bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Parallel Acquisition Technology on the Robustness of Magnetic Resonance Imaging Radiomic Features
Authors: Hu Kui , Deng Wenyou , Li Ning , Cai Qian , Yuan Zilong , Li Ling , Liu Yulin 
Published: June 2022

Objective
The aim of this study was to investigate the impact of integrated parallel acquisition technology (iPAT) on the robustness of magnetic resonance imaging radiomic features.

Methods
A phantom and 6 healthy volunteers were scanned on a clinical 3-T system using T1-weighted (S1), T1-weighted fluid-attenuated (S2), T2-weighted fluid-attenuated (S3), and T2-weighted (S4); 2 iPAT flavors (generalized autocalibration partially parallel acquisitions and modified sensitivity encoding [mSENSE]) and their different acceleration factors R. Radiomic features were extracted, and their robustness was assessed using coefficient of variation (CV), and differences between sequences and region of interest (ROI) were evaluated using the χ
2 test.

Results
One volunteer was excluded because of movement during imaging acquisition. Generalized autocalibration partially parallel acquisitions provided more radiomic features with excellent robustness than mSENSE. Radiomic features with excellent robustness, unaffected by iPAT across different sequences and ROIs, in 92 radiomic features for phantom and healthy volunteers are 6.5% and 2.2%. For phantom, difference in the robustness degree between 4 sequences/P-ROIs was significant according to χ
2 test; S2 and S3 could provide more excellent robust radiomic features than S1 and S4, and P-ROI3 filled with the biggest polystyrene particles could provide the most radiomic features with excellent robustness than the other P-ROIs. For healthy volunteers, only the difference in the degree of robustness between the 4 V-ROIs was significant, and V-ROI3 in white matter region of the left frontal lobe, which was located at periphery in image, could provide the most robust radiomic features compared with other V-ROIs.

Conclusions
Integrated parallel acquisition technology had a significant impact on the robustness of radiomic features. Generalized autocalibration partially parallel acquisitions delivered a more robust substrate for radiomic analyses than mSENSE.
COVID-19 Infection With the Omicron SARS-CoV-2 Variant in a Cohort of Kidney and Kidney Pancreas Transplant Recipients: Clinical Features, Risk Factors, and Outcomes
Authors: Wong Germaine , Rowlandson Matthew , Sabanayagam Dharshana , Ginn Andrew N. , Kable Kathy , Sciberras Frederika , Au Eric , Draper Jenny , Arnott Alicia , Sintchenko Vitali , Dwyer Dominic E. , Chen Sharon C.A. , Kok Jen 
Published: June 2022

Background.
Since November 2021, a new variant of concern (VOC), the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.1.529 (Omicron) has emerged as the dominant coronavirus disease 2019 (COVID-19) infection worldwide. We describe the clinical presentation, risk factors, and outcomes in a cohort of kidney and kidney pancreas transplant recipients with COVID-19 caused by Omicron infection.

Methods.
We included all kidney and kidney pancreas transplant recipients diagnosed with SARS-CoV-2 Omicron infections between December 26, 2021, and January 14, 2022, in a single transplant center in Australia. Identification of the VOC Omicron was confirmed using phylogenetic analysis of SARS-CoV-2 sequences.

Results.
Forty-one patients with kidney (6 living and 33 deceased) and kidney pancreas transplants were diagnosed with the VOC Omicron (lineage B.1.1.529/BA.1) infection during the study period. The mean age (SD) at the time of diagnosis was 52 (11.1) y; 40 (out of 41) (98%) had received at least 2 doses of COVID-19 vaccine. Cough was the most frequent symptom (80.5%), followed by myalgia (70.7%), sore throat (63.4%), and fever (58.5%). After a follow-up time of 30 d, 1 (2.4%) patient died, 2 (4.9%) experienced multiorgan failure, and 5 (12.2%) had respiratory failure; 11 (26.8%) patients developed other superimposed infections. Compared with recipients who did not receive sotrovimab antibody therapy, the odds ratio (95% confidence interval) for hospitalization among patients who received sotrovimab was 0.05 (0.005-0.4).

Conclusions.
Despite double or triple dose vaccination, VOC Omicron infections in kidney and kidney pancreas transplant recipients are not necessarily mild. Hospitalization rates remained high (around 56%), and sotrovimab use may prevent hospitalization.
Assessment of Factors Associated with Morbidity and Textbook Outcomes of Laparoscopic Liver Resection in Obese Patients: A French Nationwide Study
Authors: Genser Laurent , Lim Chetana , Barbier Louise , Regimbeau Jean-Marc , Hobeika Christian , Goumard Claire , Laurent Alexis , Fuks David , Chiche Laurence , Vibert Eric , Scatton Olivier ,   for the AFC-LLR-2018 Study Group
Published: June 2022

BACKGROUND:
Liver surgeons need to know the expected outcomes of laparoscopic liver resection (LLR) in obese patients.

OBJECTIVE:
The purpose of the present study is to assess morbidity, mortality and textbook outcomes (TO) after LLR in obese patients.

METHODS:
This is a French multicenter study of patients undergoing LLR between 1996 and 2018. Obesity was defined by a BMI at or above 30 kg/m2. Short-term outcomes and TO were compared between obese (ob) and nonobese (non-ob) patients. Factors associated with severe morbidity and TO were investigated.

RESULTS:
Of 3,154 patients included, 616 (19.5%) were obese. Ob-group patients had significantly higher American Society of Anesthesiologists (ASA) score and higher incidence of metabolic syndrome and chronic liver disease and were less likely to undergo major hepatectomy. Mortality rates were similar between ob and non-ob groups (0.8 vs 1.1%; p = 0.66). Overall morbidity and hospital stay were significantly increased in the ob group compared with the non-ob group (39.4 vs 34.7%, p = 0.03; and 9.5 vs 8.6 days, p = 0.02), whereas severe 90-day morbidity (at or above Clavien–Dindo grade III) was similar between groups (8% in both groups; p = 0.90). TO rate was significantly lower for the ob group than the non-ob group (58.3 vs 63.7%; p = 0.01). In multivariate analysis, obesity did not emerge as a risk factor for severe 90-day morbidity but was associated with a lower TO rate after LLR (odds ratio = 0.8, 95% CI 0.7–1.0; p = 0.03).

CONCLUSIONS:
LLR in obese patients is safe and effective with acceptable mortality and morbidity. Obesity had no impact on severe morbidity but was a factor for failing to achieve TO after LLR.
On the prediction of arginine glycation using artificial neural networks
Authors: Que-Salinas Ulices , Martinez-Peon Dulce , Reyes-Figueroa A. D. , Ibarra Ivonne , Scheckhuber Christian Quintus 
Published: June 2022

ABSTRACTOne of the hallmarks of diabetes is an increased modification of cellular proteins. The most prominent type of modification stems from the reaction of methylglyoxal with arginine and lysine residues, leading to structural and functional impairments of target proteins. For lysine glycation, several algorithms allow a prediction of occurrence, thus making it possible to pinpoint likely targets. However, according to our knowledge, no approaches have been published for predicting the likelihood of arginine glycation. There are indications that arginine and not lysine is the most prominent target for the toxic dialdehyde. One of the reasons why there is no arginine glycation predictor is the limited availability of quantitative data. Here we used a recently published high-quality dataset of arginine modification probabilities to employ an artificial neural network strategy. Despite the limited data availability, our results achieve an accuracy of about 75% of correctly predicting the exact value of the glycation probability of an arginine-containing peptide without setting thresholds upon whether it is decided if a given arginine is modified or not. This contribution suggests a possible solution for predicting arginine glycation. Our approach will greatly aid researchers in narrowing down possible glycation sites in protein targets. This strategy could improve the structural and functional characterization of proteins of interest.
Forecasting hospital-level COVID-19 admissions using real-time mobility data
Authors: Klein Brennan , Zenteno Ana C. , Joseph Daisha , Zahedi Mohammadmehdi , Hu Michael , Copenhaver Martin , Kraemer Moritz U.G. , Chinazzi Matteo , Klompas Michael , Vespignani Alessandro , Scarpino Samuel V. , Salmasian Hojjat 
Published: June 2022

AbstractFor each of the COVID-19 pandemic waves, hospitals have had to plan for deploying surge capacity and resources to manage large but transient increases in COVID-19 admissions. While a lot of effort has gone into predicting regional trends in COVID-19 cases and hospitalizations, there are far fewer successful tools for creating accurate hospital-level forecasts. At the same time, anonymized phone-collected mobility data proved to correlate well with the number of cases for the first two waves of the pandemic (spring 2020, and fall-winter 2021). In this work, we show how mobility data could bolster hospital-specific COVID-19 admission forecasts for five hospitals in Massachusetts during the initial COVID-19 surge. The high predictive capability of the model was achieved by combining anonymized, aggregated mobile device data about users’ contact patterns, commuting volume, and mobility range with COVID hospitalizations and test-positivity data. We conclude that mobility-informed forecasting models can increase the lead-time of accurate predictions for individual hospitals, giving managers valuable time to strategize how best to allocate resources to manage forthcoming surges.
The L. pneumophila effector PieF modulates mRNA stability through association with eukaryotic CCR4-NOT
Authors: Mount Harley O’Connor , Zangari Francesco , Gingras Anne-Claude , Ensminger Alexander W. 
Published: June 2022

ABSTRACTThe eukaryotic CCR4-NOT deadenylase complex is a highly conserved regulator of mRNA metabolism that influences the expression of the complete transcriptome, representing a prime target for a generalist bacterial pathogen. We show that a translocated bacterial effector protein, PieF (Lpg1972) of L. pneumophila Str. Philadelphia-1, interacts specifically with the CNOT7/8 nuclease module of CCR4-NOT, with a dissociation constant in the low nanomolar range. PieF inhibits the catalytic deadenylase subunit CNOT7 of the CCR4-NOT complex in a stoichiometric, dose-dependent manner in vitro. In transfected cells, PieF can silence reporter gene expression and reduce mRNA steady-state levels when artificially tethered. PieF demonstrates molecular similarities to another family of CNOT7-associated factors but demonstrates divergence concerning the interaction interface with CNOT7. In addition, we show that PieF overexpression changes the subcellular localization of CNOT7 and displaces the CNOT6/6L nucleases from CCR4-NOT. Finally, PieF expression phenocopies knockout of the CNOT7 ortholog in S. cerevisiae, resulting in 6-azauracil sensitivity. Collectively, this work suggests that L. pneumophila targets host mRNA stability and expression through a highly conserved host pathway not previously associated with Legionella pathogenesis.
NtcA, LexA and heptamer repeats involved in the multifaceted regulation of DNA repair genes recF, recO and recR in the cyanobacterium Nostoc PCC7120
Authors: Pradhan Mitali , Kumar Arvind , Kirti Anurag , Pandey Sarita , Rajaram Hema 
Published: June 2022

ABSTRACTRegulation of DNA repair genes in cyanobacteria is an unexplored field despite some of them exhibit high radio-resistance. With the RecF pathway speculated to be the major double strand break repair pathway in Nostoc sp. strain PCC7120, the regulation of recF, recO and recR genes was investigated. Bioinformatic approach-based identification of promoter and regulatory elements was validated using qRT-PCR analysis, reporter gene and DNA binding assays. Different deletion constructs of the upstream regulatory regions of these genes were analysed in host Nostoc as well as heterologous system Escherichia coli. Studies revealed: (1) Positive regulation of all three genes by NtcA, (2) Negative regulation by LexA, (3) Involvement of contiguous heptamer repeats with/without its yet to be identified interacting partner in regulating (i) binding of NtcA and LexA to recO promoter and its translation, (ii) transcription or translation of recF, (4) Translational regulation of recF and recO through non-canonical and distant S.D. sequence and of recR through a rare initiation codon. Presence of NtcA either precludes binding of LexA to AnLexA-Box or negates its repressive action resulting in higher expression of these genes under nitrogen-fixing conditions in Nostoc. Thus, in Nostoc, expression of recF, recO and recR genes is intricately regulated through multiple regulatory elements/proteins. Contiguous heptamer repeats present across the Nostoc genome in the vicinity of start codon or promoter is likely to have a global regulatory role. This is the first report on the involvement of NtcA and heptamer repeats in regulation of DNA repair genes in any organism.
Cortical synapses of the world’s smallest mammal: an FIB/SEM study in the Etruscan shrew
Authors: Alonso-Nanclares Lidia , Rodríguez J. Rodrigo , Merchan-Perez Ángel , González-Soriano Juncal , Plaza-Alonso Sergio , Cano-Astorga Nicolás , Naumann Robert K. , Brecht Michael , DeFelipe Javier 
Published: June 2022

ABSTRACTThe main aim of the present study was to determine if synapses from the exceptionally small brain of the Etruscan shrew show any peculiarities compared to the much larger human brain. This study constitutes the first description of the Etruscan shrew synaptic characteristics using Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM). We analyzed the synaptic density and a variety of structural characteristics of 7,239 3D reconstructed synapses, obtaining the following major results: (i) cortical synaptic density was very high, particularly in layer I; (ii) the vast majority of synapses were excitatory, with the highest proportion found in layer I; (iii) excitatory synapses were larger than inhibitory synapses in all layers except in layer VI; and (iv) synapses were either randomly distributed in space or showed a slight tendency to be organised in a regular arrangement. Some of these general synaptic characteristics are remarkably similar to those found in the human cerebral cortex. However, the cortical volume of the human brain is about 50,000 times larger than the cortical volume of the Etruscan shrew, while the total number of cortical synapses in human is only 20,000 times the number of synapses in the shrew, and synaptic junctions are 35% smaller in the Etruscan shrew. Thus, the differences in the number and size of synapses cannot be attributed to a brain size scaling effect but rather to adaptations of synaptic circuits to particular functions. The present work provides a quantitative dataset from the Etruscan shrew synapses — not only contributing to the knowledge of the ultrastructure of the mammalian cortex, but also identifying common and differing principles of synaptic organization.
Microglial STAT1-sufficiency is required for resistance to toxoplasmic encephalitis
Authors: Cowan M.N. , Kovacs M.A. , Sethi I. , Babcock I.W. , Still K. , Batista S.J. , O’Brien C.A. , Thompson J.A. , Sibley L.A. , Labuzan S. A. , Harris T.H. 
Published: June 2022

AbstractToxoplasma gondiiis a ubiquitous intracellular protozoan parasite that establishes a life-long chronic infection largely restricted to the central nervous system (CNS). Constant immune pressure, notably IFN-γ-STAT1 signaling, is required for preventing fatal pathology duringT. gondiiinfection. Here, we report that abrogation of STAT1 signaling in microglia, the resident immune cells of the CNS, is sufficient to induce a loss of parasite control in the CNS and susceptibility to toxoplasmic encephalitis during the early stages of chronic infection. Using a microglia-specific genetic labeling and targeting system that discriminates microglia from blood-derived myeloid cells that infiltrate the brain during infection, we find that, contrary to previousin vitroreports, microglia do not express inducible nitric-oxide synthase (iNOS) duringT. gondiiinfectionin vivo. Instead, transcriptomic analyses of microglia reveal that STAT1 regulates both (i) a transcriptional shift from homeostatic to “disease-associated microglia” (DAM) phenotype conserved across several neuroinflammatory models, includingT. gondiiinfection, and (ii) the expression of anti-parasitic cytosolic molecules that are required for eliminatingT. gondiiin a cell-intrinsic manner. Further, genetic deletion ofStat1from microglia duringT. gondiichallenge leads to fatal pathology despite largely equivalent or enhanced immune effector functions displayed by brain-infiltrating immune populations. Finally, we show that microglial STAT1-deficiency results in the overrepresentation of the highly replicative, lytic tachyzoite form ofT. gondii, relative to its quiescent, semi-dormant bradyzoite form typical of chronic CNS infection. Our data suggest an overall protective role of CNS-resident microglia againstT. gondiiinfection, illuminating (i) general mechanisms of CNS-specific immunity to infection (ii) and a clear role for IFN-STAT1 signaling in regulating a microglial activation phenotype observed across diverse neuroinflammatory disease states.
Protein-protein interaction (PPI) network analysis reveals important hub proteins and sub-network modules for root development in rice (Oryza sativa)
Authors: Wimalagunasekara Samadhi , Tirimanne Shamala , Fernando Pasan Chinthana 
Published: June 2022

AbstractThe root system is vital to plant growth and survival. Therefore, genetic improvement of the root system is beneficial for developing stress-tolerant and improved plant varieties. This requires the identification of proteins that significantly contributes to root development. Analyzing protein-protein interaction (PPI) networks is vastly beneficial in studying developmental phenotypes, such as root development because a phenotype is an outcome of several interacting proteins. PPI networks can be analyzed to identify modules and get a global understanding of important proteins governing the phenotypes. PPI network analysis for root development in rice has not been performed before and has the potential to yield new findings to improve stress tolerance. Therefore, in this research, the network module for the root development was extracted from a PPI network retrieved from the STRING database. Novel protein candidates were predicted, and hub proteins and sub-modules were identified from the extracted module. The validation of the predictions yielded 75 novel candidate proteins, 6 sub-modules, 20 intramodular hubs, and 2 intermodular hubs. These results show how the PPI network module is organized for root development and can be used for future wet-lab studies for producing improved rice varieties.
Hallucinating structure-conditioned antibody libraries for target-specific binders
Authors: Mahajan Sai Pooja , Ruffolo Jeffrey A. , Frick Rahel , Gray Jeffrey J. 
Published: June 2022

AbstractAntibodies are widely developed and used as therapeutics to treat cancer, infectious disease, and inflammation. During development, initial leads routinely undergo additional engineering to increase their target affinity. Experimental methods for affinity maturation are expensive, laborious, and time-consuming and rarely allow the efficient exploration of the relevant design space. Deep learning (DL) models are transforming the field of protein engineering and design. While several DL-based protein design methods have shown promise, the antibody design problem is distinct, and specialized models for antibody design are desirable. Inspired by hallucination frameworks that leverage accurate structure prediction DL models, we propose the FvHallucinator for designing antibody sequences, especially the CDR loops, conditioned on an antibody structure. Such a strategy generates targeted CDR libraries that retain the conformation of the binder and thereby the mode of binding to the epitope on the antigen. On a benchmark set of 60 antibodies, FvHallucinator generates sequences resembling natural CDRs and recapitulates perplexity of canonical CDR clusters. Furthermore, the FvHallucinator designs amino acid substitutions at the VH-VL interface that are enriched in human antibody repertoires and therapeutic antibodies. We propose a pipeline that screens FvHallucinator designs to obtain a library enriched in binders for an antigen of interest. We apply this pipeline to the CDR H3 of the Trastuzumab-HER2 complex to generate in silico designs improving upon the binding affinity and interfacial properties of the original antibody. Thus, the FvHallucinator pipeline enables generation of inexpensive, diverse, and targeted antibody libraries enriched in binders for antibody affinity maturation.
The Brain/MINDS Marmoset Connectivity Atlas: exploring bidirectional tracing and tractography in the same stereotaxic space
Authors: Skibbe Henrik , Rachmadi Muhammad Febrian , Nakae Ken , Gutierrez Carlos Enrique , Hata Junichi , Tsukada Hiromichi , Poon Charissa , Doya Kenji , Majka Piotr , Rosa Marcello G. P. , Okano Hideyuki , Yamamori Tetsuo , Ishii Shin , Reisert Marco , Watakabe Akiya 
Published: June 2022

AbstractWe report on the implementation and features of the Brain/MINDS Marmoset Connectivity Atlas, BMCA, a new resource that provides access to anterograde neuronal tracer data in the prefrontal cortex of a marmoset brain. Neuronal tracers combined with fluorescence microscopy are a key technology for the systematic mapping of structural brain connectivity. We selected the prefrontal cortex for mapping due to its important role in higher brain functions. This work introduces the BMCA standard image preprocessing pipeline and tools for exploring and reviewing the data. We developed the BMCA-Explorer, which is an online image viewer designed for data exploration. Unlike other existing image explorers, it visualizes the data of different individuals in a common reference space at an unprecedented high resolution, facilitating comparative studies. To foster the integration with other marmoset brain image databases and cross-species comparisons, we added fiber tractography data from diffusion MRI, retrograde neural tracer data from the Marmoset Brain Connectivity Atlas project, and tools to map image data between marmoset and the human brain image space. This version of BMCA allows direct comparison between the results of 52 anterograde and 164 retrograde tracer injections in the cortex of the marmoset.