide chips with the aim to reduce the divergence of light that arises from the waveguide in both horizontal and vertical directions. Fabrication of the lenses is based on photoresist reflow which is a procedure that allows for the use of photolithography for careful alignment of the lenses with respect to the waveguides and enables mass production. We present in detail the design and fabrication procedures. Optical characterization of the fabricated micro-ball lenses demonstrates a good performance in terms of beam-size reduction and beam shape. The beam half divergence angle of 1544 nm light is reduced from 12.4 degrees to 1.85 degrees.
14.	Chang, Shu-Chieh, et al. (author) The Gram-positive bacterium Romboutsia ilealis harbors a polysaccharide synthase that can produce (1,3;1,4)-β-D-glucans 2023 In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1 Journal article (peer-reviewed)abstract (1,3;1,4)-β-D-Glucans are widely distributed in the cell walls of grasses (family Poaceae) and closely related families, as well as some other vascular plants. Additionally, they have been found in other organisms, including fungi, lichens, brown algae, charophycean green algae, and the bacterium Sinorhizobium meliloti. Only three members of the Cellulose Synthase-Like (CSL) genes in the families CSLF, CSLH, and CSLJ are implicated in (1,3;1,4)-β-D-glucan biosynthesis in grasses. Little is known about the enzymes responsible for synthesizing (1,3;1,4)-β-D-glucans outside the grasses. In the present study, we report the presence of (1,3;1,4)-β-D-glucans in the exopolysaccharides of the Gram-positive bacterium Romboutsia ilealis CRIBT. We also report that RiGT2 is the candidate gene of R. ilealis that encodes (1,3;1,4)-β-D-glucan synthase. RiGT2 has conserved glycosyltransferase family 2 (GT2) motifs, including D, D, D, QXXRW, and a C-terminal PilZ domain that resembles the C-terminal domain of bacteria cellulose synthase, BcsA. Using a direct gain-of-function approach, we insert RiGT2 into Saccharomyces cerevisiae, and (1,3;1,4)-β-D-glucans are produced with structures similar to those of the (1,3;1,4)-β-D-glucans of the lichen Cetraria islandica. Phylogenetic analysis reveals that putative (1,3;1,4)-β-D-glucan synthase candidate genes in several other bacterial species support the finding of (1,3;1,4)-β-D-glucans in these species.
15.	Chiang, Cho-Han, et al. (author) Performance of the European Society of Cardiology 0/1-Hour, 0/2-Hour, and 0/3-Hour Algorithms for Rapid Triage of Acute Myocardial Infarction : An International Collaborative Meta-analysis 2022 In: Annals of Internal Medicine. - 0003-4819. ; 175:1, s. 101-113 Research review (peer-reviewed)abstract BACKGROUND: The 2020 European Society of Cardiology (ESC) guidelines recommend using the 0/1-hour and 0/2-hour algorithms over the 0/3-hour algorithm as the first and second choices of high-sensitivity cardiac troponin (hs-cTn)-based strategies for triage of patients with suspected acute myocardial infarction (AMI).PURPOSE: To evaluate the diagnostic accuracies of the ESC 0/1-hour, 0/2-hour, and 0/3-hour algorithms.DATA SOURCES: PubMed, Embase, Cochrane Central Register of Controlled Trials, Web of Science, and Scopus from 1 January 2011 to 31 December 2020. (PROSPERO: CRD42020216479).STUDY SELECTION: Prospective studies that evaluated the ESC 0/1-hour, 0/2-hour, or 0/3-hour algorithms in adult patients presenting with suspected AMI.DATA EXTRACTION: The primary outcome was index AMI. Twenty unique cohorts were identified. Primary data were obtained from investigators of 16 cohorts and aggregate data were extracted from 4 cohorts. Two independent authors assessed each study for methodological quality.DATA SYNTHESIS: A total of 32 studies (20 cohorts) with 30 066 patients were analyzed. The 0/1-hour algorithm had a pooled sensitivity of 99.1% (95% CI, 98.5% to 99.5%) and negative predictive value (NPV) of 99.8% (CI, 99.6% to 99.9%) for ruling out AMI. The 0/2-hour algorithm had a pooled sensitivity of 98.6% (CI, 97.2% to 99.3%) and NPV of 99.6% (CI, 99.4% to 99.8%). The 0/3-hour algorithm had a pooled sensitivity of 93.7% (CI, 87.4% to 97.0%) and NPV of 98.7% (CI, 97.7% to 99.3%). Sensitivity of the 0/3-hour algorithm was attenuated in studies that did not use clinical criteria (GRACE score <140 and pain-free) compared with studies that used clinical criteria (90.2% [CI, 82.9 to 94.6] vs. 98.4% [CI, 88.6 to 99.8]). All 3 algorithms had similar specificities and positive predictive values for ruling in AMI, but heterogeneity across studies was substantial. Diagnostic performance was similar across the hs-cTnT (Elecsys; Roche), hs-cTnI (Architect; Abbott), and hs-cTnI (Centaur/Atellica; Siemens) assays.LIMITATION: Diagnostic accuracy, inclusion and exclusion criteria, and cardiac troponin sampling time varied among studies.CONCLUSION: The ESC 0/1-hour and 0/2-hour algorithms have higher sensitivities and NPVs than the 0/3-hour algorithm for index AMI.PRIMARY FUNDING SOURCE: National Taiwan University Hospital.
16.	Do, Ron, et al. (author) Common variants associated with plasma triglycerides and risk for coronary artery disease 2013 In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:11, s. 1345- Journal article (peer-reviewed)abstract Triglycerides are transported in plasma by specific triglyceride-rich lipoproteins; in epidemiological studies, increased triglyceride levels correlate with higher risk for coronary artery disease (CAD). However, it is unclear whether this association reflects causal processes. We used 185 common variants recently mapped for plasma lipids (P < 5 x 10(-8) for each) to examine the role of triglycerides in risk for CAD. First, we highlight loci associated with both low-density lipoprotein cholesterol (LDL-C) and triglyceride levels, and we show that the direction and magnitude of the associations with both traits are factors in determining CAD risk. Second, we consider loci with only a strong association with triglycerides and show that these loci are also associated with CAD. Finally, in a model accounting for effects on LDL-C and/or high-density lipoprotein cholesterol (HDL-C) levels, the strength of a polymorphism's effect on triglyceride levels is correlated with the magnitude of its effect on CAD risk. These results suggest that triglyceride-rich lipoproteins causally influence risk for CAD.
17.	Esmaeil Zadeh, Iman, et al. (author) Superconducting nanowire single-photon detectors : A perspective on evolution, state-of-the-art, future developments, and applications 2021 In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 118:19 Journal article (peer-reviewed)abstract Two decades after their demonstration, superconducting nanowire single-photon detectors (SNSPDs) have become indispensable tools for quantum photonics as well as for many other photon-starved applications. This invention has not only led to a burgeoning academic field with a wide range of applications but also triggered industrial efforts. Current state-of-the-art SNSPDs combine near-unity detection efficiency over a wide spectral range, low dark counts, short dead times, and picosecond time resolution. The present perspective discusses important milestones and progress of SNSPDs research, emerging applications, and future challenges and gives an outlook on technological developments required to bring SNSPDs to the next level: a photon-counting, fast time-tagging imaging, and multi-pixel technology that is also compatible with quantum photonic integrated circuits.
18.	Frazier-Wood, Alexis C., et al. (author) Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses 2016 In: Nature Genetics. - : Nature Research (part of Springer Nature). - 1061-4036 .- 1546-1718. ; 48, s. 624- Journal article (peer-reviewed)abstract Very few genetic variants have been associated with depression and neuroticism, likely because of limitations on sample size in previous studies. Subjective well-being, a phenotype that is genetically correlated with both of these traits, has not yet been studied with genome-wide data. We conducted genome-wide association studies of three phenotypes: subjective well-being (n = 298,420), depressive symptoms (n = 161,460), and neuroticism (n = 170,911). We identify 3 variants associated with subjective well-being, 2 variants associated with depressive symptoms, and 11 variants associated with neuroticism, including 2 inversion polymorphisms. The two loci associated with depressive symptoms replicate in an independent depression sample. Joint analyses that exploit the high genetic correlations between the phenotypes (vertical bar(p) over cap vertical bar approximate to 0.8) strengthen the overall credibility of the findings and allow us to identify additional variants. Across our phenotypes, loci regulating expression in central nervous system and adrenal or pancreas tissues are strongly enriched for association.
19.	Ganesh, Santhi K., et al. (author) Loci influencing blood pressure identified using a cardiovascular gene-centric array 2013 In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 22:8, s. 1663-1678 Journal article (peer-reviewed)abstract Blood pressure (BP) is a heritable determinant of risk for cardiovascular disease (CVD). To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP) and pulse pressure (PP), we genotyped 50 000 single-nucleotide polymorphisms (SNPs) that capture variation in 2100 candidate genes for cardiovascular phenotypes in 61 619 individuals of European ancestry from cohort studies in the USA and Europe. We identified novel associations between rs347591 and SBP (chromosome 3p25.3, in an intron of HRH1) and between rs2169137 and DBP (chromosome1q32.1 in an intron of MDM4) and between rs2014408 and SBP (chromosome 11p15 in an intron of SOX6), previously reported to be associated with MAP. We also confirmed 10 previously known loci associated with SBP, DBP, MAP or PP (ADRB1, ATP2B1, SH2B3/ATXN2, CSK, CYP17A1, FURIN, HFE, LSP1, MTHFR, SOX6) at array-wide significance (P 2.4 10(6)). We then replicated these associations in an independent set of 65 886 individuals of European ancestry. The findings from expression QTL (eQTL) analysis showed associations of SNPs in the MDM4 region with MDM4 expression. We did not find any evidence of association of the two novel SNPs in MDM4 and HRH1 with sequelae of high BP including coronary artery disease (CAD), left ventricular hypertrophy (LVH) or stroke. In summary, we identified two novel loci associated with BP and confirmed multiple previously reported associations. Our findings extend our understanding of genes involved in BP regulation, some of which may eventually provide new targets for therapeutic intervention.
20.	Gourgues, Ronan, et al. (author) Superconducting nanowire single photon detectors operating at temperature from 4 to 7 K 2019 In: Optics Express. - : OPTICAL SOC AMER. - 1094-4087. ; 27:17, s. 24601-24609 Journal article (peer-reviewed)abstract We experimentally investigate the performance of NbTiN superconducting nanowire single photon detectors above the base temperature of a conventional Gifford-McMahon cryocooler (2.5 K). By tailoring design and thickness (8-13 nm) of the detectors, high performance, high operating temperature, single-photon detection from the visible to telecom wavelengths are demonstrated. At 4.3 K, a detection efficiency of 82 % at 785 nm wavelength and a timing jitter of 30 +/- 0.3 ps are achieved. In addition, for 1550 nm and similar operating temperature we measured a detection efficiency as high as 64 %. Finally, we show that at temperatures up to 7 K, unity internal efficiency is maintained for the visible spectrum. Our work is particularly important to allow for the large scale implementation of superconducting single photon detectors in combination with heat sources such as free-space optical windows, cryogenic electronics, microwave sources and active optical components for complex quantum optical experiments and bio-imaging.
21.	LaRue, Jerry, et al. (author) Symmetry-resolved CO desorption and oxidation dynamics on O/Ru(0001) probed at the C K-edge by ultrafast x-ray spectroscopy 2022 In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 157:16 Journal article (peer-reviewed)abstract We report on carbon monoxide desorption and oxidation induced by 400 nm femtosecond laser excitation on the O/Ru(0001) surface probed by time-resolved x-ray absorption spectroscopy (TR-XAS) at the carbon K-edge. The experiments were performed under constant background pressures of CO (6 × 10−8 Torr) and O2 (3 × 10−8 Torr). Under these conditions, we detect two transient CO species with narrow 2π* peaks, suggesting little 2π* interaction with the surface. Based on polarization measurements, we find that these two species have opposing orientations: (1) CO favoring a more perpendicular orientation and (2) CO favoring a more parallel orientation with respect to the surface. We also directly detect gas-phase CO2 using a mass spectrometer and observe weak signatures of bent adsorbed CO2 at slightly higher x-ray energies than the 2π* region. These results are compared to previously reported TR-XAS results at the O K-edge, where the CO background pressure was three times lower (2 × 10−8 Torr) while maintaining the same O2 pressure. At the lower CO pressure, in the CO 2π* region, we observed adsorbed CO and a distribution of OC–O bond lengths close to the CO oxidation transition state, with little indication of gas-like CO. The shift toward “gas-like” CO species may be explained by the higher CO exposure, which blocks O adsorption, decreasing O coverage and increasing CO coverage. These effects decrease the CO desorption barrier through dipole–dipole interaction while simultaneously increasing the CO oxidation barrier.
22.	McKay, James D., et al. (author) A Genome-Wide Association Study of Upper Aerodigestive Tract Cancers Conducted within the INHANCE Consortium 2011 In: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 7:3 Journal article (peer-reviewed)abstract Genome-wide association studies (GWAS) have been successful in identifying common genetic variation involved in susceptibility to etiologically complex disease. We conducted a GWAS to identify common genetic variation involved in susceptibility to upper aero-digestive tract (UADT) cancers. Genome-wide genotyping was carried out using the Illumina HumanHap300 beadchips in 2,091 UADT cancer cases and 3,513 controls from two large European multi-centre UADT cancer studies, as well as 4,821 generic controls. The 19 top-ranked variants were investigated further in an additional 6,514 UADT cancer cases and 7,892 controls of European descent from an additional 13 UADT cancer studies participating in the INHANCE consortium. Five common variants presented evidence for significant association in the combined analysis (p <= 5 x 10(-7)). Two novel variants were identified, a 4q21 variant (rs1494961, p = 1 x 10(-8)) located near DNA repair related genes HEL308 and FAM175A (or Abraxas) and a 12q24 variant (rs4767364, p = 2 x 10(-8)) located in an extended linkage disequilibrium region that contains multiple genes including the aldehyde dehydrogenase 2 (ALDH2) gene. Three remaining variants are located in the ADH gene cluster and were identified previously in a candidate gene study involving some of these samples. The association between these three variants and UADT cancers was independently replicated in 5,092 UADT cancer cases and 6,794 controls non-overlapping samples presented here (rs1573496-ADH7, p = 5 x 10(-8); rs1229984-ADH1B, p = 7 x 10(-9); and rs698-ADH1C, p = 0.02). These results implicate two variants at 4q21 and 12q24 and further highlight three ADH variants in UADT cancer susceptibility.
23.	Nayagam, Jeremy S, et al. (author) Maternal liver-related symptoms during pregnancy in primary sclerosing cholangitis. 2023 In: JHEP reports : innovation in hepatology. - 2589-5559. ; 6:1 Journal article (peer-reviewed)abstract Although worsening liver-related symptoms during pregnancy can occur in primary sclerosing cholangitis (PSC), there are insufficient data to effectively counsel patients on their pre-conception risk and no clear recommendations on monitoring and management during pregnancy. We aimed to describe maternal liver-related symptoms in pregnancy, both before and after PSC diagnosis, and explore factors associated with worsening symptoms and liver-related outcomes.We conducted a multicentre retrospective observational study of females with PSC and known pregnancy with live birth, via the International PSC Study Group. We included 450 patients from 12 European centres. Data included clinical variables, liver-related symptoms (pruritus and/or cholangitis) during pregnancy, and liver biochemistry. A composite primary endpoint of transplant-free survival from time of PSC diagnosis was used.There were 266 pregnancies in 178 patients following PSC diagnosis. Worsening liver-related symptoms were reported in 66/228 (28.9%) pregnancies; they had a reduced transplant-free survival (p= 0.03), which retained significance on multivariate analysis (hazard ratio 3.02, 95% CI 1.24-7.35; p= 0.02).Abnormal biochemistry and/or liver-related symptoms (pruritus and/or cholangitis) were noted during pregnancy before PSC diagnosis in 21/167 (12.6%) patients. They had a reduced transplant-free survival from pregnancy (p= 0.01), which did not retain significance in a multivariable model (hazard ratio 1.10, 95% CI 0.43-2.85; p= 0.84).Liver-related symptoms are frequently encountered during pregnancies before the diagnosis of PSC, and pregnancy may expose the pre-clinical phase of PSC in some patients. Worsening liver-related symptoms were seen in a third of our cohort with known PSC during pregnancy; and this subgroup had a poorer prognosis, which may be related to more advanced liver disease at time of pregnancy and/or a more severe disease phenotype.Patients with PSC can develop worsening of their liver-related symptoms during pregnancy; however, risk factors for this and the long-term implications are not known. We identified that there is a significant risk of these symptoms in pregnancy, both before and after PSC has been diagnosed, particularly in patients with elevated alkaline phosphatase. Furthermore, our findings suggest that worsening symptoms during pregnancy may be associated with adverse long-term clinical outcomes of liver transplantation and death in patients with known PSC. This may be related to the presence of more advanced liver disease at time of pregnancy. This information can be used to counsel patients with PSC before conception and identify patients who need close follow-up after delivery.
24.	Schreck, Simon, et al. (author) Atom-Specific Probing of Electron Dynamics in an Atomic Adsorbate by Time-Resolved X-Ray Spectroscopy 2022 In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 129:27 Journal article (peer-reviewed)abstract The electronic excitation occurring on adsorbates at ultrafast timescales from optical lasers that initiate surface chemical reactions is still an open question. Here, we report the ultrafast temporal evolution of x-ray absorption spectroscopy (XAS) and x-ray emission spectroscopy (XES) of a simple well-known adsorbate prototype system, namely carbon (C) atoms adsorbed on a nickel [Ni(100)] surface, following intense laser optical pumping at 400 nm. We observe ultrafast (∼100 fs) changes in both XAS and XES showing clear signatures of the formation of a hot electron-hole pair distribution on the adsorbate. This is followed by slower changes on a few picoseconds timescale, shown to be consistent with thermalization of the complete C/Ni system. Density functional theory spectrum simulations support this interpretation.
25.	Tragante, Vinicius, et al. (author) Gene-centric Meta-analysis in 87,736 Individuals of European Ancestry Identifies Multiple Blood-Pressure-Related Loci. 2014 In: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297. ; 94:3, s. 349-360 Journal article (peer-reviewed)abstract Blood pressure (BP) is a heritable risk factor for cardiovascular disease. To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP), we genotyped ∼50,000 SNPs in up to 87,736 individuals of European ancestry and combined these in a meta-analysis. We replicated findings in an independent set of 68,368 individuals of European ancestry. Our analyses identified 11 previously undescribed associations in independent loci containing 31 genes including PDE1A, HLA-DQB1, CDK6, PRKAG2, VCL, H19, NUCB2, RELA, HOXC@ complex, FBN1, and NFAT5 at the Bonferroni-corrected array-wide significance threshold (p < 6 × 10(-7)) and confirmed 27 previously reported associations. Bioinformatic analysis of the 11 loci provided support for a putative role in hypertension of several genes, such as CDK6 and NUCB2. Analysis of potential pharmacological targets in databases of small molecules showed that ten of the genes are predicted to be a target for small molecules. In summary, we identified previously unknown loci associated with BP. Our findings extend our understanding of genes involved in BP regulation, which may provide new targets for therapeutic intervention or drug response stratification.
26.	Watson, Hunna J., et al. (author) Common Genetic Variation and Age of Onset of Anorexia Nervosa 2022 In: BIOLOGICAL PSYCHIATRY: GLOBAL OPEN SCIENCE. - : Elsevier BV. - 2667-1743. ; 2:4, s. 368-378 Journal article (peer-reviewed)abstract BACKGROUND: Genetics and biology may influence the age of onset of anorexia nervosa (AN). The aims of this study were to determine whether common genetic variation contributes to age of onset of AN and to investigate the genetic associations between age of onset of AN and age at menarche.METHODS: A secondary analysis of the Psychiatric Genomics Consortium genome-wide association study (GWAS) of AN was performed, which included 9335 cases and 31,981 screened controls, all from European ancestries. We conducted GWASs of age of onset, early-onset AN (,13 years), and typical-onset AN, and genetic correlation, genetic risk score, and Mendelian randomization analyses.RESULTS: Two loci were genome-wide significant in the typical-onset AN GWAS. Heritability estimates (single nucleotide polymorphism-h2) were 0.01-0.04 for age of onset, 0.16-0.25 for early-onset AN, and 0.17-0.25 for typical-onset AN. Early-and typical-onset AN showed distinct genetic correlation patterns with putative risk factors for AN. Specifically, early-onset AN was significantly genetically correlated with younger age at menarche, and typical-onset AN was significantly negatively genetically correlated with anthropometric traits. Genetic risk scores for age of onset and early-onset AN estimated from independent GWASs significantly predicted age of onset. Mendelian randomization analysis suggested a causal link between younger age at menarche and early -onset AN.CONCLUSIONS: Our results provide evidence consistent with a common variant genetic basis for age of onset and implicate biological pathways regulating menarche and reproduction.
27.	Willer, Cristen J., et al. (author) Discovery and refinement of loci associated with lipid levels 2013 In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:11, s. 1274-1283 Journal article (peer-reviewed)abstract Levels of low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides and total cholesterol are heritable, modifiable risk factors for coronary artery disease. To identify new loci and refine known loci influencing these lipids, we examined 188,577 individuals using genome-wide and custom genotyping arrays. We identify and annotate 157 loci associated with lipid levels at P < 5 x 10(-8), including 62 loci not previously associated with lipid levels in humans. Using dense genotyping in individuals of European, East Asian, South Asian and African ancestry, we narrow association signals in 12 loci. We find that loci associated with blood lipid levels are often associated with cardiovascular and metabolic traits, including coronary artery disease, type 2 diabetes, blood pressure, waist-hip ratio and body mass index. Our results demonstrate the value of using genetic data from individuals of diverse ancestry and provide insights into the biological mechanisms regulating blood lipids to guide future genetic, biological and therapeutic research.
28.	Zadeh, Iman Esmaeil, et al. (author) Efficient Single-Photon Detection with 7.7 ps Time Resolution for Photon-Correlation Measurements 2020 In: ACS Photonics. - : AMER CHEMICAL SOC. - 2330-4022. ; 7:7, s. 1780-1787 Journal article (peer-reviewed)abstract A broad range of scientific and industrial disciplines require precise optical measurements at very low light levels. Single-photon detectors combining high efficiency and high time resolution are pivotal in such experiments. By using relatively thick films of NbTiN (8-11 nm) and improving the pattern fidelity of the nanostructure of the superconducting nanowire single-photon detectors (SNSPD), we fabricated devices demonstrating superior performance over all previously reported detectors in the combination of efficiency and time resolution. Our findings prove that small variations in the nanowire width, in the order of a few nanometers, can lead to a significant penalty on their temporal response. Addressing these issues, we consistently achieved high time resolution (best device 7.7 ps, other devices similar to 10-16 ps) simultaneously with high system detection efficiencies (80-90%) in the wavelength range of 780-1000 nm, as well as in the telecom bands (1310-1550 nm). The use of thicker films allowed us to fabricate large-area multipixel devices with homogeneous pixel performance. We first fabricated and characterized a 100 x 100 mu m(2) 16-pixel detector and showed there was little variation among individual pixels. Additionally, to showcase the power of our platform, we fabricated and characterized 4-pixel multimode fiber-coupled detectors and carried out photon-correlation experiments on a nanowire quantum dot resulting in g(2) (0) values lower than 0.04. The multipixel detectors alleviate the need for beamsplitters and can be used for higher order correlations with promising prospects not only in the field of quantum optics, but also in bioimaging applications, such as fluorescence microscopy and positron emission tomography.
29.	Zichi, Julien, et al. (author) Optimizing the stoichiometry of ultrathin NbTiN films for high-performance superconducting nanowire single-photon detectors 2019 In: Optics Express. - : OPTICAL SOC AMER. - 1094-4087. ; 27:19, s. 26579-26587 Journal article (peer-reviewed)abstract The requirements in quantum optics experiments for high single-photon detection efficiency. low timing jitter, low dark count rate and short dead time have been fulfilled with the development of superconducting nanowire single-photon detectors. Although they offer a detection efficiency above 90%, achieving a high time resolution in devices made of amorphous materials is a challenge, particularly at temperatures above 0.8 K. Devices made from niobium nitride and niobium titanium nitride allow us to reach the best timing jitter but. in turn, have stronger requirements in terms of film quality to achieve a high efficiency. Here we take advantage of the flexibility of reactive co-sputter deposition to tailor the composition of NbxTi1-xN superconducting films and show that a Nb fraction of x = 0.62 allows for the fabrication of detectors from films as thick as 9 nm and covering an active area of 20 mu m. with a wide detection saturation plateau at telecom wavelengths and in particular at 1550 nm. This is a signature of an internal detection efficiency saturation, achieved while maintaining the high time resolution associated with NbTiN and operation at 2.5K. With our optimized recipe, we reliably fabricated detectors with high critical current densities reaching a saturation plateau at 1550 nm with 80% system detection efficiency and with a FWHM timing jitter as low as 19.5 ps. Open Access Publishing Agreement

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