Miracle-dz/UniFAR-FTUs huggingface dataset:
Lognormal distribution of pause length in ataxic dysarthria

Previous investigations indicated that pauses in ataxic dysarthric speech are abnormal, but little is known about the nature of their variation or whether it can be characterized by a common distribution. The following types of pauses were measured in spontaneous monologues of 16 speakers with ataxic dysarthria: pauses that contained evidence of respiration, pauses that occurred between words, between phonemes, within phonemes, and those associated with stop consonants. Results showed that the duration of pauses not associated with stop consonants can be modeled with two distinct lognormal distributions. The lognormal distribution predicted duration across pause types within 1.67% standard error, with the exception of pauses that occurred within phonemes. Distributional parameters pointed to some fundamental similarities between pauses that occur within words. The robustness of the lognormal distribution across pause types strongly supports this distribution as a viable and useful method of analysis. We hope this work will encourage others to consider the lognormal distribution.
Dose-related effects of smallpox vaccine.

BACKGROUND We conducted a double-blind, randomized trial of three dilutions of vaccinia virus vaccine in previously unimmunized adults in order to assess the clinical success rates, humoral responses, and virus-specific activity of cytotoxic T cells and interferon-gamma-producing T cells. METHODS Sixty healthy adults were inoculated intradermally by bifurcated needle with undiluted vaccine (dose, 10(7.8) plaque-forming units [pfu] per milliliter), a 1:10 dilution (dose, 10(6.5) pfu per milliliter), or a 1:100 dilution (dose, 10(5.0) pfu per milliliter); there were 20 subjects in each group. The subjects were monitored with respect to vesicle formation (an indicator of successful vaccination), the viral titer at the time of peak lesion formation, antiviral antibodies, and cellular immune responses. RESULTS A vaccinia vesicle developed in 19 of the 20 subjects who received undiluted vaccine (95 percent), 14 of the 20 who received the 1:10 dilution (70 percent), and 3 of the 20 who received the 1:100 dilution (15 percent). One month after vaccination, 34 of 36 subjects with vesicles had antibody responses, as compared with only 1 of 24 subjects without clinical evidence of vaccinia virus replication. Vigorous cytotoxic T-cell and interferon-gamma responses occurred in 94 percent of subjects with vesicles, and a cytotoxic T-cell response occurred in only one subject without a vesicle. CONCLUSIONS The vaccinia virus vaccine (which was produced in 1982 or earlier) still has substantial potency when administered by a bifurcated needle to previously unvaccinated adults. Diluting the vaccine reduces the rate of successful vaccination. The development of vesicular skin lesions after vaccination correlates with the induction of the antibody and T-cell responses that are considered essential for clearing vaccinia virus infections.
Quantitative flow cytometry of ZAP‐70 levels in chronic lymphocytic leukemia using molecules of equivalent soluble fluorochrome

ZAP‐70 has emerged as a potential pivotal prognostic marker for patients with chronic lymphocytic leukemia (CLL), which could replace immunoglobulin heavy chain mutation status. Although several flow cytometry assays have been described for assessing ZAP‐70 in CLL, certain technical and scientific issues remain unsolved, which have prevented results of this crucial test from being reported, even in the best routine flow cytometry laboratories. In this report, we aimed to solve some of these issues by providing a computerized quantitative flow cytometric assay for ZAP‐70 within the entire CLL population, which would be easy to perform and enable standardization between laboratories.
Impact of the unfolded protein response on the pathogenicity of the necrotrophic fungus Alternaria brassicicola

The unfolded protein response (UPR) is an important stress signalling pathway involved in the cellular development and environmental adaptation of fungi. We investigated the importance of the UPR pathway in the pathogenicity of the plant necrotrophic fungus Alternaria brassicicola, which causes black spot disease on a wide range of Brassicaceae. We identified the AbHacA gene encoding the major UPR transcription regulator in A. brassicicola. Deletion of AbHacA prevented induction of the UPR in response to endoplasmic reticulum stress. Loss of UPR in mutants resulted in a complete loss of virulence and was also associated with a cell wall defect and a reduced capacity for secretion. In addition, our results showed that the UPR was triggered by treatment of mycelia with camalexin, i.e. the major Arabidopsis thaliana phytoalexin, and that strains lacking functional AbHacA exhibited increased in vitro susceptibility to antimicrobial plant metabolites. We hypothesize that the UPR plays a major role in fungal virulence by altering cell protection against host metabolites and by reducing the ability of the fungus to assimilate nutrients required for growth in the host environment. This study suggests that targeting the UPR pathway would be an effective plant disease control strategy.
Ensemble Methods for Native Language Identification

Our team—Uvic-NLP—explored and evaluated a variety of lexical features for Native Language Identification (NLI) within the framework of ensemble methods. Using a subset of the highest performing features, we train Support Vector Machines (SVM) and Fully Connected Neural Networks (FCNN) as base classifiers, and test different methods for combining their outputs. Restricting our scope to the closed essay track in the NLI Shared Task 2017, we find that our best SVM ensemble achieves an F1 score of 0.8730 on the test set.
Endoscopic ultrasound-guided rendezvous for biliary access after failed cannulation

Introduction: Selective cannulation fails in approximately 3 % of endoscopic retrograde cholangiography (ERC) procedures. An endoscopic ultrasound-guided rendezvous technique (EUS – RV) may salvage failed cannulation. The aims of the current study were to determine the safety and efficacy of EUS – RV. Methods: A total of 40 patients underwent salvage EUS – RV. EUS – RV was attempted immediately after failed biliary cannulation. A dilated intra- or extra-hepatic biliary duct (IHBD or EHBD) was punctured from the stomach or the small intestine under EUS guidance followed by cholangiography and antegrade manipulation of the guide wire into the small intestine. Finally, the echoendoscope was exchanged for an appropriate endoscope and biliary cannulation was achieved over or adjacent to the guide wire. Result: EUS–RV appears safe and effective and may be considered as a primary salvage technique after failed cannulation. Antegrade manipulation of the guide wire into the small intestine was achieved in 29 of 40 patients (73 %; EHBD 25 /31 and IHBD 4/9). The reasons for failure were inability to advance the guide wire through an obstruction or a native ampulla. Re-attempt at ERC immediately after failed EUS – RV was made in seven of the 11 patients, and was successful in four. The remaining seven patients underwent percutaneous drainage within 3 days. Complications occurred in five patients (13 %), including pancreatitis, abdominal pain, pneumoperitoneum, and sepsis/death, which was unlikely to be related to the procedure. Conclusion: EUS – RV is safe and effective and should be considered as a primary salvage technique after failed cannulation. Immediate re-attempt at ERC after failed EUS – RV is warranted, as EUS-guided cholangiogram can facilitate biliary cannulation in some cases. Finally, prompt alternative biliary drainage should be available.
Aromatase Promoter I.f is Regulated by Estrogen Receptor Alpha (ESR1) in Mouse Hypothalamic Neuronal Cell Lines1

Aromatase (CYP19A1) catalyzes the conversion of C19 steroids to estrogens. Aromatase and its product estradiol (E2) are crucial for the sexually dimorphic development of the fetal brain and the regulation of gonadotropin secretion and sexual interest in adults. The regulation of aromatase expression in the brain is not well understood. The aromatase (Cyp19a1) gene is selectively expressed in distinct neurons of the hypothalamus through a distal brain-specific promoter I.f located ∼36 kb upstream of the coding region. Here, we investigated a short feedback effect of E2 on aromatase mRNA expression and enzyme activity using estrogen receptor alpha (ESR1; also known as ERalpha)-positive or ESR1-negative mouse embryonic hypothalamic neuronal cell lines that express aromatase via promoter I.f. Estradiol regulated aromatase mRNA expression and enzyme activity in a time- and dose-dependent manner, whereas an E2 antagonist reversed these effects. The nucleotide −200/−1 region of promoter I.f conferred E2 responsiveness. Two activator protein 1 (AP-1) elements in this region were essential for induction of promoter activity by E2. ESR1 and JUN (c-Jun) bound to these AP-1 motifs in intact cells and under cell-free conditions. The addition of an ESR1 mutant that interacts with JUN but not directly with DNA enhanced E2-dependent promoter I.f activity. Independently, we demonstrated an interaction between ESR1 and JUN in hypothalamic cells. Knockdown of ESR1 abolished E2-induced aromatase mRNA and enzyme activity. Taken together, E2 regulates Cyp19a1 expression via promoter I.f by enhanced binding of an ESR1/JUN complex to distinct AP-1 motifs in hypothalamic cells. We speculate that this mechanism may, in part, regulate gonadotropin secretion and sexual activity.
Aerosol ultraviolet absorption experiment (2002 to 2004), part 1: ultraviolet multifilter rotating shadowband radiometer calibration and intercomparison with CIMEL sunphotometers

Radiative transfer calculations of UV irradiance from total ozone mapping spectrometer (TOMS) satellite data are frequently over- estimated compared to ground-based measurements because of the presence of undetected absorbing aerosols in the planetary boundary layer. To reduce these uncertainties, an aerosol UV absorption closure experiment has been conducted at the National Aeronautics and Space Administration/Goddard Space Flight Center (NASA/GSFC) site in Greenbelt, Maryland, using 17 months of data from a shadowband radi- ometer (UV-multifilter rotating shadowband radiometer (UV-MFRSR), U.S. Department of Agriculture (USDA) UV-B Monitoring and Research Network) colocated with a group of three sun-sky CIMEL radiometers (rotating reference instruments of the NASA Aerosol Robotic Network (AERONET)). We describe an improved UV-MFRSR on-site calibration method augmented by AERONET-CIMEL measurements of aerosol ex- tinction optical thickness (t a) interpolated or extrapolated to the UV- MFRSR wavelengths and measurement intervals. The estimated t a is used as input to a UV-MFRSR spectral-band model, along with indepen- dent column ozone and surface pressure measurements, to estimate zero air mass voltages V0 in three longer wavelength UV-MFRSR chan- nels (325, 332, 368 nm). Daily mean ^V0&, estimates and standard de- viations are obtained for cloud-free conditions and compared with the on-site UV-MFRSR Langley plot calibration method. By repeating the calibrations on clear days, relatively good stability (62% in ^V0& )i s found in summer, with larger relative changes in fall-winter seasons. The changes include systematic day-to-day ^V0& decline for extended peri- ods along with step jump changes after major precipitation periods (rain or snow) that affected the diffuser transmission. When daily ^V0& values are used to calculate t a for individual 3-min UV-MFRSR measurements on the same days, the results compare well with interpolated AERONET t a measurements (at 368 nm most daily 1s root mean square (rms) differences were within 0.01). When intercalibrated against an AERO- NET sunphotometer, the UV-MFRSR is proven reliable to retrieve t a , and hence can be used to retrieve aerosol column absorption in the UV. The advantage of the shadowband technique is that the calibration ob- tained for direct-sun voltage can then be applied to diffuse-radiance volt- age to obtain total and diffuse atmospheric transmittances. These trans- mittances, in combination with accurate t a data, provide the basis for estimating aerosol column absorption at many locations of the USDA UV-B Monitoring and Research network and for correction of satellite estimations of surface UV irradiance. © 2005 Society of Photo-Optical Instru-
Frequent microsatellite instability and mismatch repair gene mutations in young Chinese patients with colorectal cancer.

BACKGROUND The incidence of colorectal cancer in persons under 46 years of age is substantially higher in Hong Kong than in Scotland and many other countries. Consequently, we examined whether there is a hereditary predisposition for colorectal cancer in this Southern Chinese population. METHODS We investigated the incidence of microsatellite instability (MSI) at 10 DNA sites in 117 colorectal cancer specimens from Chinese patients of various ages. Those tumors with new alleles at 40% or more of the sites investigated were identified as highly unstable MSI (MSI-H). In young patients, we also searched for germline mutations in three mismatch repair genes (hMSH2, hMLH1, and hMSH6). RESULTS The incidence of MSI-H varied statistically significantly with age, being observed in more than 60% of those younger than age 31 years at diagnosis and in fewer than 15% of those age 46 years or older. In 15 patients (<46 years old) whose colorectal cancers showed MSI-H, eight possessed germline mutations in either hMSH2 or hMLH1. When mutations in hMSH6 were included, more than 80% of Chinese colorectal cancer patients younger than 31 years had germline mutations in mismatch repair genes. We found a novel germline missense mutation in hMSH6 in a 29-year-old man whose tumor showed no MSI. Two patients had a 4-base-pair insertion in exon 10 causing a truncated protein; this insertion is a common polymorphism with a population allele frequency in Chinese of 5.6%. CONCLUSIONS Our results indicate that germline mutations in mismatch repair genes contribute substantially to the pathogenesis and high incidence of colorectal cancer in young Hong Kong Chinese. However, because young Chinese and Caucasians show similar proportions of colorectal cancers with MSI-H, despite the higher incidence in the former, additional factors may underlie the high susceptibility of young Chinese to colorectal cancer.
Intraoperative Radiofrequency Ablation of Chronic Atrial Fibrillation: A Left Atrial Curative Approach by Elimination of Anatomic “Anchor” Reentrant Circuits

Intraoperative Ablation of Atrial Fibrillation. Introduction: The percutaneous approach to radiofrequency (RF) catheter ablation for curative treatment of atrial fibrillation (AF) is an investigational technique, and the optimal composition of lesion lines is unknown. We tested an intraoperative RF ablation concept with elimination of left atrial anatomic “anchor” reentrant circuits.
Seroprevalence of Mycobacterium avium subspecies paratuberculosis in cows in Umbria, Italy

JOHNE'S disease, a chronic granulomatous enteritis of ruminants and camelids caused by the bacterium Mycobacterium avium subspecies paratuberculosis (MAP), is a major cause of economic losses in the cattle industry ([Johnston and others 2004][1]). There have been discussions in Europe regarding
Evidências dE validadE do tEstE dE PfistEr Para avaliação dE crianças

Resumo O objetivo deste trabalho foi verificar a validade do teste das pirâmides de Pfister em criancas, mais especificamente, sua sensibilidade para identificar diferencas no desenvolvimento cognitivo e emocional. Foram avaliadas 85 criancas de 6 e 12 anos, de ambos os sexos. As aplicacoes foram feitas nas escolas e de forma individual. Compararam-se os dados quanto a frequencia das cores, sindromes cromaticas e o aspecto formal. As criancas menores tiveram uma frequencia significati vamente maior de amarelo e sindrome de estimulo, assim como tapetes puros e com inicio de ordem. As criancas maiores apresentaram aumento das cores branca e preta em relacao as criancas menores, assim como mais estruturas em manto. Esses achados demonstram que o teste de Pfister e sensivel para revelar indicadores de maior controle emocional decorrentes do desenvolvimento cognitivo, conforme esperado teoricamente, o que constitui uma evidencia de validade para o seu uso na populacao infantil. Palavras-chave: avaliacao psicologica; Pfister; pirâmides coloridas; criancas.
Modelling convective processes during the suppressed phase of a Madden–Julian oscillation: Comparing single‐column models with cloud‐resolving models

The role of convective processes in moistening the atmosphere during suppressed periods of the suppressed phase of a Madden–Julian oscillation is investigated in cloud‐resolving model (CRM) simulations, and the impact of moistening on the subsequent evolution of convection is assessed as part of a Global Energy and Water Cycle Experiment Cloud System Study (GCSS) intercomparison project. The ability of single‐column model (SCM) versions of a number of state‐of‐the‐art climate and numerical weather prediction models to capture these convective processes is also evaluated. During the suppressed periods, the CRMs are found to simulate a maximum moistening around 3 km, which is associated with a predominance of shallow convection. All SCMs produce adequate amounts of shallow convection during the suppressed periods, comparable to that seen in CRMs, but the relatively drier SCMs have higher precipitation rates than the relatively wetter SCMs and CRMs. The relatively drier SCMs dry, rather than moisten, the lower troposphere below the melting level. During the transition periods, convective processes act to moisten the atmosphere above the level at which mean advection changes from moistening to drying, despite an overall drying effect for the column. The SCMs capture some essence of this moistening at upper levels. A gradual transition from shallow to deep convection is simulated by the CRMs and the wetter SCMs during the transition periods, but the onset of deep convection is delayed in the drier SCMs. This results in lower precipitation rates for these SCMs during the active periods, although much better agreement exists between the models at this time. Copyright © 2010 Royal Meteorological Society
Stereology of the Neocortex in Odontocetes: Qualitative, Quantitative, and Functional Implications

We investigated the quantitative morphology of the neocortex (gray matter) in 2 toothed whale (odontocete) species (harbor porpoise, Phocoena phocoena; bottlenose dolphin, Tursiops truncatus) with stereological methods. The 4 primary projection areas (motor, somatosensory, auditory, and visual fields) are analyzed for their cell densities in layers III and V with standard design-based stereology methods. Along cortical areas M1, S1, A1, and V1 in Tursiops, neuron density is always higher in layer III than in layer V, whereas the data in Phocoena are variable. Moreover, neuron density in layer III is generally around 1.5 times higher in Tursiops than in Phocoena. Maximal density values are seen in layer III of A1 and V1 in Tursiops and the ratio of layer III/layer V density is maximal in A1 of this species. Thus, layer III could have a higher capacity in the bottlenose dolphin with regard to intrinsic connectivity. Extant knowledge on toothed whale neurobiology and behavior suggests that quantitative/stereological differences between the 2 odontocete species regarding the neuron density of standard cortical units may be correlated with specific adaptations to their respective habitats. In contrast to layers V and VI which mainly serve as an executive system, layer III could represent an intermediate level in sensory and premotor processing which works more tangentially in the cortices via horizontal connections with other cortical areas, respectively. The generally higher density of cortical layer III in Tursiops suggests a higher connectivity of this layer in view of the more agile and complicated behavior of these gregarious animals including versatile phonation by complex sound and ultrasound signals.
Cholinergic chemosensory cells in the trachea regulate breathing

In the epithelium of the lower airways, a cell type of unknown function has been termed “brush cell” because of a distinctive ultrastructural feature, an apical tuft of microvilli. Morphologically similar cells in the nose have been identified as solitary chemosensory cells responding to taste stimuli and triggering trigeminal reflexes. Here we show that brush cells of the mouse trachea express the receptors (Tas2R105, Tas2R108), the downstream signaling molecules (α-gustducin, phospholipase Cβ2) of bitter taste transduction, the synthesis and packaging machinery for acetylcholine, and are addressed by vagal sensory nerve fibers carrying nicotinic acetylcholine receptors. Tracheal application of an nAChR agonist caused a reduction in breathing frequency. Similarly, cycloheximide, a Tas2R108 agonist, evoked a drop in respiratory rate, being sensitive to nicotinic receptor blockade and epithelium removal. This identifies brush cells as cholinergic sensors of the chemical composition of the lower airway luminal microenvironment that are directly linked to the regulation of respiration.
Detecting Residual/Recurrent Head Neck Squamous Cell Carcinomas Using PET or PET/CT

Objective To evaluate the diagnostic accuracy of positron emission tomography (PET) and PET/computed tomography (CT) for detecting residual and/or recurrent local and regional disease and distant metastases in patients with head and neck squamous cell carcinomas (HNSCCs) following radiotherapy with or without chemotherapy. Data Sources A systematic review with no language restrictions was conducted using PREMEDLINE, MEDLINE, EMBASE, and Google Scholar. Review Methods Only prospective studies with histopathological and/or clinical follow-up that assessed the diagnostic accuracy of PET and PET/CT in detecting residual and/or recurrent disease following radiotherapy with or without chemotherapy in patients with HNSCCs were included. Results Twenty-seven studies were identified. The pooled sensitivity and specificity of PET and PET/CT for detecting residual or recurrent disease at the primary site was 86.2% and 82.3%, respectively. For residual and recurrent neck disease, the sensitivity and specificity were 72.3% and 88.3%, while for distant metastases, the values were 84.6% and 94.9%. Conclusions PET and PET/CT are highly accurate in detecting residual and/or recurrent HNSCC. PET/CT is more specific than PET alone. Specificity is also greater for scans performed more than 12 weeks after radiotherapy with or without chemotherapy. The authors support the use of PET/CT after 12 weeks posttreatment for the assessment of residual or recurrent disease.