Miracle-dz/UniFAR-FTUs huggingface dataset:
KIF26B-AS1 Regulates TLR4 and Activates the TLR4 Signaling Pathway to Promote Malignant Progression of Laryngeal Cancer

Laryngeal cancer is one of the highest incidence, most prevalently diagnosed head and neck cancers, making it critically necessary to probe effective targets for laryngeal cancer treatment. Here, real-time quantitative reverse transcription PCR (qRT-PCR) and western blot analysis were used to detect gene expression levels in laryngeal cancer cell lines. Fluorescence in situ hybridization (FISH) and subcellular fractionation assays were used to detect the subcellular location. Functional assays encompassing Cell Counting Kit-8 (CCK-8), 5-ethynyl-2’-deoxyuridine (EdU), transwell and wound healing assays were performed to examine the effects of target genes on cell proliferation and migration in laryngeal cancer. The in vivo effects were proved by animal experiments. RNA-binding protein immunoprecipitation (RIP), RNA pulldown and luciferase reporter assays were used to investigate the underlying regulatory mechanisms. The results showed that KIF26B antisense RNA 1 (KIF26B-AS1) propels cell proliferation and migration in laryngeal cancer and regulates the toll-like receptor 4 (TLR4) signaling pathway. KIF26B-AS1 also recruits FUS to stabilize TLR4 mRNA, consequently activating the TLR4 signaling pathway. Furthermore, KIF26B-AS1 plays an oncogenic role in laryngeal cancer via upregulating TLR4 expression as well as the FUS/TLR4 pathway axis, findings which offer novel insight for targeted therapies in the treatment of laryngeal cancer patients.
Safety of paclitaxel-coated devices in the femoropopliteal arteries: A systematic review and meta-analysis

Background Clinical benefit of paclitaxel-coated devices for patients with peripheral arterial disease has been confirmed in randomized controlled trials (RCTs). A meta-analysis published in 2018 identified late mortality risk over a long follow-up period due to use of paclitaxel-coated devices in the femoropopliteal arteries, which caused enormous controversy and debates globally. This study aims to further evaluate the safety of paclitaxel-coated devices by incorporating the most recently published data. Methods We searched for candidate studies in PubMed (MEDLINE), Scopus, EMBASE (Ovid) online databases, government web archives and international cardiovascular conferences. Safety endpoints of interest included all-cause mortality rates at one, two and five years and the risk ratio (RR) was used as the summary measure. The primary analysis was performed using random-effects models to account for potential clinical heterogeneity. Findings Thirty-nine RCTs including 9164 patients were identified. At one year, the random-effects model yielded a pooled RR of 1.06 (95% CI [0.87, 1.29]) indicating no difference in short-term all-cause deaths between the paclitaxel and control groups (crude mortality, 4.3%, 214/5025 versus 4.5%, 177/3965). Two-year mortality was reported in 26 RCTs with 382 deaths out of 3788 patients (10.1%) in the paclitaxel arm and 299 out of 2955 patients (10.1%) in the control arm and no association was found between increased risk of death and usage of paclitaxel-coated devices (RR 1.08, 95% CI [0.93, 1.25]). Eight RCTs recorded all-cause deaths up to five years and a pooled RR of 1.18 (95% CI [0.92, 1.51]) demonstrated no late mortality risk due to use of paclitaxel-coated devices (crude mortality, paclitaxel 18.2%, 247/1360 versus control 15.2%, 122/805). Conclusions We found no significant difference in either short- or long-term all-cause mortalities between patients receiving paclitaxel-coated and uncoated devices. Further research on the longer-term safety of paclitaxel usage (e.g., 8- or 10-year) is warranted. Registration PROSPERO, CRD42021246291.
Whole-Genome Sequencing and Annotation of Fibrobacter succinogenes HC4, Isolated from the Horse Cecum

Fibrobacter succinogenes is a major cellulolytic bacterial species living in the large intestines of herbivores. This study reports the genome sequencing, assembly, and annotation of F. succinogenes HC4 (DSM 33656), a strain isolated from horse cecal contents. The genome comprised a total of 3.74 Mbp, with a G+C content of 48.96%. ABSTRACT Fibrobacter succinogenes is a major cellulolytic bacterial species living in the large intestines of herbivores. This study reports the genome sequencing, assembly, and annotation of F. succinogenes HC4 (DSM 33656), a strain isolated from horse cecal contents. The genome comprised a total of 3.74 Mbp, with a G+C content of 48.96%.
A morphological study of the shape of the corpus callosum in normal, schizophrenic and bipolar patients

Abnormalities in the morphology of the corpus callosum have been found to be involved in cognitive impairments or abnormal behaviour in patients with mental disorders such as schizophrenia and bipolar disorder. The present study investigated morphological shape differences of the corpus callosum in a large cohort of 223 participants between normal, schizophrenic and bipolar patients on MRI scans, CT scans and cadaver samples. Healthy samples were compared to a mental disorder population sample to determine morphological shapes variations associated with schizophrenia and bipolar disorder. Landmark‐based methodology was used to contour the corpus callosum shape that served as standard positions to allow for radial and thickness partitioning in order to determine shape variations within the specific localised anatomical sections of the corpus callosum. Shape analysis was performed using Ordinary Procrustes averaging and superimposing landmarks to define an average landmark position for the specific regions of the corpus callosum. No significant global shape differences were found between the different mental disorders. Schizophrenia and bipolar shapes differed mostly in the genu‐rostrum, posterior body, isthmus and splenium. Sample group comparisons yielded significant differences between all groups and global measurement parameters and in various sub‐regions. The findings of the present study suggest that the corpus callosum in schizophrenia and bipolar differs significantly compared to healthy controls, specifically in the anterior body and isthmus for schizophrenia and only in the isthmus for bipolar disorder. Shape changes in these regions may possibly, in part, be responsible for the symptoms and cognitive impairments observed in schizophrenia and bipolar disorder.
Digital Spectro-Correlator System for the Atacama Compact Array of the Atacama Large Millimeter/submillimeter Array

We have developed an FX-architecture digital spectro-correlator for the Atacama Compact Array (ACA) of the Atacama Large Millimeter/submillimeter Array. The correlator is able to simultaneously process four pairs of dual polarization signals with the bandwidth of 2 GHz, which are received by up to sixteen antennas. It can calculate auto- and cross-correlation spectra including cross-polarization in all combinations of all the antennas, and output correlation spectra with flexible spectral configuration such as multiple frequency ranges and multiple frequency resolutions. Its spectral dynamic range is estimated to be higher than 10^4 relative to Tsys from processing results of thermal noise for eight hours with a typical correlator configuration. The sensitivity loss is also confirmed to be 0.9 % with the same configuration. In this paper, we report the detailed design of the correlator and the verification results of the developed hardware.
Atomic layer deposition of Zr-sandwiched ZnO thin films for transparent thermoelectrics

Atomic layer deposited (ALD) transparent thermoelectric materials enable the introduction of energy harvesting and sensing devices onto surfaces of various shapes and sizes in imperceptible manner. Amongst these materials, ZnO has shown promising results in terms of both thermoelectric and optical characteristics. The thermoelectric performance of ZnO can be further optimized by introducing extrinsic doping, to the realization of which ALD provides excellent control. Here, we explore the effects of sandwiching of ZrO2 layers with ZnO on glass substrates. The room-temperature thermoelectric power factor is maximised at 116μW m−1 K−2 with samples containing a 2% nominal percentage of ZrO2. The addition of ZrO2 layers is further shown to reduce the thermal conductivity, resulting in a 20.2% decrease from the undoped ZnO at 2% doping. Our results contribute to increasing the understanding of the effects of Zr inclusion in structural properties and growth of ALD ZnO, as well as the thermal and thermoelectric properties of Zr-doped ZnO films in general.
The effect of hadron irradiation on the electrical properties of particle detectors made from various silicon materials

Les detecteurs au silicium, dont l'utilisation est prevue dans les futures experiences de physique des hautes energies (lhc au cern) devront soutenir un tres haut niveau de radiation. La defaillance des detecteurs plus exposes est attendue apres quelques annees d'operations. Un grand interet est pourtant devolue a l'etude des changements provoques par les radiations dans les detecteurs et a l'amelioration de la resistance aux radiations de ceux-ci. L'introduction d'impuretes dans le cristal de silicium peut influencer la tenue aux radiations. Les impuretes forment des complexes avec les defauts primaires induits par les radiations. Ces complexes peuvent etre electriquement actifs ou inactifs. Dans ce dernier cas, les defauts n'affectent pas les proprietes electriques du detecteur. Une grande concentration d'impuretes qui forment des complexes inactifs peut reduire la vitesse de degradation des detecteurs. Les plus importants parametres electriques qui changent en fonction de la fluence sont la densite effective de dopage, le courant inverse et l'efficacite de collection de charge. Cette these presente une etude detaillee des changements de ces parametres en fonction de la fluence hadronique et du temps apres les irradiations, pour des cristaux de silicium contenant differentes teneurs en impuretes. Le role de l'o, c et sn sur la tenue aux radiations est evalue. L'etude a ete faite en utilisant comme detecteur de simples diodes (p#+-n-n#+). Certains changements des caracteristiques electriques de ces diodes apres des forts niveaux d'irradiation ne peuvent pas etre expliques par la theorie de la jonction p-n d'un semi-conducteur. Un modele de distribution du champ electrique est propose pour expliquer les proprietes de collection de charge des detecteurs irradies.
Experimental Methods for Generating Two-Dimensional Quantum Turbulence in Bose-Einstein Condensates

Bose–Einstein condensates of dilute gases are well-suited for investigations of vortex dynamics and turbulence in quantum fluids, yet there has been little experimental research into the approaches that may be most promising for generating states of two-dimensional turbulence in these systems. Here we give an overview of techniques for generating the large and disordered vortex distributions associated with two-dimensional quantum turbulence. We focus on describing methods explored in our Bose–Einstein condensation laboratory, and discuss the suitability of these methods for studying various aspects of two-dimensional quantum turbulence. We also summarize some of the open questions regarding our own understanding of these mechanisms of two-dimensional quantum turbulence generation in condensates. We find that while these disordered distributions of vortices can be generated by a variety of techniques, further investigation is needed to identify methods for obtaining quasisteady-state quantum turbulence in condensates.
Three-Dimensional Modeling and Augmented Reality and Virtual Reality Simulation of Fiber Dissection of the Cerebellum and Brainstem

BACKGROUND: Surgeons must understand the complex anatomy of the cerebellum and brainstem and their 3-dimensional (3D) relationships with each other for surgery to be successful. To the best of our knowledge, there have been no fiber dissection studies combined with 3D models, augmented reality (AR), and virtual reality (VR) of the structure of the cerebellum and brainstem. In this study, we created freely accessible AR and VR simulations and 3D models of the cerebellum and brainstem. OBJECTIVE: To create 3D models and AR and VR simulations of cadaveric dissections of the human cerebellum and brainstem and to examine the 3D relationships of these structures. METHODS: Ten cadaveric cerebellum and brainstem specimens were prepared in accordance with the Klingler's method. The cerebellum and brainstem were dissected under the operating microscope, and 2-dimensional and 3D images were captured at every stage. With a photogrammetry tool (Qlone, EyeCue Vision Technologies, Ltd.), AR and VR simulations and 3D models were created by combining several 2-dimensional pictures. RESULTS: For the first time reported in the literature, high-resolution, easily accessible, free 3D models and AR and VR simulations of cerebellum and brainstem dissections were created. CONCLUSION: Fiber dissection of the cerebellum-brainstem complex and 3D models with AR and VR simulations are a useful addition to the goal of training neurosurgeons worldwide.
The natural language processing of radiology requests and reports of chest imaging: Comparing five transformer models’ multilabel classification and a proof-of-concept study

Background Radiology requests and reports contain valuable information about diagnostic findings and indications, and transformer-based language models are promising for more accurate text classification. Methods In a retrospective study, 2256 radiologist-annotated radiology requests (8 classes) and reports (10 classes) were divided into training and testing datasets (90% and 10%, respectively) and used to train 32 models. Performance metrics were compared by model type (LSTM, Bertje, RobBERT, BERT-clinical, BERT-multilingual, BERT-base), text length, data prevalence, and training strategy. The best models were used to predict the remaining 40,873 cases’ categories of the datasets of requests and reports. Results The RobBERT model performed the best after 4000 training iterations, resulting in AUC values ranging from 0.808 [95% CI (0.757–0.859)] to 0.976 [95% CI (0.956–0.996)] for the requests and 0.746 [95% CI (0.689–0.802)] to 1.0 [95% CI (1.0–1.0)] for the reports. The AUC for the classification of normal reports was 0.95 [95% CI (0.922–0.979)]. The predicted data demonstrated variability of both diagnostic yield for various request classes and request patterns related to COVID-19 hospital admission data. Conclusion Transformer-based natural language processing is feasible for the multilabel classification of chest imaging request and report items. Diagnostic yield varies with the information in the requests.
Study of paraquat-induced pulmonary fibrosis using biomimetic micro-lung chips

Paraquat (PQ) poisoning induces pulmonary fibrosis in vivo. The pathogenesis of pulmonary fibrosis is complex, which has prevented the development of specific treatments. Pulmonary fibrosis shows several characteristics including epithelial-mesenchymal transition (EMT), fibroblast activation, and extracellular matrix (ECM) deposition. To investigate pulmonary fibrosis, we designed a biomimetic multichannel micro-lung chip to imitate the in vivo interface between the lung epithelium and the lung interstitium. In our model, A549 (lung epithelial cells) and MRC-5 (fetal lung fibroblasts) cells were used to test the efficacy of our chip-based model. Rat tail type I collagen and hyaluronic acid were used to simulate ECM and to provide a 3D microenvironment. The micro-lung chips were cultured with PQ (0, 75, 150, 300, and 400 µM). The viability of A549 and MRC-5 cells significantly decreased with increasing PQ concentrations. There were significant changes in surfactant proteins C (SP-C), alpha smooth muscle actin protein (α-SMA), and vimentin protein levels during PQ-induced pulmonary fibrosis. SP-C levels were decreased in A549 cells, while those of α-SMA and vimentin were increased in A549 cells and MRC-5 cells treated with PQ in the micro-lung chip. We also designed a reference model without interaction between the lung epithelial cells and fibroblasts. Compared to the non-contact model, co-culturing A549 and MRC-5 cells in chips induced more severe EMT in A549 cells after treatment with 75 µM PQ and together defended against PQ-induced damage. Thus, our novel co-culture micro-lung chip that models the lung epithelium and interstitium may provide a new approach for studying lung fibrosis and will facilitate drug development.
LE-UDA: Label-Efficient Unsupervised Domain Adaptation for Medical Image Segmentation

While deep learning methods hitherto have achieved considerable success in medical image segmentation, they are still hampered by two limitations: (i) reliance on large-scale well-labeled datasets, which are difficult to curate due to the expert-driven and time-consuming nature of pixel-level annotations in clinical practices, and (ii) failure to generalize from one domain to another, especially when the target domain is a different modality with severe domain shifts. Recent unsupervised domain adaptation (UDA) techniques leverage abundant labeled source data together with unlabeled target data to reduce the domain gap, but these methods degrade significantly with limited source annotations. In this study, we address this underexplored UDA problem, investigating a challenging but valuable realistic scenario, where the source domain not only exhibits domain shift w.r. t. the target domain but also suffers from label scarcity. In this regard, we propose a novel and generic framework called “Label-Efficient Unsupervised Domain Adaptation” (LE-UDA). In LE-UDA, we construct self-ensembling consistency for knowledge transfer between both domains, as well as a self-ensembling adversarial learning module to achieve better feature alignment for UDA. To assess the effectiveness of our method, we conduct extensive experiments on two different tasks for cross-modality segmentation between MRI and CT images. Experimental results demonstrate that the proposed LE-UDA can efficiently leverage limited source labels to improve cross-domain segmentation performance, outperforming state-of-the-art UDA approaches in the literature.
Comparing two methods of regularization of the kinetic energy density

In this paper we will compare two different methods of regularizing the kinetic energy density for a massless scalar field in the presence of a static scalar potential. One method of regularization is to subtract the cosmological constant from the "naive" expression for the kinetic energy density. The other method is to use point split regularization. It is found that the two methods yield different results. The result obtained using point split regularization includes an extra ambiguous term.
Augmenting chemotherapy with low-dose decitabine through an immune-independent mechanism

The DNA methyltransferase inhibitor decitabine has classically been used to reactivate silenced genes and as a pretreatment for anticancer therapies. In a variation of this idea, this study explores the concept of adding low-dose decitabine (DAC) following administration of chemotherapy to bolster therapeutic efficacy. We find that addition of DAC following treatment with the chemotherapy agent gemcitabine improves survival and slows tumor growth in a mouse model of high-grade sarcoma. Unlike prior studies in epithelial tumor models, DAC did not induce a robust antitumor T cell response in sarcoma. Furthermore, DAC synergizes with gemcitabine independently of the immune system. Mechanistic analyses demonstrate that the combination therapy induces biphasic cell cycle arrest and apoptosis. Therapeutic efficacy was sequence dependent, with gemcitabine priming cells for treatment with DAC through inhibition of ribonucleotide reductase. This study identifies an apparently unique application of DAC to augment the cytotoxic effects of conventional chemotherapy in an immune-independent manner. The concepts explored in this study represent a promising paradigm for cancer treatment by augmenting chemotherapy through addition of DAC to increase tolerability and improve patient response. These findings have widespread implications for the treatment of sarcomas and other aggressive malignancies.
TOWARD A COMPREHENSIVE MODEL FOR FEEDBACK BY ACTIVE GALACTIC NUCLEI: NEW INSIGHTS FROM M87 OBSERVATIONS BY LOFAR, FERMI, AND H.E.S.S.

Feedback by active galactic nuclei (AGNs) appears to be critical in balancing radiative cooling of the low-entropy gas at the centers of galaxy clusters and in mitigating the star formation of elliptical galaxies. New observations of M87 enable us to put forward a comprehensive model for the physical heating mechanism. Low-frequency radio observations by LOFAR revealed the absence of fossil cosmic-ray (CR) electrons in the radio halo surrounding M87. This puzzle can be resolved by accounting for the CR release from the radio lobes and the subsequent mixing of CRs with the dense ambient intracluster gas, which thermalizes the electrons on a timescale similar to the radio halo age of 40 Myr. Hadronic interactions of similarly injected CR protons with the ambient gas should produce an observable gamma-ray signal in accordance with the steady emission of the low state of M87 detected by Fermi and H.E. S.S. Hence, we normalize the CR population to the gamma-ray emission, which shows the same spectral slope as the CR injection spectrum probed by LOFAR, thereby supporting a common origin. We show that CRs, which stream at the Alfvén velocity with respect to the plasma rest frame, heat the surrounding thermal plasma at a rate that balances that of radiative cooling on average at each radius. However, the resulting global thermal equilibrium is locally unstable and allows for the formation of the observed cooling multi-phase medium through thermal instability. Provided that CR heating balances cooling during the emerging “cooling flow,” the collapse of the majority of the gas is halted around 1 keV—in accordance with X-ray data. We show that both the existence of a temperature floor and the similar radial scaling of the heating and cooling rates are generic predictions of the CR heating model.
Comparing advance care planning between older adults with and without HIV

ABSTRACT We compared completion of advance directives (AD), designation of a healthcare proxy, and stage in the advance care planning process (pre-contemplation/contemplation, preparation/action) between older adults with (N = 110) and without (N = 50) HIV. Participants’ mean age was 61.3, most identified as male (82%) and sexual minorities (74%), were racially/ethnically diverse (44% white, 28% Latinx, 16% Black); 37% had an AD and 44% had a healthcare proxy. In adjusted logistic regressions, HIV− individuals had higher odds of being in preparation/action for having an AD (aOR: 2.6) and healthcare proxy (aOR: 3.6) compared to people living with HIV. Older age (aOR: 1.1) and having a sense of greater purpose in life (aOR: 2.1) were also positively associated with being in the preparation/action stage for having a healthcare proxy.