Miracle-dz/UniFAR-FTUs huggingface dataset:
Meal Replacements for Weight-Related Complications in Type 2 Diabetes: What Is the State of the Evidence?

Comprehensive lifestyle management is a fundamental aspect of diabetes care. Clinical practice guidelines for the nutritional management of diabetes have evolved considerably over the last 25 years shifting from a focus on single nutrients to food- and dietary pattern-based recommendations. Use of meal replacements as a temporary short-term strategy to induce weight loss and then transitioning to a healthier dietary pattern (e.g., Mediterranean or Portfolio) for weight loss maintenance fits well with this new shift in focus of clinical practice guidelines. As adherence is the most important determinant for attaining the benefits of any diet, health professionals should recommend evidence-based dietary patterns (including meal replacements) that align best with the patient’s values, preferences, and treatment goals.
Biomechanical assessment of the ipsilesional upper limb in post-stroke patients during multi-joint reaching tasks: A quantitative study

In hemiplegic patients with stroke, investigating the ipsilesional limb may shed light on the upper limb motor control, impairments and mechanisms of functional recovery. Usually investigation of motor impairment and rehabilitative interventions in patients are performed only based on the contralesional limb. Previous studies found that also the ipsilesional limb presents motor deficits, mostly evaluated with clinical scales which could lack of sensibility. To quantitatively evaluate the performance of the ipsilesional limb in patient with stroke, we conducted an observational study in which 49 hemiplegic patients were enrolled, divided in subgroups based on the severity of impairment of the contralesional limb, and assessed with a kinematic, dynamic and motor control evaluation protocol on their ipsilesional upper limb during reaching movements. Measurements were repeated in the acute and subacute phases and compared to healthy controls. Our results showed that the ipsilesional limb presented lower kinematic and dynamic performances with respect to the healthy controls. Patients performed the movements slower and with a reduced range of motion, indicating a difficulty in controlling the motion of the arm. The energy and the power outputs were lower in both shoulder and elbow joint with a high significance level, confirming the limitation found in kinematics. Moreover, we showed that motor deficits were higher in the acute phase with respect to the subacute one and we found higher significant differences in the group with a more severe contralesional limb impairment. Ipsilesional upper limb biomechanics adds significant and more sensible measures for assessments based on multi-joints dynamics, providing a better insight on the upper limb motor control after stroke. These results could have clinical implications while evaluating and treating ipsilesional and contralesional upper limb impairments and dysfunctions in patients with stroke.
Genetic sources and diversity of the paddy field carp in the Pearl River basin inferred from two mitochondrial loci

Paddy field carp (PF-carp) is an economically important fish cocultured with rice in traditional agricultural systems. Several distinctive strains of PF-carp have been formed through years of artificial and cross breeding. There is a concern about the status of germplasm resources among PF-carp, since little is known about the genetic sources, diversity, or differentiation. In this study we collected 17 PF-carp populations covering Daotian carp (DTL), Ru Yuan No. 1 (RY), Jinbian carp (JBL), Shaijiang carp (SJL), and Wu carp (WL) along the Pearl River basin to explore their genetic sources and diversity using concatenated sequences of the mitochondrial cytochrome b gene and the D-Loop region. According to the haplotype network analyses, 1, 9, and 57 haplotypes originated from Cyprinus carpio carpio, Cyprinus carpio haematopterus and Cyprinus carpio rubrofuscus, respectively, confirming that genetic introgression has occurred in Pearl River PF-carp populations and Cyprinus carpio carpio was the most common species for genetic origin. The results showed that RY exhibited the lowest level of nucleotide diversity (π = 0.0011) due to high-intensity breeding and was significantly differentiated from the other four strains. PF-carp strains in these remote traditional systems tended to experience artificial selection and a lack of farmer connection that gradually increased genetic differentiation among strains. Notably, three populations of JBL exhibited significant high-level differentiation, since they originated from mountainous areas hindering farmers from fry exchange. In contrast, no significant differentiation was uncovered in the WL populations, since this strain is the most popular cultured strain and has undergone artificial exchange of parents and fry in many cultured regions. This study helps us to understand the status of germplasm resources among PF-carp and to trace their genetic origin before being introduced for local cultivation.
The dynamic transcriptome during maturation of biofilms formed by methicillin-resistant Staphylococcus aureus

Background Methicillin-resistant Staphylococcus aureus (MRSA), a leading cause of chronic infections, forms prolific biofilms which afford an escape route from antibiotic treatment and host immunity. However, MRSA clones are genetically diverse, and mechanisms underlying biofilm formation remain under-studied. Such studies form the basis for developing targeted therapeutics. Here, we studied the temporal changes in the biofilm transcriptome of three pandemic MRSA clones: USA300, HEMRSA-15, and ST239. Methods Biofilm formation was assessed using a static model with one representative strain per clone. Total RNA was extracted from biofilm and planktonic cultures after 24, 48, and 72 h of growth, followed by rRNA depletion and sequencing (Illumina Inc., San Diego, CA, United States, NextSeq500, v2, 1 × 75 bp). Differentially expressed gene (DEG) analysis between phenotypes and among early (24 h), intermediate (48 h), and late (72 h) stages of biofilms was performed together with in silico co-expression network construction and compared between clones. To understand the influence of SCCmec and ACME on biofilm formation, isogenic mutants containing deletions of the entire elements or of single genes therein were constructed in USA300. Results Genes involved in primarily core genome-encoded KEGG pathways (transporters and others) were upregulated in 24-h biofilm culture compared to 24-h planktonic culture. However, the number of affected pathways in the ST239 24 h biofilm (n = 11) was remarkably lower than that in USA300/EMRSA-15 biofilms (USA300: n = 27, HEMRSA-15: n = 58). The clfA gene, which encodes clumping factor A, was the single common DEG identified across the three clones in 24-h biofilm culture (2.2- to 2.66-fold). In intermediate (48 h) and late (72 h) stages of biofilms, decreased expression of central metabolic and fermentative pathways (glycolysis/gluconeogenesis, fatty acid biosynthesis), indicating a shift to anaerobic conditions, was already evident in USA300 and HEMRSA-15 in 48-h biofilm cultures; ST239 showed a similar profile at 72 h. Last, SCCmec+ACME deletion and opp3D disruption negatively affected USA300 biofilm formation. Conclusion Our data show striking differences in gene expression during biofilm formation by three of the most important pandemic MRSA clones, USA300, HEMRSA-15, and ST239. The clfA gene was the only significantly upregulated gene across all three strains in 24-h biofilm cultures and exemplifies an important target to disrupt early biofilms. Furthermore, our data indicate a critical role for arginine catabolism pathways in early biofilm formation.
A miR-137-XIAP axis contributes to the sensitivity of TRAIL-induced cell death in glioblastoma

Glioblastoma (GBM) is the most lethal primary brain tumor in the central nervous system with limited therapeutic strategies to prolong the survival rate in clinic. TNF-related apoptosis-inducing ligand (TRAIL)-based strategy has been demonstrated to induce cell death in an extensive spectrum of tumor cells, including GBM, while a considerable proportion of malignant cells are resistant to TRAIL-induced apoptosis. MiR-137 is highly expressed in the brain, but significantly decreases with advanced progression of GBM. However, the functional link between miR-137 and TRAIL-induced apoptosis in GBM cells has not been established. Here, GBM cells were transfected with miR-137, and gene expression levels were examined by qRT-PCR and western blot. Apoptotic cells were measured by Annexin-V staining and TUNEL assay. Our data showed that miR-137 sensitizes GBM cells to the TRAIL-mediated apoptosis. Mechanistically, we identified that XIAP is a bona fide target of miR-137, which is essential for miR-137-regulated sensitivity of TRAIL-induced cell death in GBM cells. Finally, in a xenograft model, combined utilization of miR-137 and TRAIL potently suppresses tumor growth in vivo. Collectively, we demonstrate that a miR-137-XIAP axis is required for the sensitivity of TRAIL-induced cell death and shed a light on the avenue for the treatment of GBM.
Bacterial and fungal communities in indoor aerosols from two Kuwaiti hospitals

The airborne transmission of COVID-19 has drawn immense attention to bioaerosols. The topic is highly relevant in the indoor hospital environment where vulnerable patients are treated and healthcare workers are exposed to various pathogenic and non-pathogenic microbes. Knowledge of the microbial communities in such settings will enable precautionary measures to prevent any hospital-mediated outbreak and better assess occupational exposure of the healthcare workers. This study presents a baseline of the bacterial and fungal population of two major hospitals in Kuwait dealing with COVID patients, and in a non-hospital setting through targeted amplicon sequencing. The predominant bacteria of bioaerosols were Variovorax (9.44%), Parvibaculum (8.27%), Pseudonocardia (8.04%), Taonella (5.74%), Arthrospira (4.58%), Comamonas (3.84%), Methylibium (3.13%), Sphingobium (4.46%), Zoogloea (2.20%), and Sphingopyxis (2.56%). ESKAPEE pathogens, such as Pseudomonas, Acinetobacter, Staphylococcus, Enterococcus, and Escherichia, were also found in lower abundances. The fungi were represented by Wilcoxinia rehmii (64.38%), Aspergillus ruber (9.11%), Penicillium desertorum (3.89%), Leptobacillium leptobactrum (3.20%), Humicola grisea (2.99%), Ganoderma sichuanense (1.42%), Malassezia restricta (0.74%), Heterophoma sylvatica (0.49%), Fusarium proliferatum (0.46%), and Saccharomyces cerevisiae (0.23%). Some common and unique operational taxonomic units (OTUs) of bacteria and fungi were also recorded at each site; this inter-site variability shows that exhaled air can be a source of this variation. The alpha-diversity indices suggested variance in species richness and abundance in hospitals than in non-hospital sites. The community structure of bacteria varied spatially (ANOSIM r2 = 0.181–0.243; p < 0.05) between the hospital and non-hospital sites, whereas fungi were more or less homogenous. Key taxa specific to the hospitals were Defluvicoccales, fungi, Ganodermataceae, Heterophoma, and H. sylvatica compared to Actinobacteria, Leptobacillium, L. leptobacillium, and Cordycipitaceae at the non-hospital site (LefSe, FDR q ≤ 0.05). The hospital/non-hospital MD index > 1 indicated shifts in the microbial communities of indoor air in hospitals. These findings highlight the need for regular surveillance of indoor hospital environments to prevent future outbreaks.
The Topological Nature Of Defects

The subject of topological defects has become a very attractive field of study given its apparent relevance to as diverse systems as the early universe and condensed matter. As usually envisaged the topology of the manifold M of the minima of the relevant to our physical system effective potential V, provides reliable information about the capacity of that system to accommodate topological defects. Here we will examine the premises for that statement to be true.
Grain-filling characteristics and yield formation of wheat in two different soil fertility fields in the Huang–Huai–Hai Plain

Clarifying factors that underpinning the variation in wheat yield components between high and middle soil fertility fields is critical to increase grain production and narrow yield gap for smallholder farming systems in the Huang–Huai–Hai Plain (3HP), which characterized by a large variation in soil fertility. Two-year field experiments were conducted to investigate wheat tillering, leaf photosynthesis, and grain filling characteristics in different soil fertility fields: high soil fertility field (HF) and middle soil fertility field (MF). Results showed that the spike formation rate in HF was 12.7%–13.0% higher than that in MF, leading to an 18.0%–19.8% increase in spike number. In addition, HF improved canopy light interception and leaf photosynthesis characteristics after anthesis and delayed leaf senescence, contributing to the increase in both the active grain filling period and grain filling rate. This resulted in a higher 1,000 grain weight in HF, which was 8.2%–8.3% higher than that in MF. Compared to MF, HF obtained higher yields at 9,840 kg ha−1 in 2017/18 and 11,462 kg ha−1 in 2018/19, respectively. In summary, higher spike number and 1,000-grain weight, which were mediated by spike-formation rate, maximization of light interception and improved leaf photosynthesis. These results would have important implications for narrowing yield gap between MF and HF in the 3HP.
May the force be with your (immune) cells: an introduction to traction force microscopy in Immunology

For more than a couple of decades now, “force” has been recognized as an important physical parameter that cells employ to adapt to their microenvironment. Whether it is externally applied, or internally generated, cells use force to modulate their various actions, from adhesion and migration to differentiation and immune function. T lymphocytes use such mechano-sensitivity to decipher signals when recognizing cognate antigens presented on the surface of antigen presenting cells (APCs), a critical process in the adaptive immune response. As such, many techniques have been developed and used to measure the forces felt/exerted by these small, solitary and extremely reactive cells to decipher their influence on diverse T cell functions, primarily activation. Here, we focus on traction force microscopy (TFM), in which a deformable substrate, doped with reporters and exhibiting surface ligands, mimics a partner substrate such as an APC, and allows force measurements on the cellular scale. This technique has recently become a center of interest for many groups in the “ImmunoBiophysics” community and, as a consequence, has been subjected to refinements for its application to immune cells. Here, we present an overview of TFM, the precautions and pitfalls, and the most recent developments in the context of T cell immunology.
Package ‘CARBayes’

Description Implements a class of univariate and multivariate spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, multinomial, Poisson or zero-inﬂated Poisson (ZIP), and spatial autocorrelation is modelled by a set of random effects that are assigned a conditional autoregressive (CAR) prior distribution. A number of different models are available for univariate spatial data, including models with no random effects as well as random effects modelled by different types of CAR prior, including the BYM model (Be-sag et 1991, and Leroux model (Ler-oux et al., 2000, Additionally, a multivariate CAR (MCAR) model for multivariate spatial data is available, as is a two-level hierarchical model for modelling data relating to individuals within areas. Full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development has been supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1, ESRC grant ES/K006460/1, Innovate UK / Natural Environment Research Council (NERC) grant NE/N007352/1 and the TB Alliance.
The Performance of Biometric Attendance System (BAS): CTU-Tuburan Campus as case study

- This study aimed to evaluate the performance of the Biometric Attendance System (BAS) of Cebu Technological University-Tuburan Campus during the calendar year 2018 as basis for a proposed system improvement. This study used the quantitative research employing descriptive method that assessed the performance of the Biometric Attendance System as to timeliness, accuracy, graphical user-interface and system maintenance. The study was conducted at Cebu Technological University-Tuburan Campus, Tuburan, Cebu. There were 96 teaching staff and 48 non-teaching personnel who were chosen randomly to evaluate the performance of the Biometric Attendance System. Weighted mean was used to analyze and interpret the data. This study revealed the following findings: the BAS has six (6) features which are touch-screen user interface (TUI), system setup, administrators, finger registration, clock configuration and DTR pint menu. The overall performance of the biometric system was very satisfactory in terms of timeliness, accuracy, and graphical-user interface. Hence, biometric system has always ensured employees’ timeliness,
The syntax of inner aspect in Hungarian 1

This paper is concerned with the syntactic representation of inner aspect in Hungarian. We contribute to the extant research on inner aspectual markers by providing an analysis of entailed versus implied telicity as well as the (non)maximality e ﬀ ects with which telic predicates are associated. Although we focus on the grammar of Hungarian, we also draw parallels between typologically di ﬀ erent languages like Finno-Ugric (e.g. Hungarian and Finnish) and Germanic (e.g. English) regarding their inner aspectual marking strategies, and the interaction of inner aspect and case assignment.
Reply on RC1

knows what these abbreviations (SSP126 and SSP585) mean without context or the full spelling Reply: We have supplemented the abbreviations as follows (Lines 18–20): “In this study, we aimed to project future snow changes and their impacts on the hydrology in the upstream region of Salween (USR) under two shared socioeconomic pathway scenarios (SSP126 and SSP585) using a physically-based cryosphere–hydrology model. ” Line 51: I’m unsure what ‘all walks of life’ means in this context. Reply: For this unclear expression, we have revised it as follows (Line 51): “Accordingly, it not only has a strong effect on the regional hydrological cycle, but also provides abundant water resources for the industry, agriculture and residents in basins and supports about one-sixth of the world’s population. ” Line 84: The sentence beginning on this line is long and complex, consider splitting apart for clarity. Reply: We shall do this as follows (Line 84): “Previous studies have assessed several snow variables (e.g., snowfall, snow storage, SC, and snowmelt) and the hydrological processes related to snow under climate change on the TP based on in-situ observations and land surface snow/hydrological models. However, the impact of future snow changes on runoff is still unclear due to a lack of reliable data. ” Line 99-100: Consider ‘study area’ instead of ‘research object. ’ Reply: We have made revisions as follows (Line 95–97): “To better understand the effect of snow changes on the TP on runoff under climate change, in this study, the upstream region of Salween (USR) was selected as the study area. ” Line 101: This is vague, I am not sure what the authors mean by 'complex underlying surface. ' Same with line 105 ‘underlying surface. ’ Reply: The meaning of 'complex underlying surface' mentioned in the text is the same as 'the underlying surface', both refer to the diverse and complex surface environment in the basin. In order to avoid ambiguity, we unified the two expressions, using 'complex underlying surface'. Line 144: Use ‘observational’ instead of ‘observation’
Association of vitamin D deficiency during pregnancy with pre-eclampsia and eclampsia- A Case control study

Background: The etiology of pre-eclampsia (PE) is not yet fully known, although current literature indicates an inflammatory mediators produced by the placenta as a potential causal mechanism. Vitamin D is emerging as a promising agent for pre-eclampsia prevention. This study was done to determine whether vitamin D deficiency is an independent risk factor for pre-eclampsia/eclampsia. Methods: A prospective case-control study was conducted on 60 cases and 60 controls (with same age and sex matched without risk of pre-eclampsia) groups pregnant women admitted to our tertiary care hospital between July 2016 and august 2017. Detailed history and complete physical examination was done in all patients. It was recorded on a pre planned record sheet. All the Investigations carried out at were recorded in this record sheet throughout the duration of the study. Hypertension is diagnosed when 2 B.P. (Blood pressure) readings of 140/90 mm Hg or greater are noted 6 hours apart within a 1-week period. Results: This study showed a very high prevalence of vitamin D deficiency in pregnant women, 90% women with preeclampsia and eclampsia had Vitamin D deficiency (vit D<20ng/ml) as compared to 3.33% in the control group, which was statistically significant (p value < 0.05). Mean serum vit. D concentration was lower in women who subsequently developed preeclampsia and eclampsia (12.65±5.112) compared with controls (51.15±16.357), statistically significant (p<0.05). Mean S.calcium level was lower in pre eclampsia and eclampsia (7.65±0.732) as compared to control (8.87±1.186) which was also statistically significant (p<0.05). Conclusion: Maternal vitamin D deficiency may be an independent risk factor for preeclampsia. Vitamin D and calcium supplementation in early pregnancy should be given for preventing pre-eclampsia /eclampsia and to promote neonatal well-being.