bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection and Analysis of Proteins Modified by O‐Linked N‐Acetylglucosamine
Authors: Fahie Kamau , Narayanan Bhargavi , Zahra Fiddia , Reeves Russell , Fernandes Steve M. , Hart Gerald W. , Zachara Natasha E. 
Published: May 2021

AbstractO‐GlcNAc is a common post‐translational modification of nuclear, mitochondrial, and cytoplasmic proteins that regulates normal physiology and the cell stress response. Dysregulation of O‐GlcNAc cycling is implicated in the etiology of type II diabetes, heart failure, hypertension, and Alzheimer's disease, as well as cardioprotection. These protocols cover simple and comprehensive techniques for detecting proteins modified by O‐GlcNAc and studying the enzymes that add or remove O‐GlcNAc. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Increasing the stoichiometry of O‐GlcNAc on proteins before analysisBasic Protocol 2: Detection of proteins modified by O‐GlcNAc using antibodiesBasic Protocol 3: Detection of proteins modified by O‐GlcNAc using the lectin sWGASupport Protocol 1: Control for O‐linked glycosylationBasic Protocol 4: Detection and enrichment of proteins using WGA‐agaroseSupport Protocol 2: Digestion of proteins with hexosaminidaseAlternate Protocol: Detection of proteins modified by O‐GlcNAc using galactosyltransferaseSupport Protocol 3: Autogalactosylation of galactosyltransferaseSupport Protocol 4: Assay of galactosyltransferase activityBasic Protocol 5: Characterization of labeled glycans by β‐elimination and chromatographyBasic Protocol 6: Detection of O‐GlcNAc in 96‐well platesBasic Protocol 7: Assay for OGT activitySupport Protocol 5: Desalting of O‐GlcNAc transferaseBasic Protocol 8: Assay for O‐GlcNAcase activity
P‐tau/Aβ42 and Aβ42/40 ratios in CSF are equally predictive of amyloid PET status
Authors: Campbell Michelle R. , Ashrafzadeh‐Kian Susan , Petersen Ronald C. , Mielke Michelle M. , Syrjanen Jeremy A. , van Harten Argonde C. , Lowe Val J. , Jack Clifford R. , Bornhorst Joshua A. , Algeciras‐Schimnich Alicia 
Published: May 2021

AbstractIntroductionMeasurement of amyloid beta (Aβ40 and Aβ42) and tau (phosphorylated tau [p‐tau] and total tau [t‐tau]) in cerebrospinal fluid (CSF) can be utilized to differentiate clinical and preclinical Alzheimer's disease dementia (AD) from other neurodegenerative processes.MethodsCSF biomarkers were measured in 150 participants from the Mayo Clinic Study of Aging and the Alzheimer's Disease Research Center. P‐tau/Aβ42 (Roche Elecsys, Fujirebio LUMIPULSE) and Aβ42/40 (Fujirebio LUMIPULSE) ratios were compared to one another and to amyloid positron emission tomography (PET) classification.ResultsStrong correlation was observed between LUMIPULSE p‐tau/Aβ42 and Aβ42/40, as well as Elecsys and LUMIPULSE p‐tau/Aβ42 and Aβ42/40 (Spearman's ρ = –0.827, –0.858, and 0.960, respectively). Concordance between LUMIPULSE p‐tau/Aβ42 and Aβ42/40 was 96% and between Elecsys p‐tau/Aβ42 and both LUMIPULSE ratios was 97%. All ratios had > 94% overall, positive, and negative percent agreement with amyloid PET classification.DiscussionThese data suggest that p‐tau/Aβ42 and Aβ42/40 ratios provide similar clinical information in the assessment of amyloid pathology.
Spindle cell neoplasms of the upper gastrointestinal tract, hepatobiliary tract, and pancreas by fine needle aspiration: A single institutional experience of 15 years with follow‐up data
Authors: McHugh Kelsey E , Odronic Shelley I , Smith Amber , Springer Bridgette , Aramouni Ghada , Chute Deborah J , Reynolds Jordan P 
Published: May 2021

AbstractBackgroundThe diagnosis of spindle cell neoplasms (SCN) of the upper gastrointestinal (GI) tract, hepatobiliary tract, and pancreas detected by fine needle aspiration (FNA) is challenging. We describe a single‐center experience of these samples with follow‐up data and characterization of the morphologic findings.MethodsWe retrospectively reviewed pathology records for all FNAs diagnostic for or suggestive of SCN on esophagus, stomach, small bowel, liver, and pancreas in a 15 year period. All cases with at least 6 month follow‐up were included. Surgical material (biopsy or resection) was the diagnostic gold standard. All FNAs with subsequent surgical specimens were reviewed and assessed for cellularity, architectural features, and nuclear features.ResultsIn 15 years, 5101 FNAs of the upper GI tract, hepatobiliary tract, and pancreas were performed. SCN was diagnosed in 98 (2%) patients. Seventy‐two patients had definitive pathologic diagnoses: 68 were neoplastic and four were non‐neoplastic. Cytomorphologic review in relationship to final diagnosis revealed three statistically significant features: low cellularity favors a benign process (P = .00544), epithelioid nuclear morphology favors malignancy (P = .00278), and identification of perinuclear vacuoles favors a diagnosis of GIST over non‐GIST SCN (P = .04236).ConclusionsAmong cases with follow‐up, final pathologic diagnoses were SCN in 94% of cases diagnosed as SCN on FNA of upper GI, hepatobiliary tract, and pancreas. Although some cytomorphologic criteria are more suggestive of malignancy, arriving at a specific diagnosis relies on collaboration of clinical, radiologic, cytomorphologic, and immunohistochemical data.
Cryptic species and hidden ecological interactions of halictine bees along an elevational gradient
Authors: Mayr Antonia V. , Keller Alexander , Peters Marcell K. , Grimmer Gudrun , Krischke Beate , Geyer Mareen , Schmitt Thomas , Steffan‐Dewenter Ingolf 
Published: May 2021

AbstractChanges of abiotic and biotic conditions along elevational gradients represent serious challenges to organisms which may promote the turnover of species, traits and biotic interaction partners. Here, we used molecular methods to study cuticular hydrocarbon (CHC) profiles, biotic interactions and phylogenetic relationships of halictid bees of the genus Lasioglossum along a 2,900 m elevational gradient at Mt. Kilimanjaro, Tanzania. We detected a strong species turnover of morphologically indistinguishable taxa with phylogenetically clustered cryptic species at high elevations, changes in CHC profiles, pollen resource diversity, and a turnover in the gut and body surface microbiome of bees. At high elevations, increased proportions of saturated compounds in CHC profiles indicate physiological adaptations to prevent desiccation. More specialized diets with higher proportions of low‐quality Asteraceae pollen imply constraints in the availability of food resources. Interactive effects of climatic conditions on gut and surface microbiomes, CHC profiles, and pollen diet suggest complex feedbacks among abiotic conditions, ecological interactions, physiological adaptations, and phylogenetic constraints as drivers of halictid bee communities at Mt. Kilimanjaro.
Automatic detection of fish and tracking of movement for ecology
Authors: Lopez‐Marcano Sebastian , L. Jinks Eric , Buelow Christina A. , Brown Christopher J. , Wang Dadong , Kusy Branislav , M. Ditria Ellen , Connolly Rod M. 
Published: May 2021

Abstract

Animal movement studies are conducted to monitor ecosystem health, understand ecological dynamics, and address management and conservation questions. In marine environments, traditional sampling and monitoring methods to measure animal movement are invasive, labor intensive, costly, and limited in the number of individuals that can be feasibly tracked. Automated detection and tracking of small‐scale movements of many animals through cameras are possible but are largely untested in field conditions, hampering applications to ecological questions.

Here, we aimed to test the ability of an automated object detection and object tracking pipeline to track small‐scale movement of many individuals in videos. We applied the pipeline to track fish movement in the field and characterize movement behavior. We automated the detection of a common fisheries species (yellowfin bream, Acanthopagrus australis) along a known movement passageway from underwater videos. We then tracked fish movement with three types of tracking algorithms (MOSSE, Seq‐NMS, and SiamMask) and evaluated their accuracy at characterizing movement.

We successfully detected yellowfin bream in a multispecies assemblage (F1 score =91%). At least 120 of the 169 individual bream present in videos were correctly identified and tracked. The accuracies among the three tracking architectures varied, with MOSSE and SiamMask achieving an accuracy of 78% and Seq‐NMS 84%.

By employing this integrated object detection and tracking pipeline, we demonstrated a noninvasive and reliable approach to studying fish behavior by tracking their movement under field conditions. These cost‐effective technologies provide a means for future studies to scale‐up the analysis of movement across many visual monitoring systems.
Range‐wide breeding habitat use of the critically endangered Yellow‐breasted Bunting Emberiza aureola after population collapse
Authors: Beermann Ilka , Thomas Alexander , Anisimov Yury , Bastardot Marc , Batbayar Nyambayar , Davaasuren Batmunkh , Gerasimov Yury , Hasebe Makoto , Nakul Gleb , Nergui Jugdernamjil , Ktitorov Pavel , Kulikova Olga , Heim Wieland 
Published: May 2021

AbstractThe population of the Yellow‐breasted Bunting Emberiza aureola, a formerly widely distributed and abundant songbird of northern Eurasia, suffered a catastrophic decline and a strong range contraction between 1980 and 2013. There is evidence that the decline was driven by illegal trapping during migration, but potential contributions of other factors to the decline, such as land‐use change, have not yet been evaluated. Before the effects of land‐use change can be evaluated, a basic understanding of the ecological requirements of the species is needed. We therefore compared habitat use in ten remaining breeding regions across the range, from European Russia to Japan and the Russian Far East. We also assessed large‐scale variation in habitat parameters across the breeding range. We found large variation in habitat use, within and between populations. Differences were related to the cover and height of trees and shrubs at Yellow‐breasted Bunting territories. In many regions, Yellow‐breasted Buntings occupied early successional stages, including anthropogenic habitats characterized by mowing, grazing, or fire regimes. We found that the probability of presence can be best predicted with the cover of shrubs, herbs, and grasses. Highest probabilities were found at shrub cover values of 40%–70%. Differences in habitat use along a longitudinal gradient were small, but we found strong differences across latitudes, possibly related to habitat availability. We conclude that the remaining Yellow‐breasted Bunting populations are not limited to specific habitat types. Our results provide important baseline information to model the range‐wide distribution of this critically endangered species and to guide targeted conservation measures.
Simulating seasonal drivers of aphid dynamics to explore agronomic scenarios
Authors: Thierry Hugo , Monteil Claude , Parry Hazel , Vialatte Aude 
Published: May 2021

AbstractWith the regulation of pesticides in European agricultural landscapes, it is important to understand how pest populations respond to climate and landscape variables in the absence of pesticides at different spatial–temporal scales. While models have described individual biological processes, few have simulated complete life cycles at such scales. We developed a spatially explicit simulation model of the dynamics of the bird cherry–oat aphid (Rhopalosiphum padi) in a pesticide‐free simulated landscape using data from an agricultural landscape located in southwest France. Using GLMMs, we ran two statistical methods, one at the crop level, focusing on aphid densities within each crop individually (wheat and its regrowth, corn, and sorghum), and another at the landscape level where aphid densities were not differentiated by crops. For each season, we analyzed how temperature, immigration, and habitat availability impacted on aphid densities. Predictors of aphid densities varied between crops and between seasons, and models for each individual crop resulted in better predictions of aphid densities than landscape‐level models. Aphid immigration and temperature were important predictors of aphid densities across models but varied in the directionality of their effects. Moreover, landscape composition was a significant predictor in only four of the nine seasonal crop models. This highlights the complexity of pest–landscape interactions and the necessity of considering fine spatial–temporal scales to identify key factors that influence aphid densities, essential for developing future regulation methods. We used our model to explore the potential effects of two agronomic scenarios on aphid densities: (1) replacement of corn with sorghum, where increases in available sorghum led to the dilution of aphid populations in sorghum in spring and their concentration in summer, and (2) abandonment of pastures for wheat fields, which had no significant effect on aphid densities at the landscape scale. By simulating potential future agronomic practices, we can identify the risks of such changes and inform policy and decision‐makers to better anticipate pest dynamics in the absence of pesticides. This approach can be applied to other systems where agronomic and land cover data are available, and to other pest species for which biological processes are described in the literature.
Chiral separation in the class of proton pump inhibitors by chromatographic and electromigration techniques: An overview
Authors: Papp Lajos Attila , Hancu Gabriel , Kelemen Hajnal , Tóth Gergő 
Published: May 2021

AbstractProton pump inhibitors (PPIs) are benzimidazole‐derivative chiral sulfoxides, frequently used in the treatment of gastric hyperacidity‐related disorders. Due to their stereoselective metabolism, the eutomeric forms of PPIs can present a more advantageous pharmacokinetic profile by comparison with the distomers or racemates. Moreover, two representatives of the class are used in therapy both as racemates and as pure enantiomers (esomeprazole, dexlansoprazole). A relatively large number of enantioseparation methods employed for the stereoselective determination of PPIs from pharmaceutical, biological, and environmental matrices were published in the past three decades. The purpose of the current overview is to provide a systematic survey of the available chiral separation methods published since the introduction of PPIs in the therapy up to the present. Analytical and bioanalytical methods using different chromatographic and electromigration techniques reported for the enantioseparation of omeprazole, lansoprazole, pantoprazole, rabeprazole, ilaprazole, and tenatoprazole are included. The analytical conditions of the presented methods are summarized in three comprehensive tables, while a critical discussion of the applied techniques, possible mechanism of enantiorecognition, and future perspectives on the topic are also presented.
In Situ Effects of a Microplastic Mixture on the Community Structure of Benthic Macroinvertebrates in a Freshwater Pond
Authors: Stanković Jelena , Milošević Djuradj , Jovanović Boris , Savić-Zdravković Dimitrija , Petrović Ana , Raković Maja , Stanković Nikola , Stojković Piperac Milica 
Published: May 2021

Abstract
Benthic communities contain some of the most threatened organisms in aquatic habitats due to different anthropogenic pressures. The high abundance of microplastics in sediments will continue to increase in the future, further increasing the probability of interactions between macroinvertebrates and microplastics. In the present study, a benthic community in a relatively pristine shallow pond was exposed either to an environmentally relevant high concentration of a microplastic mixture of 80 g m–2 in the sediment, or a control sediment, without the addition of microplastics. The mixture of microplastics contained irregularly shaped polyethylene, polyvinyl chloride, and polyamide in a ratio of 50:25:25%, respectively. The in situ experiment lasted for 100 d. The total number of taxa that colonized the microcosms was 22 (17 in the control and 18 in the microplastic treatment), and the colonization was not affected by the treatment. The most dominant group within the macroinvertebrate community was the dipteran family Chironomidae, in both the control and the microplastic treatment. No significant differences in the abundance and biomass at a community level were recorded between the groups by permutational multivariate analysis of variance (F = 0.993, p = 0.456 and F = 0.344, p = 0.797, respectively). The mixture of microplastics did not influence the abundance or biomass of the functional feeding groups (F = 1.810, p = 0.137 and F = 0.377, p = 0.736, respectively). The species richness, species abundance, species biomass, Shannon's diversity index, and Simpson's index of diversity showed no statistically significant differences between the control and treatment groups. Czekanowski's quantitative similarity index indicated that 84% of the community remained unaffected after microplastic exposure. Environ Toxicol Chem 2022;41:888–895. © 2021 SETAC
Abstract
Exposure of freshwater benthic macroinvertebrate community to a high concentration of a microplastic mixture of irregular shaped polyethylene (PE), polyvinylchloride (PVC), and polyamide (PA), with control on the right.
Index modulation based decision gathering schemes for wireless sensor networks
Authors: Alhasanat Abdullah , Althunibat Saud , Alhasanat Mohanad , Alsafasfeh Moath 
Published: May 2021

AbstractDecision gathering process in target‐detection wireless sensor networks (WSNs) has an essential impact on the overall performance. Among the different decision gathering approaches, a recently proposed scheme, denoted by index modulation based WSN (IM‐WSN), has shown a significant enhancement in the decision error rate (DER). The IM‐WSN scheme exploits the concept of IM to convey sensing results from distributed clusters in cluster‐based WSNs. In this work, we aim at further enhancing the decision accuracy of IM‐WSN by improving the transmit diversity of each cluster. Specifically, two schemes, referred to as group‐based IM (GIM‐WSN) and combination‐based IM (CIM‐WSN), are proposed. Both schemes rely on increasing transmit diversity by allowing more than one node to act as cluster head and forward sensing results to the sink node. The average decision rate is formulated in a unified closed form expression for both schemes. In comparison with the state‐of‐art schemes, simulation results show that the proposed schemes exhibit better performance in terms of DER without additional complexity or energy consumption.
How cerebral cortex protects itself from interictal spikes: The alpha/beta inhibition mechanism
Authors: Pellegrino Giovanni , Hedrich Tanguy , Sziklas Viviane , Lina Jean‐Marc , Grova Christophe , Kobayashi Eliane 
Published: May 2021

AbstractInteractions between interictal epileptiform discharges (IEDs) and distant cortical regions subserve potential effects on cognition of patients with focal epilepsy. We hypothesize that “healthy” brain areas at a distance from the epileptic focus may respond to the interference of IEDs by generating inhibitory alpha and beta oscillations. We predict that more prominent alpha‐beta oscillations can be found in patients with less impaired neurocognitive profile. We performed a source imaging magnetoencephalography study, including 41 focal epilepsy patients: 21 with frontal lobe epilepsy (FLE) and 20 with mesial temporal lobe epilepsy. We investigated the effect of anterior (i.e., frontal and temporal) IEDs on the oscillatory pattern over posterior head regions. We compared cortical oscillations (5–80 Hz) temporally linked to 3,749 IEDs (1,945 frontal and 1,803 temporal) versus an equal number of IED‐free segments. We correlated results from IED triggered oscillations to global neurocognitive performance. Only frontal IEDs triggered alpha‐beta oscillations over posterior head regions. IEDs with higher amplitude triggered alpha‐beta oscillations of higher magnitude. The intensity of posterior head region alpha‐beta oscillations significantly correlated with a better neuropsychological profile. Our study demonstrated that cerebral cortex protects itself from IEDs with generation of inhibitory alpha‐beta oscillations at distant cortical regions. The association of more prominent oscillations with a better cognitive status suggests that this mechanism might play a role in determining the cognitive resilience in patients with FLE.
Admission Urinary and Serum Metabolites Predict Renal Outcomes in Hospitalized Patients With Cirrhosis
Authors: Bajaj Jasmohan S. , Garcia‐Tsao Guadalupe , Reddy K. Rajender , O’Leary Jacqueline G. , Vargas Hugo E. , Lai Jennifer C. , Kamath Patrick S. , Tandon Puneeta , Subramanian Ram M. , Thuluvath Paul , Fagan Andrew , Sehrawat Tejasav , de la Rosa Rodriguez Randolph , Thacker Leroy R. , Wong Florence 
Published: May 2021

Background and Aims
Acute kidney injury (AKI) has a poor prognosis in cirrhosis. Given the variability of creatinine, the prediction of AKI and dialysis by other markers is needed. The aim of this study is to determine the role of serum and urine metabolomics in the prediction of AKI and dialysis in an inpatient cirrhosis cohort.

Approach and Results
Inpatients with cirrhosis from 11 North American Consortium of End‐stage Liver Disease centers who provided admission serum/urine when they were AKI and dialysis‐free were included. Analysis of covariance adjusted for demographics, infection, and cirrhosis severity was performed to identify metabolites that differed among patients (1) who developed AKI or not; (2) required dialysis or not; and/pr (3) within AKI subgroups who needed dialysis or not. We performed random forest and AUC analyses to identify specific metabolite(s) associated with outcomes. Logistic regression with clinical variables with/without metabolites was performed. A total of 602 patients gave serum (218 developed AKI, 80 needed dialysis) and 435 gave urine (164 developed AKI, 61 needed dialysis). For AKI prediction, clinical factor–adjusted AUC was 0.91 for serum and 0.88 for urine. Major metabolites such as uremic toxins (2,3‐dihydroxy‐5‐methylthio‐4‐pentenoic acid [DMTPA], N2N2dimethylguanosine, uridine/pseudouridine) and tryptophan/tyrosine metabolites (kynunerate, 8‐methoxykyunerate, quinolinate) were higher in patients who developed AKI. For dialysis prediction, clinical factor–adjusted AUC was 0.93 for serum and 0.91 for urine. Similar metabolites as AKI were altered here. For dialysis prediction in those with AKI, the AUC was 0.81 and 0.79 for serum/urine. Lower branched‐chain amino‐acid (BCAA) metabolites but higher cysteine, tryptophan, glutamate, and DMTPA were seen in patients with AKI needing dialysis. Serum/urine metabolites were additive to clinical variables for all outcomes.

Conclusions
Specific admission urinary and serum metabolites were significantly additive to clinical variables to predict AKI development and dialysis initiation in inpatients with cirrhosis. These observations can potentially facilitate earlier initiation of renoprotective measures.