bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations between substandard housing and depression: Insights from the Korea Welfare Panel Study
Authors: KIM Selin , Jeong Wonjeong , Jang Bich Na , Park Eun-Cheol , Jang Sungin 
Published: June 2020

Abstract
Background
Housing is an important social determinant of health. Poor housing conditions are associated with a wide range of health conditions, including mental health. The study aimed to investigate the association between substandard housing and depression.
Methods
We used panel data collected by the Korea Welfare Panel Study and a sample drawn from waves 11 (2016) to 13 (2018). Substandard housing was defined via three criteria: the minimum residential area and number of rooms by application, essential facility standards, and environmental standards. Depression was measured with the CESD-11. A generalized estimating equation model was used to investigate associations between substandard housing and CESD-11 scores.
Results
Participants living in substandard housing have higher depression scores (male: β = 0.63, female: β = 0.40) than participants who do not live in substandard housing. Participants who do not meet environmental standards have higher depression scores (male: β = 0.85, female: β = 0.66) than participants who do not live in substandard housing; the findings are seen in both men and women.
Conclusion
This study identified an association between substandard housing and depression by gender, and the results were significant. We found that among the three criteria, environmental standards are most likely to be associated with depression. In practical terms, we should consider improving environmental factors of housing to mitigate mental health issues related to substandard housing.
Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species
Authors: Nielsen Erica , Henriques Romina , Beger Maria , Toonen Robert , Heyden Sophie von der 
Published: June 2020

Abstract
Background: As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare the dominant environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin ( Parechinus angulosus ), Common shore crab ( Cyclograpsus punctatu s), and Granular limpet ( Scutellastra granularis ). Results: Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus . Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus , but not for C. punctatus . Conclusion: The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses better predict evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.
Clinical Characteristics and prognostic implications of BRCA-Associated Tumors in Males: A Pan-tumor Survey
Authors: Sun Peng , Li Yue , Chao Xue , Li Jibin , Luo Rongzhen , Li Mei , He Jiehua 
Published: June 2020

Abstract
PurposeBRCA mutations (BRCAm) in males have been reported to confer a higher risk in the development of various tumors. However, little is known about the characteristics and prognosis of BRCA-associated tumors in males.DesignWe conducted a pan-tumor survey on BRCA-associated tumors in males (n=346). Comparative analyses with female BRCAm carriers (n=349) and male non-BRCAm carriers (n=4577) were proceed.ResultsSimilar BRCAm incidence and diagnostic age were observed in male and female patients. Carcinomas of lung (19.4%), bladder (15.6%), stomach (11.9%), and cutaneous melanoma (16.3%) were the frequent tumors demonstrating BRCAm in males. The majority were stage II/III diseases with a higher frequency of BRCA2 mutation (65.6%). A total of 127 BRCA1 and 311 BRCA2 mutations were identified in males, of which 21.8% and 28.6% were deleterious, respectively. Deleterious variants were commonly identified in cancer of breast, colorectum, prostate, and stomach. Recurrent BRCA2 mutations at P606L/S, E832K/G, and T3033Lfs*29 were detected in males, while N1784K/Tfs*3 were frequently observed in both males and females. BRCAm in males was associated with a decrease OS and PFS than in females, as well as an increased OS than in non-BRCAm carriers. Subgroup analysis demonstrated that BRCAm was associated with increased OS in gastric and bladder cancer, decreased PFS in cancer of prostate, esophagus, head and neck, and a decreased OS in glioma/glioblastoma in males.ConclusionOur findings provide an overview of the distinct characteristics and clinical outcomes in BRCA-associated tumors in males, suggesting the importance of further BRCA testing in males.
Genomic signatures in pediatric advanced stage Burkitt lymphoma/ leukemia in Chinese population by next generation sequencing
Authors: Lei Xiaoying , Yin Nange , Guo Yuxia , Song Ling , Zhu Jin , Xiao Jianwen 
Published: June 2020

Abstract
Background: Burkitt lymphoma/leukemia (BL/BAL) is the most common lymphoma in chidren and sporadic subtype is dominant in Chinese population. MYC gene translocation is essential for sporadic BL/BAL (sBL/BAL), whereas other gene mutations also play important roles in the development of sBL/BAL. Methods: The clinical data of ten Chinese children with sBL/BAL were collected; next generation sequencing of tumor tissues were detected. BL and diffused large B cell lymphoma (DLBCL) database was also collected and bioinformatics analyzed was done.Results: Nine male and one female were enrolled in the study, including six BL patients (stage III) and four BAL patients (stage IV). Average age at diagnosis was 100.10±13.39mon; overexpression of CD20 was detectable, MYC rearrangement were confirmed. The patients received combination treatment of chemotherapy and Rituximab, complete remission was achieved and all the patients survived. Germline causal gene mutations were detected in four (40%) patients by whole exome sequencing (WES); ID3, BRCA2, ARID1A and SMARCA4 mutations, except MYC mutation, were the most common somatic mutations. The gene functions in pathopoiesis were differ from BL to DLBCL in dataset. These identified mutated genes were enriched and connected by GO or KEGG pathway, it seemed that PI3K-Akt signaling pathway or EGFR-TKI resistance pathway play important roles in the pathopoiesis of sBL/BAL. Conclusion: sBL/BAL is a highly aggressive but curable lymphoma; the pathophysiolopoiesis is still in research. The molecular hallmark of sBL/BAL is MYC translocation, whereas additional chromosomal abnormalities and gene mutations also occur and play roles in the progression of the disease. PI3K-Akt signaling pathway seems play important roles in the pathopoiesis of sBL/BAL, and sBL/BAL may be inhibited by such signaling pathway; EGFR-TKI resistance pathway was also analyzed in sBL/BAL patients, it reveals that EGFR-TKI treatment is invalid. Further research is needed for the hypothesis and possible mechanisms.
Low-level expression of necroptosis factors indicative of a poor prognosis of squamous cell carcinoma subtype of non-small-cell lung cancer
Authors: Lim Jun Hyeok , Oh Sekyung , Kim Lucia , Suh Young Ju , Ha Yu-Jin , Kim Jung Soo , Kim Hyun-Jung , Park Mi Hwa , Kim Young Sam , Cho Yunjung , Kwak Seung Min , Lee Hong Lyeol , Kim You-Sun , Ryu Jeong-Seon 
Published: June 2020

Abstract
Background

A programmed cell death pathway, necroptosis may synergize with DNA damage response (DDR) in opposing tumor progression. While our basic mechanistic understanding of necroptotic cell death advances rapidly, its prognostic implications have not been thoroughly examined in cancer.
Methods

We measured expression level of nine proteins involved in necroptosis and DDR in primary stage I non-small-cell lung carcinoma (NSCLC) samples from 394 patients using a tissue microarray.
Results

We find that low-level expression of the necroptosis markers RIPK3 and PELI1 is associated with increased risk of patient death and that high-level expression of the key DDR factor p53 enhances this risk. These effects appear to be specific to squamous cell carcinoma (SCC) subtype of NSCLC patients but not observable in non-SCC patients.
Conclusions

Low-level expression of such necroptosis factors as RIPK3 and PELI1 in combination with high-level expression of the DDR factor p53 can serve as a critical indicator in predicting survival of patients with stage I SCC.
Energy Replenishment Diversification Under Marine Spatial Planning Connects Big Data, Artificial Intelligence, Internet of Things for Coastal Community Sustainability
Authors: Liao Victor Te Cheng 
Published: June 2020

Abstract
Background Controversial coal power plant restart and non-nuke policy were rejected by referendum in Taiwan on 24 Nov 2018. Outcomes affecting energy replenishment and undermining economic stability are criticized politicization because coal energy is detrimental but no nuke beneficial for the environment. These policies could be contradictory. Problem No autonomous energy puts the country into extreme risk and is controlled by foreigners. Developing energy faces a traditional tradeoff between economic development and environmental protection. Purpose The assumption an innovative energy diversification linking Big Data, artificial intelligence (AI), and the Internet of Things (IoT) is encouraged. The paper investigates upgrading liquified petroleum gas (LPG) to liquified natural gas (LNG) under marine spatial planning (MSP) for energy replenishment and creating an energy diversification framework through integrated coastal zone management (ICZM) linking Big Data, IoT, AI whether are supported. Results Online sampling investigation results, enhancing LPG to LNG at the ecologically biologically significant area (EBSA) under MSP was less encouraged but linking Big Data, IoT, AI innovation through ICZM was overwhelmingly supported and consistent with goalkeepers interview. Research finding gender, the environment, age revealed no significant difference from LNG through MSP and AI under ICZM. Males more support LNG energy replenishment and energy diversification. Energy deficiency, environmental protection, and economic development were interrelated. Conclusion The results LPG to LNG revealed less encouraging and implicates many coastal communities in favor of tangible stable electricity without blackout is important than the intangible slogan EBSA protection, or perhaps renewable energy is an alternative approach. An autonomous energy diversification framework through ICZM links Big Data, IoT, AI for sustainable coastal community development (SCCD) indicating no significant difference from gender, environment, age, and is consistent with the goalkeepers' interview results supporting energy diversification. The finding males more support LNG and energy diversification. Finally, the study suggests that legislative enforcement establishment designate expertise teamwork to coordinate administration, integrate programs of energy replenishment, creating an autonomous energy diversification framework for monitoring energy demand, supplies, replenishment, and connect Big Data, IoT, AI innovation for SCCD.
NMR Elucidation of Non-productive Binding Sites of 13C-Labeled Lignin Models with Carbohydrate Binding Module of Cellobiohydrolase I for Efficient Biomass Conversion
Authors: Tokunaga Yuki , Nagata Takashi , Kondo Keiko , Katahira Masato , Watanabe Takashi 
Published: June 2020

Abstract
Background: Highly efficient enzymatic saccharification of pretreated lignocellulose is a primary key step in achieving lignocellulosic biorefinery. Cellobiohydrolase I (Cel7A) secreted by Trichoderma reesei is an industrially used cellulase possessing carbohydrate binding module 1 (TrCBM1) as the C-terminal domain. Non-productive binding of TrCBM1 to lignin significantly decreases enzymatic saccharification efficiency and enhance cost of biomass conversion due to required additional enzymes. Understanding of the interaction mechanism between lignin and TrCBM1 is essentially required to realize cost-effective biofuels production, but the binding sites in lignin have not been clearly elucidated. Results: Three types of 13C-labeled b-O-4 lignin oligomer models were synthesized and characterized. The 2D 1H-13C HSQC spectra of the 13C-labeled lignin models exhibited that 13C-labels were correctly incorporated in the (1) aromatic rings and b positions, (2) a positions, and (3) methoxy groups, respectively. The TrCBM1 binding sites in lignin were analyzed by observing NMR chemical shift perturbations (CSPs) using the synthetic 13C-labeled b-O-4 lignin oligomer models. Obvious CSPs were observed in signals from the aromatic regions in oligomers bound to TrCBM1, whereas perturbations in the signals from aliphatic regions and methoxy groups were insignificant. This indicated that hydrophobic interactions and p–p stacking were dominating factors in non-productive binding. The synthetic lignin models have two configurations whose terminal units were differently aligned and donated C(I) and C(II). The C(I) ring showed remarkable perturbation compared with C(II), which indicated that binding of TrCBM1 is evidently affected by configuration of lignin models. Long-chain lignins (DP 4.16–4.70) clearly bound to TrCBM1. Interactions with short-chain lignins (DP 2.64–3.12) were insignificant, indicating that a DP greater than 4 was necessary for TrCBM1 binding. Conclusion: The CSP analysis using 13C-labeled b-O-4 lignin oligomer models enabled us to identify TrCBM1 binding sites in lignin at the atomic level. This specific interaction analysis will lead to new molecular design of cellulase having controlled affinity to cellulose and lignin for cost-effective biorefinery process.
Impact of negative energy balance on transcriptomic profiles of three endometrial cell types isolated by laser capture microdissection in postpartum dairy cows
Authors: Chankeaw Wiruntita , Lignier Sandra , Richard Christophe , Ntallaris Theodoros , Raliou Mariam , Guo Yongzhi , Plassard Damien , Bevilacqua Claudia , Sandra Olivier , Andersson Goran , Humblot Patrice , Charpigny Gilles 
Published: June 2020

Abstract
Background: In postpartum dairy cows, the energy needs to satisfy high milk production induces a more or less pronounced Negative Energy Balance (NEB) status. NEB associated with fat mobilization impairs reproductive function. This study investigated the specific impact of NEB on gene expression in the three main types of endometrial cells at time planned for insemination and implantation. Endometrial cell types (stromal, glandular and luminal epithelial cells) were isolated by laser micro-dissection allowing the study of constitutive gene expression and their specific response to NEB. Methods: Nine Swedish Red cows receiving a control diet or a mild restricted diet to induce differences of energy balance were categorized into mild (MNEB, n = 5) and severe negative energy balance (SNEB, n = 4). The three endometrial cell types: luminal (LE), glandular (GE) epithelium and stroma (ST) were collected by laser microdissection from endometrial biopsies performed at 80 days postpartum. Results: Transcriptome profiles obtained by RNA sequencing revealed differences in constitutive gene expression between the three cells types and also differences in specific responses related to the severity of NEB. Number of differentially expressed genes between SNEB and MNEB cows was higher in ST than in LE and GE, respectively. SNEB was associated with differential expression of genes related to metabolic processes and embryo-maternal interactions in ST. Under-expression of genes related to cell structure was found in GE whereas genes related to pro-inflammatory pathways were over-expressed. Genes associated to adaptive immunity were under-expressed in LE. Conclusion: The three different main cells types of the endometrium, have very different patterns of gene expression. The severity of NEB after calving is associated with changes in gene expression at time of breeding. Specific alterations in GEs are associated with activation of pro-inflammatory mechanisms. Concomitantly, changes in the expression of genes related to cell to cell interactions and maternal recognition of pregnancy takes place in ST. The combination of these effects possibly altering the uterine environment and embryo maternal interactions may negatively influence the establishment of pregnancy.
Understanding the Physiological Functions of the Host Xenobiotic-sensing Nuclear Receptors PXR and CAR on the Gut Microbiome using Genetically Modified Mice
Authors: Little Mallory , Dutta Moumita , Li Hao , Matson Adam , Shi Xiaojian , Gu Haiwei , Mani Sridhar , Cui Julia Yue 
Published: June 2020

Abstract
Background: Pharmacological activation of the host xenobiotic-sensing nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) is well-known to increase drug metabolism and reduce inflammation. Little is known regarding the physiological functions of PXR and CAR on the gut microbiome, which is an important regulator for the host immune surveillance and bile acid (BA) metabolism. We examined the gut microbiome composition and BA metabolites in high vs. low PXR/CAR-expressing mice, and in mice that are deficient in PXR, CAR, or both, at two developmental ages. We also utilized humanized PXR transgenic (hPXR-TG) mice to compare the species-specific effect of PXR on the gut microbiome. Results: We discovered bivalent hormetic functions of PXR and CAR in modulating the richness of the gut microbiome and inflammatory biomarkers: the high PXR/CAR expressers had higher microbial richness, pro-inflammatory bacteria (distinct taxa in Helicobacteraceae and Helicobacter), and fecal pro-inflammatory cytokines, suggesting higher immune surveillance to prevent the colonization of harmful bacteria. Interestingly, the absence of PXR or CAR also increased the microbial richness, and absence of both receptors synergistically increased the microbial richness. PXR and CAR deficiency increased the pro-inflammatory bacteria (Helicobacteraceae and Helicobacter). Most notably, deficiency in both PXR and CAR markedly increased the relative abundance of Lactobacillus, which is capable of bile salt hydrolase (BSH) activity. This corresponded to a decrease in major primary taurine-conjugated bile acids (BAs) in feces, which may lead to higher internal burden of taurine and unconjugated BAs, both of which are linked to inflammation, oxidative stress, and cytotoxicity. hPXR-TG mice had a distinct microbial profile as compared to wild-type mice, including a higher representation of Prevotella. hPXR-TG mice also had higher 12-OH BAs but lower 6-OH BAs, suggesting PXR’s species-specific role in modulating host hepatic BA synthesis. Conclusions: This study is the first to show that the host PXR and CAR profoundly influence the composition of the gut microbiome and its BA metabolites, with a bivalent hormetic relationship between PXR/CAR levels and microbial richness, unveiling the involvement of PXR/CAR-microbiome interactions in host immune surveillance and BA metabolism.
Clinicopathological and prognostic significance of Fusobacterium nucleatum infection in colorectal cancer: a meta-analysis
Authors: Huangfu Shuchen , Zhang Wen-bin , Zhang haoran , Li Yang , Zhang Yiran , Chu Xiaodong , Nie Jinling , Chen Changshun , Jiang Hai-ping , Pan Jing-hua 
Published: June 2020

Abstract
Background: Accumulating evidences about the association between Fusobacterium nucleatum (F. nucleatum) and colorectal cancer (CRC) has been reported in various studies. However, the definite relationship between abundance of F. nucleatum with clinical characteristics and prognosis of CRC is still controversial. Methods: PubMed, Embase and Web of Science were searched for relevant articles up to April 7, 2020. Outcomes of interest included clinical characteristics, molecular characteristic and survival analysis. HR (OR), odds ratios (OR) and 95% confidence interval (CI) were calculated to explore the prognostic value and relationship of clinical characteristics of Fusobacterium nucleatum in CRC.Results: A total of 3626 patients with CRC from 13 eligible studies were included. High abundance of F. nucleatum was associated with worse prognosis on overall survival (OS) (HR= 1.40, P < 0.0001), disease-free survival (DFS) (HR = 1.71, P = 0.0002) and cancer-specific survival (OR= 1.93, P <0.0001). In addition, F. nucleatum abundance was related with T (T3-T4) stage(OR = 2.20, P < 0.00001), M (M1) stage (OR = 2.11, P = 0.005), poor tumor differentation(OR = 1.83, P =0.02), microsatellite instability (MSI) -high (OR = 2.53, P = 0.0003) and KRAS mutation (OR =1.27, P=0.05).Conclusion: The present evidences revealed that high abundance of F. nucleatum is inclined to indicate worse prognosis and is associated with tumor growth, distant Impact: This study highlights the risk factor of F. nucleatum for worse prognosis of CRC.
Comparative genomic analysis of head and body/tail of pancreatic ductal adenocarcinoma at early and late stages
Authors: Zhang Xueyou , Feng Shi , Wang Qian , Huang Haitao , Xie Qinfen , Zhang Wu , Wang Aodi , Zhang Shuirong , Wang Lingjian , Yao Ming , Ling Qi 
Published: June 2020

Abstract
Background

Pancreatic ductal adenocarcinoma (PDAC), one of the most lethal human cancers, can be divided into head and body/tail cancers according to the anatomy. We previously reported a prognostic relevance of tumor location in resectable PDAC. This study is aimed to further explore the mechanism underlying the molecular diversity between the head and body/tail of PDACs.
Methods

We detected tumor genomes in 154 resectable (surgery) and non-resectable (biopsy) PDACs using a next-generation sequencing panel. Wilcoxon rank test or Fisher exact test was used for evaluating associations between clinical characteristics, mutation frequency, and survival probability between the two cohorts.
Results

Compared with pancreatic head cancers, pancreatic body/tail cancers showed significantly more enriched genomic alterations in KRAS (97.1% vs. 82.4%, p = 0.004) and SMAD4 (42.0% vs. 21.2%, p = 0.008). At early stages (I-II), the SMAD4 mutation rate was significantly higher in pancreatic body/tail cancers than pancreatic head cancers (56.0% vs. 26.5%, p = 0.021). At late stages (III-IV), pancreatic body/tail cancers presented significantly higher KRAS mutation rate (100.0% vs. 75.8%, p = 0.001), higher frequency of MAPK pathway mutation (100% vs. 87.8%, p = 0.040) and lower rates of druggable genomic alterations (30.8% vs. 57.6%, p = 0.030) than pancreatic head cancers.
Conclusions

The molecular diversity exists between pancreatic head and body/tail cancers in both tumor initiation and progression. Pancreatic body/tail cancer seems to be more malignant than pancreatic head cancer at late stages.