bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protocol for a hybrid type 3 cluster randomized trial of a technical assistance system supporting coalitions and evidence-based drug prevention programs
Authors: Brown Louis D. , Chilenski Sarah M. , Wells Rebecca , Jones Eric C. , Welsh Janet A. , Gayles Jochebed G. , Fernandez Maria E. , Jones Damon E. , Mallett Kimberly A. , Feinberg Mark E. 
Published: June 2021

Abstract
Background
Over 5000 community anti-drug coalitions operating in the USA serve as a cornerstone of federal drug prevention. These coalitions, however, have demonstrated effectiveness in preventing substance use only when they use technical assistance (TA) and implement evidence-based programs (EBPs). The absence of TA and EBP implementation by coalitions is a key research-to-practice gap. The Coalition Check-Up TA system is designed to fill this gap by supporting community coalition implementation of EBPs. Existing TA models for evidence-based coalition approaches are resource intensive and coalition model specific. The Coalition Check-Up is a lower cost strategy that works with a variety of types of coalitions to support sustainable implementation of EBPs. This study protocol describes a hybrid type 3 effectiveness-implementation trial applying Wandersman’s Interactive Systems Framework to test the effects of the Coalition Check-Up on coalition EBP implementation capacity and outcomes. The Interactive Systems Framework outlines how the prevention support system—especially TA—bolsters EBP dissemination and implementation.

Methods
Using a cluster randomized controlled design, this trial will test the overall effectiveness of the Coalition Check-Up, including how it contributes to EBP implementation and prevention of youth substance use. The first aim is to estimate the impact of the Coalition Check-Up on coalitions’ capacity to do their work. We will recruit 68 anti-drug coalitions for random assignment to the Coalition Check-Up or “TA as usual” condition. We will evaluate whether the Coalition Check-Up improves coalition capacity using measures of coalition member responses about team processes, coalition network composition, and collaborative structure. Our second aim is to estimate the impact of the Coalition Check-Up on implementation of EBPs, and our third aim is to estimate the impact of the Coalition Check-Up on youth substance use.

Discussion
This project will clarify how the Coalition Check-Up, a scalable approach to TA due to its low cost, affects coalition capacity to support EBP implementation. Analyses also provide insight into causal pathways from the prevention support system to the prevention delivery system outlined by the Interactive Systems Framework. Results will build the evidence-base for how to support community coalitions’ sustainable implementation of evidence-based prevention programs and policies.

Trial registration
Clinicaltrials.gov registration number NCT04592120. Registered on October 19, 2020.
Retrospective analysis of recurrence patterns and clinical outcome of grade II meningiomas following postoperative radiotherapy
Authors: Hoffmann Elgin , Clasen Kerstin , Frey Bettina , Ehlers Jakob , Behling Felix , Skardelly Marco , Bender Benjamin , Schittenhelm Jens , Reimold Matthias , Tabatabai Ghazaleh , Zips Daniel , Eckert Franziska , Paulsen Frank 
Published: June 2021

Abstract
Background
Atypical meningiomas exhibit a high tendency for tumor recurrence even after multimodal therapy. Information regarding recurrence patterns after additive radiotherapy is scarce but could improve radiotherapy planning and therapy decision. We conducted an analysis of recurrence patterns with regard to target volumes and dose coverage assessing target volume definition and postulated areas of tumor re-growth origin. Prognostic factors contributing to relapse were evaluated.

Methods
The clinical outcome of patients who had completed additive, somatostatin receptor (SSTR)-PET/CT-based fractionated intensity-modulated radiotherapy for atypical meningioma between 2007 and 2017 was analyzed. In case of tumor recurrence/progression, treatment planning was evaluated for coverage of the initial target volumes and the recurrent tumor tissue. We proposed a model evaluating the dose distribution in postulated areas of tumor re-growth origin. The median of proliferation marker MIB-1 was assessed as a prognostic factor for local progression and new distant tumor lesions.

Results

Data from 31 patients who had received adjuvant (n = 11) or salvage radiotherapy (n = 20) were evaluated. Prescribed dose ranged from 54.0 to 60.0 Gy. Local control at five years was 67.9%. Analysis of treatment plans of the eight patients experiencing local failure proved sufficient extent of target volumes and coverage of the prescribed dose of at least 50.0 Gy as determined by mean dose, D98, D2, and equivalent uniform dose (EUD) of all initial target volumes, postulated growth-areas, and areas of recurrent tumor tissue. In all cases, local failure occurred in high-dose volumes. Tumors with a MIB-1 expression above the median (8%) showed a higher tendency for re-growth.

Conclusions
The model showed adequate target volume and relative dose distribution but absolute dose appears lower in recurrent tumors without reaching statistical significance. This might provide a rationale for dose escalation studies. Biological factors such as MIB-1 might aid patients’ stratification for dose escalation.
Development of the Fabry Disease Patient-Reported Outcome (FD-PRO): a new instrument to measure the symptoms and impacts of Fabry Disease
Authors: Hamed Alaa , DasMahapatra Pronabesh , Lyn Nicole , Gwaltney Chad , Hopkin Robert J. 
Published: June 2021

Abstract
Background
The systematic collection of disease-specific symptoms and impacts on the lives of patients with Fabry Disease (FD) can offer unique insights into the patient experience, yet no disease-specific tool to measure FD symptoms exists. This study describes the development of the Fabry Disease Patient-Reported Outcome (FD-PRO).

Methods
A targeted literature search, interviews with key opinion leaders (KOLs), and concept elicitation (CE) interviews with patients identified the most frequent signs and symptoms associated with FD and their impact on daily life. Cognitive interviews evaluated patients’ ability to understand the FD-PRO instructions and respond to the items on the draft FD-PRO instrument.

Results
The targeted literature search identified key signs and symptoms in domains that were confirmed in KOL interviews. In CE interviews with 37 treated and treatment-naïve patients, neuropathic pain symptoms (95% treated, 82% treatment-naïve), temperature intolerance (95% treated, 88% treatment-naïve), energy difficulties (95% treated, 94% treatment-naïve), hearing/vision impairment (95% treated, 71% treatment-naïve), and gastrointestinal symptoms (80% treated, 59% treatment-naïve) were most frequently mentioned. Results were similar for men and women in both treated and treatment-naïve groups. While treatment-naïve patients in general expressed fewer and milder symptoms compared to treated patients, the overall sets of symptoms expressed by the two groups were similar. The most severe symptoms were neuropathic pain, stomach pain, burning pain, and fatigue. The most bothersome symptoms were stomach pain, breathing difficulty, fatigue, neuropathic pain, and constipation. The most frequent impacts were in the work/school limitations domain for both treated and treatment-naïve patients. The impacts with the highest difficulty ratings were stress, limited outdoor activity, and guilt. Cognitive interviews with 14 treated and treatment-naïve patients resulted in the refinement of FD-PRO items and language.

Conclusions
The FD-PRO is a novel, disease-specific instrument that measures the patient experience in Fabry disease. Such tools are valuable in capturing the burden of disease in patients with FD and demonstrating the value of treatment in clinical trials.
A proteomic network approach resolves stage-specific molecular phenotypes in chronic traumatic encephalopathy
Authors: Gutierrez-Quiceno Laura , Dammer Eric B. , Johnson Ashlyn Grace , Webster James A. , Shah Rhythm , Duong Duc , Yin Luming , Seyfried Nicholas T. , Alvarez Victor E. , Stein Thor D. , McKee Ann C. , Hales Chadwick M. 
Published: June 2021

Abstract
Background
There is an association between repetitive head injury (RHI) and a pathologic diagnosis of chronic traumatic encephalopathy (CTE) characterized by the aggregation of proteins including tau. The underlying molecular events that cause these abnormal protein accumulations remain unclear. Here, we hypothesized that identifying the human brain proteome from serial CTE stages (CTE I-IV) would provide critical new insights into CTE pathogenesis. Brain samples from frontotemporal lobar degeneration due to microtubule associated protein tau (FTLD-MAPT) mutations were also included as a distinct tauopathy phenotype for comparison.

Methods
Isobaric tandem mass tagged labeling and mass spectrometry (TMT-MS) followed by integrated differential and co-expression analysis (i.e., weighted gene co-expression network analysis (WGCNA)) was used to define modules of highly correlated proteins associated with clinical and pathological phenotypes in control (n = 23), CTE (n = 43), and FTLD-MAPT (n = 12) post-mortem cortical tissues. We also compared these findings to network analysis of AD brain.

Results
We identified over 6000 unique proteins across all four CTE stages which sorted into 28 WGCNA modules. Consistent with Alzheimer’s disease, specific modules demonstrated reduced neuronal protein levels, suggesting a neurodegeneration phenotype, while other modules were increased, including proteins associated with inflammation and glial cell proliferation. Notably, unique CTE-specific modules demonstrated prominent enrichment of immunoglobulins, including IGHM and IGLL5, and extracellular matrix (ECM) proteins as well as progressive protein changes with increasing CTE pathologic stage. Finally, aggregate cell subtype (i.e., neurons, microglia, astrocytes) protein abundance levels in CTE cases were similar in expression to AD, but at intermediate levels between controls and the more exaggerated phenotype of FTLD-MAPT, especially in astrocytes.

Conclusions
Overall, we identified thousands of protein changes in CTE postmortem brain and demonstrated that CTE has a pattern of neurodegeneration in neuronal-synaptic and inflammation modules similar to AD. We also identified unique CTE progressive changes, including the enrichment of immunoglobulins and ECM proteins even in early CTE stages. Early and sustained changes in astrocyte modules were also observed. Overall, the prominent overlap with FTLD-MAPT cases confirmed that CTE is on the tauopathy continuum and identified CTE stage specific molecular phenotypes that provide novel insights into disease pathogenesis.
The development of lived experience-centered word clouds to support research uncertainty gathering in degenerative cervical myelopathy: results from an engagement process and protocol for their evaluation, via a nested randomized controlled trial
Authors: Davies Benjamin M. , Mowforth Oliver D. , Khan Danyal Z. , Yang Xiaoyu , Stacpoole Sybil R. L. , Hazenbiller Olesja , Gronlund Toto , Tetreault Lindsay , Kalsi-Ryan Sukhvinder , Starkey Michelle L. , Sadler Iwan , Sarewitz Ellen , Houlton Delphine , Carter Julia , Howard Evangeline , Rahimi-Movaghar Vafa , Guest James D. , Aarabi Bizhan , Kwon Brian K. , Kurpad Shekar N. , Harrop James , Wilson Jefferson R. , Grossman Robert , Smith Emma K. , McNair Angus G.K. , Fehlings Michael G. , Kotter Mark R. N. 
Published: June 2021

Abstract
Objectives
AO Spine REsearch objectives and Common Data Elements for Degenerative Cervical Myelopathy [RECODE-DCM] is a multi-stakeholder consensus process aiming to promote research efficiency in DCM. It aims to establish the top 10 research uncertainties, through a James Lind Alliance Priority Setting Partnership [PSP]. Through a consensus process, research questions are generated and ranked. The inclusion of people with cervical myelopathy [PwCM] is central to the process. We hypothesized that presenting PwCM experience through word cloud generation would stimulate other key stakeholders to generate research questions better aligned with PwCM needs. This protocol outlines our plans to evaluate this as a nested methodological study within our PSP.

Methods
An online poll asked PwCM to submit and vote on words associated with aspects of DCM. After review, a refined word list was re-polled for voting and word submission. Word clouds were generated and an implementation plan for AO Spine RECODE-DCM PSP surveys was subsequently developed.

Results
Seventy-nine terms were submitted after the first poll. Eighty-seven refined words were then re-polled (which added a further 39 words). Four word clouds were generated under the categories of diagnosis, management, long-term effects, and other. A 1:1 block randomization protocol to assess word cloud impact on the number and relevance of PSP research questions was generated.

Conclusions
We have shown it is feasible to work with PwCM to generate a tool for the AO Spine RECODE-DCM nested methodological study. Once the survey stage is completed, we will be able to evaluate the impact of the word clouds. Further research will be needed to assess the value of any impact in terms of stimulating a more creative research agenda.
SCAPP: an algorithm for improved plasmid assembly in metagenomes
Authors: Pellow David , Zorea Alvah , Probst Maraike , Furman Ori , Segal Arik , Mizrahi Itzhak , Shamir Ron 
Published: June 2021

AbstractBackgroundMetagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples.ResultsWe developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids.We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets.ConclusionsSCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from:https://github.com/Shamir-Lab/SCAPP.
Depletion of acetate-producing bacteria from the gut microbiota facilitates cognitive impairment through the gut-brain neural mechanism in diabetic mice
Authors: Zheng Hong , Xu Pengtao , Jiang Qiaoying , Xu Qingqing , Zheng Yafei , Yan Junjie , Ji Hui , Ning Jie , Zhang Xi , Li Chen , Zhang Limin , Li Yuping , Li Xiaokun , Song Weihong , Gao Hongchang 
Published: June 2021

AbstractBackgroundModification of the gut microbiota has been reported to reduce the incidence of type 1 diabetes mellitus (T1D). We hypothesized that the gut microbiota shifts might also have an effect on cognitive functions in T1D. Herein we used a non-absorbable antibiotic vancomycin to modify the gut microbiota in streptozotocin (STZ)-induced T1D mice and studied the impact of microbial changes on cognitive performances in T1D mice and its potential gut-brain neural mechanism.ResultsWe found that vancomycin exposure disrupted the gut microbiome, altered host metabolic phenotypes, and facilitated cognitive impairment in T1D mice. Long-term acetate deficiency due to depletion of acetate-producing bacteria resulted in the reduction of synaptophysin (SYP) in the hippocampus as well as learning and memory impairments. Exogenous acetate supplement or fecal microbiota transplant recovered hippocampal SYP level in vancomycin-treated T1D mice, and this effect was attenuated by vagal inhibition or vagotomy.ConclusionsOur results demonstrate the protective role of microbiota metabolite acetate in cognitive functions and suggest long-term acetate deficiency as a risk factor of cognitive decline.
Prevalence of intestinal schistosomiasis in pre-school aged children: a pilot survey in Marolambo District, Madagascar
Authors: Sheehy Caitlin , Lawson Heather , Andriamasy Emmanuel H. , Russell Hannah J. , Reid Alice , Raderalazasoa Gina U. , Dodge Graham , Kornitschky Robbie , Penney James M. StJ. , Ranaivoson Tahiry N. , Andrianiaina Antsa , Emmanoela Jenny S. , Bustinduy Amaya L. , Stothard J. Russell , Andrianjaka Louis , Spencer Stephen A. 
Published: June 2021

AbstractSchool-aged children (SAC) have a considerable burden of intestinal schistosomiasis in Madagascar yet its burden in pre-school aged children (PSAC) is currently overlooked. To assess the at-risk status of PSAC, we undertook a pilot epidemiological survey in June 2019 examining children (n = 89), aged 2–4-years of balanced gender, in six remote villages in Marolambo District, Madagascar. Diagnosis included use of urine-circulating cathodic antigen (CCA) dipsticks and coproscopy of stool with duplicate Kato-Katz (K-K) thick smears. Prevalence of intestinal schistosomiasis by urine-CCA was 67.4% (95% confidence interval [CI]: 56.5–77.2%) and 35.0% (95% CI: 24.7–46.5%) by K-K. The relationship between faecal eggs per gram (epg) and urine-CCA G-scores (G1 to G10) was assessed by linear regression modelling, finding for every increment in G-score, epg increased by 20.4 (6.50–34.4, P = 0.006). Observed proportions of faecal epg intensities were light (78.6%), moderate (17.9%) and heavy (3.6%). Soil-transmitted helminthiasis was noted, prevalence of ascariasis was 18.8% and trichuriasis was 33.8% (hookworm was not reported). Co-infection of intestinal schistosomiasis and soil-transmitted helminthiasis occurred in 36.3% of PSAC. These results provide solid evidence highlighting the overlooked burden of intestinal schistosomiasis in PSAC, and they also offer technical guidance for better surveillance data for the Madagascan national control programme.
STEAM in education: a bibliometric analysis of performance and co-words in Web of Science
Authors: Marín-Marín José-Antonio , Moreno-Guerrero Antonio-José , Dúo-Terrón Pablo , López-Belmonte Jesús 
Published: June 2021

Abstract
Background
Emerging methodologies that apply and integrate science, technology, engineering, art, and math (STEAM) in education have appeared in recent years as a pedagogical alternative providing more holistic and attractive education.

Method
The research methodology used in this work is of a bibliometric nature. Specifically, an academic performance analysis and a co-word analysis has been carried out. The term STEAM was analyzed in the Web of Science (WoS) database. The WoS programs Analyze Results, Creation Citation Report, and SciMAT were used. A total of 1116 manuscripts were analyzed.

Results
The results show that studies in the field education of STEAM began in 2006 and have continued uninterruptedly up to the present day, although interest generated in the scientific community has been irregular.

Conclusions
It can be concluded that STEAM studies have not had an established and robust line of research over time, although it can be observed that the trends in this aspect are focused on the scientific branch of education. In addition, the topics of study on STEAM include points related to gender differences, the influence of STEAM on people of different races, the skills developed by students, and training teachers to implement teaching and learning processes with STEAM.
Amelioration of hemodialysis-induced oxidative stress and fatigue with a hemodialysis system employing electrolyzed water containing molecular hydrogen
Authors: Satta Hidehisa , Iwamoto Tamio , Kawai Yuki , Koguchi Naoaki , Shibata Kazuhiko , Kobayashi Nobuteru , Yoshida Mariko , Nakayama Masaaki 
Published: June 2021

Abstract
Background
A novel hemodialysis (HD) system employing electrolyzed water containing molecular hydrogen (E-HD) has been developed to improve the bio-compatibility of HD. This study examined the impact of E-HD on changes in redox state during HD and HD-related fatigue.

Method
This single-arm, prospective observational study examined 63 patients on chronic HD (41 males; mean age, 72 ± 9 years; median duration of HD, 7 years). Redox parameters (serum myeloperoxidase [MPO], malondialdehyde-protein adduct [MDA-a], thioredoxin 1 [TRX]) during HD were compared between control HD (C-HD) and E-HD after 8 weeks. Fatigue was evaluated using a numerical rating scale (NRS) during the 8-week course.

Results
In C-HD, an increase in serum MPO accompanied increases in both oxidative products (MDA-a) and anti-oxidant molecules (TRX). In E-HD, although increases in MPO were accentuated during HD, changes in MDA-a and TRX were ameliorated as compared with C-HD. In patients who showed HD-related fatigue (47%) during C-HD, change in MDA-a by HD was a risk factor for the presence of fatigue. During the 8 weeks of observation on E-HD, those patients displayed significant decreases in fatigue scores.

Conclusion
E-HD ameliorates oxidative stress and supports anti-oxidation during HD, suggesting improved bio-compatibility of the HD system. E-HD may benefit patients with HD-related fatigue, but the mechanisms underlying changes to oxidative stress have yet to be clarified.