bluuebunny/crossref_metadata_2025_split huggingface dataset:
A bloody interaction: plasma proteomics reveals gilthead sea bream (Sparus aurata) impairment caused by Sparicotyle chrysophrii
Authors: Riera-Ferrer Enrique , Piazzon M. Carla , Del Pozo Raquel , Palenzuela Oswaldo , Estensoro Itziar , Sitjà-Bobadilla Ariadna 
Published: September 2022

Abstract
Background
Sparicotylosis is an enzootic parasitic disease that is well established across the Mediterranean Sea. It is caused by the polyopisthocotylean monogenean Sparicotyle chrysophrii and affects the gills of gilthead sea bream (GSB; Sparus aurata). Current disease management, mitigation and treatment strategies are limited against sparicotylosis. To successfully develop more efficient therapeutic strategies against this disease, understanding which molecular mechanisms and metabolic pathways are altered in the host is critical. This study aims to elucidate how S. chrysophrii infection modulates the plasma proteome of GSB and to identify the main altered biological processes involved.

Methods
Experimental infections were conducted in a recirculating aquaculture system (RAS) in which naïve recipient GSB ([R]; 70 g; n = 50) were exposed to effluent water from S. chrysophrii-infected GSB (98 g; n = 50). An additional tank containing unexposed naïve fish (control [C]; 70 g; n = 50) was maintained in parallel, but with the open water flow disconnected from the RAS. Haematological and infection parameters from sampled C and R fish were recorded for 10 weeks. Plasma samples from R fish were categorised into three different groups according to their infection intensity, which was based on the number of worms fish−1: low (L: 1–50), medium (51–100) and high (H: > 100). Five plasma samples from each category and five C samples were selected and subjected to a SWATH-MS proteome analysis. Additional assays on haemoglobin, cholesterol and the lytic activity of the alternative complement pathway were performed to validate the proteome analysis findings.

Results
The discriminant analysis of plasma protein abundance revealed a clear separation into three groups (H, M/L and C). A pathway analysis was performed with the differentially quantified proteins, indicating that the parasitic infection mainly affected pathways related to haemostasis, the immune system and lipid metabolism and transport. Twenty-two proteins were significantly correlated with infection intensity, highlighting the importance of apolipoproteins, globins and complement component 3. Validation assays of blood and plasma (haemoglobin, cholesterol and lytic activity of alternative complement pathway) confirmed these correlations.

Conclusions
Sparicotylosis profoundly alters the haemostasis, the innate immune system and the lipid metabolism and transport in GSB. This study gives a crucial global overview of the pathogenesis of sparicotylosis and highlights new targets for further research.

Graphical Abstract
Synoviocytes and skin fibroblasts show opposite effects on IL-23 production and IL-23 receptor expression during cell interactions with immune cells
Authors: Noack Mélissa , Miossec Pierre 
Published: September 2022

Abstract
Background
The IL-23/IL-17 axis is involved in inflammatory diseases including arthritis and psoriasis. However, the response to IL-23 or IL-17 inhibitors is different depending on the disease. The aim was to compare the effects of interactions between immune and stromal cells on the IL-23 axis to understand these differences.

Methods
Peripheral blood mononuclear cells were co-cultured with RA synoviocytes or Pso skin fibroblasts, with or without phytohemagglutinin, IL-23, or anti-IL-23 antibody. Production of IL-6, IL-1β, IL-23, IL-17, IL-12, and IFNγ was measured by ELISA. IL-23 and cytokine receptor gene expression (IL-17RA, IL-17RC, IL-12Rβ1, IL-12Rβ2, and IL-23R) was analyzed by RT-qPCR. IL-12Rβ1 and IL-23R subunits were analyzed by flow cytometry.

Results
The production of IL-6, IL-1β, IL-17, IL-12, and IFNγ with synoviocytes or skin fibroblasts was rather similar, and cell interactions with immune cells increased their production, specifically that of IL-17. A major difference was observed for IL-23. Interactions with synoviocytes but not with skin fibroblasts decreased IL-23 secretion while mRNA level was increased, mainly with synoviocytes, reflecting a major consumption difference. IL-23 addition had only one effect, the increase of IL-17 secretion. Cell activation induced similar effects on cytokine receptor gene expression in co-cultures with synoviocytes or skin fibroblasts. The key difference was the cell interaction effects depending on the stromal cell origin. Interactions with synoviocytes increased the expression of both IL-23 receptor subunits at mRNA levels and IL-23R at the surface expression level while interactions with skin fibroblasts decreased their expression at the mRNA level and had no effect at the surface expression level.

Conclusion
Interactions between immune and stromal cells are crucial in cytokine production and their receptor expression. The origin of stromal cells had a major influence on the production of IL-23 and its receptor expression. Such differences may explain part of the heterogeneity in treatment response.
Bacterial and archaeal communities within the alkaline soda Langaco Lake in the Qinghai-Tibet Plateau
Authors: Wang Mingxiang , Zhang Xin , Shu Zhiwan , Wang Zhibo , Tao Yujie , Lv Chuanbo , Zhu Derui , Shen Guoping 
Published: September 2022

Abstract
Purpose
Langaco Lake (LGL) is a soda lake located at an altitude of 4548 m in the Qinghai-Tibet Plateau in China. LGL exhibits unique hydrochemical characteristics among soda lakes, but little is known about the microbial diversity of LGL and the microbial interactions with environmental factors.

Methods
The water samples were filtered using chemical-grade cellulose acetate membrane (pore size of 0.45 μm), and the hydrochemical characteristics were analyzed. Community DNA was extracted, and then high-throughput sequencing of 16S rRNA genes was conducted to evaluate the composition of the microbial community.

Results
The high-throughput sequencing of 16S rRNA genes revealed that the bacterial diversity in LGL consisted of 327 genera in 24 phyla (4871 operational taxonomic units (OTUs); Shannon index values of 5.20–6.07), with a significantly higher diversity than that of the Archaea (eight phyla and 29 genera comprising 1008 OTUs; Shannon index values of 2.98–3.30). The bacterial communities were dominated by Proteobacteria (relative abundances of 42.79–53.70%), followed by Bacteroidetes (11.13–15.18%), Planctomycetes (4.20–12.82%), Acidobacteria (5.91–9.50%), Actinobacteria (2.60–5.80%), and Verrucomicrobia (2.11–4.08%). Furthermore, the archaeal communities were dominated by Crenarchaeota (35.97–58.29%), Euryarchaeota (33.02–39.89%), and Woesearchaeota (6.50–21.57%). The dominant bacterial genus was Thiobacillus (8.92–16.78%), and its abundances were most strongly correlated with the total phosphorus (TP) content, pH value, CO32− concentration, and temperature. The most abundant archaeal genus was Methanoregula (21.40–28.29%), and its abundances were the most highly correlated with the total organic carbon (TOC) content, total salinity (TS), and K+ and Na+ concentrations.

Conclusions
The results of this study provide valuable insights for developing a more comprehensive understanding of microbial diversity in these unique carbonate alkaline environments, as well as a better understanding of the microbial resources on the Qinghai-Tibet Plateau.
Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis
Authors: Park Hong-Tae , Lee Sang-Mok , Ko Seyoung , Kim Suji , Park Hyun-Eui , Shin Min-Kyoung , Kim Donghyuk , Yoo Han Sang 
Published: September 2022

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne’s disease, a chronic debilitating disease in ruminants. To control this disease, it is crucial to understand immune evasion and the mechanism of persistence by analyzing the early phase interplays of the intracellular pathogens and their hosts. In the present study, host–pathogen interactions at the transcriptomic level were investigated in an in vitro macrophage infection model. When differentiated human THP-1 cells were infected with MAP, the expression of various genes associated with stress responses and metabolism was altered in both host and MAP at 3 h post-infection. MAP upregulates stress-responsive global gene regulators, such as two-component systems and sigma factors, in response to oxidative and cell wall stress. Downstream genes involved in type VII secretion systems, cell wall synthesis (polyketide biosynthesis proteins), and iron uptake were changed in response to the intracellular environment of macrophages. On the host side, upregulation of inflammatory cytokine genes was observed along with pattern recognition receptor genes. Notably, alterations in gene sets involved in arginine metabolism were observed in both the host and MAP, along with significant downregulation of NOS2 expression. These observations suggest that the utilization of metabolites such as arginine by intracellular MAP might affect host NO production. Our dual RNA-seq data can provide novel insights by capturing the global transcriptome with higher resolution, especially in MAP, thus enabling a more systematic understanding of host–pathogen interactions.
QKI degradation in macrophage by RNF6 protects mice from MRSA infection via enhancing PI3K p110β dependent autophagy
Authors: Zhai Dongsheng , Wang Wenwen , Ye Zichen , Xue Ke , Chen Guo , Hu Sijun , Yan Zhao , Guo Yanhai , Wang Fang , Li Xubo , Xiang An , Li Xia , Lu Zifan , Wang Li 
Published: September 2022

Abstract
Background
Sepsis is a fatal condition commonly caused by Methicillin-resistant Staphylococcus aureus (MRSA) with a high death rate. Macrophages can protect the host from various microbial pathogens by recognizing and eliminating them. Earlier we found that Quaking (QKI), an RNA binding protein (RBP), was involved in differentiation and polarization of macrophages. However, the role of QKI in sepsis caused by pathogenic microbes, specifically MRSA, is unclear. This study aimed to investigate the role of QKI in regulation of host–pathogen interaction in MRSA-induced sepsis and explored the underlying mechanisms.

Methods
Transmission electron microscope and immunofluorescence were used to observe the autophagy level in macrophages. Real-time PCR and western blot were used to analyzed the expression of mRNA and protein respectively. The potential protein interaction was analyzed by iTRAQ mass spectrometry and Immunoprecipitation. RNA fluorescence in situ hybridization, dual-luciferase reporter assay and RNA immunoprecipitation were used to explore the mechanism of QKI regulating mRNA of PI3K-p110β.

Results
The mRNA level of QKI was aberrantly decreased in monocytes and PBMCs of septic patients with the increasing level of plasma procalcitonin (PCT). Then the mice with myeloid specific knockout of QKI was challenged with MRSA or Cecal Ligation and Puncture (CLP). Mice in these two models displayed higher survival rates and lower bacterial loads. Mechanistically, QKI deletion promoted phagocytosis and autophagic degradation of MRSA via activating p110β (a member of Class IA phosphoinositide 3-kinases) mediated autophagic response. QKI expression in macrophages led to the sequestration of p110β in mRNA processing (P) bodies and translational repression. Upon infection, the direct interaction of RNF6, a RING-type E3 ligase, mediated QKI ubiquitination degradation and facilitated PI3K-p110β related autophagic removal of pathogen. The administration of nanoparticles with QKI specific siRNA significantly protected mice from MRSA infection.

Conclusions
This study disclosed the novel function of QKI in the P body mRNA regulation during infection. QKI degradation in macrophage by RNF6 protects mice from MRSA infection via enhancing PI3K-p110β dependent autophagy. It suggested that QKI may serve as a potential theranostic marker in MRSA-induced sepsis.

Graphical Abstract
Identification of a novel de novo pathogenic variant in GFAP in an Iranian family with Alexander disease by whole-exome sequencing
Authors: Heshmatzad Katayoun , Naderi Niloofar , Masoumi Tannaz , Pouraliakbar Hamidreza , Kalayinia Samira 
Published: September 2022

Abstract
Background
Alexander disease (AxD) is a rare leukodystrophy with an autosomal dominant inheritance mode. Variants in GFAP lead to this disorder and it is classified into three distinguishable subgroups: infantile, juvenile, and adult-onset types.

Objective
The aim of this study is to report a novel variant causing AxD and collect all the associated variants with juvenile and adult-onset as well.

Methods
We report a 2-year-old female with infantile AxD. All relevant clinical and genetic data were evaluated. Search strategy for all AxD types was performed on PubMed. The extracted data include total recruited patients, number of patients carrying a GFAP variant, nucleotide and protein change, zygosity and all the clinical symptoms.

Results
A novel de novo variant c.217A > G: p. Met73Val was found in our case by whole-exome sequencing. In silico analysis categorized this variant as pathogenic. Totally 377 patients clinically diagnosed with juvenile or adult-onset forms were recruited in these articles, among them 212 patients were affected with juvenile or adult-onset form carrier of an alteration in GFAP. A total of 98 variants were collected. Among these variants c.262C > T 11/212 (5.18%), c.1246C > T 9/212 (4.24%), c.827G > T 8/212 (3.77%), c.232G > A 6/212 (2.83%) account for the majority of reported variants.

Conclusion
This study highlighted the role of genetic in AxD diagnosing. It also helps to provide more information in order to expand the genetic spectrum of Iranian patients with AxD. Our literature review is beneficial in defining a better genotype–phenotype correlation of AxD disorder.
Impacts of a home garden intervention in Bangladesh after one, three and six years
Authors: Baliki Ghassan , Schreinemachers Pepijn , Brück Tilman , Uddin Nasir Md. 
Published: September 2022

Abstract
Background
Training women in home gardening and nutrition has been shown to increase household production and consumption of nutritious food and contribute to women’s empowerment, but evidence is limited to short-term effects. Here, we investigate whether home garden support leads to long-term improvements in household nutrition and women’s empowerment. To do this we use four waves of household-level survey data collected over a 7-year period (2013–2019) from an intervention (n = 395) and a control (n = 224) group in four rural districts of Bangladesh. We estimate the intent-to-treat effect using a difference-in-difference estimator.

Results
We find an immediate increase in the quantity of vegetables harvested from home gardens (+ 29.6 kg/year; p = 0.01) and this effect is sustained in years three (+ 42.3 kg; p < 0.01) and six (+ 37.0 kg; p < 0.01). The nutrient yield from the gardens also remained positive and significant, but the effect declined due to changes in the composition of vegetables. The effect on per capita vegetable intake, significant in years one and three, turned not significant in year six. Effects on nutrition knowledge, food preparation practices, and women’s empowerment all remained significant in year six.

Conclusions
Home garden interventions in Bangladesh create sustained impact on a range of social, economic and nutritional outcomes. Refresher training after 5 or 6 years may help to maintain the full range of impacts observed.
Development and validation of Foreign Language Teacher Support Scale (FLTSS)
Authors: Sadoughi Majid , Hejazi S. Yahya 
Published: September 2022

AbstractTeacher support, as an essential type of social support and an important antecedent of many key outcomes in L2 learning, can significantly contribute to foreign language achievement. Although teacher support has received considerable attention in education and educational psychology, it has drawn scanty attention in foreign language and applied linguistics research. Therefore, the present study aimed to fill in this research gap by developing and validating a domain-specific scale to measure the types of teacher support perceived by English as a Foreign Language (EFL) learners. An initial item pool was constructed based on some generic measures of teacher support and semi-structured interviews with EFL learners. Then, the items were submitted to a panel of experts and their content validity was checked using the content validity index. After a series of exploratory and confirmatory factor analyses, the final version of the Foreign Language Teacher Support Scale (FLTSS) measuring four types of perceived teacher support, namely, emotional, instrumental, appraisal, and informational, was prepared. The results of examining different types of validity and reliability indicated that the scale is suitable for measuring different types of perceived teacher support. Some suggestions for further research are presented.
Formative vs. summative assessment: impacts on academic motivation, attitude toward learning, test anxiety, and self-regulation skill
Authors: Ismail Seyed M. , Rahul D. R. , Patra Indrajit , Rezvani Ehsan 
Published: September 2022

AbstractAs assessment plays an important role in the process of teaching and learning, this research explored the impacts of formative and summative assessments on academic motivation, attitude toward learning, test anxiety, and self-regulation skill of EFL students in Iran. To fulfill the objectives of this research, 72 Iranian EFL learners were chosen based on the convenience sampling method assigned to two experimental groups (summative group and formative group) and a control group. Then, the groups took the pre-tests of test anxiety, motivation, and self-regulation skill. Then, one experimental group was trained by following the rules of the formative assessment and the other experimental group was taught according to the summative assessment. The control group was instructed without using any preplanned assessment. After a 15-session treatment, the post-tests of the test anxiety, motivation, and self-regulation skill were administered to all groups to assess the impacts of the instruction on their language achievement. Lastly, a questionnaire of attitude was administered to both experimental groups to examine their attitudes towards the impacts of formative and summative assessment on their English learning improvement. The outcomes of one-way ANOVA and Bonferroni tests revealed that both summative and formative assessments were effective but the formative one was more effective on academic motivation, test anxiety, and self-regulation skill. The findings of one sample t-test indicated that the participants had positive attitudes towards summative and formative assessments. Based on the results, it can be concluded that formative assessment is an essential part of teaching that should be used in EFL instructional contexts. The implications of this study can help students to detect their own weaknesses and target areas that need more effort and work.
Assessing the evidence for the comparability of socioeconomic status between students with and without immigrant background in Norway and Sweden
Authors: Mittal Oleksandra , Scherer Ronny , Nilsen Trude 
Published: September 2022

AbstractThe prerequisite for meaningful comparisons of educational inequality indicators across immigration status is the comparability of socioeconomic status (SES) measures. The Programme for International Student Assessment (PISA) uses its index of economic, social, and cultural status (ESCS) to provide insights into the problems of inequality across students’ socioeconomic and immigration statuses. However, missing evidence regarding the comparability of the ESCS index or its components across students with and without immigrant background challenges the accuracy of empirical inferences. Our study sheds light on the comparability of the index of household possessions (HOMEPOS) across immigration status in Norway and Sweden—two countries that continue to be two largest recipients of immigration flows among their Nordic neighbours. We tested the PISA 2018 HOMEPOS scale for the overall measurement invariance and possible differential item functioning (DIF) across three student groups with first-generation, second-generation, or no immigrant background. Several HOMEPOS items exhibited DIF within these countries. Moreover, we examined how four strategies to deal with DIF items may affect the inferences regarding educational inequalities across immigration status. The strength of the HOMEPOS–achievement association was sensitive to the choice of approach for 15-year-old immigrant students, while it remained stable and moderate for native students. Our findings encourage researchers using the HOMEPOS scale to consider the invariance testing to avoid measurement bias and provide robust evidence characterizing immigrant achievement gaps.
Malnutrition and inflammatory parameters in patients with chronic kidney disease stages 3–5 from northern India
Authors: Sheikh Rayees Yousuf , Samoon Hamad Jeelani , Bhat Nucksheeba Aziz , Wani Imtiyaz 
Published: September 2022

Abstract
Background
Malnutrition is highly prevalent in chronic kidney disease (CKD). This study is conducted to find out the prevalence of malnutrition and its association with inflammation in patients with CKD stages 3–5.

Method
This is a hospital-based cross-sectional study conducted at the Sri Ram Murti Smarak Institute of Medical Science, Uttar Pradesh, India. CKD stages 3–5 patients were included. The nutritional status was assessed by subjective global assessment (SGA). Anthropometric and biochemical measurements were also checked at the time of enrollment.

Results
A total of 213/354 (60.2%) of patients were malnourished. The triceps skinfold thickness (TSFT) was 8.2 ± 1.2 mm and 10.9 ± 1.2 mm in the malnourished and well-nourished groups, respectively; p < 0.001. TSFT was ≤ 10 mm in 91.1% of patients with malnutrition. Mid-arm muscle circumference (MAMC) was 21.3 ± 2.2 cm and 24 ± 2.9 cm, and the body mass index (BMI) was 19.8 ± 1.5 and 22.5 ± 1.4 kg/m2 in the malnourished and well-nourished group, respectively; p < 0.001. A significant direct correlation between BMI, TSFT, MAMC, and eGFR was noted. Median eGFR was 11.9 ml/min/1.73 m2 in the malnourished compared to 24.2 ml/min/1.73 m2 in the well-nourished group; p < 0.001. Serum ferritin level was 246.77 ± 18.24 mg/L in the malnourished group, higher than the well-nourished group at 237.23 ± 16.13 mg/L; p < 0.001. CRP was elevated (> 0.6 mg/dl) in 53.5% patients with malnutrition; p 0.003.

Conclusions
Malnutrition is highly prevalent in the CKD population. The incidence increases as the eGFR decrease. TSFT ≤ 10 mm compares favorably with SGA in detecting malnutrition (sensitivity > 90%), and BMI > 20 kg/m2 compares favorably with SGA in ruling out malnutrition (specificity 97%). Malnutrition and inflammation often coexist. Early detection and appropriate management are crucial.