Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Treatment Intensity on Outcomes in Acquired Apraxia of Speech.

Purpose This investigation was designed to examine the effects of treatment intensity (i.e., dose frequency) on the outcomes of Sound Production Treatment (SPT) for acquired apraxia of speech. Method Five men with chronic apraxia of speech and aphasia received both intense SPT (3 hr per day/3 days per week) and nonintense/traditional SPT (SPT-T; 1 hr per day/3 days per week) in the context of single-case experimental designs. Each treatment was applied separately to a designated set of experimental words with 1 treatment applied at a time. Twenty-seven treatment sessions were conducted with each phase of treatment. Accuracy of articulation of target sounds within treated and untreated experimental words was measured during the course of the investigation. Results All participants demonstrated improved articulation with both treatment intensities. Better maintenance of gains for treated items was found with SPT-T for 2 participants as measured at an 8-week posttreatment retention probe. Superior maintenance of increased accuracy of production of untreated items was also observed with SPT-T for all participants. Conclusion A less intense (distributed) application of SPT facilitated better maintenance of improved articulatory accuracy for untreated items, and in some cases treated items, than intense SPT. Supplemental Materials https://doi.org/10.23641/asha.5734053.
Cryptococcus gattii in the United States: Genotypic Diversity of Human and Veterinary Isolates

Background Cryptococcus gattii infections are being reported in the United States (US) with increasing frequency. Initially, US reports were primarily associated with an ongoing C . gattii outbreak in the Pacific Northwest (PNW) states of Washington and Oregon, starting in 2004. However, reports of C . gattii infections in patients from other US states have been increasing since 2009. Whether this is due to increasing frequency of disease, greater recognition within the clinical community, or both is currently unknown. Methodology/Principal Findings During 2005–2013, a total of 273 C . gattii isolates from human and veterinary sources in 16 US states were collected. Of these, 214 (78%) were from the Pacific Northwest (PNW) and comprised primarily the clonal C . gattii genotypes VGIIa (64%), VGIIc (21%) and VGIIb (9%). The 59 isolates from outside the PNW were predominantly molecular types VGIII (44%) and VGI (41%). Genotyping using multilocus sequence typing revealed small clusters, including a cluster of VGI isolates from the southeastern US, and an unrelated cluster of VGI isolates and a large cluster of VGIII isolates from California. Most of the isolates were mating type MATα, including all of the VGII isolates, but one VGI and three VGIII isolates were mating type MATa . Conclusions/Significance We provide the most comprehensive report to date of genotypic diversity of US C . gattii isolates both inside and outside of the PNW. C . gattii may have multiple endemic regions in the US, including a previously-unrecognized endemic region in the southeast. Regional clusters exist both in California and the Southeastern US. VGII strains associated with the PNW outbreak do not appear to have spread substantially beyond the PNW.
Effect of seismic source bandwidth on reflection sections to image water structure

The seismic reflection profile is the convolution of the seismic acquisition impulse response and the target impedance contrasts. In the ocean, these contrasts are mainly determined by the widths and gradients of the temperature transitions between the different water masses. Hence seismic oceanography profiles are sensitive to the frequency bandwidth of the seismic acquisition system. We tested a novel seismic source that allowed us to simultaneously profile the ocean with differing impulse responses. We show that frequencies ∼20 Hz are best to delineate large impedance contrasts that occur over a vertical scale of several tens of meters whereas frequencies ∼80 Hz image the boundaries of layers of around 10 m. We demonstrate a towed acquisition system that can operate from a research vessel to give a bandwidth from 10 to 120 Hz that could, if required, be modified to provide frequencies up to 200 Hz.
Association Test Based on SNP Set: Logistic Kernel Machine Based Test vs. Principal Component Analysis

GWAS has facilitated greatly the discovery of risk SNPs associated with complex diseases. Traditional methods analyze SNP individually and are limited by low power and reproducibility since correction for multiple comparisons is necessary. Several methods have been proposed based on grouping SNPs into SNP sets using biological knowledge and/or genomic features. In this article, we compare the linear kernel machine based test (LKM) and principal components analysis based approach (PCA) using simulated datasets under the scenarios of 0 to 3 causal SNPs, as well as simple and complex linkage disequilibrium (LD) structures of the simulated regions. Our simulation study demonstrates that both LKM and PCA can control the type I error at the significance level of 0.05. If the causal SNP is in strong LD with the genotyped SNPs, both the PCA with a small number of principal components (PCs) and the LKM with kernel of linear or identical-by-state function are valid tests. However, if the LD structure is complex, such as several LD blocks in the SNP set, or when the causal SNP is not in the LD block in which most of the genotyped SNPs reside, more PCs should be included to capture the information of the causal SNP. Simulation studies also demonstrate the ability of LKM and PCA to combine information from multiple causal SNPs and to provide increased power over individual SNP analysis. We also apply LKM and PCA to analyze two SNP sets extracted from an actual GWAS dataset on non-small cell lung cancer.
Vegetative Rhombic Pattern Formation Driven by Root Suction for an Interaction-Diffusion Plant-Ground Water Model System in an Arid Flat Environment

A rhombic planform nonlinear cross-diffusive instability analysis is applied to a particular interaction-diffusion plant-ground water model system in an arid flat environment. This model contains a plant root suction effect as a cross-diffusion term in the ground water equation. In addition a threshold-dependent paradigm that differs from the usually employed implicit zero-threshold methodology is introduced to interpret stable rhombic patterns. These patterns are driven by root suction since the plant equation does not yield the required positive feedback necessary for the generation of standard Turing-type self-diffusive instabilities. The results of that analysis can be represented by plots in a root suction coefficient versus rainfall rate dimensionless parameter space. From those plots regions corresponding to bare ground and vegetative patterns consisting of isolated patches, rhombic arrays of pseudo spots or gaps separated by an intermediate rectangular state, and homogeneous distributions from low to high density may be identified in this parameter space. Then, a morphological sequence of stable vegetative states is produced upon traversing an experimentally-determined root suction characteristic curve as a function of rainfall through these regions. Finally, that predicted sequence along a rainfall gradient is compared with observational evidence relevant to the occurrence of leopard bush, pearled bush, or labyrinthine tiger bush vegetative patterns, used to motivate an aridity classification scheme, and placed in the context of some recent biological nonlinear pattern formation studies.
Investigation of the tableting behavior of Ibuprofen DC 85 W

Abstract The aim of the present study was to investigate the tableting behavior of Ibuprofen DC 85 W with special focus on the tablet disintegration time, the tablet crushing strength, and the sticking tendency to punch surfaces. To simulate production conditions, tableting was conducted on a rotary press, equipped with three compaction stations. An I-optimal design of experiments was used to analyze the influence of the pre-compaction, the intermediate compaction, and the main compaction force on the two responses: tablet disintegration time and crushing strength. It was shown that Ibuprofen DC 85 W showed a good tableting behavior with regard to both responses. The tablet disintegration was considerably affected by the maximum compaction force applied, but was also slightly affected by preceding compaction events. The tablet crushing strength was mainly affected by the maximum applied compaction force independent of the order of these forces. The sticking tendency of Ibuprofen DC 85 W was compared with that two other ibuprofen powder formulations in long-term tableting runs. Compared to the other two formulations, sticking was considerably lower with Ibuprofen DC 85 W. The sticking tendency was not influenced by the addition of an intermediate compaction force, but was remarkably reduced by the choice of the punch tip coating.
CNN oriented fast QTBT partition algorithm for JVET intra coding

In this paper, a novel fast coding unit depth decision algorithm based on convolution neural network is presented for JVET future video coding. JVET employs quad-tree plus binary-tree (QTBT) block partitioning structure, which can support much more flexibility for coding units partition shapes, and improve the coding performance significantly than the HEVC standard. However, the flexible partitioning structure also introduces a tremendous computation complexity. To address this issue, we model the QTBT partition depth range as a multi-class classification problem, and try to predict the depth range of 32×32 block directly, rather than to judge split or not at each depth level. To the best of our knowledge, it is the first framework to formulate the QTBT partition range as a multi classification task, and optimized by an end-to-end learning model. For training optimization, we design an objective function consists of class penalty term and L2 HingeLoss function, which leverage the characteristics of category settings, can further boost the classification accuracy. Experimental results demonstrate the effectiveness of our proposed method, which can achieve 42.80% complexity reduction with only 0.65% Bjontegaard Delta bitrate (BD-rate) increase.
Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System

The p53 transcription factor is a regulator of key cellular processes including DNA repair, cell cycle arrest, and apoptosis. In this theoretical study, we investigate how the complex circuitry of the p53 network allows for stochastic yet unambiguous cell fate decision-making. The proposed Markov chain model consists of the regulatory core and two subordinated bistable modules responsible for cell cycle arrest and apoptosis. The regulatory core is controlled by two negative feedback loops (regulated by Mdm2 and Wip1) responsible for oscillations, and two antagonistic positive feedback loops (regulated by phosphatases Wip1 and PTEN) responsible for bistability. By means of bifurcation analysis of the deterministic approximation we capture the recurrent solutions (i.e., steady states and limit cycles) that delineate temporal responses of the stochastic system. Direct switching from the limit-cycle oscillations to the “apoptotic” steady state is enabled by the existence of a subcritical Neimark—Sacker bifurcation in which the limit cycle loses its stability by merging with an unstable invariant torus. Our analysis provides an explanation why cancer cell lines known to have vastly diverse expression levels of Wip1 and PTEN exhibit a broad spectrum of responses to DNA damage: from a fast transition to a high level of p53 killer (a p53 phosphoform which promotes commitment to apoptosis) in cells characterized by high PTEN and low Wip1 levels to long-lasting p53 level oscillations in cells having PTEN promoter methylated (as in, e.g., MCF-7 cell line).
Prediction of days in hospital for children using random forest

In this study, a method was developed to predict the number of hospitalization days of infant patients. The random forest algorithm, along with a data set consisted by records extracted from a hospital information system, was utilized to develop a model to predict the days in hospital. When half of randomly selected records was used as training set to train the random forest algorithm and the other half was used as testing set to test the trained model, the random forest method achieved good predictive accuracy with RMSE being 0.314, R2 being 0.706, |R| being 0.545, and Acc±1 being 71%, which is better than the results obtained by Adaboost method and Bagging method. Experiment on three subgroups of records: a group with all data, a group with records having less than or equal to 14 days in hospital, and a group with records having greater than 14 days in hospital, shows that the prediction of the developed method on the group having more than 14 days in hospital was better than predictions on other groups. Analysis to the importance of three different types of feature sets to the accuracy of prediction reveals that the feature set relating to personal information contribute more to the prediction than other types of features.
Phosphine Resistance in Cryptolestes ferrugineus (Coleoptera: Laemophloeidae) Collected From Grain Storage Facilities in Oklahoma, USA.

Phosphine gas (PH3) is one of the most commonly used fumigants for controlling stored-grain pests worldwide. We estimated the discriminating dose for Cryptolestes ferrugineus (Stephens) (Coleoptera: Laemophloeidae) adult insects using a laboratory susceptible strain. This discriminating dose was then used to determine presence or absence of PH3 resistance (resistance frequencies) in 19 field-collected populations of C. ferrugineus from Oklahoma, United States. The discriminating dose was estimated as 56.2 ppm of PH3 over a 20-h exposure period at 25 °C. Discriminating dose bioassay results showed that PH3 resistance was present in all 19 populations of C. ferrugineus tested. However, five populations-Stillwater (Stil), Enid Terminal 1 (ET-1), Enid Terminal 2 (ET-2), Johnson-Enid population (JE), and DK Farm 20 population (DK Farm 20) had ≥90% resistance frequencies. LC99 values estimated by probit analyses of dose-response mortality data for the laboratory susceptible strain (Lab-S), JE, and DK Farm 20 were 7.3, 636.4, and 968.6 ppm, respectively, over a 3-d exposure period. The level of resistance in DK Farm 20, the most resistant population, was 133.5 times that of the susceptible laboratory strain. This study shows that PH3 resistance in C. ferrugineus may be widespread in Oklahoma. Based on this study, there is a need for a wider PH3 resistance survey in grain-growing regions of Oklahoma and United States. Furthermore, results show there is a need to develop PH3 resistance management strategies for C. ferrugineus and other stored-product insect pest species to combat resistance and ensure continued effective future use of PH3.
A major change in North Atlantic deep water circulation 1.6 million years ago

Abstract. The global ocean–climate system has been highly sensitive to the formation and advection of deep overflow water from the Nordic Seas as integral part of the Atlantic Meridional Overturning Circulation (AMOC) but its evolution over the Pliocene–Pleistocene global cooling is not fully understood. In particular, changes in the sources and mixing of prevailing deep waters that were involved in driving overturning throughout the Pliocene–Pleistocene climate transitions are not well constrained. Here we investigate the evolution of a substantial deep southward return overflow of the AMOC over the last 4 million years. We present new records of the bottom-water radiogenic neodymium isotope (vNd) variability obtained from three sediment cores (DSDP site 610 and ODP sites 980/981 and 900) at water depths between 2170 and 5050 m in the northeast Atlantic. We find that prior to the onset of major Northern Hemisphere glaciation (NHG) ∼3 million years ago (Ma), vNd values primarily oscillated between −9 and −11 at all sites, consistent with enhanced vertical mixing and weak stratification of the water masses during the warmer-than-today Pliocene period. From 2.7 Ma to ∼2.0 Ma, the vNd signatures of the water masses gradually became more distinct, which documents a significant advection of Nordic Seas overflow deep water coincident with the intensification of NHG. Most markedly, however, at ∼1.6 Ma the interglacial vNd signatures at sites 610 (2420 m water depth (w.d.)) and 980/981 (2170 m w.d.) synchronously and permanently shifted by 2 to 3 vNd units to less radiogenic values, respectively. Since then the difference between glacial and interglacial vNd values has been similar to the Late Quaternary at each site. A decrease of ∼2vNd units at 1.6 Ma was also recorded for the deepest water masses by site 900 (∼5050 m w.d.), which thereafter, however, evolved to more radiogenic values again until the present. This major vNd change across the 1.6 Ma transition reflects a significant reorganization of the overturning circulation in the northeast Atlantic paving the way for the more stratified water column with distinct water masses prevailing thereafter.
MSMB gene rs10993994 polymorphism increases the risk of prostate cancer

Genome-wide association studies (GWASs) identified microseminoprotein-β (MSMB) gene rs10993994 polymorphism was significantly associated with prostate cancer (PC) risk. However, the association between MSMB gene rs10993994 polymorphism and PC risk remains controversial. Therefore, we performed a systematic review and meta-analysis by searching in the databases of PubMed, and Embase. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by using fixed-effect or random-effect models. A total of 11 publications containing 13 case-control studies for rs10993994 polymorphism were included in our analysis. Our data indicated that MSMB gene rs10993994 polymorphism was associated with an increased risk of PC. Stratification analyses of ethnicity suggested rs10993994 polymorphism increased the risk of PC among Caucasians, but not among Asians. In conclusion, this meta-analysis indicates that MSMB gene rs10993994 polymorphism increases the risk of PC.
Origin and fate of the secondary nitrite maximum in the Arabian Sea

Abstract. The Arabian Sea harbours one of the three major oxygen minimum zones (OMZs) in the world's oceans, and it alone is estimated to account for ~10–20 % of global oceanic nitrogen (N) loss. While actual rate measurements have been few, the consistently high accumulation of nitrite (NO2−) coinciding with suboxic conditions in the central-northeastern part of the Arabian Sea has led to the general belief that this is the region where active N-loss takes place. Most subsequent field studies on N-loss have thus been drawn almost exclusively to the central-NE. However, a recent study measured only low to undetectable N-loss activities in this region, compared to orders of magnitude higher rates measured towards the Omani Shelf where little NO2− accumulated (Jensen et al., 2011). In this paper, we further explore this discrepancy by comparing the NO2−-producing and consuming processes, and examining the relationship between the overall NO2− balance and active N-loss in the Arabian Sea. Based on a combination of 15N-incubation experiments, functional gene expression analyses, nutrient profiling and flux modeling, our results showed that NO2− accumulated in the central-NE Arabian Sea due to a net production via primarily active nitrate (NO3−) reduction and to a certain extent ammonia oxidation. Meanwhile, NO2− consumption via anammox, denitrification and dissimilatory nitrate/nitrite reduction to ammonium (NH4+) were hardly detectable in this region, though some loss to NO2− oxidation was predicted from modeled NO3− changes. No significant correlation was found between NO2− and N-loss rates (p>0.05). This discrepancy between NO2− accumulation and lack of active N-loss in the central-NE Arabian Sea is best explained by the deficiency of labile organic matter that is directly needed for further NO2− reduction to N2O, N2 and NH4+, and indirectly for the remineralized NH4+ required by anammox. Altogether, our data do not support the long-held view that NO2− accumulation is a direct activity indicator of N-loss in the Arabian Sea or other OMZs. Instead, NO2− accumulation more likely corresponds to long-term integrated N-loss that has passed the prime of high and/or consistent in situ activities.
Evaluation of virus reduction at a large-scale wastewater reclamation plant by detection of indigenous F-specific RNA bacteriophage genotypes

ABSTRACT Evaluating the reduction of virus load in water reclamation plants is important to ensuring the hygienic safety of the reclaimed water. A virus-spiking test is usually used to estimate virus reduction but is not practicable at large-scale plants. Thus, we evaluated virus reduction by ultrafiltration (UF) plus ultraviolet (UV) irradiation at a large-scale reclamation plant (1000 m3/d) by quantifying indigenous F-specific RNA bacteriophages (FRNAPHs). To detect the infectious FRNAPH, we used both plaque assay and integrated culture–reverse-transcription polymerase chain reaction combined with the most probable number assay, which can detect infectious FRNAPH genotypes. For comparison, we determined reductions of indigenous FRNAPHs and spiked MS2 at a small-scale pilot plant (10 m3/d) at the same time. Reductions by UF were not significantly different among the bacteriophages at pilot plants. This result suggests that indigenous bacteriophages could be used for evaluating virus reduction by UF at large-scale plants. Indigenous Genotype I (GI) FRNAPH showed the highest UV resistance, followed by GII, GIII, and GIV. The resistance of GI-FRNAPH was equivalent to that of spiked MS2. The reduction of the total infectious FRNAPHs determined by plaque assay was affected by the predominant FRNAPH genotype, presumably because of their different UV resistances. Our results reveal that indigenous GI-FRNAPH can be a good alternative indicator to spiked MS2 in view of virus reduction during water reclamation. The reclaimed water from our large-scale reclamation plant could be used for irrigation because the expected reduction (6.3 log10) of indigenous GI-FRNAPH achieved the Title 22 (>5 log10).
The Assessment of the Integrated Antioxidant System of the Body in the Course of Radon Therapy: A Pilot Study

Introduction The sources of Reactive Oxidative Species (ROS) in the organism are the respiratory processes occurring in cells catalyzed by different enzymes. Operation of ROS is balanced by antioxidants, the compounds; although present in low concentrations, they significantly inhibit the degree of oxidation of particular molecules. The Aim of the Study The aim of this study was to assess the changes in the integrated antioxidant system under the influence of radon therapy in osteoarthritis patients. Material and Methods Observation included 35 patients suffering from degenerative joints and disc disease (mean age 56.5 years) undergoing radon water therapy and control group that consisted of 15 osteoarthritis patients (mean age 54.2) without contact with radon water. Before therapy and after 18 days of treatment, serum total antioxidant status (TAS) was assessed with the use of standard colorimetric assay. Results In the study group, we observed trends to increase TAS concentration, whereas, in the control group, TAS concentration was decreasing. Conclusions (1) Radon waters treatment influenced the level of TAS of osteoarthritis patients treated with the radon water. (2) The change in TAS concentrations in the study group may be the result of low doses of ionizing radiation, but further studies on larger patient's groups are demanded. This study is registered with number NCT03274128.