Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Architecture of Full-length TRF1 Favors Its Interaction with DNA*

Telomeres are specific DNA-protein structures found at both ends of eukaryotic chromosomes that protect the genome from degradation and from being recognized as double-stranded breaks. In vertebrates, telomeres are composed of tandem repeats of the TTAGGG sequence that are bound by a six-subunit complex called shelterin. Molecular mechanisms of telomere functions remain unknown in large part due to lack of structural data on shelterins, shelterin complex, and its interaction with the telomeric DNA repeats. TRF1 is one of the best studied shelterin components; however, the molecular architecture of the full-length protein remains unknown. We have used single-particle electron microscopy to elucidate the structure of TRF1 and its interaction with telomeric DNA sequence. Our results demonstrate that full-length TRF1 presents a molecular architecture that assists its interaction with telometic DNA and at the same time makes TRFH domains accessible to other TRF1 binding partners. Furthermore, our studies suggest hypothetical models on how other proteins as TIN2 and tankyrase contribute to regulate TRF1 function.
Condom Use to Prevent Incident STDs: The Validity of Self‐Reported Condom Use

Background Studies of sexual behavior and of interventions designed to reduce human immunodeficiency virus risk usually depend on self-report. Validation of self-reported condom use measures has not been previously reported in an urban population at high risk for sexually transmitted diseases and human immunodeficiency virus. Methods A prospective cohort study was performed in subjects recruited from sexually transmitted disease clinics in Baltimore. At enrollment, a questionnaire was administered that assessed human immunodeficiency virus risk factors and sexually transmitted disease history, and used a retrospective calendar to assess sexual events and condom use over the previous 30 days. Clinical evaluation was performed for sexually transmitted diseases. At follow-up 3 months later, the same procedures were repeated. Incident sexually transmitted diseases at follow-up were defined as new culture or serologically documented diagnoses of gonorrhea, chlamydia, syphilis, or trichomoniasis. Results In the 323 male and 275 female (total = 598) subjects who completed a follow-up visit, 21% reported using condoms for every act of sexual intercourse over the previous 30 days, 21% reported occasionally using condoms, and 59% reported not using condoms. At follow-up, 21% of subjects had new incident gonorrhea, chlamydia, syphilis, or trichomoniasis. Fifteen percent of the men who were “always” condom users had incident sexually transmitted diseases compared with 15.3% of “never users;” 23.5% of women who were “always” users had incident sexually transmitted diseases compared with 26.8% of “never” users. Conclusions In this high-risk population, self-reported condom use is not associated with lower sexually transmitted disease incidence. This finding suggests that self-reported condom use measures, even in a research setting, may be subject to substantial reporting bias.
Understanding Innovation Deployment and Evaluation in Healthcare: The Triality Framework

This chapter encompasses two objectives. The first objective is to understand different conceptualisation of technology, context and the user according to various theoretical perspectives within information systems (IS) literature and in the field of healthcare/medical informatics; and in addition, outline perspectives that have expounded the nature of relationship between these three entities. The need to explore such notions stems from authors’ interest to elicit how these theoretical perspectives and concepts have been applied in the field of healthcare to understand technological innovation deployment and evaluation processes by taking the tacit, ephemeral, and complicated nature of healthcare work practices into account.
Position-Dependent Threshold-Voltage Variation by Random Telegraph Noise in  nand Flash Memory Strings

The position dependence of threshold-voltage change (ΔV<sub>th</sub>) in floating-gate NAND Flash cell strings due to random telegraph noise was characterized. It was found that the cumulative distribution of ΔV<sub>th</sub>'s measured from 100 cell devices at word line 31 (WL31) is broader than that at WL0 due to smaller transconductance (G<sub>m</sub>). As the position of a read cell in the string is changed from WL0 to WL31, maximum G<sub>m</sub> decreases by ~50% since the equivalent source resistance (R<sub>s</sub>) of the read cell increases. Decreasing G<sub>m</sub> makes the slope of the I<sub>read</sub> - V<sub>read</sub> curve low, which increases ΔV<sub>th</sub> at the same noise current fluctuation. It was also shown that the G<sub>m</sub> (finally, ΔV<sub>th</sub>) of a read cell can be changed by controlling the pass bias since the pass bias changes the channel resistance (≈ R<sub>s</sub>) of the pass cells.
The value of infrared thermography for research on mammals: previous applications and future directions

Infrared thermography (IRT) involves the precise measurement of infrared radiation which allows surface temperature to be determined according to simple physical laws. This review describes previous applications of IRT in studies of thermal physiology, veterinary diagnosis of disease or injury and population surveys on domestic and wild mammals. 2. IRT is a useful technique because it is non-invasive and measurements can be made at distances of 1000 m to count large mammals. Detailed measurements of surface temperature variation can be made where large numbers of temperature sensors would otherwise be required and where conventional solid sensors can give false readings on mammal coats. Studies need to take into account sources of error due to variation in emissivity, evaporative cooling and radiative heating of the coat. 3. Recent advances in thermal imaging technology have produced lightweight, portable systems that store digital images with high temperature and spatial resolution. For these reasons,therearemanyfurtheropportunitiesforIRTinstudiesofcaptiveandwildmammals.
Neurobiology and Effectiveness of Antipsychotic Drugs in Resistant Obsessive-Compulsive Disorder: A Systematic Review

A systematic review of the literature was conducted using PRISMA criteria. The paradigm search was “obsessive compulsive disorder and antipsychotic agents”. Medline, Cochrane and Web of science databases were explored without date or language restriction. Case reports, open label studies and randomized double-blind controlled trials were included in the qualitative review. Unlike the classical serotonergic hypothesis, OCD may result from striatal dopaminergic hyperactivity, modulated in some patients by an underlying serotonergic hypo activity. In the treatment of resistant OCD, most studies report the effectiveness of first-generation antipsychotic (haloperidol, amisulpride) and some second-generation antipsychotics (risperidone, olanzapine, aripiprazole, quetiapine) in combination with an SSRI. Moreover, in case reports, recrudescence or onset of OCD symptoms in patients with schizophrenia have been described in a switch from first generation antipsychotic medication to olanzapine, risperidone, aripiprazole or clozapine, but not within a switch to amisulpride or quetiapine.
Media and Stress in Adolescent Boys in Germany

The study is on the effects of entertainment media on physiological and psychological indicators of stress. The concept of stress is considered to play a key role in the explanation of the effects of media use on aggression, academic performance, and health. Two types of media (television and video games) and violent versus nonviolent content were compared. Differential effects on physiological measures (heart rate [HR], heart rate variability [HRV], cortisol, salivary alpha-amylase [sAA]) and subjective experience were expected. Study participants consisted of 98 boys, aged 11 to 14. Physiological stress reactions were higher for video games than for television with regards to HR and HRV. Violent content had greater effects on physiological stress than nonviolent content, when measured in terms of sAA, cortisol, and HRV. Violent content, in general, was rated as being more stressful but also more enjoyable. The results underline that certain types of media use are associated with subjective and physiological indices of stress.
A taxonomy for grid applications

The concept of Grid Computing addresses the next evolutionary step of distributed computing. Offering storage and computation capabilities to users not having those resources is the ultimate goal of grid computing. In this paper we introduce a taxonomy for grid applications, aiming at a better understanding of the categories of applications that could benefit from gridification. The proposed taxonomy captures in a simple and straightforward way the concepts of control parallelism and data parallelism.
Blood Chemistry of Normal Full-term Infants in the First 48 Hours of Life

nations Cord 7-79 5-6-12-0 ±2-0 14 1 6-78 5-3-7-8 ± 0-71 13 2 6-65 5-2-8-4 ±0-83 13 3 7-0 5-7-9-7 ±0-94 13 5 6-84 5-1-7-5 ±0-73 11 7 6-4 5-3-7-3 ±0-64 12 9 6-71 5-3-8-0 +0-79 13 11 6-6 5-3-7-9 ±0-79 13 18 6-33 5-3-8-9 ±0-78 13 24 6-19 5-3-7-7 0-73 14 36 6-03 5-2-7-3 ±0-63 14 48 5-92 5-0-7-7 +0-8 14
Early exposure of dams to a westernized diet has long-term consequences on food intake and physiometabolic homeostasis of the rat offspring

Abstract This study evaluated the long-term effects of a westernized diet during pregnancy and lactation. Female Wistar rats (n = 12) were divided into two groups according to their food intake, namely, control (C) or westernized (W) diet, throughout pregnancy/lactation. On the 21st day, the male pups were weaned on a standard diet as follows: Control diet (CC) (n = 8) and westernized diet in perinatal life followed by control diet post weaning (WC) (n = 8). The levels of fasting (12 h) serum glucose, triglycerides (TG), and total cholesterol and fraction in the pups were determined. During weaning, the WC group showed 14% greater body weight (p < 0.001). In the adulthood, the offspring from dams fed on westernized diet showed hyperphagia, hyperinsulinism, hypertriglyceridemia, higher fat visceral weight, higher very-low-density-lipoprotein cholesterol level, decreased high-density-lipoprotein cholesterol level, and altered glucose tolerance test. In conclusion, maternal western-style diet in early life altered long-term food intake, visceral fat pad, insulin, glucose and lipid serum, and increased risk of metabolic disorders.
Msx2 and Twist cooperatively control the development of the neural crest-derived skeletogenic mesenchyme of the murine skull vault

The flat bones of the vertebrate skull vault develop from two migratory mesenchymal cell populations, the cranial neural crest and paraxial mesoderm. At the onset of skull vault development, these mesenchymal cells emigrate from their sites of origin to positions between the ectoderm and the developing cerebral hemispheres. There they combine, proliferate and differentiate along an osteogenic pathway. Anomalies in skull vault development are relatively common in humans. One such anomaly is familial calvarial foramina, persistent unossified areas within the skull vault. Mutations in MSX2 and TWIST are known to cause calvarial foramina in humans. Little is known of the cellular and developmental processes underlying this defect. Neither is it known whether MSX2 and TWIST function in the same or distinct pathways. We trace the origin of the calvarial foramen defect in Msx2 mutant mice to a group of skeletogenic mesenchyme cells that compose the frontal bone rudiment. We show that this cell population is reduced not because of apoptosis or deficient migration of neural crest-derived precursor cells, but because of defects in its differentiation and proliferation. We demonstrate, in addition, that heterozygous loss of Twist function causes a foramen in the skull vault similar to that caused by loss of Msx2 function. Both the quantity and proliferation of the frontal bone skeletogenic mesenchyme are reduced in Msx2-Twist double mutants compared with individual mutants. Thus Msx2 and Twist cooperate in the control of the differentiation and proliferation of skeletogenic mesenchyme. Molecular epistasis analysis suggests that Msx2 and Twist do not act in tandem to control osteoblast differentiation, but function at the same epistatic level.
Intracellular Enhanced Cyan Fluorescent Protein/Angiotensin II Does Not Modify Angiotensinogen Accumulation in Transgenic Mice.

BACKGROUND Several studies suggest that extracellular angiotensin can upregulate renin and angiotensinogen (AGT). We have shown that enhanced cyan fluorescent protein/angiotensin II (ECFP/AngII) transgenic mice, in which AngII is fused downstream of ECFP and regulated by the mouse metallothionein housekeeping gene, possess elevated blood pressure and kidney thrombotic microangiopathy. The present study evaluated the effect of intracellular AngII on AGT messenger RNA (mRNA) and protein levels in ECFP/AngII transgenic mice. METHODS The traditional guanidinium thiocyanate method was used to extract total mRNA. Proteins were extracted by homogenization in a tissue extraction reagent buffer. Northern blots for AGT mRNA and an 18S ribosomal RNA control were performed. Immunoblots for AGT protein levels with actin and tubulin controls were evaluated. RESULTS Northern blot densitometry showed liver mRNA levels an average of 12-fold greater than levels in the brain or kidney in both Lines A and D (different copies of the transgene) with no quantifiable differences between wild-type (WT) and homozygous (HO) transgenic mice. Immunoblots showed liver AGT protein levels 3.2-fold greater than levels in the brain or kidney, with no differences observed between WT and HO transgenic mice. CONCLUSION ECFP/AngII transgene expression does not alter AGT mRNA or protein levels in major organs (kidney, liver, and brain) of transgenic mice. The altered blood pressure and kidney thrombosis observed in these transgenic mouse lines are not the result of increased intracellular AGT synthesis and resultant increases in free extracellular AngII. This finding is consistent with our published studies that indicate no increase in circulating AngII by radioimmunoassay.
Pre-Clinical Pharmacological Profile of the Novel Glycoconjugate Org 36764 with both Factor Xa and Thrombin (IIa) Inhibitory Activities

Summary Org 36764, is an antithrombin III (AT) and thrombin binding carbohydrate, which accelerates the inactivation of both factor Xa and thrombin by AT. It displays in buffer an anti-Xa and anti-thrombin activity of 415 and 2 U/mg, respectively, compared to 172 and 114 U/mg, respectively, for unfractionated heparin (UFH). Org 36764 does not cross-react with HIT (heparin induced thrombocytopenia) antibodies and is not neutralised by PF4. In experimental models in rats, on a molar basis, Org 36764 was more active than the pentasaccharide SanOrg 34006 (= AT binding domain of Org 36764) in arterial thrombosis, but both were equally active in venous thrombosis. In arterial thrombosis following endothelial damage by ferric chloride, Org 36764 was more active than the LMW heparin enoxaparin and SanOrg 34006 and similar active to UFH. At AT saturating doses the bleeding enhancement was not more than 3.5 times the control value. Org 36764 was more active in suppressing in vivo thrombus formation on stents than UFH, SanOrg 34006 or a combination of ticlopidine and aspirin. The results indicate that the novel drug Org 36764 is a drug with antithrombotic potential against venous and arterial thrombosis.
Analyzing public transportation mobility data for networking purposes

Utilizing vehicles for networking purposes has always been a challenge. This is mainly due to the minimum density of connected-vehicles required. The locations of these vehicles should be shareable and reasonably predictable for efficient position-based routing protocols to be implemented. Their Vehicle-to-Vehicle (V2V) communication cooperation should be well-incentivized for efficient networking to be realized. Regular vehicles struggle to have all of these properties. Public transportation vehicles, on the other hand, are well-positioned in this regard; their number is proportional to the number of city residents while being uniformly distributed throughout the day, their locations have no privacy concerns while being highly predictable and their V2V communication cooperation is easily enforceable by the single administration authority they usually have. With efficient networking, public transportation vehicles can become the reliable communication backbone for other vehicle categories. In order to investigate their networking potential, we present for the firs time, in this paper, a data analysis study of realistic public transportation mobility datasets representing the Grand River Transit bus service offered throughout the Region of Waterloo, Ontario, Canada. We show both the data preprocessing and processing phases. The processing phase is mainly based on discovering bus groups using hierarchical clustering. This is done while varying the minimum degree of intra-cluster connectivity and the maximum intra-cluster communication range. Based on this data analysis approach, we show the promising networking potential of public transportation vehicles and provide design guidelines for future networking solutions utilizing them.
A Survey on Intelligentized Technologies for Visual Information Acquirement, modeling and Control of Arc Welding Pool Dynamics

This paper presents a sequential research work on visual information acquirement and intelligent control of arc welding pool dynamics. The visual information acquirement methods are focused in computer vision sensing, image processing and characteristic extraction of the weld pool surface from the single-item pool images by particular algorithms; Based on acquired visual characteristics of weld pool and established neural network, nonlinear and knowledge models for predicting weld pool dynamics during arc welding process, corresponding control methods, such as neural network, self-learning and other composite intelligent control strategies are developed to control welding pool dynamics during pulsed GTAW.
3D Ultrasound Imaging: Fast and Cost-effective Morphometry of Musculoskeletal Tissue

The developmental goal of 3D ultrasound imaging (3DUS) is to engineer a modality to perform 3D morphological ultrasound analysis of human muscles. 3DUS images are constructed from calibrated freehand 2D B-mode ultrasound images, which are positioned into a voxel array. Ultrasound (US) imaging allows quantification of muscle size, fascicle length, and angle of pennation. These morphological variables are important determinants of muscle force and length range of force exertion. The presented protocol describes an approach to determine volume and fascicle length of m. vastus lateralis and m. gastrocnemius medialis. 3DUS facilitates standardization using 3D anatomical references. This approach provides a fast and cost-effective approach for quantifying 3D morphology in skeletal muscles. In healthcare and sports, information on the morphometry of muscles is very valuable in diagnostics and/or follow-up evaluations after treatment or training.
Noninvasive Monitoring of Pneumococcal Meningitis and Evaluation of Treatment Efficacy in an Experimental Mouse Model*

Noninvasive real-time in vivo bioluminescent imaging was used to assess the spread of Streptococcus pneumoniae throughout the spinal cord and brain during the acute stages of bacterial meningitis. A mouse model was established by lumbar (LP) or intracisternal (IC) injection of bioluminescent S. pneumoniae into the subarachnoid space. Bacteria replicated initially at the site of inoculation and spread progressively from the spinal cord to the brain or from the brain down to the cervical part of the spinal column and to the lower vertebral levels. After 24 hr, animals showed strong bioluminescent signals throughout the spinal canal, indicating acute meningitis of the intracranial and intraspinal meninges. A decline in bacterial cell viability, as judged by a reduction in the bioluminescent signal, was observed over time in animals treated with ceftriaxone, but not in untreated groups. Mice treated with the antibiotic survived infection, whereas all mice in untreated groups became moribund, first in the IC group then in the LP group. No untreated animal survived beyond 48 hr after induction of infection. Colony counts of infected cerebrospinal fluid (CSF) correlated positively with bioluminescent signals. This methodology is especially appealing because it allows detecting infected mice as early as 3 hr after inoculation, provide temporal, sequential, and spatial distribution of bacteria within the brain and spinal cord throughout the entire disease process and the rapid monitoring of treatment efficacy in a nondestructive manner. Moreover, it avoids the need to sacrifice the animals for CSF sampling and the potential manipulative damage that can occur with other conventional methods.
Adenovirus-pulsed dendritic cells stimulate human virus-specific T-cell responses in vitro

Adenovirus infections cause significant morbidity and mortality in immunocompromised patients, yet little is known about the immune response to adenovirus infections. We established a system for the generation of a cytotoxic immune response to adenovirus in vitro. Cytotoxic T cells (CTLs) were derived from normal donors by using peripheral blood dendritic cells as antigen-presenting cells. The CTLs were found to contain a mixture of effector cells that recognized virus peptides in the context of both class I and class II antigens. Endogenous viral gene expression was not required to sensitize cells to lysis by adenovirus-specific CTLs. CTLs raised against subgroup C adenovirus type 5 can lyse cells infected with subgroup B adenovirus type 11, indicating that viruses of different subgroups have epitopes in common. This system holds promise for defining the human immune response to adenovirus, including characterization of the viral protein(s) against which the response is generated, and the identity of the effector cells. Such studies are in progress.
Residual-based inspection/replacement policy for a deteriorating system with Markovian covariates

This paper investigates a residual-based maintenance policy for a stochastic deteriorating system, which is influenced by a Markovian covariates process. The baseline stochastic deterioration is modeled by a Gamma process, and the covariates process is assumed to be a time-homogeneous finite-state Markov chain. A model similar to the proportional hazards model is used to represent the influence of the covariates. A residual-based inspection scheme, depending on the degradation level as well as the covariates state, is proposed. We derive the optimal maintenance threshold, optimal inspection scheme to minimize the expected average maintenance cost. By Monte Carlo simulations the efficiency of our method is studied.