bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meta-analysis of SNPs determining litter traits in pigs
Authors: Sell-Kubiak E. , Dobrzański J. , Derks M.F.L. , Lopes M. S. , Szwaczkowski T. 
Published: July 2022

Abstract
Background: Nearly 2,000 SNPs associated with pig litter size traits were so far reported based on genome-wide association studies (GWAS). The aims of this study were to gather and integrate previously reported associations between SNPs and five litter traits: total number born (TNB), number born alive (NBA), number of stillborn (SB), litter birthweight (LWT), and corpus luteum number (CLN) to evaluate their common genetic background, and to perform the meta-analysis (MA) of GWAS for total number born (TNB) recorded on animals from five pig populations. Results: In this study, the genes with the largest number of associations with evaluated litter traits were GABRG3, RBP7, PRKD1, and STXBP6. Only 21 genes out of 233 associated with the evaluated litter traits were reported in more than one population or for more than one trait. Based on this evaluation the most interesting candidate gene is PRKD1, which has an association with SB and TNB. Based on GO term analysis, PRKD1 was shown to be involved in angiogenesis as well. As a result of the MA, two new genomic regions, that have not been previously reported, were found to be associated with TNB. One SNP was located on Sus scrofa chromosome (SSC) 14 in the intron of the FAM13C gene. The second SNP was located on SSC9 within the intron of the AGMO gene. Functional analysis revealed a strong candidate causal gene underlying the QTL on SSC9. The third best hit and the most promising candidate gene for litter size was found within the SOSTDC1 gene associated with lower male fertility in rats.Conclusions: We showed that litter traits studied across pig populations have only a few genomic regions in common based on candidate genes comparison. PRKD1 could be an interesting candidate gene with wider association with fertility. The MA identified new genomic regions on SSC9 and SSC14 associated with TNB. Further functional analysis indicated the most promising gene being SOSTDC1 that was confirmed to affect male fertility in other mammals. This is an important finding as litter traits are by default linked with females rather than males.
Assessment of surface water quality during different tides and an anthropogenic impact on coastal water at Gulf of Kachchh, West Coast of India
Authors: Panseriya Haresh , Gosai Haren , Gavali Deepa , Dave Bharti 
Published: July 2022

Abstract
The port-based activity is often associated with industrial growth in the hinterland and similar phenomenon is reported from the Gulf of Kachchh, India. The establishment of industrial clusters close to the coastline is a matter of concern as the release of effluents which influenced the marine ecosystem. The present paper tries to evaluate the variation in the water quality during the high tide and low tide in relation with the anthropogenic or natural influence in Gulf of Kachchh. The tidal variation is important as it reflects the influence of the land-based activity on the coastal waters. To prove this logic a series of stations were taken along the coastal water and statistical analysis viz., Pearson correlation, Box plot, Hierarchical Cluster Analysis (HCA) and Factor Analysis (PCA/FA) were conducted. Pearson correlation and Box plot represents visual impact of parameter variations in respected tides. The chemometric analysis i.e. HCA and PCA/FA clearly indicates an anthropogenic impact on coastal water. Surface water temperature 32.1–34.1°C, pH 7.9–8.7, EC 6.3–9.9 mS/cm, salinity 36.0–52.0 ppt, DO 2.43–6.91, BOD 1.63–4.49 mgO2/L, TSS 1.88–6.98 g/L and turbidity 3–32 NTU. Similarly nutrient concentrations in the gulf of Kachchh were phosphates 0.10–1.54 mg/L, total nitrogen 0.38–0.63 mg/L and sulphate 23.66–37.35 mg/L. The results of HCA revealed that major anthropogenic and domestic impact were found at various stations during low tide. The PCA/FA supported the HCA and justify most of variation in coastal ecosystem were mainly attributed due to the land based activities and sewage outfall points. Overall, the study reveals that water quality parameters like pH, salinity, dissolved solid, oxygen, turbidity, sulphate and nutrients are impacted by the anthropogenic activities and tidal influence. The findings of the paper will be useful for developing effective management strategies for policy maker or stakeholders operational in the coastal area.
The First Toxicological Report of Bigeye Thresher Alopias superciliosus Lowe, 1841
Authors: ÇİFTÇİ Nuray , AYAS Deniz , CİCİK Bedii 
Published: July 2022

Abstract
Cartilaginous fish species have ecological and economic importance, and ecotoxicological studies on these species are quite insufficient. In this study, Al, Cr, Mn, Fe, Cu, Zn, As, Pb, Cd, and Sr levels were determined in muscle, liver, gill, kidney, spleen, stomach, and gonad tissues of Alopias superciliosus (Female, 240 cm TL) caught from Mersin Bay. Tissue metal analysis was determined by Inductively Coupled Plasma Mass Spectrometry (ICP-MS). The SPSS package program was used for statistical analysis and the Duncan test was applied. A statistical difference was found among the tissues in terms of the metals. Fe was determined the highest level in all tissues (p<0.05). The relation between tissues in terms of Fe level was determined as Liver>Gill>Spleen>Gonad>Kidney>Stomach>Muscle. Zn was detected at higher levels in the liver and stomach, and As in other tissues after Fe. Al has the highest level after Zn and As and was mostly found in the gills. The tissue Cu and Zn levels were found in the same order from highest to lowest as Liver>Gonad>Kidney>Spleen≥ Stomach>Gill>Muscle. Sr was higher in the stomach, gonad, and kidney than the other tissues. Cd levels were found in higher than Pb levels in the examined tissues. Liver Cd level was determined as 57.37 µg g-1 dw. Except for the liver, Mn was found at a low level after Cr in the examined tissues. The distinction between the tissue levels of the investigated elements has changed depending on the functional differences between the tissues and metal metabolisms.
Color appearance in rotational material jetting
Authors: Golhin Ali Payami , Sole Aditya Suneel , Strandlie Are 
Published: July 2022

Abstract
Material jetting (MJT) is a popular additive manufacturing (AM) method to combine various materials and create a wide range of designed appearances. However, the measured color of MJT objects is frequently different from the color provided in the printer software. As a result, estimating the color quality and the measured color attributes of an object before printing is vital for accurate color reproduction. This study investigates the color variation based on the texture in an object 3D printed using the MJT method on a rotary tray. The novel radial shape of the rotary tray build platform and variation in the layers structure were targeted as the main factors that can increase the uncertainty in accurate color reproduction. The influence of the PolyJet printer setup has been examined by thickness variation of the colored layers, location on the tray (swath selection), ink color, and finish type between layers. Color quality was assessed by comparing the produced object color by calculating spectral and colorimetric differences. Spearman rank correlation coefficient and principal component analysis (PCA) methods were used to analyze the direct or indirect influence of independent categorical factors on the measured color variables. Based on the studied parameters, switching swathes did not fail printer objects for industrial color matching. In contrast, a thickness variation as small as 0.5 mm could cause CIEDE2000 above 5 for most models, resulting in unnatural color reproduction. Color differences in most objects might be discernible to inexperienced observers, depending on the 3D printing parameters.
An Exclusive NEMO B Mutation Leads to NF-κB-linked Recurrent Pneumonia by Disrupting the NEMO/IKK Complex
Authors: Xu Li , Xu Jing , Guo Xiaoman , Tan Yun , Qiu Tianyi , Tao Jie , Tao Shuai , Liao Yixin , Zhang Lin , Tian Di , Ma Yuanyuan , Ye Peiyan , Hao Yi , Zhang Jianliang , Okada Satoshi , Liu Jialin , Lu Hongzhou , Liu TieFu , Ling Yun 
Published: July 2022

Abstract
Purpose
A number of NEMO mutations in the shared sequences of NEMO isoform A and B have been associated with NF-κB-linked diseases. Here, we first report an exclusive NEMO B mutation as the genetic etiology of a male case with recurrent bacterial pneumonia and explore the underlying mechanism.
Methods
The genomic protein-coding regions of genes were analyzed using the whole exome sequencing (WES) technique, and the rare gene variant was confirmed by Sanger sequence analysis; activation of NF-kB signaling pathway was assessed by co-immunoprecipitation, western blotting, and single-cell RNA-seq analysis; glycolytic changes of peripheral immune cells were evaluated by extracellular acidification rate assay; protein-protein binding affinity and stability were estimated by structure modeling and molecular docking analysis.
Results
A c.20T > C mutation in exon 1 of the IKBKG germline sequence (NM_001099856.2) resulted in a Val7Ala replacement in the exclusive N-terminal sequence of NEMO B. This mutation significantly decreased the binding affinity and stability of NEMO B with IKKα/β, leading to the failure to form functional NEMO/IKK complex and the subsequent inhibition of RelA phosphorylation and nuclear translocation to initiate pro-inflammatory TNF-α and IL-1β gene transcription and metabolic support by glycolysis in response to the TLR4 agonist LPS. Single-cell sequencing analysis revealed abnormalities in monocyte and T-lymphocyte function and B-cell hyperplasia.
Conclusions
The exclusive N-terminal sequence of NEMO B is essential for a functional NEMO/IKKa/IKKb complex to activate NF-κB-dependent antibacterial immunity.
Evolutionary implications of new Postopsyllidiidae from mid-Cretaceous amber from Burma and sternorrhynchan nymphal conservatism
Authors: Drohojowska Jowita , Zmarzły Marzena , Szwedo Jacek 
Published: July 2022

Abstract
Nymphs of extinct sternorrhynchan hemipterans are extremely scarce, however very important for understanding of evolutionary trait of these insects. A protopsyllidioid nymph, placed in the family Postopsyllidiidae is the first found in the fossil record, based on an inclusion in mid-Cretaceous amber from Kachin, Burma. Postopsyllidiidae so far comprised the sole genus Postopsyllidium with a few species: P. rebeccae, P. grimaldii and P. burmaticum from Kachin amber (Cenomanian) and P. emilyae from Turonian amber of New Jersey. Here we are reporting a new genus and species of the postopsyllid Megalophthallidion burmapteron gen. et sp. nov. (imago) and first known nymph of the family ascribed to the same genus. An overview of fossil record of sternorrhynchan nymphs and their evolutionary implications are presented. This finding unlocked new and complementary window to understanding the evolutionary traits of Protopsyllidioidea and other Sternorrhyncha hemipterans.
The “whole ingredients extract” of Astragali Radix improves the symptoms of dextran sulfate sodium (DSS)-induced ulcerative colitis in mice through systemic immunomodulation
Authors: Linghu Ke-Gang , Ma Qiushuo , Xiong Shi Hang , Zhao Mingming , Chen Qiling , Xu Wen , Chen Meiwan , Zhang Jian-Ye , Hu Yuanjia , Xu Wei , Yu Hua 
Published: July 2022

Abstract
Background
Ulcerative colitis (UC) is a common inflammatory intestinal disease. Astragali Radix (AR) is one of the traditional Chinese medicines used in clinic for UC treatment. In our previous study, the whole ingredient extract (WIE) from AR have been proved to possess better immunomodulatory effects on immunosuppressed mice compared with the traditional water extraction (WAE). At our present study, we further evaluated the systemic immune regulation and therapeutic effects of WIE compared with the WAE in the dextran sodium sulfate (DSS)-induced UC mice.
Methods
Gradient solvent extraction has been used to prepare the WIE of Astragalus. The HPLC-MS analysis approach has been employed to analyze and compare the chemical differences between WAE and WIE. UC model was reproduced in 3% DSS-induced C57BL/6 mice for 6 days. Flow cytometric analysis for splenic lymphocyte subset. Elisa kits were used to determine the cytokines in the serum and colon tissues. The histopathological characteristics of colon were evaluated by hematoxylin-eosin staining and immunohistochemistry
Results
The chemical compositions of WIE were more abundant than that in WAE, and amount of main active ingredients in WIE is higher than that in WAE. The WIE treatment altered a better action on reducing colitis disease activity index (DAI) and histological scores, as well as the recovered body weight and increased colon length in mice compared to the WAE group. Additionally, WIE showed a better effects than WAE in recovering the levels of white blood cells in peripheral blood and cytokines (IL-2, IL-6 and MCP-1) in serum or colon tissues, improving the percentage of CD3 + and the ratio of CD4+/CD8 + in the spleen, and inhibiting the spleen enlargement in DSS-induced UC mice.
Conclusions
WIE has a more complete chemical composition than WAE. Meanwhile, WIE possesses better therapeutic effect on UC and the resuming effect on dysfunctional immunity than WAE at the same dosage in mice.
Association Between Obstructive Sleep Apnea and Depression
Authors: Roh Eun Hak , Jang Hyewon , Hwang Kyuchul , Hurh Kyungduk , Park Eun-Cheol 
Published: July 2022

Abstract
Background
Depression is the leading cause of mental health disorders. Obstructive sleep apnea (OSA) is a common sleep disorder, with a recent increase in prevalence. This study aimed to determine the association between OSA and depressive symptoms.
Methods
A total of 1,681 men and 2,112 women aged > 40 years from the Korea National Health and Nutrition Examination Survey (2020) were analyzed using multiple logistic regression. OSA was measured using snoring. In addition, apnea and depressive symptoms were measured using the Patient Health Questionnaire-9.
Results
Individuals with OSA showed a higher likelihood of experiencing depressive symptoms among men (odds ratio [OR]: 1.59, 95% confidence interval [CI]: 1.01–2.48) and women (OR: 2.00, 95% CI: 1.35–2.95). Among men, those who responded to both symptoms of snoring and observed apnea showed a higher likelihood than those who only reported one of the symptoms (OR: 2.10, 95% CI: 1.12–3.92). Women showed more association with those who reported both symptoms (OR: 3.20, 95% CI: 1.58–6.47).
Conclusions
This study found that OSA increased depressive symptoms. This study suggests the treatment of sleep disorders may be used as a method for preventing depression.
The COVID-19 Pandemic in the Nawalparasi District of Nepal: A Mixed Methods Assessment of Increased Alcohol Use and Intimate Partner Violence
Authors: Cornell Alia , Diamond-Smith Nadia , Mitchell Ashley , Puri Mahesh 
Published: July 2022

Abstract
Background In Nepal and across the globe, the COVID-19 pandemic has primed an environment for increased rates of intimate partner violence (IPV). This paper examines how the upstream factors of alcohol use and economic insecurity in the Nawalparasi district of Nepal has brought about higher rates of IPV among newly married women. Methods This study is a secondary analysis of data obtained from the Sumadhur Intervention pilot study that has been previously described and demonstrates successful implementation of group-based, household-level intervention for women’s empowerment and sexual and reproductive health education (1). Our three sets of data were collected before and during the COVID-19 pandemic. The first set is from a longitudinal cohort of 200 newly married women who were surveyed twice a year from February 2017 through July 2020. The second data set is from a cohort of newly married women, their husbands, and their mothers-in-law (31 women, 31 husbands and 31 mothers-in-law) who participated in Sumadhur in January 2021. The third data set was obtained through in-depth interviews in July 2021 from 15 households following Sumadhur. The interviews were thematically coded, and subthemes were identified. The survey data was analyzed for change over time. Results In households in the Nawalparasi district of Nepal, between 2019 and 2020 there was an increase in alcohol consumption with reports of drinking every day increasing from 9.2% to 13.6%. In July 2020, 30% (N=31/102) of newly married women said their husbands’ alcohol consumption had increased since the pandemic. In 2019, 47.06% (N=88/187) of participants reported that they had experienced any form of IPV. In July 2021, 74% (N=23/31) of women reported being physically forced to have sexual intercourse with their husband when they did not want to and in the past four months, 68% (N=21/31) reported being forced to perform sexual acts against their will. The interviews highlighted the presence of alcohol use in the community as well as increased concerns over economic insecurity. Mothers-in-law consistently described increased rates of IPV and community violence since the pandemic. Conclusions The pandemic has led to precarious economic situations that have influenced alcohol use among men, and instances of IPV among young, newly married women. We have demonstrated a need for urgent programmatic and policy responses aimed at reducing IPV, which has increased during the pandemic. Family interventions centering on women, such as Sumadhur, are critical to implement along with community-wide emergency preparedness to ensure autonomy, safety, and wellbeing now and in future times of uncertainty.
Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia
Authors: Silva Cinthy Jimenez , Rivero Ricardo , Douglas Jordan , Bouckaert Remco , Arenas Christian Julian Villabona , Atkins Katherine , Gastelbondo Bertha , Calderon Alfonso , Guzman Camilo , Hoz Daniel Echeverri-De la , Muñoz Marina , Ballesteros Nathalia , Castañeda Sergio , Patiño Luz , Ramirez Angie , Luna Nicolas , Paniz-Mondolfi Alberto , Serrano-Coll Hector , Ramirez Juan David , Mattar Salim , Drummond Alexei 
Published: July 2022

Abstract
The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere. To provide a better understanding of the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia, and performed Bayesian phylodynamic analyses to estimate the time of variants introduction, their respective effective reproductive number, and effective population size, and the impact of disease control measures. We detected a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the start of the pandemic. We showed that the effective reproduction number oscillated drastically throughout the first two years of the pandemic, with Mu showing the highest transmissibility (Re and growth rate estimation). Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions towards the emergence and circulation of novel SARS-CoV-2 variants.
The Royal College of Ophthalmologists’ National Ophthalmology Database Study of Cataract Surgery: report 11, Techniques and Complications of Local Anaesthesia
Authors: Neo Yan Ning , Gruszka-Goh Marta , Braga Alice , De Klerk Tim , Lindfield Dan , Nestel Achim , Stewart Stephen , Donachie Paul , Buchan John 
Published: July 2022

Abstract
Objective:
To describe variation in local anaesthesia techniques and complications over a 10-year period for cataract surgery in the United Kingdom.
Methods:
Data from the Royal College of Ophthalmologists National Ophthalmology Database was used. Eligible for analysis were 1 195 882 cataract operations performed using local anaesthesia between 01/04/2010 and 31/03/2020 in 80 centres.
Results:
Overall, topical anaesthesia alone was used in 152 321 (12.7%) operations, combined topical and intracameral anaesthesia in 522 849 (43.7%), sub-Tenon’s in 461 175 (38.6%), and peribulbar/retrobulbar anaesthesia in 59 537 (5.0%). In National Health Service (NHS) institutions, 48.3% operations were topical with/without intracameral vs 88.7% in independent sector treatment centres (ISTC). 45.9% were sub-Tenon’s in NHS vs 9.6% in ISTC. 5.8% were peribulbar/retrobulbar in NHS vs 1.7% in ISTC. Anaesthetic complication rates decreased from 2.7% in the 2010 NHS year to 1.5% in the 2019 NHS year (overall, 2.1% for NHS; 0.2% for ISTC). Overall anaesthetic complication rates were 0.3%, 0.3%, 3.5% and 3.1% for topical alone, combined topical/intracameral, sub-Tenon’s and peribulbar/retrobulbar respectively. Complication rates were higher for sharp needle anaesthesia (peribulbar/retrobulbar) in patients taking warfarin rather than direct oral anticoagulants (4.8% vs 3.1%; p = 0.024). Considerable variation was observed between centres on anaesthetic choices and anaesthetic complication rates.
Conclusions:
Combined topical and intracameral is the most common choice of anaesthesia for cataract surgery in the United Kingdom and is associated with lower anaesthetic-related complication rates than sub-Tenon’s and peribulbar/retrobulbar anaesthesia. Variation in anaesthetic choice exists between centres and between NHS & ISTC sectors.
Improving pre-harvest sprouting resistance in rice by editing OsABA8ox using CRISPR/Cas9
Authors: Fu Kai , Song Weihan , Chen Cheng , Mou Changling , Huang Yunshuai , Zhang Fulin , Hao Qixian , Wang Ping , Ma Tengfei , Chen Yaping , Zhu Ziyan , Zhang Min , Tong Qikai , Liu Xi , Jiang Ling , Wan Jianmin 
Published: July 2022

Abstract
Pre-harvest sprouting (PHS) in cereal crops, is a universal phenomenon that affects grain yield and quality (Tai et al. 2021). Breeders use different methods to strengthen seed dormancy to prevent PHS including genome editing. Abscisic acid is one of the phytohormones that promote seed dormancy. ABA8ox genes encode abscisic acid 8’ hydroxylase (ABA8OX) which determines the level of ABA content by catabolizing ABA (Vallabhaneni and Wurtzel 2010). Three genes in rice encode ABA8’ hydroxylases, namely OsABA8ox1 (LOC_Os02g47470), OsABA8ox2 (LOC_Os08g36860) and OsABA8ox3 (LOC_Os09g28390) (Kushiro et al. 2004; Cai et al. 2015; Zhang et al. 2020). Each gene is expressed in different tissues of rice.
An amplitude-dependent vibration model of thin plate made of fiber metal laminates with partial constraint layer damping treatments
Authors: Xu Zhuo , Xu Pei-yao , Li Hui , Gu Da-wei , Zhang Yong-feng , Liu Zi-ming , Li He , Han Qing-kai , Wen Bang-chun 
Published: July 2022

Abstract
In this study, considering the amplitude-dependence, a nonlinear vibration model of fiber metal laminates thin plate treated with partial constraint layer damping treatments is proposed. Based on the Jones-Nelson nonlinear theory, the model is established by deducing the stress-strain relationships among four layers including fiber layer, metal layer, viscoelastic layer and constraint layer. Then, the nonlinear vibration characters are solved by utilizing the energy method and the Newton-Raphson technique. Next, the damping character is acquired based on complex modulus method. The experimental example of a TA2/TC500 fiber metal laminates plate treated stainless steel/Zn-33 constraint layer damping is performed to validate the presented nonlinear vibration model. Besides, the affections of the treating factors on the nonlinear vibration characteristics of FMLs plate is discussed as well.