bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of Copeptin With Sense of Coherence in Individuals With Varying Degrees of Glucose Intolerance
Authors: Madhu Sri Venkata , Aslam Mohammad , Siddiqui Azaz Ahmad , Goyal Sandeep , Mishra Brijesh Kumar 
Published: November 2019

ABSTRACT

Objective
This study aimed to examine the association of serum copeptin levels, a surrogate marker of arginine-vasopressin secretion with sense of coherence (SOC) among individuals with varying degrees of glucose intolerance.

Methods
The study was conducted in 120 age- and sex-matched individuals who were divided equally into three groups. Group A included individuals with normal glucose tolerance; group B, individuals with prediabetes (impaired glucose tolerance and/or impaired fasting glucose); and group C, individuals with newly detected diabetes mellitus (NDDM). SOC, perceived stress scale (PSS), copeptin, anthropometry, glycated hemoglobin, insulin, and salivary cortisol were measured in all study participants.

Results
The SOC score was found to be significantly lower in group C compared with group A (p < .001) and group B (p = .006). The PSS score was found to be significantly higher in group C compared with group A (p = .002). No significant difference was found between PSS scores of groups B and C (p = .25). Copeptin levels were found to be significantly higher in group C compared with group A (p = .016). Copeptin levels in group C did not differ significantly from those in group B (p = .056). There was a significant negative correlation between serum copeptin levels and SOC in the NDDM group C (r = 0.31, p = .048) and overall (r = 0.19, p = .037). In multiple regression analysis, SOC emerged as the variable with the strongest association with 2-hour postprandial plasma glucose and glycated hemoglobin.

Conclusion
Individuals with NDDM displayed significantly higher serum copeptin levels that inversely correlated with SOC, a global measure of stress coping ability.
Hospital Admissions Associated With Medication-Related Problems in Thai Older Patients: A Multicenter Prospective Observational Study
Authors: Dechanont Supinya , Jedsadayanmata Arom , Butthum Bodin , Kongkaew Chuenjid 
Published: November 2019

Objective
The aim of the study was to estimate the prevalence rate and risk factors of medication-related problems (MRPs) leading to hospital admissions in Thai older patients.

Methods
A prospective observational study was carried out in nine hospitals in Lower Northern Thailand. Participants admitted to internal medicine units were screened for suspected MRPs by clinical pharmacists using medical record review and patient interview. Three experts evaluated suspected MRPs independently using the following four criteria: contribution of MRPs to hospital admissions, causality, severity, and preventability.

Results
Of 1776 patients admitted during the study period, 56 patients (3.2%) were deemed to have causal MRPs; 24 (42.9%) were judged as preventable. The medication groups most commonly associated with MRPs were those targeting the endocrine system, especially antidiabetic medications, such as metformin and glipizide. Preventable MRPs were usually manifest as hypoglycemia (n = 15, 62.5%). The variables that contributed to hospital admissions associated with MRPs were age (odds ratio = 1.92; 95% confidence interval [CI] = 1.06–3.47), starting a new drug within 1 week (odds ratio = 2.31; 95% CI = 1.08–4.95), or within 1 month (odds ratio = 2.17; 95% CI = 1.05–4.48).

Conclusions
Hospital admissions associated with MRPs in Thai older patients continue to burden the Thai healthcare system of which nearly half were preventable. Further studies should consider analysis of costs and include hepatic and renal function status of participants.
A comparison between the TEG 6s and TEG 5000 analyzers to assess coagulation in trauma patients
Authors: Neal Matthew D. , Moore Ernest E. , Walsh Mark , Thomas Scott , Callcut Rachael A. , Kornblith Lucy Z. , Schreiber Martin , Ekeh Akpofure Peter , Singer Adam J. , Lottenberg Lawrence , Foreman Michael , Evans Susan , Winfield Robert D. , Goodman Michael D. , Freeman Carl , Milia David , Saillant Noelle , Hartmann Jan , Achneck Hardean E. 
Published: November 2019

BACKGROUNDTrauma-induced coagulopathy is a major driver of mortality following severe injury. Viscoelastic goal-directed resuscitation can reduce mortality after injury. The TEG 5000 system is widely used for viscoelastic testing. However, the TEG 6s system incorporates newer technology, with encouraging results in cardiovascular interventions. The purpose of this study was to validate the TEG 6s system for use in trauma patients.METHODSMulticenter noninvasive observational study for method comparison conducted at 12 US Levels I and II trauma centers. Agreement between the TEG 6s and TEG 5000 systems was examined using citrated kaolin reaction time (CK.R), citrated functional fibrinogen maximum amplitude (CFF.MA), citrated kaolin percent clot lysis at 30 minutes (CK.LY30), citrated RapidTEG maximum amplitude (CRT.MA), and citrated kaolin maximum amplitude (CK.MA) parameters in adults meeting full or limited trauma team criteria. Blood was drawn ≤1 hour after admission. Assays were repeated in duplicate. Reliability (TEG 5000 vs. TEG 6s analyzers) and repeatability (interdevice comparison) was quantified. Linear regression was used to define the relationship between TEG 6s and TEG 5000 devices.RESULTSA total of 475 patients were enrolled. The cohort was predominantly male (68.6%) with a median age of 49 years. Regression line slope estimates (ß) and linear correlation estimates (p) were as follows: CK.R (ß = 1.05,ρ= 0.9), CFF.MA (ß = 0.99,ρ= 0.95), CK.LY30 (ß = 1.01,ρ= 0.91), CRT.MA (TEG 6s) versus CK.MA (TEG 5000) (ß = 1.06,ρ= 0.86) as well as versus CRT.MA (TEG 5000) (ß = 0.93,ρ= 0.93), indicating strong reliability between the devices. Overall, within-device repeatability was better for TEG 6s versus TEG 5000, particularly for CFF.MA and CK.LY30.CONCLUSIONThe TEG 6s device appears to be highly reliable for use in trauma patients, with close correlation to the TEG 5000 device and equivalent/improved within-device reliability. Given the potential advantages of using the TEG 6s device at the site of care, confirmation of agreement between the devices represents an important advance in diagnostic testing.LEVEL OF EVIDENCEDiagnostic test, level II.
Sound sequences in birdsong: how much do birds really care?
Authors: Fishbein Adam R. , Idsardi William J. , Ball Gregory F. , Dooling Robert J. 
Published: November 2019

The complex and melodic nature of many birds' songs has raised interest in potential parallels between avian vocal sequences and human speech. The similarities between birdsong and speech in production and learning are well established, but surprisingly little is known about how birds perceive song sequences. One popular laboratory songbird, the zebra finch (Taeniopygia guttata), has recently attracted attention as an avian model for human speech, in part because the male learns to produce the individual elements in its song motif in a fixed sequence. But psychoacoustic evidence shows that adult zebra finches are relatively insensitive to the sequential features of song syllables. Instead, zebra finches and other birds seem to be exquisitely sensitive to the acoustic details of individual syllables to a degree that is beyond human hearing capacity. Based on these findings, we present a finite-state model of zebra finch perception of song syllable sequences and discuss the rich informational capacity of their vocal system. Furthermore, we highlight the abilities of budgerigars (Melopsittacus undulatus), a parrot species, to hear sequential features better than zebra finches and suggest that neurophysiological investigations comparing these species could prove fruitful for uncovering neural mechanisms for auditory sequence perception in human speech.This article is part of the theme issue ‘What can animal communication teach us about human language?’
Some cautions regarding the phonological continuity hypothesis
Authors: Idsardi William J. 
Published: November 2019

We consider the Phonological Continuity Hypothesis (PCH) of Fitch (2018) in light of a broader range of formal systems. A consideration of the learning and generalization of simple patterns such as AAB from Marcus (Marcus 2000Curr. Dir.9, 145–147(doi:10.1111/1467-8721.00080)) shows that finite-state automata defined in the standard way fail to generalize in a compatible fashion. However, pushdown automata with finite-memory limits do show compatible generalization capabilities. The third class of formal systems—tree automata—provide yet another possibility for the processing of words within sentences. We conclude that there are additional possible formal differences between sound patterns and sentence patterns, which will make testing the PCH even more difficult.This article is part of the theme issue ‘What can animal communication teach us about human language?’
Prediction of GPI-Anchored proteins with pointer neural networks
Authors: Gíslason Magnús Halldór , Nielsen Henrik , Almagro Armenteros José Juan , Johansen Alexander Rosenberg 
Published: November 2019

ABSTRACTGPI-anchors constitute a very important post-translational modification, linking many proteins to the outer face of the plasma membrane in eukaryotic cells. Since experimental validation of GPI-anchoring signals is slow and costly, computational approaches for predicting them from amino acid sequences are needed. However, the most recent GPI predictor is more than a decade old and considerable progress has been made in machine learning since then. We present a new dataset and a novel method, NetGPI, for GPI signal prediction. NetGPI is based on recurrent neural networks, incorporating an attention mechanism that simultaneously detects GPI-anchoring signals and points out the location of their ω-sites. The performance of NetGPI is superior to existing methods with regards to discrimination between GPI-anchored proteins and other secretory proteins and approximate (±1 position) placement of the ω-site.NetGPI is available at: https://services.healthtech.dtu.dk/service.php?NetGPIThe code repository is available at: https://github.com/mhgislason/netgpi-1.1
A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses
Authors: Worthington Margaret , Perez Juan Guillermo , Mussurova Saule , Silva-Cordoba Alexander , Castiblanco Valheria , Jones Charlotte , Fernandez-Fuentes Narcis , Skot Leif , Dyer Sarah , Tohme Joe , Di Palma Federica , Arango Jacobo , Armstead Ian , De Vega Jose J 
Published: November 2019

ABSTRACTToxic concentrations of aluminium cations and low phosphorus availability are the main yield-limiting factors in acidic soils, which represent half of the potentially available arable land. Brachiaria grasses, which are commonly sown as a forage in the tropics because of their resilience and low demand for nutrients, have a greater tolerance to high concentrations of aluminium cations than most other grass crops. In this work, we explored the natural variation in tolerance to aluminium cations (Al3+) between high and low tolerant Brachiaria species and characterised their transcriptional differences during stress. We also identified three QTLs associated with root vigour during Al3+ stress in their hybrid progeny. By integrating these results with a new Brachiaria reference genome, we have identified 30 genes responsible for Al3+ tolerance in Brachiaria. We also observed differential expression during stress of genes involved in RNA translation, response signalling, cell wall composition and vesicle location genes homologous to aluminium-induced proteins involved in limiting uptake or localizing the toxin. However, there was limited regulation of malate transporters in Brachiaria, which are associated with external tolerance mechanisms to Al3+ stress in other grasses. The contrasting regulation of RNA translation and response signalling suggests response phasing is critical to Al3+ tolerance.HIGHLIGHTWe identified QTLs, genes and molecular responses in high and low tolerant Brachiaria grasses associated with aspects of response to aluminium stress, such as regulation, cell-wall composition and active transport.
Robust banded protoxylem pattern formation through microtubule-based directional ROP diffusion restriction
Authors: Jacobs Bas , Molenaar Jaap , Deinum Eva E. 
Published: November 2019

AbstractIn plant vascular tissue development, different cell wall patterns are formed, offering different mechanical properties optimised for different growth stages. Critical in these patterning processes are Rho of Plants (ROP) proteins, a class of evolutionarily conserved small GTPase proteins responsible for local membrane domain formation in many organisms. While the spotted metaxylem pattern can easily be understood as a result of a Turing-style reaction-diffusion mechanism, it remains an open question how the consistent orientation of evenly spaced bands and spirals as found in protoxylem is achieved. We hypothesise that this orientation results from an interaction between ROPs and an array of transversely oriented cortical microtubules that acts as a directional diffusion barrier. Here, we explore this hypothesis using partial differential equation models with anisotropic ROP diffusion and show that a horizontal microtubule array acting as a vertical diffusion barrier to active ROP can yield a horizontally banded ROP pattern. We then study the underlying mechanism in more detail, finding that it can only orient curved pattern features but not straight lines. This implies that, once formed, banded and spiral patterns cannot be reoriented by this mechanism. Finally, we observe that ROPs and microtubules together only form ultimately static patterns if the interaction is implemented with sufficient biological realism.
A genetic map of the response to DNA damage in human cells
Authors: Olivieri Michele , Cho Tiffany , Álvarez-Quilón Alejandro , Li Kejiao , Schellenberg Matthew J. , Zimmermann Michal , Hustedt Nicole , Rossi Silvia Emma , Adam Salomé , Melo Henrique , Heijink Anne Margriet , Sastre-Moreno Guillermo , Moatti Nathalie , Szilard Rachel , McEwan Andrea , Ling Alexanda K. , Serrano-Benitez Almudena , Ubhi Tajinder , Delgado-Sainz Irene , Ferguson Michael W. , Brown Grant W. , Cortés-Ledesma Felipe , Williams R. Scott , Martin Alberto , Xu Dongyi , Durocher Daniel 
Published: November 2019

SUMMARYThe response to DNA damage is critical for cellular homeostasis, tumor suppression, immunity and gametogenesis. In order to provide an unbiased and global view of the DNA damage response in human cells, we undertook 28 CRISPR/Cas9 screens against 25 genotoxic agents in the retinal pigment epithelium-1 (RPE1) cell line. These screens identified 840 genes whose loss causes either sensitivity or resistance to DNA damaging agents. Mining this dataset, we uncovered that ERCC6L2, which is mutated in a bone-marrow failure syndrome, codes for a canonical non-homologous end-joining pathway factor; that the RNA polymerase II component ELOF1 modulates the response to transcription-blocking agents and that the cytotoxicity of the G-quadruplex ligand pyridostatin involves trapping topoisomerase II on DNA. This map of the DNA damage response provides a rich resource to study this fundamental cellular system and has implications for the development and use of genotoxic agents in cancer therapy.
Physiological responses to light explain competition and facilitation in a tree diversity experiment
Authors: Kothari Shan , Montgomery Rebecca , Cavender-Bares Jeannine 
Published: November 2019

AbstractEcologists often invoke interspecific facilitation to help explain positive biodiversity-ecosystem function relationships in plant communities, but seldom test how it occurs. One mechanism through which one species may facilitate another is by ameliorating abiotic stress. Physiological experiments show that a chronic excess of light can cause stress that depresses carbon assimilation. If shading by a plant’s neighbors reduces light stress enough, it may facilitate that plant’s growth. If light is instead most often a limiting factor for photosynthesis, shading may have an adverse, competitive effect.In a temperate tree diversity experiment, we measured stem growth rates and photosynthetic physiology in broadleaf trees across a gradient of light availability imposed by their neighbors. At the extremes, trees experienced nearly full sun (monoculture), or were shaded by nearby fast-growing conifers (shaded biculture).Most species had slower growth rates with larger neighbors, implying a net competitive effect. On the other hand, the two most shade-tolerant species (Tilia americanaandAcer negundo) and the most shade-intolerant one (Betula papyrifera) had faster stem growth rates with larger neighbors. The two most shade-tolerant species had large increases in photoinhibition (reduced dark-acclimated Fv/Fm) across the gradient of increasing light availability, which suggests they are more vulnerable to chronic light stress. While most species had lower carbon assimilation rates in the shaded biculture treatment,T. americanahad rates up to 25% higher.T. americanaalso dropped its leaves 3-4 weeks earlier in monocultures, curtailing its growing season. We conclude that although large neighbors can cause light limitation in shade-intolerant species, they can also increase growth through abiotic stress amelioration in shade-tolerant species. Finally, in shade-intolerantB. papyrifera, we find a pattern of stem elongation in trees with larger neighbors, which may suggest that a shade avoidance response accounts for the apparent positive trend in stem volume.Synthesis: Both positive and negative species interactions in our experiment can be explained in large part by the photosynthetic responses of trees to the light environment created by their neighbors. We show that photosynthetic physiology can help explain the species interactions that underlie biodiversity-ecosystem function relationships. The insights that ecologists gain by searching for such physiological mechanisms may help us forecast species interactions under environmental change.
Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Authors: Petek Marko , Zagorščak Maja , Ramšak Živa , Sanders Sheri , Tomaž Špela , Tseng Elizabeth , Zouine Mohamed , Coll Anna , Gruden Kristina 
Published: November 2019

AbstractAlthough the reference genome ofSolanum tuberosumGroup Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using severalde novoassemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes.
Effects of advanced age upon astrocyte-specific responses to acute traumatic brain injury in mice
Authors: Early Alexandria N. , Gorman Amy A. , Van Eldik Linda J. , Bachstetter Adam D. , Morganti Josh M. 
Published: November 2019

AbstractBackgroundOlder-age individuals are at the highest risk for disability from a traumatic brain injury (TBI). Astrocytes are the most numerous glia in the brain, necessary for brain function, yet there is little known about unique responses of astrocytes in the aged-brain following TBI.MethodsOur approach examined astrocytes in young adult, 4-month-old, versus aged, 18-month-old mice, at 1, 3, and 7 days post-TBI. We selected these time points to span the critical period in the transition from acute injury to presumably irreversible tissue damage and disability. Two approaches were used to define the astrocyte contribution to TBI by age interaction: 1) tissue histology and morphological phenotyping, and 2) transcriptomics on enriched astrocytes from the injured brain.ResultsAging was found to have a profound effect on the TBI-induced loss of homeostatic astrocyte function needed for maintaining water transport and edema – namely, aquaporin-4. The loss of homoeostatic responses was coupled with a progressive exacerbation of astrogliosis in the aged brain as a function of time after injury. Moreover, clasmatodendrosis, an underrecognized astrogliopathy, was found to be significantly increased in the aged brain, but not in the young brain. As a function of TBI, we observed a transitory refraction in the number of these astrocytes, which rebounded by 7 days post-injury in the aged brain. The transcriptomics found disproportionate changes in genes attributed to reactive astrocytes, inflammatory response, complement pathway, and synaptic support in aged mice following TBI compared to young mice. Additionally, our data highlight that TBI did not evoke a clear alignment with previously defined “A1/A2” dichotomy of reactive astrogliosis.ConclusionsOverall, our findings point toward a progressive phenotype of aged astrocytes following TBI that we hypothesize to be maladaptive, shedding new insights into potentially modifiable astrocyte-specific mechanisms that may underlie increased fragility of the aged brain to trauma.