bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice
Authors: Pan Yinghua , Liang Haifu , Gao Lijun , Dai Gaoxing , Chen Weiwei , Yang Xinghai , Qing Dongjin , Gao Ju , Wu Hao , Huang Juan , Zhou Weiyong , Huang Chengcui , Liang Yuntao , Deng Guofu 
Published: August 2020

Abstract
Background
Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold.

Results
This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12–4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29,128 and 30,131 genes in genotypes 253 and Y12–4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis (WGCNA) revealed Y12–4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice.

Conclusion
Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.
Patient-individual cancer cell lines and tissue analysis delivers no evidence of sequences from DNA viruses in colorectal cancer cells
Authors: Gock Michael , Kordt Marcel , Matschos Stephanie , Mullins Christina S. , Linnebacher Michael 
Published: August 2020

AbstractBackgroundSeveral DNA viruses are highly suspicious to have oncogenic effects in humans. This study investigates the presence of potentially oncogenic viruses such as SV40, JCV, BKV and EBV in patient-derived colorectal carcinoma (CRC) cells typifying all molecular subtypes of CRC.MethodsSample material (gDNA and cDNA) of a total of 49 patient-individual CRC cell lines and corresponding primary material from 11 patients, including normal, tumor-derived and metastasis-derived tissue were analyzed for sequences of SV40, JVC, BKV and EBV using endpoint PCR. In addition, the susceptibility of CRC cells to JCV and BKV was examined using a long-term cultivation approach of patient-individual cells in the presence of viruses.ResultsNo virus-specific sequences could be detected in all specimens. Likewise, no morphological changes were observed and no evidence for viral infection or integration could be provided after long term CRC cell cultivation in presence of viral particles.ConclusionsIn summary, the presented data suggest that there is no direct correlation between tumorigenesis and viral load and consequently no evidence for a functional role of the DNA viruses included into this analysis in CRC development.
Nutrition assessment and geriatric associated conditions among community dwelling Iranian elderly people
Authors: Bakhtiari Afsaneh , pourali Mahbobeh , Omidvar Shabnam 
Published: August 2020

Abstract
Background
Although malnutrition risk is well documented in elderly care institutions, few studies have been conducted to address concerns regarding community-dwelling elderly people. This study has been aimed to describe the nutritional status and its related socioeconomic and geriatric factors in community-dwelling elders with malnutrition.

Method
For this study, a randomized sampling among people aged 60 has been done (n = 326). Information on nutrition status (full MNA) and health information, like cognitive status (MMSE), daily functional status (ADL and IADL scales) and frailty was obtained. Multiple logistic regression analyses have been carried out, in order to identify the association of demographical and clinical factors with malnutrition.

Results
28.1% of the participants suffered from poor nutrition. In the binary analysis, low MNA scores were associated with increasing age, female gender, lower education level, financial dependence, solitary life, poor self-rated health, multiple physical disabilities and chronic disease, polypharmacy, smoking, functional and cognitive decrease and frailty. In the final model of the multivariate analysis, living alone (OR:1.249,CI:1.105–2.620), multiple physical disabilities (OR:2.183,CI:1.246 ± 3..250) and chronic disease (OR: 2.148,CI:1.167–2.879) were independently associated with malnutrition. Also financial independency (OR:0.625,CI:0.233–0.938), functional ability on ADL (OR:0.536,CI:0.327–0.976) and IADL (OR:0.319,CI:0.194–0.856), normal cognitive (OR:0.456,CI:0.293–0.934) and no frailty (OR:0.253,CI:0.117–0.729) independently were inversely associated with malnutrition. The model was adjusted for all socio- demographic and health variables that were significantly related in the previous models.

Conclusions
Our results indicated a strong correlation between malnutrition and health status. Identifying predictive factors can potentially improve prevention and management strategies used for malnutrition in elderly.
Relocation experiences of the elderly to a long-term care facility in Taiwan: a qualitative study
Authors: Wu Chia-Shan , Rong Jiin-Ru 
Published: August 2020

Abstract
Background
Relocation to a long-term care (LTC) facility is a major life change for most elderly people. Following relocation, many elderly experience difficulties in adapting to changes in the living environment. Taiwan is increasingly becoming an “aging society” and the numbers of those who relocate from family residences to long-term residential care facilities have increased over years. However, in-depth evidence on the experiences of the elderly of their stay in LTC facilities in Taiwan is relatively sparse. This study aimed to explore the relocation experiences of the elderly to a LTC facility to inform policy and practice to address their needs effectively.

Methods
A qualitative study, using semi-structured in-depth interviews, was conducted to explore the experiences of 16 elderly people who have relocated to and lived in a LTC facility in Taiwan for up to a period of 12 months. All interviews were recorded, transcribed, and analyzed using grounded theory approach.

Results
Participants’ accounts reflected four interrelated key themes: wish to minimize the burden, but stay connected with the family; perceived barriers to adaptation; valuing tailored care; and acceptance and engagement. Each theme included interrelated subthemes that influenced one another and represented the different stages in the relocation journey. Most participants viewed relocation as a way of minimizing the burden of their care from family members, but desired to keep a close connection with family and friends. Participants recounted experiences of psychological resistance while making the decision to relocate. Fear of losing autonomy and the ability to perform self-care was a major reason for resistance to adapt. Provision of tailored care was accorded much value by the participants. The decision to accept the relocation and to adapt themselves to the new environment due to their needs for constant care was explicit in some accounts.

Conclusions
Relocation to LTC facility is a dynamic process in the first year of moving into the facility, and involves a range of emotions, feelings and experiences. Adaptation of the elderly into the LTC facility can be maximized if the relocation is well planned with provisions for individually tailored care and family involvement.
Renal function in Ethiopian HIV-positive adults on antiretroviral treatment with and without tenofovir
Authors: Yilma Daniel , Abdissa Alemseged , Kæstel Pernille , Tesfaye Markos , Olsen Mette F. , Girma Tsinuel , Ritz Christian , Friis Henrik , Andersen Åse B. , Kirk Ole 
Published: August 2020

AbstractBackgroundLimited data are available on the effect of antiretroviral treatment (ART) or Tenofovir disoproxil fumarate (TDF) on renal function in Ethiopians. We aimed to assess factors associated with renal function changes during the first year of ART with special focus on TDF.MethodsHIV positive persons who were ≥ 18 years of age and eligible for ART initiation were recruited. Creatinine measurement to estimate glomerular filtration rate (eGFR) and spot urine analyses were performed at baseline and after 3, 6 and 12 months of ART. Univariate and multivariate linear regression and univariate logistic regression were used to determine factors associated with eGFR as continuous and categorical variable respectively. A linear mixed model was used to assess 12 month eGFR difference in TDF and non-TDF based regimen.ResultOf 340 ART-naïve HIV patients with baseline renal function tests, 82.3% (279/339) were initiated on a TDF based ART regimen. All patients were on non-nucleoside reverse transcriptase inhibitors (NNRTI) based ART regimen. The median (IQR) change in eGFR with 12 months of ART was 0.8 (− 11.1; 10.0) ml/min/1.73m2. About 41 and 26.9% of HIV patients had a drop of greater than 3 and 10 mL/min/1.73 m2in eGFR at 12 month, respectively. However, none of the HIV patients declined to< 60 ml/min/1.73m2within 12 months. Moreover, none of the HIV patients had persistent proteinuria or glycosuria. Older HIV patients especially age > 45 years and those with unsuppressed viral load at 6 month of ART had a significantly lower eGFR at 12 months of ART initiation. However, there was no difference in 12 month eGFR between HIV patients initiated on TDF based regimen and non-TDF based regimen.ConclusionRenal function remained stable with no difference between HIV patients treated with TDF or non-TDF NNRTI based ART regimen over 12 months. However, older HIV patients and those with unsuppressed viral load deserve special focus on renal monitoring. Data on long-term safety of TDF (> 1 year) is still warranted in this population.
Impact of individual and neighborhood social capital on the physical and mental health of pregnant women: the Japan Environment and Children’s Study (JECS)
Authors: Morozumi Ryoko , Matsumura Kenta , Hamazaki Kei , Tsuchida Akiko , Takamori Ayako , Inadera Hidekuni ,   the Japan Environment and Children’s Study (JECS) Group, Kamijima Michihiro , Yamazaki Shin , Ohya Yukihiro , Kishi Reiko , Yaegashi Nobuo , Hashimoto Koichi , Mori Chisato , Ito Shuichi , Yamagata Zentaro , Inadera Hidekuni , Nakayama Takeo , Iso Hiroyasu , Shima Masayuki , Kurozawa Youichi , Suganuma Narufumi , Kusuhara Koichi , Katoh Takahiko 
Published: August 2020

Abstract
Background
Previous studies revealed positive, negative, and no influence of social capital on the health outcomes of pregnant women. It was considered that such differences were caused by the disparities of outcome measures and sample sizes between studies. Our chief aim was to verify the positive influence of social capital on the health condition of pregnant women using established health outcome measures and large-scale nationwide survey data.

Methods
We employed questionnaire survey data from 79,210 respondents to the Japan Environment and Children’s Study, and physical and mental component summary scores from the 8-Item Short-Form Health Survey as outcome measures. We estimated the effect of individual and neighborhood social capitals on physical and mental component summary scores. To consider the property that the richness of social capital would be generally determined by individual characteristics, and to estimate the causal influence of social capital on health without bias caused by said property, we adopted average treatment effect estimation with inverse probability weighting. Generally, average treatment effects are based on the difference of average outcomes between treated and untreated groups in an intervention. In this research, we reckoned individuals’ different levels of social capital as a kind of non-randomized treatment for respective individuals, and we applied average treatment effect estimation. The analysis regarded pregnant women with the lowest level of social capital as untreated samples and women with other levels of social capitals as treated samples.

Results
For mental component summary score, the maximum average treatment effects in the comparison between the lowest and highest levels of social capital were approximately 4.4 and 1.6 for individual and neighborhood social capital, respectively. The average treatment effects for the physical component summary score were negligible for both social capital types.

Conclusions
Social capital particularly contributes to improving mental component summary score in pregnant women. The likelihood of a mentally healthy pregnancy may be increased by enhancing social capital.
Spontaneous regression of ALK fusion protein-positive non-small cell lung carcinoma: a case report and review of the literature
Authors: Walls Maria , Walls Gerard M. , James Jacqueline A. , Crawford Kyle T. , Abdulkhalek Hossam , Lynch Tom B. , Peace Aaron J. , McManus Terry E. , Evans O. Rhun 
Published: August 2020

Abstract
Background
ALK-rearrangement is observed in < 5% non-small cell lung cancer (NSCLC) cases and prior to the advent of oral tyrosine kinase inhibitors, the natural history of oncogenic NSCLC was typically poor. Literature relating to regression of treatment-naïve NSCLC is limited, and regression without treatment has not been noted in the ALK-rearranged sub-population.

Case presentation
A 76 year old ‘never smoker’ female with an ALK-rearranged left upper lobe T2 N0 NSCLC experienced a stroke following elective DC cardioversion for new atrial fibrillation. Following a good recovery, updated imaging demonstrated complete regression of the left upper lobe lesion and a reduction of the previously documented mediastinal lymph node. Remaining atelectasis was non-avid on repeat PET-CT imaging, 8 months from the baseline PET-CT. When the patient developed new symptoms 6 months later a further PET-CT demonstrated FDG-avid local recurrence. She completed 55 Gy in 20 fractions but at 18 months post-radiotherapy there was radiological progression in the lungs with new pulmonary metastases and effusion and new bone metastases. Owing to poor performance status, she was not considered fit for targeted therapy and died 5 months later.

Conclusion
All reported cases of spontaneous regression in lung cancer have been collated within. Documented precipitants of spontaneous regression across tumour types include biopsy and immune reconstitution; stroke has not been reported previously. The favourable response achieved with radical radiotherapy alone in this unusual case of indolent oncogenic NSCLC reinforces the applicability of radiotherapy in locally advanced ALK-rearranged tumours, in cases not behaving aggressively. As a common embolic event affecting the neurological and pulmonary vasculature is less likely, an immune-mediated mechanism may underpin the phenomenon described in this patient, implying that hitherto unharnessed principles of immuno-oncology may have relevance in oncogenic NSCLC. Alternatively, high electrical voltage applied percutaneously adjacent to the tumour during cardioversion in this patient may have induced local tumour cell lethality.
Burden of pelvic organ prolapse in Ethiopia: a systematic review and meta-analysis
Authors: Gedefaw Getnet , Demis Asmamaw 
Published: August 2020

Abstract
Background
Pelvic organ prolapse can significantly affect a woman’s quality of life by compromising physical, social, psychological and sexual function. Pelvic organ disorders and its consequences have higher economic burden to the patient as well to the country. Therefore, this systematic review and met- analysis aimed to estimate the burden of POP in Ethiopia.

Methods
International databases (MEDLINE/Pub Med, Hinari, Scopus, Google scholar, African journals and literatures were searched and seven eligible cross sectional and two case control studies were included in this systematic review and meta-analysis. Eggers test and funnel plot were computed to check publication bias across the studies. Publication bias was computed using a funnel plot and eggers test. Heterogeneity of the studies was checked using Cochrane Q-test and I2 statistic. Subgroup analysis was computed for the evidence of heterogeneity.

Results
This systematic review and meta-analysis revealed that the overall national prevalence of pelvic organ prolapse in Ethiopia was 23.52% (95% CI: 61.04, 80.24). Being rural resident (AOR = 3.29; 95% CI: 1.38–7.85), I2 = 47.5%, P = 0.167), having < 18.5 BMI (AOR = 2.59; 95% CI: 1.53–4.4), I2 = 59.9%, P = 0.64), and age > 40(AOR = 7.43; 95% CI: 2.27–24.29), I2 = 75.9%, P = 0.016) were the associated risk factors for pelvic organ prolapse.

Conclusions
The pooled prevalence of pelvic organ prolapse was high. Residence, body mass index and age of the women were the predictors of pelvic organ prolpase. Creating awareness and identifying the modifiable and non modifiable risk factors for pelvic organ prolpase is a crucial strategy to prevent further complications and risk of operation.
Standardized ethanol extract of Tinospora crispa upregulates pro-inflammatory mediators release in LPS-primed U937 human macrophages through stimulation of MAPK, NF-κB and PI3K-Akt signaling networks
Authors: Haque Md. Areeful , Jantan Ibrahim , Harikrishnan Hemavathy , Ahmad Waqas 
Published: August 2020

Abstract
Background
Immunomodulatory effects of Tinospora crispa have been investigated due to its traditional use to treat several inflammatory disorders associated to the immune system. The present study reports the underlying mechanisms involved in the stimulation of 80% ethanol extract of T. crispa stems on pro-inflammatory mediators release in lipopolysaccharide (LPS)-primed U937 human macrophages via MyD88-dependent pathways.

Methods
Release of interleukin (IL)-1β and tumor necrosis factor (TNF)-α, and production of prostaglandin E2 (PGE2) were determined by using enzyme-linked immunosorbent assay (ELISA). Immunoblot technique was executed to determine the activation of MAPKs molecules, NF-κB, PI3K-Akt and cyclooxygenase-2 (COX-2) protein. Determination of pro-inflammatory cytokines and COX-2 relative gene expression levels was by performing the real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). A reversed-phase HPLC method was developed and validated to standardize the T. crispa extract and chemical profiling of its secondary metabolites was performed by LC-MS/MS.

Results
Qualitative and quantitative analyses of chromatographic data indicated that syringin and magnoflorine were found as the major components of the extract. T. crispa-treatment prompted activation of NF-κB by enhancing IKKα/β and NF-κB (p65) phosphorylation, and degradation of IκBα. The extract upregulated COX-2 protein expression, release of pro-inflammatory mediators and MAPKs (ERK, p38 and JNK) phosphorylation as well as Akt dose-dependently. T. crispa extract also upregulated the upstream signaling adaptor molecules, toll-like receptor 4 (TLR4) and MyD88. T. crispa-treatment also upregulated the pro-inflammatory markers mRNA expression.

Conclusion
The results suggested that T. crispa extract stimulated the MyD88-dependent signaling pathways by upregulating the various immune inflammatory related parameters.
A synthetic peptide sensitizes multi-drug resistant Pseudomonas aeruginosa to antibiotics for more than two hours and permeabilizes its envelope for twenty hours
Authors: Rázquin-Olazarán Iosu , Shahrour Hawraa , Martínez-de-Tejada Guillermo 
Published: August 2020

Abstract
Background
Pseudomonas aeruginosa is a Gram-negative pathogen that frequently causes life-threatening infections in immunocompromised patients. We previously showed that subinhibitory concentrations of short synthetic peptides permeabilize P. aeruginosa and enhance the lethal action of co-administered antibiotics.

Methods
Long-term permeabilization caused by exposure of multidrug-resistant P. aeruginosa strains to peptide P4–9 was investigated by measuring the uptake of several antibiotics and fluorescent probes and by using confocal imaging and atomic force microscopy.

Results
We demonstrated that P4–9, a 13-amino acid peptide, induces a growth delay (i.e. post-antibiotic effect) of 1.3 h on a multidrug-resistant P. aeruginosa clinical isolate. Remarkably, when an independently P4–9-treated culture was allowed to grow in the absence of the peptide, cells remained sensitive to subinhibitory concentrations of antibiotics such as ceftazidime, fosfomycin and erythromycin for at least 2 h. We designated this persistent sensitization to antibiotics occurring in the absence of the sensitizing agent as Post-Antibiotic Effect associated Permeabilization (PAEP). Using atomic force microscopy, we showed that exposure to P4–9 induces profound alterations on the bacterial surface and that treated cells need at least 2 h of growth to repair those lesions. During PAEP, P. aeruginosa mutants overexpressing either the efflux pump MexAB-OprM system or the AmpC β-lactamase were rendered sensitive to antibiotics that are known substrates of those mechanisms of resistance. Finally, we showed for the first time that the descendants of bacteria surviving exposure to a membrane disturbing peptide retain a significant level of permeability to hydrophobic compounds, including propidium iodide, even after 20 h of growth in the absence of the peptide.

Conclusions
The phenomenon of long-term sensitization to antibiotics shown here may have important therapeutic implications for a combined peptide-antibiotic treatment because the peptide would not need to be present to exert its antibiotic enhancing activity as long as the target organism retains sensitization to the antibiotic.
TAK-242 ameliorates DSS-induced colitis by regulating the gut microbiota and the JAK2/STAT3 signaling pathway
Authors: Wang Jiajia , Zhu Guannan , Sun Cheng , Xiong Kangwei , Yao Tingting , Su Yuan , Fang Haiming 
Published: August 2020

AbstractBackgroundThe goal of the present study was to investigate the effects of TAK-242 on the gut microbiota and the TLR4/JAK2/STAT3 signaling pathway in mice with dextran sulfate sodium (DSS)-induced colitis.ResultsAt the phylum level,Bacteroidetes,Firmicutes,Actinobacteria,Cyanobacteria,EpsilonbacteraeotaandProteobacteriawere the primary microbiota in the five groups. TAK-242 treatment significantly enhancedVerrucomicrobiaandActinobacteria; significantly decreasedCyanobacteria, EpsilonbacteraeotaandProteobacteria; and particularly promoted the growth ofAkkermansia. TAK-242 markedly alleviated DSS-induced colitis symptoms and colonic lesions by promoting IL-10 release, inhibiting IL-17 release, downregulating TLR4 and JAK2/STAT3 mRNA and protein expression and increasing JAK2/STAT3 phosphorylation.ConclusionTAK-242 modulates the structure of the gut microbiota in colitis and may be a novel therapeutic candidate for ulcerative colitis.