Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationship of sociodemographic and lifestyle factors and diet habits with metabolic syndrome (MetS) in a multi-ethnic Asian population

Objectives Literature shows a high prevalence of MetS among Malaysians, varying across major ethnicities. As sociodemographic characteristics, lifestyle factors and diet habits of such communities have been reported to be diverse, the study objective was to investigate the association of various sociodemographic characteristics, lifestyle factors and diet habits on MetS overall and among the three major ethnic communities in Malaysia. Materials and Methods We conducted a cross-sectional study among 481 Malaysians of age 18 years and above living in Johor, Malaysia. Information on demographics, lifestyle and diet habits was collected using a structured questionnaire. MetS was diagnosed among the subjects using the Harmonized criteria. Multiple logistic regression was used to analyse associations between sociodemographic and lifestyle factors and dietary behaviours with MetS. Results MetS was found among 32.2% of the respondents, more prevalent among the Indians (51.9%), followed by Malays (36.7%) and Chinese (20.2%). Overall, increasing age (AOR=2.44[95%CI=1.27-4.70] at 40-49 years vs. AOR=4.14[95%CI=1.97-8.69] at 60 years and above) and Indian ethnicity (AOR=1.95[95%CI=1.12-3.38)] increased, while higher education (AOR = 0.44[95%CI = 0.20-0.94] reduced the odds of MetS in this population. Quick finishing of meals (AOR=2.17[95%CI=1.02-4.60]) and low physical activity (AOR=4.76[95%CI=1.49-15.26]) was associated with an increased odds of MetS among the Malays and Chinese, respectively. Conclusion The population in Johor is diverse in these factors, and some of these are associated with MetS in certain ethnicities. In light of such differences, ethnic specific measures are needed to reduce the prevalence of MetS in this population.
Organic matter and nutrients associated with fine root turnover in a white oak stand. [Quercus albus]

Organic matter and nutrients cycled by fine root turnover were quantified in a mature white oak (Quercus alba L.) stand and compared to contributions from litterfall. The budget method, a revised version of the traditional repeated sampling method, was used to measure root turnover. The magnitude of the live and dead pools of three size classes of fine (<5 mm diameter) roots were monitored bimonthly for 14 months. Decomposition rates over these intervals were also measured, while production and mortality were calculated. Litterfall was collected simultaneously, and the nutrient concentrations of the various detritus components determined. Root pools fluctuated less, and total root turnover biomass (220 g m/sup -2/ yr/sup -1/) was also less than previously noted in most other stands studied. Fine root turnover accounted for 30% of the total detritus production and 20-40% of the turnover of the five macronutrients (N, P, K, Ca, Mg) studied. Differences with previous studies suggest that there may be rather large species and/or site-related differences in the amount of energy various stands allocate for fine root maintenance. For. Sci. 33(2):330-346.
Phosphorylation of Parkin by the autophagy initiating kinase ULK1 regulates mitochondrial homeostasis

Author(s): Lombardo, Portia Sachi | Advisor(s): Shaw, Reuben J | Abstract: Our laboratory recently identified the autophagy initiating kinase ULK1 as a novel AMPK substrate, which directly connects the highly conserved AMPK-mediated energy sensing pathway to the regulation of autophagy. Genetic deletion of ULK1 led to an accumulation of mitochondria with abnormal morphology, supporting a role for ULK1 kinase activity in the maintenance of mitochondrial homeostasis, yet few mammalian ULK1 substrates have been identified beyond those involved in the canonical initiation of autophagy. Here we have identified and validated the E3 ligase Parkin, a known mediator of mitochondrial quality control and the most commonly mutated gene in autosomal recessive early-onset Parkinson’s disease, as a direct ULK1 substrate. ULK1-mediated phosphorylation of Parkin was required for maximal Parkin activity in multiple assays of Parkin function. These data reveal an important role for ULK1-mediated Parkin phosphorylation in the regulation of mitochondrial homeostasis, as this modification seems to prime Parkin for maximal activity following depolarization. Further studies using mouse models have indicated that Parkin is phosphorylated in vivo in mouse livers and primary hepatocytes in response to activators of the AMPK/ULK1 pathway, including Metformin, the most widely prescribed drug for the treatment of Type II diabetes. These data suggest the potential for profound in vivo relevance for the regulation of Parkin function downstream of the AMPK/ULK1 signaling cascade.
Evaluation of the fermentation properties of different soybean (Glycine max L.) cultivars

The enzymatic activity (EA) and amino-type nitrogen (ATN), viscous substance (VS), organic acid (OA), free amino acid (FAA), and volatile compound (VC) content in fermented soybeans of six cultivars (Glycine max L. ‘Taekwangkong’ [TKK], ‘Daechankong’ [DCK], ‘Misokong’ [MSK], ‘Seonpungkong’ [SPK], ‘Uramkong’ [URK], and ‘Chamolkong’ [COK]) were compared. Fermentation increased the quality indices such as EA, ATN and VS in soybean, and their highest content were observed in DCK. The content of major OAs decreased in the following order: lactic acid > acetic acid > fumaric acid. The essential amino acid (EAA) content was increased by fermentation, and FAA production had a positive effect on the abundance of the fermentation metabolites ã-amino-n-butyric acid and ornithine. The content of the VS pyrazine differed with cultivar. Overall, soybean cultivars showed differences in the composition and fermentation properties, with raw DCK soybeans being particularly suitable for fermentation.
The complete mitochondrial genome of Argiope ocula (Araneae: Araneidae) and its phylogeny

Abstract The complete mitochondrial genome of Argiope ocula (GenBank accession number MN331657) is a circular molecule of 14,079 bp in length, comprising of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes, and a control region. Ten intergenic spacer regions and 19 reading frame overlaps were found in the mitogenome of A. ocula. Ten tRNAs (trnD, trnF, trnK, trnR, trnT, trnW, trnE, trnG, trnL1, and trnM) lacked the TΨC arm stem, whereas three tRNAs (trnA, trnS1, and trnS2) lost the dihydrouracil (DHU) arm. Phylogenetic analysis suggested that A. ocula had the closest evolutionary relationship with A. perforata.
Opportunistically collected photographs can be used to estimate large-scale phenological trends

Premise Research on large-scale patterns of phenology have utilized multiple sources of data to analyze the timing of events such as flowering, fruiting, and leaf out. In-situ observations from standardized surveys are ideal, but remain spatially sparse. Herbarium records and phenology-focused citizen science programs provide a source of historic data and spatial replication, but the sample sizes for any one season are still relatively low. A novel and rapidly growing source of broad-scale phenology data are photographs from the iNaturalist platform, but methods utilizing these data must generalize to a range of different species with varying season lengths and occurring across heterogenous areas. They must also be robust to different sample sizes and potential biases toward well travelled areas such as roads and towns. Methods/Results We developed a spatially explicit model, the Weibull Grid, to estimate flowering onset across large-scales, and utilized a simulation framework to test the approach using different phenology and sampling scenarios. We found that the model is ideal when the underlying phenology is non-linear across space. We then use the Weibull Grid model to estimate flowering onset of two species using iNaturalist photographs, and compare those estimates with independent observations of greenup from the Phenocam network. The Weibull Grid model estimate consistently aligned with Phenocam greenup across four years and broad latitudes. Conclusion iNaturalist observations can considerably increase the amount of phenology observations and also provide needed spatial coverage. We showed here they can accurately describe large-scale trends as long as phenological and sampling processes are considered.
Adhesion-free cell migration by topography-based force transduction

Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force-coupling is usually mediated by transmembrane adhesion receptors, especially these of the integrin family, amoeboid cells like leukocytes can migrate extremely fast despite very low adhesive forces1. We show that leukocytes cannot only migrate under low adhesion but indeed can transduce forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographic features of the substrate to propel themselves. Here, the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating shear forces sufficient to drive deformations towards the back of the cell. Notably, adhesion dependent and adhesion independent migration are not exclusive but rather variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate simultaneously. As adhesion free migration is independent of the chemical composition of the environment it renders cells completely autonomous in their locomotive behavior.
Morphometric variability of dentition of the Late Pleistocene Voles (Arvicolidae, Rodentia) from Bacho Kiro Cave (Bulgaria)

A b s t r a c t . The paper comprises a description of the morphotypical variation in the dentition (chiefly M,) and dimensions of seven arvicolid species. The frequency of particular morphotypes has been calculated and conclusions as to the microevolutionary changes in some species (e.g. Microtus nivalis and Lagurus lagurus) have been drawn. The method of analysis of morphotypes made it possible to treat the specimens described previously under the name of Microtus cf. oeconomus as extre­ me variants of Microtus nivalis and to include them in this last species. Two forms (M. arvalis and M. agrestis), described earlier as M. arvalis, have also been shown to be present in the fossil materials, although they could not be separated entirely on the basis of either morphology or measurements. In view of the well-established stratigraphy of the locality an analysis and discussion of changes in the length of Mlr occurring in particular species from the Early Würm up to the Holocene, have been carried out. These changes were not connected with climatic fluctuations and so they had been brought about by a selective factor other than climatic conditions.
Characterization and phylogenetic relationship of the complete mitochondrial genome of Black-cheeked Lovebird, Agapornis Nigrigenis

Abstract The complete mitochondrial genome of Agapornis nigrigenis was obtained using Sanger sequencing. The mitochondrial genome from A. nigrigenis is 16,718 bp in length. Its genome with an overall GC content of 48.86%, contained 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and 1 control region. The phylogenetic position of A. nigrigenis based on the 18 parrots species showed it was sister to the same genus specie Agapornis roseicollis. The results obtained here can contribute to molecular evolution and phylogeny of parrots further.
Linking influenza virus evolution within and between human hosts

Influenza viruses rapidly diversify within individual human infections. Several recent studies have deep-sequenced clinical influenza infections to identify viral variation within hosts, but it remains unclear how within-host mutations fare in the global viral population. Here, we compare viral variation within and between hosts to link influenza’s evolutionary dynamics across scales. Synonymous sites evolve at similar rates at both scales, indicating that global evolution at these putatively neutral sites results from the accumulation of within-host variation. However, nonsynonymous mutations are depleted in global viral populations compared to within hosts, suggesting that selection purges many of the protein-altering changes that arise within hosts. The exception is at antigenic sites, where selection detectably favors nonsynonymous mutations at the global scale, but not within hosts. These results suggest that selection against deleterious mutations and selection for antigenic change are the main forces that transform influenza’s within-host genetic variation into global evolution.
Physiological analysis and gene expression analysis of ZmDBP3, ZmALDH9, ZmAN13, and ZmDREB2A in maize lines

The objective of this study was to evaluate gene expression related to water deficit tolerance in maize lines. For this, lines previously classified as tolerant (91-T and 32-T) and non-tolerant (24-NT and 57-NT) to water deficit were used. The seeds of the four lines were evaluated for emergence and emergence speed index, and the seedlings were evaluated for root and shoot length under two conditions of water availability (70 and 10% substrate water retention capacity). In transcript analysis, the expression of several genes associated with water deficit tolerance, ZmDBP3, ZmALDH9, ZmAN13, and ZmDREB2A, was evaluated by qRT-PCR for the 91-T and 57-NT lines. It can be concluded that soil water deficiency did not reduce root development. However, the shoot length was significantly lower under dry conditions. Through transcript analysis, the genes ZmDBP3 and ZmAN13 were identified as potential markers for the early selection of maize lines tolerant to water deficit.
miR-181a Regulates p62/SQSTM1, Parkin and Protein DJ-1 Promoting Mitochondrial Dynamics in Skeletal Muscle Ageing

One of the key mechanisms underlying skeletal muscle functional deterioration during ageing is disrupted mitochondrial dynamics. Regulation of mitochondrial dynamics is essential to maintain a healthy mitochondrial population and prevent the accumulation of damaged mitochondria, however the regulatory mechanisms are poorly understood. We demonstrated loss of mitochondrial content and disrupted mitochondrial dynamics in muscle during ageing concomitant with dysregulation of miR-181a target interactions. Using functional approaches and mitoQc assay, we have established that miR-181a is an endogenous regulator of mitochondrial dynamics through concerted regulation of Park2, p62/SQSTM1 and DJ-1 in vitro. Downregulation of miR-181a with age was associated with an accumulation of autophagy-related proteins and abnormal mitochondria. Restoring miR-181a levels in old mice prevented accumulation of p62, DJ-1 and PARK2, improved mitochondrial quality and muscle function. These results provide physiological evidence for the potential of microRNA-based interventions for age-related muscle atrophy and of wider significance for diseases with disrupted mitochondrial dynamics.
Metagenomics coupled with biogeochemical rates measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments

High‐throughput sequencing has enabled robust shotgun metagenomic sequencing that informs our understanding of the genetic basis of important biogeochemical processes. Slower to develop, however, are the application of these tools in a controlled experimental framework that pushes the field beyond exploratory analysis toward hypothesis‐driven research. We performed flow‐through reactor experiments to examine how salt marsh sediments from varying depths respond to nitrate addition and linked biogeochemical processes to this underlying genetic foundation. Understanding the mechanistic basis of carbon and nitrogen cycling in salt marsh sediments is critical for predicting how important ecosystem services provided by marshes, including carbon storage and nutrient removal, will respond to global change. Prior to the addition of nitrate, we used metagenomics to examine the functional potential of the sediment microbial community that occurred along a depth gradient, where organic matter reactivity changes due to decomposition. Metagenomic data indicated that genes encoding enzymes involved in respiration, including denitrification, were higher in shallow sediments, and genes indicative of resource limitation were greatest at depth. After 92 d of nitrate enrichment, we measured cumulative increases in dissolved inorganic carbon production, denitrification, and dissimilatory nitrate reduction to ammonium; these rates correlated strongly with genes that encode essential enzymes in these important pathways. Our results highlight the importance of controlled experiments in linking biogeochemical rates to underlying genetic pathways. Furthermore, they indicate the importance of nitrate as an electron acceptor in fueling microbial respiration, which has consequences for carbon and nitrogen cycling and fate in coastal marine systems.
Molecular Detection of Serine Carbapenemase Genes in Carbapenem-Resistant Isolates of Pseudomonas aeruginosa Recovered from Patients in Al-Diwaniyah Province, Iraq

The present study aimed at investigating the spread of serine carbapenemase-producing isolates of Pseudomonas aeruginosa recovered from some hospitals and specialized health centers in Al-Diwaniyah City, Iraq. Using morphological and molecular methods, 630 clinical samples (244 burn swabs, 163 sputa, 115 urine samples, and 108 ear swabs) were tested. The current work also explored the carbapenemase production ability of the carbapenemresistant (CR) isolates using morphological and molecular methods. A monoplex polymerase chain reaction (MPCR) technique targeting 4 different serine carbapenemase (SCMs) coding genes was followed. The study also explored the nucleotide sequences of the SCM genes. The API 20 E and Vitek 2 system showed that 100 of the isolates belonged to P. aeruginosa. With different severity of resistance by percentages of isolates to various antibiotics, only 24% of the isolates displayed resistance against carbapenem. The results of the SCM-related MPCR showed the occurrence of the blaGES, blasMe, blaKPC, and blaOXA-48 genes in 20 (83.3%), 19 (79.1%), 11 (45.8%), 18 (75%), respectively, of the isolates. The phylogenetic study analysis revealed high, 99%, identity with NCBI-related world strains. According to the best of our knowledge, this is the first study in Iraq that detects a group of encoding genes of serine carbapenemase in carbapenem-resistant isolates.
Variabilidade genética de Spondias lutea L. em uma população do baixo São Francisco sergipano, por meio de isoenzimas

A conservacao genetica de uma especie requer o previo conhecimento de seu sistema de reproducao, estrutura e diversidade genetica. Assim, este estudo foi realizado com o objetivo de determinar a diversidade genetica existente em uma populacao de Spondias lutea L. localizada na Regiao do Baixo Sao Francisco sergipano, por meio de marcadores isoenzimaticos, visando a elaboracao de estrategias de producao de sementes para a recuperacao de mata ciliar. Para a realizacao deste estudo foram coletadas folhas jovens de 16 individuos de Spondias lutea L. A diversidade genetica foi caracterizada a partir das estimativas das frequencias alelicas (Pij) e dos Indices de diversidade heterozigosidade media observada (H0 ), heterozigosidade media esperada (He ), numero medio de alelos por loco (Â) e porcentagem de locos polimorficos. Tambem foi calculado o indice de fixacao F de Wright. Dos 28 alelos detectados 12 (42,85%) tinham baixa frequencia. A porcentagem de locos polimorficos foi igual a 90% e o numero medio de alelos por loco igual a 2,80. A heterozigosidade media observada foi maior do que a esperada, indicando que ha mais heterozigotos na populacao do que o esperado pelo Equilibrio de Hardy-Weinberg, o que pode ser visualizado pelo valor negativo do indice de fixacao (F(IS) = - 0,0658). Devido ao elevado polimorfismo a populacao estudada tem elevado potencial para a conservacao in situ.
Natural image reconstruction from brain waves: a novel visual BCI system with native feedback

Here we hypothesize that observing the visual stimuli of different categories trigger distinct brain states that can be decoded from noninvasive EEG recordings. We introduce an effective closed-loop BCI system that reconstructs the observed or imagined stimuli images from the co-occurring brain wave parameters. The reconstructed images are presented to the subject as a visual feedback. The developed system is applicable to training BCI-naïve subjects because of the user-friendly and intuitive way the visual patterns are employed to modify the brain states.
Assessment of low-velocity impact damage in composites by the measure of second-harmonic guided waves with the phase-reversal approach

Structural strength and integrity of composites can be considerably affected by the low-velocity impact damage due to the unique characteristics of composites, such as layering bonded by adhesive and the weakness to impact. For such damage, there is an urgent need to develop advanced nondestructive testing approaches. Despite the fact that the second harmonics could provide information sensitive to the structural health condition, the diminutive amplitude of the measured second-order harmonic guided wave still limits the applications of the second-harmonic generation–based nonlinear guided wave approach. Herein, laminated composites suffered from low-velocity impact are characterized by use of nonlinear guided waves. An enhancement in the signal-to-noise ratio for the measure of second harmonics is achieved by a phase-reversal method. Results obtained indicate a monotonic correlation between the impact-induced damage in composites and the relative acoustic nonlinear indicator of guided waves. The experimental finding in this study shows that the measure of second-order harmonic guided waves with a phase-reversal method can be a promising indicator to impact damage rendering in an improved and reliable manner.
Invasive meningococcal disease in north Queensland, 1990-1994

All episodes of invasive meningococcal disease (n=69) that occurred in north Queensland over the five-year period 1990-1994 are described. Aboriginal and Torres Strait Islander people had a considerably greater annual incidence (20.2 cases per 100,000) than did all other people (1.6 per 100,000 population). All three deaths were of young Aboriginal males. The majority (70%) of the isolates were serogroup C. Five outbreaks of serogroup C disease were identified, and these outbreaks accounted for nearly half of all the cases of serogroup C disease. (author abstract)
Early Polycomb-target deregulations in Hutchinson-Gilford Progeria Syndrome revealed by heterochromatin analysis

Hutchinson-Gilford progeria syndrome (HGPS) is characterized by the progressive accumulation of progerin, an aberrant form of Lamin A. This leads to chromatin structure disruption, in particular by interfering with Lamina Associated Domains. Although several cellular and molecular alterations have been characterized, it is still unclear how chromatin structural changes translate into premature senescence in HGPS. Moreover, early events in chromatin remodeling have not been detected so far. We developed a new high-throughput sequencing-based method, named SAMMY-seq, for genome-wide characterization of heterochromatin accessibility changes. Using SAMMY-seq, we detected early stage alterations of chromatin structure in HGPS primary fibroblasts. Of note, these structural changes do not disrupt the distribution of H3K9me3 but are associated with site-specific H3K27me3 variations and transcriptional dysregulation of Polycomb target genes. Our results show that SAMMY-seq represents a novel and sensitive tool to characterize heterochromatin alterations. Moreover, we found that the assembly of lamin associated domains is strictly connected to the correct Polycomb repression, rapidly lost in early HGPS pathogenesis.