| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
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| 3. |
- Forsen, E, et al.
(författare)
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Fabrication of cantilever based mass sensors integrated with CMOS using direct write laser lithography on resist
- 2004
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Ingår i: Nanotechnology. - : IOP Publishing. - 0957-4484 .- 1361-6528. ; 15:10, s. 628-633
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Tidskriftsartikel (refereegranskat)abstract
- A CMOS compatible direct write laser lithography technique has been developed for cantilever fabrication on pre-fabricated standard CMOS. We have developed cantilever based sensors for mass measurements in vacuum and air. The cantilever is actuated into lateral vibration by electrostatic excitation and the resonant frequency is detected by capacitive readout. The device is integrated on standard CMOS circuitry. In the work a new direct write laser lithography (DWL) technique is introduced. This laser lithography technique is based on direct laser writing on substrates coated with a resist bi-layer consisting of poly(methyl methacrylate) (PMMA) on lift-off resist (LOR). Laser writing evaporates the PMMA, exposing the LOR. A resist solvent is used to transfer the pattern down to the substrate. Metal lift-off followed by reactive ion etching is used for patterning the structural poly-Si layer in the CMOS. The developed laser lithography technique is compatible with resist exposure techniques such as electron beam lithography. We demonstrate the fabrication of sub-micrometre wide suspended cantilevers as well as metal lift-off with feature line widths down to approximately 500 nm.
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| 4. |
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| 5. |
- Forsen, E, et al.
(författare)
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Ultrasensitive mass sensor fully integrated with complementary metal-oxide-semiconductor circuitry
- 2005
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 87:4
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Tidskriftsartikel (refereegranskat)abstract
- Nanomechanical resonators have been monolithically integrated on preprocessed complementary metal-oxide-semiconductor (CMOS) chips. Fabricated resonator systems have been designed to have resonance frequencies up to 1.5 MHz. The systems have been characterized in ambient air and vacuum conditions and display ultrasensitive mass detection in air. A mass sensitivity of 4 ag/Hz has been determined in air by placing a single glycerine drop, having a measured weight of 57 fg, at the apex of a cantilever and subsequently measuring a frequency shift of 14.8 kHz. CMOS integration enables electrostatic excitation, capacitive detection, and amplification of the resonance signal directly on the chip.
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| 6. |
- Brissot, Eolia, et al.
(författare)
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Tyrosine kinase inhibitors improve long-term outcome of allogeneic hematopoietic stem cell transplantation for adult patients with Philadelphia chromosome positive acute lymphoblastic leukemia.
- 2015
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Ingår i: Haematologica. - : Ferrata Storti Foundation (Haematologica). - 1592-8721 .- 0390-6078. ; 100:3, s. 392-399
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Tidskriftsartikel (refereegranskat)abstract
- This study aimed to determine the impact of tyrosine-kinase inhibitors given pre- and post-allogeneic stem cell transplantation on long term outcome of patients allografted for Philadelphia chromosome-positive acute lymphoblastic leukemia. This retrospective analysis from the Acute Leukemia Working Party of EBMT included 473 de novo Philadelphia chromosome-positive acute lymphoblastic leukemia patients in first complete remission who underwent an allogeneic stem cell transplantation using an human leucocyte antigen-identical sibling or human leucocyte antigen-matched unrelated donor between 2000 and 2010. Three hundred ninety patients received tyrosine-kinase inhibitors before transplant, 329 at induction and 274 at consolidation. The Kaplan-Meier estimates of leukemia-free survival, overall survival, cumulative incidences of relapse incidence, and non-relapse mortality at 5 years were 38%, 46%, 36% and 26%, respectively. In multivariate analysis, tyrosine-kinase inhibitors given before allogeneic stem cell transplantation was associated with a better overall survival (HR=0.68; P=.04) and was associated with lower relapse incidence (HR=0.5; P=.01). In the post-transplant period, multivariate analysis identified prophylactic tyrosine-kinase inhibitors administration to be a significant factor for improved leukemia-free survival (HR=0.44; P=.002) and overall survival (HR=0.42; P=.004), and a lower relapse incidence (HR=0.40; P=.01). In conclusion, over the past decade, tyrosine-kinase inhibitors administration before allogeneic stem cell transplantation has significantly improved the long term allogeneic stem cell transplantation outcome of adult Philadelphia chromosome-positive acute lymphoblastic leukemia. Prospective studies will be of great interest to further confirm the potential benefit of the prophylactic use of tyrosine-kinase inhibitors in the post-transplant setting.
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| 7. |
- Ghatnekar-Nilsson, Sara, et al.
(författare)
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Resonators with integrated CMOS circuitry for mass sensing applications, fabricated by electron beam lithography
- 2005
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Ingår i: Nanotechnology. - : IOP Publishing. - 0957-4484 .- 1361-6528. ; 16:1, s. 98-102
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Tidskriftsartikel (refereegranskat)abstract
- A resonator system has been fabricated directly on a pre-processed CMOS chip. The system is to be used for high sensitivity mass sensing applications in air and vacuum. The resonator system, corresponding of a cantilever and structures for electrostatic actuation and capacitive read-out, have been defined by electron beam lithography on top of a charge and radiation sensitive CMOS layer in predefined areas as a post-process step. This has been accomplished without affecting the electronic properties of the pre-processed CMOS circuits. The subsequent etching steps to fully release the cantilevers have been obtained without stiction of the cantilevers to the substrate. Cantilevers are driven at their mechanical resonance in a lateral mode, and the frequency is monitored by capacitive read-out on the chip. CMOS integration enables signal detection directly on the chip, which radically decreases the parasitic capacitances. Consequently, low-noise electrical measurements with a very high mass sensitivity are obtained. Fabricated resonator systems were characterized to have resonance frequencies of approximately 1.49 MHz, which is in good agreement with a theoretical estimation of 1.41 MHz. The theoretical mass resolution, partial derivativem/partial derivativef, is approximately 17 ag Hz(-1) using a Young modulus value of 160 GPa.
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| 8. |
- Lazarevic, Vladimir Lj, et al.
(författare)
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Relatively favorable outcome after allogeneic stem cell transplantation for BCR-ABL1-positive AML : A survey from the acute leukemia working party of the European Society for blood and marrow transplantation (EBMT)
- 2018
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Ingår i: American Journal of Hematology. - : Wiley. - 0361-8609 .- 1096-8652. ; 93:1, s. 31-39
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Tidskriftsartikel (refereegranskat)abstract
- The aim of the study was to assess the role of allogeneic stem cell transplantation (SCT) in patients diagnosed with BCR-ABL1-positive acute myeloid leukemia (AML). Fifty-seven patients (median age, 48 years, range: 19-67) with BCR-ABL1 positive AML undergoing SCT were identified. The majority of the patients (70%) received a TKI before the transplant. At SCT 48 patients were in CR (45 in CR1), while 9 patients were transplanted in a more advanced stage of the disease. MRD was negative (BCR-ABL1/ABL<104) at time of SCT in 36.1% (14/40). After SCT, 16 (61.5%) out of 26 patients with MRD positive at transplantation reached MRD negativity. After a median follow-up of 6.3 years (0.7-14.2), NRM, RI, LFS, OS, and GRFS at 5 years were 18.1%, 37%, 44.2%, 53.8%, and 32.1%, respectively. The cumulative incidence of acute GvHD grade II-IV was 16.4%, incidence of chronic GvHD 24.9%, and of extensive cGvHD 21.4%, respectively. In patients who received SCT in CR1, 5-yr NRM, RI, LFS, OS, and GRFS were 15.9%, 36.4%, 46.5%, 59.4%, and 34.9%, respectively. Univariate analysis showed that age (<50 vs. ≥50 years) was associated with RI (5-yr: 22.7 vs. 50%), LFS (5-yr: 61.9 vs. 31.8%), and GRFS (5-yr: 52.4 vs. 18.2%), whereas MRD-negative status before SCT was associated with an improved GRFS (38.9 vs. 16.7%). We conclude that the outcome of patients <50 years of age with BCR-ABL1-positive AML receiving allogeneic SCT in CR is relatively favorable, possibly reflecting the beneficial effect of the use of TKI.
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| 9. |
- Zheng, Tenghao, et al.
(författare)
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Human Leukocyte Antigen Signatures as Pathophysiological Discriminants of Microscopic Colitis Subtypes
- 2024
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Ingår i: Journal of Crohn's and Colitis. - : OXFORD UNIV PRESS. - 1873-9946 .- 1876-4479. ; 18:3, s. 349-359
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Tidskriftsartikel (refereegranskat)abstract
- Background and Aims: Microscopic colitis [MC] is currently regarded as an inflammatory bowel disease that manifests as two subtypes: collagenous colitis [CC] and lymphocytic colitis [LC]. Whether these represent a clinical continuum or distinct entities is, however, an open question. Genetic investigations may contribute important insight into their respective pathophysiologies. Methods: We conducted a genome-wide association study [GWAS] meta-analysis in 1498 CC, 373 LC patients, and 13 487 controls from Europe and the USA, combined with publicly available MC GWAS data from UK Biobank and FinnGen [2599 MC cases and 552 343 controls in total]. Human leukocyte antigen [HLA] alleles and polymorphic residues were imputed and tested for association, including conditional analyses for the identification of key causative variants and residues. Genetic correlations with other traits and diagnoses were also studied. Results: We detected strong HLA association with CC, and conditional analyses highlighted the DRB1*03:01 allele and its residues Y26, N77, and R74 as key to this association (best p = 1.4 × 10-23, odds ratio [OR] = 1.96). Nominally significant genetic correlations were detected between CC and pneumonia [rg = 0.77; p = 0.048] and oesophageal diseases [rg = 0.45, p = 0.023]. An additional locus was identified in MC GWAS analyses near the CLEC16A and RMI2 genes on chromosome 16 [rs35099084, p = 2.0 × 10-8, OR = 1.31]. No significant association was detected for LC. Conclusion: Our results suggest CC and LC have distinct pathophysiological underpinnings, characterised by an HLA predisposing role only in CC. This challenges existing classifications, eventually calling for a re-evaluation of the utility of MC umbrella definitions.
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