Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-Genome Shotgun Sequence of Streptococcus agalactiae Sequence Type 176 Strain 3966RFQB from a Dairy Herd in Selangor, Malaysia

Streptococcus agalactiae, commonly known as group B streptococcus (GBS), is among the most implicated pathogens in bovine mastitis worldwide. Proper control measures can curb both economic and public health effects it may cause. ABSTRACT Streptococcus agalactiae, commonly known as group B streptococcus (GBS), is among the most implicated pathogens in bovine mastitis worldwide. Proper control measures can curb both economic and public health effects it may cause. Here, we report the sequenced genome of S. agalactiae sequence type 167 (ST167) strain 3966RFQB obtained from a bovine mastitis case at a dairy herd in Banting, Selangor, Malaysia (longitude 2.8121°N, latitude 101.5026°E).
EBV miR-BART10-3p Promotes Cell Proliferation and Migration by Targeting DKK1

In Epstein-Barr virus (EBV)-infected epithelial cancers, BamHI A rightward transcript (BART) miRNAs are highly expressed. However, only a few target genes of BART miRNAs have been investigated. Our mRNA microarray data showed that DKK1 was markedly down-regulated in EBV-associated gastric carcinoma (EBVaGC) cells. Using luciferase reporter assay we tested whether miR-BART10-3p regulates DKK1 by directly targeting the 3'-UTR of DKK1 mRNA. We observed that miR-BART10-3p transfection decreased DKK1 expression, while an LNA inhibitor of miR-BART10-3p (LNA-miR-BART10-3p(i)) increased DKK1 expression. Furthermore, miR-BART10-3p and siDKK1 promoted cell proliferation and migration. In contrast, transfecting GC cells with LNA-miR-BART10-3p(i) or DKK1 over expression vector suppressed cell proliferation and migration. Our results suggest that miR-BART10-3p may be involved in the tumor progression of EBVaGC by targeting DKK1.
Polydatin Increases Radiosensitivity by Inducing Apoptosis of Stem Cells in Colorectal Cancer

This study aimed to investigate the radiosensitizing effect of polydatin (PD) on colorectal cancer (CRC) and its underlying mechanism. The C57BL/6 mouse model of CRC was induced by treatment with azoxymethane (AOM)/dextran sodium sulfate (DSS) and then divided into four groups: control, PD alone, IR alone, and combination of PD and IR. Radiation therapy (200 cGy/min, 10Gy) was performed in mice in the experimental groups for once a week with a total of four times. Thirty minutes before IR, mice were intraperitoneally injected with PD at the dose of 25mg/kg. The number and volume of CRC xenografts were calculated. Immunohistochemical staining was performed to detect the expression of Ki67 and cleaved caspase-3 in tumor tissues samples. The effects of PD on proliferation and apoptosis were evaluated in CT26 and HCT116 colon tumor cells. Leucine-rich repeat-containing G-protein coupled receptor 5 positive (Lgr5+) cancer stem cells (CSCs) were sorted from CT26 cells and the effects of PD on their proliferation and apoptosis were observed to elucidate the radiosensitizing mechanism of PD in CRC cells. Combined therapy with PD and IR significantly decreased tumor volume, inhibited proliferation and induced apoptosis of tumor cells in the mouse model of CRC compared to other three groups. Compared to the IR group, in vitro assay showed that PD combined with IR inhibited proliferation and promoted apoptosis of CT26 and HCT116 colon tumor cells as well as Lgr5+ CSCs. However, addition of the bone morphogenetic protein (BMP) type I receptor inhibitor K02288 (6.4nM) dramatically increased proliferation of Lgr5+ CSCs and abolished the cytotoxic effect of PD combined with IR on Lgr5+ CSCs. The in vivo and in vitro experiments demonstrated that IR combined treatment with PD could inhibit proliferation and promote apoptosis of CRC cells and Lgr5+ CSCs, and BMP signaling pathway was involved in the radiosensitizing effect of PD.
Neuroimaging findings in obsessive–compulsive disorder: A narrative review to elucidate neurobiological underpinnings

Obsessive compulsive disorder (OCD) is a common psychiatric illness and significant research has been ongoing to understand its neurobiological basis. Neuroimaging studies right from the 1980s have revealed significant differences between OCD patients and healthy controls. Initial imaging findings showing hyperactivity in the prefrontal cortex (mainly orbitofrontal cortex), anterior cingulate cortex and caudate nucleus led to the postulation of the cortico-striato-thalamo-cortical (CSTC) model for the neurobiology of OCD. However, in the last two decades emerging evidence suggests the involvement of widespread associative networks, including regions of the parietal cortex, limbic areas (including amygdala) and cerebellum. This narrative review discusses findings from structural [Magnetic Resonance Imaging (MRI), Diffusion Tensor Imaging(DTI)], functional [(functional MRI (fMRI), Single photon emission computed tomography (SPECT), Positron emission tomography (PET), functional near-infrared spectroscopy (fNIRS)], combined structural and functional imaging studies and meta-analyses. Subsequently, we collate these findings to describe the neurobiology of OCD including CSTC circuit, limbic system, parietal cortex, cerebellum, default mode network and salience network. In future, neuroimaging may emerge as a valuable tool for personalised medicine in OCD treatment.
Communication lower bounds using directional derivatives

We study the set disjointness problem in the most powerful bounded-error model: the number-on-the-forehead model with k parties and arbitrary classical or quantum communication. We obtain a communication lower bound of Omega(√(n)/2k*k) bits, which is essentially optimal. Proving it was a longstanding open problem even in restricted settings, such as one-way classical protocols with k=4 parties (Wigderson 1997). The proof contributes a novel technique for lower bounds on multiparty communication, based on directional derivatives of communication protocols over the reals.
การใช้เซลล์ต้นก าเนิดชนิดเมสเซลไคมอลจากไขกระดูกในการรักษาโรคเข่าเสื่อม ตุลยพฤกษ์ ถาวรสวัสดิ์รักษ,์ พบ , ไตร พรหมแสง , พบ , ปวณี ตั้งจิตต์พิสุทธิ์ , พบ , พงศ์ศักดิ์ ยกุตะนันทน์ , พบ ปัจจุบันผู้ป่วยโรคข้อเข่าเสื่อมมีจ านวนสูงขึ้น เนื่องจากจ านวนประชากรผู้สูงอายุที่มากขึ้นในประเทศ การรักษา โดยการใช้เซล

Forty percent of people over 70 years of age suffer from knee osteoarthritis. Stem cell based therapy is one of a number of promising strategies for osteoarthritis treatment. Mesenchymal stromal /stem cells (MSCs) derived from the bone marrow are the most commonly described source of MSCs and have been widely used to promote tissue regeneration in orthopaedic conditions, particularly in osteoarthritis. A fundamental knowledge of stem cells is very important prior to translating this technology into clinical practice. Although the mechanism of MSC therapy is still uncertain, several studies have reported on the safety and outcome of using bone marrow-derived MSCs for treating osteoarthritis. However, we still cannot conclude that MSCs can regenerate long lasting cartilage tissue. The long term clinical studies need to be evaluated in the future.
The effect of saltfree - salt diet on the reproductive performance of Ile de France ewes

The aim of the present study was to establish the effect of salt-free - salt diet (SFSD) on the size of antral follicles during salt consumption, the duration of controlled breeding campaign and the fertilities of ewes from the Ile de France breed. Тhe experiment was carried out with 57 ewes, which were divided into 3 groups (19 ewes in each) depending on whether they were subjected to SFSD and their contacts with rams during the first 8 days of the beginning of breeding: Group I – SFSD + ram contact; Group II – only SFSD; Group III – no SFSD, only ram contacts. The first day of the salt diet coincided with the first day of ram contacts. Transrectal ultrasound examinations of the ovaries were done on days 1, 2, 3, 5, 6 and 7. The time of manifestation of estrus (in days), pregnancy rate and fecundity were studied. A significant effect of time (P<0.05) and diet (P<0.01) on the size of follicles was established. The onset of the first estrus, the shortest terms of breeding campaign, the fertility and the fecundity results gave us reason to favour the scheme applied to Group II. A stimulatory effect of the diet in that study was demonstrated, but the pattern was different from our previous studies.
Causes of Re-admission in Medical ward within 30 days of discharge among hospitalized Saudi and Non-Saudi patients

Hospital readmissions within 30 days of initial discharge occur frequently. In studies of elderly patients receiving Medicare, readmissions have been associated with poor-quality inpatient care, ineffective hospital-tohome transitions, patient characteristics, disease burden, and socioeconomic status. Among adult family medicine patients spanning a wide age range, we hypothesize that previous hospitalizations, length of stay, number of discharge medications, medical comorbidities, and patient demographics are associated with a greater risk of hospital readmission within 30 days. A retrospective case-control study of 253 family medicine inpatients was conducted to determine the factors associated with 30-day re-admission. Odds ratio and one sample T-test were computed to determine the risk factors for unscheduled re-admittance. The results indicated that Patients who were admitted again in 30 days had additional related morbidities (2.1 vs 1.2; P < .0001), and the characteristic associated morbidities of congestive heart failure, coronary artery disease, chronic obstructive pulmonary ailment, presence of a psychiatric disorder and recent cancer were all additionally widespread amongst cases. Also the study results indicated that unscheduled re-admittance is related to patient’s features. Patients with heart disease, cancer, pneumonia, septicaemia and liver diseases were more prone to admitted again. The proportion of re-admittance was associated with extended stay in the hospital, increased morbidity rate and hospital expenses. [Maimoona Mushtaq Ahmed and Sami M Bahlas. Causes of Re-admission in Medical ward within 30 days of discharge among hospitalized Saudi and Non-Saudi patients. Life Sci J 2014;11(6):98-104]. (ISSN:1097-8135). http://www.lifesciencesite. com. 14
High-dimensional similarity retrieval using dimensional choice

There are several pieces of information that can be utilized in order to improve the efficiency of similarity searches on high-dimensional data. The most commonly used information is the distribution of the data itself but the use of dimensional choice based on the information in the query as well as the parameters of the distribution can provide an effective improvement in the query processing speed and storage. The use of this method can produce dimension reduction by as much as a factor of n, the number of data points in the database, over sequential search. We demonstrate that the curse of dimensionality is not based on the dimension of the data itself but primarily upon the effective dimension of the distance function. We also introduce a new distance function that utilizes fewer dimensions of the higher dimensional space to produce a maximal lower bound distance in order to approximate the full distance function. This work has demonstrated significant dimension reduction, up to 70% reduction with an improvement in accuracy or over 99% with only a 6% loss in accuracy on a prostate cancer data set.
The Role of IL-10 in Malaria: A Double Edged Sword

IL-10 produced by CD4+ T cells suppresses inflammation by inhibiting T cell functions and the upstream activities of antigen presenting cells (APCs). IL-10 was first identified in Th2 cells, but has since been described in IFNγ-producing Tbet+ Th1, FoxP3+ CD4+ regulatory T (Treg) and IL-17-producing CD4+ T (Th17) cells, as well as many innate and innate-like immune cell populations. IL-10 production by Th1 cells has emerged as an important mechanism to dampen inflammation in the face of intractable infection, including in African children with malaria. However, although these type I regulatory T (Tr1) cells protect tissue from inflammation, they may also promote disease by suppressing Th1 cell-mediated immunity, thereby allowing infection to persist. IL-10 produced by other immune cells during malaria can also influence disease outcome, but the full impact of this IL-10 production is still unclear. Together, the actions of this potent anti-inflammatory cytokine along with other immunoregulatory mechanisms that emerge following Plasmodium infection represent a potential hurdle for the development of immunity against malaria, whether naturally acquired or vaccine-induced. Recent advances in understanding how IL-10 production is initiated and regulated have revealed new opportunities for manipulating IL-10 for therapeutic advantage. In this review, we will summarize our current knowledge about IL-10 production during malaria and discuss its impact on disease outcome. We will highlight recent advances in our understanding about how IL-10 production by specific immune cell subsets is regulated and consider how this knowledge may be used in drug delivery and vaccination strategies to help eliminate malaria.
Cell Type-Specific Transcriptomics of Lateral Root Formation and Plasticity

Lateral roots are a major determinant of root architecture and are instrumental for the efficient uptake of water and nutrients. Lateral roots consist of multiple cell types each expressing a unique transcriptome at a given developmental stage. Therefore, transcriptome analyses of complete lateral roots provide only average gene expression levels integrated over all cell types. Such analyses have the risk to mask genes, pathways and networks specifically expressed in a particular cell type during lateral root formation. Cell type-specific transcriptomics paves the way for a holistic understanding of the programming and re-programming of cells such as pericycle cells, involved in lateral root initiation. Recent discoveries have advanced the molecular understanding of the intrinsic genetic control of lateral root initiation and elongation. Moreover, the impact of nitrate availability on the transcriptional regulation of lateral root formation in Arabidopsis and cereals has been studied. In this review, we will focus on the systemic dissection of lateral root formation and its interaction with environmental nitrate through cell type-specific transcriptome analyses. These novel discoveries provide a better mechanistic understanding of postembryonic lateral root development in plants.
Increased Regulatory T-Cell Activity and Enhanced T-Cell Homeostatic Signaling in Slow Progressing HIV-infected Children

Pediatric slow progressors (PSP) are rare ART-naïve, HIV-infected children who maintain high CD4 T-cell counts and low immune activation despite persistently high viral loads. Using a well-defined cohort of PSP, we investigated the role of regulatory T-cells (TREG) and of IL-7 homeostatic signaling in maintaining normal-for-age CD4 counts in these individuals. Compared to children with progressive disease, PSP had greater absolute numbers of TREG, skewed toward functionally suppressive phenotypes. As with immune activation, overall T-cell proliferation was lower in PSP, but was uniquely higher in central memory TREG (CM TREG), indicating active engagement of this subset. Furthermore, PSP secreted higher levels of the immunosuppressive cytokine IL-10 than children who progressed. The frequency of suppressive TREG, CM TREG proliferation, and IL-10 production were all lower in PSP who go on to progress at a later time-point, supporting the importance of an active TREG response in preventing disease progression. In addition, we find that IL-7 homeostatic signaling is enhanced in PSP, both through preserved surface IL-7receptor (CD127) expression on central memory T-cells and increased plasma levels of soluble IL-7receptor, which enhances the bioactivity of IL-7. Combined analysis, using a LASSO modeling approach, indicates that both TREG activity and homeostatic T-cell signaling make independent contributions to the preservation of CD4 T-cells in HIV-infected children. Together, these data demonstrate that maintenance of normal-for-age CD4 counts in PSP is an active process, which requires both suppression of immune activation through functional TREG, and enhanced T-cell homeostatic signaling.
LSEC Fenestrae Are Preserved Despite Pro-inflammatory Phenotype of Liver Sinusoidal Endothelial Cells in Mice on High Fat Diet

Healthy liver sinusoidal endothelial cells (LSECs) maintain liver homeostasis, while LSEC dysfunction was suggested to coincide with defenestration. Here, we have revisited the relationship between LSEC pro-inflammatory response, defenestration, and impairment of LSEC bioenergetics in non-alcoholic fatty liver disease (NAFLD) in mice. We characterized inflammatory response, morphology as well as bioenergetics of LSECs in early and late phases of high fat diet (HFD)-induced NAFLD. LSEC phenotype was evaluated at early (2–8 week) and late (15–20 week) stages of NAFLD progression induced by HFD in male C57Bl/6 mice. NAFLD progression was monitored by insulin resistance, liver steatosis and obesity. LSEC phenotype was determined in isolated, primary LSECs by immunocytochemistry, mRNA gene expression (qRT-PCR), secreted prostanoids (LC/MS/MS) and bioenergetics (Seahorse FX Analyzer). LSEC morphology was examined using SEM and AFM techniques. Early phase of NAFLD, characterized by significant liver steatosis and prominent insulin resistance, was related with LSEC pro-inflammatory phenotype as evidenced by elevated ICAM-1, E-selectin and PECAM-1 expression. Transiently impaired mitochondrial phosphorylation in LSECs was compensated by increased glycolysis. Late stage of NAFLD was featured by prominent activation of pro-inflammatory LSEC phenotype (ICAM-1, E-selectin, PECAM-1 expression, increased COX-2, IL-6, and NOX-2 mRNA expression), activation of pro-inflammatory prostaglandins release (PGE2 and PGF2α) and preserved LSEC bioenergetics. Neither in the early nor in the late phase of NAFLD, were LSEC fenestrae compromised. In the early and late phases of NAFLD, despite metabolic and pro-inflammatory burden linked to HFD, LSEC fenestrae and bioenergetics are functionally preserved. These results suggest prominent adaptive capacity of LSECs that might mitigate NAFLD progression.
Gut Microbiota and Chronic Constipation: A Review and Update

Background: Chronic constipation, including functional constipation and constipation-type irritable bowel syndrome, is a prevalent, multifactorial gastrointestinal disorder, and its etiology and pathophysiology remain poorly understood. Recently studies using 16S rRNA-based microbiota profiling have demonstrated dysbiosis of gut microbiota in chronic constipation. Aims: To provide an overview of recent studies for microbiota in chronic constipation and treatments for chronic constipation using probiotics, prebiotics, synbiotics, antibiotics and fecal microbiota transplantation (FMT). Methods: PubMed searches were performed up to 1 August 2018 using keywords: “IBS,” “IBS-C,” “irritable bowel syndrome,” “irritable bowel syndrome with constipation,” “functional constipation,” “chronic constipation” in combination with “gut microbiota,” “dysbiosis,” “gut microflora” for microbiota in chronic constipation, and in combination with “probiotics,” “prebiotics,” “synbiotics,” “antibiotics,” and “fecal microbiota transplantation. ” Results: The findings of gut microbiota in functional constipation are inconsistent, and currently no consensus exists. Although no clear consensus exists, compared with healthy subjects, IBS-C patients have a lower level of Actinobacteria, including Bifidobacteria, in their fecal samples and a higher level of Bacteroidetes in their mucosa. In most randomized controlled and parallel-group trials, probiotics, prebiotics, synbiotics, antibiotics, and FMT therapy for chronic constipation were effective with few side effects. However, there are many studies in a small number and the types of probiotics are different, it is difficult to evaluate the effect. Conclusions: Evidence indicates that dysbiosis of gut microbiota may contribute to functional constipation and constipation-type irritable bowel syndrome. Targeting treatments for the dysbiosis of constipation by probiotics, prebiotics, synbiotics, antibiotics, and FMT may be a new option, especially for refractory constipation to conventional therapies.
KLF4-Induced Connexin40 Expression Contributes to Arterial Endothelial Quiescence

Shear stress, a blood flow-induced frictional force, is essential in the control of endothelial cell (EC) homeostasis. High laminar shear stress (HLSS), as observed in straight parts of arteries, assures a quiescent non-activated endothelium through the induction of Krüppel-like transcription factors (KLFs). Connexin40 (Cx40)-mediated gap junctional communication is known to contribute to a healthy endothelium by propagating anti-inflammatory signals between ECs, however, the molecular basis of the transcriptional regulation of Cx40 as well as its downstream effectors remain poorly understood. Here, we show that flow-induced KLF4 regulated Cx40 expression in a mouse EC line. Chromatin immunoprecipitation in ECs revealed that KLF4 bound to three predicted KLF consensus binding sites in the Cx40 promoter. HLSS-dependent induction of Cx40 expression was confirmed in primary human ECs. The downstream effects of Cx40 modulation in ECs exposed to HLSS were elucidated by an unbiased transcriptomics approach. Cell cycle progression was identified as an important downstream target of Cx40 under HLSS. In agreement, an increase in the proportion of proliferating cell nuclear antigen (PCNA)-positive ECs and a decrease in the proportion of ECs in the G0/G1 phase were observed under HLSS after Cx40 silencing. Transfection of communication-incompetent HeLa cells with Cx40 demonstrated that the regulation of proliferation by Cx40 was not limited to ECs. Using a zebrafish model, we finally showed faster intersegmental vessel growth and branching into the dorsal longitudinal anastomotic vessel in embryos knock-out for the Cx40 orthologs Cx41.8 and Cx45.6. Most significant effects were observed in embryos with a mutant Cx41.8 encoding for a channel with reduced gap junctional function. Faster intersegmental vessel growth in Cx41.8 mutant embryos was associated with increased EC proliferation as assessed by PH3 immunostaining. Our data shows a novel evolutionary-conserved role of flow-driven KLF4-dependent Cx40 expression in endothelial quiescence that may be relevant for the control of atherosclerosis and diseases involving sprouting angiogenesis.