| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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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.
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| 2. |
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| 3. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 17. |
- Thomas, M, et al.
(author)
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Combining Asian-European Genome-Wide Association Studies of Colorectal Cancer Improves Risk Prediction Across Race and Ethnicity
- 2023
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In: medRxiv : the preprint server for health sciences. - : Cold Spring Harbor Laboratory.
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Journal article (other academic/artistic)abstract
- Polygenic risk scores (PRS) have great potential to guide precision colorectal cancer (CRC) prevention by identifying those at higher risk to undertake targeted screening. However, current PRS using European ancestry data have sub-optimal performance in non-European ancestry populations, limiting their utility among these populations. Towards addressing this deficiency, we expanded PRS development for CRC by incorporating Asian ancestry data (21,731 cases; 47,444 controls) into European ancestry training datasets (78,473 cases; 107,143 controls). The AUC estimates (95% CI) of PRS were 0.63(0.62-0.64), 0.59(0.57-0.61), 0.62(0.60-0.63), and 0.65(0.63-0.66) in independent datasets including 1,681-3,651 cases and 8,696-115,105 controls of Asian, Black/African American, Latinx/Hispanic, and non-Hispanic White, respectively. They were significantly better than the European-centric PRS in all four major US racial and ethnic groups (p-values<0.05). Further inclusion of non-European ancestry populations, especially Black/African American and Latinx/Hispanic, is needed to improve the risk prediction and enhance equity in applying PRS in clinical practice.
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| 24. |
- Do, Ron, et al.
(author)
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Common variants associated with plasma triglycerides and risk for coronary artery disease
- 2013
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:11, s. 1345-
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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.
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| 28. |
- Garcia-Alonso, L, et al.
(author)
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Single-cell roadmap of human gonadal development
- 2022
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 607:7919, s. 540-
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Journal article (peer-reviewed)abstract
- Gonadal development is a complex process that involves sex determination followed by divergent maturation into either testes or ovaries1. Historically, limited tissue accessibility, a lack of reliable in vitro models and critical differences between humans and mice have hampered our knowledge of human gonadogenesis, despite its importance in gonadal conditions and infertility. Here, we generated a comprehensive map of first- and second-trimester human gonads using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays and fluorescent microscopy. We extracted human-specific regulatory programmes that control the development of germline and somatic cell lineages by profiling equivalent developmental stages in mice. In both species, we define the somatic cell states present at the time of sex specification, including the bipotent early supporting population that, in males, upregulates the testis-determining factor SRY and sPAX8s, a gonadal lineage located at the gonadal–mesonephric interface. In females, we resolve the cellular and molecular events that give rise to the first and second waves of granulosa cells that compartmentalize the developing ovary to modulate germ cell differentiation. In males, we identify human SIGLEC15+ and TREM2+ fetal testicular macrophages, which signal to somatic cells outside and inside the developing testis cords, respectively. This study provides a comprehensive spatiotemporal map of human and mouse gonadal differentiation, which can guide in vitro gonadogenesis.
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| 31. |
- Li, Ci, et al.
(author)
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The Poses for Equine Research Dataset (PFERD)
- 2024
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In: Scientific Data. - : Springer Nature. - 2052-4463. ; 11:1
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Journal article (peer-reviewed)abstract
- Studies of quadruped animal motion help us to identify diseases, understand behavior and unravel the mechanics behind gaits in animals. The horse is likely the best-studied animal in this aspect, but data capture is challenging and time-consuming. Computer vision techniques improve animal motion extraction, but the development relies on reference datasets, which are scarce, not open-access and often provide data from only a few anatomical landmarks. Addressing this data gap, we introduce PFERD, a video and 3D marker motion dataset from horses using a full-body set-up of densely placed over 100 skin-attached markers and synchronized videos from ten camera angles. Five horses of diverse conformations provide data for various motions from basic poses (eg. walking, trotting) to advanced motions (eg. rearing, kicking). We further express the 3D motions with current techniques and a 3D parameterized model, the hSMAL model, establishing a baseline for 3D horse markerless motion capture. PFERD enables advanced biomechanical studies and provides a resource of ground truth data for the methodological development of markerless motion capture.
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| 32. |
- Li, X., et al.
(author)
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Adaptive Resilient Secondary Control for Microgrids With Communication Faults
- 2021
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In: IEEE Transactions on Cybernetics. - : Institute of Electrical and Electronics Engineers (IEEE). - 2168-2267 .- 2168-2275. ; , s. 1-11
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Journal article (peer-reviewed)abstract
- In this article, we consider the resilience problem in the presence of communication faults encountered in distributed secondary voltage and frequency control of an islanded alternating current microgrid. Such faults include the partial failure of communication links and some classes of data manipulation attacks. This practical and important yet challenging issue has been taken into limited consideration by existing approaches, which commonly assume that the measurement or communication between the distributed generations (DGs) is ideal or satisfies some restrictive assumptions. To achieve communication resilience, a novel adaptive observer is first proposed for each individual DG to estimate the desired reference voltage and frequency under unknown communication faults. Then, to guarantee the stability of the closed-loop system, voltage and frequency restoration, and accurate power sharing regardless of unknown communication faults, sufficient conditions are derived. Some simulation results are presented to verify the effectiveness of the proposed secondary control approach.
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| 33. |
- Li, Xiaolei, et al.
(author)
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Resilience for Communication Faults in Reactive Power Sharing of Microgrids
- 2021
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In: IEEE Transactions on Smart Grid. - : Institute of Electrical and Electronics Engineers (IEEE). - 1949-3053 .- 1949-3061. ; 12:4, s. 2788-2799
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Journal article (peer-reviewed)abstract
- In this paper, we consider the distributed reactive power sharing control problem for an autonomous inverter-based microgrid with resilience for communication faults, which may be caused by partial communication link failures or some channel manipulation attacks. Under the standard decoupling approximation for bus angle differences, the reactive power flow of each inverter can be controlled by manipulating the voltage amplitudes of itself and its neighbour inverters. By designing an adaptive resilient cooperative control scheme, accurate reactive power sharing can be guaranteed even in the presence of communication faults. Some simulation results are presented to verify the superiority of the proposed control approach compared with the existing methods.
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| 34. |
- Lin, Ci, et al.
(author)
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Direct Band Gap in Multilayer Transition Metal Dichalcogenide Nanoscrolls with Enhanced Photoluminescence
- 2022
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In: ACS Materials Letters. - : American Chemical Society (ACS). - 2639-4979. ; 4:8, s. 1547-1555
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Journal article (peer-reviewed)abstract
- A direct band gap that solely exists in monolayer semiconducting transition metal dichalcogenides (TMDs) endows strong photoluminescence (PL) features, whereas multilayer TMD structures exhibit quenched PL due to the direct-to-indirect band gap transition. We demonstrate multi-layer TMD (such as MoS2 and WS2) nanoscrolls with a preserved direct band gap fabricated by an effective and facile method of solvent-driven self-assembly. The resultant multi-layer nanoscrolls, exhibiting up to 11 times higher PL intensity than the remanent monolayer, are carefully characterized using PL spectroscopy. Significantly enlarged interlayer distances and modulated interlayer coupling in the fabricated nanostructures are unveiled by cross-sectional scanning transmission electron microscopy, atomic force microscopy, and Raman spectroscopy. The preservation of direct band gap features is further evidenced by density functional theory calculations using the simplified bilayer model with an experimentally obtained 15 & ANGS; interlayer distance. The modulation of the PL intensity as an indicator of the band gap crossover in the TMD nanoscrolls is demonstrated by removing the acetone molecules trapped inside the interlayer space. The general applicability of the method presents an opportunity for large-scale fabrication of a plethora of multilayer TMD nanoscrolls with direct band gaps.
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| 44. |
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| 45. |
- Wang, Baicun, et al.
(author)
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Human Digital Twin in the context of Industry 5.0
- 2024
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In: Robotics and Computer-Integrated Manufacturing. - : Elsevier Ltd. - 0736-5845 .- 1879-2537. ; 85
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Research review (peer-reviewed)abstract
- Human-centricity, a core value of Industry 5.0, places humans in the center of production. It leads to the prioritization of human needs, spanning from health and safety to self-actualization and personal growth. The concept of the Human Digital Twin (HDT) is proposed as a critical method to realize human-centricity in smart manufacturing systems towards Industry 5.0. HDTs are digital representations of humans, aiming to change the practice of human-system integration by coupling humans’ characteristics directly to the system design and its performance. In-depth analysis, critical insights, and application guidelines of HDT are essential to realize the concept of Industry 5.0 in practice and evolve the smart manufacturing paradigm in modern factories. However, the investigation on the development of HDT to evolve humans’ roles and develop humans to their full potential is limited to date. Recent studies are rarely geared towards designing a standardized framework and architecture of HDT for diverse real-world applications. Thus, this work aims to close this research gap by carrying out a comprehensive survey on HDT in the context of Industry 5.0, summarizing the ongoing evolution, and proposing a proper connotation of HDT, before discussing the conceptual framework and system architecture of HDT and analyzing enabling technologies and industrial applications. This work provides guidance on possible avenues as well as challenges for the further development of HDT and its related concepts, allowing humans to reach their potential and accommodating their diverse needs in the futuristic smart manufacturing systems shaped by Industry 5.0.
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| 46. |
- Wang, Ci, et al.
(author)
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Twinning pathways in Fe and Fe-Cr alloys from first-principles theory
- 2021
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In: Acta Materialia. - : Elsevier BV. - 1359-6454 .- 1873-2453. ; 215
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Journal article (peer-reviewed)abstract
- Using density-functional theory, we determine the generalized stacking fault energy (GSFE) for the {1 (1) over bar 12} < 1 (1) over bar 11 > twinning system in ferromagnetic (FM) body-centered cubic Fe and Fe-Cr alloys with molar fraction of Cr <= 0.5. We adopt both reflection and isosceles twinning pathways and reveal the magnetic ordering effects on the GSFE by contrasting the FM results to those obtained for the magnetically disordered paramagnetic (PM) state. The results show that the isosceles twin boundary configuration is energetically preferred in this binary. The loss of long-range magnetic order lowers the GSFE amplitude but increases the twin boundary migration (TBM) energy regardless of the Cr content. The twin boundary formation (TBF) energy and the TBM energy show non-linear dependences on Cr content in the FM and PM states, and the effect of Cr on these properties critically depends on the magnetic state. We discuss our results in regard to the stable twin boundary structure and deformation twinning experimentally observed in homogeneous Fe-50 wt.% Cr alloy up to temperatures slightly above the magnetic ordering temperature.
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| 47. |
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| 48. |
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| 49. |
- Willer, Cristen J., et al.
(author)
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Discovery and refinement of loci associated with lipid levels
- 2013
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:11, s. 1274-1283
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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.
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