bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opium Use and Cancer Risk: A Comprehensive Systematic Review and Meta-Analysis of Observational Studies
Authors: Mansouri Masoume , Naghshi Sina , Parsaeian Mahbobeh , G Sepanlou Sadaf , Poustchi Hossein , Momayez Sanat Zahra , Sadeghi Omid , Pourshams Akram 
Published: February 2022

Background. Epidemiological studies have reported inconsistent associations between opium use and cancer risk. We therefore conducted a systematic review and meta-analysis to investigate the relationship between opium use and cancer risk. Methods. We searched PubMed, Scopus, ISI Web of Knowledge, and Google Scholar until February 2021 and references of retrieved relevant articles for observational studies that reported the risk of cancer in relation to opium use. Random-effects models were used to calculate pooled effect sizes (ESs) as well as 95% confidence intervals (CIs) for the association between opium use and cancer risk by considering opium doses and types, duration of consumption, and routes of opium use. Results. In total, 21 observational articles, with a total sample size of 64,412 individuals and 6,658 cases of cancer, were included in this systematic review and meta-analysis. Ever opium users, compared with never opium users, had 3.53 times greater risk of overall cancer (pooled ES: 3.53, 95% CI: 2.60–4.79,

P

≤ 0.01). This positive association was also seen for some individual types of cancers except for esophageal and colon cancers. Also, we found that higher opium doses and higher duration of consumption were associated with an increased risk of overall and individual types of cancer. However, the associations between opium doses and the risk of head and neck and larynx cancers were not significant. In terms of the routes of opium use, both opium ingestion and smoking were positively associated with the risk of cancer. Regarding opium types, we found that using teriak, but not shireh, could increase the risk of cancer. Conclusions. Our findings showed that opium use, particularly in the form of teriak, is a risk factor for cancer.
Lansoprazole-induced osteoporosis via the IP3R- and SOCE-mediated calcium signaling pathways
Authors: Cheng Ziping , Liu Yangjie , Ma Mengyuan , Sun Shiyu , Ma Zengqing , Wang Yu , Yu Liyuan , Qian Xuping , Sun Luning , Zhang Xuehui , Liu Yun , Wang Yongqing 
Published: February 2022

Abstract
Background
Many clinical studies have shown a correlation between proton pump inhibitors (PPIs) and osteoporosis or fractures. The purpose of this study was to establish a murine model of chronic oral PPI administration to verify whether PPIs caused bone metabolic impairment and investigate the relevant molecular mechanism underlying the effects of PPIs on MC3T3-E1 murine osteoblasts.

Methods
A lansoprazole-induced bone loss model was used to investigate the damaging effects of PPIs. In vivo, immunohistochemistry, Hematoxylin–Eosin (HE) staining, micro-CT analysis, and blood biochemical analyses were used to evaluate the effect of lansoprazole on bone injury in mice. In vitro, the effects of lansoprazole and related signaling pathways in MC3T3-E1 cells were investigated by CCK-8 assays, EdU assays, flow cytometry, laser confocal microscopy, patch clamping, reverse transcription-quantitative polymerase chain reaction and Western blotting.

Results
After 6 months of lansoprazole gavage in ICR mice, the micro-CT results showed that compared with that in the vehicle group, the bone mineral density (BMD) in the high-dose group was significantly decreased (P < 0.05), and the bone microarchitecture gradually degraded. Biochemical analysis of bone serum showed that blood calcium and phosphorus were both decreased (P < 0.01). We found that long-term administration of lansoprazole impaired skeletal function in mice. In vitro, we found that lansoprazole (LPZ) could cause calcium overload in MC3T3-E1 cells leading to apoptosis, and 2-APB, an inhibitor of IP3R calcium release channel and SOCE pathway, effectively blocked increase in calcium caused by LPZ, thus protecting cell viability.

Conclusions
Longterm administration of LPZ induced osteoporotic symptoms in mice, and LPZ triggered calcium increases in osteoblasts in a concentration-dependent manner. Intracellular calcium ([Ca2+]i) persisted at a high concentration, thereby causing endoplasmic reticulum stress (ERS) and inducing osteoblast apoptosis.
Phosphorylation of BCL2 at the Ser70 site mediates RANKL-induced osteoclast precursor autophagy and osteoclastogenesis
Authors: Ke Dianshan , Yu Yunlong , Li Chenglong , Han Junyong , Xu Jie 
Published: February 2022

Abstract
Background
Phosphorylation modification of BCL2 is involved in receptor activator of nuclear factor-κB ligand (RANKL)-induced autophagy of osteoclast precursors (OCPs) and osteoclastogenesis. As an antiapoptotic molecule, the role of BCL2 phosphorylation in osteoclastogenesis is unknown. This study aimed to explore how BCL2 phosphorylation at specific sites regulates osteoclastogenesis.

Methods
We first examined the effects of RANKL on BCL2 phosphorylation at different sites (Ser70 and Ser87) in OCPs. In vivo, transgenic mice overexpressing RANKL (Tg-hRANKL mice) were used to observe the effects of RANKL on phosphorylated BCL2 at different sites in OCPs of trabecular bone. Subsequently, using site-directed mutagenesis, we observed the respective effect of BCL2 mutations at different phosphorylation sites in OCPs on osteoclastogenesis, apoptosis, autophagy and the affinity between BCL2 and Beclin1/BAX under RANKL intervention.

Results
RANKL promoted BCL2 phosphorylation at the Ser70 (S70) site, but not the Ser87 (S87) site, in OCPs. Moreover, Tg-hRANKL mice had stronger BCL2 phosphorylation capacity at S70, not S87, in the OCPs of trabecular bone than wild-type mice in the same nest. Furthermore, BCL2 mutation at S70, not S87, inhibited RANKL-induced osteoclast differentiation and bone resorption activity. In addition, BCL2 mutation at S70 promoted OCP apoptosis, while BCL2 mutation at S87 showed the opposite effect. Remarkably, the BCL2 mutation at S70, not S87, inhibited OCP autophagic activity. Furthermore, BCL2 mutation at S70 enhanced the coimmunoprecipitation of BCL2 and Beclin1, whereas BCL2 mutation at S87 enhanced the coimmunoprecipitation of BCL2 and BAX in OCPs. More importantly, OCP autophagy, osteoclast differentiation and resorption pits inhibited by BCL2 mutation at S70 could be reversed by Beclin1 upregulation with TAT-Beclin1.

Conclusion
RANKL activates OCP autophagy through BCL2 phosphorylation at S70, thereby promoting osteoclastogenesis, which indicates that the inactivation of BCL2 at S70 in OCPs may be a therapeutic strategy for pathological bone loss.
Post-traumatic headache after mild traumatic brain injury in a one-year follow up study – risk factors and return to work
Authors: Kraemer Yvonn , Mäki Kaisa , Marinkovic Ivan , Nybo Taina , Isokuortti Harri , Huovinen Antti , Korvenoja Antti , Melkas Susanna , Harno Hanna 
Published: February 2022

Abstract
Background
Post-traumatic headache (PTH) is a common symptom following mild traumatic brain injury (mTBI). Patients at risk to develop acute PTH (aPTH) and further persistent PTH (pPTH) need to be recognized.

Methods
This is a one-year follow-up of 127 patients with mTBI, aged 18 to 68, referred to outpatient clinic in the Helsinki University Hospital. Symptoms were assessed at the emergency department (ED), with structured interview at outpatient clinic visit and with Rivermead post-concussion symptom questionnaire at one, three, and 12 months after injury. Psychiatric disorders were assessed with Structured Clinical Interview for DSM-IV Axis I disorders at 3-4 months and return to work (RTW) from patient records.

Results
At one month, 77/127 patients (61%) had aPTH. According to multiple logistic regression analysis, risk factors for aPTH were headache at the emergency department (ED) (OR 5.43), other pain (OR 3.19), insomnia (OR 3.23), and vertigo (OR 5.98). At three months, 17 patients (22% of aPTH patients) had developed pPTH, and at one year, 4 patients (24% of pPTH patients) still presented with pPTH. Risk factors for pPTH at three months were older age (OR 1.06) and current insomnia (OR 12.3). The frequency of psychiatric disorders did not differ between the groups. pPTH patients performed worse on their RTW.

Conclusions
Risk factors for aPTH were insomnia, headache at ED, other pain, and vertigo and for pPTH, insomnia and older age. RTW rate was lower among pPTH patients.
Exploring neuronal mechanisms involved in the scratching behavior of a mouse model of allergic contact dermatitis by transcriptomics
Authors: Liu Boyu , Chen Ruixiang , Wang Jie , Li Yuanyuan , Yin Chengyu , Tai Yan , Nie Huimin , Zeng Danyi , Fang Junfan , Du Junying , Liang Yi , Shao Xiaomei , Fang Jianqiao , Liu Boyi 
Published: February 2022

Abstract
Background
Allergic contact dermatitis (ACD) is a common skin condition characterized by contact hypersensitivity to allergens, accompanied with skin inflammation and a mixed itch and pain sensation. The itch and pain dramatically affects patients’ quality of life. However, still little is known about the mechanisms triggering pain and itch sensations in ACD.

Methods
We established a mouse model of ACD by sensitization and repetitive challenge with the hapten oxazolone. Skin pathological analysis, transcriptome RNA sequencing (RNA-seq), qPCR, Ca2+ imaging, immunostaining, and behavioral assay were used for identifying gene expression changes in dorsal root ganglion innervating the inflamed skin of ACD model mice and for further functional validations.

Results
The model mice developed typical ACD symptoms, including skin dryness, erythema, excoriation, edema, epidermal hyperplasia, inflammatory cell infiltration, and scratching behavior, accompanied with development of eczematous lesions. Transcriptome RNA-seq revealed a number of differentially expressed genes (DEGs), including 1436-DEG mRNAs and 374-DEG-long noncoding RNAs (lncRNAs). We identified a number of DEGs specifically related to sensory neuron signal transduction, pain, itch, and neuroinflammation. Comparison of our dataset with another published dataset of atopic dermatitis mouse model identified a core set of genes in peripheral sensory neurons that are exclusively affected by local skin inflammation. We further found that the expression of the pain and itch receptor MrgprD was functionally upregulated in dorsal root ganglia (DRG) neurons innervating the inflamed skin of ACD model mice. MrgprD activation induced by its agonist β-alanine resulted in exaggerated scratching responses in ACD model mice compared with naïve mice.

Conclusions
We identified the molecular changes and cellular pathways in peripheral sensory ganglia during ACD that might participate in neurogenic inflammation, pain, and itch. We further revealed that the pain and itch receptor MrgprD is functionally upregulated in DRG neurons, which might contribute to peripheral pain and itch sensitization during ACD. Thus, targeting MrgprD may be an effective method for alleviating itch and pain in ACD.
An efficient and pragmatic approach for regulatory aquatic mixture risk assessment of pesticides
Authors: Dietrich Christian , Wang Magnus , Ebeling Markus , Gladbach Anja 
Published: February 2022

AbstractThe current regulatory approach to address aquatic mixture toxicity for pesticides in the EU (EFSA J 11:3290, 2013) is rather complex: in typical cases it requires conducting the entire mixture risk assessment scheme for every exposure scenario separately (e.g. 6–8 ecotoxicological endpoints, for each of the nine exposure scenarios for the European Central Zone with 24 common mitigation measure combinations result in over 1700 sub-scenarios to be assessed). This article discusses the available concepts for a mixture toxicity assessment, the key questions raised and the implementation of these questions in existing risk assessment approaches. Based on this, an alternative, more efficient assessment scheme for aquatic mixture risk assessment (AMiRA) is proposed with the aim of facilitating the practical conduct and interpretation of the assessment while addressing the key questions and preserving the level of protection. The scheme assesses product risk (including a check for non-additive effects), the presence of a risk driver and gains efficiency by the straightforward use of risk quotients (RQ) to calculate mixture risk quotients (RQmix) that are equivalent to the calculation of exposure toxicity ratios for a mixture (ETRmix,CA = Exposure-Toxicity-Ratio for mixtures based on concentration addition) proposed by EFSA (EFSA J 11:3290, 2013). A case study is provided underlining the equivalence of the proposed approach to the EFSA (EFSA J 11:3290, 2013) decision tree.
Coronavirus disease (COVID-19) and conjunctival sac swab findings
Authors: Vesely Pavol , Novakova Elena , Stubna Michal , Trnka Michal , Jurenova Denisa , Lyskova Darina , Furda Robert , Plesnikova Paulina , Himic Vratko , Furdova Alena 
Published: February 2022

Abstract
Background
The purpose of this article is to evaluate the positivity of conjunctival sac swab by PCR (Polymerase chain reaction) test in COronaVIrus Disease 19 (COVID-19) patients.

Methods
Inclusion criteria of our study were COVID-19 patients hospitalized during March 2021 in inpatient wards at University Hospitals in towns Bratislava and Zilina, Slovakia. The conjunctival sac swabs collected by four ophthalmologists were stored for 24 h, then analyzed in the laboratory of the Department of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University, Slovakia. The sampling apparatus, used for conjunctival sac swab, was the Dacron polyester swab.

Results
We examined one group of 302 COVID-19 patients, 168 Male (56%) and 134 Female (44%). The patients’ mean age was 66.3 ± 13.66 years, ranging from 25 to 96 years, and the mean length of hospital stay in our patients with a nasopharyngeal positive PCR test was 7.33 ± 4.76, from 2 to 24 days.
The PCR tests from the conjunctival sac swabs were positive in 33 patients (11%), negative in 259 patients (86%), and ten patients (3%) were with the unclear result. In the group of 33 positive patients were 17 males with a mean age of 74.6 ± 13.59 years and 16 females with a mean age of 70.63 ± 14.17 years.
The cycle threshold (CT) values differed significantly between conjunctival sac swabs from the nasopharynx and the conjunctiva. Medians of the values were 25.1 (14.1, 32.1) and 31.5 (22.6, 36.6) (P <  0.001), respectively.

Conclusion
This study affirmed that in COVID-19 patients the SARS-CoV-2 was detectable with PCR test in conjunctival sac swab, but the positivity rate was only about one to ten cases (11%).
Comparison of the choice of animals for re-sequencing in two maternal pig lines
Authors: Dauben Christina M. , Große-Brinkhaus Christine , Heuß Esther M. , Henne Hubert , Tholen Ernst 
Published: February 2022

AbstractNext-generation sequencing is a promising approach for the detection of causal variants within previously identified quantitative trait loci. Because of the costs of re-sequencing experiments, this application is currently mainly restricted to subsets of animals from already genotyped populations. Imputation from a lower to a higher marker density could represent a useful complementary approach. An analysis of the literature shows that several strategies are available to select animals for re-sequencing. This study demonstrates an animal selection workflow under practical conditions. Our approach considers different data sources and limited resources such as budget and availability of sampling material. The workflow combines previously described approaches and makes use of genotype and pedigree information from a Landrace and Large White population. Genotypes were phased and haplotypes were accurately estimated with AlphaPhase. Then, AlphaSeqOpt was used to optimize selection of animals for re-sequencing, reflecting the existing diversity of haplotypes. AlphaSeqOpt and ENDOG were used to select individuals based on pedigree information and by taking into account key animals that represent the genetic diversity of the populations. After the best selection criteria were determined, a subset of 57 animals was selected for subsequent re-sequencing. In order to evaluate and assess the advantage of this procedure, imputation accuracy was assessed by setting a set of single nucleotide polymorphism (SNP) chip genotypes to missing. Accuracy values were compared to those of alternative selection scenarios and the results showed the clear benefits of a targeted selection within this practical-driven approach. Especially imputation of low-frequency markers benefits from the combined approach described here. Accuracy was increased by up to 12% compared to a randomized or exclusively haplotype-based selection of sequencing candidates.
GWAS and genomic prediction of milk urea nitrogen in Australian and New Zealand dairy cattle
Authors: van den Berg Irene , Ho Phuong N. , Nguyen Tuan V. , Haile-Mariam Mekonnen , MacLeod Iona M. , Beatson Phil R. , O’Connor Erin , Pryce Jennie E. 
Published: February 2022

Abstract
Background
Urinary nitrogen leakage is an environmental concern in dairy cattle. Selection for reduced urinary nitrogen leakage may be done using indicator traits such as milk urea nitrogen (MUN). The result of a previous study indicated that the genetic correlation between MUN in Australia (AUS) and MUN in New Zealand (NZL) was only low to moderate (between 0.14 and 0.58). In this context, an alternative is to select sequence variants based on genome-wide association studies (GWAS) with a view to improve genomic prediction accuracies. A GWAS can also be used to detect quantitative trait loci (QTL) associated with MUN. Therefore, our objectives were to perform within-country GWAS and a meta-GWAS for MUN using records from up to 33,873 dairy cows and imputed whole-genome sequence data, to compare QTL detected in the GWAS for MUN in AUS and NZL, and to use sequence variants selected from the meta-GWAS to improve the prediction accuracy for MUN based on a joint AUS-NZL reference set.

Results
Using the meta-GWAS, we detected 14 QTL for MUN, located on chromosomes 1, 6, 11, 14, 19, 22, 26 and the X chromosome. The three most significant QTL encompassed the casein genes on chromosome 6, PAEP on chromosome 11 and DGAT1 on chromosome 14. We selected 50,000 sequence variants that had the same direction of effect for MUN in AUS and MUN in NZL and that were most significant in the meta-analysis for the GWAS. The selected sequence variants yielded a genetic correlation between MUN in AUS and MUN in NZL of 0.95 and substantially increased prediction accuracy in both countries.

Conclusions
Our results demonstrate how the sharing of data between two countries can increase the power of a GWAS and increase the accuracy of genomic prediction using a multi-country reference population and sequence variants selected based on a meta-GWAS.
Functionally prioritised whole-genome sequence variants improve the accuracy of genomic prediction for heat tolerance
Authors: Cheruiyot Evans K. , Haile-Mariam Mekonnen , Cocks Benjamin G. , MacLeod Iona M. , Mrode Raphael , Pryce Jennie E. 
Published: February 2022

Abstract
Background
Heat tolerance is a trait of economic importance in the context of warm climates and the effects of global warming on livestock production, reproduction, health, and well-being. This study investigated the improvement in prediction accuracy for heat tolerance when selected sets of sequence variants from a large genome-wide association study (GWAS) were combined with a standard 50k single nucleotide polymorphism (SNP) panel used by the dairy industry.

Methods
Over 40,000 dairy cattle with genotype and phenotype data were analysed. The phenotypes used to measure an individual’s heat tolerance were defined as the rate of decline in milk production traits with rising temperature and humidity. We used Holstein and Jersey cows to select sequence variants linked to heat tolerance. The prioritised sequence variants were the most significant SNPs passing a GWAS p-value threshold selected based on sliding 100-kb windows along each chromosome. We used a bull reference set to develop the genomic prediction equations, which were then validated in an independent set of Holstein, Jersey, and crossbred cows. Prediction analyses were performed using the BayesR, BayesRC, and GBLUP methods.

Results
The accuracy of genomic prediction for heat tolerance improved by up to 0.07, 0.05, and 0.10 units in Holstein, Jersey, and crossbred cows, respectively, when sets of selected sequence markers from Holstein cows were added to the 50k SNP panel. However, in some scenarios, the prediction accuracy decreased unexpectedly with the largest drop of − 0.10 units for the heat tolerance fat yield trait observed in Jersey cows when 50k plus pre-selected SNPs from Holstein cows were used. Using pre-selected SNPs discovered on a combined set of Holstein and Jersey cows generally improved the accuracy, especially in the Jersey validation. In addition, combining Holstein and Jersey bulls in the reference set generally improved prediction accuracy in most scenarios compared to using only Holstein bulls as the reference set.

Conclusions
Informative sequence markers can be prioritised to improve the genomic prediction of heat tolerance in different breeds. In addition to providing biological insight, these variants could also have a direct application for developing customized SNP arrays or can be used via imputation in current industry SNP panels.
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules
Authors: Kropiwnicki Eryk , Lachmann Alexander , Clarke Daniel J. B. , Xie Zhuorui , Jagodnik Kathleen M. , Ma’ayan Avi 
Published: February 2022

AbstractBackgroundPubMed contains millions of abstracts that co-mention terms that describe drugs with other biomedical terms such as genes or diseases. Unique opportunities exist for leveraging these co-mentions by integrating them with other drug-drug similarity resources such as the Library of Integrated Network-based Cellular Signatures (LINCS) L1000 signatures to develop novel hypotheses.ResultsDrugShot is a web-based server application and an Appyter that enables users to enter any biomedical search term into a simple input form to receive ranked lists of drugs and other small molecules based on their relevance to the search term. To produce ranked lists of small molecules, DrugShot cross-references returned PubMed identifiers (PMIDs) with DrugRIF or AutoRIF, which are curated resources of drug-PMID associations, to produce an associated small molecule list where each small molecule is ranked according to total co-mentions with the search term from shared PubMed IDs. Additionally, using two types of drug-drug similarity matrices, lists of small molecules are predicted to be associated with the search term. Such predictions are based on literature co-mentions and signature similarity from LINCS L1000 drug-induced gene expression profiles.ConclusionsDrugShot prioritizes drugs and small molecules associated with biomedical search terms. In addition to listing known associations, DrugShot predicts additional drugs and small molecules related to any search term. Hence, DrugShot can be used to prioritize drugs and preclinical compounds for drug repurposing and suggest indications and adverse events for preclinical compounds. DrugShot is freely and openly available at:https://maayanlab.cloud/drugshotandhttps://appyters.maayanlab.cloud/#/DrugShot.