Miracle-dz/UniFAR-FTUs huggingface dataset:
The high mobility group transcription factor Sox8 is a negative regulator of osteoblast differentiation

Bone remodeling is an important physiologic process that is required to maintain a constant bone mass. This is achieved through a balanced activity of bone-resorbing osteoclasts and bone-forming osteoblasts. In this study, we identify the high mobility group transcription factor Sox8 as a physiologic regulator of bone formation. Sox8-deficient mice display a low bone mass phenotype that is caused by a precocious osteoblast differentiation. Accordingly, primary osteoblasts derived from these mice show an accelerated mineralization ex vivo and a premature expression of osteoblast differentiation markers. To confirm the function of Sox8 as a negative regulator of osteoblast differentiation we generated transgenic mice that express Sox8 under the control of an osteoblast-specific Col1a1 promoter fragment. These mice display a severely impaired bone formation that can be explained by a strongly reduced expression of runt-related transcription factor 2, a gene encoding a transcription factor required for osteoblast differentiation. Together, these data demonstrate a novel function of Sox8, whose tightly controlled expression is critical for bone formation.
Association between the circulating leptin levels and the biomarkers of oxidative stress and inflammation among Iranian overweight and obese adults

Background: Oxidative stress in obese people is an important pathogenic mechanism of an obesity-associated metabolic syndrome. We evaluated the association between circulating leptin levels with biomarkers of oxidative stress in overweight and obese participants. Methods: This study was performed on 189 overweight and obese people aged 18-60 years old. Serum leptin, superoxide dismutase (SOD), high-sensitivity C-reactive protein (hs-CRP), homocysteine (Hcy), thiobarbituric acid reactive substances (TBARS) and amyloid A (SAA) concentrations were measured. Pearson correlation and multiple linear regressions were used to assess the relationships. Results: We found that among the biomarkers of oxidative stress and inflammation in participants, serum hs-CRP and SAA were positively correlated with BMI (β=0.003, P<0.001 and β=7.83, P<0.001, respectively). This relationship remained significant even after controlling other oxidative stress and inflammatory indicators (β=0.003, p<0.001 for hs-CRP), but this association disappeared for SAA. In addition, serum hs-CRP was positively correlated with leptin (β=0.001, p=0.003). Regression analysis showed that there was no association between serum Hcy, SAA, TBARS and SOD with serum leptin concentrations Conclusion: Overall, the current study demonstrated that serum hs-CRP and SAA levels were independently correlated with BMI. Furthermore, serum hs-CRP was positively correlated with leptin. Focusing on such strategies may lead to promises for alleviating obesity and its co-morbidities.
An Enhanced Segmentation Technique for Blood Vessel in Retinal Images

of the major symptoms of many blood related diseases like diabetes or cardiovascular disease is the change in blood vessel features. These diseases can be detected by analyzing features of retinal vessels and proper treatment can be provided to patient in early stages of disease. Cost associated in detecting these changes and inconsistency in the detection procedure led to the automation of this process. Among other tasks, retinal blood vessel segmentation is the foremost and very challenging task from which various features are analyzed to detect the disease. In this paper, an effective blood vessel segmentation method from coloured retinal fundus images is presented. Segmentation is done by extracting the green channel from RGB retinal image. Firstly the vessel structure is estimated using morphological operations and then noise is removed using Rician Denoise method. After removing the noise, segmentation of blood vessels is carried out using thresholding method. Segmented image needs to be post-processed before considering it for examining any disease. Proposed segmentation method was evaluated on two publicly available DRIVE and STARE datasets. Segmentation process achieves high level of accuracy than most of the previous techniques. Further, results have demonstrated that the proposed method is applicable for segmenting retinal vessels and taking measurements from it. Advantages of this method are its simplicity, fast segmentation process, high efficiency and scalability to deal with coloured retinal images of high resolution.
14-3-3 transits to the nucleus and participates in dynamic nucleocytoplasmic transport

14-3-3 proteins regulate the cell cycle and prevent apoptosis by controlling the nuclear and cytoplasmic distribution of signaling molecules with which they interact. Although the majority of 14-3-3 molecules are present in the cytoplasm, we show here that in the absence of bound ligands 14-3-3 homes to the nucleus. We demonstrate that phosphorylation of one important 14-3-3 binding molecule, the transcription factor FKHRL1, at the 14-3-3 binding site occurs within the nucleus immediately before FKHRL1 relocalization to the cytoplasm. We show that the leucine-rich region within the COOH-terminal α-helix of 14-3-3, which had been proposed to function as a nuclear export signal (NES), instead functions globally in ligand binding and does not directly mediate nuclear transport. Efficient nuclear export of FKHRL1 requires both intrinsic NES sequences within FKHRL1 and phosphorylation/14-3-3 binding. Finally, we present evidence that phosphorylation/14-3-3 binding may also prevent FKHRL1 nuclear reimport. These results indicate that 14-3-3 can mediate the relocalization of nuclear ligands by several mechanisms that ensure complete sequestration of the bound 14-3-3 complex in the cytoplasm.
"Generation of Induced Pluripotent Stem Cells Using Recombinant Proteins" (2009), by Hongyan Zhou et al

Induced pluripotent stem cells [5] (iPSCs) are studied carefully by scientists not just because they are a potential source of stem cells [5] that circumvents ethical controversy involved with experimentation on human embryos, but also because of their unique potential to advance the field of regenerative medicine [6]. First generated in a lab by Kazutoshi Takahashi [7] and Shinya Yamanaka [8] in 2006, iPSCs have the ability to differentiate into cells of all types. If scientists discover how to induce differentiated cells to return to a pluripotent state using a method that leaves the iPSCs safe for transplantation, then patients could receive stem cell transplants with cells containing their own DNA. This would presumably remove the danger of transplant rejection that comes with foreign cell transplantation.
Translating the Research in Insulin Injection Technique

Purpose Glucose variability leading to suboptimal glycemic control is common among people using injection therapies. Advanced technology and new studies have identified important issues related to injection technique: needle length and gauge, body mass index, skin and subcutaneous tissue thickness, adequate resuspension of cloudy insulins, leakage, choice of injection site and rotation, pinching a skinfold, and lipohypertrophy. All these issues can affect pain and bruising, insulin absorption, and blood glucose levels. The purpose of this article is to review current and past research regarding insulin injection therapy and to provide practical, translational information regarding injection technique, teaching/learning techniques specific to insulin administration, and implications for diabetes self-management education and support. Conclusion International injection recommendations for patients with diabetes have recently been published and have identified specific recommendations for health care professionals. This article provides an evidence-based translational and practical review of the research regarding injection technique and teaching/learning theory. Diabetes educators need to reevaluate how they provide instruction for the administration of insulin and other injectable medications. Research regarding skin and subcutaneous thickness reveals that shorter needles may be appropriate for the majority of patients regardless of body mass index. Periodic reassessment of injection technique, including suspension of cloudy insulins and inspection of injection sites for lipohypertrophy, is a critical aspect of the role of the diabetes educator. An injection checklist is provided as a guide for diabetes educators.
Articulatory Information and Multiview Features for Large Vocabulary Continuous Speech Recognition

This paper explores the use of multi-view features and their discriminative transforms in a convolutional deep neural network (CNN) architecture for a continuous large vocabulary speech recognition task. Mel-filterbank energies and perceptually motivated forced damped oscillator coefficient (DOC) features are used after feature-space maximum-likelihood linear regression (fMLLR) transforms, which are combined and fed as a multi-view feature to a single CNN acoustic model. Use of multi-view feature representation demonstrated significant reduction in word error rates (WERs) compared to the use of individual features by themselves. In addition, when articulatory information was used as an additional input to a fused deep neural network (DNN) and CNN acoustic model, it was found to demonstrate further reduction in WER for the Switchboard subset and the CallHome subset (containing partly non-native accented speech) of the NIST 2000 conversational telephone speech test set, reducing the error rate by 12% relative to the baseline in both cases. This work shows that multi-view features in association with articulatory information can improve speech recognition robustness to spontaneous and non-native speech.
In situ TEM probing properties of individual one-dimensional nanostructures

One-dimensional nanomaterials are a fundamental component of nanoscience and nanotechnology. Property measurements of individual one-dimensional nanostructures, including nanowires and nanotubes, are challenging due to their small size, which constrains the applications of the well-established testing and measurement techniques. We have developed an alternative novel approach that allows the direct measurements of the mechanical and physical properties of individual nanostructures inside high-resolution transmission electron microscopy (TEM), by which microstructures of the nanomaterials can be characterised in situ. Thus the properties of nanostructures can be directly correlated with their well-defined structures by this technique. This paper will review our progress in using in situ TEM method to measure the mechanical and field emission properties of individual nanowires and nanotubes. Mechanical resonance of zinc oxide (ZnO) nanobelt, as a new important class of nanowire, was induced by an alternating electric field. Due to the rectangular cross-section of the nanobelt, two fundamental resonance modes have been observed, corresponding to the two orthogonal transverse vibration directions, showing the versatile applications of nanobelts as nanocantilevers and nanoresonators. The elastic modulus of the ZnO nanobelts was measured to be ∼52 GPa and the damping time constant of the resonance in vacuum of 10-8 Torr was ∼1.2 ms. Field emission properties of individual carbon nanotubes have been systematically studied. The field emission behaviours have been directly linked with in situ nanotube tip morphology and their real work function. The dynamic field emission of a nanotube at mechanical resonance was also studied by in situ TEM method.
Genetic analysis of the role of G protein–coupled receptor signaling in electrotaxis

Cells display chemotaxis and electrotaxis by migrating directionally in gradients of specific chemicals or electrical potential. Chemotaxis in Dictyostelium discoideum is mediated by G protein–coupled receptors. The unique Gβ is essential for all chemotactic responses, although different chemoattractants use different receptors and Gα subunits. Dictyostelium amoebae show striking electrotaxis in an applied direct current electric field. Perhaps electrotaxis and chemotaxis share similar signaling mechanisms? Null mutation of Gβ and cAMP receptor 1 and Gα2 did not abolish electrotaxis, although Gβ-null mutations showed suppressed electrotaxis. By contrast, G protein signaling plays an essential role in chemotaxis. G protein–coupled receptor signaling was monitored with PHcrac–green fluorescent protein, which translocates to inositol phospholipids at the leading edge of cells during chemotaxis. There was no intracellular gradient of this protein during electrotaxis. However, F-actin was polymerized at the leading edge of cells during electrotaxis. We conclude that reception and transduction of the electrotaxis signal are largely independent of G protein–coupled receptor signaling and that the pathways driving chemotaxis and electrotaxis intersect downstream of heterotrimeric G proteins to invoke cytoskeletal elements.
Interspinous Spacer versus Traditional Decompressive Surgery for Lumbar Spinal Stenosis: A Systematic Review and Meta-Analysis

Background Dynamic interspinous spacers, such as X-stop, Coflex, DIAM, and Aperius, are widely used for the treatment of lumbar spinal stenosis. However, controversy remains as to whether dynamic interspinous spacer use is superior to traditional decompressive surgery. Methods Medline, Embase, Cochrane Library, and the Cochrane Controlled Trials Register were searched during August 2013. A track search was performed on February 27, 2014. Study was included in this review if it was: (1) a randomized controlled trial (RCT) or non-randomized prospective comparison study, (2) comparing the clinical outcomes for interspinous spacer use versus traditional decompressive surgery, (3) in a minimum of 30 patients, (4) with a follow-up duration of at least 12 months. Results Two RCTs and three non-randomized prospective studies were included, with 204 patients in the interspinous spacer (IS) group and 217 patients in the traditional decompressive surgery (TDS) group. Pooled analysis showed no significant difference between the IS and TDS groups for low back pain (WMD: 1.2; 95% CI: −10.12, 12.53; P = 0.03; I2 = 66%), leg pain (WMD: 7.12; 95% CI: −3.88, 18.12; P = 0.02; I2 = 70%), ODI (WMD: 6.88; 95% CI: −14.92, 28.68; P = 0.03; I2 = 79%), RDQ (WMD: −1.30, 95% CI: −3.07, 0.47; P = 0.00; I2 = 0%), or complications (RR: 1.39; 95% CI: 0.61, 3.14; P = 0.23; I2 = 28%). The TDS group had a significantly lower incidence of reoperation (RR: 3.34; 95% CI: 1.77, 6.31; P = 0.60; I2 = 0%). Conclusion Although patients may obtain some benefits from interspinous spacers implanted through a minimally invasive technique, interspinous spacer use is associated with a higher incidence of reoperation and higher cost. The indications, risks, and benefits of using an interspinous process device should be carefully considered before surgery.
CloudETL: scalable dimensional ETL for hive

Extract-Transform-Load (ETL) programs process data into data warehouses (DWs). Rapidly growing data volumes demand systems that scale out. Recently, much attention has been given to MapReduce for parallel handling of massive data sets in cloud environments. Hive is the most widely used RDBMS-like system for DWs on MapReduce and provides scalable analytics. It is, however, challenging to do proper dimensional ETL processing with Hive; e.g., the concept of slowly changing dimensions (SCDs) is not supported (and due to lacking support for UPDATEs, SCDs are complex to handle manually). Also the powerful Pig platform for data processing on MapReduce does not support such dimensional ETL processing. To remedy this, we present the ETL framework CloudETL which uses Hadoop to parallelize ETL execution and to process data into Hive. The user defines the ETL process by means of high-level constructs and transformations and does not have to worry about technical MapReduce details. CloudETL supports different dimensional concepts such as star schemas and SCDs. We present how CloudETL works and uses different performance optimizations including a purpose-specific data placement policy to co-locate data. Further, we present a performance study and compare with other cloud-enabled systems. The results show that CloudETL scales very well and outperforms the dimensional ETL capabilities of Hive both with respect to performance and programmer productivity. For example, Hive uses 3.9 times as long to load an SCD in an experiment and needs 112 statements while CloudETL only needs 4.
Assessing neuronal density in peri‐infarct cortex with PET: Effects of cortical topology and partial volume correction

The peri‐infarct cortex (PIC) is the site of long‐term physiologic changes after ischemic stroke. Traditional methods for delineating the peri‐infarct gray matter (GM) have used a volumetric Euclidean distance metric to define its extent around the infarct. This metric has limitations in the case of cortical stroke, i.e., those where ischemia leads to infarction in the cortical GM, because the vascularization of the cerebral cortex follows the complex, folded topology of the cortical surface. Instead, we used a geodesic distance metric along the cortical surface to subdivide the PIC into equidistant rings emanating from the infarct border and compared this new approach to a Euclidean distance metric definition. This was done in 11 patients with [F‐18]‐Flumazenil ([18‐F]‐FMZ) positron emission tomography (PET) scans at 2 weeks post‐stroke and at 6 month follow‐up. FMZ is a PET radiotracer with specific binding to the alpha subunits of the type A γ‐aminobutyric acid (GABAA) receptor. Additionally, we used partial‐volume correction (PVC) of the PET images to compensate for potential cortical thinning and long‐term neuronal loss in follow‐up images. The difference in non‐displaceable binding potential (BPND) between the stroke unaffected and affected hemispheres was 35% larger in the geodesic versus the Euclidean peri‐infarct models in initial PET images and 48% larger in follow‐up PET images. The inter‐hemispheric BPND difference was approximately 17–20% larger after PVC when compared to uncorrected PET images. PET studies of peri‐infarct GM in cortical strokes should use a geodesic model and include PVC as a preprocessing step. Hum Brain Mapp 38:326–338, 2017. © 2016 Wiley Periodicals, Inc.
Different molecular approaches used for detection of Escherichia coli O157:H7 from different sources

Escherichia coli (E. coli) O157:H7 was first recognized in 1982 after investigation of two cases of hemorrhagic colitis and hemolytic uremic syndrome. E. coli O157:H7 the shiga toxin producing strain of E. coli are most commonly involved in many outbreaks of human and animal diseases with low infectious dose. Human infections caused by E. coli O157:H7 are due to consumption of undercooked ground beef, raw milk and raw milk products, water, cold sandwiches, vegetables, raw apple cider and person to person contact. Due to low infectious dose and different mode of transmission it is essential to develop more rapid and sensitive methods for detection of shiga toxin producing E. coli. In this review different molecular based detection methods are discussed. PCR speeds up the analysis time and amplify small number of microbes are described along different variations of PCR following DPCR, omitting the tedious step of DNA extraction. Genomic techniques are reviewed along further epidemiological typing like phage typing and biotyping. Biosensors provide real time detection described along with use of fluorescence and microscopy. Emerging technologies including microarray, molecular beacons and lab-on-a-chip are described along with new improvements in molecular beacons. Merits and demerits of each approach discussed are examined throughout the article.
Dermatan Sulfate-Free Mice Display Embryological Defects and Are Neonatal Lethal Despite Normal Lymphoid and Non-Lymphoid Organogenesis

The epimerization of glucuronic acid into iduronic acid adds structural variability to chondroitin/dermatan sulfate polysaccharides. Iduronic acid-containing domains play essential roles in processes such as coagulation, chemokine and morphogen modulation, collagen maturation, and neurite sprouting. Therefore, we generated and characterized, for the first time, mice deficient in dermatan sulfate epimerase 1 and 2, two enzymes uniquely involved in dermatan sulfate biosynthesis. The resulting mice, termed DKO mice, were completely devoid of iduronic acid, and the resulting chondroitin sulfate chains were structurally different from the wild type chains, from which a different protein binding specificity can be expected. As a consequence, a vast majority of the DKO mice died perinatally, with greatly variable phenotypes at birth or late embryological stages such as umbilical hernia, exencephaly and a kinked tail. However, a minority of embryos were histologically unaffected, with apparently normal lung and bone/cartilage features. Interestingly, the binding of the chemokine CXCL13, an important modulator of lymphoid organogenesis, to mouse DKO embryonic fibroblasts was impaired. Nevertheless, the development of the secondary lymphoid organs, including the lymph nodes and spleen, was normal. Altogether, our results indicate an important role of dermatan sulfate in embryological development and perinatal survival.
An enhanced passivation layer for secure consumer integrated circuit devices

Consumer electronics devices have a common point called integrated circuit (IC). Among the most advanced integrated circuits are the microprocessors which control everything from computers and cellular phones to the USB. In this paper, a novel manufacturing technique to enhance the passivation layer which protects the ICs is presented where a stronger passivation layer is made from Ni-TiO2 composite coating and Tetraethyl orthosilicate compound (TEOS/O2). The Ni-TiO2 will provide a high wear resistance and improve the hardness while the Tetraethyl orthosilicate will protect the microprocessor against ultraviolet attack on the ICs passivation layer.
Fundamentals and Methods for T- and B-Cell Epitope Prediction

Adaptive immunity is mediated by T- and B-cells, which are immune cells capable of developing pathogen-specific memory that confers immunological protection. Memory and effector functions of B- and T-cells are predicated on the recognition through specialized receptors of specific targets (antigens) in pathogens. More specifically, B- and T-cells recognize portions within their cognate antigens known as epitopes. There is great interest in identifying epitopes in antigens for a number of practical reasons, including understanding disease etiology, immune monitoring, developing diagnosis assays, and designing epitope-based vaccines. Epitope identification is costly and time-consuming as it requires experimental screening of large arrays of potential epitope candidates. Fortunately, researchers have developed in silico prediction methods that dramatically reduce the burden associated with epitope mapping by decreasing the list of potential epitope candidates for experimental testing. Here, we analyze aspects of antigen recognition by T- and B-cells that are relevant for epitope prediction. Subsequently, we provide a systematic and inclusive review of the most relevant B- and T-cell epitope prediction methods and tools, paying particular attention to their foundations.