bluuebunny/crossref_metadata_2025_split huggingface dataset:
An anti-inflammatory diet intervention for knee osteoarthritis: a feasibility study
Authors: Cooper Indiana , Brukner Peter , Devlin Brooke L. , Reddy Anjana J. , Fulton Melanie , Kemp Joanne L. , Culvenor Adam G. 
Published: January 2022

Abstract
Background
Knee osteoarthritis has an inflammatory component that is linked to pain and joint pathology, yet common non-surgical and non-pharmacological interventions (e.g., exercise, calorie restricting diets) do not typically target inflammation. We aimed to evaluate the feasibility of a telehealth delivered anti-inflammatory diet intervention for knee osteoarthritis.

Methods
This 9-week single-arm feasibility study recruited participants aged 40–85 years with symptomatic knee osteoarthritis (inclusion criteria: average pain ≥4/10 or maximal pain ≥5/10 during past week). All participants received a telehealth-delivered anti-inflammatory dietary education intervention involving 1:1 consultations at baseline, 3- and 6-week follow-up. The diet emphasised nutrient-dense wholefoods and minimally processed anti-inflammatory foods and discouraged processed foods considered to be pro-inflammatory. The primary outcome of feasibility was assessed via: i) eligibility, recruitment and retention rates; ii) self-reported dietary adherence; iii) adverse events; and iv) treatment satisfaction. Post-intervention interviews evaluated the acceptability of the dietary intervention delivered via telehealth. Secondary outcomes included changes in self-reported body mass, Knee injury and Osteoarthritis Outcome Score (KOOS), health-related quality of life (EuroQoL-5D), analgesic use and global rating of change. Worthwhile effects were determined by the minimal detectable change (MDC) for all five KOOS-subscales (pain, symptoms, activities of daily living, sport/recreation, quality of life) being contained within the 95% confidence interval.

Results
Forty-eight of seventy-three (66%) individuals screened were eligible and 28 enrolled over 2 months (82% female, mean age 66 ± 8 years, body mass index 30.7 ± 4.8 kg.m−2). Six participants withdrew prior to final follow-up (21% drop-out). Of those with final follow-up data, attendance at scheduled telehealth consultations was 99%. Self-reported adherence to diet during the 9-week intervention period: everyday = 27%, most of time = 68% and some of time = 5%. Two minor adverse events were reported. Change scores contained the MDC within the 95% confidence interval for all five KOOS subscales. Suggestions to improve study design and limit drop-out included an initial face-to-face consultation and more comprehensive habitual dietary intake data collection.

Conclusion
This study supports the feasibility of a full-scale randomised controlled trial to determine the efficacy of a primarily telehealth-delivered anti-inflammatory dietary education intervention in adults with symptomatic knee osteoarthritis.

Trial registration
ACTRN12620000229976 prospectively on 25/2/2020.
The effect of Kappaphycus alvarezii active fraction on oxidative stress and inflammation in streptozotocin and nicotinamide-induced diabetic rats
Authors: Yulianti Evy , Sunarti  , Wahyuningsih Mae Sri Hartati 
Published: January 2022

Abstract
Background
High glucose concentration increases the glycation process which leads to oxidative stress and inflammation, that can cause complications in diabetes. Several medicinal plants have been used in the treatment of diabetes and its complications. One of them is Kappaphycus alvarezii, an algae that has known antidiabetic abilities. This study aimed to examine the effect of K. alvarezii active fraction on plasma hydrogen peroxide (H2O2) and Tumor Necrosis Factor α (TNFα) levels, renal NADPH oxidase 4 (NOX4) and Nuclear Factor κ B (NFκB) gene expressions.

Methods
Active fraction was obtained from bioassay-guided fractionation with antiglycation ability. In vivo study was performed on twenty Wistar male rats. The level of H2O2 was measured using H2O2 Assay Kit, the Optical Density value measured using spectrophotometer at a wavelength of 405 nm. Plasma TNFα level was measured using ELISA. Renal NOX4 and NFκB gene expression was analyzed using qPCR.

Results
Active fraction significantly reduced plasma H2O2 but not TNFα levels. Furthermore, renal NOX4 gene expression was lower in the diabetic rat group treated with active fraction compared to the untreated group but not NFκB gene expression.

Conclusions
K. alvarezii active fraction has an activity to reduce plasma H2O2 as well as renal NOX4 gene expression. Therefore, this fraction could be developed as a potential candidate for diabetes treatment through oxidative stress mechanisms.
Student usage of open educational resources and social media at a Sri Lanka Medical School
Authors: Hettige Samankumara , Dasanayaka Eshani , Ediriweera Dileepa Senajith 
Published: January 2022

Abstract
Background
The use of Open Educational Resources (OER) and Social Media (SM) for academic information seeking is common among undergraduates nowadays. There is limited data on OER and SM use for education in Sri Lanka. This study was aimed at evaluating the OER and SM use for education among the medical students at the Faculty of Medicine, University of Kelaniya, Sri Lanka.

Methods
A cross-sectional study was conducted at the Faculty of Medicine, University of Kelaniya. Stratified random sampling was used to select students from the first year to the final year. A self-administrated questionnaire was used to collect data.

Results
The study included 257 responses (response rate: 89.5%), of which 185 (72.0%) were females. The OER and SM use for educational purposes at least once a month among students was 96.1% (95%CI: 93.7–98.5%) and 88.3% (95%CI: 84.4–92.3%) respectively. There was no gender difference in OER and SM use. The main reasons for accessing OER were the availability of information at any time (36.1%) and ease of information access (31.5%). Wiki sites (84.4%) and Facebook (79.8%) were the highest accessed OER and SM platforms. The majority of students were in view that the information on wiki sites (51.4%) and results of general non-specific web searches (56.0%) were reliable. Only 33.9% of students searched information from educational and government-related sources and 18.7% had accessed e-journals. Through SM, 79.0% joined educational groups and 77.0% followed the medical-related sites, pages and people. More than one-third of students (35.8%) could not find academic information from SM due to the information overload and 31.1% mentioned that SM distracted their education.

Conclusion
The majority of the students used OER and SM for education; however, only a minority accessed reliable information. Students accepted information available in wiki sites and general non-specific web searchers without considering the credibility of sources. The majority of the students did not refer to e-journals. Distractions to academic work and the difficulty to access accurate information were major concerns of using SM. This study highlights the importance of improving information literacy among medical students.
Cost-savings and potential cost-savings through the distribution of generic antiretroviral drugs within the statutory health insurance market of Germany between January 2017 and June 2019
Authors: Lottes Matthäus , Bremer Viviane , Prugger Christof , Kollan Christian , Schmidt Daniel 
Published: January 2022

Abstract

Background
Recent patent losses for antiretroviral drugs (ARV) have led to the debate of cost-saving through the replacement of patented drugs with generic drugs. The split of recommended single-tablet regimens (STR) into their single substance partners is one of the considerations mentioned in said debate. Particularly, generic tenofovir disoproxil/emtricitabine (TDF/FTC) is expected to hold untapped cost-saving potential, which may curb increasing overall expenditures for combined antiretroviral therapy (cART) within the statutory health insurance (SHI) of Germany.

Methods
Data of ARV reimbursed by the SHI were used to describe the trends of defined daily doses (DDD) as well as the revenue within the German ARV market. They were also used to determine the cost-savings of moving to generic drugs. The time period observed was between January 2017 and June 2019. The potential cost-savings were determined with following assumption in mind: the maximum possible use of generic ARV, including 1) the split of STR and replacing all substance partners with generic ones, and 2) replacing patented tenofovir alafenamide/emtricitabine (TAF/FTC) with generic TDF/FTC.

Results
Throughout the observation period, the DDD of generic ARV increased nearly five-fold while their revenue increased more than four-fold. Total cost-saving showed a sharp increase over the same period, with generic TDF/FTC accounting for a share of around 70%. The largest potential cost-saving could have been achieved through replacing patented TAF/FTC with generic TDF/FTC, peaking at nearly 10% of total revenue, but showing decreasing trends in general.

Conclusion
The progressive distribution of generic ARV ensured increasing cost-savings, but consequently curbed the potential cost-savings. Unique price reductions of generic TDF/FTC have played a pivotal role for these effects. In any case, substituting with generic ARV should not fail to adhere to the treatment guidelines and continue to consider the medical requirements for the treatment.
Conventional laboratory housing increases morbidity and mortality in research rodents: results of a meta-analysis
Authors: Cait Jessica , Cait Alissa , Scott R. Wilder , Winder Charlotte B. , Mason Georgia J. 
Published: January 2022

AbstractBackgroundOver 120 million mice and rats are used annually in research, conventionally housed in shoebox-sized cages that restrict natural behaviours (e.g. nesting and burrowing). This can reduce physical fitness, impair thermoregulation and reduce welfare (e.g. inducing abnormal stereotypic behaviours). In humans, chronic stress has biological costs, increasing disease risks and potentially shortening life. Using a pre-registered protocol (https://atrium.lib.uoguelph.ca/xmlui/handle/10214/17955), this meta-analysis therefore tested the hypothesis that, compared to rodents in ‘enriched’ housing that better meets their needs, conventional housing increases stress-related morbidity and all-cause mortality.ResultsComprehensive searches (via Ovid, CABI, Web of Science, Proquest and SCOPUS on May 24 2020) yielded 10,094 publications. Screening for inclusion criteria (published in English, using mice or rats and providing ‘enrichments’ in long-term housing) yielded 214 studies (within 165 articles, using 6495 animals: 59.1% mice; 68.2% male; 31.8% isolation-housed), and data on all-cause mortality plus five experimentally induced stress-sensitive diseases: anxiety, cancer, cardiovascular disease, depression and stroke. The Systematic Review Center for Laboratory animal Experimentation (SYRCLE) tool assessed individual studies’ risks of bias. Random-effects meta-analyses supported the hypothesis: conventional housing significantly exacerbated disease severity with medium to large effect sizes: cancer (SMD = 0.71, 95% CI = 0.54–0.88); cardiovascular disease (SMD = 0.72, 95% CI = 0.35–1.09); stroke (SMD = 0.87, 95% CI = 0.59–1.15); signs of anxiety (SMD = 0.91, 95% CI = 0.56–1.25); signs of depression (SMD = 1.24, 95% CI = 0.98–1.49). It also increased mortality rates (hazard ratio = 1.48, 95% CI = 1.25–1.74; relative median survival = 0.91, 95% CI = 0.89–0.94). Meta-regressions indicated that such housing effects were ubiquitous across species and sexes, but could not identify the most impactful improvements to conventional housing. Data variability (assessed via coefficient of variation) was also not increased by ‘enriched’ housing.ConclusionsConventional housing appears sufficiently distressing to compromise rodent health, raising ethical concerns. Results also add to previous work to show that research rodents are typically CRAMPED (cold, rotund, abnormal, male-biased, poorly surviving, enclosed and distressed), raising questions about the validity and generalisability of the data they generate. This research was funded by NSERC, Canada.
Modular evolution of secretion systems and virulence plasmids in a bacterial species complex
Authors: Chou Lin , Lin Yu-Chen , Haryono Mindia , Santos Mary Nia M. , Cho Shu-Ting , Weisberg Alexandra J. , Wu Chih-Feng , Chang Jeff H. , Lai Erh-Min , Kuo Chih-Horng 
Published: January 2022

Abstract
Background
Many named species as defined in current bacterial taxonomy correspond to species complexes. Uncertainties regarding the organization of their genetic diversity challenge research efforts. We utilized the Agrobacterium tumefaciens species complex (a.k.a. Agrobacterium biovar 1), a taxon known for its phytopathogenicity and applications in transformation, as a study system and devised strategies for investigating genome diversity and evolution of species complexes.

Results
We utilized 35 genome assemblies, including 14 newly generated ones, to achieve a phylogenetically balanced sampling of A. tumefaciens. Our genomic analysis suggested that the 10 genomospecies described previously are distinct biological species and supported a quantitative guideline for species delineation. Furthermore, our inference of gene content and core-genome phylogeny allowed for investigations of genes critical in fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition and thought to be conserved, we detected multiple losses and one horizontal gene transfer. For the tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion system (T4SS) that are essential for agrobacterial phytopathogenicity, we uncovered novel diversity and hypothesized their involvement in shaping this species complex. Intriguingly, for both T6SS and T4SS, genes encoding structural components are highly conserved, whereas extensive diversity exists for genes encoding effectors and other proteins.

Conclusions
We demonstrate that the combination of a phylogeny-guided sampling scheme and an emphasis on high-quality assemblies provides a cost-effective approach for robust analysis in evolutionary genomics. We show that the T6SS VgrG proteins involved in specific effector binding and delivery can be classified into distinct types based on domain organization. The co-occurrence patterns of VgrG-associated domains and the neighboring genes that encode different chaperones/effectors can be used to infer possible interacting partners. Similarly, the associations between plant host preference and the pTi type among these strains can be used to infer phenotype-genotype correspondence. Our strategies for multi-level investigations at scales that range from whole genomes to intragenic domains and phylogenetic depths from between- to within-species are applicable to other bacteria. Furthermore, modularity observed in the molecular evolution of genes and domains is useful for inferring functional constraints and informing experimental works.
Modelling upper respiratory viral load dynamics of SARS-CoV-2
Authors: Challenger Joseph D. , Foo Cher Y. , Wu Yue , Yan Ada W. C. , Marjaneh Mahdi Moradi , Liew Felicity , Thwaites Ryan S. , Okell Lucy C. , Cunnington Aubrey J. 
Published: January 2022

AbstractRelationships between viral load, severity of illness, and transmissibility of virus are fundamental to understanding pathogenesis and devising better therapeutic and prevention strategies for COVID-19. Here we present within-host modelling of viral load dynamics observed in the upper respiratory tract (URT), drawing upon 2172 serial measurements from 605 subjects, collected from 17 different studies. We developed a mechanistic model to describe viral load dynamics and host response and contrast this with simpler mixed-effects regression analysis of peak viral load and its subsequent decline. We observed wide variation in URT viral load between individuals, over 5 orders of magnitude, at any given point in time since symptom onset. This variation was not explained by age, sex, or severity of illness, and these variables were not associated with the modelled early or late phases of immune-mediated control of viral load. We explored the application of the mechanistic model to identify measured immune responses associated with the control of the viral load. Neutralising antibodies correlated strongly with modelled immune-mediated control of viral load amongst subjects who produced neutralising antibodies. Our models can be used to identify host and viral factors which control URT viral load dynamics, informing future treatment and transmission blocking interventions.
Chicken hepatomegaly and splenomegaly associated with novel subgroup J avian leukosis virus infection
Authors: Xu Moru , Hang Fusen , Qian Kun , Shao Hongxia , Ye Jianqiang , Qin Aijian 
Published: January 2022

Abstract
Background
Subgroup J avian leukosis virus (ALV-J) is an oncovirus which can induce multiple types of tumors in chicken. In this report, we found novel ALV-J infection is closely associated with serious hepatomegaly and splenomegaly in chicken.

Case presentation
The layer chickens from six flocks in Jiangsu province, China, showed serious hemoperitoneum, hepatomegaly and splenomegaly. Histopathological results indicated focal lymphocytic infiltration, cell edema and congestion in the liver, atrophy and depletion of lymphocyte in the spleen. Tumor cells were not detected in all the organs. avian hepatitis E virus (aHEV), which is thought to be the cause of a very similar disease, big liver and spleen disease (BLS), was not detected. Other viruses causing tumors or liver damage including Marek’s disease virus (MDV), reticuloendotheliosis virus (REV), fowl adenovirus (FAdV) and chicken infectious anemia virus (CIAV) were also proved negative by either PCR or RT-PCR. However, we did detect ALV-J in those chickens using PCR. Only novel ALV-J strains were efficiently isolated from these chicken livers.

Conclusions
This is the first report that chicken hepatomegaly and splenomegaly disease was closely associated with novel ALV-J, highlighting the importance of ALV-J eradication program in China.
Enhanced production of ectoine from methane using metabolically engineered Methylomicrobium alcaliphilum 20Z
Authors: Cho Sukhyeong , Lee Yun Seo , Chai Hanyu , Lim Sang Eun , Na Jeong Geol , Lee Jinwon 
Published: January 2022

Abstract
Background
Ectoine (1,3,4,5-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) is an attractive compatible solute because of its wide industrial applications. Previous studies on the microbial production of ectoine have focused on sugar fermentation. Alternatively, methane can be used as an inexpensive and abundant resource for ectoine production by using the halophilic methanotroph, Methylomicrobium alcaliphilum 20Z. However, there are some limitations, including the low production of ectoine from methane and the limited tools for the genetic manipulation of methanotrophs to facilitate their use as industrial strains.

Results
We constructed M. alcaliphilum 20ZDP with a high conjugation efficiency and stability of the episomal plasmid by the removal of its native plasmid. To improve the ectoine production in M. alcaliphilum 20Z from methane, the ectD (encoding ectoine hydroxylase) and ectR (transcription repressor of the ectABC-ask operon) were deleted to reduce the formation of by-products (such as hydroxyectoine) and induce ectoine production. When the double mutant was batch cultured with methane, ectoine production was enhanced 1.6-fold compared to that obtained with M. alcaliphilum 20ZDP (45.58 mg/L vs. 27.26 mg/L) without growth inhibition. Notably, a maximum titer of 142.32 mg/L was reached by the use of an optimized medium for ectoine production containing 6% NaCl and 0.05 μM of tungsten without hydroxyectoine production. This result demonstrates the highest ectoine production from methane to date.

Conclusions
Ectoine production was significantly enhanced by the disruption of the ectD and ectR genes in M. alcaliphilum 20Z under optimized conditions favoring ectoine accumulation. We demonstrated effective genetic engineering in a methanotrophic bacterium, with enhanced production of ectoine from methane as the sole carbon source. This study suggests a potentially transformational path to commercial sugar-based ectoine production.

Graphical Abstract
Six-sigma and quality planning of TORCH tests in the Peruvian population: a single-center cross-sectional study
Authors: Moya-Salazar Jeel , SantaMaria Bianca M. , Moya-Salazar Marcia M. , Rojas-Zumaran Víctor , Chicoma-Flores Karina , Contreras-Pulache Hans 
Published: January 2022

AbstractObjectiveTo ensure the health of newborns, it is necessary to perform high-quality diagnostic tests. The TORCH panel is a set of tests that identifies infectious pathogens such as Toxoplasma (Toxo) and Cytomegalovirus (CMV) that are common in low-setting populations. We performed TORCH panel quality planning using six sigma in a reference laboratory at Peru.ResultsThis was a cross-sectional study. TORCH tests include Toxo, Rubella, CMV, and Herpes. We processed all samples by fourth-generation ELISA on the GEMINI XCR200 analyzer (Diatron, Budapest, Hungary). We obtained the imprecision from the annual data of the external quality assessment plan and we used the CLSI EP12-A3 guideline. In a total of 44,788 analyses, the average imprecision was 3.69 ± 1.47%, and CMV had lower imprecision (2.3 and 2.6% for IgM and IgG, respectively). Quality planning of the TORCH panel allowed estimating the sigma value that ranged from 4 to 10 (average 7 ± 2 sigma), where rubella had the highest values (10 for IgM and 8 for IgG) while HSV2 had the lowest values (4 for IgM and 5 for IgG). Our results suggest the optimal performance of half of the markers including Toxoplasma, Rubella, and CMV in the Peruvian population.