Miracle-dz/UniFAR-FTUs huggingface dataset:
The regulation of tDNA transcription during the directed differentiation of stem cells

The human genome consists of 625 tDNA copies that encode 51 distinct isoacceptor families. Recent studies demonstrated that changes in chromatin structure during cellular differentiation can alter the expression of these tDNA. However, the mechanism by which tDNA can be differentially regulated remains unclear. Here we used the directed differentiation of pluripotent human embryonic stem cells (hESCs) towards the endoderm lineage as a model system to study the developmental regulation of individual tDNA. We demonstrated a significant change in the Pol III occupancy at 49 tDNA (22 reduced and 27 increased). The regulation of tDNA did not correlate with changes in TFIIIB or TFIIIC occupancy, H3K4me3, or H3K27me3 levels. However, tDNA that had an increase in Pol III binding were preferentially found within strong CTCF-COHESIN chromatin loops. The knockdown of either Ctcf or Rad21 in mouse tail tip fibroblasts had similar effects on changes in tRNA levels. We identified 7 isoacceptors that were differentially expressed during the directed differentiation of hESCs. The open reading frames of the ribosomal protein genes, which are translationally repressed during hESC differentiation, are enriched for codons that are decoded by these downregulated isoacceptors. Thus, translation efficiency during cellular differentiation may be affected by changes in tDNA regulation.
Robust finite-frequency ℋ2 analysis

Finite-frequency ℋ2 analysis is relevant to a number of problems in which a priori information is available on the frequency domain of interest. This paper addresses the problem of analyzing robust finite-frequency ℋ2 performance of systems with structured uncertainties. An upper bound on this measure is provided by exploiting convex optimization tools for robustness analysis and the notion of finite-frequency Gramians. An application to a comfort analysis problem for an aircraft aeroelastic model is presented.
Joint optimization of transmit beamforming and processor sleeping for green C-RAN

Cloud radio access network (C-RAN) is perceived as an energy-efficient solution for the next mobile network. The cloud-based baseband unit (BBU) pool is capable of dynamically provisioning computational resources for mobile users to improve hardware utilization such that unused processors can be switched off for power saving in the BBU pool. Besides, cooperative radio among remote radio heads (RRHs) can optimize transmit beamforming to reduce power consumption at RRHs. Thus, to achieve more judicious system power saving, this is need to consider power consumption in the BBU pool and that at RRHs together. In this paper, we aim to minimize system power consumption by jointly exploiting transmit beamforming and processor sleeping. Specifically, we formulate a mixed integer non-linear system power minimization problem, which is hard to solve. For tractability purpose, we transform this problem to an equivalent clustering problem embedded with a series of transmit beamforming problems and processor sleeping problems. On this basis, we first focus on solving the embedded problems with the given clustering and then propose a low-complexity clustering algorithm to search out the optimal clustering with minimum system power consumption. Finally, simulation results show that our proposed algorithms can save system power significantly.
The Proteolytic Landscape of an Arabidopsis Separase-Deficient Mutant Reveals Novel Substrates Associated With Plant Development

Digestive proteolysis executed by the proteasome plays an important role in plant development. Yet, the role of limited proteolysis in this process is still obscured due to the absence of studies. Previously, we showed that limited proteolysis by the caspase-related protease separase (EXTRA SPINDLE POLES [ESP]) modulates development in plants through the cleavage of unknown substrates. Here we used a modified version of the positional proteomics method COmbined FRActional DIagonal Chromatography (COFRADIC) to survey the proteolytic landscape of wild-type and separase mutant RADIALLY SWOLLEN 4 (rsw4) root tip cells, as an attempt to identify targets of separase. We have discovered that proteins involved in the establishment of pH homeostasis and sensing, and lipid signalling in wild-type cells, suggesting novel potential roles for separase. We also observed significant accumulation of the protease PRX34 in rsw4 which negatively impacts growth. Furthermore, we observed an increased acetylation of N-termini of rsw4 proteins which usually comprise degrons identified by the ubiquitin-proteasome system, suggesting that separase intersects with additional proteolytic networks. Our results hint to potential pathways by which separase could regulate development suggesting also novel proteolytic functions.
Necrotizing Fasciitis of the Eyelids

Necrotizing fasciitis is a destructive soft tissue infection that rarely involves the eyelids. Three cases of necrotizing fasciitis of the eyelids are described. Necrotizing fasciitis was preceded by minor forehead soft tissue trauma in two cases and occurred spontaneously in one. In two patients necrotizing fasciitis was bilateral and involved both the upper and lower eyelids. Review of these cases, in addition to 18 cases previously reported in the English literature, reveals a predominance in females, preceding minor local soft tissue trauma, frequent bilateral involvement, and an association with alcohol abuse and diabetes. In all of the patients, group A β-hemolytic streptococci were cultured from the wound. Early recognition of the disease process, prompt surgical debridement of the necrotic tissue, aggressive antimicrobial therapy, and delayed skin grafting combine to minimize morbidity.
Association between caffeine consumption and nonalcoholic fatty liver disease: a systemic review and meta-analysis

Objectives: Caffeine consumption is reported to be associated with reduced hepatic fibrosis in patients with chronic liver diseases. We performed a systematic review and meta-analysis to assess the association between caffeine consumption and prevalence or hepatic fibrosis of nonalcoholic fatty liver disease (NAFLD) in observational studies. Methods: We searched the literature of all languages from PubMed, EMBASE, and the Cochrane library from 1 January 1980 through 10 January 2015. Total caffeine consumption was defined as the daily intake of caffeine (mg/day) from all caffeine-containing products. Combined and subgroup analyses stratified by study designs, study locations, and type of caffeine intake were performed. Results: Four cross-sectional and two case control studies with a total of 20,064 subjects were included in the meta-analysis. Among these, three studies with 18,990 subjects were included in the analysis for prevalence of NAFLD while the other three studies with 1074 subjects were for hepatic fibrosis. Total caffeine consumption (mg/day) was not significantly associated with either the prevalence [pooled mean difference (MD) 2.36; 95% confidence interval (CI) −35.92 to 40.64] or hepatic fibrosis (higher versus lower stages; pooled MD −39.95; 95% CI −132.72 to 52.82) of NAFLD. Subgroup analyses stratified by study designs and locations were also not significant. However, after stratifying by type of caffeine intake, regular coffee caffeine intake (mg/day) was significantly associated with reduced hepatic fibrosis of NAFLD (pooled MD −91.35; 95% CI −139.42 to −43.27; n = 2 studies). Conclusion: Although total caffeine intake is not associated with the prevalence or hepatic fibrosis of NAFLD, regular coffee caffeine consumption may significantly reduce hepatic fibrosis in patients with NAFLD.
Finite Element Modeling of Bone by Using Hydroxyapatite As Bioactive Nanomaterial in Bone Grafting, Bone Healing and the Reduction of Mechanical Failure in the Bone Surgery

Biomaterials engineered at the nano level play a significant role in human health care, in particular bone – related therapy, because of their unique functional properties. In this work we explained bone grafting, bone healing, Preparation of hydoxy apatite (HA) and finite element model for bone grafting and simulation. Finite Element Model (FEM) is useful for surgery and reduces failures. The main aim of this study is to provide a patient specific model where the surgical gestures were considered and to evaluate its relevance as a
Antibacterial Activity and Cytotoxicity of Three Lectins Purified from Drumstick ( Moringa oleifera Lam.) Leaves

Context: Plant materials contain glycoproteins (phytolectins) that are toxic in nature may play a key role in the control of various normal and pathological processes in living organisms and have diverse biochemical and diagnostic applications. Objectives: Screening of three lectins SLL-1, SLL-2 and SLL-3 purified from Drumstick ( Moringa oleifera Lam.) leaves for their antibacterial activities and brine shrimp lethality bioassay. Materials and Methods: Three bioactive lectins were purified from Drumstick leaves by conventional chromatographic methods. The lectins were tested for their antibacterial activities against three pathogenic bacteria- Escherichia coli (gram-negative) Shigella dysenteriae (gram-negative) and Staphylococcus aureus (gram-positive) using the standard disc-diffusion method. Mortality of the brine shrimp naupli was assessed by hality bioassay. Results: All the lectins showed antibacterial activity against E. coli , Sh. dysenteriae and St. aureus . They also showed cytotoxic effect in brine shrimp ( Artemia salina L.) lethality bioassay. The LC 50 values of SLL-1, SLL-2 and SLL-3 were found to be 15.8, 17.78 and 14.12 μg/ml respectively. The experimental results revealed that SLL-3 is more cytotoxic than other lectins. The lectin SLL-3 showed lowest activity whereas SLL-1 showed highest activity against the three bacteria. Conclusion: Results suggest that the extracts from M. oleifera leaf can be a source of natural antimicrobials with potential applications in pharmaceutical industry to control coliform bacteria. Key words: Drumstick; Moringa oleifera ; lectins; antibacterial activity; brine shrimp; bioassay DOI: 10.3329/jbs.v17i0. 7112 J. bio-sci. 17: 89-94, 2009
Association between NAFLD and Risk of Colorectal Adenoma in Chinese Han Population

Abstract Background and Aims: Colorectal cancer is associated with non-alcoholic fatty liver disease (NAFLD) and other metabolic syndromes, such as obesity, abnormal blood glucose, and dyslipidemia. The relationship of NAFLD and colorectal adenoma, which is the precursor of colorectal cancer, is worthy of discussion. The aim of this study was to investigate the association between colorectal adenoma and NAFLD, colorectal adenoma and metabolic syndrome in a Chinese Han population. Methods: This retrospective study analyzed the relationship between NAFLD and colorectal adenoma in 1089 patients in Qingdao municipal hospital. Subjects were divided into a colorectal adenoma group (n = 267) and a control group (n = 822). NAFLD and the controlled attenuation parameter (CAP) value were determined by abdominal ultrasound and FibroScan. Results: Patients with NAFLD in the colorectal adenoma group and the control group represented 142 cases (53.2%) and 360 cases (43.8%), respectively. The mean CAP value in the colorectal adenoma group was significantly higher than that in the control group. The values of body mass index, triglyceride, high-density lipoprotein cholesterol, aspartate aminotransferase, fasting plasma glucose, and uric acid were also significantly higher in the colorectal adenoma group than in the control group. Multifactor logistic regression analysis showed that the sex, NAFLD, CAP, body mass index, triglyceride, aspartate aminotransferase, and fasting plasma glucose were significant risk factors for colorectal adenoma. Besides, NAFLD and CAP value were significant risk factors for colorectal adenoma in males but not in females. Conclusions: NAFLD and metabolic syndrome were tightly associated with the risk of colorectal adenoma in this Chinese Han population. The effect of NAFLD on colorectal adenoma was prominent in males rather than in females.
Cardiovascular MRI for the assessment of heart failure: Focus on clinical management and prognosis

Cardiovascular MR (CMR) has an emerging role in the noninvasive diagnostic assessment of heart failure (HF). Different imaging sequences allow for a detailed assessment of cardiac morphology, function, myocardial perfusion, tissue characterization, and blood flow measurement. This article reviews the key applications of CMR in HF, with special focus on how CMR may influence the diagnostic and therapeutic approach of HF patients. J. Magn. Reson. Imaging 2011;33:275–286. © 2011 Wiley‐Liss, Inc.
Reconstitution of the U1 small nuclear ribonucleoprotein particle

Although the U1 small nuclear ribonucleoprotein particle (snRNP) was the first mRNA-splicing cofactor to be identified, the manner in which it functions in splicing is not precisely understood. Among the information required to understand how U1 snRNP participates in splicing, it will be necessary to know its structure. Here we describe the in vitro reconstitution of a particle that possesses the properties of native U1 snRNP. 32P-labeled U1 RNA was transcribed from an SP6 promoter-human U1 gene clone and incubated in a HeLa S100 fraction. A U1 particle formed which displayed the same sedimentation coefficient (approximately 10S) and buoyant density (1.40 g/cm3) as native U1 snRNP. The latter value reflects the ability to withstand isopycnic banding in Cs2SO4 without prior fixation, a property shared by native U1 snRNP. The reconstituted U1 particle reacted with both the Sm and RNP monoclonal antibodies, showing that these two classes of snRNP proteins were present. Moreover, the reconstituted U1 snRNP particle was found to display the characteristic Mg2+ switch of nuclease sensitivity previously described for native U1 snRNP: an open, nuclease-sensitive conformation at a low Mg2+ concentration (3 mM) and a more compact, nuclease-resistant organization at a higher concentration (15 mM). The majority of the U1 RNA in the reconstituted particle did not contain hypermethylated caps, pseudouridine, or ribose 2-O-methylation, showing that these enigmatic posttranscriptional modifications are not essential for reconstitution of the U1 snRNP particle. The extreme 3' end (18 nucleotides) of U1 RNA was required for reconstitution, but loop II (nucleotides 64 to 77) was not. Interestingly, the 5' end (15 nucleotides) of U1 RNA that recognizes pre-mRNA 5' splice sites was not required for U1 snRNP reconstruction.
Relationship between vitamin D status and response to hepatitis C virus therapy

We thank Drs. Jaeschke and Du for their comments and insight regarding our recent manuscript highlighting a protective role for benzyl alcohol (BA) in a murine model of acetaminophen-induced liver injury. We appreciate their attention to our findings and agree that the time course of protection of BA in this preclinical model suggests a limited utility of BA as a potential late therapeutic subsequent to acetaminophen overdose. However, our interest in acute sterile liver injury, including acetaminophen-induced hepatotoxicity, continues to stimulate our investigations into the understanding of innate immune signaling in liver injury, as well as the role of BA and other therapeutics to influence these immune responses. Moreover, we agree that the protective effects of BA in this preclinical model may be greatly influenced by inhibition of P450 enzymatic activity. However, the findings that the hepatoprotective influence of BA in this model was lost in mice deficient in Tolllike receptor 4 (TLR4), and, more specifically, in mice deficient in TLR4 expression on myeloid cells, suggests a role for modulation of innate immune signaling as a contributive mechanism. With regard to the role of inflammasome signaling and acetaminophen-induced liver injury, our findings of decreased liver injury in mice lacking Nalp3 or caspase-1 expression were consistent with those of other investigators, as pointed out in Drs. Jaeschke and Du’s letter. We agree that the levels of interleukin (IL)-1b were modest and may not contribute substantially to liver injury in acetaminophen toxicity. Additionally, hepatocytes express and activate the inflammasome, but do not produce IL-1b or IL-18 at high levels, thus the complexity of inflammasome signaling may not be solely dependent upon these cytokines. Therefore, further investigation of the role of the inflammasome and other pattern recognition receptors should be further investigated for their role in contributing to the pathophysiology in sterile liver injury, as well as the potential to target these receptors for therapeutic benefit. Again, we appreciate their comments and the opportunity to respond.
Pulpal effects of enamel ablation with a microsecond pulsed λ = 9.3‐µm CO2 laser

In vitro studies have shown that CO2 lasers operating at the highly absorbed 9.3 and 9.6‐µm wavelengths with a pulse duration in the range of 10–20‐microsecond are well suited for the efficient ablation of enamel and dentin with minimal peripheral thermal damage. Even though these CO2 lasers are highly promising, they have yet to receive FDA approval. Clinical studies are necessary to determine if excessive heat deposition in the tooth may have any detrimental pulpal effects, particularly at higher ablative fluencies. The purpose of this study was to evaluate the pulpal safety of laser irradiation of tooth occlusal surfaces under the conditions required for small conservative preparations confined to enamel.
Enhanced segmentation of EOG signals

Extraction of certain events from a signal is a very common problem in the field of medical signal processing. This paper presents a combined method to extract events from electro-oculogram (EOG) signal that are characterized by a band of frequencies. The method uses a combination of mean weighted instantaneous frequency and Pan-Tompkins algorithm. The goal is to improve specifically the identification of the start and end of the detected event. The algorithm is tested and applied on the Electro-oculogram signals and the results are presented.
The dynamics of primate M retinal ganglion cells

The retinal ganglion cells (RGCs) of the primate form at least two classes—M and P—that differ fundamentally in their functional properties. M cells have temporal-frequency response characteristics distinct from P cells (Benardete et al., 1992; Lee et al., 1994). In this paper, we elaborate on the temporal-frequency responses of M cells and focus in detail on the contrast gain control (Shapley & Victor, 1979a,b). Earlier data showed that the temporal-frequency response of M cells is altered by the level of stimulus contrast (Benardete et al., 1992). Higher contrast shifts the peak of the frequency-response curve to higher temporal frequency and produces a phase advance. In this paper, by fitting the data to a linear filter model, the effect of contrast on the temporal-frequency response is subsumed into a change in a single parameter in the model. Furthermore, the model fits are used to predict the response of M cells to steps of contrast, and these predictions demonstrate the dynamic effect of contrast on the M cells' response. We also present new data concerning the spatial organization of the contrast gain control in the primate and show that the signal that controls the contrast gain must come from a broadly distributed network of small subunits in the surround of the M-cell receptive field.
Universal Exoskeleton Arm Design for Rehabilitation

This paper proposes the design of a 4 DOF exoskeleton robotic arm for rehabilitation. This proposed robot arm can be used easily with either the user’s left or right arm. This robot arm is designed to have low inertia, high stiffness link, and zero backlash transmissions. It supports the patient’s arm during rehabilitation which is a repetitive task and takes a period of time. Each joint of this exoskeleton can be rotated from -90 to 90 degrees. From the result of joint trajectory of exoskeleton, this exoskeleton can support the daily movement of human arm and can be utilized for both arms. Furthermore, this proposed robot arm can be applied as a therapeutic and diagnostics device for physiotherapy, assistive device for human power amplifications, a haptic device for virtual reality simulation, and a master-slave device for teleportation.
The health of teenagers: a focused ethnographic study.

This study, a focused community analysis, was conducted to determine the health needs and status of the aggregate of school-aged adolescents (13–18 years) using a method combining an epidemiologic approach with an ethnographic field method. Health was defined broadly, assumed to be interrelated with environmental, economic, social, educational, and cultural variables influencing adolescent life. The research involved five steps: collection of available secondary epidemiologic and census data; interviews with key informants, such as teachers, parents, school nurses, and other adults working with teenagers; participant observation and ethnographic interviews with primary informants, that is, teenagers from a variety of backgrounds; and finally, analysis and reporting of secondary and ethnographic data. Of the many themes generated in the data collection, four are reported here: lifestyle, health, pregnancy, and substance abuse. Findings included a typology of subgroups of the adolescent population that influenced lifestyles and led to different attitudes toward health, pregnancy, and substance abuse. The ethnographic approach facilitated an understanding of the health needs and attitudes of teenagers, implying a need for altered interventions and approaches by adults teaching and caring for them.
A design method of fuzzy weighted median filters

Stack filters are a class of nonlinear filters and include rank order filters, morphological filters, weighted median filters, and so on. The stack filter is defined by a Boolean function. The output of the Boolean function is restricted to two values (i.e., 0 or 1). We attempt to enlarge the class of stack filters by defining the output of the Boolean function from 0 to 1 continuously. We call this filter the fuzzy stack filter. Fuzzy center weighted median filters which are one type of fundamental fuzzy stack filters, have been proposed. We propose fuzzy weighted median (FWM) filters which are more general stack filters, and show the design method of those. The FWM filter is synthesized by two factors, the fuzzy Boolean function and the filter weights. We approximate the fuzzy Boolean function by a sigmoidal function. Furthermore, we approximate the weights of the proposed filter by the S-type function which is used in the field of fuzzy theory. As a result, the FWM filter is defined by only four parameters. The proposed filter can be derived by the LMS algorithm under the mean squared error criterion.
Essential Role of Vascular Endothelial Growth Factor in Angiotensin II–Induced Vascular Inflammation and Remodeling

Angiotensin II (Ang II) upregulates vascular endothelial growth factor (VEGF) and activates vascular inflammation. However, the decisive role of VEGF in Ang II–induced vascular inflammation and remodeling has not been addressed. Ang II infusion to wild-type mice increased local expression of VEGF and its receptors in cells of aortic wall and plasma VEGF, and caused aortic inflammation (monocyte infiltration) and remodeling (wall thickening and fibrosis). Hypoxia-inducible factor-1&agr; colocalized with VEGF-positive cell types. Blockade of VEGF by the soluble VEGF receptor 1 (sFlt-1) gene transfer attenuated the Ang II–induced inflammation and remodeling. The sFlt-1 gene transfer also inhibited the increased expression of VEGF and inflammatory factors such as monocyte chemoattractant protein-1. In contrast, sFlt-1 gene transfer did not affect Ang II–induced arterial hypertension and cardiac hypertrophy. VEGF is an essential mediator in Ang II–induced vascular inflammation and structural changes through its proinflammatory actions.