Miracle-dz/UniFAR-FTUs huggingface dataset:
The Dose-Response Relationship between Alcohol Consumption and the Risk of Type 2 Diabetes among Asian Men: A Systematic Review and Meta-Analysis of Prospective Cohort Studies

The objective of this review was to provide a summary of the literature on the dose-response relationship between alcohol consumption and risk of type 2 diabetes (T2D) in Asian populations, particularly men. The present study was recorded in PROSPERO as CRD 42019121073. We searched the PubMed-Medline, Web of Science, and Cochrane Library for studies published in any language since the database inception to January 2019. Prospective cohort studies were included in the meta-analysis. Relative risks (RRs) and 95% confidence intervals (CIs) were calculated for random-effects models and dose-response meta-analyses. In total, 8 prospective cohort studies were included. High alcohol intake was significantly associated with increased risk of T2D (RR = 1.16, 95% CI: 1.04–1.29; Q statistic p = 0.326) compared to the lowest category of alcohol intake. Nonlinear association was observed between alcohol consumption and T2D risk in men (p = 0.003). Dose-wise, consuming ≤57 g/day of alcohol was not associated with the risk of T2D in this study; however, alcohol intake >57 g/day was associated with increased risk of T2D in men. Overall, the association between alcohol consumption and T2D among Asian men was J-shaped. Lifestyle recommendations for prevention of T2D should include advice on limiting alcohol intake. This trial is registered with Prospero registration: CRD 42019121073.
Determination and Pharmacokinetics of Okanin in Rat Plasma by UltraHigh Performance Liquid Chromatography Coupled with Triple-Quadrupole Tandem Mass Spectrometry

Okanin is a major flavonoid found in Coreopsis tinctoria Nutt. , arousing huge interest recently for its considerable biological characteristics including antioxidant, antineurotoxic, and antidiabetic activities. An ultrahigh performance liquid chromatography triple-quadrupole tandem mass spectrometry (UPLC-MS) was successfully used to determine okanin in rat plasma after oral administration of okanin. Bavachalcone acted as an internal standard (IS). By gradient elution, IS and analyte were separated on a C18 column for 7 min at a flow rate of 0.25 mL/min with acetonitrile-0.1% acetic acid mobile phase. The stability, matrix effect, extraction recovery, accuracy, precision, linearity, and selectivity of the method were firstly demonstrated. The major pharmacokinetic parameters of okanin in rat plasma were then measured using the developed UPLC-MS method. An UPLC-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) was finally established to obtain the specific and accurate mass of okanin in rat plasma after oral administration, and its proposed fragmentation was further elaborated.
Stomatal and Metabolic Limitations to Photosynthesis Resulting from NaCl Stress in Perennial Ryegrass Genotypes Differing in Salt Tolerance

Plants possess abiotic stress responses that alter photosynthetic metabolism under salinity stress. The objective of this study was to identify the stomatal and metabolic changes associated with photosynthetic responses to NaCl stress in perennial ryegrass (Lolium perenne). Five-week-old seedlings of two perennial ryegrass genotypes, PI 516605 (salt-sensitive) and BARLP 4317 (salt-tolerant), were subjected to 0 and 250 mM NaCl for 8 days. The salt tolerance in perennial ryegrass was significantly associated with leaf relative water content (RWC) and photosyn- thetic capacity through the maintenance of greater metabolic activities under prolonged salt stress. BARLP 4317 maintained greater turf quality, RWC, and stomatal limitations but a lower level of lipid peroxidation (malondialde- hyde (MDA)) and intercellular CO2 concentration than PI 516605 at 8 days after treatment (DAT). Ribulose-1, 5-bisphosphate carboxylase:oxygenase (Rubisco) activity and activation state, transcriptional level of rbcL gene, and expression level of Rubisco large subunit (LSU) declined in stressed perennial ryegrass but were higher in salt- tolerant genotype at 8 DAT. Furthermore, photosynthetic rate increased linearly with increasing Rubisco activity, Rubisco activation state, and RWC in both genotypes. The same linear relationship was found between RWC and Rubiscoactivity.However,MDAcontentdecreasedlinearlywithincreasingRWCinbothgenotypes.Salinity-induced inhibition of photosynthesis in perennial ryegrass was mainly the result of stomatal limitation during early salt stress and metabolic limitation associated with the inhibition of RWC, activity of Rubisco, expression level of rbcLgene, and LSU under a prolonged period of severe salinity.
Giant benign phyllodes breast tumour with pulmonary nodule mimicking malignancy: A case report

BACKGROUND Phyllodes tumours (PTs) are fibroepithelial breast tumours, which can be classified as benign, borderline or malignant, according to their histological characteristics. While various huge borderline or malignant PTs have been previously described, a benign PT with a pulmonary nodule mimicking malignancy has not yet been reported. In order that doctors may have a comprehensive understanding of super-giant benign PTs (≥ 20 cm), we also performed a literature review to summarize the clinical features, differential diagnosis, and treatment of this disease. CASE SUMMARY A 42-year-old woman with severe anaemia presented with a rapidly enlarging right breast mass, measuring approximately 30 cm × 25 cm × 20 cm that was first noticed 1 year previously. A region of skin ulceration and necrosis (20 cm × 15 cm) was observed on the lateral side of the mass. Computed tomography (CT) of the chest revealed a pulmonary nodule, which initially suggested a diagnosis of metastasis. CT showed that the boundaries between the pectoralis major and the mass were blurred, which was presumed to be due to tumour invasion. However, two core needle biopsies of the mass showed no evidence of malignancy. Following these results, the tumour was removed by mastectomy of the right breast. Interestingly, postoperative pathology finally proved the diagnosis of a benign PT. After 1 year of follow-up, wedge resection of the small pulmonary nodule was performed, and it was confirmed that the lung nodule was actually adenocarcinoma rather than metastatic breast cancer. The patient recovered very well without any postoperative treatment. CONCLUSION This case is unique in that the giant breast mass initially mimicking a malignant clinical presentation was eventually pathologically confirmed to be a benign PT, which misled the diagnosis and complemented the atypical features of benign PTs. The pathological and immunohistochemical results were important in the differential diagnosis. In addition, total mastectomy should be recommended due to difficulty in the precise diagnosis of PTs, especially in large breast masses. In the literature, almost one-half of super-giant benign cases were thought to be malignant tumours before surgery. This finding is a reminder to consider all conditions in order to make an accurate diagnosis and avoid excessive treatment.
Functional Constraints and rbcL Evidence for Land Plant Phylogeny

Although the proportion of «functional» DNA in eukaryotic genomes is both debatable and subject to definition, most sequences gathered for phylogenetic purposes are indisputably functional. For example, patterns of variation are likely to be strongly constrained in ribosomal RNAs because of their structural and catalytic roles in protein translation, and in protein-coding genes, because of protein function itself. Although seemingly obvious, these concerns are usually ignored by workers producing gene trees. We have examined the extent of functional constraints in land-plant rbcL sequences. Not only do rbcL sequences appear to change with essentially clocklike regularity, but nucleotide-based cladograms imply tbat approximately 97.5% of codon changes on internal branches are functionally neutral (i.e., synonymous or functionally labile)
Using Ancestral Information to Inform Analyses of Complex Data Sets

Over the last decade, improvements in sequencing technologies coupled with active development of association mapping methods have made it possible to link genotypes and quantitative traits in humans. Despite substantial progress in the ability to generate and analyze large data sets, however, genotype-phenotype associations are often difficult to find, even in studies with large numbers of individuals and genetic markers. This is due, in part, to the fact that effects of individual loci can be small and/or dependent on genetic variation at other loci or the environment. Tree-based mapping, which uses the evolutionary relatedness of sampled individuals to gain information during association mapping, has the potential to significantly improve our ability to detect loci impacting human traits. However, current tree-based methods are too computationally intensive and inflexible to be of practical use. Here, we compare tree-based methods with more classical approaches for association mapping and discuss how the limitations of these newer methods might be addressed. Ultimately, these advances have the potential to advance our understanding of the molecular mechanisms underlying complex diseases.
Association analysis between chronic obstructive pulmonary disease and polymorphisms in circadian genes

Background Circadian genes have been suggested to play an important role in lung pathology. However, it remains unknown whether polymorphisms of these genes are associated with chronic obstructive pulmonary disease (COPD). Here, we aimed to investigate the association of circadian genes polymorphisms with COPD in a case-control study of 477 COPD patient and 323 control Han Chinese persons. Methods Genotyping assays were carried out for nine single nucleotide polymorphisms (SNPs) from five circadian genes (PER3, CLOCK, RORB, BMAL1 and CRY2) that were previously identified in lung pathology. Age, sex, BMI and smoking status and comorbidities were recorded for all subjects. Results No significant association was found in all SNP sites in overall subjects and no significant difference was found in age, sex, smoking status stratification analysis. Discussion The findings of this investigation indicated the effect of circadian genes polymorphisms on COPD susceptibility may only be small and possibly dependent on the subject factors, such as age and sex.
Spatial Distributions, Characteristics, and Applications of Craniofacial Stem Cells

Stem cells play an irreplaceable role in the development, homeostasis, and regeneration of the craniofacial bone. Multiple populations of tissue-resident craniofacial skeletal stem cells have been identified in different stem cell niches, including the cranial periosteum, jawbone marrow, temporomandibular joint, cranial sutures, and periodontium. These cells exhibit self-renewal and multidirectional differentiation abilities. Here, we summarized the properties of craniofacial skeletal stem cells, based on their spatial distribution. Specifically, we focused on the in vivo genetic fate mapping of stem cells, by exploring specific stem cell markers and observing their lineage commitment in both the homeostatic and regenerative states. Finally, we discussed their application in regenerative medicine.
Extraction and Characterization of Novel Natural Hydroxyapatite Bioceramic by Thermal Decomposition of Waste Ostrich Bone

A novel natural hydroxyapatite (HAp) bioceramic was extracted from the ostrich cortical bone by the thermal decomposition method. HAp was characterized by different analytical tools such as thermogravimetric analysis (TGA), Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) analysis, and scanning electron microscopy (SEM). Removal of organic impurities from the bone powder was confirmed by TGA analysis. FTIR spectra of HAp confirmed the presence of the major functional groups such as phosphate (PO43−), hydroxyl (OH−), and carbonate (CO32−) in the bioceramic. The XRD data revealed that the HAp was the crystalline phase obtained by calcination of the bone powder at 950°C, and the SEM analyses confirmed the typical plate-like texture of the nanosized HAp crystals.
Changes in Blood Profile from Steady State in Patients with Sickle Cell Anemia Admitted for Vaso-occlusive Crisis and Acute Chest Syndrome

Close to half of all patients with sickle cell disease (SCD) will have at least one episode of acute chest syndrome (ACS) during their lifetime. Multiple cells and molecules involved with the inflammatory cascade play a role in the development of ACS. We found that patients with SCD who developed ACS as a complication of a vaso-occlusive crisis (VOC) had a significant increase in leukocytes and decrease in platelets from their steady state when compared with a separate admission for VOC without ACS development. No significant change from steady state hemoglobin or reticulocyte count was noted between the two admissions. These results indicate that trending laboratory markers may be useful to predict patients at risk for ACS development.
Mitochondrial Dysfunction and Therapeutic Targets in Auditory Neuropathy

Sensorineural hearing loss (SNHL) becomes an inevitable worldwide public health issue, and deafness treatment is urgently imperative; yet their current curative therapy is limited. Auditory neuropathies (AN) were proved to play a substantial role in SNHL recently, and spiral ganglion neuron (SGN) dysfunction is a dominant pathogenesis of AN. Auditory pathway is a high energy consumption system, and SGNs required sufficient mitochondria. Mitochondria are known treatment target of SNHL, but mitochondrion mechanism and pathology in SGNs are not valued. Mitochondrial dysfunction and pharmacological therapy were studied in neurodegeneration, providing new insights in mitochondrion-targeted treatment of AN. In this review, we summarized mitochondrial biological functions related to SGNs and discussed interaction between mitochondrial dysfunction and AN, as well as existing mitochondrion treatment for SNHL. Pharmaceutical exploration to protect mitochondrion dysfunction is a feasible and effective therapeutics for AN.
A rapid and low-cost method for genomic DNA extraction from the cyanobacterium Synechocystis

Abstract A two-step method is reported for preparation of genomic DNA from the model cyanobacterium Synechocystis that can be performed with minimal equipment and reagents in about an hour. High yields of genetic material can be obtained (200–450 ng/μl) with reasonable purity. A further ethanol precipitation step can be included but is not necessary if template is simply required for polymerase chain reaction (PCR) or digestion. This new protocol is helpful for amplification of genes of interest in early-stage research projects and for low throughput screening of transformants. It is more reliable than colony PCR of Synechocystis cultures, and less involved and cheaper than existing clean-DNA preparation methods. It represents an unusually simple and reliable extraction protocol for the growing body of research making use of this cyanobacterium.
Damage to grape flowers and berries by Lobesia botrana larvae (Denis & Schiffernüller) (Lepidoptera: Tortricidae), and relation to larval age

Background and Aims Evaluation of pest damage and the population age of the pest are key factors in integrated pest management. Gaining such knowledge, however, can be time consuming and difficult in larvae that have cryptic habits, such as the European grapevine moth (EGVM, Lobesia botrana). An alternative is to measure the damage caused by different larval instars. Damage caused by different EGVM larval instars was described over 3 consecutive years. Methods and Results The first two larval generations of wild EGVM were sampled in an experimental vineyard in the Bordeaux area, France; 1945 samples of larval damage to inflorescences were collected and instars determined. Significant correlations were described between both in each generation. Conclusions Quantification of plant damage monitoring has potential to assist with assessing the characteristics of EGVM populations. Significance of the Study Using crop injury or damage to determine larval stage should provide a rapid and convenient method for pest management.
Identification and Characterization of Copy Number-Associated Driver Genes in Esophageal Squamous Cell Carcinoma

Background Esophageal squamous cell carcinoma (ESCC) is a leading malignancy with both high incidence and mortality worldwide. However, the molecular mechanisms of the poor prognosis in ESCC are still unclear. Methods We conducted differential expression analysis between ESCC and normal tissues and between ESCC samples with and without CNAs in a given gene. Overrepresentation enrichment and gene set enrichment analyses were used to identify the oncogenic pathways and abnormal transcription factors (TFs). The survival analysis was employed to identify the genes associated with overall survival. Results In this study, we aimed to identify and interpret the driver genes triggered by the copy number alterations (CNAs), including CCND1, TEAD4, EIF4EBP1, EGFR, FGFR3, and FZD6. Furthermore, we identified oncogenic pathways, including RTK-RAS, WNT, PI3K, Hippo, and cell cycle, and key TFs including TEAD4, a transcription factor in the Hippo signaling pathway, and LEF1 in the WNT signaling pathway. Furthermore, we observed that upregulations of FGFR3 and EIF4EBP1 were significantly associated with shorter overall survival in ESCC. Conclusion In conclusion, the driver genes triggered by CNAs not only exhibited critical functionality but also were clinically relevant in ESCC, which greatly improved our understanding of the molecular mechanisms in ESCC.
Targeted Next-Generation Sequencing Identifies Separate Causes of Hearing Loss in One Deaf Family and Variable Clinical Manifestations for the p.R161C Mutation in SOX10

Hearing loss is the most common sensory deficit in humans. Identifying the genetic cause and genotype-phenotype correlation of hearing loss is sometimes challenging due to extensive clinical and genetic heterogeneity. In this study, we applied targeted next-generation sequencing (NGS) to resolve the genetic etiology of hearing loss in a Chinese Han family with multiple affected family members. Targeted sequencing of 415 deafness-related genes identified the heterozygous c.481C>T (p.R161C) mutation in SOX10 and the homozygous c.235delC (p.L79Cfs∗3) mutation in GJB2 as separate pathogenic mutations in distinct affected family members. The SOX10 c.481C>T (p.R161C) mutation has been previously reported in a Caucasian patient with Kallmann syndrome that features congenital hypogonadotropic hypogonadism with anosmia. In contrast, family members carrying the same p.R161C mutation in this study had variable Waardenburg syndrome-associated phenotypes (hearing loss and/or hair hypopigmentation) without olfactory or reproductive anomalies. Our results highlight the importance of applying comprehensive diagnostic approaches such as NGS in molecular diagnosis of hearing loss and show that the p.R161C mutation in SOX10 may be associated with a wide range of variable clinical manifestations.
Reduced predation of artificial nests in border-edge cuts on woodlots

Forest fragmentation has resulted in abrupt, artificial edges that may not provide transitional shrub habitat needed by edge- and shrub-nesting species. The creation of border-edge cuts (shrub transitional zones 15-40 m wide) at woodlot edges increases horizontal and vertical understory cover, and may affect habitat suitability for edgenesting species. Using artificial nests, we tested the hypothesis that predation rates in border-edge cuts were lower than in uncut edges. During May-June 1997, we placed 10 artificial nests containing 2 northern bobwhite (Colinus virginianus) eggs in each edge. Nests were monitored for depredation for 14 days. Most nest predation was attributed to avian predators, snakes, and small mammals, with a few nests depredated by large mammals. Mean predation rates were more than twice as high in uncut edges (88 ± 7%; x ± SE) as in border-edge cuts (36 ± 11%). Vegetation cover from 0 to 2 m at the nest site was greater at nests in border-edge cuts (85.6 ± 4.1%) than in uncut edges (59.5 ± 3.3%). Predation rates within edges were negatively correlated with mean cover from 0 to 2 m at the nest site (r= -0.90) and mean cover at nest height (r= -0.86). However, predation rates on natural nests found the previous year in both edge types did not follow the same trend, indicating that further research is needed on both the differences in individual bird species' productivity and predator, communities between the 2 edge types.
Improved antioxidant status among HIV-infected injecting drug users on potent antiretroviral therapy.

Low serum antioxidant levels in HIV-infected people have been attributed to altered metabolism associated with excess oxidative stress. We conducted a study to examine serum antioxidant levels in 175 HIV-positive and 210 HIV-negative injecting drug users (IDUs) in Baltimore, Maryland. At the time of data collection, 30 of the HIV-positive IDUs were receiving antiretroviral therapies (ART) including a protease inhibitor (PI), 43 ART without a PI, 22 monotherapies, and 80 not on any ART. Serum antioxidants examined included retinol, alpha-tocopherol and gamma-tocopherol, alpha-carotene and beta-carotene, lycopene, lutein/zeaxanthin, and beta-cryptoxanthin. Mean serum levels of lycopene and lutein/zeaxanthin were significantly lower in HIV-positive IDUs than HIV-negative IDUs. Contrary to the findings in other studies, however, levels of the remaining antioxidants in HIV-positive study subjects were not lower than in HIV-negative study subjects. In fact, serum alpha-tocopherol levels were significantly higher in HIV-positive IDUs than HIV-negative IDUs (medians = 744 microg/dl and 718 microg/dl, respectively; p = .04). Among HIV-positive study subjects, there were significant differences in antioxidant levels by ART regimen. In multivariate models adjusting for injecting drug use, dietary intake, supplement intake, gender, and alcohol intake, significant overall differences by ART regimen were observed for alpha-tocopherol, beta-carotene, and beta-cryptoxanthin. Serum levels of these three antioxidants were significantly higher in the PI group than in the other three ART groups combined (p = .0008, 0.02, and 0.02, respectively). These data provide indirect evidence of the effectiveness of PIs in lowering oxidative stress levels in HIV-positive IDUs.
Effects of duration and combination of drought and flood conditions on leaf photosynthesis, growth and sugar content in sugarcane

Abstract Global climate change will result in extreme environments, such as droughts and floods. We investigated the individual and combined effects of droughts and floods of varying duration on sugarcane (Saccharum spp.) growth using a pot experiment under glasshouse conditions with the following six treatments: drought for 15 d, prolonged drought for 30 d, flood for 15 d, prolonged flood for 30 d, short flood followed by prolonged drought, and prolonged flood followed by prolonged drought. Plants that were subjected to drought conditions, including drought after a flood, had reduced CO2 assimilation (through stomatal closure) and leaf areas, whereas flood conditions showed no effect. During flooding, some roots died, and adventitious roots with well-developed aerenchyma appeared from the submerged nodes. At the time of harvest, there were no significant differences in stem fresh weight, sucrose content, or sugar yield between the treatments. However, ion content analysis revealed that flood conditions caused an accumulation of sodium in the bottom of stems and adventitious roots. Therefore, under flood conditions, plants may develop adventitious roots, which may offset the negative effects of root death, helping them to maintain their growth and yield.