bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serum Factor V Is a Continuous Biomarker of Graft Dysfunction and a Predictor of Graft Loss After Liver Transplantation
Authors: Gorgen Andre , Prediger Carolina , Prediger João E. , Chedid Marcio F. , Backes Ariane N. , de Araujo Alexandre , Grezzana-Filho Tomaz J.M. , Leipnitz Ian , Chedid Aljamir D. , Alvares-da-Silva Mario R. , Sapisochin Gonzalo , Kruel Cleber R.P. 
Published: August 2018

Background.
Factor V has never been compared to a validated early allograft dysfunction (EAD) definition. We aimed to assess factor V as a biomarker of EAD and a predictor of graft loss after liver transplantation (LT).

Methods.
We retrospectively assessed the serum factor V levels on postoperative day 1 after LT. Patients were divided according to their factor V levels into the ≤36.1 U/mL and > 36.1 U/mL groups. The primary outcome was graft loss within 1, 3, and 6 months. The secondary outcome was EAD, as defined by Olthoff et al. Predictors of outcomes were identified by multivariable logistic regression.

Results.
Two hundred twenty-seven patients were included in the study: 74 with factor V of 36.1 U/mL or less and 153 with factor V >36.1 U/mL. EAD was diagnosed in 41 (55.4%) of 74 patients with factor V of 36.1 U/mL or less and in 20/153 (13.1%) patients with factor V >36.1 U/mL (P < 0.001). According to the multivariable regression model, factor V was a continuous marker of EAD (odds ratio [OR], 0.96; 95% confidence interval [CI], 0.94-0.98 per U/mL). Among the study groups, the 1-, 3-, and 6-month graft survival rates were 82%, 74%, and 74%, respectively, for patients with factor V of 36.1 U/mL or less and 98%, 95%, and 95%, respectively, for patients with factor V >36.1 U/mL (P = 0.001). Factor V was a continuous predictor for 3- and 6-month graft losses (OR, 0.96; 95% CI, 0.94-0.99 and OR, 0.97; 95% CI, 0.94-0.99 per U/mL), whereas EAD was not significant when adjusted for factor V.

Conclusion.
Factor V is an early marker for EAD and is a continuous predictor of short-term graft loss after LT.
Blood, sweat and tears: a review of non-invasive DNA sampling
Authors: Lefort M.C. , Cruickshank R.H. , Descovich K. , Adams N.J. , Barun A. , Emami-Khoyi A. , Ridden J. , Smith V.R. , Sprague R. , Waterhouse B. , Boyer S. 
Published: August 2018

AbstractThe use of DNA data is ubiquitous across animal sciences. DNA may be obtained from an organism for a myriad of reasons including identification and distinction between cryptic species, sex identification, comparisons of different morphocryptic genotypes or assessments of relatedness between organisms prior to a behavioural study. DNA should be obtained while minimizing the impact on the fitness, behaviour or welfare of the subject being tested, as this can bias experimental results and cause long-lasting effects on wild animals. Furthermore, minimizing impact on experimental animals is a key Refinement principle within the ‘3Rs’ framework which aims to ensure that animal welfare during experimentation is optimised. The term ‘non-invasive DNA sampling’ has been defined to indicate collection methods that do not require capture or cause disturbance to the animal, including any effects on behaviour or fitness. In practice this is not always the case, as the term ‘non-invasive’ is commonly used in the literature to describe studies where animals are restrained or subjected to aversive procedures. We reviewed the non-invasive DNA sampling literature for the past six years (380 papers published in 2013-2018) and uncovered the existence of a significant gap between the current use of this terminology (i.e. ‘non-invasive DNA sampling’) and its original definition. We show that 58% of the reviewed papers did not comply with the original definition. We discuss the main experimental and ethical issues surrounding the potential confusion or misuse of the phrase ‘non-invasive DNA sampling’ in the current literature and provide potential solutions. In addition, we introduce the terms ‘non-disruptive’ and ‘minimally disruptive’ DNA sampling, to indicate methods that eliminate or minimise impacts not on the physical integrity/structure of the animal, but on its behaviour, fitness and welfare, which in the literature reviewed corresponds to the situation for which an accurate term is clearly missing. Furthermore, we outline when these methods are appropriate to use.
40 Hz acoustic stimulation decreases amyloid beta and modulates brain rhythms in a mouse model of Alzheimer’s disease
Authors: Lee Juho , Ryu Seungjun , Kim Hyun-Ju , Jung Jieun , Lee Boreom , Kim Tae 
Published: August 2018

AbstractIntroductionThe accumulation of amyloid-beta (Aβ) is one of the neuropathologic hallmarks of Alzheimer’s disease (AD) and abnormal gamma band oscillations and brain connectivity have been observed. Recently, a therapeutic potential of gamma entrainment of the brain was reported by Iaccarino et al. However, the affected areas were limited to hippocampus and visual cortex. Therefore, we sought to test the effects of acoustic stimulation in a mouse model of AD.MethodsFreely moving 6-month-old 5XFAD mice with electroencephalogram (EEG) electrodes were treated with daily two-hour acoustic stimulation at 40Hz for 2 weeks. Aβ and microglia were evaluated by immunohistochemistry and ELISA. Evoked and spontaneous gamma power were analyzed by wavelet analysis. Coherence, phase locking value (PLV), and cross-frequency coupling were analyzed.ResultsThe number of Aβ plaques decreased in the pre-and infralimbic (PIL) and hippocampus regions and soluble Aβ-40 and Aβ-42 peptides in PIL in the acoustic stimulation group. We also found that the number of microglia increased in PIL and hippocampus. In EEG analysis, evoked gamma power was decreased and spontaneous gamma power was increased. Gamma coherence and phase locking value did not show significant changes. Cross-frequency coupling was shifted from gamma-delta to gamma-theta rhythm.ConclusionIn summary, we found that acoustic stimulation at 40Hz can reduce Aβ in the brain and restore the gamma band oscillations and the frontoparietal connectivity. Our data suggest that acoustic stimulation might alter the natural deterioration processes of AD and have a therapeutic potential in AD.
The role of the fornix in human navigational learning
Authors: Hodgetts Carl J. , Stefani Martina , Williams Angharad N. , Kolarik Branden S. , Yonelinas Andrew P. , Ekstrom Arne D. , Lawrence Andrew D. , Zhang Jiaxiang , Graham Kim S. 
Published: August 2018

AbstractStudies in rodents have demonstrated that transecting the white matter pathway linking the hippocampus and anterior thalamic nuclei - the fornix - impairs flexible navigational learning in the Morris Water Maze (MWM), as well as similar spatial learning tasks. While diffusion MRI studies in humans have linked fornix microstructure to scene discrimination and memory, its role in human navigation is currently unknown. We used high-angular resolution diffusion MRI to ask whether inter-individual differences in fornix microstructure would be associated with spatial learning in a virtual MWM task. To increase sensitivity to individual learning across trials, we adopted a novel curve fitting approach to estimate a single index of learning rate. We found a significant correlation between learning rate and the microstructure (mean diffusivity) of the fornix, but not that of a control tract linking occipital and anterior temporal cortices (the inferior longitudinal fasciculus, ILF). Further, this correlation remained significant when controlling for hippocampal volume. These findings extend previous animal studies by demonstrating the functional relevance of the fornix for human navigational learning, and highlight the importance of a distributed neuroanatomical network, underpinned by key white matter pathways, such as the fornix, in complex spatial behaviour.
Sterile spikelets assimilate carbon in sorghum and related grasses
Authors: AuBuchon-Elder Taylor , Coneva Viktoriya , Goad David M. , Allen Doug K. , Kellogg Elizabeth A. 
Published: August 2018

ABSTRACTSorghum and its relatives in the grass tribe Andropogoneae bear their flowers in pairs of spikelets, in which one spikelet (seed-bearing, or SS) of the pair produces a seed and the other is sterile or male (staminate). This division of function does not occur in other major cereals such as wheat or rice. Additionally, one bract of the seed-bearing spikelet often produces a long extension, the awn, which is in the same position as but independently derived from that of wheat and rice. The function of the sterile spikelet is unknown and that of the awn has not been tested in Andropogoneae. We used radioactive and stable isotopes of carbon, as well as RNA-seq of metabolically important enzymes to show that the sterile spikelet assimilates carbon, which is translocated to the largely heterotrophic SS, thereby functioning as a nurse tissue. The awn shows no evidence of photosynthesis. These results apply to distantly related species of Andropogoneae. Thus, the sterile spikelet, but not the awn, could affect yield in the cultivated species and fitness in the wild ones.
Interpretable multimodal deep learning for real-time pan-tissue pan-disease pathology search on social media
Authors: Schaumberg Andrew J. , Juarez-Nicanor Wendy C. , Choudhury Sarah J. , Pastrián Laura G. , Pritt Bobbi S. , Pozuelo Mario Prieto , Sánchez Ricardo Sotillo , Ho Khanh , Zahra Nusrat , Sener Betul Duygu , Yip Stephen , Xu Bin , Annavarapu Srinivas Rao , Morini Aurélien , Jones Karra A. , Rosado-Orozco Kathia , Mukhopadhyay Sanjay , Miguel Carlos , Yang Hongyu , Rosen Yale , Ali Rola H. , Folaranmi Olaleke O. , Gardner Jerad M. , Rusu Corina , Stayerman Celina , Gross John , Suleiman Dauda E. , Sirintrapun S. Joseph , Aly Mariam , Fuchs Thomas J. 
Published: August 2018

AbstractPathologists are responsible for rapidly providing a diagnosis on critical health issues. Challenging cases benefit from additional opinions of pathologist colleagues. In addition to on-site colleagues, there is an active worldwide community of pathologists on social media for complementary opinions. Such access to pathologists worldwide has the capacity to improve diagnostic accuracy and generate broader consensus on next steps in patient care. From Twitter we curate 13,626 images from 6,351 tweets from 25 pathologists from 13 countries. We supplement the Twitter data with 113,161 images from 1,074,484 PubMed articles. We develop machine learning and deep learning models to (i) accurately identify histopathology stains, (ii) discriminate between tissues, and (iii) differentiate disease states. Area Under Receiver Operating Characteristic is 0.805-0.996 for these tasks. We repurpose the disease classifier to search for similar disease states given an image and clinical covariates. We report precision@k=1 = 0.7618±0.0018 (chance 0.397±0.004, mean±stdev). The classifiers find texture and tissue are important clinico-visual features of disease. Deep features trained only on natural images (e.g. cats and dogs) substantially improved search performance, while pathology-specific deep features and cell nuclei features further improved search to a lesser extent. We implement a social media bot (@pathobot on Twitter) to use the trained classifiers to aid pathologists in obtaining real-time feedback on challenging cases. If a social media post containing pathology text and images mentions the bot, the bot generates quantitative predictions of disease state (normal/artifact/infection/injury/nontumor, pre-neoplastic/benign/ low-grade-malignant-potential, or malignant) and lists similar cases across social media and PubMed. Our project has become a globally distributed expert system that facilitates pathological diagnosis and brings expertise to underserved regions or hospitals with less expertise in a particular disease. This is the first pan-tissue pan-disease (i.e. from infection to malignancy) method for prediction and search on social media, and the first pathology study prospectively tested in public on social media. We will share data throughpathobotology.org. We expect our project to cultivate a more connected world of physicians and improve patient care worldwide.
A highly conserved complete accessoryEscherichia colitype III secretion system 2 is widespread in bloodstream isolates of the ST69 lineage
Authors: Fox S. , Goswami C. , Holden M. , Connolly J.P.R. , Roe A. , Connor M. , Leanord A. , Evans T.J. 
Published: August 2018

AbstractBacterial type III secretion systems (T3SS) play an important role in pathogenesis of Gram-negative infections. Enteropathogenic and enterohemorrhagicEscherichia colicontain a well-defined T3SS but in addition a second T3SS termedE. coliT3SS 2 (ETT2) has been described in a number of strains ofE. coli.The majority ofE. colicontain elements of a genetic locus encoding ETT2, but which has undergone significant mutational attrition rendering it without predicted function. Only a very few strains have been reported to contain an intact ETT2 locus. To investigate the occurrence of the ETT2 locus in strains of human pathogenicE. coli, we carried out genomic sequencing of 162 isolates obtained from patient blood cultures in Scotland. We found that all 26 ST69 isolates from this collection contained an intact ETT2 together with an associatedeiplocus which encodes putative secreted ETT2 effectors as well aseilA, a gene encoding a putative transcriptional regulator of ETT2 associated genes. Using a reporter gene foreilAactivation, we defined conditions under which this gene was differentially activated. However, comparison of secreted proteins from ST69 strains under high and loweilAactivation failed to identify any ETT2 secreted substrates. The conservation of the genes encoding ETT2 in human pathogenic ST69 strains strongly suggests it has functional importance in infection, although its exact functional role remains obscure.ImportanceOne of the commonest bacteria causing bloodstream infections in humans isEscherichia coli, which has a significant morbidity and mortality. Better understating of the mechanisms by which this microbe can invade blood could lead to more effective prevention and treatment. One mechanism by which some strains cause disease is by elaboration of a specialized secretion system, the type III secretion system (T3SS), encoded by the locus of enterocyte effacement (LEE). In addition to this well-defined T3SS, a second T3SS has been found in someE. colistrains termedE. colitype III secretion system 2 (ETT2). Most strains carry elements of the ETT2 locus, but with significant mutational attrition rendering it functionless. The significance of our work is that we have discovered that human bloodstream isolates ofE. coliof sequence type 69 contain a fully intact ETT2 and associated genes, strongly suggesting its functional importance in human infection.
Individual variation in longitudinal postnatal development of the primate brain
Authors: Ball G. , Seal M. L. 
Published: August 2018

AbstractQuantifying individual variation in postnatal brain development can provide insight into cognitive diversity within a population and the aetiology of common neuropsychiatric and neurodevelopmental disorders that are associated with adverse conditions in early life. Non-invasive studies of the non-human primate can aid understanding of human brain development, facilitating longitudinal analysis during early postnatal development when comparative human populations are difficult to sample.In this study, we perform analysis of a longitudinal MRI dataset of 32 macaques, each with up to five magnetic resonance imaging (MRI) scans acquired between 1 and 36 months of age. Using nonlinear mixed effects model we derive growth trajectories for whole brain, cortical and subcortical grey matter, cerebral white matter and cerebellar volume. We then test the association between individual variation in postnatal tissue volumes and birth weight.We report nonlinear growth models for all tissue compartments, as well as significant variation in total intracranial volume between individuals. We also demonstrate that subcortical grey matter varies both in total volume and rate of change between individuals and is associated with differences in birth weight. This supports evidence that subcortical grey matter is specifically vulnerable to adverse conditions in utero and highlights the importance of longitudinal MRI analysis in developmental studies.
Mitochondrial DNA and their nuclear copies in parasitic waspPteromalus puparum: A comparative analysis in Chalcidoidea
Authors: Yan Zhichao , Fang Qi , Tian Yu , Wang Fang , Chen Xuexin , Werren John H. , Ye Gongyin 
Published: August 2018

AbstractChalcidoidea (chalcidoid wasps) are an abundant and megadiverse insect group with both ecological and economical importance. Here we report a complete mitochondrial genome in Chalcidoidea fromPteromalus puparum(Pteromalidae). Eight tandem repeats followed by 6 reversed repeats were detected in its 3,308 bp control region. This long and complex control region may explain failures of amplifying and sequencing of complete mitochondrial genomes in some chalcidoids. In addition to 37 typical mitochondrial genes, an extra identical isoleucine tRNA (trnI) was detected. We speculate this recent mitochondrial gene duplication indicates that gene arrangements in chalcidoids are ongoing. A comparison among available chalcidoid mitochondrial genomes, reveals rapid gene order rearrangements overall, and high substitution rate inP. puparum. In addition, we identified 24 nuclear sequences of mitochondrial origin (NUMTs) inP. puparum, summing up to 9,989 bp, with 3,617 bp of these NUMTs originating from mitochondrial coding regions. NUMTs abundance inP. puparumis only one-twelfth of that in its relative,Nasonia vitripennis. Based on phylogenetic analysis, we provide evidence that a faster nuclear degradation rate contributes to the reduced NUMT numbers inP. puparum. Overall, our study shows unusually high rates of mitochondrial evolution and considerable variation in NUMT accumulation in Chalcidoidea.
Farmers’ perceptions on the causes of cassava root bitterness in konzo-affected areas of Mtwara Region, Tanzania
Authors: Imakumbili Matema L.E. , Semu Ernest , Semoka Johnson M.R. , Abass Adebayo , Mkamilo Geoffrey 
Published: August 2018

AbstractThe agronomic factors influencing increased cyanogenic glucoside levels, particularly in bitter cassava varieties during periods without water stress, in areas where konzo (a cassava cyanide related paralytic disorder also called spastic paraparesis) persists, are hardly known. However, through their assessment of bitter taste, farmers may have noticed factors unrelated to water stress and variety type that additionally influence cassava root cyanogenic glucoside content in these environments. Bitterness in cassava is usually associated with high cyanogenic glucoside levels. Using some konzo-affected areas in Mtwara region of Tanzania as a case study, a survey was thus carried out to identify the factors, hitherto overlooked, that may additionally influence cyanogenic glucoside levels in cassava. A total of 120 farmers were interviewed. A number of factors unrelated to water stress and variety type that could be additionally influencing cyanogenic glucoside production in cassava plants were mentioned. The mentioned factors included nutrient poor soils, plant age at harvest, weeds, piecemeal harvesting, and branch pruning; the factors, respectively, constituted 14.2%, 7.5%, 0.8%, 0.8%, and 0.8% of the total responses given. The revealed factors constitute permanent environmental characteristics and commonly used crop management practices by farmers living in konzo-prone Mtwara region of Tanzania that could be additionally resulting in high cyanogenic glucoside levels in cassava, regardless of water stress.
A comprehensive genomics solution for HIV surveillance and clinical monitoring in a global health setting
Authors: Bonsall David , Golubchik Tanya , Cesare Mariateresa de , Limbada Mohammed , Kosloff Barry , MacIntyre-Cockett George , Hall Matthew , Wymant Chris , Ansari M Azim , Abeler-Dörner Lucie , Schaap Ab , Brown Anthony , Barnes Eleanor , Piwowar-Manning Estelle , Wilson Ethan , Emel Lynda , Hayes Richard , Fidler Sarah , Ayles Helen , Bowden Rory , Fraser Christophe 
Published: August 2018

AbstractHigh-throughput viral genetic sequencing is needed to monitor the spread of drug resistance, direct optimal antiretroviral regimes, and to identify transmission dynamics in generalised HIV epidemics. Public health efforts to sequence HIV genomes at scale face three major technical challenges: (i) minimising assay cost and protocol complexity, (ii) maximising sensitivity, and (iii) recovering accurate and unbiased sequences of both the genome consensus and the within-host viral diversity. Here we present a novel, high-throughput, virus-enriched sequencing method and computational pipeline tailored specifically to HIV (veSEQ-HIV), which addresses all three technical challenges, and can be used directly on leftover blood drawn for routine CD4 testing. We demonstrate its performance on 1,620 plasma samples collected from consenting individuals attending 10 large urban clinics in Zambia, partners of HPTN 071 (PopART). We show that veSEQ-HIV consistently recovers complete HIV genomes from the majority of samples of different subtypes, and is also quantitative: the number of HIV reads per sample obtained by veSEQ-HIV estimates viral load without the need for additional testing. Both quantitativity and sensitivity were assessed on a subset of 126 samples with clinically measured viral loads, and with standardized quantification controls (VL 100 – 5,000,000 RNA copies/ml). Complete HIV genomes were recovered from 93% (85/91) of samples when viral load was over 1,000 copies per ml. The quantitative nature of the assay implies that variant frequencies estimated with veSEQ-HIV are representative of true variant frequencies in the sample. Detection of minority variants can be exploited for epidemiological analysis of transmission and drug resistance, and we show how the information contained in individual reads of a veSEQ-HIV sample can be used to detect linkage between multiple mutations associated with resistance to antiretroviral therapy. Less than 2% of reads obtained by veSEQ-HIV were identified as in silico contamination events using updates to the phyloscanner software (phyloscanner clean) that we show to be 95% sensitive and 99% specific at ‘decontaminating’ NGS data. The cost of the assay — approximately 45 USD per sample — compares favourably with existing VL and HIV genotyping tests, and provides the additional value of viral load quantification and inference of drug resistance with a single test. veSEQ-HIV is well suited to large public health efforts and is being applied to all ∼9000 samples collected for the HPTN 071-2 (PopART Phylogenetics) study.
Docclustering: An Implementation of the Novel Ps-Document Clustering Algorithm a Preprint
Authors: Dörpinghaus Jens , Schaaf Sebastian , Jacobs Marc 
Published: August 2018

ABSTRACTDocument clustering is widely used in science for data retrieval and organisation. DocClustering is developed to include and use a novel algorithm called PS-Document Clustering that has been first introduced in 2017. This method combines approaches of graph theory with state of the art NLP-technologies. This new heuristic has been shown to be superior to conventional algorithms and it provides – given a suiting similarity measure – a more accurate clustering on biological and medical data.Since the application is written for research on biomedical literature, interfaces for PubMed and SCAIView are available. In this brief report the source code as well as a short overview about the new features, novel heuristics and approaches are provided.The software can be obtained from the authors or directly downloaded from GitHub, see https://github.com/jd-s/DocClustering.