bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping Sea Ice Surface Topography in High Fidelity With ICESat‐2
Authors: Farrell S. L. , Duncan K. , Buckley E. M. , Richter‐Menge J. , Li R.
Published: October 2020

The Advanced Topographic Laser Altimeter System on Ice, Cloud and land Elevation Satellite 2 (ICESat‐2) offers a new remote sensing capability to measure complex sea ice surface topography. We demonstrate the retrieval of six sea ice parameters from ICESat‐2/Advanced Topographic Laser Altimeter System data: surface roughness, ridge height, ridge frequency, melt pond depth, floe size distribution, and lead frequency. Our results establish that these properties can be observed in high fidelity, across broad geographic regions and ice conditions. We resolve features as narrow as 7 m and achieve a vertical height precision of 0.01 m, representing a significant advance in resolution over previous satellite altimeters. ICESat‐2 employs a year‐round observation strategy spanning all seasons, across both the Arctic and Southern Oceans. Because of its higher resolution, coupled with the spatial and temporal extent of data acquisition, ICESat‐2 observations may be used to investigate time‐varying, dynamic, and thermodynamic sea ice processes.
Flow‐to‐Friction Transition in Simulated Calcite Gouge: Experiments and Microphysical Modeling
Authors: Chen Jianye , Verberne B. A. , Niemeijer A. R.
Published: October 2020

A (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

This 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

The 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

There 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

Recent 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

In 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

The 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

Exome 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

To 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

Coffee 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

Incidental 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

Stress 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

The 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

Progressive 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

We 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.
Genassemblage 2.0 software facilitates conservation of genetic variation of captively propagated species
Authors: Kaczmarczyk Dariusz , Wolnicki Jacek
Published: October 2020

In conservation of captively propagated species, conserving genetic diversity is important. Here, we present an example of the use of Genassemblage 2.0 software in conserving the genetic variation of the lake minnow (Eupallasella percnurus). This fish has low genetic variation and is at risk of extinction in the western edge of its range, which includes Poland. Fish from one Polish population were captured (23 males, 25 females). Fin clips were taken, and DNA was extracted. Polymorphic microsatellites (13) were used to prepare genetic profiles, assess genetic variation in the fish and estimate genetic diversity in their progeny. Alleles were scored using an automatic capillary sequencer. The four and eight best variants of spawning pairs, and the optimal sets for group volitional breeding (four males, four females; eight males, eight females) were identified using Genassemblage 2.0. In the sets of 8 and 16 fish for group breeding, the mean heterozygosity, the number of alleles, and the share of “weak” heterozygotes (0.493, 24, 0.239 and 0.479, 23, 0.257, respectively) were better than the mean values for the progeny of all potential breeding pairs. For group volitional breeding, one set of four males and four females, and numerous sets of eight males and eight females would enable transmission of all 33 alleles identified in the potential broodstock and an expected progeny heterozygosity of 0.441 and 0.414, respectively. These expected heterozygosity values are higher than those in the broodstock. For practical purposes, the larger sets would be preferable for avoiding a future inbreeding and genetic drift.
ENSO diversity driving low-frequency change in mesoscale activity off Peru and Chile
Authors: Conejero Carlos , Dewitte Boris , Garçon Véronique , Sudre Joël , Montes Ivonne
Published: October 2020

Transient mesoscale oceanic eddies in Eastern Boundary Upwelling Systems are thought to strongly affect key regional scale processes such as ocean heat transport, coastal upwelling and productivity. Understanding how these can be modulated at low-frequency is thus critical to infer their role in the climate system. Here we use 26 years of satellite altimeter data and regional oceanic modeling to investigate the modulation of eddy kinetic energy (EKE) off Peru and Chile by ENSO, the main mode of natural variability in the tropical Pacific. We show that EKE tends to increase during strong Eastern Pacific (EP) El Niño events along the Peruvian coast up to northern Chile and decreases off central Chile, while it is hardly changed during Central Pacific El Niño and La Niña events. However the magnitude of the EKE changes during strong EP El Niño events is not proportional to their strength, with in particular the 1972/1973 El Niño event standing out as an extreme event in terms of EKE increase off Peru reaching an amplitude three times as large as that during the 1997/1998 El Niño event, and the 2015/2016 El Niño having instead a weak impact on EKE. This produces decadal changes in EKE, with a similar pattern than that of strong EP El Niño events, resulting in a significant negative (positive) long-term trend off Peru (central Chile).
Electrophysiological correlates of the brain-derived neurotrophic factor (BDNF) Val66Met polymorphism
Authors: Roy Nikita , Barry Robert J. , Fernandez Francesca E. , Lim Chai K. , Al-Dabbas Mahmoud A. , Karamacoska Diana , Broyd Samantha J. , Solowij Nadia , Chiu Christine L. , Steiner Genevieve Z.
Published: October 2020

The brain-derived neurotrophic factor (BDNF) protein is essential for neuronal development. Val66Met (rs6265) is a functional polymorphism at codon 66 of the BDNF gene that affects neuroplasticity and has been associated with cognition, brain structure and function. The aim of this study was to clarify the relationship between BDNF Val66Met polymorphism and neuronal oscillatory activity, using the electroencephalogram (EEG), in a normative cohort. Neurotypical (N = 92) young adults were genotyped for the BDNF Val66Met polymorphism and had eyes open resting-state EEG recorded for four minutes. Focal increases in right fronto-parietal delta, and decreases in alpha-1 and right hemispheric alpha-2 amplitudes were observed for the Met/Met genotype group compared to Val/Val and Val/Met groups. Stronger frontal topographies were demonstrated for beta-1 and beta-2 in the Val/Met group versus the Val/Val group. Findings highlight BDNF Val66Met genotypic differences in EEG spectral amplitudes, with increased cortical excitability implications for Met allele carriers.
Inhibition of NLRP3 inflammasome by MCC950 improves the metabolic outcome of islet transplantation by suppressing IL-1β and islet cellular death
Authors: Matsuoka Taisuke , Yoshimatsu Gumpei , Sakata Naoaki , Kawakami Ryo , Tanaka Tomoko , Yamada Teppei , Yoshida Yoichiro , Hasegawa Suguru , Kodama Shohta
Published: October 2020

Early rejection is a critical issue to be overcome to achieve successful islet transplantation. NLRP3 inflammasome is a protein complex that mediates the maturation of pro-interleukin (IL)-1β and pro-IL-18 to IL-1β and IL-18, respectively, which induce cellular death. Here, we investigated the impact of NLRP3 inflammasome and the effect of its inhibition by MCC950 in a rodent model of islet transplantation. We assessed the therapeutic effects of MCC950, a specific inhibitor of NLRP3 inflammasome, on gene expression, islet survival ratio and viability, and islet transplantation in mice. NLRP3 inflammasome-related gene (Nlrp3 and Il1b) expression was upregulated in islets stimulated with proinflammatory cytokines and suppressed when incubated with MCC950. Survival ratio and viability of incubated islets were reduced by cytokine stimulation and improved by MCC950. Regarding islet transplantation, the number of apoptotic cells in transplanted islets was reduced by MCC950. Furthermore, the expression of IL-1β in transplanted islets, migration of macrophages around islets, and fluctuation of blood glucose levels were suppressed by MCC950. Our study revealed that NLRP3 inflammasome worsened the therapeutic outcomes of islet transplantation and that MCC950 administration improved glycaemic control in syngeneic mice that underwent islet transplantation by inhibiting inflammation, which suppressed islet death.
Newly established gastrointestinal cancer cell lines retain the genomic and immunophenotypic landscape of their parental cancers
Authors: Hirsch Daniela , Seyfried Steffen , Staib Tobias , Fiedler David , Sauer Christian , Ried Thomas , Witt Stephanie , Rueckert Felix , Gaiser Timo
Published: October 2020

Human cancer cell lines are frequently used as model systems to study molecular mechanisms and genetic changes in cancer. However, the model is repeatedly criticized for its lack of proximity to original patient tumors. Therefore, understanding to what extent cell lines cultured under artificial conditions reflect the phenotypic and genomic profiles of their corresponding parental tumors is crucial when analyzing their biological properties. To directly compare molecular alterations between patient tumors and derived cell lines, we have established new cancer cell lines from four patients with gastrointestinal tumors. Tumor entities comprised esophageal cancer, colon cancer, rectal cancer and pancreatic cancer. Phenotype and genotype of both patient tumors and derived low-passage cell lines were characterized by immunohistochemistry (22 different antibodies), array-based comparative genomic hybridization and targeted next generation sequencing (48-gene panel). The immunophenotype was highly consistent between patient tumors and derived cell lines; the expression of most markers in cell lines was concordant with the respective parental tumor and characteristic for the respective tumor entities in general. The chromosomal aberration patterns of the parental tumors were largely maintained in the cell lines and the distribution of gains and losses was typical for the respective cancer entity, despite a few distinct differences. Cancer gene mutations (e.g., KRAS, TP53) and microsatellite status were also preserved in the respective cell line derivates. In conclusion, the four examined newly established cell lines exhibited a phenotype and genotype closely recapitulating their parental tumor. Hence, newly established cancer cell lines may be useful models for further pharmacogenomic studies.
Effects of temperature variability and extremes on spring phenology across the contiguous United States from 1982 to 2016
Authors: Liu Lingling , Zhang Xiaoyang
Published: October 2020

Warming climate and its impact on vegetation phenological trends have been widely investigated. However, interannual variability in temperature is considerably large in recent decades, which is expected to trigger an increasing trend of variation in vegetation phenology. To explore the interannual phenological variation across the contiguous United States (CONUS), we first detected the onset of vegetation greenup using the time series of the daily two-band Enhanced Vegetation Index (EVI2) observed from the AVHRR Long-Term Data Record (1982–1999) and the MODIS Climate Modeling Grid (2000–2016). We then calculated the interannual variation in greenup onset during four decadal periods: 1982–1989, 1990–1999, 2000–2009 and 2010–2016. Further, the trend of interannual variation in greenup onset from 1982 to 2016 was analyzed at pixel and state levels. Extreme phenological events were also determined using a greenup onset anomaly for each pixel. Similar approaches were applied to spring temperatures to detect extreme years and to the temporal trend of interannual variation to explain the phenological variation. The results revealed that 62% of pixels show an increasing interannual variation in greenup onset, and in 44% of pixels, this variation could be explained by the temperature. Although extreme phenology occurred locally in different years, three nationwide extreme phenological years were distinguished. The extreme warm spring that occurred in 2012 resulted in the occurrence of greenup onset as much as 20 days earlier than normal in large parts of the CONUS. In contrast, greenup onset was much later (up to 30 days) in 1983 and 1996 due to cool spring temperatures. These findings suggest that interannual variation in spring phenology could be much stronger in the future in response to climate variation, which could have more significant impacts on terrestrial ecosystems than the regular long-term phenological trend.
Pre-movement changes in sensorimotor beta oscillations predict motor adaptation drive
Authors: Darch Henry T. , Cerminara Nadia L. , Gilchrist Iain D. , Apps Richard
Published: October 2020

Beta frequency oscillations in scalp electroencephalography (EEG) recordings over the primary motor cortex have been associated with the preparation and execution of voluntary movements. Here, we test whether changes in beta frequency are related to the preparation of adapted movements in human, and whether such effects generalise to other species (cat). Eleven healthy adult humans performed a joystick visuomotor adaptation task. Beta (15–25 Hz) scalp EEG signals recorded over the motor cortex during a pre-movement preparatory phase were, on average, significantly reduced in amplitude during early adaptation trials compared to baseline, late adaptation, or aftereffect trials. The changes in beta were not related to measurements of reaction time or reach duration. We also recorded local field potential (LFP) activity within the primary motor cortex of three cats during a prism visuomotor adaptation task. Analysis of these signals revealed similar reductions in motor cortical LFP beta frequencies during early adaptation. This effect was present when controlling for any influence of the reaction time and reach duration. Overall, the results are consistent with a reduction in pre-movement beta oscillations predicting an increase in adaptive drive in upcoming task performance when motor errors are largest in magnitude and the rate of adaptation is greatest.
Alterations in the mucosal immune system by a chronic exhausting exercise in Wistar rats
Authors: Ruiz-Iglesias Patricia , Estruel-Amades Sheila , Camps-Bossacoma Mariona , Massot-Cladera Malén , Castell Margarida , Pérez-Cano Francisco J.
Published: October 2020

Exhausting exercise can disturb immune and gastrointestinal functions. Nevertheless, the impact of it on mucosal-associated lymphoid tissue has not been studied in depth. Here, we aim to establish the effects of an intensive training and exhausting exercise on the mucosal immunity of rats and to approach the mechanisms involved. Rats were submitted to a high-intensity training consisting of running in a treadmill 5 days per week for 5 weeks, involving 2 weekly exhaustion tests. At the end, samples were obtained before (T), immediately after (TE) and 24 h after (TE24) an additional final exhaustion test. The training programme reduced the salivary production of immunoglobulin A, impaired the tight junction proteins’ gene expression and modified the mesenteric lymph node lymphocyte composition and function, increasing the ratio between Tαβ+ and B lymphocytes, reducing their proliferation capacity and enhancing their interferon-γ secretion. As a consequence of the final exhaustion test, the caecal IgA content increased, while it impaired the gut zonula occludens expression and enhanced the interleukin-2 and interferon-γ secretion. Our results indicate that intensive training for 5 weeks followed or not by an additional exhaustion disrupts the mucosal-associated lymphoid tissue and the intestinal epithelial barrier integrity in rats.
MicroRNA-941 regulates the proliferation of breast cancer cells by altering histone H3 Ser 10 phosphorylation
Authors: Surapaneni Sunil Kumar , Bhat Zahid Rafiq , Tikoo Kulbhushan
Published: October 2020

Breast cancer including triple negative breast cancer (TNBC) represents an important clinical challenge, as these tumours often develop resistance to conventional chemotherapeutics. MicroRNAs play a crucial role in cell-cycle regulation, differentiation, apoptosis, and migration. Herein, we performed Affymetrix Gene Chip miRNA 4.0 microarray and observed differential regulation of miRNAs (75 upregulated and 199 downregulated) in metastatic MDA-MB-231 cells as compared to immortalized human non-tumorigenic breast epithelial (MCF-10A) cells. MicroRNA-941 was significantly upregulated in MDA-MB-231 cells (almost nine-fold increase) in comparison to MCF-10A cells. Transfection of MiRNA-941 inhibitor significantly decreased the proliferation and migration of MDA-MB-231 cells by altering the expressions of p21, Cyclin D1, PP2B-B1, E-cadherin and MMP-13. Interestingly, we provide first evidence that inhibiting miR-941 prevents cell proliferation and phosphorylation of histone H3 at Ser10 residue. Xenograft model of breast cancer was developed by subcutaneous injection of MDA-MB-231 cells into the mammary fat pad of female athymic nude mice (Crl:NU-Foxn1nu). The tumours were allowed to grow to around 60 mm3, thereafter which we divided the animals into seven groups (n = 5). Notably, intratumoral injection of miR-941 inhibitor significantly abolished the tumour growth in MDA-MB-231 xenograft model. 5-Fluorouracil (10 mg/kg, i.p.) was used as positive control in our study. To the best of our knowledge, we report for the first time that targeting miR-941 improves the sensitivity of MDA-MB-231 cells to 5-fluorouracil. This can be of profound clinical significance, as it provides novel therapeutic approach for treating variety of cancers (overexpressing miRNA-941) in general and breast cancers in particular.
Behaviours indicating cannibalistic necrophagy in ants are modulated by the perception of pathogen infection level
Authors: Maák István , Tóth Eszter , Lenda Magdalena , Lőrinczi Gábor , Kiss Anett , Juhász Orsolya , Czechowski Wojciech , Torma Attila
Published: October 2020

Cannibalistic necrophagy is rarely observed in social hymenopterans, although a lack of food could easily favour such behaviour. One of the main supposed reasons for the rarity of necrophagy is that eating of nestmate corpses carries the risk of rapid spread of pathogens or parasites. Here we present an experimental laboratory study on behaviour indicating consumption of nestmate corpses in the antFormica polyctena. We examined whether starvation and the fungal infection level of the corpses affects the occurrence of cannibalistic necrophagy. Our results showed that the ants distinguished between corpses of different types and with different levels of infection risk, adjusting their behaviour accordingly. The frequency of behaviours indicating cannibalistic necrophagy increased during starvation, although these behaviours seem to be fairly common inF. polyctenaeven in the presence of other food sources.The occurrence and significance of cannibalistic necrophagy deserve further research because, in addition to providing additional food, it may be part of the hygienic behaviour repertoire. The ability to detect infections and handle pathogens are important behavioural adaptations for social insects, crucial for the fitness of both individual workers and the entire colony.
The endangered California Condor (Gymnogyps californianus) population is exposed to local haemosporidian parasites
Authors: Pacheco M. Andreína , Parish Chris N. , Hauck Timothy J. , Aguilar Roberto F. , Escalante Ananias A.
Published: October 2020

The endangered California Condor (Gymnogyps californianus) is the largest New World Vulture in North America. Despite recovery program success in saving the species from extinction, condors remain compromised by lead poisoning and limited genetic diversity. The latter makes this species especially vulnerable to infectious diseases. Thus, taking advantage of the program of blood lead testing in Arizona, condor blood samples from 2008 to 2018 were screened for haemosporidian parasites using a nested polymerase chain reaction (PCR) protocol that targets the parasite mitochondrial cytochrome b gene. Plasmodium homopolare (Family Plasmodiidae, Order Haemosporida, Phylum Apicomplexa), was detected in condors captured in 2014 and 2017. This is the first report of a haemosporidian species infecting California Condors, and the first evidence of P. homopolare circulating in the Condor population from Arizona. Although no evidence of pathogenicity of P. homopolare in Condors was found, this study showed that the California Condors from Arizona are exposed to haemosporidian parasites that likely are spilling over from other local bird species. Thus, active surveillance should be an essential part of conservation efforts to mitigate the impact of infectious diseases, an increasingly recognized cause of global wildlife extinctions worldwide, particularly in avian populations considered vulnerable or endangered.
New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment
Authors: Milan David T. , Mendes Izabela S. , Damasceno Júnio S. , Teixeira Daniel F. , Sales Naiara G. , Carvalho Daniel C.
Published: October 2020

The megadiverse Neotropical fish fauna lacks a comprehensive and reliable DNA reference database, which hampers precise species identification and DNA based biodiversity assessment in the region. Here, we developed a mitochondrial 12S ribosomal DNA reference database for 67 fish species, representing 54 genera, 25 families, and six major Neotropical orders. We aimed to develop mini-barcode markers (i.e. amplicons with less than 200 bp) suitable for DNA metabarcoding by evaluating the taxonomic resolution of full-length and mini-barcodes and to determine a threshold value for fish species delimitation using 12S. Evaluation of the target amplicons demonstrated that both full-length library (565 bp) and mini-barcodes (193 bp) contain enough taxonomic resolution to differentiate all 67 fish species. For species delimitation, interspecific genetic distance threshold values of 0.4% and 0.55% were defined using full-length and mini-barcodes, respectively. A custom reference database and specific mini-barcode markers are important assets for ecoregion scale DNA based biodiversity assessments (such as environmental DNA) that can help with the complex task of conserving the megadiverse Neotropical ichthyofauna.
Mitigation potential of selenium nanoparticles and riboflavin against arsenic and elevated temperature stress in Pangasianodon hypophthalmus
Authors: Kumar Neeraj , Gupta Sanjay Kumar , Chandan Nitish Kumar , Bhushan Shashi , Singh Dilip Kumar , Kumar Paritosh , Kumar Prem , Wakchaure Goraksha C. , Singh Narendra Pratap
Published: October 2020

Climate change impact has disturbed the rainfall pattern worsening the problems of water availability in the aquatic ecosystem of India and other parts of the world. Arsenic pollution, mainly through excessive use of groundwater and other anthropogenic activities, is aggravating in many parts of the world, particularly in South Asia. We evaluated the efficacy of selenium nanoparticles (Se-NPs) and riboflavin (RF) to ameliorate the adverse impacts of elevated temperature and arsenic pollution on growth, anti-oxidative status and immuno-modulation in Pangasianodon hypophthalmus. Se-NPs were synthesized using fish gill employing green synthesis method. Four diets i.e., Se-NPs (0 mg kg−1) + RF (0 mg kg−1); Se-NPs (0.5 mg kg−1) + RF (5 mg kg−1); Se-NPs (0.5 mg kg−1) + RF (10 mg kg−1); and Se-NPs (0.5 mg kg−1) + RF (15 mg kg−1) were given in triplicate in a completely randomized block design. The fish were treated in arsenic (1/10th of LC50, 2.68 mg L−1) and high temperature (34 °C). Supplementation of the Se-NPs and RF in the diets significantly (p < 0.01) enhanced growth performance (weight gain, feed efficiency ratio, protein efficiency ratio, and specific growth rate), anti-oxidative status and immunity of the fish. Nitroblue tetrazolium (NBT), total immunoglobulin, myeloperoxidase and globulin enhanced (p < 0.01) with supplementation (Se-NPs + RF) whereas, albumin and albumin globulin (A:G) ratio (p < 0.01) reduced. Stress biomarkers such as lipid peroxidation in the liver, gill and kidney, blood glucose, heat shock protein 70 in gill and liver as well as serum cortisol reduced (p < 0.01) with supplementation of Se-NPs and RF, whereas, acetylcholine esterase and vitamin C level in both brain and muscle significantly enhanced (p < 0.01) in compared to control and stressors group (As + T) fed with control diet. The fish were treated with pathogenic bacteria after 90 days of experimental trial to observe cumulative mortality and relative survival for a week. The arsenic concentration in experimental water and bioaccumulation in fish tissues was also determined, which indicated that supplementation of Se-NPs and RF significantly reduced (p < 0.01) bioaccumulation. The study concluded that a combination of Se-NPs and RF has the potential to mitigate the stresses of high temperature and As pollution in P. hypophthalmus.