Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical Factors Influencing Pleasant Touch during Tactile Exploration

Background When scanning surfaces, humans perceive some of their physical attributes. These percepts are frequently accompanied by a sensation of (un)pleasantness. We therefore hypothesized that aspects of the mechanical activity induced by scanning surfaces with fingertips could be objectively associated with a pleasantness sensation. Previously, we developed a unidimensional measure of pleasantness, the Pleasant Touch Scale, quantifying the pleasantness level of 37 different materials. Findings of this study suggested that the sensation of pleasantness was influenced by the average magnitude of the frictional forces brought about by sliding the finger on the surface, and by the surface topography. In the present study, we correlated (i) characteristics of the fluctuations of frictional forces resulting from the interaction between the finger and the surface asperities as well as (ii) the average friction with the sensation of pleasantness. Results Eight blindfolded participants tactually explored twelve materials of the Pleasant Touch Scale through lateral sliding movements of their index fingertip. During exploration, the normal and tangential interaction force components, fN and fT, as well as the fingertip trajectory were measured. The effect of the frictional force on pleasantness sensation was investigated through the analysis of the ratio fT to fN, i.e. the net coefficient of kinetic friction, μ. The influence of the surface topographies was investigated through analysis of rapid fT fluctuations in the spatial frequency domain. Results showed that high values of μ were anticorrelated with pleasantness. Furthermore, surfaces associated with fluctuations of fT having higher amplitudes in the low frequency range than in the high one were judged to be less pleasant than the surfaces yielding evenly distributed amplitudes throughout the whole spatial frequency domain. Conclusion Characteristics of the frictional force fluctuations and of the net friction taking place during scanning can reliably be correlated with the pleasantness sensation of surfaces.
MetAmyl: A METa-Predictor for AMYLoid Proteins

The aggregation of proteins or peptides in amyloid fibrils is associated with a number of clinical disorders, including Alzheimer's, Huntington's and prion diseases, medullary thyroid cancer, renal and cardiac amyloidosis. Despite extensive studies, the molecular mechanisms underlying the initiation of fibril formation remain largely unknown. Several lines of evidence revealed that short amino-acid segments (hot spots), located in amyloid precursor proteins act as seeds for fibril elongation. Therefore, hot spots are potential targets for diagnostic/therapeutic applications, and a current challenge in bioinformatics is the development of methods to accurately predict hot spots from protein sequences. In this paper, we combined existing methods into a meta-predictor for hot spots prediction, called MetAmyl for METapredictor for AMYLoid proteins. MetAmyl is based on a logistic regression model that aims at weighting predictions from a set of popular algorithms, statistically selected as being the most informative and complementary predictors. We evaluated the performances of MetAmyl through a large scale comparative study based on three independent datasets and thus demonstrated its ability to differentiate between amyloidogenic and non-amyloidogenic polypeptides. Compared to 9 other methods, MetAmyl provides significant improvement in prediction on studied datasets. We further show that MetAmyl is efficient to highlight the effect of point mutations involved in human amyloidosis, so we suggest this program should be a useful complementary tool for the diagnosis of these diseases.
Using ILD or ITD Cues for Sound Source Localization and Speech Understanding in a Complex Listening Environment by Listeners With Bilateral and With Hearing-Preservation Cochlear Implants.

PURPOSE To assess the role of interaural time differences and interaural level differences in (a) sound-source localization, and (b) speech understanding in a cocktail party listening environment for listeners with bilateral cochlear implants (CIs) and for listeners with hearing-preservation CIs. METHODS Eleven bilateral listeners with MED-EL (Durham, NC) CIs and 8 listeners with hearing-preservation CIs with symmetrical low frequency, acoustic hearing using the MED-EL or Cochlear device were evaluated using 2 tests designed to task binaural hearing, localization, and a simulated cocktail party. Access to interaural cues for localization was constrained by the use of low-pass, high-pass, and wideband noise stimuli. RESULTS Sound-source localization accuracy for listeners with bilateral CIs in response to the high-pass noise stimulus and sound-source localization accuracy for the listeners with hearing-preservation CIs in response to the low-pass noise stimulus did not differ significantly. Speech understanding in a cocktail party listening environment improved for all listeners when interaural cues, either interaural time difference or interaural level difference, were available. CONCLUSIONS The findings of the current study indicate that similar degrees of benefit to sound-source localization and speech understanding in complex listening environments are possible with 2 very different rehabilitation strategies: the provision of bilateral CIs and the preservation of hearing.
University of New Hampshire Scholars' Repository University of New Hampshire Scholars' Repository

The point scattering model offers a parameterization of the reverberation probability density function (pdf) in terms of the coefficient of excess (kurtosis) and a coherent component represented by a harmonic process with random phase. In this paper the potential utility of this parametrization is investigated in the context of seafloor characterization. The problem of separating out the effect of each parameter is discussed. Computer simulations are used to verify model predictions on the reverberation quadrature, envelope, and phase pdf. As part of the verification study, the scatterer density was determined from the kurtosis of the reverberation quadrature pdfi A statistical analysis of this procedure points to reduced estimate accuracy with decreasing kurtosis. Additional computer simulations show that the chosen pdf family, developed under the assumption of a Poisson scatterer distribution, is flexible enough to fit reverberation data generated by non-Poisson scatterer distributions exhibiting a degree of clustering or regularity. A computer experiment demonstrates how this parametdy(cid:127)tion can be used in conjunction with a simple sonar geometry to generate acoustic signatures for seafloor classification. In addition, real reverberation data collected by a Sea Beam sonar system in two different seafloor areas are interpreted according to the chosen parametrization.
Glutamate and GABA in Vestibulo-Sympathetic Pathway Neurons

The vestibulo-sympathetic reflex (VSR) actively modulates blood pressure during changes in posture. This reflex allows humans to stand up and quadrupeds to rear or climb without a precipitous decline in cerebral perfusion. The VSR pathway conveys signals from the vestibular end organs to the caudal vestibular nuclei. These cells, in turn, project to pre-sympathetic neurons in the rostral and caudal ventrolateral medulla (RVLM and CVLM, respectively). The present study assessed glutamate- and GABA-related immunofluorescence associated with central vestibular neurons of the VSR pathway in rats. Retrograde FluoroGold tract tracing was used to label vestibular neurons with projections to RVLM or CVLM, and sinusoidal galvanic vestibular stimulation (GVS) was employed to activate these pathways. Central vestibular neurons of the VSR were identified by co-localization of FluoroGold and cFos protein, which accumulates in some vestibular neurons following galvanic stimulation. Triple-label immunofluorescence was used to co-localize glutamate- or GABA- labeling in the identified VSR pathway neurons. Most activated projection neurons displayed intense glutamate immunofluorescence, suggestive of glutamatergic neurotransmission. To support this, anterograde tracer was injected into the caudal vestibular nuclei. Vestibular axons and terminals in RVLM and CVLM co-localized the anterograde tracer and vesicular glutamate transporter-2 signals. Other retrogradely-labeled cFos-positive neurons displayed intense GABA immunofluorescence. VSR pathway neurons of both phenotypes were present in the caudal medial and spinal vestibular nuclei, and projected to both RVLM and CVLM. As a group, however, triple-labeled vestibular cells with intense glutamate immunofluorescence were located more rostrally in the vestibular nuclei than the GABAergic neurons. Only the GABAergic VSR pathway neurons showed a target preference, projecting predominantly to CVLM. These data provide the first demonstration of two disparate chemoanatomic VSR pathways.
Transmission of Mycobacterium tuberculosis between Farmers and Cattle in Central Ethiopia

Background Transmission of Mycobacterium tuberculosis (M. tuberculosis) complex could be possible between farmers and their cattle in Ethiopia. Methodology/Principal Findings A study was conducted in mixed type multi-purposes cattle raising region of Ethiopia on 287 households (146 households with case of pulmonary tuberculosis (TB) and 141 free of TB) and 287 herds consisting of 2,033 cattle belonging to these households to evaluate transmission of TB between cattle and farmers. Interview, bacteriological examinations and molecular typing were used for human subjects while comparative intradermal tuberculin (CIDT) test, post mortem and bacteriological examinations, and molecular typing were used for animal studies. Herd prevalence of CIDT reactors was 9.4% and was higher (p<0.01) in herds owned by households with TB than in herds owned by TB free households. Animal prevalence was 1.8% and also higher (p<0.01) in cattle owned by households with TB case than in those owned by TB free households. All mycobacteria (141) isolated from farmers were M. tuberculosis, while only five of the 16 isolates from cattle were members of the M. tuberculosis complex (MTC) while the remaining 11 were members of non-tuberculosis mycobacteria (NTM). Further speciation of the five MTC isolates showed that three of the isolates were M. bovis (strain SB1176), while the remaining two were M. tuberculosis strains (SIT149 and SIT53). Pathology scoring method described by “Vordermeier et al. (2002)” was applied and the average severity of pathology in two cattle infected with M. bovis, in 11 infected with NTM and two infected with M. tuberculosis were 5.5, 2.1 and 0.5, respectively. Conclusions/Significance The results showed that transmission of TB from farmers to cattle by the airborne route sensitizes the cows but rarely leads to TB. Similarly, low transmission of M. bovis between farmers and their cattle was found, suggesting requirement of ingestion of contaminated milk from cows with tuberculous mastitis.
Nonmelanoma Skin Cancer With Aggressive Subclinical Extension in Immunosuppressed Patients.

IMPORTANCE Immunosuppression (IS), such as in solid-organ transplant recipients (SOTRs) and patients with human immunodeficiency virus (HIV) or hematologic malignant neoplasms, increases the risk of developing nonmelanoma skin cancers (NMSCs). However, it is unknown whether IS patients are at increased risk of developing NMSCs with aggressive subclinical extensions (NMSC-ASE), which may extend aggressively far beyond conventional surgical margins. OBJECTIVE To study clinical characteristics of NMSC-ASE among immunocompetent (IC) and various subgroups of IS patients and to suggest a predictive model for NMSC-ASE lesions. DESIGN, SETTING, AND PARTICIPANTS A 6-year retrospective review of 2998 NMSC cases between February 26, 2007, and February 17, 2012, at the Dermatologic and Mohs Micrographic Surgery Unit of the University of California, San Diego, Medical Center. Nonmelanoma skin cancers that required at least 3 Mohs micrographic surgery stages with final surgical margins of at least 10 mm were defined as ASE lesions. All cases were categorized into 1 of 2 groups, IS or IC. Immunosuppressed cases were further subcategorized into 3 subgroups: SOTRs and patients with HIV or hematologic malignant neoplasm. The data were analyzed in December 2012. MAIN OUTCOMES AND MEASURES We evaluated the odds ratio of having NMSC-ASE lesions in IS patients (SOTRs, HIV, hematologic malignant neoplasm) compared with IC patients. Other clinical characteristics and preoperative risks were analyzed and compared. RESULTS Of all 2998 cases, we identified 805 NMSC-ASE cases: 137 IS and 668 IC. Immunosuppressed patients had an odds ratio of 1.94 of having ASE lesions compared with IC patients (95% CI, 1.54-2.44; P < .001). Additionally, the SOTR subgroup was associated with a 2.74 odds of having NSMC-ASE compared with non-SOTRs (95% CI, 2.00-3.76; P < .001), and the presence of hematologic malignant neoplasm was associated with 1.74 times the odds compared with IC patients (95% CI, 1.04-2.90; P = .04). Multivariate analysis found older age (P < .001), lesion locations such as zone 1 (OR, 1.39 [95% CI, 1.04-1.85]; P = .02) or zone 2 (OR, 1.45 [95% CI, 1.08-1.94]; P = .01), and IS status (OR, 1.94 [95% CI, 1.54-2.44]; P < .001) to be significant predictors of ASE. CONCLUSIONS AND RELEVANCE The findings of this study suggest an increased risk for NMSC-ASE lesions in IS patients, especially in SOTRs and those with hematologic malignant neoplasm, but not patients with HIV. Statistically significant predictors of NMSC-ASE lesions such as age, location, and IS status can help physicians choose the most appropriate treatment modalities and optimize surgical planning.
Selective outcome reporting in obesity clinical trials: a cross‐sectional review

Selective outcome reporting is a form of bias resulting from discrepancies between outcomes presented in a trial's registration and the published report. We investigate this selective bias in obesity clinical trials. A PubMed search was conducted to identify randomized controlled trials (RCTs) published in four obesity journals from 2013 to 2015. Primary, secondary and tertiary outcomes were recorded for each trial and compared to pre‐specified outcomes in each trial's registration. Of the 392 identified articles, 142 were included in the final analysis; 22 (15%) RCTs demonstrated major outcome discrepancies between registration and publication: No primary outcomes were demoted to a secondary or tertiary outcome; 14 (36.84%) primary outcomes were omitted; 14 (36.84%) primary outcomes were added: 5 (13.16%) secondary outcomes were upgraded to primary outcomes; and timing of assessment for a primary outcome changed 5 (13.16%) times. Out of the 63 prospectively registered studies, 53 had no discrepancies. A total of 76 of the studies (29.80%) were unregistered or did not have an associated registration number. Our results suggest that selective outcome reporting may be a concern in obesity clinical trials. As selective outcome reporting may distort clinical findings and limit outcomes in systematic reviews, we encourage trialists and journal editors to work towards solutions to mitigate this issue.
Hypogonadism alters cecal and fecal microbiota in male mice

ABSTRACT Low testosterone levels increase the risk for cardiovascular disease in men and lead to shorter life spans. Our recent study showed that androgen deprivation via castration altered fecal microbiota and exacerbated risk factors for cardiovascular disease, including obesity, impaired fasting glucose, excess hepatic triglyceride accumulation, and thigh muscle weight loss only in high-fat diet (HFD)-fed male mice. However, when mice were administered antibiotics that disrupted the gut microbiota, castration did not increase cardiovascular risks or decrease the ratio of dried feces to food intake. Here, we show that changes in cecal microbiota (e.g., an increased Firmicutes/Bacteroidetes ratio and number of Lactobacillus species) were consistent with changes in feces and that there was a decreased cecal content secondary to castration in HFD mice. Castration increased rectal body temperature and plasma adiponectin, irrespective of diet. Changes in the gut microbiome may provide novel insight into hypogonadism-induced cardiovascular diseases.
Molecular Signature of High Yield (Growth) Influenza A Virus Reassortants Prepared as Candidate Vaccine Seeds

Background Human influenza virus isolates generally grow poorly in embryonated chicken eggs. Hence, gene reassortment of influenza A wild type (wt) viruses is performed with a highly egg adapted donor virus, A/Puerto Rico/8/1934 (PR8), to provide the high yield reassortant (HYR) viral ‘seeds’ for vaccine production. HYR must contain the hemagglutinin (HA) and neuraminidase (NA) genes of wt virus and one to six ‘internal’ genes from PR8. Most studies of influenza wt and HYRs have focused on the HA gene. The main objective of this study is the identification of the molecular signature in all eight gene segments of influenza A HYR candidate vaccine seeds associated with high growth in ovo. Methodology The genomes of 14 wt parental viruses, 23 HYRs (5 H1N1; 2, 1976 H1N1-SOIV; 2, 2009 H1N1pdm; 2 H2N2 and 12 H3N2) and PR8 were sequenced using the high-throughput sequencing pipeline with big dye terminator chemistry. Results Silent and coding mutations were found in all internal genes derived from PR8 with the exception of the M gene. The M gene derived from PR8 was invariant in all 23 HYRs underlining the critical role of PR8 M in high yield phenotype. None of the wt virus derived internal genes had any silent change(s) except the PB1 gene in X-157. The highest number of recurrent silent and coding mutations was found in NS. With respect to the surface antigens, the majority of HYRs had coding mutations in HA; only 2 HYRs had coding mutations in NA. Significance In the era of application of reverse genetics to alter influenza A virus genomes, the mutations identified in the HYR gene segments associated with high growth in ovo may be of great practical benefit to modify PR8 and/or wt virus gene sequences for improved growth of vaccine ‘seed’ viruses.
Increase in suicides the months after the death of Robin Williams in the US

Investigating suicides following the death of Robin Williams, a beloved actor and comedian, on August 11th, 2014, we used time-series analysis to estimate the expected number of suicides during the months following Williams’ death. Monthly suicide count data in the US (1999–2015) were from the Centers for Disease Control and Prevention Wide-ranging ONline Data for Epidemiologic Research (CDC WONDER). Expected suicides were calculated using a seasonal autoregressive integrated moving averages model to account for both the seasonal patterns and autoregression. Time-series models indicated that we would expect 16,849 suicides from August to December 2014; however, we observed 18,690 suicides in that period, suggesting an excess of 1,841 cases (9.85% increase). Although excess suicides were observed across gender and age groups, males and persons aged 30–44 had the greatest increase in excess suicide events. This study documents associations between Robin Williams’ death and suicide deaths in the population thereafter.
Vertebrate Ssu72 Regulates and Coordinates 3′-End Formation of RNAs Transcribed by RNA Polymerase II

In eukaryotes, the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is composed of tandem repeats of the heptapeptide YSPTSPS, which is subjected to reversible phosphorylation at Ser2, Ser5, and Ser7 during the transcription cycle. Dynamic changes in CTD phosphorylation patterns, established by the activities of multiple kinases and phosphatases, are responsible for stage-specific recruitment of various factors involved in RNA processing, histone modification, and transcription elongation/termination. Yeast Ssu72, a CTD phosphatase specific for Ser5 and Ser7, functions in 3′-end processing of pre-mRNAs and in transcription termination of small non-coding RNAs such as snoRNAs and snRNAs. Vertebrate Ssu72 exhibits Ser5- and Ser7-specific CTD phosphatase activity in vitro, but its roles in gene expression and CTD dephosphorylation in vivo remain to be elucidated. To investigate the functions of vertebrate Ssu72 in gene expression, we established chicken DT40 B-cell lines in which Ssu72 expression was conditionally inactivated. Ssu72 depletion in DT40 cells caused defects in 3′-end formation of U2 and U4 snRNAs and GAPDH mRNA. Surprisingly, however, Ssu72 inactivation increased the efficiency of 3′-end formation of non-polyadenylated replication-dependent histone mRNA. Chromatin immunoprecipitation analyses revealed that Ssu72 depletion caused a significant increase in both Ser5 and Ser7 phosphorylation of the Pol II CTD on all genes in which 3′-end formation was affected. These results suggest that vertebrate Ssu72 plays positive roles in 3′-end formation of snRNAs and polyadenylated mRNAs, but negative roles in 3′-end formation of histone mRNAs, through dephosphorylation of both Ser5 and Ser7 of the CTD.
Ability of Cicer arietinum (L.) for Bioremoval of Lead and Chromium from Soil

Intensive industrial activity has resulted in contamination of soils with high concentrations of heavy metals and toxic elements, potentially bioaccumulated in crop and causing serious health and socio-economic problems. Soil pollution not only leads to pollution of water resources but also restricts the use of a site or can lead to soil degeneration. The present study is considered to take the advantage of bioaccumulative nature of heavy metals for soil remediation. The experimentation involves the usage of Chickpea (Cicer arietinum (L.)) for the phytoextraction of Pb and Cr. The seeds were sown in artificially contaminated soil separately with 25, 50, 75, 100 and 150 mg/Kg Cr and 50, 100, 200, 400 and 600 mg/Kg Pb. The plants were allowed to grow for a period of 30 days and bioaccumulation was analyzed at interval of 10 days. Higher bioaccumulation was observed for higher heavy metal concentration and longer growth periods. An attempt has been made in the present paper to compare the extent of soil cleanup with time.
Movement and Heat/Mass Transfer of a Polymer in the Feed and Melting Delay Zones of the Extruder

Polymer movement and heating at the beginning of a plasticating extruder, i.e. in the feed and melting delay zones, are studied numerically in this paper. Consideration is given to the pressure distribution along the solid bed and the temperature distribution in the depth of the channel. For the melting delay zone, the distribution of the rate of melting in the polymer film is plotted. It is shown how the length of the feed and melting delay zones is influenced by screw speed, extruder throughput, heat temperature of the barrel and rheological and thermophysical properties of the polymer.