bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data Augmentation and Deep Learning Techniques to Improve Interface Noise Tolerance of Myoelectric Pattern Recognition Controllers
Authors: Teh Yuni , Hargrove Levi J. 
Published: February 2022

Abstract
Background: Clinically available myoelectric PR controllers deteriorate under conditions that generate interface noise, such as electrode liftoff or wire failure. Previous solutions relied on additional processing steps like signal denoising and controller adaptation to mitigate these negative effects. However, there are no clinically practical controllers that are inherently robust to interface noise. This paper investigated the use of data-driven methods to build clinically practical, noise tolerant PR control strategies for transradial prostheses.Methods: We developed a data augmentation protocol to increase training data variability and two deep neural networks (MLP and CNN) to compress redundancies across a six-channel EMG array to a latent space that is robust to noise. Using data from fourteen intact limb subjects and seven below-elbow amputee subjects, we evaluated five control strategies: an LDA classifier (LDA), an existing adaptive LDA classifier that recalibrates after discarding noisy EMG channels (LDA-), an LDA classifier trained with an augmented data set (LDA+), an LDA classifier trained with MLP-aligned latent variables of an augmented data set (MLP-LDA), and an LDA classifier trained with CNN-aligned latent variables of an augmented data set (CNN-LDA). We computed the classification accuracies on clean signals and signals that had interface noise in up to four channels.Results: Compared to the baseline LDA method, LDA+ and MLP-LDA significantly increased classification accuracy on noisy data but decreased accuracy on clean data. On the other hand, LDA- and CNN-LDA improved noise tolerance while maintaining high performance with clean data. Conclusion: The CNN-LDA control strategy is robust to multichannel interface noise and can improve the reliability and usability of PR-based upper limb prostheses.
Prognostic factors for the successful conservative management of nonocclusive mesenteric ischemia
Authors: Toda Yoko , Komatsu Shunichiro , Fukami Yasuyuki , Saito Takuya , Matsumura Tatsuki , Osawa Takaaki , Kurahashi Shintaro , Uchino Tairin , Kato Shoko , Yasui Kohe , Hanazawa Takaaki , Kaneko Kenitiro , Sano Tsuyoshi 
Published: February 2022

Abstract
Background: The criteria for deciding upon non-operative management for nonocclusive mesenteric ischemia (NOMI) are poorly defined. The aim of this study is to determine the prognostic factors for survival in conservative treatment of NOMI.Methods: Patients with bowel ischemia were identified by searching for “ICD-10 code K550” in the Diagnosis Procedure Combination database between June 2015 and May 2020. A total of 457 patients were extracted and their medical records, including the clinical factors, imaging findings and outcomes, were analyzed retrospectively. Diagnosis of NOMI was confirmed by the presence of specific findings in contrast-enhanced multidetector-row CT. Twenty six patients with conservative therapy for NOMI, including four cases of explorative laparotomy or laparoscopy, were enrolled.Results: Among the 26 cases without surgical intervention, eight patients (31%) survived to discharge. The level of albumin was significantly higher and the levels of lactate dehydrogenase, total bilirubin, C-reactive protein, and lactate were significantly lower in the survivors than the non-survivors. Sepsis-related Organ Failure Assessment (SOFA) score was significantly lower in the survivors than the non-survivors. The most reliable predictor of survival for NOMI was SOFA score (cutoff value =<3 points), which had the highest AUC value (0.899) with odds ratio of 0.075 (CI: 0.0096-0.58).Conclusions: The SOFA score and several biological markers are promising predictors to determine a treatment plan for NOMI and to avoid unnecessary laparotomy.
Poly(ADP) ribose polymerase promotes DNA polymerase theta-mediated end joining by activation of end resection
Authors: Luedeman Megan , Stroik Susanna , Feng Wanjuan , Luthman Adam , Gupta Gaorav , Ramsden Dale 
Published: February 2022

Abstract
The DNA polymerase theta (Polθ)-dependent end joining (TMEJ) pathway for repair of chromosomal double strand breaks (DSBs) is essential in cells deficient in other DSB repair pathways, including hereditary breast cancers defective in homologous recombination. Strand-break activated poly(ADP) ribose polymerase 1 (PARP1) has been implicated in TMEJ, but the modest specificity of existing TMEJ assays means the extent of effect and the mechanism behind it remain unclear. We describe here a series of TMEJ assays with improved specificity and show ablation of PARP activity reduces TMEJ activity 2-4-fold. The reduction in TMEJ is attributable to a reduction in the 5’ to 3’ resection of DSB ends that is essential for engagement of this pathway and is compensated by increased repair by the nonhomologous-end joining pathway. This limited role for PARP activity in TMEJ helps better rationalize the combined employment of inhibitors of PARP and Polθ in cancer therapy.
Brain Dural Arteriovenous Fistulas in the Covid-19 era: a warning and rationale for association
Authors: Garcia-Garcia Sergio , Cepeda Santiago , Arrese Iñaki , Sarabia Rosario 
Published: February 2022

Abstract
Background
Brain dural arteriovenous fistulas(bDAVFs) are anomalous connections between dural arteries and cerebral veins or sinuses. Cerebral venous thrombosis(CVT) often precedes or coincides with bDAVFs and is considered a risk factor for these vascular malformations. Recently, vaccine-induced thrombotic thrombocytopenia causing CVTs has been associated with COVID-19 vaccines. Concurrently with the start of massive vaccination in our region, we have observed a fivefold increase in the average incidence of bDAVFs.
Objective
To raise awareness of the potential involvement of COVID-19 vaccines in the pathogenesis of bDAVF.
Methods
A retrospective review of demographic, clinical, radiological, COVID-19 infection and vaccination data of patients diagnosed with bDAVFs between 2011-2021 was conducted. Patients were divided into two cohorts according to their belonging to pre- or post-COVID-19 vaccination times. Cohorts were compared for bDAVFs incidences and demographic and clinical features.
Results
Twenty-one bDAVFs were diagnosed between 2011- 2021, 7 of which were diagnosed in 2021. The mean age was 57.7 years, and 62% were males. All cases except one were treated; of them, 85% were exclusively managed with surgery. All treated cases were successfully occluded. The incidence in 2021 was significantly higher than that in the prevaccination period (1.72 vs 0.35/100,000/year;p=0.036; 95%Confidence Interval=0.09-2.66). Cohorts were not different in age, sex, hemorrhagic presentation, dural sinus thrombosis or presence of prothrombotic or cardiovascular risk factors.
Conclusion
The significant increase in the incidence of bDAVF following general vaccination policies against COVID-19 observed in our region suggests a potential correlation between these two facts. Our findings need confirmation from larger cohorts and further pathogenic research.
Excitatory drive of cortical fast-spiking GABAergic interneurons is set by D-serine acting on NMDA receptors
Authors: Lecouflet Pierre , Maldera Steeve , Potier Brigitte , Pollegioni Loredano , Mothet Jean-Pierre 
Published: February 2022

Abstract
N-methyl-D-aspartate receptors (NMDARs) populate GABAergic interneurons, where they play a critical role in shaping circuit motifs and memory. However, we are largely ignoring whether and how NMDARs at GABAergic interneurons are gated by signals released in their surrounding microenvironment. Here we explore the dynamics of the co-agonist site occupancy by D-serine and glycine at glutamatergic synapses onto parvalbumin positive GABAergic interneurons in the adolescent prefrontal cortex, an area central to complex cognitive operation. We discovered that D-serine but not glycine is required for maintaining the activity of NMDAR at the GABAergic interneurons and that the identity of the co-agonist is not determined by the synaptic regime. Our study extends the physiological implications of D-serine in brain physiopathology by uncovering its control of inhibitory synaptic networks through NMDARs.
The molluscs’ periodic table: Elemental analysis reveals distinct mineralization patterns in radular teeth
Authors: Krings Wencke , Brütt Jan-Ole , Gorb Stanislav N. 
Published: February 2022

Abstract
The molluscan phylum is the second specious animal group inhabiting various habitats and feeding on a variety of food sources. The latter is enabled by the radula, a small chitinous membrane with embedded teeth, one important molluscan autapomorphy. Between species, radulae can vary in their morphology, mechanical, and chemical properties. With regard to radular chemical composition, some taxa (Polyplacophora and Patellogastropoda) were studied extensively in the past decades, due to their specificity to incorporate high proportions of iron, calcium, and silicon. There is, however, a huge lack of knowledge about radular chemical composition in other molluscan taxa. The work presented here aims at shedding light on the radular chemistry by performing energy-dispersive X-ray spectroscopy (EDX) analyses on overall 24 molluscan species, thereof two Polyplacophora, two Cephalopoda, and 20 Gastropoda. The elements, which are not part of chitin, and their proportions were documented for overall 1448 individual, mature teeth and hypotheses about potential biomineralizations types were proposed. The here presented work additionally comprises a detailed record on past studies about the chemical composition of molluscan teeth, which is an important basis for further investigation of the radular chemistry. The found disparity in elements detected, in their distribution and proportions highlights the diversity of evolutionary solutions, as it depicts multiple biomineralization types present within Mollusca.
Gravitational cells and gravitational strings. Obtaining new physical formulas and calculating the gravitational constant, the mass of the hydrogen atom, the mass of the electron, the graviton energy, the length and frequency of gravitational waves, the distance of action of gravitational forces, etc.
Authors: Chernov Andrey 
Published: February 2022

Abstract
This study introduces scientific concepts such as gravitational cells and gravitational strings. This innovation made it possible to move from general ideas about gravitational interaction to a deeper and more detailed understanding of this physical process, as well as to obtain significant scientific results. These results include: obtaining the formula for the gravitational constant, determining the fixed graviton energy, obtaining the length and frequency of gravitational waves, obtaining the formula for the mass of an electron and the formula for the mass of a hydrogen atom through fundamental physical constants, obtaining formulas for the minimum and maximum distance of action of gravitational forces, obtaining a new relativistic formula the speed of a body in a gravitational field, etc. The calculations made according to the new formulas completely coincided with the known scientific and experimental data. In this work, Planck's constant was successfully applied to the gravitational field (with its help, the minimum distance of action of gravitational forces was determined, the mass of the hydrogen atom was calculated with an accuracy of 10−7, the frequency and length of gravitational waves were determined, etc.). Through the synthesis of the theory of gravitational cells and the relativistic formula of Einstein's total energy, a new formula for the velocity of a body in a gravitational field was obtained, which is conveniently used for calculations. A distinctive feature of this study is the fact that only fundamental physical constants are present in the new formulas.
Ecogenomics Sheds Light on Diverse Lifestyle Strategies in Freshwater CPR
Authors: Chiriac Maria-Cecilia , Bulzu Paul-Adrian , Andrei Adrian-Stefan , Okazaki Yusuke , Nakano Shin-ichi , Haber Markus , Kavagutti Vinicius Silva , Layoun Paul , Ghai Rohit , Salcher Michaela M. 
Published: February 2022

Abstract
Background. The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR, or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome and cell sizes, and a general host-associated lifestyle was proposed for the radiation. So far, most CPR genomes were obtained from groundwaters, however, their diversity, abundance, and role in surface freshwaters is largely unexplored. Here we attempt to close these knowledge gaps by deep metagenomic sequencing of 119 samples of 17 different freshwater lakes located in Europe and Asia. Moreover, we applied Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) for a first visualization of distinct CPR lineages in freshwater samples.Results. A total of 174 dereplicated metagenome-assembled genomes (MAGs) of diverse CPR lineages were recovered from the investigated lakes, with a higher prevalence from hypolimnion samples (162 MAGs). They have reduced genomes (median size 1 Mbp) and were generally found in low abundances (0.02 – 14.36 coverage/Gb) and with estimated slow replication rates. The analysis of genomic traits and CARD-FISH results showed that the radiation is an eclectic group in terms of metabolic capabilities and potential lifestyles, ranging from what appear to be free-living lineages to host- or particle-associated groups. Although some complexes of the electron transport chain were present in the CPR MAGs, together with ion-pumping rhodopsins and heliorhodopsins, we believe that they most probably adopt a fermentative metabolism. Terminal oxidases might function in O2 scavenging, while heliorhodopsins could be involved in mitigation against oxidative stress. Conclusions. A high diversity of CPR MAGs was recovered, and distinct CPR lineages did not seem to be limited to lakes with specific trophic states. Their reduced metabolic capacities resemble the ones described for genomes in groundwater and animal-associated samples, apart from Gracilibacteria that possesses more complete metabolic pathways. Even though this radiation is mostly host-associated, we also observed organisms from different clades (ABY1, Paceibacteria, Saccharimonadia) that appear to be unattached to any other organisms or were associated with ‘lake snow’ particles (ABY1, Gracilibacteria), suggesting a broad range of potential life-strategies in this phylum.
Does aquatic products trade waste or save water resources? An analysis of virtual water trade
Authors: Xu Xuan , Yang Zhengyong 
Published: February 2022

Abstract
China is the largest producer and exporter of aquatic products. While earning foreign exchange, its implied water resources output could not be denied. Against the background of promoting water resources and food security, whether aquatic products trade can also achieve the purpose of water-saving has become a topic worthy of attention. Based on the idea of the quality and energy conservation law, this study uses the physical value input–output table and the fish growth model, and calculates the output and input of China's aquatic products virtual water trade indirectly by fishery water coefficient and virtual water of feed crops. The results show that while China's aquatic products trade is water-saving in general, it is water-wasting in some parts, and its environmental function needs to be improved. In particular, the aquatic products trade with South Asia, Central Asia, Northern Europe, North America, South America and Oceania is virtual water net import, while that with other regions is virtual water net export. The trade of shellfish and marine fish is water-saving, while that of mollusk, crustacean and freshwater fish is water-wasting. China, as a globally responsible power, should try to dynamically optimize the trade structure of aquatic products.
Analysis of the variation of costs for sewage sludge transport, recovery and disposal in Northern Italy: a recent survey (2015–2021)
Authors: Domini M. , Abbà A. , Bertanza G. 
Published: February 2022

Abstract
The cost for the recovery/disposal of residues produced by wastewater treatment plants (WWTPs) represents a relevant aspect in the economics of WWTP management. We elaborated and applied a desk-based methodology to analyze tender processes and to investigate quantitatively and qualitatively the variability of unit costs for sewage sludge (EWC 190805) management in Northern Italy from 2015 to 2021. We conducted a qualitative survey for operators of the sector. Unit costs for sludge management increased over time. The unit cost was mostly affected by the type of sludge recovery/disposal being the cost for recovery in agriculture (direct or by composting) lower than incineration and landfilling. Other variables influencing the cost were the distance and discount offered by the contractor. Regulatory and judiciary events determined a sudden increase of sludge disposal costs in Italy between 2017 and 2019. Recovery in agriculture, when practicable, remains the preferable option. Results can orient and support the optimization of sludge management costs and be of interest for future studies at national or European level.
A Comprehensive Investigation of Molecular Signatures and Pathways
Linking Alzheimer’s Disease and Epilepsy via Bioinformatic Approaches
Authors: Wu Jiao , Zhu Shu , Zhao Chenyang , Xu Xiaoxue 
Published: February 2022

Background:
Epileptic activity frequently occurs in patients with Alzheimer’s disease
(AD), which may accelerate AD progression; however, the relationship between AD and epilepsy remains
unclear.

Objective:
We aimed to investigate the molecular pathways and genes linking AD and epilepsy using
bioinformatics approaches.

Methods:
Gene expression profiles of AD (GSE1297) and epilepsy (GSE28674) were derived from
the Gene Expression Omnibus (GEO) database. The top 50% expression variants were subjected to
weighted gene co-expression network analysis (WGCNA) to identify key modules associated with
these diseases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses
for the key modules were performed, and the intersected terms of functional enrichment and common
genes within the key modules were selected. The overlapping genes were subjected to analyses of
protein-protein interaction (PPI) network, transcription factor (TF)-mRNA network, microRNA
(miRNA)-mRNA network, and drug prediction.

Results:
We identified 229 and 1187 genes in the AD-associated purple and epilepsy-associated blue
modules, respectively. Six shared functional terms between the two modules included “calcium ion
binding” and “calcium signaling pathway.” According to 17 common genes discovered, 130 TFmRNA
pairs and 56 miRNA-mRNA pairs were established. The topological analyses of the constructed
regulatory networks suggested that TF - FOXC1 and miRNA - hsa-mir-335-5p might be vital
co-regulators of gene expression in AD and epilepsy. In addition, CXCR4 was identified as a hub
gene, becoming the putative target for 20 drugs.

Conclusion:
Our study provided novel insights into the molecular connection between AD and epilepsy,
which might be beneficial for exploring shared mechanisms and designing disease-modifying therapies.
In Silico Evaluation of Some Commercially Available Flavonoids as Galactofuranoyltransferase-
2 Inhibitors in the Management of Tuberculosis
Authors: Madeswaran Arumugam , Midhuna Premavathi Gunasekaran 
Published: February 2022

Background:
Background: Galactofuranoyltransferase-2 (GlfT2) enzyme involved in the galactan polymerization of the arabinogalactan (AG) region of the mycolylarabinogalactan-peptidoglycan (mAGP) complex, an important component of the mycobacterial cell wall

Objective:
Objective: With the existing challenge the study focused into identifying certain commercially available flavonoids through molecular docking studies against the Galactofuranoyltransferase-2 enzyme.

Methods:
Methods: The initial pharmacokinetic screening was carried out using Lipinski’s rule of 5 with the help of Molinspiration software. In this perspective, Apigenin, Kaempferol, Rutin, Silibinin and Vitexicarpin were selected for the current study. Except for rutin all other selected flavonoids did not show any violations and thereby selected for the docking studies using AutoDock 4.2.

Results:
Results: The docking results showed that the selected flavonoids have excellent binding energy values between −8.98 to −6.58 kcal/mol against the GlfT2 enzyme. The theoretical inhibition constant was found to be in the range of 260.90 nM to 15.13 µM which coincides with the binding energies of the selected compounds.

Conclusion:
Conclusion: From the selected flavonoids, Silibinin showed excellent binding scores and it has the potential to inhibit the GlfT2 enzyme. Silibinin could act as a novel GlfT2 inhibitor with promising therapeutic activity with low toxicity profile against tuberculosis
Drug Resistance in the HIV-1 Subtype C Protease Enzyme: A High Throughput Virtual Screening Approach in Search of New Ligands with Activity
Authors: Sarron Arthur , Lobb Kevin A. 
Published: February 2022

Background:HIV-1 subtype C protease is a strategic target for antiretroviral treatment. However, resistance to protease inhibitors appears after months of treatment. Chromones and 2- biscoumarin derivatives show potential for inhibition of the HIV- subtype C protease.Objective:Different heterocyclic structures from the ZINC database were docked against Human Immunodeficiency Virus-1 (HIV) subtype C protease crystal structure 2R5Q and 2R5P. The 5 best molecules were selected to be docked against 62 homology models based on HIV-protease sequences from infants failing antiretroviral protease treatment. This experimentation was performed with two molecular docking programs: Autodock and Autodock Vina. These molecules were modified by substituting protons with different moieties, and the derivatives were docked against the same targets. Ligand-protein interactions, physical/chemical proprieties of the molecules, and dynamics simulations were analyzed.Methods:Docking of all of the molecules was performed to find out the binding sites of HIV-1 subtype C proteases. An in-house script was made to substitute protons of molecules with different moieties. According to the Lipinski rule of five, physical and chemical properties were determined. Complexes of certain ligands-protease were compared to the protein alone in molecular dynamics simulations.Results:From the first docking results, the 5 best (lowest energy) ligands (dibenz[a,h]acridine, dibenz[a, i]acridine, NSC114903, dibenz[c,h]acridine, benzo[a]acridine) were selected. The binding energy of the modified ligands increased, including the poorest-performing molecules. A correlation between nature, the position, and the resulting binding energy was observed. According to the Lipinski rules, the physico-chemical characteristics of the five best-modified ligands are ideal for oral bioavailability. Molecular dynamics simulations show that some lead-protease complexes were stable.Conclusion:Dibenz[a,h]acridine, dibenz[a, i]acridine, NSC114903, dibenz[c,h]acridine, benzo[ a]acridine and their derivatives might be considered as promising HIV-1 subtype C protease inhibitors. This could be confirmed through synthesis and subsequent in vitro assays.