Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

The ever-increasing number of available microbial genomes and metagenomes provide new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, notably for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we first showed that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We then managed to identify clusters of adjacent genes that display specific distribution patterns in the field (CAGs) and are thus potentially involved in the adaptation to particular environmental niches. Several CAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine or phosphonates, which might be either directly used by cells, for e.g. the biosynthesis of proteins or DNA, or degraded into inorganic nitrogen and/or phosphorus forms. We also highlight the frequent presence of CAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas, which are absent in low-iron regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in these areas. In contrast, Prochlorococcus populations thriving in iron-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) into Fe(II). Together, this study provides insights into how these key members of the phytoplankton community might behave in response to ongoing global change. Significance Statement Picocyanobacteria face various environmental conditions in the ocean and numerous studies have shown that genetically distinct ecotypes colonize different niches. Yet the functional basis of their adaptation remains poorly known, essentially due to the large number of genes of yet unknown function, many of which have little or no beneficial effect on fitness. Here, by combining comparative genomics and metagenomics approaches, we have identified not only single genes but also entire gene clusters, potentially involved in niche adaptation. Although being sometimes present in only one or a few sequenced strains, they occur in a large part of the population in specific ecological niches and thus constitute precious targets for elucidating the biochemical function of yet unknown niche-related genes.
Detection of circulating carcinoma cells in peripheral blood collected from patients with ovarian cancer by using different molecular markers - a preliminary report

Introduction: Efficient techniques enabling the ovarian cancer patients’ diagnosis, prognosis and therapy remain far from perfection. Especially, the prognostic significance of circulating tumour cells’ (CTC) presence remains to some extent unclear. Latest findings on this matter suggest a need to revise the modern persuasion about the meaning of single tumour cell detection in peripheral blood (PB) or bone marrow (BM) by using standard cancer diagnostic procedures, as standard histopathological, immunohisto- and immunocytochemical procedures. However, that negative state induced the investigation of mRNA transcripts present in tumour diseases, which could be easily detected by using real-time RT-PCR method. The RNA markers used in this study were: cytokeratin 19 (CK19), telomerase catalytic subunit (hTERT) and two markers thought to be tissue-specific for ovaries: steroidogenic acute regulatory protein (StAR) and creatine kinase B (CKB). Materials and methods: The blood samples from 20 women were collected in two parts (blood from each 10-person group was used either to perform real-time RT-PCR, or TA PCR-ELISA [enzyme-linked immunosorbent assay]). Results: Both real-time RT-PCR and TA PCR-ELISA methods showed some degree of specificity in this study, but not enough to be put in practice. Conclusions: Both results of our study and the small number of articles on molecular markers suitable for detecting CTCs in PB of patients with OC show that this aim will be hard to achieve by using standard molecular biology tools, like PCR or even real-time PCR. However, these attempts should not be terminated, because if any of them succeeds, the diagnostic value of this technique will be great.
Prevalence and Associated Factors of Pterygium Among Adults Living in Kolla Diba Town, Northwest Ethiopia

Background: Pterygium is a dis ﬁ guring disease that can potentially lead to blindness. It is more common in warm, windy and dry climates of tropical and sub-tropical regions of Africa. Globally, the prevalence ranging from 0.07% to 53%. Studies conducted on the prevalence of pterygium in developing countries were limited with a wider discrepancy between them. In this study, we aimed to assess the prevalence of pterygium and its associated factors among adults in Kolla Diba town. Methods: A community-based cross-sectional study was done in Kolla Diba town from May 30-June 16, 2019. A systematic random sampling technique was used to select 627 study participants. The basic ophthalmic examination was performed using portable slit lamp, 3x magnifying loop with torch light and a pretested structured questionnaire was completed. The data entered into EPI INFO version 7 and analyzed using SPSS version 20. Descriptive statistics and binary logistic regression analysis were employed. P-values of <0.05 were considered statistically signi ﬁ cant. Results: A total of 605 study participants were involved with a response rate of 96.5%. Among them, 317 (52.4%) participants were males. The mean age of the respondents was 38.18 ± 15.56 with a range of (18 – 95) in years. The overall prevalence of pterygium was 112 (18.5% (95% CI (15.6 – 21.7)). Being widowed (AOR = 7.32 (95% CI: 2.88, 18.57)), outdoor occupation (AOR = 2.50 (95% CI: 1.46, 4.29)), sun exposure (AOR = 2.38 (95% CI: 1.28, 4.43)), wind exposure (AOR = 1.97 (95% CI: 1.04, 3.72)), alcohol drinking (AOR = 2.26 (95% CI: 1.48, 4.63)), and severe blepharitis (AOR = 2.45 (95% CI: 1.48, 4.05)) had statistically signi ﬁ cant positive association with pterygium. Conclusion: The prevalence of pterygium was relatively higher. Being widowed, outdoor occupation, sun exposure, wind exposure, alcohol drinking, and severe blepharitis were signi ﬁ cantly associated with the development of pterygium.
Distributed learning with indefinite kernels

We investigate the distributed learning with coefficient-based regularization scheme under the framework of kernel regression methods. Compared with the classical kernel ridge regression (KRR), the algorithm under consideration does not require the kernel function to be positive semi-definite and hence provides a simple paradigm for designing indefinite kernel methods. The distributed learning approach partitions a massive data set into several disjoint data subsets, and then produces a global estimator by taking an average of the local estimator on each data subset. Easy exercisable partitions and performing algorithm on each subset in parallel lead to a substantial reduction in computation time versus the standard approach of performing the original algorithm on the entire samples. We establish the first mini-max optimal rates of convergence for distributed coefficient-based regularization scheme with indefinite kernels. We thus demonstrate that compared with distributed KRR, the concerned algorithm is more flexible and effective in regression problem for large-scale data sets.
Study of Conjugate Heat Transfer from Heated Plate by Turbulent Offset
 Jet in Presence of Freestream Motion using Low-Reynolds Number
 Modeling

The present study deals with conjugate heat transfer from a heated flat plate by a turbulent offset jet in presence of freestream motion. The turbulent convection in fluid and conduction in solid is solved in a coupled manner by simultaneously satisfying the equality of temperature and heat flux at the solid-fluid interface. The computations have been carried out using low-Reynolds number (LRN) k −ω SST model in the fluid region. The capability of LRN modeling have enabled to solve the entire boundary layer including the thin viscous sublayer due to which Moffatt vortices (secondary recirculation regions) have been captured near the corner of the wall where the turbulence Reynolds number is low. The bottom surface of solid plate is maintained at a constant temperature higher than the jet inlet temperature whereas the jet inlet temperature is same as that of the ambient. The present investigation reports the effects of offset ratio of jet (OR), Reynolds number of flow (Re), solid to fluid thermal conductivity ratio (K), solid slab thickness (S) and freestream velocity (U∞) on conjugate heat transfer arises due to solid and fluid interaction. The offset ratio is varied in the range OR = 3 − 11, Reynolds number in the range Re = 10000 − 25000, solid to fluid thermal conductivity ratio in the range K = 1 − 2000, solid slab thickness in the range S = 1−20 and freestream velocity in the range U∞ = 0.1 − 0.25. The effects of various parameters on the near-wall velocity profile, solid-fluid interface temperature, local Nusselt number variation along the plate, heat flux variation along the plate, etc. have been discussed in detail.
Improving food security through environmental management in Ibadan: the case of the Ayeye community.

www.ruaf. org The Sustainable Ibadan Project (SIP) was established in 1994 (together with 11 similar projects across the world) by UNCHS (HABITAT) as part of the Sustainable Cities Programme. Participants at a City Consultative Forum in 1995 concluded that waste management and conversion to organic fertiliser were top priorities for Ibadan and jointly identified aerobic composting technology using windrows as a viable method to collect and recycle waste, generate income, and use compost for urban agriculture.
Distribution and fixed-precision sampling plans for diamondback moth (Lepidoptera: Plutellidae), on winter–spring cabbage

The diamondback moth (Plutella xylostella L.) is the most destructive insect pest on cabbage (Brassica oleracea var. capitata L.). Infestation by this pest usually results in the indiscriminate use of insecticides by farmers due to a lack of sampling plans for this pest. Sampling plans for P. xylostella management decisions on winter–spring cabbage in the Eastern Cape Province of South Africa were developed, through population monitoring that comprised weekly counts of immature stages of P. xylostella on 60 plants for 11 wk each during the winter and spring seasons. The mean density–variance relationship was used to describe the distribution of the pest, and number of infested plants was used to develop a fixed-precision sampling plan. All plant growth stages preceding maturation were vulnerable to P. xylostella damage resulting in yield losses. A high aggregation of P. xylostella on cabbage was observed in spring than in winter. The average sample number to estimate P. xylostella density within a 15% standard error of the mean was 35 plants. Furthermore, the estimated plant proportion action threshold (AT) was 51% with density action thresholds of 0.50 and 0.80 for spring and winter, respectively. Fitting P. xylostella cumulative counts in the winter and spring sampling plans resulted in 100% and 45% reduction in insecticide treatments. The similarity of sample size and ATs between both seasons provides evidence that a single sampling plan is practical for all cabbage growing seasons. The similarity of the estimated ATs to those acceptable in established integrated pest management programs indicates reliability.
Comorbidity and mortality in systemic sclerosis and matched controls: Impact of interstitial lung disease. A population based cohort study based on health registry data

Objective This population-based, matched cohort study evaluates the impact of comorbidities on mortality among systemic sclerosis (SSc) patients with and without interstitial lung disease (ILD). Method Patients with a first-time SSc diagnosis between 2002 and 2015 were identified in the Danish National Patient Registry, separated into two cohorts – with ILD (SSc-ILD) and without ILD (non-ILD SSc), and matched 1:4 with controls from the general population on age, sex, residency and marital status. Comorbidity and mortality data were obtained from national registries. The Deyo-Charlson comorbidity score (DCcs) was used for assessment of the burden of comorbidities. Results 1732 patients with SSc and 6919 controls were included; 258 (14.9%) patients had SSc-ILD. The hazard ratio (HR) for death was 2.8 (95% CI 2.4–3.3) in SSc, and especially increased in SSc-ILD (HR 4.2 (95% CI 3.2–5.4)), males (HR 3.1 95% CI 2.4–4.1) and younger adults (aged 18–40 (HR 6.9, 95% CI 3.4–14.2) and 41–50 (HR 7.7, 95% CI 3.8–15.6)). In non-ILD SSc, mortality increased with increasing DCcs. Cancer was the most frequent cause of death in SSc (24.9% of deaths) and in controls (33.5%), in SSc followed by musculoskeletal and connective tissue diseases (22.7%); the cause of only 0.8% of deaths among controls. Conclusion The high prevalence of comorbidities in SSc had extensive impact on mortality. Mortality was increased in males, in young adults and in SSc-ILD, underlining the excess mortality associated with ILD. These findings emphasise the importance of timely diagnosis and optimal management of organ involvement and comorbidities in SSc.
G1P3/IFI6, an interferon stimulated protein, promotes the association of RAB5+ endosomes with mitochondria in breast cancer cells

G1P3/IFI6 is an interferon stimulated gene with antiapoptotic, prometastatic, and antiviral functions. Despite its pleiotropic functions, subcellular localization of G1P3 remains unclear. Using biochemical‐ and confocal microscopic approaches, this study identified the localization of G1P3 in organelles of the endomembrane system and in the mitochondria of breast cancer cells. In cell fractionation studies, both interferon‐induced endogenous‐ and stably expressed G1P3 cofractionated with affinity‐isolated mitochondria. Results of the protease protection assay have suggested that ~24% of mitochondrial G1P3 resides within the mitochondria. Conforming to this, confocal microscopy studies of cells stably expressing epitope‐tagged G1P3 (MCF‐7/G1P3‐FLAG), identified its localization in mitochondria (~38%) as well as in ER, trans‐Golgi network (TGN), lysosomes, and in RAB5 positive (RAB5+) endosomes. These results suggested the trafficking of G1P3 from TGN into endolysosomes. Both G1P3 and RAB5 were known to confer apoptosis resistance through mitochondrial stabilization. Therefore, the effects of G1P3 on the localization of RAB5 in mitochondria were tested. Compared to vector control, the co‐occurrence of RAB5 with the mitochondria was increased by 1.5‐fold in MCF‐7/G1P3‐FLAG expressing cells (p ≤ .005). Taken together, our results demonstrate a role for G1P3 to promote the association of RAB5+ endosomes with mitochondria and provide insight into yet another mechanism of G1P3‐induced cancer cell survival.
Perioperative interventions to improve early mobilisation and physical function after hip fracture: a systematic review and meta-analysis

Abstract Background Perioperative interventions could enhance early mobilisation and physical function after hip fracture surgery. Objective Determine the effectiveness of perioperative interventions on early mobilisation and physical function after hip fracture. Methods Ovid MEDLINE, CINAHL, Embase, Scopus and Web of Science were searched from January 2000 to March 2022. English language experimental and quasi-experimental studies were included if patients were hospitalised for a fractured proximal femur with a mean age 65 years or older and reported measures of early mobilisation and physical function during the acute hospital admission. Data were pooled using a random effect meta-analysis. Results Twenty-eight studies were included from 1,327 citations. Studies were conducted in 26 countries on 8,192 participants with a mean age of 80 years. Pathways and models of care may provide a small increase in early mobilisation (standardised mean difference [SMD]: 0.20, 95% confidence interval [CI]: 0.01–0.39, I2 = 73%) and physical function (SMD: 0.07, 95% CI 0.00 to 0.15, I2 = 0%) and transcutaneous electrical nerve stimulation analgesia may provide a moderate improvement in function (SMD: 0.65, 95% CI: 0.24–1.05, I2 = 96%). The benefit of pre-operative mobilisation, multidisciplinary rehabilitation, recumbent cycling and clinical supervision on mobilisation and function remains uncertain. Evidence of no effect on mobilisation or function was identified for pre-emptive analgesia, intraoperative periarticular injections, continuous postoperative epidural infusion analgesia, occupational therapy training or nutritional supplements. Conclusions Perioperative interventions may improve early mobilisation and physical function after hip fracture surgery. Future studies are needed to model the causal mechanisms of perioperative interventions on mobilisation and function after hip fracture.
The Impact of Floods on Firms’ Performance

We estimate the short-run impact of a major flood that hit the region of Veneto in 2010 on firms' performance. Using firm level data and a difference in difference approach we compare the value added growth of hit firms to the one of a control group of companies that are not exposed to the flood. The results indicate that the value added growth of affected firms is 6.9% higher two years after the flood. We further investigate the role of aid transfers in the aftermath of the disaster event. Considering both the flood and the aid treatment, we construct four mutually exclusive and exhaustive groups. The results indicate that, among firms exposed to the flood, both the ones that benefit from financial aid and the ones that don't grow faster than the reference groups of firms that neither are exposed to the flood, nor receive financial aid. We also find a 2% additional growth effect that is attributable to the contribution of aid in the recovery phase.
TAM receptors in phagocytosis: Beyond the mere internalization of particles

TYRO3, AXL, and MERTK constitute the TAM family of receptor tyrosine kinases, activated by their ligands GAS6 and PROS1. TAMs are necessary for adult homeostasis in the immune, nervous, reproductive, skeletal, and vascular systems. Among additional cellular functions employed by TAMs, phagocytosis is central for tissue health. TAM receptors are dominant in providing phagocytes with the molecular machinery necessary to engulf diverse targets, including apoptotic cells, myelin debris, and portions of live cells in a phosphatidylserine‐dependent manner. Simultaneously, TAMs drive the release of anti‐inflammatory and tissue repair molecules. Disruption of the TAM‐driven phagocytic pathway has detrimental consequences, resulting in autoimmunity, male infertility, blindness, and disrupted vascular integrity, and which is thought to contribute to neurodegenerative diseases. Although structurally and functionally redundant, the TAM receptors and ligands underlie complex signaling cascades, of which several key aspects are yet to be elucidated. We discuss similarities and differences between TAMs and other phagocytic pathways, highlight future directions and how TAMs can be harnessed therapeutically to modulate phagocytosis.
A phospho‐deficient α3 glycine receptor mutation alters synaptic glycine and GABA release in mouse spinal dorsal horn neurons

Glycine receptors (GlyRs), together with GABAA receptors, mediate postsynaptic inhibition in most spinal cord and hindbrain neurons. In several CNS regions, GlyRs are also expressed in presynaptic terminals. Here, we analysed the effects of a phospho‐deficient mutation (S346A) in GlyR α3 subunits on inhibitory synaptic transmission in superficial spinal dorsal horn neurons, where this subunit is abundantly expressed. Unexpectedly, we found that not only were the amplitudes of evoked glycinergic inhibitory postsynaptic currents (IPSCs) significantly larger in GlyRα3(S346A) mice than in mice expressing wild‐type α3GlyRs (GlyRα3(WT) mice), but so were those of GABAergic IPSCs. Decreased frequencies of spontaneously occurring glycinergic and GABAergic miniature IPSCs (mIPSCs) with no accompanying change in mIPSC amplitudes suggested a change in presynaptic transmitter release. Paired‐pulse experiments on glycinergic IPSCs revealed an increased paired‐pulse ratio and a smaller coefficient of variation in GlyRα3(S346A) mice, which together indicate a reduction in transmitter release probability and an increase in the number of releasable vesicles. Paired‐pulse ratios of GABAergic IPSCs recorded in the presence of strychnine were not different between genotypes, while the coefficient of variation was smaller in GlyRα3(S346A) mice, demonstrating that the decrease in release probability was readily reversible by GlyR blockade, while the difference in the size of the pool of releasable vesicles remained. Taken together, our results suggest that presynaptic α3 GlyRs regulate synaptic glycine and GABA release in superficial dorsal horn neurons, and that this effect is potentially regulated by their phosphorylation status.
Kinesiophobia and physical activity: A systematic review and meta-analysis

OBJECTIVE. Physical activity is known to reduce the risk of disability, disease, and mortality. However, in some patients, an excessive, irrational, and debilitating fear of movement (i.e., kinesiophobia) is thought to induce avoidance behaviors, contributing to decreased engagement in physical activity. The aim of this study was to examine whether kinesiophobia is negatively associated with physical activity and what factors influence this relationship. METHODS. Three databases were searched for articles including both a measure of kinesiophobia and physical activity. Two reviewers screened articles for inclusion, assessed risk of bias, and extracted data from each study. Pearson product-moment correlations were pooled from eligible studies using the generic inverse pooling and random effects method to examine the relationship between kinesiophobia and physical activity. RESULTS. Forty-nine articles were included in the systematic review and 41 studies (n = 4,848) in the meta-analysis. Results showed a moderate negative correlation between kinesiophobia and physical activity (r = -0.31; 95% CI: -0.42 to -0.20; I2 = 1.8%; p < 0.0001). Subgroup meta-analyses revealed that the correlation was statistically significant only in patients with a cardiovascular or arthritis condition and in studies using a self-reported measure of physical activity. There was no evidence of an effect of age, gender, or pain. CONCLUSIONS. Higher levels of kinesiophobia were moderately associated with lower levels of physical activity. However, between-study heterogeneity was considerable, and results showed no evidence of this association when physical activity was assessed with accelerometers or pedometers. Additional studies using device-based measures of physical activity are required to confirm these results and to understand the factors and mechanisms influencing this potential relationship. IMPACT. Our results suggest that kinesiophobia could be considered as a limiting factor when developing physical activity promotion strategies for inactive patients.