Miracle-dz/UniFAR-FTUs huggingface dataset:
Recurrent falls in elder patients: risk factors and effect on care giving family members

BACKGROUND: Care giving produces great amounts of caregiver burden and stress. Falls are a common and complex geriatric syndrome that cause considerable mortality, morbidity, reduced functioning, and premature nursing home admissions. AIM: To evaluate the risk factors of recurrent falls and effect on care giving family members. MATERIALS AND METHODS: Case control study, performed with structured questionnaire conducted in an outpatient geriatric unit on 150 elder patients, divided into 2 groups; first: cases (100 subjects), second: controls (50 subjects). Comprehensive geriatric assessment and Timed Up and Go test (TUG) were applied. Caregiver burden and potential determinants were measured in all participant partners using Caregiver Burden Questionnaire. RESULTS: The mean age of the cases was 69.6 ± 6.8, while for controls was 67.2 ± 4.7, [P: 0.02]. Sex did not show a significant difference between cases and controls [P: 0.123]. The mean BMI of the cases was 26.03 ± 6.4, and of controls: 29.1 ± 6.8, [P: 0.007]. The functional state assessed by ADL showed significant difference between cases and controls, [P: CONCLUSION: Age, lower BMI, functional impairment, polypharmacy, depression and use of assistive device are risk factors for recurrent falls in older adults, and the caregiver stress is more prevalent in those with recurrent falls especially with increase in the number of falls, the presence of depression and functional impairment. So we recommend assessment of these risk factors for falls in all older patients and also assessment of caregiver stress especially in the elders with recurrent falls. Key words: recurrent falls, elderly patients, care giving family members Language: en
New allele of C. elegans gene spch-3 (T27A3.4), called xc2

Description We created a new mutant allele, named xc2, of the gene spch-3 (T27A3.4). spch-3 encodes one of three C. elegans small, highly basic proteins that resemble invertebrate protamines and associate with sperm meiotic chromosomes (Chu et al., 2006). The alleles were isolated from gene mutations generated by Non-Homologous End Joining (NHEJ) mediated repair of Cas9-generated breaks (Dickinson et al., 2013; Ran et al., 2013). The alleles were discovered using PCR with the following primers 5’CCCTCGTCTTCTCTACTAGA -3’ and 5’CATAGCTTCACAGGGAGAAG -3’. Next Generation Sequencing let us identify 30 bp flanking sequences of the xc2 allele as GTCCGTCAACCCGCCGTTCGTCGTCTCGTC [191 bp deletion] TCTCGTCATCGCTCATCTTCGAAGGCTCGT. Wildtype spch-3 has 2 exons. The xc2 mutation is located in the second exon (Fig. 1A). In the mutant, while the first 97 amino acids of the mutant protein remain wildtype, they are followed by the deletion causing a frameshift mutation that adds 25 mutant amino acids (LSSSLIFEGSWTSCVDCKEDSCQKT) before the first resulting stop codon (Fig. 1B). Therefore, out of the 203 amino acids in the wildtype SPCH-3 protein, only the first 97 remain in the xc2 allele. Although the additional 25 amino acids may have an effect that is yet to be determined, the mutation in the second exon changes about 52% of the protein providing a unique opportunity to understand the function of SPCH-3 through mutant studies.
Opioids depress breathing through two small brainstem sites

The rates of opioid overdose in the United States quadrupled between 1999 and 2017, reaching a staggering 130 deaths per day. This health epidemic demands innovative solutions that require uncovering the key brain areas and cell types mediating the cause of overdose—opioid respiratory depression. Here, we identify two primary changes to breathing after administering opioids. These changes implicate the brainstem’s breathing circuitry which we confirm by locally eliminating the μ-Opiate receptor. We find the critical brain site is the origin of the breathing rhythm, the preBötzinger Complex, and use genetic tools to reveal that just 70-140 neurons in this region are responsible for its sensitivity to opioids. Future characterization of these neurons may lead to novel therapies that prevent respiratory depression while sparing analgesia.
Home range, population density, and foraging behaviour of the Yellow-breasted Warbling-Antbird (Hypocnemis subflava) in forest fragments in southwestern Brazilian Amazonia

ABSTRACT Hypocnemis subflava is endemic to southwestern Amazonia, where it prefers habitats dominated by bamboo. We estimated the home range size and population density of this species, and described its foraging behaviour and occurrence in bamboo. We collected data within 1 – ha plots located in three different 16-ha grids. The mean home range of the species was 0.65 ± 0.26 ha (mean ± SE). The population density was 0.44–0.75 individuals per hectare and 0.22–0.37 pairs per hectare within the different study plots. The birds foraged primarily in bamboo leaves (65%), using ‘reach’ and ‘sally’ movements, and foraging was most frequent at a height of 1.1–2 m. Logistic regression analysis indicated that the probability of occurrence of the species increases with the density of culms and percentage bamboo cover per ha. The home range of H. subflava is one of the smallest yet reported for a thamnophilid species, while the density of the bamboo-dwelling populations among the highest recorded for any Amazonian thamnophilid, including other bamboo forest specialists. The high degree of habitat specificity of H. subflava for bamboo-dominated environments makes the species vulnerable to the loss of its preferred habitat in the region.
The complete chloroplast genome sequence of Canarium album

Abstract The first complete chloroplast genome (cpDNA) sequence of Canarium album was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 163,347 bp in length, contains a large single-copy (LSC) region of 87,838 bp and a small single-copy (SSC) region of 13,935 bp, which were separated by a pair of inverted repeats (IRs) regions of 30,787 bp. The genome contains 129 genes, including 84 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall guanine-cytosine (GC) content of the whole genome is 37.5%, and the corresponding values of the LSC, SSC, and IR regions are 35.8%, 32.6%, and 41.1%, respectively. Further, phylogenomic analysis showed that C. album clustered together with Boswellia sacra.
Synergistic effect: a common theme in mixed-species litter decomposition

Litter decomposition plays a key role in ecosystem nutrients cycling, yet, to date science is lacking a comprehensive understanding of the non-additive effect in mixing litter decomposition. In order to fill that gap, we compiled 69 individual studies for the purpose of performing two sub-meta-analyses on the non-additive effect. Our results show that a significantly synergistic effect occurs at global scale with the average increase by 2-4% in litter mixture decomposition; In particular, low-quality litter in mixture shows a significantly synergistic effect, while no significant change is observed with high-quality species. Additionally, the synergistic effect turns into the antagonistic effect when soil fauna is absent or litter decomposition enters into humus-near stage. In contrast to temperate and tropical areas, studies in frigid area also show a significantly antagonistic effect. Our meta-analysis provides a systematic evaluation of the non-additive effect in decomposition mixed litters, which is critical for understanding and improving the carbon forecasts and nutrient dynamics.
Mechanics of snake biting: Experiments and modelling

Among all the vertebrates, snakes possess the most sophisticated venom delivering system using their fangs. Fangs of many animals are well adapted to the mechanical loads experienced during the functions such as breaking the diet and puncturing the skin of the prey. Thus, investigation and modelling of puncturing mechanics of snakes is of importance to understand the form-function relationship of the fangs and tissue-fang interactions in detail. We have thus chosen fangs of two snake species i.e. viper (Bitis arietans) and burrowing snake (Atractaspis aterrima), with different shape and size and performed insertion experiments using tissue phantoms. Our results showed that both the species have similar mechanical properties but there was a difference in the insertion forces owing to the difference in shape of the fang. Also, our modelling of the fang-tissue interactions predicted some parameters close to the experimental values. Thus, our study can help in the development of bioinspired needles that can potentially have reduced insertion forces and less damage to the tissue.
Plant diversity and community composition in temperate northeast Atlantic salt marshes are linked to nutrient concentrations

QUESTION: Studies in the northwest Atlantic have shown that nutrient enrichment can severely impact salt marshes, undermining their broad range of high‐value ecosystem services. However, biogeographical differences in plant communities may preclude extrapolation of these findings to other regions. The few investigations of such impacts elsewhere, including in Europe, have been strongly localised, restricting generalisations, and have not addressed community‐level properties. LOCATION: South and east coasts of Ireland (northeast Atlantic). METHODS: We conducted a field survey of vascular plants and soil properties in fifteen salt marshes representing broad environmental gradients but comparable biogeographical settings, to test if salt marsh plant (a) diversity and (b) community composition are related to soil nutrients. RESULTS: Species richness and Shannon diversity were both negatively related to soil NOₓ⁻, and Shannon diversity had a hump‐shaped relationship to labile P. Multivariate community composition was highly significantly related to NOₓ⁻, to a lesser degree to P, and marginally significantly to NH₄⁺. This was most clearly evident in the positive association of the ground cover of an evergreen dwarf shrub, Atriplex portulacoides, and a weaker negative association of a forb, Plantago maritima, with NOₓ⁻, indicating competition between these key and functionally contrasting mid‐salt‐marsh species. The relationship between community composition and P was most evident through the positive association of P with the invasive cordgrass, Spartina anglica. CONCLUSIONS: Physiognomic and functional differences between the herb‐rich Pl. maritima community and monospecific A. portulacoides stands likely have implications for ecosystem services, as would a continued expansion of S. anglica. Further studies to ascertain causality could determine whether such transitions can be driven by nutrient enrichment.
Outcome of the nonrandomized patients in the FFCD 9102 trial: Chemoradiation followed by surgery compared with chemoradiation alone in squamous cancer of the esophagus

4555 Background: For locally advanced thoracic oesophageal cancers, the FFCD 9102 trial have demonstrated that for responders chemoradiation only was equivalent to chemoradiation followed by surgery in term of overall survival. What about nonrandomized patients (Bedenne L et al. J Clin Oncol 2007;25:1160–8)? Methods: Out of 451 patients, 192 were not randomized because of no objective response or improved dysphagia, contraindication to either surgery or continuation of chemo-radiation, patient’s refusal, death or no further treatment. Results: At the end of the induction chemo-radiation, there was no difference between randomized and non-randomized patients in term of age, tumor height and diameter, doses of chemotherapy or radiotherapy. However, weight loss, body surface and Spitzer QoL Index were significantly different. Duration of follow-up was identical: 47.3 months vs 48.1 months (NS). Overall survival was significantly lower in non-randomized patients: median survival 11.5 months (SE = 1.09 months).
Antifungal Effect of Thymus vulgaris Methanolic Extract on Growth of Aflatoxins Producing Aspergillus parasiticus

THIS STUDY illustrates a simple method for detection of the ability of Aspergillus parasiticus, isolated from peanut seeds, for production of aflatoxins. The indicator of aflatoxins production ability is the appearance of yellow color in colony reverse of the fungus on agar media and natural fluorescence of aflatoxin around the colony when observed under UV (black light 350BL) after three days of incubation at 28oC. The morphological identification of A. parasiticus was confirmed by molecular identification by using rDNA sequencing. The addition of β-Cyclodextrine to media enhances natural fluorescence of aflatoxin around the colony under UV. The extract of Thymus vulgaris has inhibitory effect on growth of A. parasiticus. Minimum inhibitory concentration (MIC) of Thymus extract against A. parasiticus was 80μl of Thymus extract/10ml of YSA medium. The effective concentration of Thymus extract causing a 50% inhibition of mycelial growth (EC50) was 20μl of Thymus extract/10ml of YSA medium. Chemical analysis of Thymus extract by Gas chromatography-Mass Spectroscopy (GC-MS), illustrated the high area percentage (13.8717) appeared with thymol which has known with its antiseptic properties and is responsible for the antifungal effect of Thymus extract.
Complete mitochondrial genome of the Arctic hare, Lepus arcticus

Abstract In this study, we report on the complete mitochondrial genome of the Arctic hare, Lepus arcticus (Leporidae; Lagomorpha) a large lagomorph endemic to the northernmost regions of Greenland. The complete mitogenome of L. arcticus was 16,972 bp long and was typical of genus Lepus mitogenomes in genomic content and structure, as the entire mitogenome contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one control region. The phylogenetic analysis of the Arctic hare within Leporidae confirmed the sister relationship among Lepus species. This mitogenome sequence will provide a useful resource for investigations of biogeography, phylogenetic distance, and evolutionary history in lagomorphs.
Sex is determined by XY chromosomes across the radiation of dioecious Nepenthes pitcher plants

Species with separate sexes (dioecy) are a minority among flowering plants, but dioecy has evolved multiple times independently in their history. The sex‐determination system and sex‐linked genomic regions are currently identified in a limited number of dioecious plants only. Here, we study the sex‐determination system in a genus of dioecious plants that lack heteromorphic sex chromosomes and are not amenable to controlled breeding: Nepenthes pitcher plants. We genotyped wild populations of flowering males and females of three Nepenthes taxa using ddRAD‐seq and sequenced a male inflorescence transcriptome. We developed a statistical tool (privacy rarefaction) to distinguish true sex specificity from stochastic noise in read coverage of sequencing data from wild populations and identified male‐specific loci and XY‐patterned single nucleotide polymorphsims (SNPs) in all three Nepenthes taxa, suggesting the presence of homomorphic XY sex chromosomes. The male‐specific region of the Y chromosome showed little conservation among the three taxa, except for the essential pollen development gene DYT1 that was confirmed as male specific by PCR in additional Nepenthes taxa. Hence, dioecy and part of the male‐specific region of the Nepenthes Y‐chromosomes likely have a single evolutionary origin.
MetaSanity: An integrated, customizable microbial genome evaluation and annotation pipeline

Summary As the importance of microbiome research continues to become more prevalent and essential to understanding a wide variety of ecosystems (e.g., marine, built, host-associated, etc.), there is a need for researchers to be able to perform highly reproducible and quality analysis of microbial genomes. MetaSanity incorporates analyses from eleven existing and widely used genome evaluation and annotation suites into a single, distributable workflow, thereby decreasing the workload of microbiologists by allowing for a flexible, expansive data analysis pipeline. MetaSanity has been designed to provide separate, reproducible workflows, that (1) can determine the overall quality of a microbial genome, while providing a putative phylogenetic assignment, and (2) can assign structural and functional gene annotations with varying degrees of specificity to suit the needs of the researcher. The software suite combines the results from several tools to provide broad insights into overall metabolic function and putative extracellular localization of peptidases and carbohydrate-active enzymes. Importantly, this software provides built-in optimization for “big data” analysis by storing all relevant outputs in an SQL database, allowing users to query all the results for the elements that will most impact their research. Availability and implementation MetaSanity is provided under the GNU General Public License v.3. 0 and is available for download at https://github.com/cjneely10/MetaSanity. This application is distributed as a Docker image. MetaSanity is implemented in Python3/Cython and C++. Supplementary information Supplementary data are available below.
Six‐Transmembrane Epithelial Antigen of the Prostate 3 Deficiency in Hepatocytes Protects the Liver Against Ischemia‐Reperfusion Injury by Suppressing Transforming Growth Factor‐β‐Activated Kinase 1

Hepatic ischemia‐reperfusion (I/R) injury remains a major challenge affecting the morbidity and mortality of liver transplantation. Effective strategies to improve liver function after hepatic I/R injury are limited. Six‐transmembrane epithelial antigen of the prostate 3 (Steap3), a key regulator of iron uptake, was reported to be involved in immunity and apoptotic processes in various cell types. However, the role of Steap3 in hepatic I/R‐induced liver damage remains largely unclear.
Carbon metabolism, transcriptome and RNA editome in developmental paths differentiation of Coprinopsis cinerea

The balance and interplay between sexual and asexual reproduction is one of the most attractive mysteries in fungi. The choice of developmental strategy reflects the ability of fungi to adapt to the changing environment. However, the evolution of developmental paths and the metabolic regulation during differentiation and morphogenesis are poorly understood. Here, we monitor the carbohydrate metabolism and gene expression regulation during the early differentiation process from the “fungal stem cell”, vegetative mycelium, to the highly differentiated tissue/cells, fruiting body, oidia or sclerotia, of a homokaryotic fruiting Coprinopsis cinerea strain A43mut B43mut pab1-1 #326, uncovering the systematic changes during morphogenesis and the evolutionary process of developmental strategies. Conversion between glucose and glycogen and conversion between glucose and beta-glucan are the main carbon flows in the differentiation processes. Genes related to carbohydrate transport and metabolism are significantly differentially expressed among paths. RNA editing, a novel layer of gene expression regulation, occurs in all four developmental paths and enriched in cytoskeleton and carbohydrate metabolic genes. It is developmentally regulated and evolutionarily conserved in basidiomycetes. Evolutionary transcriptomic analysis on four developmental paths showed that all transcriptomes are under purifying selection, and the more stressful the environment, the younger the transcriptome age. Oidiation has the lowest value of transcriptome age index (TAI) and transcriptome divergence index (TDI), while fruiting process has the highest of both indexes. These findings provide new insight to the regulations of carbon metabolism and gene expressions during fungal developmental paths differentiation. Importance Fungi is a group of species with high diversity and plays essential roles to the ecosystem. The life cycle of fungi is complex in structure and delicate in function. Choice of developmental strategies and internal changes within the organism are both important for the fungus to fulfill their ecological functions, reflecting the relationship between environment and the population. This study put the developmental process of vegetative growth, sexual and asexual reproduction, resistant structure formation of a classical model basidiomycetes fungus, C. cinerea, together for the first time to view the developmental paths differentiation process with physiology, transcriptomics and evolutionary prospects. Carbohydrate assays and RNA-seq showed the changes of the fungus. Our results fill the gaps on gene expression regulation during the early stage of developmental paths differentiation, and expand our understanding of the evolutionary process of life history and reproductive strategy in fungi.
A Cross-national Comparison Study of Metabolic Syndrome among Canadian and Korean Older Adults

Background: Metabolic syndrome (MetS) is a clustering of traditional cardiovascular risk factors including central obesity, dyslipidemia, insulin resistance, and hypertension. The prevalence of MetS increases risk of cardiovascular disease and type 2 diabetes and increases with age. Purpose: To compare prevalence and correlates of MetS (and components) in Canadian and Korean older adults. Methods: This study consisted of secondary data analysis, using data from the Canadian Health Measures Survey (CHMS) (cycle 1) and the Korea National Health and Nutrition Examination Survey (cycle 4). The study sample included adults aged 60 to 79 years and who provided fasting blood samples. To compare prevalence of MetS between countries, the same diagnostic criteria (Harmonizing definition) were used. Similar measures of potential explanatory variables for MetS, such as physical activity, dietary patterns, comorbidity, gender, household income adequacy, education, marital status, alcohol consumption, smoking, psychological distress, and duration of sleep were also used where possible. Univariate and multiple logistic regression models were used to examine the cross-sectional relationship between these study variables and MetS. Principal component and cluster analyses were conducted to derive dietary patterns. Results: Included were 550 (weighted N=4,886,039) and 3,040 (weighted N=4,267,182) Canadians and Koreans aged 60 to 79 years, respectively. The prevalence of MetS was 42.0% and 52.2% in the Canadian and Korean sample, respectively (p<.0001). The prevalence of MetS in Korean women was 60.5% and explained the overall increased prevalence in the Korean sample. Results of the descriptive analysis, as well as the univariate and multiple logistic regression analyses indicated that the prevalence and pattern or joint distribution of explanatory variables differed across the two populations. In the Canadian sample, the final multivariate model comprised household income, marital status, alcohol consumption and psychological distress, with evidence of an interaction between adequacy of household income and marital status. In the Korean sample, the final multivariate model comprised comorbidity, gender, education, marital status, physical activity, and dietary pattern, with evidence of an interaction between comorbidity and marital status and between gender and education. Conclusions: Findings of this study provided insight into possible underlying mechanisms that might lead to between-country differences in prevalence of MetS and to inconsistent measures of association between MetS and an individual factor like physical activity or dietary intake across studies.