bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modularity and multitasking in neuro-memristive reservoir networks
Authors: Loeffler Alon , Zhu Ruomin , Hochstetter Joel , Diaz-Alvarez Adrian , Nakayama Tomonobu , Shine James M , Kuncic Zdenka 
Published: July 2021

Abstract
The human brain seemingly effortlessly performs multiple concurrent and elaborate tasks in response to complex, dynamic sensory input from our environment. This capability has been attributed to the highly modular structure of the brain, enabling specific task assignment among different regions and limiting interference between them. Here, we compare the structure and functional capabilities of different bio-physically inspired and biological networks. We then focus on the influence of topological properties on the functional performance of highly modular, bio-physically inspired neuro-memristive nanowire networks (NWNs). We perform two benchmark reservoir computing tasks (memory capacity and nonlinear transformation) on simulated networks and show that while random networks outperform NWNs on independent tasks, NWNs with highly segregated modules achieve the best performance on simultaneous tasks. Conversely, networks that share too many resources, such as networks with random structure, perform poorly in multitasking. Overall, our results show that structural properties such as modularity play a critical role in trafficking information flow, preventing information from spreading indiscriminately throughout NWNs.
Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction
Authors: Yang Xiaodi , Yang Shiping , Lian Xianyi , Wuchty Stefan , Zhang Ziding 
Published: July 2021

Abstract

Motivation
To complement experimental efforts, machine learning-based computational methods are playing an increasingly important role to predict human–virus protein–protein interactions (PPIs). Furthermore, transfer learning can effectively apply prior knowledge obtained from a large source dataset/task to a small target dataset/task, improving prediction performance.

Results
To predict interactions between human and viral proteins, we combine evolutionary sequence profile features with a Siamese convolutional neural network (CNN) architecture and a multi-layer perceptron. Our architecture outperforms various feature encodings-based machine learning and state-of-the-art prediction methods. As our main contribution, we introduce two transfer learning methods (i.e. ‘frozen’ type and ‘fine-tuning’ type) that reliably predict interactions in a target human–virus domain based on training in a source human–virus domain, by retraining CNN layers. Finally, we utilize the ‘frozen’ type transfer learning approach to predict human–SARS-CoV-2 PPIs, indicating that our predictions are topologically and functionally similar to experimentally known interactions.

Availability and implementation
The source codes and datasets are available at https://github.com/XiaodiYangCAU/TransPPI/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Comparing effects and action mechanisms of BPA and BPS on HTR-8/SVneo placental cells
Authors: Profita Marilin , Fabbri Elena , Spisni Enzo , Valbonesi Paola 
Published: July 2021

Abstract
Bisphenol A (BPA) is one of the most investigated compound as a suspected endocrine disrupting chemical. It has been found at nM concentrations in the maternal serum, cord serum, and amniotic fluid and also permeates placental tissues. Attempts are being made to replace BPA with the analog Bisphenol S (BPS). Also BPS was found in maternal and umbilical cord serum, and urine samples from a large population of pregnant women. A few studies investigated BPA impact on the placentation process, and even less are available for BPS. This work aimed to elucidate and compare the effects of BPA and BPS on physiological functions of HTR-8/SVneo cells, derived from extravillous trophoblast of first-trimester pregnancy. Proliferation and migration ability of trophoblast cells were assessed in vitro after exposure to BPA or BPS (10−13–10−3 M). Further, induction of the inflammatory response by the bisphenols was studied. To provide insight into the molecular pathways implicated in the responses, experiments were carried out in the presence or absence of tamoxifen as estrogen receptors (ERs) blocker, and U0126 as ERK1/2 phosphorylation inhibitor. Data indicate that BPA significantly affects both proliferation and migration of HTR-8/SVneo cells, through ER and ERK1/2 mediated processes. Differently, BPS only acts on proliferation, again through ER and ERK1/2 mediated processes. BPS, but not BPA, induces secretion of interleukins 6 and 8. Such effect is inhibited by blocking ERK1/2 phosphorylation. To the best of our knowledge, these are the first data showing that BPS affects trophoblast functions through ER/MAPK modulation.
Cerebral white matter vasculature: still uncharted?
Authors: Smirnov Mykyta , Destrieux Christophe , Maldonado Igor Lima 
Published: July 2021

Abstract
White matter vasculature plays a major role in the pathophysiology of permanent neurological deficits following a stroke or progressive cognitive alteration related to small vessel disease. Thus, knowledge of the complex vascularization and functional aspects of the deep white matter territories is paramount to comprehend clinical manifestations of brain ischaemia.
This review provides a structured presentation of the existing knowledge of the vascularization of the human cerebral white matter from seminal historical studies to the current literature. First, we revisit the highlights of prenatal development of the endoparenchymal telencephalic vascular system that are crucial for the understanding of vessel organization in the adult. Second, we reveal the tangled history of debates on the existence, clinical significance and physiological role of leptomeningeal anastomoses. Then, we present how conceptions on white matter vascularization transitioned from the mixed ventriculopetal/ventriculofugal theory, in which a low-flow area was interposed in between concurrent arterial flows, to the purely ventriculopetal theory. The latter model explains variable white matter sensitivity to ischaemia by various organizations of ventriculopetal vessel terminals having different origin/length properties and interconnection patterns. Next, arteries supplying primarily the white matter are described according to their length and overall structure. Furthermore, the known distribution territories, to date, are studied in relation to primary anatomical structures of the human cerebral white matter, emphasizing the sparsity of the ‘ground truth’ data available in the literature. Finally, the implications for both large vessel occlusion and chronic small vessel disease are discussed, as well as the insights from neuroimaging.
All things considered, we identify the need for further research on deep white matter vascularization, especially regarding the arterial supply of white matter fibre tracts.
Digital Reconstruction of the Neuro-Glia-Vascular Architecture
Authors: Zisis Eleftherios , Keller Daniel , Kanari Lida , Arnaudon Alexis , Gevaert Michael , Delemontex Thomas , Coste Benoît , Foni Alessandro , Abdellah Marwan , Calì Corrado , Hess Kathryn , Magistretti Pierre Julius , Schürmann Felix , Markram Henry 
Published: July 2021

AbstractAstrocytes connect the vasculature to neurons mediating the supply of nutrients and biochemicals. They are involved in a growing number of physiological and pathophysiological processes that result from biophysical, physiological, and molecular interactions in this neuro-glia-vascular ensemble (NGV). The lack of a detailed cytoarchitecture severely restricts the understanding of how they support brain function. To address this problem, we used data from multiple sources to create a data-driven digital reconstruction of the NGV at micrometer anatomical resolution. We reconstructed 0.2 mm3 of the rat somatosensory cortex with 16 000 morphologically detailed neurons, 2500 protoplasmic astrocytes, and its microvasculature. The consistency of the reconstruction with a wide array of experimental measurements allows novel predictions of the NGV organization, allowing the anatomical reconstruction of overlapping astrocytic microdomains and the quantification of endfeet connecting each astrocyte to the vasculature, as well as the extent to which they cover the latter. Structural analysis showed that astrocytes optimize their positions to provide uniform vascular coverage for trophic support and signaling. However, this optimal organization rapidly declines as their density increases. The NGV digital reconstruction is a resource that will enable a better understanding of the anatomical principles and geometric constraints, which govern how astrocytes support brain function.
Modulation of Theta Phase Synchrony during Syllable Processing as a Function of Interactive Acoustic Experience in Infancy
Authors: Ortiz-Mantilla Silvia , Roesler Cynthia P , Realpe-Bonilla Teresa , Benasich April A 
Published: July 2021

AbstractPlasticity, a prominent characteristic of the infant brain, supports formation of cortical representations as infants begin to interact with and adapt to environmental sensory events. Enhanced acoustic processing efficiency along with improved allocation of attentional resources at 7 months and establishment of well-defined phonemic maps at 9 months have been shown to be facilitated by early interactive acoustic experience (IAE). In this study, using an oddball paradigm and measures of theta phase synchrony at source level, we examined short- and long-term effects of nonspeech IAE on syllable processing. Results demonstrated that beyond maturation alone, IAE increased the efficiency of syllabic representation and discrimination, an effect that endured well beyond the immediate training period. As compared with naive controls, the IAE-trained group at 7, 9, and 18 months showed less theta phase synchrony for the standard syllable and at 7 and 18 months for the deviant syllable. The decreased theta phase synchrony exhibited by the trained group suggests more mature, efficient, acoustic processing, and thus, better cortical representation and discrimination of syllabic content. Further, the IAE modulatory effect observed on theta phase synchrony in left auditory cortex at 7 and 9 months was differentially associated with receptive and expressive language scores at 12 and 18 months of age.
Short physical performance battery vs. 6-minute walking test in hospitalized elderly patients with heart failure
Authors: Kitai Takeshi , Shimogai Takayuki , Tang W H Wilson , Iwata Kentaro , Xanthopoulos Andrew , Otsuka Shuto , Nakada Fumika , Yokoyama Rina , Kamiya Kentaro , Saito Hiroshi , Saito Kazuya , Maekawa Emi , Konishi Masaaki , Ogasahara Yuki , Jujo Kentaro , Wada Hiroshi , Kasai Takatoshi , Momomura Shinichi , Krittanawong Chayakrit , Skoularigis John , Triposkiadis Filippos , Kagiyama Nobuyuki , Furukawa Yutaka , Matsue Yuya 
Published: July 2021

Abstract

Aims
Functional decline due to skeletal muscle abnormalities leads to poor outcomes in patients with acute heart failure (AHF). The 6-minute walking test (6MWT) reliably evaluates functional capacity, but its technical difficulty for the elderly often limits its benefits. Although the Short Physical Performance Battery (SPPB) is a comprehensive measure of physical performance, its role in AHF remains unclear. This study aimed to examine the prognostic significance of SPPB compared to the 6MWT in elderly patients hospitalized for AHF.

Methods and results
We retrospectively analysed 1192 elderly patients with AHF whose SPPB and 6MWT were measured during the hospitalization. The primary outcome measure was defined as a composite of all-cause death and heart failure readmission until 1 year after discharge. Patients with lower SPPB scores (0–6, n = 373) had significantly poorer outcomes than those with higher SPPB scores (7–12, n = 819) even after multivariable adjustment [adjusted hazard ratio (HR) 1.28, 95% confidence interval (CI) 1.01–1.61; P = 0.049], similar to those with shorter 6MWT (&lt;median) than those with longer 6MWT (adjusted HR 1.61, 95% CI 1.27–2.04; P &lt; 0.001). Although both SPPB and 6MWT [net reclassification index (NRI) 0.139, P = 0.036 and NRI 0.350, P &lt; 0.001, respectively] exhibited incremental prognostic value over conventional risk factors of HF, the additive prognostic effect of 6MWT was superior to that of SPPB (NRI 0.300, P &lt; 0.001).

Conclusions
Reduced functional capacity assessed by either the SPPB or 6MWT was associated with worse outcomes in hospitalized elderly patients with AHF. The incremental prognostic value over the conventional risk factors was higher in 6MWT than in SPPB.

Trial Registration
UMIN000023929
Intentional mentoring: maximizing the impact of underrepresented future scientists in the 21st century
Authors: Shuler Haysetta , Cazares Victor , Marshall Andrea , Garza-Lopez Edgar , Hultman Rainbo , Francis Tam'ra-Kay , Rolle Tiffany , Byndloss Mariana X , Starbird Chrystal A , Hicsasmaz Innes , AshShareef Salma , Neikirk Kit , Johnson Pamela E C , Vue Zer , Beasley Heather K , Williams Aislinn , Hinton Antentor 
Published: July 2021

ABSTRACT
Mentoring is a developmental experience intended to increase the willingness to learn and establish credibility while building positive relationships through networking. In this commentary, we focus on intentional mentoring for underrepresented mentees, including individuals that belong to minority racial, ethnic and gender identity groups in Science, Technology, Engineering, Mathematics and Medicine (STEMM) fields. Intentional mentoring is the superpower action necessary for developing harmony and comprehending the purpose and value of the mentor/mentee relationship. Regardless of a mentor's career stage, we believe the strategies discussed may be used to create a supportive and constructive mentorship environment; thereby improving the retention rates of underrepresented mentees within the scientific community.
Testing gene–environment interactions in the presence of confounders and mismeasured environmental exposures
Authors: Cheng Chao , Spiegelman Donna , Wang Zuoheng , Wang Molin 
Published: July 2021

AbstractInterest in investigating gene–environment (GxE) interactions has rapidly increased over the last decade. Although GxE interactions have been extremely investigated in large studies, few such effects have been identified and replicated, highlighting the need to develop statistical GxE tests with greater statistical power. The reverse test has been proposed for testing the interaction effect between continuous exposure and genetic variants in relation to a binary disease outcome, which leverages the idea of linear discriminant analysis, significantly increasing statistical power comparing to the standard logistic regression approach. However, this reverse approach did not take into consideration adjustment for confounders. Since GxE interaction studies are inherently nonexperimental, adjusting for potential confounding effects is critical for valid evaluation of GxE interactions. In this study, we extend the reverse test to allow for confounders. The proposed reverse test also allows for exposure measurement errors as typically occurs. Extensive simulation experiments demonstrated that the proposed method not only provides greater statistical power under most simulation scenarios but also provides substantive computational efficiency, which achieves a computation time that is more than sevenfold less than that of the standard logistic regression test. In an illustrative example, we applied the proposed approach to the Veterans Aging Cohort Study (VACS) to search for genetic susceptibility loci modifying the smoking-HIV status association.
Monotonicity Formula and Classification of Stable Solutions to Polyharmonic Lane–Emden Equations
Authors: Luo Senping , Wei Juncheng , Zou Wenming 
Published: July 2021

Abstract
In this paper, we consider polyharmonic Lane–Emden equations $$ \begin{equation*} (-\Delta )^m u=|u|^{p-1}u, \ \ \ \mbox{in} \ \ \ {\mathbb R}^n, \end{equation*}$$where $m\geq 3$. We classify the stable or stable outside a compact set solutions when $m=3$ or $4$ for any dimensions and when $m\geq 5$ for large dimensions. In the process, we exhibit the general Joseph–Lundgren exponent (including both local and nonlocal cases) in a concise form and prove related properties. The key ingredient of the proof of the classification is a monotonicity formula for general polyharmonic equations, which may have application in regularity theory for higher-order elliptic equations.
Emergence of resistantCandida glabratain Germany
Authors: Aldejohann Alexander Maximilian , Herz Michaela , Martin Ronny , Walther Grit , Kurzai Oliver 
Published: July 2021

AbstractBackgroundCandida glabrata is the second leading fungal pathogen causing candidaemia and invasive candidiasis in Europe. This yeast is recognized for its rapid ability to acquire antifungal drug resistance.ObjectivesWe systematically evaluated 176 C. glabrata isolates submitted to the German National Reference Center for Invasive Fungal Infections (NRZMyk) between 2015 and 2019 with regard to echinocandin and fluconazole susceptibility.MethodsSusceptibility testing was performed using a reference protocol (EUCAST) and a range of commercial assays. Hot spot regions of the echinocandin target FKS genes were sequenced using Sanger sequencing.ResultsIn total, 84 of 176 isolates were initially classified as anidulafungin-resistant based on EUCAST testing. Of those, 71 harboured mutations in the glucan synthase encoding FKS genes (13% in FKS1, 87% in FKS2). Significant differences in anidulafungin MICs were found between distinct mutation sites. 11 FKS wild-type (WT) isolates initially classified as resistant exhibited anidulafungin MICs fluctuating around the interpretation breakpoint upon re-testing with multiple assays. Two FKS WT isolates consistently showed high anidulafungin MICs and thus must be considered resistant despite the absence of target gene mutations. Over one-third of echinocandin-resistant strains displayed concomitant fluconazole resistance. Of those, isolates linked to bloodstream infection carrying a change at Ser-663 were associated with adverse clinical outcome.ConclusionsResistant C. glabrata strains are emerging in Germany. Phenotypic echinocandin testing can result in misclassification of susceptible strains. FKS genotyping aids in detecting these strains, however, echinocandin resistance may occur despite a wild-type FKS genotype.
Comparative Effectiveness of Lumen-Apposing Metal Stents and Plastic Stents for the Treatment of Pancreatic Walled-Off Necrosis: A Meta-analysis
Authors: Calo Natalia Causada , Bishay Kirles , Yaghoobi Mohammad , Yuan Yuhong , Mosko Jeffrey , May Gary , Chen Yen-I , Teshima Christopher 
Published: July 2021

Abstract

Background
Plastic stents (PS), lumen-apposing metal stents (LAMS) and biflanged metal stents (BFMS) are used for initial drainage of pancreatic walled-off necrosis (WON). There are no strong evidence to support the use of LAMS/BFMS over PS, and prior systematic reviews lack comparative analyses and also lack both trial data and observational studies for WON efficacy outcomes. The aim of this study is to compare the efficacy and adverse events (AEs) in LAMS/BFMS versus PS in patients with pancreatic WON.

Methods
A comprehensive search up to December 1, 2020, was performed. The primary outcome was clinical improvement after drainage. Secondary outcomes included AEs and technical failure. Pooled odds ratios (OR) with 95% confidence intervals (CI) were reported using random effects models. Heterogeneity was evaluated with the Cochrane I2 statistic. Subgroup and sensitivity analyses were performed. The quality of the evidence was assessed using Grading of Recommendations, Assessment, Development and Evaluations (GRADE).

Results
Nine studies (one randomized controlled trial and eight observational) were included for the primary outcome including 493 patients treated with LAMS/BFMS and 514 with PS. LAMS/BFMS were associated with higher odds of clinical improvement compared with PS (OR 2.58; 95% CI 1.81, 3.68; I2 = 1%). This association remained robust in sensitivity analyses. The use of LAMS/BFMS was not associated with higher AEs (OR 1.22; 0.61, 2.46; I2 = 71%). There was no difference in technical failure (OR 1.06; 0.19, 6.00; I2 = 12%).

Conclusions
LAMS/BFMS seem to result in better clinical outcomes compared with PS in patients with pancreatic WON, with comparable AEs and technical failure. Larger randomized controlled trials for this comparison are warranted.
Action-at-a-distance mutations at 5′-GpA-3′ sites induced by oxidised guanine in WRN-knockdown cells
Authors: Suzuki Tetsuya , Masuda Hiroshi , Mori Madoka , Ito Rikako , Kamiya Hiroyuki 
Published: July 2021

Abstract
G:C sites distant from 8-oxo-7,8-dihydroguanine (GO, 8-hydroxyguanine) are frequently mutated when the lesion-bearing plasmid DNA is replicated in human cells with reduced Werner syndrome (WRN) protein. To detect the untargeted mutations preferentially, the oxidised guanine base was placed downstream of the reporter supF gene and the plasmid DNA was introduced into WRN-knockdown cells. The total mutant frequency seemed higher in the WRN-knockdown cells as compared to the control cells. Mutation analyses revealed that substitution mutations occurred at the G:C pairs of 5′-GpA-3′/5′-TpC-3′ sites, the preferred sequence for the apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3)-family cytosine deaminases, in the supF gene in both control and knockdown cells. These mutations were observed more frequently at G sites than C sites on the DNA strand where the GO base was originally located. This tendency was promoted by the knockdown of the WRN protein. The present results imply the possible involvement of APOBEC3-family cytosine deaminases in the action-at-a-distance (untargeted) mutations at G:C (or G) sites induced by GO and in cancer initiation by oxidative stress.
Venous Causes of Pulsatile Tinnitus: Clinical Presentation, Clinical and Radiographic Evaluation, Pathogenesis, and Endovascular Treatments: A Literature Review
Authors: Essibayi Muhammed Amir , Oushy Soliman H , Lanzino Giuseppe , Brinjikji Waleed 
Published: July 2021

AbstractTinnitus is an abnormal perception of a sound without external stimulation. Venous pulsatile tinnitus (VPT) is a specific form of tinnitus characterized by an objective and often subjective bruit that occurs as a result of localized venous abnormalities. Clinical evaluation relies on sound quality, duration, and precipitating factors. Idiopathic intracranial hypertension (IIH) and transverse sinus stenosis (TSS) are among the most common causes of VPT. Other causes include sigmoid sinus wall abnormalities (SSWAs), jugular vein anomalies (JVAs), and emissary veins anomalies. These anomalies can be detected on magnetic resonance imaging, magnetic resonance angiography/magnetic resonance venography, and high-resolution temporal bone computed tomography. The pathogenesis behind the VPT includes turbulent blood flow as a result of luminal stenosis or abnormal dilation, amplification of internal sound due to temporal bone defects, and abnormal position of the venous sinus system structures adjacent to the bony structures of the auditive apparatus. Based on these theories, different interventional treatment modalities can be applied to treat the underlying causes. Endovascular treatments have shown high efficacy and safety among those treatments which include stenting of the lateral sinus stenosis in IIH and TSS, coiling of the SSWA and JVA, and embolization of emissary veins anomalies. Further studies are needed to understand the natural history of these anomalies and the efficacy of treatments of VPT, which—unlike other types of tinnitus—can be cured with proper treatment.