Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic epidemiological studies of congenital/prelingual deafness in Turkey: Population structure and mating type are major determinants of mutation identification

In order to evaluate the genetic epidemiology of deafness in Turkey, we first analyzed the pedigree data obtained from 2,169 families whose children were students of the schools for hearing loss/deafness in 31 cities of Turkey. Single major locus segregation analysis was performed after families were grouped according to hearing status of the parents. The results showed that sporadic phenocopies, autosomal dominant, and autosomal recessive transmission account for 18.2%, 4.9%, and 76.9% of the cases respectively, after exclusion of probands with unequivocal evidence for environmental etiologies. The high frequency of autosomal recessive transmission of this study differs from those of previous ones in Western populations. We subsequently analyzed the data from a subset of 574 unrelated families that were evaluated clinically, including mutation analysis of the GJB2 gene in 406 probands. Biallelic mutations were detected in 22.4% of all probands. They were present in 68.8% of probands whose parents were both deaf, yet in only 9.3% when both parents were hearing and consanguineous without a family history of deafness. Our study shows that GJB2 is the major gene for deafness in Turkey and was amplified in deaf by deaf matings, since assortative mating preferentially affects common genes. Deafness in the remaining families appears to result from mutations at many loci that are less frequent causes of deafness, because consanguinity has a proportionally greater effect on rare genes. Conclusions of this study may be relevant to other populations where consanguineous or assortative mating is present with various frequencies. © 2007 Wiley‐Liss, Inc.
Arthrosonography in the evaluation of osteoarticular and soft-tissue structures in rheumatology.

BACKGROUND Real-time ultrasonography is a widely available, reliable, diagnostically sensitive and specific noninvasive modality which allows measuring of the thickness of different anatomical landmarks which form joints, of the periarticular soft tissue and connective tissue structures, of their echogenicity and the amount of joint effusion. The present study was designed to assess the clinical and diagnostic applicability of high-frequency ultrasonography in rheumatology. METHODS We used SONOACE 1500 (Medison Europe GmbH) with a 7.5 MHz transducer. RESULTS We demonstrate the most characteristic ultrasonographic patterns which have diagnostic significance in the seven most common rheumatologic disorders. DISCUSSION The pathological ultrasonographic patterns of the joints, periarticular and soft-tissue structures in rheumatologic disorders we present give an insight into the clinical applicability of arthrosonography and its inherent advantages over the conventional radiological examination--namely, ultrasonography is noninvasive, uses no radiation, which allows reproducibility and follow-up, widely available and relatively inexpensive and as such can be performed at bedside or on an outpatient basis.
An ultra high-Q micromechanical in-plane tuning fork

This work presents a micromechanical in-plane tuning fork with internal vibration amplification ability that can be used as an ultra-sensitive MEMS gyroscope. The structure is designed to incorporate a thermal-piezoresistive energy pump for one of the vibration modes leading to significant amplification of vibration amplitude with the same actuation force. Up to 473X vibration amplitude enhancement has been demonstrated leading to a measured effective quality factor (Q) of 10.4×106 for the vibration mode with intrinsic mechanical Q of 22,097. This was achieved by applying a bias current of only 1.607mA to the piezoresistor embedded within the structure. The internal thermal-piezoresistive amplification is caused by coupling of mechanical strain and Joule's heating in the piezoresistor biased with a DC current. Measured effective Q values as a function of bias current agree with the theoretical predication. Theoretically there is no upper limit on the achievable effective Q provided that the bias current can be controlled with adequate precision.
Concerns of the dry-cleaning industry: a qualitative investigation of labor and management.

BACKGROUND Occupational scientists agree there are hazards associated with dry-cleaning, but do dry-cleaning owners and workers concur? Knowledge of owners' and workers' perceptions can help guide intervention efforts to reduce worker exposure. To better understand these issues, a qualitative study was conducted using focus group methodology and constant comparative analysis. METHODS Two owner and four worker focus groups were held. RESULTS Findings suggest that overall, health and safety issues were not of great concern. Owners were primarily concerned with the economic impact of regulations. Workers did express some anxiety about solvent exposure and burns, but most felt that these hazards were "just part of the job. " Also, other than the installation of air-conditioning in the shops and the provision of health benefits, workers could not think of ways health and safety on the job could be improved. CONCLUSIONS These findings will be used to develop comprehensive safety and health interventions (e.g., engineering plus education and training) in dry-cleaning shops.
GP96 C‐terminal improves Her2/neu DNA vaccine

DNA vaccines ensure protective immunity against tumors in a variety of experimental models. The favorite target tumor‐associated antigens have been those that are frequently expressed by human tumors, such as Her2. However, the efficacy of active vaccination is limited because Her2 is a self‐tolerated antigen. Many strategies have been applied to increase the efficacy of DNA vaccination, such as fusion or co‐administration of Her2 with cytokine and co‐stimulatory molecules. GP96 is involved in innate and adaptive immune responses and evokes potent activation and maturation of dendritic cells along with increased secretion of pro‐inflammatory cytokines. On the basis of previous studies, we expected the C‐terminal of GP96 to act as a package and as a suitable substitute for both cytokine and co‐stimulatory genes.
Improving Access to Chronic Pain Services Through eConsultation: A Cross-Sectional Study of the Champlain BASE eConsult Service.

OBJECTIVE To describe the impact of the Champlain BASE (Building Access to Specialists through eConsultation) eConsult service on access to specialist care for patients with chronic pain. DESIGN A cross-sectional descriptive study SETTING: The Champlain Local Health Integration Network, comprising Ottawa, Canada, and the surrounding region. SUBJECTS All eConsult cases submitted to chronic pain specialists by primary care providers between April 15, 2011 and June 30, 2015. METHODS Usage data and provider responses to a mandatory closeout survey were analyzed to determine response times, case outcomes, and provider satisfaction. RESULTS Ninety-three primary care providers submitted 199 eConsults to four chronic pain specialists during the study period. Submitted cases had median response times of 1.9 days. Thirty-six percent of cases resulted in an unnecessary referral being avoided, and over 90% of cases were rated by primary care providers as being of high or very high value for their patients and themselves. CONCLUSION The eConsult service improved access to specialist care for patients with chronic diseases. By facilitating prompt communication between primary care providers and specialists, eConsult can help mitigate the negative effects of long wait times experienced by patients with chronic pain.
A V-band planar narrow bandpass filter using a new type integrated waveguide transition

A surface mountable planar narrow bandpass filter is proposed and demonstrated at V-band. The filter is constructed using an integrated waveguide in an alumina substrate employing a novel microstrip line to waveguide transition. The insertion loss per one transition is less than 0.1 dB over 43 to 73 GHz. A fabricated three-pole Chebyshev filter exhibits an insertion loss of 3 dB with a 3.3% bandwidth at a center frequency of 62 GHz and the return loss is better than 15 dB in the passband.
Fundamental Limits on Data Acquisition: Trade-offs Between Sample Complexity and Query Difficulty

We consider query-based data acquisition and the corresponding information recovery problem, where the goal is to recover $k$ binary variables (information bits) from parity measurements of those variables. The queries and the corresponding parity measurements are designed using the encoding rule of Fountain codes. By using Fountain codes, we can design potentially limitless number of queries, and corresponding parity measurements, and guarantee that the original $k$ information bits can be recovered with high probability from any sufficiently large set of measurements of size n. In the query design, the average number of information bits that is associated with one parity measurement is called query difficulty $(\bar{d})$ and the minimum number of measurements required to recover the $k$ information bits for a fixed $\bar{d}$ is called sample complexity (n). We analyze the fundamental trade-offs between the query difficulty and the sample complexity, and show that the sample complexity of $n=c\max\{k,(k \log k)/\bar{d}\}$ for some constant $c$ > 0 is necessary and sufficient to recover $k$ information bits with high probability as $k\rightarrow\infty$. 1 A full version of this paper is accessible at arXiv:I712.00157 [I]
Increased CYP4B1 mRNA Is Associated with the Inhibition of Dextran Sulfate Sodium–Induced Colitis by Caffeic Acid in Mice

Susceptibility to inflammatory bowel diseases depends upon interactions between the genetics of the individual and induction of chronic mucosal inflammation. We hypothesized that administration of dietary phenolics, caffeic acid and rutin, would suppress upregulation of inflammatory markers and intestinal damage in a mouse model of colitis. Colitis was induced in C3H/ HeOuJ mice (8 weeks old, 6 male/6 female per treatment) with 1.25% dextran sulfate sodium (DSS) for 6 d in their drinking water. Rutin (1.0 mmol (524 mg)/kg in diet), caffeic acid (1.0 mmol (179 mg)/kg in diet), and hypoxoside extract (15 mg/d, an anticolitic phenolic control) were fed to the mice for 7 d before and during DSS treatment, as well as without DSS treatment. Body weight loss was prevented by rutin and caffeic acid during DSS treatment. Colon lengths in mice fed caffeic acid and hypoxoside during DSS treatment were similar to DSS-negative control. Food intake was improved and myeloperoxidase (MPO) was decreased with each phenolic treatment in DSS-treated mice compared with DSS treatment alone. Colonic mRNA expression of IL-17 and iNOS were inhibited when IL-4 was increased by each phenolic treatment combined with DSS, whereas CYP4B1 mRNA was increased only by caffeic acid in DSS-treated mice, compared with DSS treatment alone. Colonic and cecal histopathology scores of DSS-treated mice were significantly more severe (P < 0.01) than in mice fed caffeic acid before and during DSS treatment, based on mucosal height, necrosis, edema, erosion, and inflammatory cell infiltration. Although both rutin and caffeic acid suppressed the expression of selected inflammatory markers, only caffeic acid protected against DSS-induced colitis, in association with normalization of CYP4B1 expression. The inhibition of DSS-induced colitic pathology by caffeic acid was mediated by mechanisms in addition to anti-inflammatory effects that deserve further study.
Energetic and ecological constraints on population density of reef fishes

Population ecology has classically focused on pairwise species interactions, hindering the description of general patterns and processes of population abundance at large spatial scales. Here we use the metabolic theory of ecology as a framework to formulate and test a model that yields predictions linking population density to the physiological constraints of body size and temperature on individual metabolism, and the ecological constraints of trophic structure and species richness on energy partitioning among species. Our model was tested by applying Bayesian quantile regression to a comprehensive reef-fish community database, from which we extracted density data for 5609 populations spread across 49 sites around the world. Our results indicate that population density declines markedly with increases in community species richness and that, after accounting for richness, energetic constraints are manifested most strongly for the most abundant species, which generally are of small body size and occupy lower trophic groups. Overall, our findings suggest that, at the global scale, factors associated with community species richness are the major drivers of variation in population density. Given that populations of species-rich tropical systems exhibit markedly lower maximum densities, they may be particularly susceptible to stochastic extinction.
Chronic adrenaline treatment fails to down‐regulate the Del301–303‐α2B‐adrenoceptor in neuronal cells

Background and purpose: A polymorphism of the human α2B‐adrenoceptor (Del301–303‐α2B‐adrenoceptor) has been described, and this receptor exhibits reduced G‐protein‐coupled receptor kinase (GRK) phosphorylation and impaired short‐term desensitization. Expression of the Del301–303‐α2B‐adrenoceptor also is associated with an increased risk for myocardial infarction in humans. Recent evidence from our laboratory suggests a quantitative relationship between cellular GRK3 expression levels and the sensitivity of the α2B‐adrenoceptor to agonist‐induced down‐regulation. Therefore, the present study was undertaken to study agonist‐induced down‐regulation of the wild‐type (WT)‐ and Del301–303‐α2B‐adrenoceptor in a neuronal cell model.
Does size of one’s community affect likelihood of being drafted into the NHL? Analysis of 25 years of data

Abstract The consistency of community size effects in North American contexts but not elsewhere, reinforces the notion that the effect is driven by socio-cultural factors specific to the country under examination. In order to identify and understand the various forces driving the community size effect, it is important to determine whether the effect has changed over time. Stability or instability over time would assist researchers in identifying the specific socio-cultural mechanisms driving these effects. This study compared the influence of community size on the likelihood of being drafted into the National Hockey League (NHL) among Canadian ice hockey players drafted to play in the NHL between 1985 and 2009. Although there was some variability over the timespan examined, most notably in communities with between 250,000 and 499,999 inhabitants and over 1,000,000 inhabitants, trends were generally stable over time, suggesting that the socio-cultural mechanisms may have also been relatively stable, although further work is necessary to confirm this assumption.
Mobility of the First Tarsometatarsal Joint in Hallux Valgus Patients: A Radiographic Analysis

Hypermobility of the first tarsometatarsal (TMT 1) joint in the sagittal plane plays a role in the etiology and treatment of the hallux valgus complex. However, objective quantification of this mobility is still a problem. We performed a radiographic analysis of TMT 1 mobility in the sagittal plane in 94 hallux valgus patients aged 15 to 65 years. We examined 94 feet with symptomatic hallux valgus deformity requiring operative correction. Excluded were patients with osteoarthritis, inflammatory diseases or previous operations on the foot. The TMT 1 mobility was tested with a clinical test and by radiographic measurement using the modified Coleman block test. The mean mobility of the TMT 1 joint in the sagittal plane in the patient group was 12.9° (SD 4.80). In addition, there was a statistically significant difference between two sub-groups: patients with and without clinical TMT 1 hypermobility. No correlation of TMT 1 (hyper)mobility and radiographic second ray hypertrophy was found. This simple method can produce additional information to the clinical TMT 1 hypermobility test in the sagittal plane.
Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches

Based on integrative computational hybrid approaches that combined statistical coupling analysis (SCA), molecular dynamics (MD), and normal mode analysis (NMA), evolutionarily coupled residues involved in functionally relevant motion in the adenylate kinase protein family were identified. The hybrids identified four top‐ranking site pairs that belong to a conserved hydrogen bond network that is involved in the enzyme's flexibility. A second group of top‐ranking site pairs was identified in critical regions for functional dynamics, such as those related to enzymatic turnover. The high consistency of the results obtained by SCA with NMA (SCA.NMA) and by SCA.MD hybrid analyses suggests that suitable replacement of the matrix of cross‐correlation analysis of atomic fluctuations (derived by using NMA) with those based on MD contributes to the identification of such sites by means of a fast computational calculation. The analysis presented here strongly supports the hypothesis that evolutionary forces, such as coevolution at the sequence level, have promoted functional dynamic properties of the adenylate kinase protein family. Finally, these hybrid approaches can be used to identify, at the residue level, protein motion coordination patterns not previously observed, such as in hinge regions. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Contributions of the Domains of the Bacillus subtilis Response Regulator Spo0A to Transcription Stimulation of the spoIIG Operon*

Spo0A is a response regulator that controls entry into sporulation by specifically stimulating or repressing transcription of critical developmental genes. Response regulators have at least two domains: an output transcription regulation domain and a receiver domain that inhibits the output domain. Phosphorylation of the receiver domain relieves the inhibition. We examined the in vitro transcription activation mechanism for Spo0A, phosphorylated Spo0A (Spo0A∼P), and a deletion mutant that consists solely of the C-terminal output domain (Spo0ABD). Both Spo0A∼P and Spo0ABD stimulated transcription from thespoIIG promoter 10-fold more efficiently than Spo0A. Spo0A∼P and Spo0ABD induced DNA denaturation by RNA polymerase in the −10 recognition region, whereas Spo0A did not. DNase I footprint assays revealed that phosphorylation enhanced binding of intact Spo0A to the 0A boxes, while the binding of Spo0ABD was similar to that of Spo0A. Thus, activation of Spo0A by phosphorylation is not primarily due to enhanced DNA binding. The presence of a phosphorylated N terminus increased the stability of the ternary complex at thespoIIG promoter. We propose that the primary effect of phosphorylation is to expose an RNA polymerase interaction domain to promote transcription from PspoIIG.
Syndromic approach to detection of gonococcal and chlamydial infections among female sex workers in two Philippine cities.

BACKGROUND In many developing countries, STD control efforts often involve registration and periodic examinations of female sex workers (FSW). Non-availability of sensitive and specific diagnostic tests frequently constrain this approach. METHODS A model for detection of Chlamydia trachomatis or Neisseria gonorrhoeae in FSW on the basis of risk assessment and examination was developed from data gathered in Manila and evaluated in a second city (Cebu) in the Republic of the Philippines. RESULTS Gonococcal or chlamydial cervical infection was found in 23.3% of FSW in Manila and 37.0% in Cebu. Unregistered and younger FSW had greatest risk of chlamydial infection and/or gonorrhoea in both cities. In Manila, where gynaecologists performed the pelvic examinations, signs of cervical mucopus or cervical motion, uterine or cervical motion tenderness in women under < 25 years old or unregistered had positive predictive value (PPV) of 0.60 and sensitivity of 42.1% for cervical infection. In Cebu, where women were not examined by gynaecologists, the same model had high PPV, but a sensitivity of only 12.3%. CONCLUSIONS Experience and training of clinicians undoubtedly can influence the yield of examination in syndromic management of cervical infection. Nevertheless, inexpensive and diagnostic tests are needed for detection of cervical infection in this population.
Computerized measures of finger tapping: Reliability, malingering and traumatic brain injury

We analyzed computerized finger tapping metrics in four experiments. Experiment 1 showed tapping-rate differences associated with hand dominance, digits, sex, and fatigue that replicated those seen in a previous, large-scale community sample. Experiment 2 revealed test–retest correlations (r = .91) that exceeded those reported in previous tapping studies. Experiment 3 investigated subjects simulating symptoms of traumatic brain injury (TBI); 62% of malingering subjects produced abnormally slow tapping rates. A tapping-rate malingering index, based on rate-independent tapping patterns, provided confirmatory evidence of malingering in 48% of the subjects with abnormal tapping rates. Experiment 4 compared tapping in 24 patients with mild TBI (mTBI) and a matched control group; mTBI patients showed slowed tapping without evidence of malingering. Computerized finger tapping measures are reliable measures of motor speed, useful in detecting subjects performing with suboptimal effort, and are sensitive to motor abnormalities following mTBI.
In vivo and in vitro analyses of Myc for differential promoter activities of the human telomerase (hTERT) gene in normal and tumor cells.

Induction of the catalytic subunit of human telomerase, hTERT, plays a critical role in the activation of telomerase during tumorigenesis. Here, we isolate the hTERT gene promoter and define the functional promoter region, which is inactive in normal cells but active in tumor cells. Myc directly interacts with the hTERT promoter and activates its transcription both in vivo and in vitro. Activation or repression of Myc can alter hTERT promoter activities in normal or tumor cells. Furthermore, we detect high levels of Myc protein in tumor cells compared with normal cells. The ability of Myc to modulate the activity of the hTERT promoter and, hence, the telomerase enzyme may contribute to its ability to promote tumor formation.
Genome-scale transcriptional regulatory network models for the mouse and human striatum predict roles for SMAD3 and other transcription factors in Huntington’s disease

Transcriptional changes occur presymptomatically and throughout Huntington’s Disease (HD), motivating the study of transcriptional regulatory networks (TRNs) in HD. We reconstructed a genome-scale model for the target genes of 718 TFs in the mouse striatum by integrating a model of the genomic binding sites with transcriptome profiling of striatal tissue from HD mouse models. We identified 48 differentially expressed TF-target gene modules associated with age‐ and Htt allele-dependent gene expression changes in the mouse striatum, and replicated many of these associations in independent transcriptomic and proteomic datasets. Strikingly, many of these predicted target genes were also differentially expressed in striatal tissue from human disease. We experimentally validated a key model prediction that SMAD3 regulates HD-related gene expression changes using chromatin immunoprecipitation and deep sequencing (ChIP-seq) of mouse striatum. We found Htt allele-dependent changes in the genomic occupancy of SMAD3 and confirmed our model’s prediction that many SMAD3 target genes are down-regulated early in HD. Importantly, our study provides a mouse and human striatal-specific TRN and prioritizes a hierarchy of transcription factor drivers in HD.