bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Fetal Alcohol Exposure by Analysis of Meconium Fatty Acid Ethyl Esters; A National Canadian Study
Authors: Delano Kaitlyn , Koren Gideon , Zack Martin , Kapur Bhushan M. 
Published: February 2019

AbstractOur study aimed to estimate the prevalence of heavy fetal alcohol exposure through the analysis of meconium FAEEs as an objective biomarker of fetal exposure. We conducted a study on meconium samples collected nationwide through the Maternal-Infant Research on Environmental Chemicals (MIREC) Study Group. FAEE in meconium was quantified by an established headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (SPME GC-MS). Out of 1315 samples collected in 10 Canadian obstetric units coast to coast between 2008-2011, the estimated prevalence of positive meconium FAEE ranged between 1.16% and 2.40%, translating into at least 1800 new cases of FASD in Canada each year. Positive maternal self- reports of heavy alcohol use were tenfold lower (0.24%). Use of meconium FAEE revealed tenfold more cases of heavy exposure to maternal drinking than did maternal reports. The use of objective measures of maternal alcohol exposure is critical in accurately estimating risks and in monitoring effective prevention of FASD.
Low-cost Fabrication of Tunable Band Gap Composite Indium and Gallium Nitrides
Authors: McInnes Andrew , Sagu Jagdeep S. , Mehta Diana , Wijayantha K. G. U. 
Published: February 2019

AbstractIII-nitride materials have been linked with a vast number of exciting applications from power electronics to solar cells. Herein, polycrystalline InN, GaN and systematically controlled InxGa1−xN composite thin films are fabricated on FTO glass by a facile, low-cost and scalable aerosol assisted chemical vapor deposition technique. Variation of the indium content in the composite films leads to a dramatic shift in the optical absorbance properties, which correlates with the band edges shifting between those of GaN to InN. Moreover, the photoelectrochemical properties are shown to vary with indium content, with the 50% indium composite having an external quantum efficiency of around 8%. Whilst the overall photocurrent is found to be low, the photocurrent stability is shown to be excellent, with little degradation seen over 1 hour. These findings demonstrate a new and low-cost method for fabricating polycrystalline III-nitrides, which have a range of interesting properties that are highly sought after for many applications.
Peripheral CD39-expressing T regulatory cells are increased and associated with relapsing-remitting multiple sclerosis in relapsing patients
Authors: Álvarez-Sánchez Nuria , Cruz-Chamorro Ivan , Díaz-Sánchez María , Lardone Patricia Judith , Guerrero Juan Miguel , Carrillo-Vico Antonio 
Published: February 2019

AbstractCD39, an ectonucleotidase that hydrolyses pro-inflammatory ATP, is a marker of highly active and suppressive T regulatory cells (Tregs). Although CD39 has a role in Treg suppression and might be important in the control of neuroinflammation in relapsing-remitting multiple sclerosis (RR-MS), to date, there are contradictory reports concerning the Tregs expression of CD39 in RR-MS patients. Thus, our objectives were to assess the activity and expression of CD39, especially in Tregs from peripheral blood mononuclear cells (PBMCs) of relapsing RR-MS patients compared with control subjects and to evaluate the association of CD39+ Tregs with disability and the odds of RR-MS. The activity and expression of CD39 and the CD39+ Treg frequency were measured in PBMCs from 55 relapsing RR-MS patients (19 untreated and 36 receiving immunomodulatory treatment) and 55 age- and sex-paired controls. Moreover, the association between CD39+ Tregs and RR-MS was assessed by multivariate logistic regression. CD39 activity and the frequency of CD39-expressing Tregs were elevated in relapsing RR-MS patients. Moreover, CD39+ Tregs were significantly correlated with the EDSS score and were independently associated with the odds of RR-MS. Our results highlight the relevance of CD39+ Treg subset in the clinical outcomes of RR-MS.
In vivo characterisation of fluorescent proteins in budding yeast
Authors: Botman Dennis , de Groot Daan Hugo , Schmidt Phillipp , Goedhart Joachim , Teusink Bas 
Published: February 2019

AbstractFluorescent proteins (FPs) are widely used in many organisms, but are commonly characterised in vitro. However, the in vitro properties may poorly reflect in vivo performance. Therefore, we characterised 27 FPs in vivo using Saccharomyces cerevisiae as model organism. We linked the FPs via a T2A peptide to a control FP, producing equimolar expression of the 2 FPs from 1 plasmid. Using this strategy, we characterised the FPs for brightness, photostability, photochromicity and pH-sensitivity, achieving a comprehensive in vivo characterisation. Many FPs showed different in vivo properties compared to existing in vitro data. Additionally, various FPs were photochromic, which affects readouts due to complex bleaching kinetics. Finally, we codon optimized the best performing FPs for optimal expression in yeast, and found that codon-optimization alters FP characteristics. These FPs improve experimental signal readout, opening new experimental possibilities. Our results may guide future studies in yeast that employ fluorescent proteins.
Diabetic endothelial colony forming cells have the potential for restoration with glycomimetics
Authors: Langford-Smith Alexander W. W. , Hasan Ahmad , Weston Ria , Edwards Nicola , Jones Alan M. , Boulton Andrew J. M. , Bowling Frank L. , Rashid S. Tawqeer , Wilkinson Fiona L. , Alexander M. Yvonne 
Published: February 2019

AbstractEndothelial colony forming progenitor cell (ECFC) function is compromised in diabetes, leading to poor vascular endothelial repair, which contributes to impaired diabetic foot ulcer healing. We have generated novel glycomimetic drugs with protective effects against endothelial dysfunction. We investigated the effect of glycomimetic C3 on the functional capacity of diabetic ECFCs. ECFCs were isolated from healthy controls and patients with diabetes with neuroischaemic (NI) or neuropathic (NP) foot ulcers. Functionally, diabetic ECFCs demonstrated delayed colony formation (p < 0.02), differential proliferative capacity (p < 0.001) and reduced NO bioavailability (NI ECFCs; p < 0.05). Chemokinetic migration and angiogenesis were also reduced in diabetic ECFCs (p < 0.01 and p < 0.001), and defects in wound closure and tube formation were apparent in NP ECFCs (p < 0.01). Differential patterns in mitochondrial activity were pronounced, with raised activity in NI and depressed activity in NP cells (p < 0.05). The application of glycomimetic improved scratch wound closure in vitro in patient ECFCs (p < 0.01), most significantly in NI cells (p < 0.001), where tube formation (p < 0.05) was also improved. We demonstrate restoration of the deficits in NI cells but not NP cells, using a novel glycomimetic agent, which may be advantageous for therapeutic cell transplantation or as a localised treatment for NI but not NP patients.
Genomic Features, Comparative Genomics, and Antimicrobial Susceptibility Patterns of Elizabethkingia bruuniana
Authors: Lin Jiun-Nong , Lai Chung-Hsu , Yang Chih-Hui , Huang Yi-Han , Lin Hsi-Hsun 
Published: February 2019

AbstractElizabethkingia bruuniana is a novel species of the Elizabethkingia genus. There is scant information on this microorganism. Here, we report the whole-genome features and antimicrobial susceptibility patterns of E. bruuniana strain EM798-26. Elizabethkingia strain EM798-26 was initially identified as E. miricola. This isolate contained a circular genome of 4,393,011 bp. The whole-genome sequence-based phylogeny revealed that Elizabethkingia strain EM798-26 was in the same group of the type strain E. bruuniana G0146T. Both in silico DNA-DNA hybridization and average nucleotide identity analysis clearly demonstrated that Elizabethkingia strain EM798-26 was a species of E. bruuniana. The pan-genome analysis identified 2,875 gene families in the core genome and 5,199 gene families in the pan genome of eight publicly available E. bruuniana genome sequences. The unique genes accounted for 0.2–12.1% of the pan genome in each E. bruuniana. A total of 59 potential virulence factor homologs were predicted in the whole-genome of E. bruuniana strain EM798–26. This isolate was nonsusceptible to multiple antibiotics, but susceptible to aminoglycosides, minocycline, and levofloxacin. The whole-genome sequence analysis of E. bruuniana EM798-26 revealed 29 homologs of antibiotic resistance-related genes. This study presents the genomic features of E. bruuniana. Knowledge of the genomic characteristics provides valuable insights into a novel species.
Novel model of secreted human tau protein reveals the impact of the abnormal N-glycosylation of tau on its aggregation propensity
Authors: Losev Yelena , Paul Ashim , Frenkel-Pinter Moran , Abu-Hussein Malak , Khalaila Isam , Gazit Ehud , Segal Daniel 
Published: February 2019

AbstractAlzheimer’s disease (AD) is the most common neurodegenerative disorder and has no disease-modifying treatment yet. The hallmarks of AD are two amyloidogenic proteins: tau and amyloid β (Aβ). Tau undergoes several posttranslational modifications, including N-glycosylation. Tau was reported to be N-glycosylated in AD brains, but not in healthy counterparts, which may affect AD etiology. Here, we aimed to examine the effect of N-glycosylation on aggregation propensity of tau. To that end, a novel SH-SY5Y cell-based model was generated in which recombinant human tau (htau) is forced to be secreted from the cells. Secreted htau was found to localize in the secretory pathway compartments and to undergo N-glycosylation. Following N-glycan cleavage of the secreted htau, various biophysical results collectively indicated that the untreated N-glycosylated secreted htau is markedly less aggregative, contains thinner and shorter fibrils, as compared to treated de-glycosylated secreted htau. This finding shows that N-glycans attached to htau may affect its aggregation. This could help to better understand the effect of N-glycosylated htau on AD progression.
Recycling endosomal CD133 functions as an inhibitor of autophagy at the pericentrosomal region
Authors: Izumi Hideki , Li Yuanyuan , Shibaki Masami , Mori Daisuke , Yasunami Michio , Sato Seiji , Matsunaga Hisashi , Mae Takao , Kodama Kenji , Kamijo Takehiko , Kaneko Yasuhiko , Nakagawara Akira 
Published: February 2019

AbstractCD133 is a transmembranous protein that mainly localises to the plasma membrane in haematopoietic and neural stem cells as well as cancer stem cells. Although CD133 also localises to the cytoplasm, the mechanism of action and function of cytoplasmic CD133 currently remain unknown. We herein demonstrated that when Src family kinase activity is weak, CD133 interacts with HDAC6 and is transported to the pericentrosomal region after internalization and endosome formation via the dynein-based traffic system. Pericentrosomal CD133 is then recycled to the plasma membrane via recycling endosomes. At the pericentrosomal region, endosomal CD133 captures GABARAP, an initiator of autophagy, and inhibits GABARAP-mediated ULK1 activation and the subsequent initiation of autophagy. Furthermore, pericentrosomal CD133 suppresses cell differentiation, such as primary cilium formation and neurite outgrowth, by inhibiting autophagy. Thus, the present results provide evidence to suggest that pericentrosomal CD133 has the unique property of maintaining the undifferentiated status of cells by inhibiting autophagy.
Analysis of postmarketing safety data for proton-pump inhibitors reveals increased propensity for renal injury, electrolyte abnormalities, and nephrolithiasis
Authors: Makunts Tigran , Cohen Isaac V. , Awdishu Linda , Abagyan Ruben 
Published: February 2019

AbstractProton pump inhibitors, PPIs, are widely prescribed and sold globally. Although initially intended for time-limited treatment of acute disorders, such as gastric ulcers and esophagitis, PPIs are now commonly used for prolonged durations and are considered safe for over the counter access. Recent studies have raised concern over associations between PPI use and acute kidney injury, chronic kidney disease, end-stage renal disease, and electrolyte abnormalities. The growing concern over potentially serious adverse drug reactions warrants an evaluation of post marketing surveillance data. In this study of over ten million FDA Adverse Event Reporting System records, we provided evidence of kidney injury and electrolyte imbalances in an alarming number of patients taking PPIs. Additionally, we assessed differences between specific PPIs and observed significant electrolyte and renal abnormalities for each individual drug with varying magnitudes.
Virtual cleaning and unwrapping of non-invasively digitized soiled bamboo scrolls
Authors: Stromer Daniel , Christlein Vincent , Huang Xiaolin , Zippert Patrick , Hausotte Tino , Maier Andreas 
Published: February 2019

AbstractIn ancient China, symbols and drawings captured on bamboo and wooden slips were used as main communication media. Those documents are very precious for cultural heritage and research, but due to aging processes, the discovered pieces are sometimes in a poor condition and contaminated by soil. Manual cleaning of excavated slips is a demanding and time-consuming task in which writings can be accidentally deleted. To counter this, we propose a novel approach based on conventional 3-D X-ray computed tomography to digitize such historical documents without before manual cleaning. By applying a virtual cleaning and unwrapping algorithm, the entire scroll surface is remapped into 2-D such that the hidden content becomes readable. We show that the technique also works for heavily soiled scrolls, enabling an investigation of the content by the naked eye without the need for manual labor. This digitization also allows for recovery of potentially erased writings and reconstruction of the original spatial information.
A dynamic view of the proteomic landscape during differentiation of ReNcell VM cells, an immortalized human neural progenitor line
Authors: Song Yuyu , Subramanian Kartik , Berberich Matthew J. , Rodriguez Steven , Latorre Isabel J. , Luria Catherine M. , Everley Robert , Albers Mark W. , Mitchison Timothy J. , Sorger Peter K. 
Published: February 2019

AbstractThe immortalized human ReNcell VM cell line represents a reproducible and easy-to-propagate cell culture system for studying the differentiation of neural progenitors. To better characterize the starting line and its subsequent differentiation, we assessed protein and phospho-protein levels and cell morphology over a 15-day period during which ReNcell progenitors differentiated into neurons, astrocytes and oligodendrocytes. Five of the resulting datasets measured protein levels or states of phosphorylation based on tandem-mass-tag (TMT) mass spectrometry and four datasets characterized cellular phenotypes using high-content microscopy. Proteomic analysis revealed reproducible changes in pathways responsible for cytoskeletal rearrangement, cell phase transitions, neuronal migration, glial differentiation, neurotrophic signalling and extracellular matrix regulation. Proteomic and imaging data revealed accelerated differentiation in cells treated with the poly-selective CDK and GSK3 inhibitor kenpaullone or the HMG-CoA reductase inhibitor mevastatin, both of which have previously been reported to promote neural differentiation. These data provide in-depth information on the ReNcell progenitor state and on neural differentiation in the presence and absence of drugs, setting the stage for functional studies.
Sex-specific median life expectancies from ex situ populations for 330 animal species
Authors: Che-Castaldo Judy P. , Byrne Amy , Perišin Kaitlyn , Faust Lisa J. 
Published: February 2019

AbstractWe present life expectancy estimates for hundreds of vertebrate species based on carefully vetted studbook data from North American zoos and aquariums. These data include sex-specific median life expectancies as well as sample size and 95% confidence limits for each estimate. Existing longevity data for animals primarily consist of maximum lifespan values, which are single observations rather than statistically derived estimates of longevity. Moreover, all of our estimates are based on the same type of data and calculated using consistent, standardized methods. To derive these estimates, we conducted Kaplan-Meier survival analyses using individual-level demographic data (i.e., records of birth and mortality events) from studbook records for each ex situ population. Our species set represents a range of vertebrate taxa (primarily mammals, birds, amphibians, and reptiles) and diverse life histories. This dataset will have broad utility, not only for informing comparative demographic and life history studies, but also more broadly for any research or conservation application that requires sex- or species-specific life expectancy information.
The variable quality of metadata about biological samples used in biomedical experiments
Authors: Gonçalves Rafael S. , Musen Mark A. 
Published: February 2019

AbstractWe present an analytical study of the quality of metadata about samples used in biomedical experiments. The metadata under analysis are stored in two well-known databases: BioSample—a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples—a repository managed by the European Bioinformatics Institute (EBI). We tested whether 11.4 M sample metadata records in the two repositories are populated with values that fulfill the stated requirements for such values. Our study revealed multiple anomalies in the metadata. Most metadata field names and their values are not standardized or controlled. Even simple binary or numeric fields are often populated with inadequate values of different data types. By clustering metadata field names, we discovered there are often many distinct ways to represent the same aspect of a sample. Overall, the metadata we analyzed reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements. The significant aberrancies that we found in the metadata are likely to impede search and secondary use of the associated datasets.
Long noncoding RNA and mRNA expression profiles following igf3 knockdown in common carp, Cyprinus carpio
Authors: Song Feibiao , Wang Lanmei , Zhu Wenbin , Dong Zaijie 
Published: February 2019

AbstractAs a novel IGF system member, igf3 plays an important role in gonadal development of teleost fish. Although studies have reported the unusual expression of igf3 in fish gonad, whether the igf3 affects the expression of long noncoding RNAs (lncRNAs) in gonad remains unknown. In this study, an igf3 knockdown common carp (Cyprinus carpio) model was established by RNA interference. Then RNA sequencing of C. carpio gonad after igf3 knockdown was performed. A total of 327,169,410 and 306,305,018 clean reads were identified from control and igf3-dsRNA interference group, respectively. After a stringent filtering, RNA-seq yielded 14199 lncRNA and 106932 mRNA transcripts with 124 and 353 differentially expressed lncRNAs and mRNAs. Our dataset provides an extensive resource for understanding the potential regulatory molecular mechanism of igf3 in early stage of gonadal development in C. carpio.
Dynamic hydrolase labelling as a marker for seed quality in Arabidopsis seeds
Authors: Viñegra de la Torre Natanael , Kaschani Farnusch , Kaiser Markus , van der Hoorn Renier A. L. , Soppe Wim J. J. , Misas Villamil Johana C. 
Published: February 2019

Abstract
Seed quality is affected by different constituents of the seed. In general, seed lots are considered to be of high quality when they exhibit fast and homogeneous germination. When seeds are stored, they undergo different degrees of damage that have detrimental effects on their quality. Therefore, accurate prediction of the seed quality and viability levels of a seed lot is of high importance in the seed-producing industry. Here, we describe the use of activity-based protein profiling of proteases to evaluate the quality of artificially and naturally aged seeds of Arabidopsis thaliana. Using this approach, we have identified two protease activities with opposite behaviours in aged seeds of Arabidopsis that correlate with the quality status of the seeds. We show that vacuolar processing enzymes (VPEs) become more active during the ageing process, in both artificial and natural ageing treatments. Secondly, we demonstrate that serine hydrolases are active at the beginning of our artificial ageing treatment, but their labelling decreases along with seed viability. We present a list of candidate hydrolases active during seed germination and propose that these protease activities can be used in combination with VPEs to develop novel markers of seed quality.
Cysteine-rich granulin-3 rapidly promotes amyloid-β fibrils in both redox states
Authors: Bhopatkar Anukool A. , Ghag Gaurav , Wolf Lauren M. , Dean Dexter N. , Moss Melissa A. , Rangachari Vijayaraghavan 
Published: February 2019

Abstract
Granulins (GRNs 1–7) are cysteine-rich proteolytic products of progranulin (PGRN) that have recently been implicated in neurodegenerative diseases including frontotemporal dementia (FTD) and Alzheimer's disease (AD). Their precise mechanism in these pathologies remains uncertain, but both inflammatory and lysosomal roles have been observed for GRNs. Among the seven GRNs, GRN-3 is well characterized and is implicated within the context of FTD. However, the relationship between GRN-3 and amyloid-β (Aβ), a protein relevant in AD pathology, has not yet been explored. To gain insight into this mechanism, we investigated the effect of both oxidized and reduced GRN-3 on Aβ aggregation and found that both GRN-3 (oxidized) and rGRN-3 (reduced) bind to monomeric and oligomeric Aβ42 to promote rapid fibril formation with subtle rate differences. As low molecular weight oligomers of Aβ are well-established neurotoxins, rapid promotion of fibrils by GRN-3 mitigates Aβ42-induced cellular apoptosis. These data provide valuable insights in understanding GRN-3's ability to modulate Aβ-induced toxicity under redox control and presents a new perspective toward AD pathology. These results also prompt further investigation into the role(s) of other GRNs in AD pathogenesis.