bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flow‐to‐Friction Transition in Simulated Calcite Gouge: Experiments and Microphysical Modeling
Authors: Chen Jianye , Verberne B. A. , Niemeijer A. R. 
Published: October 2020

AbstractA (micro)physical understanding of the transition from frictional sliding to plastic or viscous flow has long been a challenge for earthquake cycle modeling. We have conducted ring‐shear deformation experiments on layers of simulated calcite fault gouge under conditions close to the frictional‐to‐viscous transition previously established in this material. Constant velocity (v) and v‐stepping tests were performed, at 550°C, employing slip rates covering almost 6 orders of magnitude (0.001–300 μm/s). Steady‐state sliding transitioned from (strong) v‐strengthening, flow‐like behavior to v‐weakening, frictional behavior, at an apparent “critical” velocity (vcr) of ~0.1 μm/s. Velocity‐stepping tests using v < vcr showed “semi‐brittle” flow behavior, characterized by high stress sensitivity (“n‐value”) and a transient response resembling classical frictional deformation. For v ≥ vcr, gouge deformation is localized in a boundary shear band, while for v < vcr, the gouge is well‐compacted, displaying a progressively homogeneous structure as the slip rate decreases. Using mechanical data and post‐mortem microstructural observations as a basis, we deduced the controlling shear deformation mechanisms and quantitatively reproduced the steady‐state shear strength‐velocity profile using an existing micromechanical model. The same model also reproduces the observed transient responses to v‐steps within both the flow‐like and frictional deformation regimes. We suggest that the flow‐to‐friction transition strongly relies on fault (micro)structure and constitutes a net opening of transient microporosity with increasing shear strain rate at v < vcr, under normal stress‐dependent or “semi‐brittle” flow conditions. Our findings shed new insights into the microphysics of earthquake rupture nucleation and dynamic propagation in the brittle‐to‐ductile transition zone.
New Approaches to Multifrequency Sp Stacking Tested in the Anatolian Region
Authors: Hua J. , Fischer K. M. , Wu M. , Blom N. A. 
Published: October 2020

AbstractThis study presents an improved approach to common‐conversion point stacking of converted body waves that incorporates scattering kernels, accurate and efficient measurement of stack uncertainties, and an alternative method for estimating free surface seismic velocities. To better separate waveforms into the P and SV components to calculate receiver functions, we developed an alternative method to measure near‐surface compressional and shear wave velocities from particle motions. To more accurately reflect converted phase scattering kernels in the common‐conversion point stack, we defined new weighting functions to project receiver function amplitudes only to locations where sensitivities to horizontal discontinuities are high. To better quantify stack uncertainties, we derived an expression for the standard deviation of the stack amplitude that is more efficient than bootstrapping and can be used for any problem requiring the standard deviation of a weighted average. We tested these improved methods on Sp phase data from the Anatolian region, using multiple band‐pass filters to image velocity gradients of varying depth extents. Common conversion point stacks of 23,787 Sp receiver functions demonstrate that the new weighting functions produce clearer and more continuous mantle phases, compared to previous approaches. The stacks reveal a positive velocity gradient at 80–150 km depth that is consistent with the base of an asthenospheric low‐velocity layer. This feature is particularly strong in stacks of longer period data, indicating it represents a gradual velocity gradient. At shorter periods, a lithosphere‐asthenosphere boundary phase is observed at 60–90 km depth, marking the top of the low‐velocity layer.
Thermal Hall conductivity in the cuprate Mott insulators Nd2CuO4 and Sr2CuO2Cl2
Authors: Boulanger Marie-Eve , Grissonnanche Gaël , Badoux Sven , Allaire Andréanne , Lefrançois Étienne , Legros Anaëlle , Gourgout Adrien , Dion Maxime , Wang C. H. , Chen X. H. , Liang R. , Hardy W. N. , Bonn D. A. , Taillefer Louis 
Published: October 2020

AbstractThe heat carriers responsible for the unexpectedly large thermal Hall conductivity of the cuprate Mott insulator La2CuO4 were recently shown to be phonons. However, the mechanism by which phonons in cuprates acquire chirality in a magnetic field is still unknown. Here, we report a similar thermal Hall conductivity in two cuprate Mott insulators with significantly different crystal structures and magnetic orders – Nd2CuO4 and Sr2CuO2Cl2 – and show that two potential mechanisms can be excluded – the scattering of phonons by rare-earth impurities and by structural domains. Our comparative study further reveals that orthorhombicity, apical oxygens, the tilting of oxygen octahedra and the canting of spins out of the CuO2 planes are not essential to the mechanism of chirality. Our findings point to a chiral mechanism coming from a coupling of acoustic phonons to the intrinsic excitations of the CuO2 planes.
A fast impedance-based antimicrobial susceptibility test
Authors: Spencer Daniel C. , Paton Teagan F. , Mulroney Kieran T. , Inglis Timothy J. J. , Sutton J. Mark , Morgan Hywel 
Published: October 2020

AbstractThere is an urgent need to develop simple and fast antimicrobial susceptibility tests (ASTs) that allow informed prescribing of antibiotics. Here, we describe a label-free AST that can deliver results within an hour, using an actively dividing culture as starting material. The bacteria are incubated in the presence of an antibiotic for 30 min, and then approximately 105 cells are analysed one-by-one with microfluidic impedance cytometry for 2–3 min. The measured electrical characteristics reflect the phenotypic response of the bacteria to the mode of action of a particular antibiotic, in a 30-minute incubation window. The results are consistent with those obtained by classical broth microdilution assays for a range of antibiotics and bacterial species.
Direct reprogramming of human umbilical vein- and peripheral blood-derived endothelial cells into hepatic progenitor cells
Authors: Inada Hiroki , Udono Miyako , Matsuda-Ito Kanae , Horisawa Kenichi , Ohkawa Yasuyuki , Miura Shizuka , Goya Takeshi , Yamamoto Junpei , Nagasaki Masao , Ueno Kazuko , Saitou Daisuke , Suyama Mikita , Maehara Yoshihiko , Kumamaru Wataru , Ogawa Yoshihiro , Sekiya Sayaka , Suzuki Atsushi 
Published: October 2020

AbstractRecent advances have enabled the direct induction of human tissue-specific stem and progenitor cells from differentiated somatic cells. However, it is not known whether human hepatic progenitor cells (hHepPCs) can be generated from other cell types by direct lineage reprogramming with defined transcription factors. Here, we show that a set of three transcription factors, FOXA3, HNF1A, and HNF6, can induce human umbilical vein endothelial cells to directly acquire the properties of hHepPCs. These induced hHepPCs (hiHepPCs) propagate in long-term monolayer culture and differentiate into functional hepatocytes and cholangiocytes by forming cell aggregates and cystic epithelial spheroids, respectively, under three-dimensional culture conditions. After transplantation, hiHepPC-derived hepatocytes and cholangiocytes reconstitute damaged liver tissues and support hepatic function. The defined transcription factors also induce hiHepPCs from endothelial cells circulating in adult human peripheral blood. These expandable and bipotential hiHepPCs may be useful in the study and treatment of human liver diseases.
Predicting aqueous stability of solid with computed Pourbaix diagram using SCAN functional
Authors: Wang Zhenbin , Guo Xingyu , Montoya Joseph , Nørskov Jens K. 
Published: October 2020

AbstractIn this work, using the SCAN functional, we develop a simple method on top of the Materials Project (MP) Pourbaix diagram framework to accurately predict the aqueous stability of solids. We extensively evaluate the SCAN functional’s performance in computed formation enthalpies for a broad range of oxides and develop Hubbard U corrections for transition-metal oxides where the standard SCAN functional exhibits large deviations. The performance of the calculated Pourbaix diagram using the SCAN functional is validated with comparison to the experimental and the MP PBE Pourbaix diagrams for representative examples. Benchmarks indicate the SCAN Pourbaix diagram systematically outperforms the MP PBE in aqueous stability prediction. We further show applications of this method in accurately predicting the dissolution potentials of the state-of-the-art catalysts for oxygen evolution reaction in acidic media.
Exome sequencing and characterization of 49,960 individuals in the UK Biobank
Authors: Van Hout Cristopher V. , Tachmazidou Ioanna , Backman Joshua D. , Hoffman Joshua D. , Liu Daren , Pandey Ashutosh K. , Gonzaga-Jauregui Claudia , Khalid Shareef , Ye Bin , Banerjee Nilanjana , Li Alexander H. , O’Dushlaine Colm , Marcketta Anthony , Staples Jeffrey , Schurmann Claudia , Hawes Alicia , Maxwell Evan , Barnard Leland , Lopez Alexander , Penn John , Habegger Lukas , Blumenfeld Andrew L. , Bai Xiaodong , O’Keeffe Sean , Yadav Ashish , Praveen Kavita , Jones Marcus , Salerno William J. , Chung Wendy K. , Surakka Ida , Willer Cristen J. , Hveem Kristian , Leader Joseph B. , Carey David J. , Ledbetter David H. ,   Geisinger-Regeneron DiscovEHR Collaboration, Cardon Lon , Yancopoulos George D. , Economides Aris , Coppola Giovanni , Shuldiner Alan R. , Balasubramanian Suganthi , Cantor Michael ,   Regeneron Genetics Center, Nelson Matthew R. , Whittaker John , Reid Jeffrey G. , Marchini Jonathan , Overton John D. , Scott Robert A. , Abecasis Gonçalo R. , Yerges-Armstrong Laura , Baras Aris 
Published: October 2020

AbstractThe UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world1. Here we describe the release of exome-sequence data for the first 49,960 study participants, revealing approximately 4 million coding variants (of which around 98.6% have a frequency of less than 1%). The data include 198,269 autosomal predicted loss-of-function (LOF) variants, a more than 14-fold increase compared to the imputed sequence. Nearly all genes (more than 97%) had at least one carrier with a LOF variant, and most genes (more than 69%) had at least ten carriers with a LOF variant. We illustrate the power of characterizing LOF variants in this population through association analyses across 1,730 phenotypes. In addition to replicating established associations, we found novel LOF variants with large effects on disease traits, including PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical importance, and show that 2% of this population has a medically actionable variant. Furthermore, we characterize the penetrance of cancer in carriers of pathogenic BRCA1 and BRCA2 variants. Exome sequences from the first 49,960 participants highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community.
Reference exome data for a Northern Brazilian population
Authors: Weeks Alexia L. , Francis Richard W. , Neri Joao I. C. F. , Costa Nathaly M. C. , Arrais Nivea M. R. , Lassmann Timo , Blackwell Jenefer M. , Jeronimo Selma M. B. 
Published: October 2020

AbstractExome sequencing is widely used in the diagnosis of rare genetic diseases and provides useful variant data for analysis of complex diseases. There is not always adequate population-specific reference data to assist in assigning a diagnostic variant to a specific clinical condition. Here we provide a catalogue of variants called after sequencing the exomes of 45 babies from Rio Grande do Nord in Brazil. Sequence data were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. A total of 612,761 variants were identified in at least one individual in this Brazilian Cohort, including 559,448 single nucleotide variants (SNVs) and 53,313 insertion/deletions. Of these, 58,111 overlapped with nonsynonymous (nsSNVs) or splice site (ssSNVs) SNVs in dbNSFP. As an aid to clinical diagnosis of rare diseases, we used the American College of Medicine Genetics and Genomics (ACMG) guidelines to assign pathogenic/likely pathogenic status to 185 (0.32%) of the 58,111 nsSNVs and ssSNVs. Our data set provides a useful reference point for diagnosis of rare diseases in Brazil. (169 words).
Sleep dissatisfaction and insufficient sleep duration in the Italian population
Authors: Varghese Nirosha Elsem , Lugo Alessandra , Ghislandi Simone , Colombo Paolo , Pacifici Roberta , Gallus Silvano 
Published: October 2020

AbstractTo investigate the prevalence and possible determinants of sleep quality and quantity, we used data from a cross-sectional study conducted in 2019 on a sample of 3120 subjects, representative of the general Italian adult population. Sleep dissatisfaction was reported by 14.2% and insufficient sleep (duration) by 29.5% of adults. Sleep dissatisfaction and insufficient sleep were directly related with age (p for trend < 0.001), and inversely related with socioeconomic class (p for trend < 0.001) and income (p for trend < 0.001). Sleep dissatisfaction was higher among women (odds ratio, OR 1.30; 95% confidence interval, CI 1.05–1.60). Insufficient sleep was inversely related to education (p for trend < 0.001) and more frequent in current compared to never smokers (OR 1.32; 95% CI 1.08–1.61). Sleep dissatisfaction was higher among divorced/separated compared with married subjects (OR 1.75; 95% CI 1.20–2.58) and lower among subjects living with children aged 0–14 years (OR 0.48, 95% CI 0.33–0.70). Pet owners more frequently had sleep dissatisfaction (OR 1.35, 95% CI 1.08–1.68) and insufficient sleep (OR 1.46, 95% CI 1.23–1.73). In Italy, self-perceived sleep problems appear to be increasing. Sleep problems can contribute to aggravating health disparities in the society. The unfavourable relationship with pets (and the favourable ones with children) should be confirmed by longitudinal studies.
Coffee consumption and cancer risk in African Americans from the Southern Community Cohort Study
Authors: Schmit Stephanie L. , Nwogu Onyekachi , Matejcic Marco , DeRenzis Amanda , Lipworth Loren , Blot William J. , Raskin Leon 
Published: October 2020

AbstractCoffee consumption has been associated with the risk of cancer at several anatomical sites, but the findings, mostly from studies of non-Hispanic whites and Asians, are inconsistent. The association between coffee consumption and the incidence of cancer has not been thoroughly examined in African Americans. We conducted a nested case–control study including 1801 cancer cases and 3337 controls among African Americans from the Southern Community Cohort Study (SCCS) to examine the association between coffee drinking, as assessed by a semi-quantitative food frequency questionnaire, and the risk of four common cancers (lung, prostate, breast, colorectal). We used logistic regression adjusted for age, sex and cancer-specific risk factors. Overall, only ≤ 9.5% of African American cases and controls from the SCCS drank regular or decaffeinated coffee ≥ 2 times/day. After adjustment for major cancer-specific risk factors, coffee consumption was not statistically significantly associated with the risk of lung, breast, colorectal, or prostate cancers (OR range 0.78–1.10; P ≥ 0.27 for ≥ 2 versus < 1 times/day) or overall cancer risk (OR 0.93; 95% CI 0.75–1.16; P = 0.52 for ≥ 2 versus < 1 times/day). Coffee consumption was not associated with the risk of cancer among African Americans in our study.
Estrogen hormone replacement therapy in incidental intracranial meningioma: a growth-rate analysis
Authors: Dresser Laura , Yuen Carlen Amy , Wilmington Andrew , Walker Matthew , Vogel Tilley Jenkins , Merrell Ryan T. , Kamson David Olayinka 
Published: October 2020

AbstractIncidental meningiomas (IMs) are the most common intracranial neoplasms, especially in perimenopausal women. There is ongoing debate on whether their incidence is increased by hormone replacement therapy. Meningiomas often express estrogen receptors, which were linked to higher proliferative activity according to some reports. Consequently, there is a theoretical risk of estrogen-based HRT (e-HRT) leading to an increase in tumor growth and thus altering the natural history of IMs. However, clinical data is lacking to support this notion. To identify differences in the natural history of IM after e-HRT exposure. We queried the NorthShore Meningioma Database for patients with ≥ 6 months of e-HRT. They were compared with age-matched IM controls. Forty patients were included in the e-HRT group (mean age 62.1 ± 12.0 years; mean duration of HRT 5.3 ± 4.5 years) and 80 in the no-HRT group (mean age 62.2 ± 12 years). Radiographic appearance was similar between groups. The average 2D tumor diameter was 35% lower in the e-HRT group (p = 0.02), with an absolute growth-rate of half of the no-HRT group (p = 0.02). Radiographic and clinical progression-free survival were 1.2 years and 3.3 years longer in the e-HRT group, respectively. These preliminary results suggest that e-HRT may be safe in incidental meningiomas.
Repeated stress exposure in mid-adolescence attenuates behavioral, noradrenergic, and epigenetic effects of trauma-like stress in early adult male rats
Authors: Chaby Lauren E. , Sadik Nareen , Burson Nicole A. , Lloyd Scott , O’Donnel Kelly , Winters Jesse , Conti Alana C. , Liberzon Israel , Perrine Shane A. 
Published: October 2020

AbstractStress in adolescence can regulate vulnerability to traumatic stress in adulthood through region-specific epigenetic activity and catecholamine levels. We hypothesized that stress in adolescence would increase adult trauma vulnerability by impairing extinction-retention, a deficit in PTSD, by (1) altering class IIa histone deacetylases (HDACs), which integrate effects of stress on gene expression, and (2) enhancing norepinephrine in brain regions regulating cognitive effects of trauma. We investigated the effects of adolescent-stress on adult vulnerability to severe stress using the single-prolonged stress (SPS) model in male rats. Rats were exposed to either (1) adolescent-stress (33–35 postnatal days) then SPS (58–60 postnatal days; n = 14), or (2) no adolescent-stress and SPS (58–60 postnatal days; n = 14), or (3) unstressed conditions (n = 8). We then measured extinction-retention, norepinephrine, HDAC4, and HDAC5. As expected, SPS exposure induced an extinction–retention deficit. Adolescent-stress prior to SPS eliminated this deficit, suggesting adolescent-stress conferred resiliency to adult severe stress. Adolescent-stress also conferred region-specific resilience to norepinephrine changes. HDAC4 and HDAC5 were down-regulated following SPS, and these changes were also modulated by adolescent-stress. Regulation of HDAC levels was consistent with the pattern of cognitive effects of SPS; only animals exposed to SPS without adolescent-stress exhibited reduced HDAC4 and HDAC5 in the prelimbic cortex, hippocampus, and striatum. Thus, HDAC regulation caused by severe stress in adulthood interacts with stress history such that seemingly conflicting reports describing effects of adolescent stress on adult PTSD vulnerability may stem in part from dynamic HDAC changes following trauma that are shaped by adolescent stress history.
Cell morphology maintenance in Bacillus subtilis through balanced peptidoglycan synthesis and hydrolysis
Authors: Sassine Jad , Sousa Joana , Lalk Michael , Daniel Richard A. , Vollmer Waldemar 
Published: October 2020

AbstractThe peptidoglycan layer is responsible for maintaining bacterial cell shape and permitting cell division. Cell wall growth is facilitated by peptidoglycan synthases and hydrolases and is potentially modulated by components of the central carbon metabolism. In Bacillus subtilis, UgtP synthesises the glucolipid precursor for lipoteichoic acid and has been suggested to function as a metabolic sensor governing cell size. Here we show that ugtP mutant cells have increased levels of cell wall precursors and changes in their peptidoglycan that suggest elevated dl-endopeptidase activity. The additional deletion of lytE, encoding a dl-endopeptidase important for cell elongation, in the ugtP mutant background produced cells with severe shape defects. Interestingly, the ugtP lytE mutant recovered normal rod-shape by acquiring mutations that decreased the expression of the peptidoglycan synthase PBP1. Together our results suggest that cells lacking ugtP must re-adjust the balance between peptidoglycan synthesis and hydrolysis to maintain proper cell morphology.
Loss of PRCD alters number and packaging density of rhodopsin in rod photoreceptor disc membranes
Authors: Sechrest Emily R. , Murphy Joseph , Senapati Subhadip , Goldberg Andrew F. X. , Park Paul S.-H. , Kolandaivelu Saravanan 
Published: October 2020

AbstractProgressive rod-cone degeneration (PRCD) is a small protein localized to photoreceptor outer segment (OS) disc membranes. Several mutations in PRCD are linked to retinitis pigmentosa (RP) in canines and humans, and while recent studies have established that PRCD is required for high fidelity disc morphogenesis, its precise role in this process remains a mystery. To better understand the part which PRCD plays in disease progression as well as its contribution to photoreceptor OS disc morphogenesis, we generated a Prcd-KO animal model using CRISPR/Cas9. Loss of PRCD from the retina results in reduced visual function accompanied by slow rod photoreceptor degeneration. We observed a significant decrease in rhodopsin levels in Prcd-KO retina prior to photoreceptor degeneration. Furthermore, ultrastructural analysis demonstrates that rod photoreceptors lacking PRCD display disoriented and dysmorphic OS disc membranes. Strikingly, atomic force microscopy reveals that many disc membranes in Prcd-KO rod photoreceptor neurons are irregular, containing fewer rhodopsin molecules and decreased rhodopsin packing density compared to wild-type discs. This study strongly suggests an important role for PRCD in regulation of rhodopsin incorporation and packaging density into disc membranes, a process which, when dysregulated, likely gives rise to the visual defects observed in patients with PRCD-associated RP.
Movement patterns of the grey field slug (Deroceras reticulatum) in an arable field
Authors: Ellis John , Petrovskaya Natalia , Forbes Emily , Walters Keith F. A. , Petrovskii Sergei 
Published: October 2020

AbstractWe report the results of an experiment on radio-tracking of individual grey field slugs in an arable field and associated data modelling designed to investigate the effect of slug population density in their movement. Slugs were collected in a commercial winter wheat field in which a 5x6 trapping grid had been established with 2m distance between traps. The slugs were taken to the laboratory, radio-tagged using a recently developed procedure, and following a recovery period released into the same field. Seventeen tagged slugs were released singly (sparse release) on the same grid node on which they had been caught. Eleven tagged slugs were released as a group (dense release). Each of the slugs was radio-tracked for approximately 10 h during which their position was recorded ten times. The tracking data were analysed using the Correlated Random Walk framework. The analysis revealed that all components of slug movement (mean speed, turning angles and movement/resting times) were significantly different between the two treatments. On average, the slugs released as a group disperse more slowly than slugs released individually and their turning angle has a clear anticlockwise bias. The results clearly suggest that population density is a factor regulating slug movement.