bluuebunny/crossref_metadata_2025_split huggingface dataset:
UniProt Tools: BLAST, Align, Peptide Search, and ID Mapping
Authors: Zaru Rossana , Orchard Sandra ,   The UniProt Consortium
Published: March 2023

AbstractThe Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data (UniProt Consortium, 2023). The UniProt website receives about 800,000 unique visitors per month and is the primary means to access UniProt. Along with various datasets that you can search, UniProt provides four main tools. These are the “BLAST” tool for sequence similarity searching, the “Align” tool for multiple sequence alignment, the “Peptide Search” tool for retrieving proteins containing a short peptide sequence, and the “Retrieve/ID Mapping” tool for using a list of identifiers to retrieve UniProt Knowledgebase (UniProtKB) proteins and to convert database identifiers from UniProt to external databases or vice versa. This article provides four basic protocols and seven alternate protocols for using UniProt tools. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Basic local alignment search tool (BLAST) in UniProtAlternate Protocol 1: BLAST through UniProt text search results pagesAlternate Protocol 2: BLAST through UniProt basketBasic Protocol 2: Multiple sequence alignment in UniProtAlternate Protocol 3: Align tool through UniProt results pages and entry pagesAlternate Protocol 4: Align tool through UniProt basketBasic Protocol 3: Peptide search in UniProtBasic Protocol 4: Batch retrieval and ID mapping in UniProtAlternate Protocol 5: Retrieve/ID Mapping tool through UniProt text search results pages and BLAST and Align results pagesAlternate Protocol 6: Retrieve/ID Mapping tool through UniProt basketAlternate Protocol 7: Retrieve/ID Mapping tool through UniProt search box
RNS processor using moduli sets of the form 2n±1
Authors: Prediger Vanessa , Bairros Fábio , Seman Laio Oriel , Bezerra Eduardo Augusto , Pettenghi Héctor 
Published: March 2023

SummaryIn recent years, research on residue number systems (RNS) has targeted larger dynamic ranges to explore their inherent parallelism further. In this paper, we start from the traditional 3‐moduli set , with an equivalent 3 ‐bit dynamic range, and propose balanced horizontal extensions by using modulus of the form and to scale the dynamic range and enhance the parallelism according to the requirements. A method to design the reverse conversion by using it is also presented. A case study of multiplier‐accumulator (MACs) in cascade for filtering applications has been analyzed to validate the RNS processor using the proposed moduli set and reverse conversion architecture. Experimental results show that the proposed approaches achieve a significant speedup compared with the state‐of‐the‐art cases for the same dynamic range purposes.
Adoptive T‐cell therapy targeting Epstein–Barr virus as a treatment for multiple sclerosis
Authors: Smith Corey , Khanna Rajiv 
Published: March 2023

AbstractEmergence of a definitive link between Epstein–Barr virus (EBV) and multiple sclerosis has provided an impetus to develop immune‐based therapies to target EBV‐infected B cells. Initial studies with autologous EBV‐specific T‐cell therapy demonstrated that this therapy is safe with minimal side effects and more importantly multiple patients showed both symptomatic and objective neurological improvements including improved quality of life, reduction of fatigue and reduced intrathecal IgG production. These observations have been successfully extended to an ‘off‐the‐shelf’ allogeneic EBV‐specific T‐cell therapy manufactured using peripheral blood lymphocytes of healthy seropositive individuals. This adoptive immunotherapy has also been shown to be safe with encouraging clinical responses. Allogeneic EBV T‐cell therapy overcomes some of the limitations of autologous therapy and can be rapidly delivered to patients with improved therapeutic potential.
Introducing the No-Significant-Effect Concentration
Authors: Fisher Rebecca , Fox David R. 
Published: March 2023

Abstract
The no-effect concentration (NEC) is the preferred threshold metric for single-species toxicity tests applied to derive safe concentration thresholds for contaminants in the environment for use in species sensitivity distributions. However, the NEC is only suitable when concentration–response (C-R) data exhibit a threshold response. We describe an alternative toxicity estimate, the no-significant-effect concentration (NSEC), which is better suited to C-R data for which the response is a monotonically decreasing function of concentration and no threshold effects are evident. We use a flexible, three-parameter sigmoidal function to describe the C-R relationship and detail both Bayesian and frequentist approaches to estimation and inference for the NSEC. While the NSEC is conceptually linked to the traditional no-observed-effect concentration (NOEC), it is a substantial improvement over the NOEC because it decouples the estimate from being directly dependent on the placement of treatment concentrations as well as admitting statements of precision of the resulting toxicity estimate. Environ Toxicol Chem 2023;42:2019–2028. © 2023 Commonwealth of Australia and The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Using Plasma Vitellogenin in Loggerhead Sea Turtles to Assess Reproductive Maturation and Estrogen-Like Contaminant Exposure
Authors: Corniuk Raquel N. , Lynch Jennifer M. , Arendt Michael D. , Braun-McNeill Joanne , Owens David W. , Valverde Roldán A. , Kucklick John R. , McClellan-Green Patricia D. 
Published: March 2023

Abstract
Vitellogenin (VTG), an egg yolk precursor, is abnormally produced by male and juvenile oviparous species after exposure to estrogens. Plasma VTG in loggerhead sea turtles (Caretta caretta) helped us understand their reproductive maturation and investigate it as a biomarker of contaminant exposure. The presence of VTG was screened in plasma from 404 loggerheads from the northwestern Atlantic Ocean using a freshwater turtle antibody in western blots. The concentrations of VTG were semiquantified using band intensities calibrated to results from a loggerhead antibody enzyme-linked immunoassay. The detection and concentrations of VTG were in (from highest to lowest): nesting females, in-water adult females, subadult females, smaller females, unknown sex, and males. Loggerheads from this region begin vitellogenesis at ≅77 cm straight carapace length. We classified VTG expression as abnormal in nine male or juvenile turtles. Organochlorine contaminant (OC) concentrations were measured in blood and/or fat biopsies of some turtles. One abnormal VTG female had the second highest fat polychlorinated biphenyl (PCB) and 4,4′-dichlorodiphenyldichloroethylene concentrations compared among 43 VTG-negative juveniles. The nine VTG-abnormal turtles had average blood PCB concentrations 8.5% higher, but not significantly different, than 46 VTG-negative juveniles (p = 0.453). In turtles less than 77 cm, blood PCB concentrations were significantly, but weakly, correlated with semiquantified VTG concentrations (tau = 0.1, p = 0.004). Greater blood OC concentrations were found in adult females than in males, which motivated the creation of a conceptual model of OC, VTG, and hormone concentrations across a reproductive cycle. A decision tree is also provided incorporating VTG as a sexing tool. Abnormal VTG expression cannot conclusively be linked to endocrine disruption caused by these OC concentrations. Studies should further investigate causes of abnormal VTG expression in wild sea turtles. Environ Toxicol Chem 2023;42:1309–1325. © 2023 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
Developing health information systems in developing countries: Lessons learnt from a longitudinal action research study in Vietnam
Authors: Nguyen Thanh Ngoc 
Published: March 2023

AbstractDesigning and implementing health information systems (HISs) in developing‐country settings is challenging. Many HISs do not go beyond the pilot stage and tend to vanish when external funding is over. In other cases, multiple fragmented HISs remain, but these are unable to talk to each other. And more often than not, data collected by HISs are not used in decision making. To better understand and address these problems, this article employs an information infrastructure (II) perspective and views HISs as parts of larger and complex social‐technical networks. This article contributes to the current knowledge with a set of rich empirical descriptions of the design and implementation of HISs in Vietnam. Theoretically, it contributes to II discussions in the information systems domain by presenting four design problems and suggesting five design principles and 15 design rules to meet them. These design principles and rules also offer practical guidance for managers and designers involved in the design and implementation of HISs in developing countries.
Simple bio‐inspired coating of ureteral stent for protein and bacterial fouling and calcium encrustation control
Authors: Gonzales Ralph Rolly , Kumagai Kazuo , Yang Zhe , Yang Youngmin , Shigemura Katsumi , Matsuyama Hideto 
Published: March 2023

AbstractEncrustation, caused by deposition of calcium and magnesium salts present in urine, is a common problem of indwelling urinary devices, such as ureteral stent. Encrustation was also found to be related to urinary tract infections; thus, it is necessary to prepare ureteral stents with antibacterial and antifouling surfaces to mitigate the occurrence of encrustation. In this study, commercial ureteral stent was coated with polydopamine (PDA), formed from self‐polymerization of dopamine. The PDA coating was optimized in terms of dopamine concentration, pH, and coating time using response surface methodology. The chosen response parameters for optimization were calcium oxalate (CaC2O4) encrustation and protein adsorption. Optimized PDA coating conditions were determined to be the following: pH 9.0, 2 mg/mL DA, and 3 days coating. The optimized PDA‐coated ureteral stent exhibited outstanding resistance against CaC2O4 encrustation, protein fouling, and bacterial adhesion due to its hydrophilic and functional coating layer. In comparison with the pristine ureteral stent, PDA coating was able to suppress approximately 97% and 87% of CaC2O4 and protein adsorption, respectively. The PDA‐coated ureteral stent was compared against those of commercially available ureteral stents and found to have superior encrustation and protein fouling mitigation performance. Finally, PDA coating was found to be highly stable for a storage period of 90 days, whether stored in wet or dry conditions.
Potent SARS‐CoV2‐specific T‐cell response in asymptomatic hemodialysis patients with hidden COVID‐19 infection history
Authors: Etemadi Jalal , Motavalli Roza , Mirghaffari Seyed Alireza , Soltani‐Zangbar Mohammad Sadegh , Hajivalili Mahsa , Ahmadian Heris Javad , Niknafs Bahram , Zununi Sepideh , Sadeghi Mohammadreza , Rasi Hashemi Sadraddin , Tayebi Khosroshahi Hamid , Yousefi Mehdi 
Published: March 2023

AbstractBackgroundCOVID‐19‐related immune responses in patients with end‐stage renal disease (ESRD) are characterized in detail by the humoral response, but their cellular immunity has not been clarified. Here, we evaluated virus‐specific T cells in parallel with serology‐related tests.MethodsIn this study, 104 ESRD patients at the hemodialysis ward of Imam Reza hospital at Tabriz (Iran) were enrolled. After blood sampling, SARS‐CoV2‐specific humoral and cellular immune responses were evaluated by SARS‐CoV2‐specific IgM/IgG ELISA and peptide/MHCI‐Tetramers flow cytometry, respectively.ResultsOur results showed that 14 (13.5%) and 45 (43.3%) patients had specific SARS‐CoV2 IgM and IgG in their sera, respectively. Immunophenotyping for SARS‐CoV2‐specific CD8+ T lymphocytes revealed that 68 (65.4%) patients had these types of cells. Among SARS‐CoV2‐specific CD8+ T lymphocytes positive subjects, 13 and 43 individuals had positive results for specific SARS‐CoV2 IgM and IgG existence, respectively. Also, there was a relationship between specific SARS‐CoV2 IgM (p = 0.031) and IgG (p < 0.0001) existence and having SARS‐CoV2‐specific TCD8+ lymphocytes in the studied population.ConclusionDespite not having clinical symptoms, a high rate of SARS‐CoV2‐specific T‐cell response in asymptomatic ESRD patients may reveal a high burden of asymptomatic COVID‐19 infection in these patients.
Mobility and HIV care engagement: a research agenda
Authors: Thorp Marguerite , Ayieko James , Hoffman Risa M. , Balakasi Kelvin , Camlin Carol S. , Dovel Kathryn 
Published: March 2023

AbstractIntroductionMobility is common and an essential livelihood strategy in sub‐Saharan Africa (SSA). Mobile people suffer worse outcomes at every stage of the HIV care cascade compared to non‐mobile populations. Definitions of mobility vary widely, and research on the role of temporary mobility (as opposed to permanent migration) in HIV treatment outcomes is often lacking. In this article, we review the current landscape of mobility and HIV care research to identify what is already known, gaps in the literature, and recommendations for future research.DiscussionMobility in SSA is closely linked to income generation, though caregiving, climate change and violence also contribute to the need to move. Mobility is likely to increase in the coming decades, both due to permanent migration and increased temporary mobility, which is likely much more common. We outline three central questions regarding mobility and HIV treatment outcomes in SSA. First, it is unclear what aspects of mobility matter most for HIV care outcomes and if high‐risk mobility can be identified or predicted, which is necessary to facilitate targeted interventions for mobile populations. Second, it is unclear what groups are most vulnerable to mobility‐associated treatment interruption and other adverse outcomes. And third, it is unclear what interventions can improve HIV treatment outcomes for mobile populations.ConclusionsMobility is essential for people living with HIV in SSA. HIV treatment programmes and broader health systems must understand and adapt to human mobility, both to promote the rights and welfare of mobile people and to end the HIV pandemic.
Mobility and ART retention among men in Malawi: a mixed‐methods study
Authors: Thorp Marguerite , Bellos MacDaphton , Temelkovska Tijana , Mphande Misheck , Cornell Morna , Hubbard Julie , Choko Augustine , Coates Thomas J. , Hoffman Risa , Dovel Kathryn 
Published: March 2023

AbstractIntroductionMobility is associated with worse outcomes across the HIV treatment cascade, especially among men. However, little is known about the mechanisms that link mobility and poor HIV outcomes and what types of mobility most increase the risk of treatment interruption among men in southern Africa.MethodsFrom August 2021 to January 2022, we conducted a mixed‐methods study with men living with HIV (MLHIV) but not currently receiving antiretroviral therapy (ART) in Malawi. Data collection was embedded within two larger trials (ENGAGE and IDEaL trials). We analysed baseline survey data of 223 men enrolled in the trials who reported being mobile (defined as spending ≥14 nights away from home in the past 12 months) using descriptive statistics and negative binomial regressions. We then recruited 32 men for in‐depth interviews regarding their travel experiences and ART utilization. We analysed qualitative data using constant comparative methods.ResultsSurvey data showed that 34% of men with treatment interruptions were mobile, with a median of 60 nights away from home in the past 12 months; 69% of trips were for income generation. More nights away from home in the past 12 months and having fewer household assets were associated with longer periods out of care. In interviews, men reported that travel was often unplanned, and men were highly vulnerable to exploitive employer demands, which led to missed appointments and ART interruption. Men made major efforts to stay in care but were often unable to access care on short notice, were denied ART refills at non‐home facilities and/or were treated poorly by providers, creating substantial barriers to remaining in and returning to care. Men desired additional multi‐month dispensing (MMD), the ability to refill treatment at any facility in Malawi, and streamlined pre‐travel refills at home facilities.ConclusionsMen prioritize ART and struggle with the trade‐offs between their own health and providing for their families. Mobility is an essential livelihood strategy for MLHIV in Malawi, but it creates conflict with ART retention, largely due to inflexible health systems. Targeted counselling and peer support, access to ART services anywhere in the country, and MMD may improve outcomes for mobile men.
Confirmatory Auditory Brainstem Responses Testing Results in Discordant Outcomes: Implications for Timely Care
Authors: Tunkel Alexandra E. , Gorelik Daniel , Behzadpour Hengameh K. , Rana Md Sohel , Ambrose Tracey , Kronzek Eve , Preciado Diego A. , Reilly Brian K. 
Published: March 2023

ObjectivesThe purpose of this study is to evaluate for discrepancies in diagnostic auditory brainstem responses (ABR) between Children's National Hospital (CNH), a pediatric medical center, and outside facilities (OSF) that referred patients to CNH for confirmatory evaluation. Such discrepancies impact early hearing detection and intervention (EHDI) timelines.MethodsA retrospective chart review was conducted from an internal database of patients who underwent diagnostic ABR from 2017 to 2021. Only patients with ABR results from both CNH and OSF were analyzed. Demographic data, external and internal test results, and intervention data were obtained. Hearing loss (HL) severity was graded on a scale of 0 to 8, where 0 indicated normal hearing and 8 indicated profound. Each ear was analyzed separately.ResultsForty‐nine patients met the inclusion criteria, and each ear was evaluated separately. Median HL severity was 1.0 [0.0, 4.3] at CNH compared to 3.0 [1.8, 6] at OSF (p = 0.004). Forty‐seven ears (48.0%) showed lower severity at CNH. Twenty‐seven patients (55%) received hearing amplification devices. The median age at time of hearing intervention was 220 days.ConclusionOur results showed statistical significance in the median severity of HL between CNH and OSF. A substantial proportion (70%) of children in our dataset who received amplification via cochlear implant or hearing aids were shown to have discrepancies in ABR findings from CNH and OSF. These findings have implications with regards to the appropriate usage of health care resources and maintaining EDHI timelines.Level of Evidence4 (Retrospective Cohort Study) Laryngoscope, 133:3571–3574, 2023
Molecular Mobility of Polyrotaxane Surfaces Alleviates Oxidative Stress‐Induced Senescence in Mesenchymal Stem Cells
Authors: Masuda Hiroki , Arisaka Yoshinori , Hakariya Masahiro , Iwata Takanori , Yoda Tetsuya , Yui Nobuhiko 
Published: March 2023

AbstractPolyrotaxane is a supramolecular assembly consisting of multiple cyclic molecules threaded by a linear polymer. One of the unique properties of polyrotaxane is molecular mobility, cyclic molecules moving along the linear polymer. Molecular mobility of polyrotaxane surfaces affects cell spreading, differentiation, and other cell‐related aspects through changing subcellular localization of yes‐associated proteins (YAPs). Subcellular YAP localization is also related to cell senescence derived from oxidative stress, which is known to cause cancer, diabetes, and heart disease. Herein, the effects of polyrotaxane surface molecular mobility on subcellular YAP localization and cell senescence following H2O2‐induced oxidative stress are evaluated in human mesenchymal stem cells (HMSCs) cultured on polyrotaxane surfaces with different molecular mobilities. Oxidative stress promotes cytoplasmic YAP localization in HMSCs on high‐mobility polyrotaxane surfaces; however, low‐mobility polyrotaxane surfaces more effectively maintain nuclear YAP localization, exhibiting lower senescence‐associated β‐galactosidase activity and senescence‐related gene expression and DNA damage than that seen with the high‐mobility surfaces. These results suggest that the molecular mobility of polyrotaxane surfaces regulates subcellular YAP localization, thereby protecting HMSCs from oxidative stress‐induced cell senescence. Applying the molecular mobility of polyrotaxane surfaces to implantable scaffolds can provide insights into the prevention and treatment of diseases caused by oxidative stress.
Automated assessment of necrosis tumor ratio in colorectal cancer using an artificial intelligence‐based digital pathology analysis
Authors: Ye Huifen , Ye Yunrui , Wang Yiting , Tong Tong , Yao Su , Xu Yao , Hu Qingru , Liu Yulin , Liang Changhong , Wang Guangyi , Zhao Ke , Fan Xinjuan , Cui Yanfen , Liu Zaiyi 
Published: March 2023

AbstractBackgroundWith the advance in digital pathology and artificial intelligence (AI)‐powered approaches, necrosis is proposed as a marker of poor prognosis in colorectal cancer (CRC). However, most previous studies quantified necrosis merely as a tissue type and patch‐level segmentation. Thus, it was worth exploring and validating the prognostic and predictive value of necrosis proportion with a pixel‐level segmentation in large multicenter cohorts.MethodsA semantic segmentation model was trained with 12 tissue types labeled by pathologists. Segmentation was performed using the U‐net model with a subsequently derived necrosis tumor ratio (NTR). We proposed the NTR score (NTR‐low or NTR‐high) to evaluate the prognostic and predictive value of necrosis for disease‐free survival (DFS) and overall survival (OS) in the development (N = 443) and validation cohorts (N = 333) using 75% as a threshold.ResultsThe 2‐category NTR was an independent prognostic factor and NTR‐low was associated with significant prolonged DFS (unadjusted HR for high vs. low 1.72 [95% CI 1.19–2.49] and 1.98 [1.22–3.23] in the development and validation cohorts). Similar trends were observed for OS. The prognostic value of NTR was maintained in the multivariate analysis for both cohorts. Furthermore, a stratified analysis showed that NTR‐high was a high risk with adjuvant chemotherapy for OS in stage II CRC (p = 0.047).ConclusionAI‐based pixel‐level quantified NTR has a stable prognostic value in CRC associated with unfavorable survival. Additionally, adjuvant chemotherapy provided survival benefits for patients with a high NTR score in stage II CRC.