bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between metabolic resistances to atrazine and mesotrione in a multiple-resistant waterhemp (Amaranthus tuberculatus) population
Authors: Jacobs Kip E , Butts-Wilmsmeyer Carrie J. , Ma Rong , O’Brien Sarah R. , Riechers Dean E. 
Published: April 2020

AbstractMetabolic resistances to atrazine (atz-R) and mesotrione (meso-R) occur in several waterhemp [Amaranthus tuberculatus (Moq.) Sauer] populations in the United States. Interestingly, although metabolic atz-R but mesotrione-sensitive A. tuberculatus populations have been reported, an Amaranthus population has not been confirmed as meso-R but atrazine-sensitive, implying an association between these traits. Experiments were designed to investigate whether the single gene conferring metabolic atz-R plays a role in meso-R. An F2 population was generated from a multiple herbicide–resistant A. tuberculatus population from McLean County, IL (MCR). A cross was made between a known meso-R male clone (MCR-6) and a herbicide-sensitive female clone from Wayne County, IL (WCS-2) to develop an F1 population. Survival of MCR-6 plants following atrazine POST treatment (14.4 kg ha−1) indicated the male parent was homozygous atz-R. F1 plants were intermated to obtain a segregating pseudo-F2 population. Dose–response and metabolic studies conducted with mesotrione using F1 plants indicated intermediate biomass reductions and metabolic rates compared with MCR-6 and WCS. F2 plants were initially treated with either mesotrione (260 g ha−1) or atrazine (2 kg ha−1) POST, and after 21 d of recovery, vegetative clones from surviving resistant plants were subsequently treated with the other herbicide. When mesotrione was applied first, the meso-R frequency was 8.2%, and when atrazine was applied first, the atz-R frequency was 75%. However, the meso-R frequency increased to 16.5% following preselection for atz-R, and 100% of surviving meso-R plants were atz-R. Our findings indicate that the gene conferring metabolic atz-R is also involved with the meso-R trait within the population tested.
Limited induction of ethylene and cyanide synthesis are observed in quinclorac-resistant barnyardgrass (Echinochloa crus-galli) in Uruguay
Authors: Diez Vignola Manuel , Sainz Martha , Saldain Néstor E. , Marchesi Claudia , Bonnecarrère Victoria , Díaz Gadea Pedro 
Published: April 2020

AbstractBarnyardgrass [Echinochloa crus-galli(L.) P. Beauv] is the foremost weed in rice (Oryza sativaL.) systems, and its control is crucial to successful rice production. Quinclorac, a synthetic auxin herbicide, has been used effectively to manageE. crus-galli. However, occurrences of quinclorac-resistant genotypes are frequently reported, and its resistance evolution has led to questions about the continued utility of quinclorac for grass control. Identification of the resistance mechanism(s) of resistant genotypes will facilitate development of integrated weed management strategies that sustain quinclorac use for management ofE. crus-galli. We evaluated the responses to quinclorac of two contrasting genotypes: E7 (resistant, R) and LM04 (susceptible, S). Quinclorac induced ethylene and cyanide biosynthesis in the S-genotype. Both genotypes responded similarly to an increasing application of exogenous 1-carboxylic acid aminocyclopropane (ACC) and potassium cyanide, and their growth was inhibited at higher doses. The key mechanism for cyanide (HCN) detoxification in plants, β-cyanoalanine synthase (β-CAS) activity, was evaluated in both genotypes, and no significant difference was observed in the basal activity. However, quinclorac significantly induced β-CAS–like activity in the S-genotype, which is consistent with the increased synthesis of ethylene and cyanide. This work suggests that the resistance to quinclorac of the E7 R-genotype is likely related to an alteration in the auxin signal transduction pathway, causing a lower stimulation of ACC synthase and, therefore, limited synthesis of ethylene and HCN after quinclorac treatment.
Akzeptanz- und Commiment-Therapie mit therapieresistenten Störungen im stationären Setting
Authors: Benoy Charles , Meyer Andrea , Knitter Barbara , Pinhard Katrin , Walter Marc , Bader Klaus , Gloster Andrew T. 
Published: April 2020

Zusammenfassung. Hintergrund: Stationäre psychotherapeutische Behandlungen haben eine große Bedeutung im Versorgungsalltag. Ihre Bewährung bei schwergradigen und komorbiden Störungsbildern ist jedoch nur lückenhaft untersucht. Dies gilt besonders für die zunehmend angewendete Akzeptanz- und Commitment-Therapie (ACT). Fragestellung: In erster Linie soll die Wirksamkeit einer stationären störungsübergreifenden ACT-basierten Behandlung in erwähnten Stichproben untersucht werden. Ergänzend wird der zeitliche Verlauf der psychischen Flexibilität (PF), dem Kernkonzept der ACT, explorativ untersucht. Methode: Eine konsekutive Stichprobe von 47 Patientinnen und Patienten mit heterogenen und komorbiden Störungsbildern in stationärer Psychotherapie wurde im Rahmen einer explorativen Beobachtungsstudie mittels wöchentlicher Verlaufsmessungen sowie umfassender Prä-Post-Vergleiche untersucht. Ergebnisse: Die Effektstärken hinsichtlich allgemeiner Symptomreduktion, der Zunahme psychischer Flexibilität sowie weiterer ACT-spezifischer Fertigkeiten sind moderat bis hoch. Die Verlaufsmessungen weisen auf lineare Verbesserungen sowie hohe Übereinstimmungen zwischen Selbst- und Fremdrating hin. Schlussfolgerungen: Die Ergebnisse zeigen positive Effekte der ACT im stationären Setting bei einer diagnostisch heterogenen Stichprobe mit einem hohen Anteil komorbider Störungen.
Contribution of common and rare damaging variants in familial forms of bipolar disorder and phenotypic outcome
Authors: Courtois Elisa , Schmid Mark , Wajsbrot Orly , Barau Caroline , Le Corvoisier Philippe , Aouizerate Bruno , Bellivier Frank , Belzeaux Raoul , Dubertret Caroline , Kahn Jean-Pierre , Leboyer Marion , Olie Emilie , Passerieux Christine , Polosan Mircea , Etain Bruno , Jamain Stéphane ,   and the FondaMental Advanced Centers of Expertise in Bipolar Disorders (FACE-BD)
Published: April 2020

AbstractGenome-wide association studies on bipolar disorders (BD) have revealed an additive polygenic contribution of common single-nucleotide polymorphisms (SNPs). However, these SNPs explain only 25% of the overall genetic variance and suggest a role of rare variants in BD vulnerability. Here, we combined high-throughput genotyping data and whole-exome sequencing in cohorts of individuals with BD as well as in multiplex families with a high density of affected individuals in order to determine the contribution of both common and rare variants to BD genetic vulnerability. Using polygenic risk scores (PRS), we showed a strong contribution of common polymorphisms previously associated with BD and schizophrenia (SZ) and noticed that those specifically associated with SZ contributed more in familial forms of BD than in non-familial ones. The analysis of rare damaging variants shared by affected individuals in multiplex families with BD revealed a single interaction network enriched in neuronal and developmental biological pathways, as well as in the regulation of gene expression. We identified four genes with a higher mutation rate in individuals with BD than in the general population and showed that mutations in two of them were associated with specific clinical manifestations. In addition, we showed a significant negative correlation between PRS and the number of rare damaging variants specifically in unaffected individuals of multiplex families. Altogether, our results suggest that common and rare genetic variants both contribute to the familial aggregation of BD and this genetic architecture may explain the heterogeneity of clinical manifestations in multiplex families.
Spectro-temporal encoded multiphoton microscopy and fluorescence lifetime imaging at kilohertz frame-rates
Authors: Karpf Sebastian , Riche Carson T. , Di Carlo Dino , Goel Anubhuti , Zeiger William A. , Suresh Anand , Portera-Cailliau Carlos , Jalali Bahram 
Published: April 2020

AbstractTwo-Photon Microscopy has become an invaluable tool for biological and medical research, providing high sensitivity, molecular specificity, inherent three-dimensional sub-cellular resolution and deep tissue penetration. In terms of imaging speeds, however, mechanical scanners still limit the acquisition rates to typically 10–100 frames per second. Here we present a high-speed non-linear microscope achieving kilohertz frame rates by employing pulse-modulated, rapidly wavelength-swept lasers and inertia-free beam steering through angular dispersion. In combination with a high bandwidth, single-photon sensitive detector, this enables recording of fluorescent lifetimes at speeds of 88 million pixels per second. We show high resolution, multi-modal - two-photon fluorescence and fluorescence lifetime (FLIM) – microscopy and imaging flow cytometry with a digitally reconfigurable laser, imaging system and data acquisition system. These high speeds should enable high-speed and high-throughput image-assisted cell sorting.
Artifact-free and high-temporal-resolution in vivo opto-electrophysiology with microLED optoelectrodes
Authors: Kim Kanghwan , Vöröslakos Mihály , Seymour John P. , Wise Kensall D. , Buzsáki György , Yoon Euisik 
Published: April 2020

AbstractThe combination of in vivo extracellular recording and genetic-engineering-assisted optical stimulation is a powerful tool for the study of neuronal circuits. Precise analysis of complex neural circuits requires high-density integration of multiple cellular-size light sources and recording electrodes. However, high-density integration inevitably introduces stimulation artifact. We present minimal-stimulation-artifact (miniSTAR) μLED optoelectrodes that enable effective elimination of stimulation artifact. A multi-metal-layer structure with a shielding layer effectively suppresses capacitive coupling of stimulation signals. A heavily boron-doped silicon substrate silences the photovoltaic effect induced from LED illumination. With transient stimulation pulse shaping, we reduced stimulation artifact on miniSTAR μLED optoelectrodes to below 50 μVpp, much smaller than a typical spike detection threshold, at optical stimulation of >50 mW mm–2irradiance. We demonstrated high-temporal resolution (<1 ms) opto-electrophysiology without any artifact-induced signal quality degradation during in vivo experiments. MiniSTAR μLED optoelectrodes will facilitate functional mapping of local circuits and discoveries in the brain.
Cytosine base editors with minimized unguided DNA and RNA off-target events and high on-target activity
Authors: Yu Yi , Leete Thomas C. , Born David A. , Young Lauren , Barrera Luis A. , Lee Seung-Joo , Rees Holly A. , Ciaramella Giuseppe , Gaudelli Nicole M. 
Published: April 2020

AbstractCytosine base editors (CBEs) enable efficient, programmable reversion of T•A to C•G point mutations in the human genome. Recently, cytosine base editors with rAPOBEC1 were reported to induce unguided cytosine deamination in genomic DNA and cellular RNA. Here we report eight next-generation CBEs (BE4 with either RrA3F [wt, F130L], AmAPOBEC1, SsAPOBEC3B [wt, R54Q], or PpAPOBEC1 [wt, H122A, R33A]) that display comparable DNA on-target editing frequencies, whilst eliciting a 12- to 69-fold reduction in C-to-U edits in the transcriptome, and up to a 45-fold overall reduction in unguided off-target DNA deamination relative to BE4 containing rAPOBEC1. Further, no enrichment of genome-wide C•G to T•A edits are observed in mammalian cells following transfection of mRNA encoding five of these next-generation editors. Taken together, these next-generation CBEs represent a collection of base editing tools for applications in which minimized off-target and high on-target activity are required.
Prefrontal reinstatement of contextual task demand is predicted by separable hippocampal patterns
Authors: Jiang Jiefeng , Wang Shao-Fang , Guo Wanjia , Fernandez Corey , Wagner Anthony D. 
Published: April 2020

AbstractGoal-directed behavior requires the representation of a task-set that defines the task-relevance of stimuli and guides stimulus-action mappings. Past experience provides one source of knowledge about likely task demands in the present, with learning enabling future predictions about anticipated demands. We examine whether spatial contexts serve to cue retrieval of associated task demands (e.g., context A and B probabilistically cue retrieval of task demands X and Y, respectively), and the role of the hippocampus and dorsolateral prefrontal cortex (dlPFC) in mediating such retrieval. Using 3D virtual environments, we induce context-task demand probabilistic associations and find that learned associations affect goal-directed behavior. Concurrent fMRI data reveal that, upon entering a context, differences between hippocampal representations of contexts (i.e., neural pattern separability) predict proactive retrieval of the probabilistically dominant associated task demand, which is reinstated in dlPFC. These findings reveal how hippocampal-prefrontal interactions support memory-guided cognitive control and adaptive behavior.
Proteogenomics analysis unveils a TFG-RET gene fusion and druggable targets in papillary thyroid carcinomas
Authors: Krishnan Aswini , Berthelet Jean , Renaud Emilie , Rosigkeit Sebastian , Distler Ute , Stawiski Eric , Wang Jing , Modrusan Zora , Fiedler Marc , Bienz Mariann , Tenzer Stefan , Schad Arno , Roth Wilfried , Thiede Bernd , Seshagiri Somasekar , Musholt Thomas J. , Rajalingam Krishnaraj 
Published: April 2020

AbstractPapillary thyroid cancer (PTC) is the most common type of endocrine malignancy. By RNA-seq analysis, we identify a RET rearrangement in the tumour material of a patient who does not harbour any known RAS or BRAF mutations. This new gene fusion involves exons 1–4 from the 5′ end of the Trk fused Gene (TFG) fused to the 3′ end of RET tyrosine kinase leading to a TFG-RET fusion which transforms immortalized human thyroid cells in a kinase-dependent manner. TFG-RET oligomerises in a PB1 domain-dependent manner and oligomerisation of TFG-RET is required for oncogenic transformation. Quantitative proteomic analysis reveals the upregulation of E3 Ubiquitin ligase HUWE1 and DUBs like USP9X and UBP7 in both tumor and metastatic lesions, which is further confirmed in additional patients. Expression of TFG-RET leads to the upregulation of HUWE1 and inhibition of HUWE1 significantly reduces RET-mediated oncogenesis.
Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria
Authors: Shaw Dario R. , Ali Muhammad , Katuri Krishna P. , Gralnick Jeffrey A. , Reimann Joachim , Mesman Rob , van Niftrik Laura , Jetten Mike S. M. , Saikaly Pascal E. 
Published: April 2020

AbstractAnaerobic ammonium oxidation (anammox) bacteria contribute significantly to the global nitrogen cycle and play a major role in sustainable wastewater treatment. Anammox bacteria convert ammonium (NH4+) to dinitrogen gas (N2) using intracellular electron acceptors such as nitrite (NO2−) or nitric oxide (NO). However, it is still unknown whether anammox bacteria have extracellular electron transfer (EET) capability with transfer of electrons to insoluble extracellular electron acceptors. Here we show that freshwater and marine anammox bacteria couple the oxidation of NH4+ with transfer of electrons to insoluble extracellular electron acceptors such as graphene oxide or electrodes in microbial electrolysis cells. 15N-labeling experiments revealed that NH4+ was oxidized to N2 via hydroxylamine (NH2OH) as intermediate, and comparative transcriptomics analysis revealed an alternative pathway for NH4+ oxidation with electrode as electron acceptor. Complete NH4+ oxidation to N2 without accumulation of NO2− and NO3− was achieved in EET-dependent anammox. These findings are promising in the context of implementing EET-dependent anammox process for energy-efficient treatment of nitrogen.
Occupational radiation exposure in femoral artery approach is higher than radial artery approach during coronary angiography or percutaneous coronary intervention
Authors: Kim Jung-Su , Lee Bong-Ki , Ryu Dong-Ryeol , Chun Kwangjin , Kwon Ho-Seok , Nam So-Ra , Kim Doo-il , Lee Sung-Yun , Jeong Jin-Ok , Bae Jang-Whan , Park Jong-Seon , Ahn Youngkeun , Chae Je-Keon , Yoon Myeong-Ho , Lee Seung-Hwan , Yoon Jeonghan , Gwon Hyeon-Cheol , Choi Donghoon , Kwon Soon-Mu , Roh Young-Hoon , Cho Byung-Ryul 
Published: April 2020

AbstractMedical radiation exposure is a significant concern for interventional cardiologists (IC). This study was aimed at estimating the radiation exposure of IC operators and assistants in real clinical practice. The radiation exposure of the operator and assistant was evaluated by conducting two types of procedures via coronary angiography (CAG) and percutaneous coronary intervention (PCI) on 1090 patients in 11-cardiovascular centers in Korea. Radiation exposure was measured using an electronic personal dosimeter (EPD). EPD were attached at 3 points on each participant: on the apron on the left anterior chest (A1), under the apron on the sternum (A2), and on the thyroid shield (T). Average radiation exposure (ARE) of operators at A1, A2, and T was 19.219 uSv, 4.398 uSv, and 16.949 uSv during CAG and 68.618 uSv, 15.213 uSv, and 51.197 uSv during PCI, respectively. ARE of assistants at A1, A2, and T was 4.941 uSv, 0.860 uSv, and 5.232 uSv during CAG and 20.517 uSv, 4.455 uSv, and 16.109 uSv during PCI, respectively. AED of operator was 3.4 times greater during PCI than during CAG.
BEHRT: Transformer for Electronic Health Records
Authors: Li Yikuan , Rao Shishir , Solares José Roberto Ayala , Hassaine Abdelaali , Ramakrishnan Rema , Canoy Dexter , Zhu Yajie , Rahimi Kazem , Salimi-Khorshidi Gholamreza 
Published: April 2020

AbstractToday, despite decades of developments in medicine and the growing interest in precision healthcare, vast majority of diagnoses happen once patients begin to show noticeable signs of illness. Early indication and detection of diseases, however, can provide patients and carers with the chance of early intervention, better disease management, and efficient allocation of healthcare resources. The latest developments in machine learning (including deep learning) provides a great opportunity to address this unmet need. In this study, we introduce BEHRT: A deep neural sequence transduction model for electronic health records (EHR), capable of simultaneously predicting the likelihood of 301 conditions in one’s future visits. When trained and evaluated on the data from nearly 1.6 million individuals, BEHRT shows a striking improvement of 8.0–13.2% (in terms of average precision scores for different tasks), over the existing state-of-the-art deep EHR models. In addition to its scalability and superior accuracy, BEHRT enables personalised interpretation of its predictions; its flexible architecture enables it to incorporate multiple heterogeneous concepts (e.g., diagnosis, medication, measurements, and more) to further improve the accuracy of its predictions; its (pre-)training results in disease and patient representations can be useful for future studies (i.e., transfer learning).
The Natural history of Epicardial Adipose Tissue Volume and Attenuation: A long-term prospective cohort follow-up study
Authors: Nerlekar Nitesh , Thakur Udit , Lin Andrew , Koh Ji Quan Samuel , Potter Elizabeth , Liu David , Muthalaly Rahul G. , Rashid Hashrul N. , Cameron James D. , Dey Damini , Wong Dennis T. L. 
Published: April 2020

AbstractEpicardial adipose tissue (EAT) is associated with cardiovascular risk. The longitudinal change in EAT volume (EATv) and density (EATd), and potential modulators of these parameters, has not been described. We prospectively recruited 90 patients with non-obstructive coronary atherosclerosis on baseline computed tomography coronary angiography (CTCA) performed for suspected coronary artery disease to undergo a repeat research CTCA. EATv in millilitres (mL) and EATd in Hounsfield units (HU) were analysed and multivariable regression analysis controlling for traditional cardiovascular risk factors (CVRF) performed to assess for any predictors of change. Secondary analysis was performed based on statin therapy. The median duration between CTCA was 4.3years. Mean EATv increased at follow-up (72 ± 33 mL to 89 ± 43 mL, p < 0.001) and mean EATd decreased (baseline −76 ± 6 HU vs. −86 ± 5 HU, p < 0.001). There were no associations between baseline variables of body mass index, age, sex, hypertension, hyperlipidaemia, diabetes or smoking on change in EATv or EATd. No difference in baseline, follow-up or delta EATv or EATd was seen in patients with (60%) or without baseline statin therapy. In this select group of patients, EATv consistently increased and EATd consistently decreased at long-term follow-up and these changes were independent of CVRF, age and statin use. Together with the knowledge of strong associations between EAT and cardiac disease, these findings may suggest that EAT is an independent parameter rather than a surrogate for cardiovascular risk.
AFP-LSE: Antifreeze Proteins Prediction Using Latent Space Encoding of Composition of k-Spaced Amino Acid Pairs
Authors: Usman Muhammad , Khan Shujaat , Lee Jeong-A 
Published: April 2020

AbstractSpecies living in extremely cold environments resist the freezing conditions through antifreeze proteins (AFPs). Apart from being essential proteins for various organisms living in sub-zero temperatures, AFPs have numerous applications in different industries. They possess very small resemblance to each other and cannot be easily identified using simple search algorithms such as BLAST and PSI-BLAST. Diverse AFPs found in fishes (Type I, II, III, IV and antifreeze glycoproteins (AFGPs)), are sub-types and show low sequence and structural similarity, making their accurate prediction challenging. Although several machine-learning methods have been proposed for the classification of AFPs, prediction methods that have greater reliability are required. In this paper, we propose a novel machine-learning-based approach for the prediction of AFP sequences using latent space learning through a deep auto-encoder method. For latent space pruning, we use the output of the auto-encoder with a deep neural network classifier to learn the non-linear mapping of the protein sequence descriptor and class label. The proposed method outperformed the existing methods, yielding excellent results in comparison. A comprehensive ablation study is performed, and the proposed method is evaluated in terms of widely used performance measures. In particular, the proposed method demonstrated a high Matthews correlation coefficient of 0.52, F-score of 0.49, and Youden’s index of 0.81 on an independent test dataset, thereby outperforming the existing methods for AFP prediction.