bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cumulative effects of exercise training and consumption of propolis on managing diabetic dyslipidemia in adult women: a single-blind, randomized, controlled trial with pre–post-intervention assessments
Authors: Moayedi Fatemeh , Taghian Farzaneh , Jalali Dehkordi Khosro , Hosseini Seyed Ali 
Published: August 2023

AbstractDyslipidemia is an imbalance of various lipids, and propolis, as a natural resinous viscos mixture made by Apis mellifera L. could improve in this condition. In this single-blind, randomized trial, 60 women with type 2 diabetes and dyslipidemia were divided into four groups: (1) the patients who did not apply the combined training and 500 mg propolis capsules supplement (Control group); (2) subjects performed combined training, including aerobic and resistance training (EXR); (3) subjects received the 500 mg propolis supplement capsules (SUPP); (4) Subjects performed combined training along with receiving the 500 mg propolis supplement capsules (EXR + SUPP). We evaluated the concentration of CTRP12, SFRP5, interleukin-6 (IL6), superoxide dismutase (SOD), malondialdehyde (MDA), adiponectin, and total antioxidant capacity (TAC) before and after the intervention. MDA, TAC, IL6, CTRP12, SFRP5 IL6, adiponectin, and lipid profile levels ameliorated in the EXR + SUPP group. We found that 8 weeks of treatment by combined exercise training and propolis supplement decreased inflammation activity and increased antioxidant defense in women with diabetic dyslipidemia.Trial registration This study was registered in the Iranian Registry of Clinical Trials; IRCT code: IRCT20211229053561N1
Temporal transcriptomic profiling elucidates sorghum defense mechanisms against sugarcane aphids
Authors: Puri Heena , Grover Sajjan , Pingault Lise , Sattler Scott E. , Louis Joe 
Published: August 2023

Abstract
Background
The sugarcane aphid (SCA; Melanaphis sacchari) has emerged as a key pest on sorghum in the United States that feeds from the phloem tissue, drains nutrients, and inflicts physical damage to plants. Previously, it has been shown that SCA reproduction was low and high on sorghum SC265 and SC1345 plants, respectively, compared to RTx430, an elite sorghum male parental line (reference line). In this study, we focused on identifying the defense-related genes that confer resistance to SCA at early and late time points in sorghum plants with varied levels of SCA resistance.

Results
We used RNA-sequencing approach to identify the global transcriptomic responses to aphid infestation on RTx430, SC265, and SC1345 plants at early time points 6, 24, and 48 h post infestation (hpi) and after extended period of SCA feeding for 7 days. Aphid feeding on the SCA-resistant line upregulated the expression of 3827 and 2076 genes at early and late time points, respectively, which was relatively higher compared to RTx430 and SC1345 plants. Co-expression network analysis revealed that aphid infestation modulates sorghum defenses by regulating genes corresponding to phenylpropanoid metabolic pathways, secondary metabolic process, oxidoreductase activity, phytohormones, sugar metabolism and cell wall-related genes. There were 187 genes that were highly expressed during the early time of aphid infestation in the SCA-resistant line, including genes encoding leucine-rich repeat (LRR) proteins, ethylene response factors, cell wall-related, pathogenesis-related proteins, and disease resistance-responsive dirigent-like proteins. At 7 days post infestation (dpi), 173 genes had elevated expression levels in the SCA-resistant line and were involved in sucrose metabolism, callose formation, phospholipid metabolism, and proteinase inhibitors.

Conclusions
In summary, our results indicate that the SCA-resistant line is better adapted to activate early defense signaling mechanisms in response to SCA infestation because of the rapid activation of the defense mechanisms by regulating genes involved in monolignol biosynthesis pathway, oxidoreductase activity, biosynthesis of phytohormones, and cell wall composition. This study offers further insights to better understand sorghum defenses against aphid herbivory.
Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population
Authors: Rouskas Konstantinos , Katsareli Efthymia A. , Amerikanou Charalampia , Dimopoulos Alexandros C. , Glentis Stavros , Kalantzi Alexandra , Skoulakis Anargyros , Panousis Nikolaos , Ongen Halit , Bielser Deborah , Planchon Alexandra , Romano Luciana , Harokopos Vaggelis , Reczko Martin , Moulos Panagiotis , Griniatsos Ioannis , Diamantis Theodoros , Dermitzakis Emmanouil T. , Ragoussis Jiannis , Dedoussis George , Dimas Antigone S. 
Published: August 2023

Abstract
Background
Expression quantitative trait loci (eQTL) studies provide insights into regulatory mechanisms underlying disease risk. Expanding studies of gene regulation to underexplored populations and to medically relevant tissues offers potential to reveal yet unknown regulatory variants and to better understand disease mechanisms. Here, we performed eQTL mapping in subcutaneous (S) and visceral (V) adipose tissue from 106 Greek individuals (Greek Metabolic study, GM) and compared our findings to those from the Genotype-Tissue Expression (GTEx) resource.

Results
We identified 1,930 and 1,515 eGenes in S and V respectively, over 13% of which are not observed in GTEx adipose tissue, and that do not arise due to different ancestry. We report additional context-specific regulatory effects in genes of clinical interest (e.g. oncogene ST7) and in genes regulating responses to environmental stimuli (e.g. MIR21, SNX33). We suggest that a fraction of the reported differences across populations is due to environmental effects on gene expression, driving context-specific eQTLs, and suggest that environmental effects can determine the penetrance of disease variants thus shaping disease risk. We report that over half of GM eQTLs colocalize with GWAS SNPs and of these colocalizations 41% are not detected in GTEx. We also highlight the clinical relevance of S adipose tissue by revealing that inflammatory processes are upregulated in individuals with obesity, not only in V, but also in S tissue.

Conclusions
By focusing on an understudied population, our results provide further candidate genes for investigation regarding their role in adipose tissue biology and their contribution to disease risk and pathogenesis.
Chromosome-level genome assemblies of two parasitoid biocontrol wasps reveal the parthenogenesis mechanism and an associated novel virus
Authors: Inwood Sarah N. , Skelly John , Guhlin Joseph G. , Harrop Thomas W.R. , Goldson Stephen L. , Dearden Peter K. 
Published: August 2023

AbstractBackgroundBiocontrol is a key technology for the control of pest species.Microctonusparasitoid wasps (Hymenoptera: Braconidae) have been released in Aotearoa New Zealand as biocontrol agents, targeting three different pest weevil species. Despite their value as biocontrol agents, no genome assemblies are currently available for theseMicroctonuswasps, limiting investigations into key biological differences between the different species and strains.Methods and findingsHere we present high-quality genomes forMicroctonus hyperodaeandMicroctonus aethiopoides, assembled with short read sequencing and Hi-C scaffolding. These assemblies have total lengths of 106.7 Mb forM. hyperodaeand 129.2 Mb forM. aethiopoides, with scaffold N50 values of 9 Mb and 23 Mb respectively. With these assemblies we investigated differences in reproductive mechanisms, and association with viruses betweenMicroctonuswasps. Meiosis-specific genes are conserved in asexualMicroctonus, within-situhybridisation validating expression of one of these genes in the ovaries of asexualMicroctonus aethiopoides. This implies asexual reproduction in theseMicroctonuswasps involves meiosis, with the potential for sexual reproduction maintained. Investigation of viral gene content revealed candidate genes that may be involved in virus-like particle production inM. aethiopoides, as well as a novel virus infectingM. hyperodae, for which a complete genome was assembled.Conclusion and significanceThese are the first published genomes forMicroctonuswasps which have been deployed as biocontrol agents, in Aotearoa New Zealand. These assemblies will be valuable resources for continued investigation and monitoring of these biocontrol systems. Understanding the biology underpinningMicroctonusbiocontrol is crucial if we are to maintain its efficacy, or in the case ofM. hyperodaeto understand what may have influenced the significant decline of biocontrol efficacy. The potential for sexual reproduction in asexualMicroctonusis significant given that empirical modelling suggests this asexual reproduction is likely to have contributed to biocontrol decline. Furthermore the identification of a novel virus inM. hyperodaehighlights a previously unknown aspect of this biocontrol system, which may contribute to premature mortality of the host pest. These findings have potential to be exploited in future in attempt to increase the effectiveness ofM. hyperodaebiocontrol.
Characterization and genomics identification of key genes involved in denitrification-DNRA-nitrification pathway of plant growth-promoting rhizobacteria (Serratia marcescens OK482790)
Authors: Hamada Marwa A. , Soliman Elham R. S. 
Published: August 2023

Abstract
Background
A wide variety of microorganisms, including bacteria, live in the rhizosphere zone of plants and have an impact on plant development both favorably and adversely. The beneficial outcome is due to the presence of rhizobacteria that promote plant growth (PGPR).

Results
In this study, a bacterial strain was isolated from lupin rhizosphere and identified genetically as Serratia marcescens (OK482790). Several biochemically and genetically characteristics were confirmed in vitro and in vivo to determine the OK482790 strain ability to be PGPR. The in vitro results revealed production of different lytic enzymes (protease, lipase, cellulase, and catalase), antimicrobial compounds (hydrogen cyanide, and siderophores), ammonia, nitrite, and nitrate and its ability to reduce nitrate to nitrite. In silico and in vitro screening proposed possible denitrification-DNRA-nitrification pathway for OK482790 strain. The genome screening indicated the presence of nitrite and nitrate genes encoding Nar membrane bound sensor proteins (NarK, NarQ and NarX). Nitrate and nitrite reductase encoding genes (NarI, NarJ, NarH, NarG and NapC/NirT) and (NirB, NirC, and NirD) are also found in addition to nitroreductases (NTR) and several oxidoreductases. In vivo results on wheat seedlings confirmed that seedlings growth was significantly improved by soil inoculation of OK482790 strain.

Conclusions
This study provides evidence for participation of S. marcescens OK482790 in nitrogen cycling via the denitrification-DNRA-nitrification pathway and for its ability to produce several enzymes and compounds that support the beneficial role of plant-microbe interactions to sustain plant growth and development for a safer environment.
Higher serum lipocalin 2 is associated with post-stroke depression at discharge
Authors: Liu Yufeng , Liu Lu , Zhi Zhongwen , Chen Rui , Wang Qing , Wang Mengchao , Wang Yuqian , Zhao Liandong 
Published: August 2023

Abstract
Background and aims
Post-stroke depression (PSD), as one of the common complications after stroke, seriously affects the physical and mental health and functional prognosis of patients. Previous studies have shown that the increase of inflammatory mediators is associated with the occurrence of PSD. Lipocalin 2 (LCN2), as an acute phase protein, is involved in the development of acute ischemic stroke (AIS), and its expression is up-regulated in patients with depression, suggesting that there is a potential correlation between serum LCN2 and depression. The aim of this study was to explore the relationship between serum LCN2 at admission and PSD at discharge.

Methods
A total of 358 AIS patients were retrospectively included. All patients had fasting venous blood taken within 24 h of admission to detect serum LCN2. The patients were evaluated by 17-item Hamilton Depression Scale (HAMD) before discharge. Patients with HAMD score > 7 were diagnosed with PSD. The correlation between serum LCN2 and PSD was tested using binary logistic regression analysis.

Results
In our study, 92 (25.7%) patients were diagnosed with PSD at discharge. According to the serum LCN2 value, the patients were divided into three layers (Tertile1 ≤ 105.24ng/ml; Tertile2: 105.24-140.12ng/ml; Tertile3 ≥ 140.12ng/ml), with T1 layer (the lowest levels) as a reference, after adjusting for multiple potential confounding factors, T3 layer (the highest levels) was independently associated with the occurrence of PSD (odds ratio [OR] = 2.639, 95% confidence interval [CI]: 1.317–5.287, P = 0.006). Similar results were found when the serum LCN2 was analyzed as a continuous variable. The optimal cut-off value of serum LCN2 at admission to predict PSD at discharge was 117.60ng/ml, at this threshold, the sensitivity was 77.2%, and the specificity was 53.4%.

Conclusions
High serum LCN2 levels at admission are an independent risk factor for PSD in patients with AIS at discharge.
Tear biomarkers for Alzheimer’s disease screening and diagnosis (the TearAD study): design and rationale of an observational longitudinal multicenter study
Authors: van de Sande Nienke , Ramakers Inez H. G. B. , Visser Pieter Jelle , Verhey Frans R. J. , Verbraak Frank D. , Bouwman Femke H. , Berendschot Tos T. J. M. , Nuijts Rudy M. M. A. , Webers Carroll A. B. , Gijs Marlies 
Published: August 2023

Abstract
Background
Alzheimer’s disease (AD) is the most common cause of dementia, and due to increasing life expectancy the number of patients is expected to grow. The diagnosis of AD involves the use of biomarkers determined by an amyloid PET scan or cerebrospinal fluid analyses that are either invasive or expensive, and not available in each hospital, thus limiting their usage as a front-line screener. The TearAD study aims to use tear fluid as a potential source for AD biomarkers. In previous reports, we demonstrated that AD biomarkers amyloid-beta and tau, are measurable in tear fluid and are associated with disease severity and neurodegeration. This study aims to validate previous results in a larger cohort and evaluate the diagnostic accuracy of tear biomarkers to discriminate between individuals with and without neurodegeneration as determined by hippocampal atrophy.

Methods
The TearAD study is an observational longitudinal multi-center study that will enroll 50 cognitively healthy controls, 50 patients with subjective cognitive decline, 50 patients with mild cognitive impairment and 50 patients with AD dementia from the memory clinic. Participants will be examined at baseline, after one year, and after two years follow-up. Study assessments include neuropsychological tests and ophthalmic examination. All participants will receive a MRI scan, and a subset of the study population will undergo cerebral spinal fluid collection and an amyloid PET scan. Tear fluid will be collected with Schirmer strips and levels of Aβ38, Aβ40, Aβ42, t-tau and p-tau in tear fluid will be determined using multiplex immunoassays. Blood samples will be collected from all participants. Images of the retina will be obtained with a standard, hyperspectral and ultra-wide field fundus camera. Additionally, macular pigment optical density will be measured with the macular pigment reflectometer, and cross-sectional images of the retina will be obtained through optical coherence tomography imaging.

Discussion
The TearAD study will provide insight into the potential diagnostic use of tear biomarkers as a minimally invasive and low cost tool for the screening and diagnosis of AD.

Trial registration
Retrospectively registered at clinicaltrials.gov (NCT05655793).
Comparative yield of molecular diagnostic algorithms for autism spectrum disorder diagnosis in India: evidence supporting whole exome sequencing as first tier test
Authors: Sheth Frenny , Shah Jhanvi , Jain Deepika , Shah Siddharth , Patel Harshkumar , Patel Ketan , Solanki Dhaval I , Iyer Anand S , Menghani Bhargavi , Mhatre Priti , Mehta Sanjiv , Bajaj Shruti , Patel Vishal , Pandya Manoj , Dhami Deepak , Patel Darshan , Sheth Jayesh , Sheth Harsh 
Published: August 2023

Abstract
Background
Autism spectrum disorder (ASD) affects 1 in 100 children globally with a rapidly increasing prevalence. To the best of our knowledge, no data exists on the genetic architecture of ASD in India. This study aimed to identify the genetic architecture of ASD in India and to assess the use of whole exome sequencing (WES) as a first-tier test instead of chromosomal microarray (CMA) for genetic diagnosis.

Methods
Between 2020 and 2022, 101 patient-parent trios of Indian origin diagnosed with ASD according to the Diagnostic and Statistical Manual, 5th edition, were recruited. All probands underwent a sequential genetic testing pathway consisting of karyotyping, Fragile-X testing (in male probands only), CMA and WES. Candidate variant validation and parental segregation analysis was performed using orthogonal methods.

Results
Of 101 trios, no probands were identified with a gross chromosomal anomaly or Fragile-X. Three (2.9%) and 30 (29.7%) trios received a confirmed genetic diagnosis from CMA and WES, respectively. Amongst diagnosis from WES, SNVs were detected in 27 cases (90%) and CNVs in 3 cases (10%), including the 3 CNVs detected from CMA. Segregation analysis showed 66.6% (n = 3 for CNVs and n = 17 for SNVs) and 16.6% (n = 5) of the cases had de novo and recessive variants respectively, which is in concordance with the distribution of variant types and mode of inheritance observed in ASD patients of non-Hispanic white/ European ethnicity. MECP2 gene was the most recurrently mutated gene (n = 6; 20%) in the present cohort. Majority of the affected genes identified in the study cohort are involved in synaptic formation, transcription and its regulation, ubiquitination and chromatin remodeling.

Conclusions
Our study suggests de novo variants as a major cause of ASD in the Indian population, with Rett syndrome as the most commonly detected disorder. Furthermore, we provide evidence of a significant difference in the diagnostic yield between CMA (3%) and WES (30%) which supports the implementation of WES as a first-tier test for genetic diagnosis of ASD in India.
Are pregnancy outcomes affected by the lack of legal status? A demographic study based on 850,288 live births in Switzerland
Authors: Montagnoli Caterina , Wanner Philippe 
Published: August 2023

Abstract
Background
In the context of increased global mobility, it is fundamental to understand migrants’ needs and how governments can ensure equal health opportunities for both regular and irregular migrants simply by applying low-cost primary health care measures. To identify health issues in which to intervene, this study analysed the impact of a mother’s lack of legal status, together with available biological and socioeconomic characteristics, on four indicators of adverse perinatal outcomes in Switzerland.

Methods
Based on the exhaustive records of the Swiss Federal Statistical Office (FSO) for its Vital Statistics (BEVNAT), different indicators of birth outcomes, including preterm birth (PTB), low and very low birth weight (LBW and VLBW), and small for gestational age (SGA), were analysed using logistic regressions on live births occurring from 2005 to 2018. These four adverse outcomes were defined as dependent variables. Statistical analysis was performed using the statistical package STATA, version 17.

Results
Selected pregnancy outcomes were conversely affected by an irregular legal status. Analysis run on the final sample showed that, compared to the neonates of mothers who are non-migrant legal residents in Switzerland, newborns of irregular migrants have higher risks of PTB (aOR 1.18 95% CI [1.05-1.32], p<0.01) and VLBW (aOR 1.43 [1.13-1.81], p < 0.01]). In contrast, we observed that in both irregular and regular migrant groups, the odds of SGA were lowered (aOR .76 [.68-.85] p<0.01) and aOR
.93 [.91-.94], p< 0.01, respectively). A similar effect was observed when controlling for any adverse outcome (any AOs) (aOR .90 [.83-.99] p 0.022; and aOR .93 [.91-.94] p< 0.01, respectively).

Conclusions
Our results, together with those from the available literature, call for a more comprehensive assessment of all pregnancy outcomes as well as of the social determinants of health for which the analysis was adjusted. Given the complexity of the migration phenomenon, future studies should account for local structural restrictions in the organization of care, the extension of a person’s network as a means of health care accessibility, diverse backgrounds and cultures and the recent arrival status of migrants. This would allow researchers to understand the long-term impact of social determinants of health on the wellbeing of a mother and child and take them into account in the adoption of health policies.
Causal association between gut microbiota and intrahepatic cholestasis of pregnancy: mendelian randomization study
Authors: Li Chuang , Li Na , Liu Caixia , Yin Shaowei 
Published: August 2023

Abstract
Background
Previous observational cohort studies have shown that the composition of the gut microbiota is related to the risk of intrahepatic cholestasis of pregnancy (ICP), although it is unclear if the association is causative. This study used Mendelian randomization (MR) to systematically examine whether the gut microbiota was causally linked to ICP.

Methods
We obtained the genome-wide association study (GWAS) summary statistics of gut microbiota and ICP from published GWASs. Maximum likelihood (ML), MR-Egger regression, weighted median, inverse variance weighted (IVW), and weighted model were used to investigate the causal association between gut microbiota and ICP. We further conducted a series of sensitivity analyses to confirm the robustness of the primary results of the MR analyses. Reverse MR analysis was performed on the bacterial taxa that were reported to be causally linked to ICP risk in forwarding MR analysis to evaluate the possibility of reverse causation.

Results
MR analysis revealed that phylum Tenericutes (OR: 1.670, 95%CI: 1.073–2.598, P = 0.023), class Bacteroidia (OR: 1.644, 95%CI: 1.031–2.622, P = 0.037), class Mollicutes (OR: 1.670, 95%CI: 1.073–2.598, P = 0.023), and order Bacteroidales (OR: 1.644, 95%CI: 1.031–2.622, P = 0.037), and were positively associated with the risk of ICP. And we identified that the relative abundance of genus Dialister (OR: 0.562, 95%CI: 0.323–0.977, P = 0.041), genus Erysipelatoclostridium (OR: 0.695, 95%CI: 0.490–0.987, P = 0.042), genus Eubacterium (brachy group) (OR: 0.661, 95%CI: 0.497–0.880, P = 0.005), genus Eubacterium (hallii group) (OR: 0.664, 95%CI: 0.451–0.977, P = 0.037), genus Holdemania (OR: 0.590, 95%CI: 0.414–0.840, P = 0.003), genus Ruminococcus (torques group) (OR: 0.448, 95%CI: 0.235–0.854, P = 0.015), and genus Veillonella (OR: 0.513, 95%CI: 0.294–0.893, P = 0.018) were related to a lower risk of ICP. Additional sensitivity analyses confirmed the robustness of the association between specific gut microbiota composition and ICP. No evidence of reverse causality from ICP to identified bacterial taxa was found in the findings of the reverse MR analyses.

Conclusions
Under MR assumptions, our findings propose new evidence of the relationship between gut microbiota and ICP risk. Our results show that the gut microbiota may be useful target of intervention for ICP.