Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthesis and Characterization of Chemically Sprayed Cu2FeSnS4 (CFTS) Thin Films: The Effect of Substrate Temperature

In this study, Cu2FeSnS4 (CFTS) thin films were deposited on glass substrates at different temperatures of 250, 300, 350, 400, and 450 °C using the chemical pyrolysis technique. This work aimed to study the effect of substrate temperature on film properties. The film's structural properties were obtained via X-ray diffraction, Raman spectroscopy, and Field Emission Scanning Electron Microscopy (FESEM). The UV-Vis spectrum determined the optical properties; and the electrical properties were obtained through observation of the Hall effect. Analysis of XRD pattern showed that the CFTS thin films have a tetragonal structure with a main peak corresponding to the direction (112). Results of Raman spectroscopy displayed a unique peak at 318 cm-1, suggesting a quaternary compound of CFTS. The FESEM tests confirmed the presence of nanoparticles of various shapes and sizes. The CFTS films have a band gap of 1.77-1.92 eV and an absorption coefficient in the visible spectrum region higher than 104 cm-1, which confirms their use as an active layer in solar cells. The mea measurements of the Hall effect of the CFTS thin films showed a p-type conductivity for all films, with the maximum charge carrier density and mobility occurring at 400 °C, making them suitable for photovoltaic applications.
Patient-centered care or osteopathic manipulative treatment as mediators of clinical outcomes in patients with chronic low back pain

Abstract Context Patient-centered care is often considered a characteristic of osteopathic medicine, in addition to the use of osteopathic manipulative treatment (OMT) in such musculoskeletal conditions as low back pain. Objectives This study aimed to determine if patient-centered care or OMT are mediators of the clinical outcomes of osteopathic medicine in patients with chronic low back pain. Methods A comparative effectiveness study was conducted within the Pain Registry for Epidemiological, Clinical, and Interventional Studies and Innovation (PRECISION Pain Research Registry). Eligible patients met the diagnostic criteria recommended by the National Institutes of Health Task Force on Research Standards for Chronic Low Back Pain and completed four consecutive quarterly encounters between April 2016 and November 2020. The Consultation and Relational Empathy instrument for patient-centered care was used at the baseline encounter and OMT use was measured at the final encounter. The clinical outcome measures included low back pain intensity on a numerical rating scale (NRS) from 0 to 10, back-related functioning on the Roland-Morris Disability Questionnaire (RMDQ), and pain impact on the National Institutes of Health Minimum Dataset for Chronic Low Back Pain (NIH-MDS). A parallel multiple mediator model was used to compute the direct and indirect effects of osteopathic medicine in achieving each of the three clinical outcomes. Results The 404 study patients had a mean age of 52.2 years (standard deviation, 13.1 years) and 288 (71.3%) were female. The 88 (21.8%) patients treated by osteopathic physicians reported more favorable scores for patient-centered care (mean, 41.3; 95% CI 39.0–43.5) than patients treated by allopathic physicians (mean, 38.0; 95% CI 36.8–39.3) (p=0.02). Fifty-six (63.6%) patients treated by osteopathic physicians used OMT. The age- and sex-adjusted outcomes for patients of osteopathic vs. allopathic physicians across all four encounters were: mean, 5.4; 95% CI 5.0–5.7 vs. mean, 5.9; 95% CI 5.7–6.1 on the NRS for pain intensity (p=0.01); mean, 11.3; 95% CI 10.1–12.6 vs. mean, 14.0; 95% CI 13.3–14.7 on the RMDQ for back-related disability (p<0.001); and mean, 26.8; 95% CI 24.9–28.7 vs. mean, 30.1; 95% CI 29.1–31.1 on the NIH-MDS for pain impact (p=0.002). Patient-centered care did not mediate any outcome of osteopathic medicine, whereas OMT mediated better outcomes in low back pain intensity. Conclusions This appears to be the first study to simultaneously address both patient-centered care and OMT as potential mediators of the effect of osteopathic medicine in treating chronic pain. Patient-centered care did not mediate the effects of osteopathic medicine and OMT only mediated outcomes relating to low back pain intensity. More research is needed to identify other aspects of osteopathic medicine that mediate its beneficial effects in patients with chronic low back pain.
A turbulence dissipation inhomogeneity scaling in the wake of two side-by-side square prisms

Abstract We experimentally study how the turbulent energy dissipation rate scales in the cross-stream direction of turbulent wake flows generated by two side-by-side square prisms. We consider three different such turbulent flows with gap ratios $G/H=1.25$, $2.4$ and $3.5$, where $G$ is the distance between the prisms and $H$ is the prism width. These three flows have a very different dynamics, inhomogeneities and large-scale features. The measurements were taken with a multi-camera particle image velocimetry system at several streamwise locations between $2.5H$ and $20H$ downstream of the prisms. After removing the large-scale most energetic coherent structures, the normalised turbulence dissipation coefficient $C'_{\epsilon }$ of the remaining incoherent turbulence is found to scale as $C'_{\epsilon } \sim (\sqrt {Re_{L}}/Re'_{\lambda })^{3/2}$ along the highly inhomogeneous cross-stream direction for all streamwise locations tested in all three flows and for all three inlet Reynolds numbers considered; $Re'_{\lambda }$ and $Re_{L}$ are, respectively, a Taylor length-based and an integral length-based Reynolds number of the remaining incoherent turbulence.
Distributed vortex-wave interactions: the relation of self-similarity to the attached eddy hypothesis

Abstract A large-Reynolds-number asymptotic reduction of the Navier–Stokes equations capable of describing a locally periodic vortex-wave array and the associated large-scale variation of the mean-shear velocity field first suggested in Hall (J. Fluid Mech., vol. 850, 2018, pp. 46–82) is extended. The sustaining process of the locally periodic coherent structures is based on the vortex-wave interaction theory of Hall & Smith (J. Fluid Mech., vol. 227, 1991, 641–666), wherein two-dimensional roll–streak fields are supported by localised nonlinear self-interactions of three-dimensional waves that are largest in size within critical layers of the streak field. The variation of the mean velocity is made possible by incorporating a slow change to the mean profile using a Wentzel–Kramers–Brillouin-type approach. As the first extension, we demonstrate that the local structure corresponds to the asymptotic limit of computations in a shearing box. A variety of solutions with different symmetry properties are found via the hybrid numerical asymptotic approach of Blackburn, Hall & Sherwin (J. Fluid Mech. vol. 721, 2013, 58–85). Moreover, some solutions show generic flow features such as uniform momentum zones and spatial intermittency known to occur in near-wall turbulent boundary layers. We extend the vortex-wave interaction array theory to show that, in addition to a Reynolds-averaged-Navier–Stokes-type relationship between the large-scale vertical variation of the mean flow and local roll–streak scale, a higher-order analysis gives a second constraint on the slow-scale dynamics. Those constraints are used for the first time to derive the logarithmic law of the wall through a closed asymptotic analysis of self-similar local coherent structures, consistent with the attached eddy hypothesis.
Cost‐effectiveness of insertable cardiac monitors for diagnosis of atrial fibrillation in cryptogenic stroke in Australia

Detection of atrial fibrillation (AF) is required to initiate oral anticoagulation (OAC) after cryptogenic stroke (CS). However, paroxysmal AF can be difficult to diagnose with short term cardiac monitoring. Taking an Australian payer perspective, we evaluated whether long‐term continuous monitoring for 3 years with an insertable cardiac monitor (ICM) is cost‐effective for preventing recurrent stroke in patients with CS.
Diagnostic Criteria and LI‐RADS for Hepatocellular Carcinoma

Most hepatocellular carcinomas (HCCs) are hypervascular tumors and occur in cirrhotic liver. These unique histological features of HCC lead to sensitive and specific imaging features and allow multiphasic computed tomography (CT) or magnetic resonance imaging (MRI) to be used as an initial diagnostic test. The CT/MRI findings are interpreted using imaging diagnostic algorithms, namely, Liver Imaging Reporting and Data System (LIRADS), for HCC diagnosis. Liver biopsy could be considered for a definite diagnosis when the imaging results remain equivocal or patients do not have cirrhosis. In this article, we discuss the diagnostic criteria of HCC and the role of LIRADS for imaging diagnosis of HCC. DiaGnOsis OF HCC
Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related microalgae

The Arctic Ocean is being impacted by warming temperatures, increasing freshwater and highly variable ice conditions. The microalgal communities underpinning Arctic marine food webs, once thought to be dominated by diatoms, include a phylogenetically diverse range of small algal species, whose biology remains poorly understood. Here, we present genome sequences of a cryptomonad, a haptophyte, a chrysophyte, and a pelagophyte, isolated from the Arctic water column and ice. Comparing protein family distributions and sequence similarity across a densely-sampled set of algal genomes and transcriptomes, we note striking convergences in the biology of distantly related small Arctic algae, compared to non-Arctic relatives; although this convergence is largely exclusive of Arctic diatoms. Using high-throughput phylogenetic approaches, incorporating environmental sequence data from Tara Oceans, we demonstrate that this convergence was partly explained by horizontal gene transfers (HGT) between Arctic species, in over at least 30 other discrete gene families, and most notably in ice-binding domains (IBD). These Arctic-specific genes have been repeatedly transferred between Arctic algae, and are independent of equivalent HGTs in the Antarctic Southern Ocean. Our data provide insights into the specialized Arctic marine microbiome, and underlines the role of geographically-limited HGT as a driver of environmental adaptation in eukaryotic algae.
HIV-1 drug resistance profiling using amino acid sequence space cartography

Human immunodeficiency virus (HIV) drug resistance is a global healthcare issue. The emergence of drug resistance demands treatment adaptation. Computational methods predicting the drug resistance profile from genomic data of HIV isolates are advantageous for monitoring drug resistance in patients. Yet, the currently existing computational methods for drug resistance prediction are either not suitable for complex mutational patterns in emerging HIV strains or lack interpretability of prediction results which is of paramount importance in clinical practice. Hence, to overcome these limitations, new approaches for the HIV drug resistance prediction combining high accuracy and interpretability are required. In this work, a new methodology for the analysis of protein sequence data based on the application of generative topographic mapping was developed and applied for HIV drug resistance profiling. It allowed achieving high accuracy of resistance predictions and intuitive interpretation of prediction results. The developed approach was successfully applied for the prediction of HIV resistance towards protease, reverse-transcriptase and integrase inhibitors and in-depth analysis of HIV resistance-inducing mutation patterns. Hence, it can serve as an efficient and interpretable tool to suggest optimal treatment regimens.
Functional characterization of two variants in the mitochondrial topoisomerase gene TOP1MT that impact regulation of the mitochondrial genome

TOP1MT encodes a mitochondrial topoisomerase that is important for mtDNA regulation, and that is involved in mitochondrial replication, transcription and translation. Two variants predicted to affect TOP1MT function (V1 - R198C and V2 - V338L) were identified by exome sequencing of a newborn with hypertrophic cardiomyopathy. As no pathogenic TOP1MT variants had been confirmed previously, we characterized these variants for their ability to rescue several TOP1MT functions in knockout cells. Consistent with these TOP1MT variants contributing to the patient phenotype, comprehensive characterization suggests that both variants had impaired activity. Critically, neither variant was able to restore steady state levels of mitochondrial-encoded proteins, nor reduced oxidative phosphorylation when re-expressed in TOP1MT knockout cells. However, the two variants behaved differently in some respects. While the V1 variant was better at restoring transcript levels, the V2 variant was able to restore mtDNA copy number and replication. These findings suggest that the different TOP1MT variants affect distinct TOP1MT functions. Altogether, these findings begin to provide insight into the many roles that TOP1MT plays in the maintenance and expression of the mitochondrial genome, and how impairments in this important protein may lead to human pathology.
Genome-wide protein-DNA interaction site mapping using a double strand DNA-specific cytosine deaminase

DNA–protein interactions (DPIs) are central to such fundamental cellular processes as transcription and chromosome maintenance and organization. The spatiotemporal dynamics of these interactions dictate their functional consequences; therefore, there is great interest in facile methods for defining the sites of DPI within cells. Here, we present a general method for mapping DPI sites in vivo using the double stranded DNA-specific cytosine deaminase toxin DddA. Our approach, which we term DddA-sequencing (3D-seq), entails generating a translational fusion of DddA to a DNA binding protein of interest, inactivating uracil DNA glycosylase, modulating DddA activity via its natural inhibitor protein, and DNA sequencing for genome-wide DPI detection. We successfully applied this method to three Pseudomonas aeruginosa transcription factors that represent divergent protein families and bind variable numbers of chromosomal locations. 3D-seq offers several advantages over existing technologies including ease of implementation and the possibility to measure DPIs at single-cell resolution.
Large differences in carbohydrate degradation and transport potential in the genomes of lichen fungal symbionts

Lichen symbioses are generally thought to be stabilized by the transfer of fixed carbon compounds from a photosynthesizing unicellular symbiont to a fungus. In other fungal symbioses, carbohydrate subsidies correlate with genomic reductions in the number of genes for plant cell wall-degrading enzymes (PCWDEs), but whether this is the case with lichen fungal symbionts (LFSs) is unknown. We predicted genes encoding carbohydrate-active enzymes (CAZymes) and sugar transporters in 17 existing and 29 newly sequenced genomes from across the class Lecanoromycetes, the largest extant clade of LFSs. Despite possessing lower mean numbers of PCWDE genes compared to non-symbiont Ascomycota, all LFS genomes possessed a robust suite of predicted PCWDEs. The largest CAZyme gene numbers, on par with model species such as Penicillium, were retained in genomes from the subclass Ostropomycetidae, which are found in crust lichens with highly specific ecologies. The lowest numbers were in the subclass Lecanoromycetidae, which are symbionts of many generalist macrolichens. Our results suggest that association with phototroph symbionts does not in itself result in functional loss of PCWDEs and that PCWDE losses may have been driven by adaptive processes within the evolution of specific LFS lineages. The inferred capability of some LFSs to access a wide range of carbohydrates suggests that some lichen symbioses may augment fixed CO2 with carbon from external sources. Significance Lichen symbioses are considered self-contained autotrophic systems in which the total carbon economy is the sum of phototroph-fixed CO2, supplied to a fungus as sugars. In other fungal-plant symbioses, such as mycorrhizae, plant-derived sugar subsidies are associated with loss of plant cell wall-degrading enzymes (PCWDEs). We compared PCWDE inventories in 46 genomes from the largest group of lichen fungal symbionts (LFSs) with non-symbionts from across Ascomycota. We found that despite lower overall gene numbers, all LFSs retain PCWDEs, and some possess gene numbers and functional diversity on par with non-symbionts. Our results suggest that association with a phototroph does not necessarily result in PCWDE loss, and some lichens may obtain carbon from sources other than CO2 fixation.
Both consumptive and non-consumptive effects of predators impact mosquito populations and have implications for disease transmission

Predator-prey interactions influence prey traits through both consumptive and non-consumptive effects, and variation in these traits can shape vector-borne disease dynamics. Meta-analysis methods were employed to generate predation effect sizes by different categories of predators and mosquito prey. This analysis showed that multiple families of aquatic predators are effective in consumptively reducing mosquito survival, and that the survival of Aedes, Anopheles, and Culex mosquitoes is negatively impacted by consumptive effects of predators. Mosquito larval size was found to play a more important role in explaining the heterogeneity of consumptive effects from predators than mosquito genus. Mosquito survival and body size were reduced by non-consumptive effects of predators, but development time was not significantly impacted. In addition, Culex vectors demonstrated predator avoidance behavior during oviposition. The results of this meta-analysis suggest that predators limit disease transmission by reducing both vector survival and vector size, and that associations between drought and human West Nile virus cases could be driven by the vector behavior of predator avoidance during oviposition. These findings are likely to be useful to infectious disease modelers who rely on vector traits as predictors of transmission.
The CHK-2 antagonizing phosphatase PPM-1.D regulates meiotic entry via catalytic and non-catalytic activities

The transition from the stem cell/progenitor fate to meiosis is mediated by several redundant post-transcriptional regulatory pathways in C. elegans. Interfering with all three branches causes tumorous germlines. SCFPROM-1 comprises one branch and mediates a scheduled degradation step at entry into meiosis. prom-1 mutants show defects in timely initiation of events of meiotic prophase I, resulting in high rates of embryonic lethality. Here, we identify the phosphatase PPM-1.D/Wip1 as crucial substrate for PROM-1. We report that PPM-1.D antagonizes CHK-2 kinase, a key regulator for meiotic prophase initiation e.g., DNA double strand breaks, chromosome pairing and synaptonemal complex formation. We propose that PPM-1.D controls the amount of active CHK-2 by both catalytic and non-catalytic activities, where strikingly the non-catalytic regulation seems to be crucial at meiotic entry. PPM-1.D sequesters CHK-2 at the nuclear periphery and programmed SCFPROM-1 mediated degradation of PPM-1.D liberates the kinase and promotes meiotic entry.
Multi-Run Concrete Autoencoder to Identify Prognostic lncRNAs for 12 Cancers

Long non-coding RNA plays a vital role in changing the expression profiles of various target genes that leads to cancer development. Thus, identifying prognostic lncRNAs related to different cancers might help in developing cancer therapy. To discover the critical lncRNAs that can identify the origin of different cancers, we proposed to use the state-of-the-art deep learning algorithm Concrete Autoencoder (CAE) in an unsupervised setting, which efficiently identifies a subset of the most informative features. However, CAE does not identify reproducible features in different runs due to its stochastic nature. We proposed a multi-run CAE (mrCAE) to identify a stable set of features to address this issue. The assumption is that a feature appearing in multiple runs carries more meaningful information about the data under consideration. The genome-wide lncRNA expression profiles of 12 different types of cancers, a total of 4,768 samples available in The Cancer Genome Atlas (TCGA), were analyzed to discover the key lncRNAs. The lncRNAs identified by multiple runs of CAE were added to the final list of key lncRNAs, which are capable of identifying 12 different cancers. Our results showed that mrCAE performs better in feature selection than single-run CAE, standard autoencoder (AE), and other state-of-the-art feature selection techniques. This study discovered a set of top-ranking 128 lncRNAs that could identify the origin of 12 different cancers with an accuracy of 95%. Survival analysis showed that 76 of 128 lncRNAs have the prognostic capability in differentiating high- and low-risk groups of patients in different cancers. The proposed mrCAE outperformed AE, which select latent features and were thought to be the best tools for dimensionality reduction. By selecting actual features instead of pseudo-features, mrCAE can be valuable for precision medicine. The identified prognostic lncRNAs (this work), mRNAs, miRNAs, and DNA methylated genes (future work) can lead to biomarkers and therapies for different cancers.
Artificial mimicry of seasonal transcriptome dynamics in Arabidopsis thaliana reveals short- and long-term responses to environmental conditions

Plants must respond to various environmental factors that change seasonally. In a previous study, seasonally oscillating genes were identified by a massive time-series transcriptome analysis in a wild population of Arabidopsis halleri ssp. gemmifera, a sister species of Arabidopsis thaliana.To analyze the function of these seasonally oscillating genes, we established an experimental system to mimic seasonal expression trends using A. thaliana. Arabidopsis thaliana plants were cultured under conditions that mimicked average monthly temperatures and daylengths in a “smart growth chamber mini,” a hand-made low-cost small chamber.Under different short-term incubations, the seasonal trends of 1627 seasonally oscillating genes were mimicked. These seasonally oscillating genes had varying temporal responsiveness (constant, transient, and incremental). Our findings suggest that plants perceive and integrate information about environmental stimuli in the field by combining seasonally oscillating genes with temporal responsiveness.