Miracle-dz/UniFAR-FTUs huggingface dataset:
Volumetric assessment of individual thalamic nuclei in patients with drug-naïve, first-episode major depressive disorder

Introduction Despite the previous inconsistent findings of structural and functional abnormalities of the thalamus in patients with major depressive disorder (MDD), the disruption of the thalamic nuclei in the pathophysiology of this disorder has not yet been adequately studied. Therefore, we investigated the volumetric changes of thalamic subregions and their nuclei in drug-naïve, first-episode MDD patients. We also investigated the association between HAM-D scores, a clinical scale frequently used to evaluate the severity of depression and thalamic nuclei volumes in MDD patients. Methods This study included 76 drug-naïve MDD patients and an equal number of healthy subjects. Magnetic resonance imaging (MRI) data were obtained using a 3T MR system and thalamic nuclei volumes were evaluated using FreeSurfer ver.7. 11. The volumetric differences were compared by one-way analysis of covariance (ANCOVA) and to ensure that effects were not accounted for by other factors, age, sex, and ETICV variables were included as covariates. Results We observed significant volume reductions of the left whole thalamus (p < 0.003) and several thalamic nuclei mostly on the left side in the MDD group compared with healthy controls (HCs). Furthermore, we have revealed weak negative correlations between several thalamic nuclei volumes and HAM-D total and subscale scores. Discussion This is the first research study to investigate alterations of the various thalamic nuclei volumes in MDD patients compared with HCs. Moreover, we first analyzed the association between individual thalamic nuclei volumes and HAM-D subscale scores. Though our study may be restricted at certain levels, especially by the demographic difference between the two groups, they possibly contribute at a preliminary level to understanding the thalamic structural changes at its subregions in patients with drug-naïve, first-episode MDD.
Measurement and Prediction of Droplet Entrainment in Inclined Liquid–Liquid Flow by PLIF Method

Inclined liquid–liquid two-phase flows widely exist in petroleum, chemical, and other important industrial processes. The study of droplet entrainment in inclined flow is of great significance for investigating the heat/mass transfer between phases and optimizing the industrial production processes. In this study, a planar laser-induced fluorescence (PLIF) system is designed to visualize the inclined liquid–liquid flows. The silicone oil (organic phase) and water/glycerol mixture (aqueous phase) are used as the experimental media. The length and amplitude of the interfacial waves are derived from the flow visualizations. The relationship between the critical wavelengths and Froude number is explored to indicate the transition from stratified flow (ST) to stratified flow with mixing at the interface (ST&MI). The wave aspect ratio is derived to characterize the instability and breakage of the interfacial wave. Meanwhile, the entrainment ratios of dispersed droplets in the continuous phases are detected, and the effects of the flow rate and the interfacial shear on the droplet entrainment are studied. Finally, a physical model is developed to predict the droplet entrainment ratios based on the force balance analysis of the interfacial wave. In general, the developed model is effective in predicting the droplet entrainment ratio with mean absolute errors of 0.015 and 0.023 for the organic and aqueous droplets, respectively.
Vortex breakdown of compressible subsonic swirling flows in a finite-length straight circular pipe

A global analysis of steady states of inviscid compressible subsonic swirling flows in a finite-length straight circular pipe is developed. A nonlinear partial differential equation for the solution of the flow stream function is derived in terms of the inlet flow specific total enthalpy, specific entropy and circulation functions. The equation reflects the complicated thermo–physical interactions in the flows. Several types of solutions of the resulting nonlinear ordinary differential equation for the columnar case together with a flow force condition describe the outlet state of the flow in the pipe. These solutions are used to form the bifurcation diagram of steady compressible flows with swirl as the inlet swirl level is increased at a fixed inlet Mach number. The approach is applied to two profiles of inlet flows, solid-body rotation and the Lamb–Oseen vortex, both with a uniform axial velocity and temperature. The computed results provide for each inlet flow profile theoretical predictions of the critical swirl levels for the appearance of vortex breakdown states as a function of the inlet Mach number, suggesting that the results are robust for a variety of inlet swirling flows. The analysis sheds light on the dynamics of compressible flows with swirl and vortex breakdown, and shows the delay in the appearance of breakdown with increase of the inlet axial flow Mach number in the subsonic range of operation. The present theory is limited to axisymmetric dynamics of swirling flows in pipes where the wall boundary layer is thin and attached and does not interact with the flow in the bulk.
Combining a Direct and Indirect Training Approach for Cross-Domain Competences: The Case of the Course “Pedagogy for Psychotherapists”

In psychology programs, students should acquire both domain-specific knowledge and cross-domain competences important for later practice (e.g., multiple document literacy). Typically, such competences are trained directly in courses explicitly devoted to them or indirectly in courses on psychological topics that require them without systematically teaching and training them (e.g., when reading multiple texts about a topic). To exploit the advantages of both direct and indirect training approaches, we combined them in a new psychology course in which students were taught domain-specific knowledge on pedagogy and psychotherapy, and they were trained in the competence facets of (a) epistemic beliefs, (b) multiple document literacy, and (c) argumentative thinking. The direct training took a tried-and-tested example-based learning approach. A central element of the indirect training consisted of course assessments requiring the application of these three competences to the contents about pedagogy and psychotherapy. The combined training approach led to significant increases in declarative knowledge, advanced epistemic beliefs, and greater self-efficacy in implementing strategies relating to multiple document literacy and argumentative thinking. This approach can be adapted to accommodate different psychological content areas or different cross-domain competences.
Emergence and genomic analysis of a novel sublineage of bovine ephemeral fever virus in Southwest China

Introduction Bovine ephemeral fever virus (BEFV), belonging to the genus Ephemerovirus under the family Rhabdoviridae, is the etiological cause for the bovine ephemeral fever (BEF) in cattle and water buffalo. Methods In this study, we report recent BEF outbreaks in Southwest China and sequence the complete genome sequence of one BEFV isolate BEFV/CQ1/2022. Results and Discussion Comparative genomic analyses between BEFV/CQ1/2022 and isolates available in GenBank revealed remarkable inter-isolate divergence. Meanwhile, the sequence divergence was related to the evolutionary relationships and geographical distribution of the isolates. Phylogenetic analysis indicated that the global BEFV isolates can be divided into 4 distinct lineages. The East Asia lineage was the most diverse and could be subdivided into 4 sublineages. Notably, BEFV/CQ1/2022 and other 10 recent isolates from Mainland China were found to be clustered in sublineage 2. Additionally, recombination analysis provided evidence of BEFV recombination among East Asian isolates for the first time. Taken together, a novel sublineage of the East Asian BEFV emerged in Southwest China, and large divergence and potential recombination among BEFV strains were investigated in this study, which may improve understanding of BEFV epidemiology and evolution.
Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study

Genome divergence by repeat proliferation and/or loss is a process that plays a crucial role in species evolution. Nevertheless, knowledge of the variability related to repeat proliferation among species of the same family is still limited. Considering the importance of the Asteraceae family, here we present a first contribution towards the metarepeatome of five Asteraceae species. A comprehensive picture of the repetitive components of all genomes was obtained by genome skimming with Illumina sequence reads and by analyzing a pool of full-length long terminal repeat retrotransposons (LTR-REs). Genome skimming allowed us to estimate the abundance and variability of repetitive components. The structure of the metagenome of the selected species was composed of 67% repetitive sequences, of which LTR-REs represented the bulk of annotated clusters. The species essentially shared ribosomal DNA sequences, whereas the other classes of repetitive DNA were highly variable among species. The pool of full-length LTR-REs was retrieved from all the species and their age of insertion was established, showing several lineage-specific proliferation peaks over the last 15-million years. Overall, a large variability of repeat abundance at superfamily, lineage, and sublineage levels was observed, indicating that repeats within individual genomes followed different evolutionary and temporal dynamics, and that different events of amplification or loss of these sequences may have occurred after species differentiation.
A mesoscale gravity wave event observed during CCOPE. III - Wave environment and probable source mechanisms

Abstract Synoptic and special mesoscale observations taken during the Cooperative Convective Precipitation Experiment (CCOPE) are used to describe the multiscale environment of a gravity wave event, understand the wave-environment interactions that led to the development of severe thunderstorms, and asses possible wave-generation mechanisms. The storms formed sequentially as a packet of gravity waves propagated across a stationary thunderstorm outflow boundary. Convection developed most rapidly in that part of the mesonetwork in which existed the combination of relatively high parcel buoyant energy, weak restraining inversion, strong storm downdraft potential, and substantial vertical wind shear (associated with a mesoscale jet streak). Synoptic-scale analysis reveals that the waves were excited north of a stationary front and within the right exit region of the jet streak as it approached a stationary ridge in the 300 mb height field. Strong indications of unbalanced flow were diagnosed within the gravit.
MicroRNA-155 and Disease-Related Immunohistochemical Parameters in Cutaneous Melanoma

Cutaneous melanoma is a severe and life-threatening form of skin cancer with growing incidences. While novel interventions have improved prognoses for these patients, early diagnosis of targeted treatment remains the most effective approach. MicroRNAs have grown to good use as potential biomarkers for early detection and as targets for treatment. miR-155 is well-studied for its role in tumor cell survival and proliferation in various tissues, although its role in melanoma remains controversial. In silico data analysis was performed in the dbDEMC v.3 to identify differentially expressed miRNA. We validated gene targets in melanoma using TarBase v8.0 and miRPath v3.0 and determined protein-protein interactions of the target genes. One hundred forty patients (age range 21–90 years) with cutaneous melanoma who underwent resection were included. Molecular assessment using Real-Time RT-qPCR, clinicopathological associations, and a literature review for the different roles of miR-155 in melanoma were performed. Analysis of the dbDEMC reveals controversial findings. While there is evidence of upregulation of miR-155 in primary and metastatic melanoma samples, others suggest decreased expression in later-stage melanoma and cases with brain metastasis. miR-155 has been overexpressed in prior cases of melanoma and precancerous lesions, and it was found to be dysregulated when compared to benign nevi. While miR-155 expression was associated with favorable outcomes in some studies, others showed an association with metastasis. Patients with high levels of miR-155 also noted reduction after receiving anti-PD-1 treatment, correlated with more prolonged overall survival. In our patient’s cohort, 22.9% relapsed during treatment, and 45% developed recurrence, associated with factors such as lymph node infiltration, high mitotic index, and positive staining for CD117. Although overall analysis revealed miR-155 downregulation in melanoma specimens compared to non-cancer tissues, increased expression of miR-155 was associated with cases of superficial spreading melanoma subtype (p = 0.005) and any melanoma with a high mitotic rate (p = 0.010). The analysis did not identify optimum cutoff values to predict relapse, recurrence, or mortality. In conclusion, miR-155 could have, in part, a potential prognostic utility in cutaneous melanoma. Further mechanistic studies are required to unravel the multifunctional role of miR-155 in melanoma.
Asymptotic Properties of Conditional Maximum‐Likelihood Estimators

The problem of obtaining consistent estimates for structural parameters in the presence of infinitely many incidental parameters was discussed first by Neyman and Scott (1948). In this paper a maximum-likelihood method based on the conditional distribution given minimal sufficient statistics for the incidental parameters is suggested. It is proved that conditional maximumlikelihood estimates in the regular case are consistent and asymptotically normally distributed with a simple asymptotic variance. The efficiency problem of this new estimator is discussed in particular with respect to some situations with ancillary information.
Novel Biomarkers for Inflammatory Bowel Disease and Colorectal Cancer: An Interplay between Metabolic Dysregulation and Excessive Inflammation

Persistent inflammation can trigger altered epigenetic, inflammatory, and bioenergetic states. Inflammatory bowel disease (IBD) is an idiopathic disease characterized by chronic inflammation of the gastrointestinal tract, with evidence of subsequent metabolic syndrome disorder. Studies have demonstrated that as many as 42% of patients with ulcerative colitis (UC) who are found to have high-grade dysplasia, either already had colorectal cancer (CRC) or develop it within a short time. The presence of low-grade dysplasia is also predictive of CRC. Many signaling pathways are shared among IBD and CRC, including cell survival, cell proliferation, angiogenesis, and inflammatory signaling pathways. Current IBD therapeutics target a small subset of molecular drivers of IBD, with many focused on the inflammatory aspect of the pathways. Thus, there is a great need to identify biomarkers of both IBD and CRC, that can be predictive of therapeutic efficacy, disease severity, and predisposition to CRC. In this study, we explored the changes in biomarkers specific for inflammatory, metabolic, and proliferative pathways, to help determine the relevance to both IBD and CRC. Our analysis demonstrated, for the first time in IBD, the loss of the tumor suppressor protein Ras associated family protein 1A (RASSF1A), via epigenetic changes, the hyperactivation of the obligate kinase of the NOD2 pathogen recognition receptor (receptor interacting protein kinase 2 [RIPK2]), the loss of activation of the metabolic kinase, AMP activated protein kinase (AMPKα1), and, lastly, the activation of the transcription factor and kinase Yes associated protein (YAP) kinase, that is involved in proliferation of cells. The expression and activation status of these four elements are mirrored in IBD, CRC, and IBD-CRC patients and, importantly, in matched blood and biopsy samples. The latter would suggest that biomarker analysis can be performed non-invasively, to understand IBD and CRC, without the need for invasive and costly endoscopic analysis. This study, for the first time, illustrates the need to understand IBD or CRC beyond an inflammatory perspective and the value of therapeutics directed to reset altered proliferative and metabolic states within the colon. The use of such therapeutics may truly drive patients into remission.
Asymmetry of the pelvis in Polish young adults

Introduction Symmetry is one of the criteria of correct body posture in upright position. The spatial positioning of the pelvic girdle is crucial to it. Functional and structural asymmetries within the lumbo-pelvic-hip complex can have a significant influence on the structure and functions of many human body organs and systems. The aim of the study was to present the results of inclinometer measurements of selected landmarks of the pelvic girdle in young adults aged 19–29. Methods The analysis of occurrence of spatial pelvic asymmetry was based on the authors’ original, clinical classification and the significance of the body mass and height for the analyzed asymmetries. The inclinometer measurements of the selected landmarks of the pelvic girdle were performed in a sample consisting of 300 young individuals. Then, the occurrences of the spatial asymmetry of the pelvis were analyzed based on the authors’ own clinical classification using alignment symmetry of the iliac crests, the anterior superior iliac spines and the trochanters major as a criterion. All study subjects with asymmetry <1 degree were treated as those with a symmetrical pelvis. Results The significance of gender, body mass and height for the analyzed asymmetries was assessed. Symmetric positioning of the iliac crests was observed in only 32% of the respondents. The iliac crest depression on the left side was more frequently observed – in 41% of the respondents. This occurred more often in women (44%) than in men (38%). In the group of women, the rotated pelvis was the most often observed (39.4%) asymmetry, while for men, it was the oblique pelvis (40%). More detailed analysis by pelvic asymmetry subtypes showed their statistical differentiation between women and men (p < 0.0001). Analysis of moderate rotation of the pelvis for men, were reported slightly higher values but these differences were not statistically significant (p = 0.253). Women, in turn, showed slightly higher mean values but here too, the differences were not statistically significant (p = 0.245). Discussion Asymmetries in the pelvis area are common; they were observed in less than three-quarters of the examined population. Oblique pelvis was found in less than a quarter of women and in more than one-third men with the predominant structural asymmetries. Rotated pelvis was observed in more than one-third of women and men with dominating functional asymmetries. There were no linear correlations between the body mass and height, and the angle of asymmetries.
Evaluation of ultrasonic C-scan attenuation image

Temporal averaging and homomorphic processing, which extract the local ultrasonic wavelet and estimate the attenuation coefficient, have been incorporated into C-scan imaging to generate and attenuation map. The variation of this map displays changes in the scattering cross section and in the absorption of materials. These processing schemes are implemented into an integrated software package designed to yield a high resolution C-scan attenuation image. Experimental results have shown that for a composite sample with fatigue damage caused by compression, the C-scan attenuation map provides an improved image of the damaged area over the conventional peak detection scheme. The benchmark of image quality (i.e., average pixel value of the damaged area over average pixel value of the nondamaged area) indicates that the C-scan attenuation map outperforms the peak-echo C-scan by a factor higher than two to one. <<ETX>>
The linear stability of oscillatory Poiseuille flow in channels and pipes

The linear stability of confined, periodic, parallel fluid flows is examined. The flow fields considered consist of a steady pressure gradient-driven velocity field combined with a purely oscillatory component generated by either an oscillatory pressure gradient or by harmonically oscillating bounding surfaces. Plane channel and circular pipe geometries are studied and all possible combinations of the steady and oscillatory flow components investigated. Neutral stability curves and critical conditions for instability are computed for a selection of steady–unsteady velocity ratios, channel half-widths and pipe radii. The results obtained confirm previous investigations into the effects of small amounts of periodic modulation on the linear stability of the underlying steady flow, but provide much more comprehensive information on the linear stability regions of unsteady parallel flows in channels and pipes.
Reduced microwave loss in trenched superconducting coplanar waveguides

Reducing the contribution of all sources of microwave loss is important for increasing coherence times in superconducting qubits. In this paper we investigate reducing the loss by systematically removing Si substrate material from the gap region in titanium nitride coplanar waveguides fabricated on intrinsic Si substrates. By exploiting the radial dependence of the etch rate in a parallel plate reactive ion etcher, otherwise identical coplanar waveguides with only the Si gaps etched to varying depth, i.e., trenched, were created in a single TiN film within a single processing step. Measurements at these multiple depths permit the study of the loss reduction in isolation to the unintentional effects caused by any single processing step. When comparing the loss from all trench depths we found that the high power loss was similar, but in the single photon limit the loss was reduced by a factor of two for deeper trenches in agreement with predictions from finite element analysis.
Bicyclist Performance on a Multiuse Trail

Bicyclist crossing time from a full stop was measured using video recording equipment at 16 diverse trail-roadway intersections (two to six lanes, stop or signal controlled, divided or undivided) of the Pinellas Trail in Pinellas County, Florida. A total of 442 bicyclists (single individuals or randomly selected individuals from a group) were timed. The cruising speed of 65 bicyclists was also determined. A linear regression model was fit to the time and crossing-distance data. A linear regression was also fit to eight 85th percentile crossing-time points that were calculated from grouped raw data. Using kinematic physics, in which bicycle acceleration and intersection crossing velocity are variables, a theoretical equation was derived to predict bicyclist crossing time for any distance. This derived equation is a linear function of distance, so the regression coefficients could then be used to estimate bicyclist crossing velocity and acceleration on the Pinellas Trail. These estimated values for bicyclist acceleration and intersection crossing velocity compare favorably with the scant available data from foreign and domestic sources. Thus, the crossing-time prediction equation can be a useful tool when designing intersections for bicyclists, with application in signal timing and crossing-sight distance calculations.
On the optimal design of k-out-of-n:G subsystems

For a k-out-of-n:G subsystem, the mathematical determination of the most economical number of components in the subsystem is sought. Optimal values of k (for fixed n) and n (for fixed k), which minimize the mean total cost of k-out-of-n:G subsystems, are given. A numerical example illustrates the results. >