bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthetic amyloid beta does not induce a robust transcriptional response in innate immune cell culture systems
Authors: Quiroga I. Y. , Cruikshank A. E. , Bond M. L. , Reed K. S. M. , Evangelista B. A. , Tseng J. H. , Ragusa J. V. , Meeker R. B. , Won H. , Cohen S. , Cohen T. J. , Phanstiel D. H. 
Published: April 2022

Abstract
Background
Alzheimer’s disease (AD) is a progressive neurodegenerative disease that impacts nearly 400 million people worldwide. The accumulation of amyloid beta (Aβ) in the brain has historically been associated with AD, and recent evidence suggests that neuroinflammation plays a central role in its origin and progression. These observations have given rise to the theory that Aβ is the primary trigger of AD, and induces proinflammatory activation of immune brain cells (i.e., microglia), which culminates in neuronal damage and cognitive decline. To test this hypothesis, many in vitro systems have been established to study Aβ-mediated activation of innate immune cells. Nevertheless, the transcriptional resemblance of these models to the microglia in the AD brain has never been comprehensively studied on a genome-wide scale.

Methods
We used bulk RNA-seq to assess the transcriptional differences between in vitro cell types used to model neuroinflammation in AD, including several established, primary and iPSC-derived immune cell lines (macrophages, microglia and astrocytes) and their similarities to primary cells in the AD brain. We then analyzed the transcriptional response of these innate immune cells to synthetic Aβ or LPS and INFγ.

Results
We found that human induced pluripotent stem cell (hIPSC)-derived microglia (IMGL) are the in vitro cell model that best resembles primary microglia. Surprisingly, synthetic Aβ does not trigger a robust transcriptional response in any of the cellular models analyzed, despite testing a wide variety of Aβ formulations, concentrations, and treatment conditions. Finally, we found that bacterial LPS and INFγ activate microglia and induce transcriptional changes that resemble many, but not all, aspects of the transcriptomic profiles of disease associated microglia (DAM) present in the AD brain.

Conclusions
These results suggest that synthetic Aβ treatment of innate immune cell cultures does not recapitulate transcriptional profiles observed in microglia from AD brains. In contrast, treating IMGL with LPS and INFγ induces transcriptional changes similar to those observed in microglia detected in AD brains.
The research output of rod-cone dystrophy genetics
Authors: Jaffal Lama , Mrad Zamzam , Ibrahim Mariam , Salami Ali , Audo Isabelle , Zeitz Christina , El Shamieh Said 
Published: April 2022

AbstractNon-syndromic rod-cone dystrophy (RCD) is the most common condition in inherited retinal diseases. The aim of this study was to evaluate the research output and productivity related to RCD genetics per countries as classified by the human development index (HDI), by analyzing publication frequency and citations, the choice of journals and publishers, since 2000 to date. We have also analyzed the use of next-generation sequencing (NGS) in publications originating from countries with different HDIs. One thousand four hundred articles focusing on non-syndromic RCD were downloaded and analyzed. Citations and published articles were adjusted per one million individuals. The research output is significantly higher in very high HDI countries (86% of the total publications and 95% of the citations) than countries with lower HDIs in all aspects. High and medium HDI countries published together 13.6% of the total articles worldwide and received 4.6% of the citations. On the publication level, the USA (26%), United Kingdom (10%), and Japan (7%) were the top 3 among very high HDI countries, while China (6%) and India (2%) ranked first in high and medium HDI countries respectively. On the citation level, similar profiles were found. Following adjustment for population size, Switzerland (~14%), Jordan (~ 1%) and Morocco (<0.2%) showed the highest rates of publications in very high, high and medium HDI countries respectively. Very high HDI countries published 71% of their papers in first quartile journals (first quartile in Scimago journal rank; Q1), and 23% in Q2 journals. High and medium HDI countries showed a similar profile in quartiles with ~ 40% of their papers published in Q1 journals and ~ 30% in Q2 journals. The first publication using NGS was issued in 2009 in very high HDI countries, while it appeared in 2012 in high HDI countries, and in 2017 in medium HDI countries, with a respective lag of 3 to 8 years compared to very high HDI countries. A profound gap exists between very high HDI countries and the rest of the world. To fill it in, we propose implementing NGS, supporting international collaborations, building capacities and infrastructures, improving accessibility of patients to services, and increasing national and international funding.
Clinical overview and outcome of the Stuve-Wiedemann syndrome: a systematic review
Authors: Warnier Hélène , Barrea Christophe , Bethlen Sarah , Schrouff Isabelle , Harvengt Julie 
Published: April 2022

Abstract
Background
Stuve-Wiedemann syndrome (SWS) is a rare and severe genetic disease characterized by skeletal anomalies and dysautonomic disturbances requiring appropriate care. Peer support is mandatory to fill the lack of clinical recommendations in such rare diseases. We report a new case and provide the first systematic review of all previous published cases.

Objective
To better describe the timeline of SWS and to improve paediatric management.

Data sources
SWS English publications available on Pubmed until 31/03/2021.

Study selection
Case description combining typical osteo-articular and dysautonomic involvement (with 2 items by categories required for children < 2 years and 3 items > 2 years).

Data extraction
Demographic, clinical, genetics and outcome data.

Results
In our cohort of 69 patients, the median age at report was 32 months. Only 46% presented antenatal signs. Mortality rate is higher during the first 2 years (42% < 2 years; 10% > 2 years) mainly due to respiratory failure, pulmonary arterial hypertension appearing to be a poor prognosis factor (mortality rate 63%). After 2 years, orthopaedic symptoms significantly increase including joint mobility restriction (81%), spinal deformations (77%) and fractures (61%).

Conclusions
Natural history of SWS is marked by a high mortality rate before 2 years due to dysautonomic disturbances. A specialized multidisciplinary approach is needed to address these early mortality risks and then adapt to the specific, mainly orthopaedic, needs of patients after 2 years of age. Further research is required to provide clinical guidelines and improve pre-natal counselling.
Development of the Clinical Gestalt Assessment: a visual clinical global impression scale for Proteus syndrome
Authors: Ours Christopher A. , Hodges Mia B. , Oden Neal , Sapp Julie C. , Biesecker Leslie G. 
Published: April 2022

AbstractBackgroundClinical outcome assessments are important tools for measuring the natural history of disease and efficacy of an intervention. The heterogenous phenotype and difficult to quantity features of Proteus syndrome present challenges to measuring clinical outcomes. To address these, we designed a global clinical assessment for Proteus syndrome, a rare mosaic overgrowth disorder. The Clinical Gestalt Assessment (CGA) aims to evaluate change over time in this phenotypically diverse disorder.ResultsWe gathered paired serial photographs and radiographs obtained at 12-to-36-month intervals from our natural history study of Proteus syndrome. The chronologic order of each set was blinded and presented to clinicians familiar with overgrowth disorders. They were asked to determine the chronologic order and, based on that response, rate global clinical change using a seven-point scale (Much Worse, Worse, Minimally Worse, No Change, Minimally Improved, Improved, Much Improved). Following a pilot, we tested the inter-rater reliability of the CGA using eight cases rated by eight clinicians. Raters identified the correct chronologic order in 53 of 64 (83%) of responses. There was low inter-rater variance and poor to moderate reliability with an intraclass correlation coefficient of 0.46 (95% CI 0.24–0.75). The overall estimate of global change was Minimally Worse over time, which is an accurate reflection of the natural history of Proteus syndrome.ConclusionsThe CGA is a tool to evaluate clinical change over time in Proteus syndrome and may be a useful adjunct to measure clinical outcomes in prospective therapeutic trials.
Administration of spruce bark (Picea abies) extracts in young lambs exhibits anticoccidial effects but reduces milk intake and body weight gain
Authors: Blomstrand Berit Marie , Enemark Heidi Larsen , Steinshamn Håvard , Aasen Inga Marie , Johanssen Juni Rosann Engelien , Athanasiadou Spiridoula , Thamsborg Stig Milan , Sørheim Kristin Marie 
Published: April 2022

Abstract
Background
Eimeria spp. are widespread apicomplexan parasites known to cause coccidiosis in livestock, resulting in reduced animal welfare and productivity, particularly in sheep. The treatment options are limited, and there is an emerging development of resistance against registered pharmaceuticals. Spruce bark is rich in plant secondary metabolites (PSM), such as condensed tannins, which are bioactive compounds previously shown to have antiparasitic activity. Here, we examined the anticoccidial properties of bark extract of Norway spruce (Picea abies) against a field isolate of ovine Eimeria spp. by treating Eimeria-infected pre-ruminant lambs with water-extracted bark daily for 12 days. We hypothesised that the bark extract would reduce the faecal oocyst excretion and, consequently, the severity of diarrhoea.

Results
Oral administration of spruce bark extract significantly reduced the excretion of Eimeria oocysts in milk-fed lambs post treatment till the end of the trial 22 days post infection. This difference in oocyst excretion between the treated and the untreated infected animals increased with time.
Compared to the untreated and the sham-infected control group, the group treated with bark extract had softer faeces and reduced milk intake during the treatment period. After discontinuing the treatment, the treated animals got a more solid and formed faeces compared to that of the untreated control group, and the milk intake increased to the level of the sham-infected, untreated control group. The bark extract treated animals had a lower body weight and a lower mean daily body weight gain throughout the whole duration of the experiment.

Conclusions
Bark extract from Norway spruce showed marked anticoccidial properties by reducing the faecal oocyst count and associated diarrhoea in young lambs. Simultaneously we experienced detrimental effects of the treatment, displayed as reduced feed intake and daily body weight gain. Therefore, we suggest conducting similar studies with lower bark extract dosage to explore the possibilities of a better trade-off to reduce the negative impact while maintaining the antiparasitic effect.
Colorectal cancer subtype identification from differential gene expression levels using minimalist deep learning
Authors: Li Shaochuan , Yang Yuning , Wang Xin , Li Jun , Yu Jun , Li Xiangtao , Wong Ka-Chun 
Published: April 2022

AbstractBackgroundCancer molecular subtyping plays a critical role in individualized patient treatment. In previous studies, high-throughput gene expression signature-based methods have been proposed to identify cancer subtypes. Unfortunately, the existing ones suffer from the curse of dimensionality, data sparsity, and computational deficiency.MethodsTo address those problems, we propose a computational framework for colorectal cancer subtyping without any exploitation in model complexity and generality. A supervised learning framework based on deep learning (DeepCSD) is proposed to identify cancer subtypes. Specifically, based on the differentially expressed genes under cancer consensus molecular subtyping, we design a minimalist feed-forward neural network to capture the distinct molecular features in different cancer subtypes. To mitigate the overfitting phenomenon of deep learning as much as possible,L1andL2regularization and dropout layers are added.ResultsFor demonstrating the effectiveness of DeepCSD, we compared it with other methods including Random Forest (RF), Deep forest (gcForest), support vector machine (SVM), XGBoost, and DeepCC on eight independent colorectal cancer datasets. The results reflect that DeepCSD can achieve superior performance over other algorithms. In addition, gene ontology enrichment and pathology analysis are conducted to reveal novel insights into the cancer subtype identification and characterization mechanisms.ConclusionsDeepCSD considers all subtype-specific genes as input, which is pathologically necessary for its completeness. At the same time, DeepCSD shows remarkable robustness in handling cross-platform gene expression data, achieving similar performance on both training and test data without significant model overfitting or exploitation of model complexity.
M2HepPrEP: study protocol for a multi-site multi-setting randomized controlled trial of integrated HIV prevention and HCV care for PWID
Authors: Martel-Laferrière Valérie , Feaster Daniel J. , Metsch Lisa R. , Schackman Bruce R. , Loignon Christine , Nosyk Bohdan , Tookes Hansel , Behrends Czarina N. , Arruda Nelson , Adigun Oluleye , Goyer Marie-Eve , Kolber Michael A. , Mary Jean-Francois , Rodriguez Allan E. , Yanez Iveth G. , Pan Yue , Khemiri Rania , Gooden Lauren , Sako Aïssata , Bruneau Julie 
Published: April 2022

Abstract
Background
Opioid use is escalating in North America and comes with a multitude of health consequences, including HIV and hepatitis C virus (HCV) outbreaks among persons who inject drugs (PWID). HIV pre-exposure prophylaxis (PrEP) and HCV treatment regimens have transformative potential to address these co-occurring epidemics. Evaluation of innovative multi-modal approaches, integrating harm reduction, opioid agonist therapy (OAT), PrEP, and HCV treatment is required. The aim of this study is to assess the effectiveness of an on-site integrated care model where delivery of PrEP and HCV treatment for PWID takes places at syringe service programs (SSP) and OAT programs compared with referring PWID to clinical services in the community through a patient navigation model and to examine how structural factors interact with HIV prevention adherence and HCV treatment outcomes.

Methods
The Miami-Montreal Hepatitis C and Pre-Exposure Prophylaxis trial (M2HepPrEP) is an open-label, multi-site, multi-center, randomized, controlled, superiority trial with two parallel treatment arms. A total of 500 persons who injected drugs in the prior 6 months and are eligible for PrEP will be recruited in OAT clinics and SSP in Miami, FL, and Montréal, Québec. Participants will be randomized to either on-site care, with adherence counseling, or referral to off-site clinics assisted by a patient navigator. PrEP will be offered to all participants and HCV treatment to those HCV-infected. Co-primary endpoints will be (1) adherence to pre-exposure prophylaxis medication at 6 months post-randomization and (2) HCV sustained virological response (SVR) 12 weeks post-treatment completion among participants who were randomized within the HCV stratum. Up to 100 participants will be invited to participate in a semi-structured interview regarding perceptions of adherence barriers and facilitators, after their 6-month assessment. A simulation model-based cost-effectiveness analysis will be performed to determine the comparative value of the strategies being evaluated.

Discussion
The results of this study have the potential to demonstrate the effectiveness and cost-effectiveness of offering PrEP and HCV treatment in healthcare venues frequently attended by PWID. Testing the intervention in two urban centers with high disease burden among PWID, but with different healthcare system dynamics, will increase generalizability of findings.

Trial registration
Clinicaltrials.gov NCT03981445. Trial registry name: Integrated HIV Prevention and HCV Care for PWID (M2HepPrEP). Registration date: June 10, 201.
Developing a theoretically informed education programme within the context of a complex implementation strategy in UK primary care: an exemplar from the IMP2ART trial
Authors: McClatchey Kirstie , Marsh Viv , Steed Liz , Holmes Steve , Taylor Stephanie J. C. , Wiener-Ogilvie Sharon , Neal Julia , Last Rhian , Saxon Ann , Pinnock Hilary ,   for the IMP2ART Programme Group
Published: April 2022

Abstract
Background
IMPlementing IMProved Asthma self-management as RouTine (IMP2ART) is a programme of work developing and evaluating a strategy for implementing supported asthma self-management in UK primary care. The strategy encompasses patient-facing resources, professional education, and organisational approaches to embed supported self-management. This paper reports the development of a theoretically informed interprofessional education programme which aims to raise awareness of and enable healthcare professionals to deliver effective supported self-management.

Methods
Aligned with the Medical Research Council (MRC) Complex Intervention Framework, the multidisciplinary team developed educational content in three phases: (1) developmental phase, identifying educational and behaviour change theory to guide development, in consultation with a professional advisory group; (2) feasibility pilot phase, testing the education using a ‘think-aloud’ method; and (3) pre-pilot phase, delivering the education within the IMP2ART strategy.

Results
The developmental phase identified educational and behaviour change theory and the need to provide two education modules: (1) a team module to raise awareness of supported asthma self-management for the whole team and (2) an individual study module for those who conduct asthma reviews with patients. The feasibility pilot highlighted content and design features in need of refinement and the pre-pilot identified substantial changes to the delivery strategy for the education modules.

Conclusions
A multi-stage development process, aligned with the MRC Framework, contributed to the module design and delivery. Prior explorative work, multi-disciplinary team discussions, and professional advisory group consultation, informed the initial development, and in-practice testing and pre-pilot stages enabled refinement. In our experience, there were important benefits of working together as an educationalist/researcher team. The education programme, a core component of the implementation strategy, is now being tested in the IMP2ART UK-wide cluster randomised controlled trial.
Effects of Jianpi Lishi Jiedu granules on colorectal adenoma patients after endoscopic treatment: study protocol for a randomized, double-blinded, placebo-controlled clinical trial
Authors: Wu Hao , Huang Yuzhen , Yang Lu , Su Kunhan , Tian Shuo , Chen Xin , Li Siyu , Liu Wanli 
Published: April 2022

Abstract
Background
Colorectal adenomas (CRAs) are precancerous lesions of the large intestine presenting as colorectal polyps. At present, the conventional treatment methods for CRA mainly include high-frequency electrocoagulation and electroexcision, biopsy forceps polypectomy, cauterization by laser and microwave, and other endoscopic interventions. The principal advantages conferred by these treatment strategies include less trauma, quick postoperative recovery, and simplicity to perform. However, the higher recurrence rates and insignificant improvement of postoperative symptoms after endoscopic surgery are considerable drawbacks to this approach. Besides, there is currently no effective pharmacotherapy to prevent the recurrence of CRA. Jianpi Lishi Jiedu (JLJ) granules are a form of traditional Chinese medicine (TCM) used to manage postoperative patients with CRA, which has shown a certain degree of efficacy in clinical practice. However, its effectiveness and safety profile have not been convincingly evaluated. The purpose of this study is to evaluate the clinical efficacy and safety profile of JLJ granules in the management of postoperative patients with CRA and to observe the recurrence rate of adenoma in these patients.

Methods
A randomized, double-blind, and placebo-controlled clinical trial is performed in this study. A total of 80 postoperative patients with CRA will be randomly classified into the Jianpi Lishi Jiedu granules group or the placebo control group. Patients in both groups shall receive 3 months of intervention, after which medical follow-up and safety evaluation will be performed for all of the patients. The primary outcome is the recurrence rate of adenomas within 12 months. The secondary outcomes are the cardinal TCM symptom scores, minor TCM symptom scores, Bristol Stool Scale, efficacy of TCM symptoms, safety indicators, and blinding assessment.

Discussion
In this study, the impact on the recurrence of adenomas and the efficacy and safety of JLJ granules in terms of improving the clinical symptoms of postoperative patients with CRA will be evaluated.

Trial registration
Trial registration Chinese Clinical Trial Registry ChiCTR 2100044297. Registered on March 16, 2021
Efficacy and safety of scopolamine compared to placebo in individuals with bipolar disorder who are experiencing a depressive episode (SCOPE-BD): study protocol for a randomised double-blind placebo-controlled trial
Authors: Miravalles Cerena , Kane Ruán , McMahon Eimear , McDonald Colm , Cannon Dara M. , Hallahan Brian 
Published: April 2022

Abstract
Background
Current treatment options for the management of depressive episodes in bipolar disorder are often sub-optimal, with some treatments either noted to be only partially effective or to require long durations of treatment prior to a therapeutic response. Therefore, pharmaco-therapeutic options that reduce depressive symptoms in a more rapid manner might provide a viable therapeutic option for some people. Intravenous (IV) scopolamine, a pan muscarinic antagonist, has been demonstrated in a number of studies to confer a rapid antidepressant effect, albeit no study to date has exclusively evaluated its potential therapeutic effect in a cohort consisting solely of individuals with bipolar disorder.

Methods
Individuals with bipolar disorder who are currently experiencing a depressive episode of at least moderate severity will be included in this study. Eligible participants will undergo a screening and placebo-run in visit and will be randomised at visit 3 to the treatment or placebo group. Participants will receive the three blinded infusions over the course of 2 weeks, with two subsequent follow-up visits, 1 and 3 weeks after the last infusion visit. The total duration of the study will be approximately 6 weeks. Patients will continue their regular treatment regime in addition to study medication. Objective and subjective mood questionnaires, cognitive assessments and other psychometric instruments will be administered and recorded.

Discussion
To our knowledge, this is the first study to investigate the antidepressant effects of IV scopolamine in an exclusively bipolar disorder cohort. Trial findings will contribute to the evidence base regarding the cholinergic hypothesis of mood disorders and specifically might result in an additional safe therapeutic option for the management of depressive episodes in bipolar disorder.

Trial registration
ClinicalTrials.gov NCT04211961. December 26, 2019. EudraCT Number 2017-003112-39