bluuebunny/crossref_metadata_2025_split huggingface dataset:
DEEP LEARNING TO PREDICT DEGREE OF INTERSTITIAL FIBROSIS AND TUBULAR ATROPHY FROM KIDNEY ULTRASOUND IMAGES – AN ARTIFICIAL INTELLIGENCE APPROACH
Authors: Athavale Ambarish M. , Hart Peter D. , Itteera Mathew , Cimbaluk David , Patel Tushar , Alabka Anas , Dunea George , Arruda Jose , Singh Ashok , Rosenberg Avi , Kulkarni Hemant 
Published: August 2020

ABSTRACTBackgroundInterstitial fibrosis and tubular atrophy (IFTA) is a strong predictor of decline in kidney function. Non-invasive test to assess IFTA is not available.MethodsWe trained, validated and tested a deep learning (DL) system to classify IFTA grade from 6,135 ultrasound images obtained from 352 patients who underwent kidney biopsy. Of 6,135 ultrasound images, 5,523 were used for training (n = 5,122) and validation (n = 401) and 612 to test the accuracy of the DL system. IFTA grade scored by nephropathologist on trichrome stained kidney biopsy slide was used as reference standard.ResultsThere were 159 patients (2,701 ultrasound images), 74 patients (1,239 ultrasound images), 41 patients (701 ultrasound images) and 78 patients (1,494 ultrasound images) with IFTA grades 1, 2, 3 and 4, respectively. The deep-learning classification system used masked images based on a 91% accurate kidney segmentation routine. The performance matrices for the deep learning classifier algorithm in the validation set showed excellent precision (90%), recall (76%), accuracy (84%) and F1-score (80%). In the independent test set also, performance matrices showed excellent precision (90%), recall (80%), accuracy (87%) and F1-score of (84%). Accuracy was highest for IFTA grade 1 (98%) and IFTA grade 4 (82%).ConclusionA DL system can accurately predict IFTA from kidney ultrasound image.
ARTIFICIAL INTELLIGENCE IN PERCUTANEOUS CORONARY INTERVENTION: IMPROVED PREDICTION OF PCI-RELATED COMPLICATIONS USING AN ARTIFICIAL NEURAL NETWORK
Authors: Kulkarni Hemant , Amin Amit P. 
Published: August 2020

AbstractImportanceComplications after percutaneous coronary intervention (PCI) are common and costly. Risk models for predicting the likelihood of acute kidney injury (AKI), bleeding, stroke and death are limited by accuracy and inability to use non-linear relationships among predictors. Additionally, if non-linear relationships among predictors can be leveraged, then the prediction of any adverse event (i.e. “the patient who will not do well with PCI”) is perhaps of greater interest to clinicians than prediction of adverse events in isolation.ObjectiveTo develop and validate a set of artificial neural networks (ANN) models to predict five adverse outcomes after PCI – AKI, bleeding, stroke, death and one or more of these four (‘any adverse outcome’).DesignCross-sectional study, using institutional NCDR CathPCI data.Setting and participants28,005 patients undergoing PCI at five hospitals in the Barnes-Jewish Hospital system.Main Outcome(s)AKI, bleeding, stroke, death, and one or more of these four (‘any adverse outcome’). We divided 28,005 PCI patients into a training cohort of 21,004 (75%) and a test cohort of 7,001 (25%). We used an artificial neural network (ANN) multilayer perceptron (MLP) model to predict each outcome based on a set of 278 encoded and preprocessed variables. Model accuracy was tested using area under the receiver-operating-characteristic curve (AUC). Performance and validation of the MLP model was compared with existing regression models using integrated discrimination improvement (IDI) and continuous net reclassification index (NRI).ResultsThe prevalence of AKI, bleeding, stroke and death in the study cohort was 4.6%, 3.6%, 0.3% and 1.1%, respectively. The fully trained MLP model achieved convergence quickly (< 10 epochs) and could predict accurately predict AKI (77.9%), bleeding (86.5%), death (90.3%) and any adverse outcome (80.6%) in the independent test set. However, prediction of stroke was not satisfactory (69.9%). Compared to the currently used models for AKI, bleeding and death prediction, our models showed a significantly higher AUC (range 1.6% – 5.6%), IDI (range 4.9% –7.2%) and NRI (range 0.07 – 0.61).Conclusions and RelevanceBy using neural network-based models, we accurately predict major adverse events after PCI. Larger studies for replicability and longitudinal studies for evidence of impact are needed to establish these artificial intelligence methods in current PCI practice.
Clinico-epidemiological characteristics of asymptomatic and symptomatic COVID-19-positive patients in Bangladesh
Authors: Hasan Mohammad Jahid , Chowdhury Sayeda Mukta , Khan Md. Abdullah Saeed , Rahaman Monjur , Fardous Jannatul , Adit Tanjir , Rahman Mustafizur , Hossain Md. Tarek , Yesmin Shakila , Raheem Enayetur , Amin Mohammad Robed 
Published: August 2020

AbstractBackgroundAs of August 15, 2020, Bangladesh lost 3591 lives since the first Coronavirus disease 2019 (COVID-19) case announced on March 8. The objective of the study was to report the clinical manifestation of both symptomatic and asymptomatic COVID-19-positive patients.MethodsA online-based cross-sectional survey was conducted for initial recruitment of participants with subsequent telephone interview by the three trained physicians in 237 adults with confirmed COVID-19 infection in Bangladesh. The study period was between 27 April to 26th May, 2020. Consent was ensured before commencing the interview. Collected data were entered in a predesigned case report form and subsequently analyzed by SPSS 20.ResultsThe mean age at presentation was 41.59±13.73 (SD) years and most of the cases were male (73%). A total of 90.29% of patients reside in urban areas. Among the positive cases, 13.1% (n = 31) were asymptomatic. Asymptomatic cases were significantly more common in households with 2 to 4 members (p = .008). Both symptomatic and asymptomatic patients shared similar ages of presentation (p = 0.23), gender differences (p = 0.30), and comorbidities (p = 0.11). Only 5.3% of patients received ICU care during their treatment. The most frequent presentation was fever (88.3%), followed by cough (69.9%), chest pain (34.5%), body ache (31.1%), and sore throat (30.1%). Thirty-nine percent (n = 92) of the patients had comorbidities, with diabetes and hypertension being the most frequently observed.ConclusionThere has been an upsurge in COVID-19 cases in Bangladesh. Patients were mostly middle-aged and male. Typical presentations were fever and cough. Maintenance of social distancing and increased testing are required to meet the current public health challenge.
Mathematical modeling of metastasis, a feasible way to detect the weakness
Authors: Guerra A. , Silva E. , Mansilla R. , Nieto-Villar J. M. 
Published: August 2020

AbstractAimCancer is one of the main causes of death worldwide. 90% of deaths caused by this disease occur due to metastasis. Two models are proposed that rescue fundamental aspects of metastasis, such as EMT (epithelial-mesenchymal transition), extravasation and colonization.MethodsTo evaluate the complexity, the Lyapunov exponents, the eigenvalues of the Jacobian matrix (stability analysis) and the Kaplan York dimension were calculated.ResultsIt was evidenced that the weakness of the metastasis lies in these stages, which indicates that they constitute potential targets in the search for an effective treatment.ConclusionThe results suggest that strengthening the immune system during EMT as well as its specialization in the detection of DTCs (disseminated tumor cells) can be effective strategies in the treatment of metastasis.
An effective, safe and cost-effective cell-based chimeric vaccine against SARS-CoV2
Authors: Cheng Zhenguo , Zhang Danhua , Liu XiaoWen , Miao Jinxin , Wang Jianyao , Guo Haoran , Yan Wenli , Zhang Zhe , Zhang Na , Wang Jingjing , Lu Shuangshuang , Zhang Zhongxian , Liu Wei , Liu Hong , Zhang Yi , Zhang Lirong , Dong Jianzeng , Lemoine Nicholas R , Wang Yaohe 
Published: August 2020

AbstractMore than one hundred vaccines against SARS-CoV-2 have been developed and some of them have entered clinical trials, but the latest results revealed that these vaccines still face great challenges. Here, we developed a novel cell-based gp96-Ig-secreting chimeric vaccine which is composed of two viral antigens, the RBD of spike protein, and a truncated nucleocapsid protein that could induce epitope-specific cytotoxic T lymphocytes but low antibody response. Syrian hamsters immunized with the cell-based vaccine produced high level of SARS-CoV-2 specific NAbs and specific T cell immunity which could eliminate RBD-truncated N-expressing cells, without the induction of antibody against N protein and other observed toxicity. This study provides a proof of concept for clinical testing of this safe, effective and cost-effective vaccine against SARS-CoV2 infection.
Modulation of flight and feeding behaviours requires presynaptic IP3Rs in dopaminergic neurons
Authors: Sharma Anamika , Hasan Gaiti 
Published: August 2020

AbstractInnate behaviours, though robust and hard wired, rely on modulation of neuronal circuits, for eliciting an appropriate response according to internal states and external cues.Drosophilaflight is one such innate behaviour that is modulated by intracellular calcium release through inositol 1,4,5-trisphosphate receptors (IP3Rs). Cellular mechanism(s) by which IP3Rs modulate neuronal function for specific behaviours remain speculative, in vertebrates and invertebrates. To address this, we generated an inducible dominant negative form of the IP3R (IP3RDN). Flies with neuronal expression of IP3RDNexhibit flight deficits. Spatiotemporal expression of IP3RDNhelped identify key flight-modulating dopaminergic neurons with axonal projections in the mushroom body. Attenuation of IP3R function in these presynaptic dopaminergic neurons resulted in flies with shortened flight bouts and a disinterest in seeking food, accompanied by reduced excitability and dopamine release upon cholinergic stimulation. Our findings suggest that the same neural circuit modulates the drive for food search and for undertaking longer flight bouts.
Enterococcus peptidoglycan remodeling promotes immune checkpoint inhibitor therapy
Authors: Griffin Matthew E. , Espinosa Juliel , Becker Jessica L. , Jha Jyoti K. , Fanger Gary R. , Hang Howard C. 
Published: August 2020

AbstractThe antitumor efficacy of cancer immunotherapy has been correlated with specific species within the gut microbiota. However, molecular mechanisms by which these microbes affect host response to immunotherapy remain elusive. Here we show that specific members of the bacterial genus Enterococcus can promote anti-PD-L1 immunotherapy in mouse tumor models. The active enterococci express and secrete orthologs of the NlpC/p60 peptidoglycan hydrolase SagA that generate immune-active muropeptides. Expression of SagA in non-protective E. faecalis was sufficient to promote antitumor activity of clinically approved checkpoint targets, and its activity required the peptidoglycan sensor Nod2. Notably, SagA-engineered probiotics or synthetic muropeptides also promoted checkpoint inhibitor antitumor activity. Our data suggest that microbiota species with unique peptidoglycan remodeling activity may enhance immunotherapy and could be leveraged for next-generation adjuvants.One Sentence SummaryA conserved family of secreted NlpC/p60 peptidoglycan hydrolases from Enterococcus promote antitumor activity of immune checkpoint inhibitors.
Detection and Characterization of Magnetosome Chains In Magnetotactic Bacteria
Authors: Vinay Bharadhwaj , Vijay Bhavya , Raghunath Surya K 
Published: August 2020

AbstractAimMagnetotactic bacteria are gram-negative, prokaryotic organisms which align themselves according to the Earth’s geomagnetic field. They contain organelles called magnetosomes which produce nano-magnetites by the mechanism of biomineralization. These nano-magnetites are arranged in the form of well-ordered chain called magnetosome chain, which are held together by intermolecular forces. The growth of these bacteria is stringent to specific oxygen gradient regions, where there is oxic-anoxic transition zone. In this paper, we report the cultivation and characterisation of magnetotactic bacteria that was accomplished under laboratory conditions and scanning electron microscope respectively.MethodologyBacterial soil samples were collected and cultivated under laboratory conditions using a precise and cost-effective media formulation using coffee bean extract and ferric chloride, which were to provide sufficient iron under the influence of external magnetic field. Experiments were conducted using media, deficient with ferric chloride and coffee bean solution, as control. Pour plate method was carried out for the growth of bacteria under the influence of external magnetic field provided on one-end of the petri-plate.ResultWe observed the growth of the cultivated bacteria in the proximity of the magnetic field only in the presence of iron in media. This emphasises that the media formulated was appropriate for the growth of bacteria under laboratory conditions. Scanning electron microscope analysis confirmed the presence of magnetosome chains in magnetotactic bacteria.InterpretationIn this research, the bacteria were able to sustain in artificial oxygen-transition zones provided in the laboratory. The coffee bean solution contained quinic acid and succinic acid, which along with ferric chloride provided iron in the form of ferric quinate, and succinic acid which are the major sources of growth for the bacteria. Even though magnetosome research has shown promising advances, one of major limitations in its commercialization is its difficulty in cultivation under laboratory conditions.
Forces experienced by instrumented animals depend on lifestyle
Authors: Wilson Rory P , Rose Kayleigh A , Gunner Richard , Holton Mark , Marks Nikki J , Bennett Nigel C , Bell Stephen H. , Twining Joshua P , Hesketh Jamie , Duarte Carlos M. , Bezodis Neil , Scantlebury D. Michael 
Published: August 2020

AbstractAnimal-attached devices have transformed our understanding of vertebrate ecology. However, to be acceptable, researchers must minimize tag-related harm. The long-standing recommendation that tag masses should not exceed 3% of the animal’s body mass ignores tag forces generated by movement. We used collar-attached accelerometers on four free-ranging carnivores, spanning two orders of magnitude in mass, to reveal that during movement, forces exerted by ‘3%’ tags were generally equivalent to 4-19% of the animals’ masses, with a record of 54% in a hunting cheetah. Controlled studies on domestic dogs revealed how the tag forces are dictated by animal gait and speed but appear largely invariant of body mass. This fundamentally changes how acceptable tag mass limits should be determined, requiring cognizance of animal athleticism.One Sentence SummaryThere can be no universal rule for collar-tag masses as a percentage of carrier mass since tag forces depend on lifestyle.
Maternal factor PABPN1L is essential for maternal mRNA degradation during maternal-to-zygotic transition
Authors: Wang Ying , Feng Tianhao , Shi Xiaodan , Liu Siyu , Wang Zerui , Zhang Xin , Zhang Jintao , Zhao Shuqin , Zhang Junqiang , Ling Xiufeng , Liu Mingxi 
Published: August 2020

AbstractInfertility affects 10% - 15% of families worldwide. However, the pathogenesis of female infertility caused by abnormal early embryonic development is not clear. We constructed a mouse model (Pabpn1l -/-) simulating the splicing abnormality of human PABPN1L and found that the female was sterile and the male was fertile. The Pabpn1l -/- oocytes can be produced, ovulated and fertilized normally, but cannot develop beyond the 2-cell stage. Using RNA-Seq, we found a large-scale upregulation of RNA in Pabpn1l -/- MII oocytes. Of the 2401 transcripts upregulated in Pabpn1l-/- MII oocytes, 1523 transcripts (63.4%) were also upregulated in Btg4 -/- MII oocytes, while only 53 transcripts (2.2%) were upregulated in Ythdf2 -/- MII oocytes. We documented that transcripts in zygotes derived from Pabpn1l -/- oocytes have a longer poly(A) tail than the control group, a phenomenon similar to that in Btg4-/- mice. Surprisingly, the poly(A) tail of these mRNAs was significantly shorter in the Pabpn1l -/- MII oocytes than in the Pabpn1l +/+. These results suggest that PABPN1L is involved in BTG4-mediated maternal mRNA degradation, and may antagonize poly(A) tail shortening in oocytes independently of its involvement in maternal mRNA degradation. Thus, PABPN1L variants could be a genetic marker of female infertility.
Activation of G-protein coupled receptors is thermodynamically linked to lipid solvation
Authors: Leonard Alison N. , Lyman Edward 
Published: August 2020

AbstractPreferential lipid solvation of the G-protein coupled A2Aadenosine receptor (A2AR) is evaluated from 35μsec of all-atom molecular dynamics simulation. A coarse-grained transition matrix algorithm is developed to overcome slow equilibration of the first solvation shell, obtaining statistically robust estimates of the free energy of solvation by different lipids for the receptor in different activation states. Results indicate preference for solvation by unsaturated chains, which favors the active receptor. A model for lipid-dependent GPCR activity is proposed in which the chemical potential of lipids in the bulk membrane modulates receptor activity. The enthalpy and entropy associated with moving saturated vs. unsaturated lipids from bulk to A2AR’s first solvation shell are compared. In the simulated mixture, saturated chains are disordered (i.e., obtain a favorable entropic contribution) when partitioning to the receptor surface, but this is outweighed by a favorable enthalpic contribution for unsaturated chains to occupy the first solvation shell.
Deep learning for species identification of modern and fossil rodent molars
Authors: Miele Vincent , Dussert Gaspard , Cucchi Thomas , Renaud Sabrina 
Published: August 2020

AbstractReliable identification of species is a key step to assess biodiversity. In fossil and archaeological contexts, genetic identifications remain often difficult or even impossible and morphological criteria are the only window on past biodiversity. Methods of numerical taxonomy based on geometric morphometric provide reliable identifications at the specific and even intraspecific levels, but they remain relatively time consuming and require expertise on the group under study. Here, we explore an alternative based on computer vision and machine learning. The identification of three rodent species based on pictures of their molar tooth row constituted the case study. We focused on the first upper molar in order to transfer the model elaborated on modern, genetically identified specimens to isolated fossil teeth. A pipeline based on deep neural network automatically cropped the first molar from the pictures, and returned a prediction regarding species identification. The deep-learning approach performed equally good as geometric morphometrics and, provided an extensive reference dataset including fossil teeth, it was able to successfully identify teeth from an archaeological deposit that was not included in the training dataset. This is a proof-of-concept that such methods could allow fast and reliable identification of extensive amounts of fossil remains, often left unstudied in archaeological deposits for lack of time and expertise. Deep-learning methods may thus allow new insights on the biodiversity dynamics across the last 10.000 years, including the role of humans in extinction or recent evolution.
Targeted knockdown of ribulose-1, 5-bisphosphate carboxylase-oxygenase in rice mesophyll cells impact on photosynthesis and growth
Authors: Maheshwari Chirag , Coe Robert A , Karki Shanta , Covshoff Sarah , Tapia Ronald , Tyagi Aruna , Hibberd Julian M. , Furbank Robert T. , Quick W Paul , Lin Hsiang-Chun 
Published: August 2020

AbstractWe generated antisense constructs targeting two of the five Rubisco small subunit genes (OsRBCS2 and 4) which account for between 30-40% of the RBCS transcript abundance in leaf blades. The constructs were driven by a maize phosphoenolpyruvate carboxylase (PEPC) promoter known to have enriched expression in mesophyll cells (MCs). In the resulting lines leaf Rubisco protein content was reduced by between 30-50% and CO2assimilation rate was limited under photorespiratory and non-photorespiratory conditions. A relationship between Rubisco protein content and CO2assimilation rate was found. This was associated with a significant reduction in dry biomass accumulation and grain yield of between 37 to 70%. In addition to serving as a resource for reducing Rubisco accumulation in a cell-preferential manner, these lines allow us to characterize gene function and isoform specific suppression on photosynthesis and growth. Our results suggest that the knockdown of multiple genes is required to completely reduce Rubisco accumulation in MCs.
Functions of Gle1 are governed by two distinct modes of self-association
Authors: Mason Aaron C. , Wente Susan R. 
Published: August 2020

AbstractGle1 is a conserved, essential regulator of DEAD-box RNA helicases, with critical roles defined in mRNA export, translation initiation, translation termination, and stress granule formation. Mechanisms that specify which, where and when DDXs are targeted by Gle1 are critical to understand. In addition to roles for stress-induced phosphorylation and inositol hexakisphosphate (IP6) binding in specifying Gle1 function, Gle1 oligomerizes via its N-terminal domain in a phosphorylation-dependent manner. However, a thorough analysis of the role for Gle1 self-association is lacking. Here, we find that Gle1 self-association is driven by two distinct regions: a coiled-coil domain and a novel ten amino acid aggregation prone region, both of which are necessary for proper Gle1 oligomerization. By exogenous expression in HeLa cells, we tested the function of a series of mutations that impact the oligomerization domains of the Gle1A and Gle1B isoforms. Gle1 oligomerization is necessary for many, but not all aspects of Gle1A and Gle1B function, and the requirements for each interaction domain differ. Whereas the coiled-coil domain and aggregation prone region additively contribute to competent mRNA export and stress granule formation, both self-association domains are independently required for regulation of translation under cellular stress. In contrast, Gle1 self-association is dispensable for phosphorylation and non-stressed translation initiation. Collectively, we reveal self-association functions as an additional mode of Gle1 regulation to ensure proper mRNA export and translation. This work also provides further insight into the mechanisms underlying humangle1disease mutants found in prenatally lethal forms of arthrogryposis.