bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contemporary limnology of the rapidly changing glacierized watershed of the world’s largest High Arctic lake
Authors: St. Pierre K. A. , St. Louis V. L. , Lehnherr I. , Schiff S. L. , Muir D. C. G. , Poulain A. J. , Smol J. P. , Talbot C. , Ma M. , Findlay D. L. , Findlay W. J. , Arnott S. E. , Gardner Alex S. 
Published: March 2019

AbstractGlacial runoff is predicted to increase in many parts of the Arctic with climate change, yet little is known about the biogeochemical impacts of meltwaters on downstream freshwater ecosystems. Here we document the contemporary limnology of the rapidly changing glacierized watershed of the world’s largest High Arctic lake (Lake Hazen), where warming since 2007 has increased delivery of glacial meltwaters to the lake by up to 10-times. Annually, glacial meltwaters accounted for 62–98% of dissolved nutrient inputs to the lake, depending on the chemical species and year. Lake Hazen was a strong sink for NO3−-NO2−, NH4+ and DOC, but a source of DIC to its outflow the Ruggles River. Most nutrients entering Lake Hazen were, however, particle-bound and directly transported well below the photic zone via dense turbidity currents, thus reinforcing ultraoligotrophy in the lake rather than overcoming it. For the first time, we apply the land-to-ocean aquatic continuum framework in a large glacierized Arctic watershed, and provide a detailed and holistic description of the physical, chemical and biological limnology of the rapidly changing Lake Hazen watershed. Our findings highlight the sensitivity of freshwater ecosystems to the changing cryosphere, with implications for future water quality and productivity at high latitudes.
Atmospheric ammonia (NH3) emanations from Lake Natron’s saline mudflats
Authors: Clarisse L. , Van Damme M. , Gardner W. , Coheur P.-F. , Clerbaux C. , Whitburn S. , Hadji-Lazaro J. , Hurtmans D. 
Published: March 2019

AbstractIn a recent global analysis of satellite-derived atmospheric NH3 data, a hotspot was observed in the vicinity of Lake Natron, Tanzania. The lake is in the centre of an endorheic (limited drainage) basin and has shallow, saline-alkaline waters. Its remote location and the absence of nearby large anthropogenic sources suggest that the observed NH3 is mainly of natural origin. Here we explore 10 years of IASI NH3 satellite data and other publicly available datasets over the area to characterize the natural NH3 emissions in this unique ecosystem. Temporal analysis reveals that the emissions are episodic and linked with the lake’s surface area. The largest NH3 column loadings generally occur at the end of the dry season in September–November over Lake Natron’s largest mudflat, that is exposed with receding water levels. The timing is different from the agricultural dominated NH3 emissions in the wider Natron area, which peak early in the year, after the first wet season. The likely source of NH3 at Lake Natron is decomposition of organic material, either from rivers and springs or produced in the lake (plankton, bird excreta). High temperatures and alkalinity are known to promote NH3 losses from soda lakes. We formulate six processes that may explain why the largest losses are observed specifically over concentrated brines and/or exposed sediments. As a by-product, we also show that hyperspectral infrared sounders such as IASI are capable of mapping different types of evaporative minerals such as trona and thermonatrite.
Intrinsic activation of cell growth and differentiation in ex vivo cultured human hair follicles by a transient endogenous production of ROS
Authors: Calvo-Sánchez María I. , Fernández-Martos Sandra , Montoya Juan José , Espada Jesús 
Published: March 2019

AbstractThe emerging variety of signalling roles for ROS in eukaryotic cells and tissues is currently a matter of intense research. Here we make use of ex vivo cultured single human hair follicles as an experimental model to demonstrate that a transient production of non-lethal endogenous ROS levels in these mini-organs promotes efficiently the entry into the growth phase (anagen). The stimulatory process implicates the specific activation of the hair follicle stem cell niche, encompassing the induction of stem cell differentiation markers (Ck15), overall cell proliferation and sustained growth of the tissue associated with expression of gen targets (Ccnd1) concomitant with the inhibition of Wnt signaling antagonists and repressors (Dkk1, Gsk3β) of Wnt signaling. As a whole, this observation indicates that, once activated, ROS signalling is an intrinsic mechanism regulating the hair follicle stem cell niche independently of any external signal.
Functional divergence of thyrotropin beta-subunit paralogs gives new insights into salmon smoltification metamorphosis
Authors: Fleming Mitchell S. , Maugars Gersende , Lafont Anne-Gaëlle , Rancon Jocelyn , Fontaine Romain , Nourizadeh-Lillabadi Rasoul , Weltzien Finn-Arne , Yebra-Pimentel Elena Santidrian , Dirks Ron , McCormick Stephen D. , Rousseau Karine , Martin Patrick , Dufour Sylvie 
Published: March 2019

AbstractSmoltification is a metamorphic event in salmon life history, which initiates downstream migration and pre-adapts juvenile salmon for seawater entry. While a number of reports concern thyroid hormones and smoltification, few and inconclusive studies have addressed the potential role of thyrotropin (TSH). TSH is composed of a α-subunit common to gonadotropins, and a β-subunit conferring hormone specificity. We report the presence and functional divergence of duplicated TSH β-subunit paralogs (tshβa and tshβb) in Atlantic salmon. Phylogeny and synteny analyses allowed us to infer that they originated from teleost-specific whole genome duplication. Expression profiles of both paralogs in the pituitary were measured by qPCR throughout smoltification in Atlantic salmon from the endangered Loire-Allier population raised in a conservation hatchery. This revealed a striking peak of tshβb expression in April, concomitant with downstream migration initiation, while tshβa expression remained relatively constant. In situ hybridization showed two distinct pituitary cell populations, tshβa cells in the anterior adenohypophysis, and tshβb cells near to the pituitary stalk, a location comparable to the pars tuberalis TSH cells involved in seasonal physiology and behaviour in birds and mammals. Functional divergence of tshβ paralogs in Atlantic salmon supports a specific role of tshβb in smoltification.
DNA DSB Repair Dynamics following Irradiation with Laser-Driven Protons at Ultra-High Dose Rates
Authors: Hanton F. , Chaudhary P. , Doria D. , Gwynne D. , Maiorino C. , Scullion C. , Ahmed H. , Marshall T. , Naughton K. , Romagnani L. , Kar S. , Schettino G. , McKenna P. , Botchway S. , Symes D. R. , Rajeev P. P. , Prise K. M. , Borghesi M. 
Published: March 2019

AbstractProtontherapy has emerged as more effective in the treatment of certain tumors than photon based therapies. However, significant capital and operational costs make protontherapy less accessible. This has stimulated interest in alternative proton delivery approaches, and in this context the use of laser-based technologies for the generation of ultra-high dose rate ion beams has been proposed as a prospective route. A better understanding of the radiobiological effects at ultra-high dose-rates is important for any future clinical adoption of this technology. In this study, we irradiated human skin fibroblasts-AG01522B cells with laser-accelerated protons at a dose rate of 109 Gy/s, generated using the Gemini laser system at the Rutherford Appleton Laboratory, UK. We studied DNA double strand break (DSB) repair kinetics using the p53 binding protein-1(53BP1) foci formation assay and observed a close similarity in the 53BP1 foci repair kinetics in the cells irradiated with 225 kVp X-rays and ultra- high dose rate protons for the initial time points. At the microdosimetric scale, foci per cell per track values showed a good correlation between the laser and cyclotron-accelerated protons indicating similarity in the DNA DSB induction and repair, independent of the time duration over which the dose was delivered.
Circadian and wake-dependent changes in human plasma polar metabolites during prolonged wakefulness: A preliminary analysis
Authors: Grant Leilah K. , Ftouni Suzanne , Nijagal Brunda , De Souza David P. , Tull Dedreia , McConville Malcolm J. , Rajaratnam Shantha M. W. , Lockley Steven W. , Anderson Clare 
Published: March 2019

AbstractEstablishing circadian and wake-dependent changes in the human metabolome are critical for understanding and treating human diseases due to circadian misalignment or extended wake. Here, we assessed endogenous circadian rhythms and wake-dependent changes in plasma metabolites in 13 participants (4 females) studied during 40-hours of wakefulness. Four-hourly plasma samples were analyzed by hydrophilic interaction liquid chromatography (HILIC)-LC-MS for 1,740 metabolite signals. Group-averaged (relative to DLMO) and individual participant metabolite profiles were fitted with a combined cosinor and linear regression model. In group-level analyses, 22% of metabolites were rhythmic and 8% were linear, whereas in individual-level analyses, 14% of profiles were rhythmic and 4% were linear. We observed metabolites that were significant at the group-level but not significant in a single individual, and metabolites that were significant in approximately half of individuals but not group-significant. Of the group-rhythmic and group-linear metabolites, only 7% and 12% were also significantly rhythmic or linear, respectively, in ≥50% of participants. Owing to large inter-individual variation in rhythm timing and the magnitude and direction of linear change, acrophase and slope estimates also differed between group- and individual-level analyses. These preliminary findings have important implications for biomarker development and understanding of sleep and circadian regulation of metabolism.
Role of Low-Affinity Calcium System Member Fig1 Homologous Proteins in Conidiation and Trap-Formation of Nematode-trapping Fungus Arthrobotrys oligospora
Authors: Zhang Weiwei , Hu Chengcheng , Hussain Muzammil , Chen Jiezuo , Xiang Meichun , Liu Xingzhong 
Published: March 2019

AbstractArthrobotrys oligospora is a typical nematode-trapping fungus capturing free-living nematodes by adhesive networks. Component of the low-affinity calcium uptake system (LACS) has been documented to involve in growth and sexual development of filamentous fungi. Bioassay showed incapacity of trap formation in A. oligospora on Water Agar plate containing 1 mM ethylene glycol tetraacetic acid (EGTA) due to Ca2+ absorbing block. The functions of homologous proteins (AoFIG_1 and AoFIG_2) of LACS were examined on conidiation and trap formation of A. oligospora. Compared with wild type, ΔAoFIG_1 (AOL_s00007g566) resulted in 90% of trap reduction, while ΔAoFIG_2 (AOL_s00004g576) reduced vegetative growth rate up to 44% and had no trap and conidia formed. The results suggest that LACS transmembrane protein fig1 homologs play vital roles in the trap-formation and is involved in conidiation and mycelium growth of A. oligospora. Our findings expand fig1 role to include development of complex trap device and conidiation.
PPARα-Mediated Positive-Feedback Loop Contributes to Cold Exposure Memory
Authors: Alfaqaan Soaad , Yoshida Tomoki , Imamura Hiromi , Tsukano Chihiro , Takemoto Yoshiji , Kakizuka Akira 
Published: March 2019

AbstractFluctuations in food availability and shifts in temperature are typical environmental changes experienced by animals. These environmental shifts sometimes portend more severe changes; e.g., chilly north winds precede the onset of winter. Such telltale signs may be indicators for animals to prepare for such a shift. Here we show that HEK293A cells, cultured under starvation conditions, can “memorize” a short exposure to cold temperature (15 °C), which was evidenced by their higher survival rate compared to cells continuously grown at 37 °C. We refer to this phenomenon as “cold adaptation”. The cold-exposed cells retained high ATP levels, and addition of etomoxir, a fatty acid oxidation inhibitor, abrogated the enhanced cell survival. In our standard protocol, cold adaptation required linoleic acid (LA) supplementation along with the activity of Δ-6-desaturase (D6D), a key enzyme in LA metabolism. Moreover, supplementation with the LA metabolite arachidonic acid (AA), which is a high-affinity agonist of peroxisome proliferator-activated receptor-alpha (PPARα), was able to underpin the cold adaptation, even in the presence of a D6D inhibitor. Cold exposure with added LA or AA prompted a surge in PPARα levels, followed by the induction of D6D expression; addition of a PPARα antagonist or a D6D inhibitor abrogated both their expression, and reduced cell survival to control levels. We also found that the brief cold exposure transiently prevents PPARα degradation by inhibiting the ubiquitin proteasome system, and starvation contributes to the enhancement of PPARα activity by inhibiting mTORC1. Our results reveal an innate adaptive positive-feedback mechanism with a PPARα-D6D-AA axis that is triggered by a brief cold exposure in cells. “Cold adaptation” could have evolved to increase strength and resilience against imminent extreme cold temperatures.
Somatic symptom load in men and women from middle to high age in the Gutenberg Health Study - association with psychosocial and somatic factors
Authors: Beutel Manfred E. , Wiltink Jörg , Ghaemi Kerahrodi Jasmin , Tibubos Ana N. , Brähler Elmar , Schulz Andreas , Wild Philipp , Münzel Thomas , Lackner Karl , König Jochem , Pfeiffer Norbert , Michal Matthias , Henning Michaela 
Published: March 2019

AbstractThe purpose of the study was (1) to determine the prevalence of somatic symptoms in men and women in the general population and (2) to identify the contributions of psychosocial factors and somatic disease on symptom reporting. A total of 7,925 participants aged 40 to 80 years underwent medical and psychological assessments, based on the PHQ-15 (Patient Health Questionnaire). We excluded 3 items in order to avoid confounding findings: 2 items overlapping with the depression measure (PHQ-9) and the menstruation complaints item which biases sex comparisons. Pain complaints (arms, legs, joints, back pain) affected the majority of men and women, and somatic symptom reporting increased with age. When confounding has been reduced, psychosocial factors (lack of social support, adverse life events, loneliness, depression, generalized anxiety, panic, social phobia) have remained the strongest predictors of somatic symptoms. As shown by the interaction between sex and depression, depression plays a smaller role for somatic symptom reporting in women vs. men. Findings highlight the complex psychosocial and somatic contributions to somatic symptom reporting.
Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins
Authors: Sobhy Haitham , Kumar Rajendra , Lewerentz Jacob , Lizana Ludvig , Stenberg Per 
Published: March 2019

AbstractIn specific cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have limited understanding of many loops identified by Chromosome Conformation Capture (such as Hi-C) analyses. In efforts to elucidate their characteristics and functions, we have identified highly interacting regions (HIRs) using intra-chromosomal Hi-C datasets with a new computational method based on looking at the eigenvector that corresponds to the smallest eigenvalue (here unity). Analysis of these regions using ENCODE data shows that they are in general enriched in bound factors involved in DNA damage repair and have actively transcribed genes. However, both highly transcribed regions as well as transcriptionally inactive regions can form HIRs. The results also indicate that enhancers and super-enhancers in particular form long-range interactions within the same chromosome. The accumulation of DNA repair factors in most identified HIRs suggests that protection from DNA damage in these regions is essential for avoidance of detrimental rearrangements.
Analyses of 202 plastid genomes elucidate the phylogeny of Solanum section Petota
Authors: Huang Binquan , Ruess Holly , Liang Qiqi , Colleoni Christophe , Spooner David M. 
Published: March 2019

AbstractOur paper analyzes full plastid DNA sequence data of 202 wild and cultivated diploid potatoes,SolanumsectionPetota, to explore its phylogenetic utility compared to prior analyses of the same accessions using genome-wide nuclear SNPs, and plastid DNA restriction site data. The present plastid analysis discovered the same major clades as the nuclear data but with some substantial differences in topology within the clades. The considerably larger plastid and nuclear data sets add phylogenetic resolution within the prior plastid DNA restriction site data, highlight plastid/nuclear incongruence that supports hypotheses of hybridization/introgression to help explain the taxonomic difficulty in the section.
Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA
Authors: Bhattacharyya Roby P. , Walker Mark , Boykin Rich , Son Sophie S. , Liu Jamin , Hachey Austin C. , Ma Peijun , Wu Lidan , Choi Kyungyong , Cummins Kaelyn C. , Benson Maura , Skerry Jennifer , Ryu Hyunryul , Wong Sharon Y. , Goldberg Marcia B. , Han Jongyoon , Pierce Virginia M. , Cosimi Lisa A. , Shoresh Noam , Livny Jonathan , Beechem Joseph , Hung Deborah T. 
Published: March 2019

AbstractRapid bacterial identification remains a critical challenge in infectious disease diagnostics. We developed a novel molecular approach to detect and identify a wide diversity of bacterial pathogens in a single, simple assay, exploiting the conservation, abundance, and rich phylogenetic content of ribosomal RNA in a rapid fluorescent hybridization assay that requires no amplification or enzymology. Of 117 isolates from 64 species across 4 phyla, this assay identified bacteria with >89% accuracy at the species level and 100% accuracy at the family level, enabling all critical clinical distinctions. In pilot studies on primary clinical specimens, including sputum, blood cultures, and pus, bacteria from 5 different phyla were identified.
Single-cell transcriptome analysis identifies distinct cell types and niche signaling in a primary gastric organoid model
Authors: Chen Jiamin , Lau Billy T. , Andor Noemi , Grimes Susan M. , Handy Christine , Wood-Bouwens Christina , Ji Hanlee P. 
Published: March 2019

AbstractThe diverse cellular milieu of the gastric tissue microenvironment plays a critical role in normal tissue homeostasis and tumor development. However, few cell culture model can recapitulate the tissue microenvironment and intercellular signalingin vitro. We used a primary tissue culture system to generate a murine p53 null gastric tissue model containing both epithelium and mesenchymal stroma. To characterize the microenvironment and niche signaling, we used single cell RNA sequencing (scRNA-Seq) to determine the transcriptomes of 4,391 individual cells. Based on specific markers, we identified epithelial cells, fibroblasts and macrophages in initial tissue explants during organoid formation. The majority of macrophages were polarized towards wound healing and tumor promotion M2-type. During the course of time, the organoids maintained both epithelial and fibroblast lineages with the features of immature mouse gastric stomach. We detected a subset of cells in both lineages expressingLgr5, one of the stem cell markers. We examined the lineage-specific Wnt signaling activation, and identified thatRspo3was specifically expressed in the fibroblast lineage, providing an endogenous source of the R-spondin to activate Wnt signaling. Our studies demonstrate that this primary tissue culture system enables one to study gastric tissue niche signaling and immune responsein vitro.
Identification of polysaccharide capsules among extensively drug-resistant genitourinary Haemophilus parainfluenzae isolates
Authors: González-Díaz Aida , Tubau Fe , Pinto Miguel , Sierra Yanik , Cubero Meritxell , Càmara Jordi , Ayats Josefina , Bajanca-Lavado Paula , Ardanuy Carmen , Marti Sara 
Published: March 2019

AbstractThe human commensal Haemophilus parainfluenzae is emerging as an opportunistic multidrug-resistant pathogen. The objectives of this work were to characterise a new capsular operon of extensively drug-resistant (XDR) H. parainfluenzae clinical isolates and study their resistance mechanisms using whole-genome sequencing. All strains were resistant to: ß-lactams, via amino acid changes in PBP3 (S385T, I442F, V511A, N526K and V562I); quinolones, by alterations in GyrA (S84F and D88Y) and ParC (S84F and S138T); chloramphenicol, through the presence of catS; macrolides, via the presence of mel and mef(E)-carrying MEGA element; and tetracycline, through the presence of tet(M) and/or tet(B). Phylogenetic analysis revealed high genomic diversity when compared to the H. parainfluenzae genomes available on the NCBI, the isolates from this study being closely related to the Swiss XDR AE-2096513. A full capsular operon showing homology to that of H. influenzae was identified, in accordance with the observation of a capsular structure by TEM. This study describes for the first time a capsular operon in H. parainfluenzae, a major determinant of pathogenicity that may contribute to increased virulence in XDR clinical isolates. Moreover, phylogenetic analysis suggests the possible spread of an XDR-encapsulated strain in Europe.
An analysis of benign human prostate offers insights into the mechanism of apocrine secretion and the origin of prostasomes
Authors: Fullwood Nigel J. , Lawlor Alan J. , Martin-Hirsch Pierre L. , Matanhelia Shyam S. , Martin Francis L. 
Published: March 2019

AbstractThe structure and function of normal human prostate is still not fully understood. Herein, we concentrate on the different cell types present in normal prostate, describing some previously unreported types and provide evidence that prostasomes are primarily produced by apocrine secretion. Patients (n = 10) undergoing TURP were prospectively consented based on their having a low risk of harbouring CaP. Scanning electron microscopy and transmission electron microscopy was used to characterise cell types and modes of secretion. Zinc levels were determined using Inductively Coupled Plasma Mass Spectrometry. Although merocrine secretory cells were noted, the majority of secretory cells appear to be apocrine; for the first time, we clearly show high-resolution images of the stages of aposome secretion in human prostate. We also report a previously undescribed type of epithelial cell and the first ultrastructural image of wrapping cells in human prostate stroma. The zinc levels in the tissues examined were uniformly high and X-ray microanalysis detected zinc in merocrine cells but not in prostasomes. We conclude that a significant proportion of prostasomes, possibly the majority, are generated via apocrine secretion. This finding provides an explanation as to why so many large proteins, without a signal peptide sequence, are present in the prostatic fluid.