bluuebunny/crossref_metadata_2025_split huggingface dataset:
White matter regeneration induced by aligned fibrin nanofiber hydrogel contributes to motor functional recovery in canine T12 spinal cord injury
Authors: Cao Zheng , Man Weitao , Xiong Yuhui , Guo Yi , Yang Shuhui , Liu Dongkang , Zhao He , Yang Yongdong , Yao Shenglian , Li Chuzhong , Zhao Lingyun , Sun Xiaodan , Guo Hua , Wang Guihuai , Wang Xiumei 
Published: December 2021

Abstract
A hierarchically aligned fibrin hydrogel (AFG) that possesses soft stiffness and aligned nanofiber structure has been successfully proven to facilitate neuroregeneration in vitro and in vivo. However, its potential in promoting nerve regeneration in large animal models that is critical for clinical translation has not been sufficiently specified. Here, the effects of AFG on directing neuroregeneration in canine hemisected T12 spinal cord injuries were explored. Histologically obvious white matter regeneration consisting of a large area of consecutive, compact and aligned nerve fibers is induced by AFG, leading to a significant motor functional restoration. The canines with AFG implantation start to stand well with their defective legs from 3 to 4 weeks postoperatively and even effortlessly climb the steps from 7 to 8 weeks. Moreover, high-resolution multi-shot diffusion tensor imaging illustrates the spatiotemporal dynamics of nerve regeneration rapidly crossing the lesion within 4 weeks in the AFG group. Our findings indicate that AFG could be a potential therapeutic vehicle for spinal cord injury by inducing rapid white matter regeneration and restoring locomotion, pointing out its promising prospect in clinic practice.
The chemoprevention of spirulina platensis and garlic against diethylnitrosamine induced liver cancer in rats via amelioration of inflammatory cytokines expression and oxidative stress
Authors: Abouzed Tarek Kamal , Althobaiti Fayez , Omran Alaa Faik , Eldomany Ehab Bedir , El-Shazly Samir Ahmed , Alharthi Fahad , Elkattawy Azza Mansour , Kahilo Khaled Abd Aleim , Dorghamm Doaa Abdallha 
Published: December 2021

Abstract
Natural antioxidant products play a vital role in the treatment and prevention of cancer disease because they have no side effects. This study aimed to compare the chemoprotective effect of Spirulina platensis (SP) and garlic against hepatocellular carcinoma (HCC) in rats. This study was being done by using 60 male Wistar rats and divided into four groups. Group (I): normal group. Group (II): HCC group induced by injection of a single dose of DEN (200 mg/kg/I.P) and after 14 days injected CCl4 (1 mg/kg/I.P) 3 times/week/six weeks. Group (III): HCC group received SP orally at a dose (500 mg/kg). Group (IV): HCC group received garlic (250 mg/kg) orally. The results revealed that the Spirulina and garlic treatment have a significant decrease in Glutamate pyruvate transaminase, Glutamate oxaloacetate transaminase, GGT, LDH, and the Malondialdehyde (MDA) activity, and furthermore, a significant increase in the total protein level, the superoxide dismutase (SOD), and Catalase (CAT) activity nearly to normal activity. Furthermore, the hepatic expression of tumor necrosis factor (TNF-α), interleukin-6 (IL-6), inducible nitric oxide synthase, transforming growth factor-beta (TGF-β1), Heat Shock Protein glycoprotein 96 (HSPgp96), and Glypican 3 (GP3) were down regulated by the Spirulina and garlic treatment in comparison with those in HCC group. All findings reported that the chemoprotective of both Spirulina and garlic that have nearly the same effect may be due to antioxidant activity and inhibition of lipid peroxidation, amelioration of pro-inflammatory cytokine, HSPgp96, and GP3.
A Comparative Study of Children with MIS-C between Admitted to the Pediatric Intensive Care Unit and Pediatric Ward: A One-Year Retrospective Study
Authors: Kıymet Elif , Böncüoğlu Elif , Şahinkaya Şahika , Cem Ela , Çelebi Miray Yılmaz , Düzgöl Mine , Kara Aybüke Akaslan , Arıkan Kamile Ötiken , Vuran Gamze Talay , Yılmazer Murat Muhtar , Sandal Özlem Saraç , Ağın Hasan , Pirinç Neslihan , Bayram Nuri , Devrim İlker 
Published: December 2021

Abstract

Objectives
This descriptive study aimed to compare the clinical and laboratory features of the children with the multisystem inflammatory syndrome in children (MIS-C), requiring pediatric intensive care unit (PICU), admission with the MIS-C patients who did not require PICU admission.

Patients and methods
This study was conducted between March 2020 and February 2021 at the University of Health Sciences Dr. Behçet Uz Children’s Hospital, a referral center for pediatric infectious diseases in the Aegean Region of Turkey. All hospitalized patients aged 18 years old or less with MIS-C according to the definition of the universal guidelines were included in the study. Data of the patients with the diagnosis of MIS-C were recorded and collected from the electronic medical records of the hospital. The data included demographic characteristics, presenting signs and symptoms, laboratory findings and clinical data.

Results
A total of 58 patients with MIS-C were included in this study. Thirty-eight (65.5%) patients were male. The median age was 6 years (2 months–16 years). The patients admitted to PICU were 15 (25.9%). The rate of pulmonary involvement was 81.3% (n = 13) in the PICU group. The median procalcitonin, C-reactive protein, erythrocyte sedimentation rate, D-Dimer and ferritin values were significantly higher in the PICU group compared to non-PICU group (p &lt; 0.001, p = 0.02, p &lt; 0.001, p = 0.006 and p = 0.031).

Conclusions
Besides the depressing cardiac functions reported before, the pulmonary involvement and signs of shock are important factors for PICU admission in children with MIS-C.
Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Enterobacterales in a hospital setting
Authors: Stoesser N , George R , Aiken Z , Phan HTT , Lipworth S , Wyllie DH , Quan TP , Mathers AJ , De Maio N , Seale AC , Eyre DW , Vaughan A , Swann J , Peto TEA , Crook DW , Cawthorne J , Dodgson A , Walker AS ,   TRACE Investigators’ Group
Published: December 2021

2.AbstractHealthcare-associated wastewater reservoirs and asymptomatic gastrointestinal patient colonisation by carbapenemase-producing Enterobacterales (CPE) contribute to nosocomial CPE dissemination. We systematically sampled wastewater sites (n=4488 sampling events; 349 sites) and patients (n=1247) across six wards over 6-12 months in 2016 to better understand blaKPC-associated CPE (KPC-E) diversity within these niches and transmission potential in an endemic healthcare setting. Up to five isolates in KPC-E-positive samples were sequenced (Illumina). Recombination-adjusted phylogenies were used to define genetically related strains; assembly and mapping-based typing approaches were used to characterise antimicrobial resistance genes, insertion sequences, and Tn4401 types/target site sequences. The wider accessory genome was evaluated in a subset of the largest clusters, and those crossing niches.Wastewater site KPC-E-positivity was substantial (101/349 sites [28.9%] positive); 228/5,601 (4.1%) patients cultured were CPE culture-positive over the same timeframe. At a genomic-level, 13 KPC-E species and 109 strains were identified, and 24% of wastewater and 26% of patient KPC-E-positive samples harboured ≥1 strain. Most diversity was explained by the individual niche, suggesting localised factors are important in selection and spread. Tn4401+target site sequence diversity was greater in wastewater sites (p<0.001), which might favour Tn4401-associated transposition/evolution. Shower/bath and sluice/mop-associated sites were more likely to be KPC-E-positive (Adjusted Odds Ratio [95% CI]: 2.69 [1.44-5.01], p=0.0019 and 2.60 [1.04-6.52], p=0.0410, respectively). Different strains had different transmission and blaKPCdissemination dynamics.There may be substantial KPC-E colonisation of wastewater sites and patients in KPC-E-endemic healthcare settings. Niche-specific factors (e.g. microbial interactions, selection pressure) likely affect carbapenemase gene persistence and evolution, and different strains and mobile genetic elements with different transmission dynamics influence carbapenemase gene dissemination; these factors should be considered in surveillance and control strategies.
Google Trends as a predictive tool for COVID-19 vaccinations in Italy: a retrospective infodemiological analysis
Authors: Rovetta Alessandro 
Published: December 2021

AbstractBackgroundGoogle Trends is an infoveillance tool widely used by the scientific community to investigate different user behaviors related to COVID-19. However, several limitations regarding its adoption are reported in the literature.ObjectiveThis brief paper aims to provide an effective and efficient approach to investigating vaccine adherence against COVID-19 via Google Trends.MethodsThrough the cross-correlational analysis of well-targeted hypotheses, we investigate the predictive capacity of web searches related to COVID-19 towards vaccinations in Italy from November 2020 to November 2021. The keyword “vaccine reservation” (VRQ) was chosen as it reflects a real intention of being vaccinated (V). Furthermore, the impact of the second-largest Italian national newspaper on vaccines-related web searches was investigated to evaluate the role of the mass media as a confounding factor.ResultsSimple and generic keywords are more likely to identify the actual web interest in COVID-19 vaccines than specific and elaborated keywords. Cross-correlations between VRQ and V were very strong and significant (min r2 = .460, P<.001, lag = 0 weeks; max r2 = .903, P < .001, lag = 6 weeks). Cross-correlations between VRQ and news about COVID-19 vaccines have been markedly lower and characterized by greater lags (min r2 = .190, P=.001, lag = 0 weeks; max r2 = .493, P < .001, lag = -10 weeks). No correlation between news and vaccinations was sought since the lag would have been too high.ConclusionsThis research provides strong evidence in favor of using Google Trends as a surveillance and prediction tool for vaccine adherence against COVID-19 in Italy. These findings prove that the search for suitable keywords is a fundamental step to reduce confounding factors. Additionally, targeting hypotheses helps diminish the likelihood of spurious correlations. It is recommended that Google Trends be leveraged as a complementary infoveillance tool by government agencies to monitor and predict vaccine adherence in this and future crises by following the methods proposed in this manuscript.
The role of Zambia’s expansive Inter-agency Coordinating Committee (ICC) in supporting evidence-based vaccine and health sector programming
Authors: Sakas Zoe , Rodriguez Katie , Hester Kyra A , Darwar Roopa , Dounebaine Bonheur , Ellis Anna S , Rosenblum Simone , Isett Kimberley R , Orenstein Walter , Freeman Matthew C , Kilembe William , Bednarczyk Robert A 
Published: December 2021

AbstractNew vaccines, technologies, and regulations, alongside increased demand for vaccines, all require prioritization and coordination from key players within the vaccine sector. Inter-agency Coordinating Committees (ICC) support decision-making and coordination at the national-level and act as key drivers for sustainable improvements in vaccination programming. We employed a qualitative case study design to investigate critical success factors for the high routine immunization coverage in Zambia from 2000-2018. Qualitative data were collected between October 2019 and February 2020, including key informant interviews (n=66) at the national, provincial, district, and health facility levels. Thematic analysis was applied to understand the role of the Zambian ICC and its impact on the policy environment overtime. Throughout our study period, the Zambian ICC demonstrated the following improvements: 1) expanded membership to include diverse representation; 2) expanded scope and mandate to include maternal and child health in decision-making; and 3) collaboration with the ZITAG through distinct roles. The diverse and expansive membership of the Zambian ICC, along with its ability to foster government commitment and lobby for additional resources, supported improvements in immunization programming. The Zambian ICC holds considerable influence on government agencies and external partners which facilitates procurement of funding, policy decisions, and strategic planning.
Developing an Antiviral Peptides Predictor with Generative Adversarial Network Data Augmentation
Authors: Lin Tzu-Tang , Sun Yi-Yun , Cheng Wei-Chih , Lu I-Hsuan , Chen Shu-Hwa , Lin Chung-Yen 
Published: December 2021

AbstractMotivationNew antiviral drugs are urgently needed because of emerging viral pathogens’ increasing severity and drug resistance. Antiviral peptides (AVPs) have multiple antiviral properties and are appealing candidates for antiviral drug development. We developed a sequence-based binary classifier to identify whether an unknown short peptide has AVP activity. We collected AVP sequence data from six existing databases. We used a generative adversarial network to augment the number of AVPs in the positive training dataset and allow our deep convolutional neural network model to train on more data.ResultsOur classifier achieved outstanding performance on the testing dataset compared with other state-of-the-art classifiers. We deployed our trained classifier on a user-friendly web server.Availability and implementationAI4AVP is freely accessible at http://axp.iis.sinica.edu.tw/AI4AVP/Contactcylin@iis.sinica.edu.twSupplementary informationSupplementary data is also available.
Heteologous saRNA-Prime, DNA Dual-Antigen-Boost SARS-CoV-2 Vaccination Elicits Robust Cellular Immunogenicity and Cross-Variant Neutralizing Antibodies
Authors: Rice Adrian , Verma Mohit , Voigt Emily , Battisti Peter , Beaver Sam , Reed Sierra , Dinkins Kyle , Mody Shivani , Zakin Lise , Tanaka Shiho , Morimoto Brett , Olson C. Anders , Gabitzsch Elizabeth , Safrit Jeffrey T. , Spilman Patricia , Casper Corey , Soon-Shiong Patrick 
Published: December 2021

ABSTRACTWe assessed if immune responses are enhanced in CD-1 mice by heterologous vaccination with two different nucleic acid-based COVID-19 vaccines: a next-generation human adenovirus serotype 5 (hAd5)-vectored dual-antigen spike (S) and nucleocapsid (N) vaccine (AdS+N) and a self-amplifying and -adjuvanted S RNA vaccine (SASA S) delivered by a nano-lipid carrier. The AdS+N vaccine encodes S modified with a fusion motif to increase cell-surface expression. The N antigen is modified with an Enhanced T-cell Stimulation Domain (N-ETSD) to direct N to the endosomal/lysosomal compartment and increase MHC class I and II stimulation potential. The S sequence in the SASA S vaccine comprises the D614G mutation, two prolines to stabilize S in the prefusion conformation, and 3 glutamines in the furin cleavage region to increase cross-reactivity across variants. CD-1 mice received vaccination by homologous and heterologous prime > boost combinations. Humoral responses to S were the highest with any regimen including the SASA S vaccine, and IgG bound to wild type and Delta (B.1.617.2) variant S1 at similar levels. An AdS+N boost of an SASA S prime particularly enhanced both CD4+ and CD8+ T-cell responses to both wild type and Delta S peptides relative to all other vaccine regimens. Sera from mice receiving SASA S homologous or heterologous vaccination were found to be highly neutralizing of all pseudovirus strains tested: Wuhan, Beta, Delta, and Omicron strain. The findings here support the clinical testing of heterologous vaccination by an SASA S > AdS+N regimen to provide increased protection against emerging SARS-CoV-2 variants.
The developing kidney actively negotiates geometric packing conflicts to avoid defects
Authors: Prahl Louis S. , Viola John M. , Liu Jiageng , Hughes Alex J. 
Published: December 2021

AbstractThe physiological functions of several organs rely on branched tubular networks, but little is known about conflicts in development between building enough tubules for adequate function and geometric constraints imposed by organ size. We show that the mouse embryonic kidney epithelium negotiates a physical packing conflict between tubule tip duplication and limited area at the organ surface. Imaging, computational, and soft material modeling of tubule ‘families’ identifies six geometric packing phases, including two defective ones. Experiments in kidney explants show that a retrograde tension on tubule families is necessary and sufficient for them to avoid defects by switching to a vertical orientation that increases packing density. These results reveal developmental contingencies in response to physical limitations, and create a framework for classifying kidney defects.One-Sentence SummaryEpithelial branching in the kidney causes a geometric packing conflict that is resolved through internally generated tensions
MaveDB v2: a curated community database with over three million variant effects from multiplexed functional assays
Authors: Rubin Alan F , Min Joseph K , Rollins Nathan J , Da Estelle Y , Esposito Daniel , Harrington Matthew , Stone Jeremy , Bianchi Aisha Haley , Dias Mafalda , Frazer Jonathan , Fu Yunfan , Gallaher Molly , Li Iris , Moscatelli Olivia , Ong Jesslyn YL , Rollins Joshua E , Wakefield Matthew J , “Sunny” Ye Shenyi , Tam Amy , McEwen Abbye E , Starita Lea M , Bryant Vanessa L , Marks Debora S , Fowler Douglas M 
Published: December 2021

AbstractA central problem in genomics is understanding the effect of individual DNA variants. Multiplexed Assays of Variant Effect (MAVEs) can help address this challenge by measuring all possible single nucleotide variant effects in a gene or regulatory sequence simultaneously. Here we describe MaveDB v2, which has become the database of record for MAVEs. MaveDB now contains a large fraction of published studies, comprising over two hundred datasets and three million variant effect measurements. We created tools and APIs to streamline data submission and access, transforming MaveDB into a hub for the analysis and dissemination of these impactful datasets.
Compositional forecasting of Chinook Salmon Evolutionarily Significant Units in bycatch for Pacific Hake fisheries
Authors: Moran Paul , Tuttle Vanessa J. , Bishop Susan , LaVoy Larrie 
Published: December 2021

ABSTRACTBycatch impacts on non-target species present significant management problems in diverse fisheries throughout the world. Despite successful efforts to minimize bycatch in US West Coast Pacific Hake fisheries, these impacts remain a concern, particularly for sensitive populations of Chinook Salmon. NOAA Fisheries needed predictive models to estimate proportions of Chinook Salmon Evolutionarily Significant Units (ESUs) expected in bycatch. We used genetic mixture analysis to estimate ESU proportions from at-sea bycatch between 2008 and 2015. Using latitude as a predictor and applying jackknife cross validation, we found Dirichlet regression more accurately estimated abundant ESUs, whereas multinomial logistic regression performed better with rare ESUs. This targeted, ESU-specific approach showed the spatial distribution of sensitive stocks in bycatch and supported NOAA’s obligations to forecast impacts on listed ESUs. The overarching goal of this continuing work is to maximize sustainable harvest while protecting threatened and endangered Chinook Salmon ESUs.
Striatal compartmentalization and clustering of different subtypes of astrocytes is altered in the zQ175 Huntington’s disease mouse model
Authors: Brown Taylor G , Thayer Mackenzie , Zarate Nicole , Gomez-Pastor Rocio 
Published: December 2021

AbstractHuntington’s disease (HD) is a devastating neurodegenerative disease that primarily affects the striatum, a brain region that controls movement and some forms of cognition. Dysfunction and loss of medium spiny neurons of the striatum is accompanied by astrogliosis (increased astrocyte density and pathology). For decades, astrocytes were considered a homogeneous cell type, but recent transcriptomic analyses revealed astrocytes are a heterogeneous population classified into multiple subtypes depending on the expression of different gene markers. Here, we studied whether three different striatal astrocyte subtypes expressing glutamine synthetase (GS), glial fibrillary acidic protein (GFAP), or S100 calcium-binding protein B (S100B) are differentially altered in HD. We conducted a comparative immunofluorescence analysis in the striatum of WT and the heterozygous zQ175 HD mouse model and found that the expression and abundance of GFAP+ and S100B+ astrocytes increased in zQ175 mice, while GS+ astrocytes showed no alteration. We then explored whether there was a differential spatial distribution of any of these subtypes within the striatum. We developed a systematic brain compartmentalization approach and found that while GS+ and S100B+ astrocytes were more homogeneously distributed throughout the striatum in zQ175 mice, GFAP+ astrocytes preferentially accumulated in the dorsomedial and dorsolateral striatum, which are regions associated with goal-directed and habitual behaviors. Additionally, GFAP+ astrocytes in zQ175 mice showed increased clustering, a parameter that indicates increased proximity and that is associated with localized inflammation and/or neurodegeneration. Our data suggest a differential susceptibility in both increased density and striatal compartmentalization of different subtypes of astrocytes in zQ175. These results highlight new potential implications for our understanding of astrocyte pathology in HD.
The decrotonylase FoSir5 facilitates mitochondrial metabolic state switching in conidial germination of Fusarium oxysporum
Authors: Zhang Ning , Song Limin , Xu Yang , Pei Xueyuan , Luisi Ben F. , Liang Wenxing 
Published: December 2021

AbstractFusarium oxysporum is one of the most important pathogenic fungi with a broad range of plant and animal hosts. The first key step of its infection cycle is conidial germination, but there is limited information available on the molecular events supporting this process. We show here that germination is accompanied by a sharp decrease in expression of FoSir5, an ortholog of the human lysine deacetylase SIRT5. We observe that FoSir5 decrotonylates a subunit of the fungal pyruvate dehydrogenase complex (FoDLAT) at K148, resulting in inhibition of the activity of the complex in mitochondria. Moreover, FoSir5 decrotonylates histone H3K18, leading to a downregulation of transcripts encoding enzymes of aerobic respiration pathways. Thus, the activity of FoSir5 coordinates regulation in different organelles to steer metabolic flux through respiration. As ATP content is positively related to fungal germination, we propose that FoSir5 negatively modulates conidial germination in F. oxysporum through its metabolic impact. These findings provide insights into the multifaceted roles of decrotonylation, catalysed by FoSir5, that support conidial germination in F. oxysporum.