Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracellular vesicles secreted by triple‐negative breast cancer stem cells trigger premetastatic niche remodeling and metastatic growth in the lungs

Tumor secreted extracellular vesicles (EVs) are potent intercellular signaling platforms. They are responsible for the accommodation of the premetastatic niche (PMN) to support cancer cell engraftment and metastatic growth. However, complex cancer cell composition within the tumor increases also the heterogeneity among cancer secreted EVs subsets, a functional diversity that has been poorly explored. This phenomenon is particularly relevant in highly plastic and heterogenous triple‐negative breast cancer (TNBC), in which a significant representation of malignant cancer stem cells (CSCs) is displayed. Herein, we selectively isolated and characterized EVs from CSC or differentiated cancer cells (DCC; EVsCSC and EVsDCC, respectively) from the MDA‐MB‐231 TNBC cell line. Our results showed that EVsCSC and EVsDCC contain distinct bioactive cargos and therefore elicit a differential effect on stromal cells in the TME. Specifically, EVsDCC activated secretory cancer associated fibroblasts (CAFs), triggering IL‐6/IL‐8 signaling and sustaining CSC phenotype maintenance. Complementarily, EVsCSC promoted the activation of α‐SMA+ myofibroblastic CAFs subpopulations and increased the endothelial remodeling, enhancing the invasive potential of TNBC cells in vitro and in vivo. In addition, solely the EVsCSC mediated signaling prompted the transformation of healthy lungs into receptive niches able to support metastatic growth of breast cancer cells.
Analyzing RNA‐Protein Interactions by Cross‐Link Rates and CLIP‐seq Libraries

UV cross‐linking‐based methods are the most common tool to explore in vivo RNA‐protein interactions. UV cross‐linking enables the freezing of direct interactions in the cell, which can then be mapped by high‐throughput sequencing through a family of methods termed CLIP‐seq. CLIP‐seq measures the distribution of cross‐link events by purifying a protein of interest and sequencing the covalently bound RNA fragments. However, there are disagreements and ambiguities as to which proteins are RNA‐binding proteins and what interactions are significant as all proteins contact all RNAs at some frequency. Here we describe a protocol for both determining RNA‐protein interactions through a combination of RNA library preparation and the measurement of absolute cross‐link rates, which helps determine what proteins are RNA‐binding proteins and what interactions are significant. This protocol, comprising an updated form of the easyCLIP protocol, describes guidelines for RNA library preparation, oligo and protein standard construction, and the measurement of cross‐link rates. These methods are easily visualizable through their fluorescent labels and can be adapted to study RNA‐binding properties of both functional, high affinity RNA‐binding proteins, and the accidental RNA interactions of non‐RNA‐binding proteins. © 2023 Wiley Periodicals LLC.
The Effectiveness of Utilizing HRV Indices as a Predictor of ACFT Performance Outcomes.

BACKGROUND The Army Combat Fitness Test (ACFT) is a performance assessment used by the U.S. Army to assess a cadet's strength, endurance, and agility with a series of six events to ensure that cadets are combat ready. Heart rate variability (HRV) is an instrument that measures cardiac autonomic modulation and has been incorporated to predict the performance of athletes in daily training and competition since acute bouts of exercise alter HRV variables. PURPOSE To assess the applicability of using HRV to predict ACFT score performance outcomes in cadets. METHODS Fifty army cadets (n = 36 male; n = 14 female; age = 20.60 ± 3.61 years; height = 173.34 ± 10.39 cm; body mass = 76.33 ± 14.68 kg; body fat percentage = 17.58 ± 5.26%) completed the ACFT and reported for HRV assessment. HRV assessment had the participant lay supine for 5 minutes, and traditional time and frequency domain variables were assessed. A Pearson's correlation and multiple linear regressions were run. RESULTS HRV time and frequency domains were not significantly correlated in linear regression models except the stress index (SI) and the 2-mile run (2MR). The standing power throw and sprint drag carry were significantly correlated with traditional HRV variables. CONCLUSIONS HRV was not a predictor of ACFT performance for individual events or overall ACFT. The SI presented predictive properties only for 2MR, with no other significant correlations between HRV variables with standing power throw and sprint drag carry. The SI ability to predict 2MR performance outcome via HRV is a promising tool to assess army cadet performance and recovery.
Patient-reported outcome and quality of life research policy: Japan Clinical Oncology Group (JCOG) policy

Abstract Assessments of patient-reported outcomes and health-related quality of life in cancer clinical trials have been increasingly emphasized recently because patient and public involvement in cancer treatment development has been promoted by regulatory authorities and academic societies. To assess patient experiences during and after cancer treatment, there is interest in implementing patient-reported outcome and health-related quality of life assessments into cancer clinical trials. The Japan Clinical Oncology Group quality of life ad hoc committee previously created a version of the Quality of Life Assessment Policy in 2006. Recently, there has been increasing demand from Japan Clinical Oncology Group researchers to assess patient-reported outcome/health-related quality of life in clinical trials. Although guidelines are available regarding planning and reporting clinical trials that include patient-reported outcome/health-related quality of life as an endpoint, there are still issues regarding the lack of consensus on standardized methods for analysing and interpreting the results. Hence, it was considered necessary to reorganize the Japan Clinical Oncology Group patient-reported outcome/quality of life research committee and to revise the former patient-reported outcome/quality of life research policy to promote patient-reported outcome/health-related quality of life research in future Japan Clinical Oncology Group trials. The purpose of this Japan Clinical Oncology Group patient-reported outcome/quality of life research policy is to define patient-reported outcome/health-related quality of life research and provide guidelines for including patient-reported outcome/health-related quality of life as an endpoint in Japan Clinical Oncology Group trials.
Ultrasound‐guided cutaneous nerve chemo‐ablation for severe access site neuropathic pain—A case report

Neuropathic pain at the cannulation site is challenging, both for the patient and the dialysis team. We present a case of a middle‐aged man on chronic hemodialysis, who developed excruciating pain at the cannulation area without incident, limiting his dialysis sessions. Multidisciplinary collaboration allowed identification of the cutaneous nerve—the inferior lateral cutaneous nerve of the arm, relaying his pain. Subsequent ultrasound‐guided phenol chemoablation resulted in the complete resolution of his pain and allowed continued use of the well‐functioning fistula for dialysis.
Changing Osteoporosis Knowledge and Behaviors Through Structured Education

Osteoporosis is a silent disease that is associated with enormous cost and can lead to disability and death. We identified that individuals who have sustained a fracture from a fall are often unaware of osteoporosis risk factors and have a knowledge deficit regarding osteoporosis. Therefore, they do not receive the proper treatment. An evidence-based practice project was completed using “pre-post” intervention tools with an educational intervention to measure osteoporosis knowledge and self-efficacy in individuals hospitalized with a fragility fracture. A convenience sample of 25 participants 50 years and older, who were admitted with a fragility fracture, received targeted education. Descriptive and comparative statistics were used for comparison of pre- and postintervention data. Hospitalized osteoporotic individuals have a gap in knowledge regarding the existence of osteoporosis. Healthcare workers can improve knowledge and self-efficacy by offering osteoporosis education for these individuals.
Power of Some Tests for Umbrella Alternatives in the Multi‐Sample Location Problem

For the c‐sample location problem with umbrella alternatives we present a modification of a test proposed by BARLOW et al. (1972) for trend alternatives. Furthermore, we study a rank version of this modified test following a proposal of CONOVER and IMAN (1981). These tests are compared with the test of MACK and WOLFE (1978) and with some so called Mack‐Wolfe‐type tests in which the Mann‐Whitney statistics are replaced by other two‐sample linear rank statistics. The comparison is referred to the power of the test assuming a broad range of distributions. It will be shown firstly, that for nonnormal data there are tests with higher power than the modification of the test of Barlow et al. and secondly, that for a special distribution there is a Mack‐Wolfe‐type test which is more efficient than is competitors. We also consider the case of unknown peak.
Drought‐induced increase in tree mortality and corresponding decrease in the carbon sink capacity of Canada's boreal forests from 1970 to 2020

Canada's boreal forests, which occupy approximately 30% of boreal forests worldwide, play an important role in the global carbon budget. However, there is little quantitative information available regarding the spatiotemporal changes in the drought‐induced tree mortality of Canada's boreal forests overall and their associated impacts on biomass carbon dynamics. Here, we develop spatiotemporally explicit estimates of drought‐induced tree mortality and corresponding biomass carbon sink capacity changes in Canada's boreal forests from 1970 to 2020. We show that the average annual tree mortality rate is approximately 2.7%. Approximately 43% of Canada's boreal forests have experienced significantly increasing tree mortality trends (71% of which are located in the western region of the country), and these trends have accelerated since 2002. This increase in tree mortality has resulted in significant biomass carbon losses at an approximate rate of 1.51 ± 0.29 MgC ha−1 year−1 (95% confidence interval) with an approximate total loss of 0.46 ± 0.09 PgC year−1 (95% confidence interval). Under the drought condition increases predicted for this century, the capacity of Canada's boreal forests to act as a carbon sink will be further reduced, potentially leading to a significant positive climate feedback effect.
Theoretical models of the electrical discharge machining process. II. The anode erosion model

As a second in a series of theoretical models for the electrical discharge machining (EDM) process, an erosion model for the anode material is presented. As with our point heat‐source model in the previous article, the present model also accepts power rather than temperature as the boundary condition at the plasma/anode interface. A constant fraction of the total power supplied to the gap is transferred to the anode. The power supplied is assumed to produce a Gaussian‐distributed heat flux on the surface of the anode material. Furthermore, the area upon which the flux is incident is assumed to grow with time. The model is capable of showing, via the determined migrating melt fronts, the rapid melting of the anodic material as well as the subsequent resolidification of the material foation from plasma dynamics modeling could improve substantially our results.
A definitive version of the local two-radii theorem

Various classes of functions with zero integrals over all balls of a fixed radius are studied. For functions in such classes a description in the form of a series in special functions is obtained and a uniqueness theorem is proved. These results make it possible to solve completely the problem of existence of a non-trivial function with zero integrals over all balls of radius assuming either of two given values.
Serum positivity of serum anti‐tissue transglutaminase immunoglobulin A antibodies in Japanese children with inflammatory bowel disease

Serum anti‐tissue transglutaminase immunoglobulin A antibody (tTG‐IgA) is a screening test for celiac disease (CeD). In recent years, there have several reports of combined inflammatory bowel disease (IBD) and CeD in children. The purposes of this study are to research the positivity of the tTG‐IgA antibody in Japanese children, and whether IBD and CeD co‐occur.
Asymptotic Efficiency of Minimum Variance Unbiased Estimators

Consider a regular $p$-dimensional exponential family such that either the distributions are concentrated on a lattice or they have a component whose $k$-fold convolution has a bounded density with respect to Lebesgue measure. Then, if a parametric function has an unbiased estimator, the minimum variance unbiased estimators are asymptotically equivalent to the maximum likelihood estimators; and, hence, are asymptotically efficient. Examples are given to show that a condition like the above is needed to obtain the asymptotic equivalence.
Effect of matrine in MAC-T cells and their transcriptome analysis: A basic study

Matrine, an alkaloid derived from herbal medicine, has a wide range of biological activities, including antibacterial. Matrine was toxic to multiple cells at high concentrations. Bovine mammary epithelial cells (MAC-T) could be used as model cells for cow breast. Matrine was a feasible option to replace antibiotics in the prevention or treatment of mastitis against the background of prohibiting antibiotics, but the safe concentration of matrine on MAC-T cells and the mechanism of action for matrine at different concentrations were still unclear. In this study, different concentrations of matrine (0.5, 1, 1.5, 2, 2.5 and 3 mg/mL) were used to treat MAC-T cells for various time periods (4, 8, 12, 16 and 24 h) and measure their lactic dehydrogenase (LDH). And then the optimal doses (2 mg/mL) were chosen to detect the apoptosis at various time periods by flow cytometry and transcriptome analysis was performed between the control and 2 mg/mL matrine-treated MAC-T cells for 8 hours. The results showed that matrine was not cytotoxic at 0.5 mg/mL, but it was cytotoxic at 1~3 mg/mL. In addition, matrine induced apoptosis in MAC-T cells at 2 mg/mL and the proportion of apoptosis cells increases with time by flow cytometry. RNA-seq analysis identified 1645 DEGs, 676 of which were expressed up-regulated and 969 were expressed down-regulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated the following pathways were linked to matrine-induced toxicity and apoptosis, including cytokine-cytokine receptor interaction pathway, viral protein interaction with cytokine and cytokine receptor, P53 and PPAR pathway. We found 7 DEGs associated with matrine toxicity and apoptosis. This study would provide a basis for the safety of matrine in the prevention or treatment of mastitis.
Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties

We outline details about an extension of the tight-binding (TB) approach to improve total energies, forces, and transferability. The method is based on a second-order expansion of the Kohn-Sham total energy in density-functional theory (DFT) with respect to charge density fluctuations. The zeroth order approach is equivalent to a common standard non-self-consistent (TB) scheme, while at second order a transparent, parameter-free, and readily calculable expression for generalized Hamiltonian matrix elements may be derived. These are modified by a self-consistent redistribution of Mulliken charges (SCC). Besides the usual ``band structure'' and short-range repulsive terms the final approximate Kohn-Sham energy additionally includes a Coulomb interaction between charge fluctuations. At large distances this accounts for long-range electrostatic forces between two point charges and approximately includes self-interaction contributions of a given atom if the charges are located at one and the same atom. We apply the new SCC scheme to problems where deficiencies within the non-SCC standard TB approach become obvious. We thus considerably improve transferability.
One year later: digitalized higher education in pandemic times. An international study of higher education faculty’s response

Abstract The paper describes the international research conducted in collaboration between the University of Padova, University of North Texas, and Windesheim University of Applied Sciences. The study explores how higher education faculty involved in professionalizing courses for the educational area perceive the pandemic-induced transition to digitalized education (DE), after one year of experience with it. This paper introduces the second phase of a research study that began as early as spring 2020, with an online survey distributed worldwide. It seeks to investigate possible changes after one year of digitalized education related to (1) perceptions of institutional support and professional training offered; (2) potential and challenges of DE; and (3) professional intentions for future uses of DE. Details on the instrument’s reliability and structure will also be provided. We are exploring how the DE is changing teachers’ routines and whether these changes are paving the way for collaborative, reflective, and student-centred approaches that could have long-term consequences. This is to help focus future training pathways to better support teachers in teaching effectively and efficiently for learning, both in times of crisis and in times of normalcy.
Zero-shot Hand-held Objects Recognition Based on Global Feature Relationships: Zero-shot Hand-held Objects Recognition Based on Global Feature Relationships

In recent years, there have been frequent terrorist attacks both at home and abroad. Accurate detection of a wide variety of handheld objects is a problem that needs an urgent solution. To better exploit the effects of handheld movements on handheld object recognition, this paper proposes a zero-shot hand-held object recognition based on global feature relations that comprise two modules: an image processing module and a semantic relations module. The image processing module learns the visual classifier of the input image to obtain the classification weights. The semantic relations module propagates structural knowledge through semantic learning through graph convolution operations on the knowledge graph and obtains the classification weights for all categories. Results indicate that this method significantly improves the recognition rate compared to traditional handheld object recognition methods.
Custom High-Performance Vector Code Generation for Data-Specific Sparse Computations

Sparse computations, such as sparse matrix-dense vector multiplication, are notoriously hard to optimize due to their irregularity and memory-boundedness. Solutions to improve the performance of sparse computations have been proposed, ranging from hardware-based such as gather-scatter instructions, to software ones such as generalized and dedicated sparse formats, used together with specialized executor programs for different hardware targets. These sparse computations are often performed on read-only sparse structures: while the data themselves are variable, the sparsity structure itself does not change. Indeed, sparse formats such as CSR have a typically high cost to insert/remove nonzero elements in the representation. The typical use case is to not modify the sparsity during possibly repeated computations on the same sparse structure. In this work, we exploit the possibility to generate a specialized executor program dedicated to the particular sparsity structure of an input matrix. It creates opportunities to remove indirection arrays and synthesize regular, vectorizable code for such computations. But, at the same time, it introduces challenges in code size and instruction generation, as well as efficient SIMD vectorization. We present novel techniques and extensive experimental results to efficiently generate SIMD vector code for data-specific sparse computations, and study the limits in terms of applicability and performance of our techniques compared to state-of-practice high-performance libraries like Intel MKL.
GPU Adaptive In-situ Parallel Analytics (GAP)

Despite the popularity of in-situ analytics in scientific computing, there is only limited work to date on in-situ analytics for simulations running on GPUs. Notably, two unaddressed challenges are 1) performing memory-efficient in-situ analysis on accelerators and 2)automatically choosing the processing resources and suitable data representation for a given query and platform. This paper addresses both problems. First, GAP makes several new contributions toward making bitmap indices suitable, effective, and efficient as a compressed data summary structure for the GPUs - this includes introducing a layout structure, a method for generating multi-attribute bitmaps, and novel techniques for bitmap-based processing of major operators that comprise complex data analytics. Second, this paper presents a performance modeling methodology, aiming to predict the placement (i.e., CPU or GPU) and the data representation choice (summarization or original) that yield the best performance on a given configuration. Our extensive evaluation of complex in-situ queries and real-world simulations shows that with our methods, analytics on GPU using bitmaps almost always outperforms other options, and the GAP performance model predicts the optimal placement and data representation for most scenarios.
Report on the 1st Workshop on Audio Collection Human Interaction (AudioCHI 2022) at CHIIR 2022

This is a report from the AudioCHI 2022 workshop which was organised in conjunction with the CHIIR conference in March 2022. The workshop was organised to bring together researchers in spoken content retrieval with expertise on human computer interaction in information access to examine opportunities and challenges for advancing technologies for search and interaction with spoken content. The workshop was originally planned to be a full day event, but due to pandemic-imposed travelling constraints, it was instead held as a virtual half day event to accommodate time zone differences for participants. Date: 14 March, 2022. Website: https://speechretrievalworkshop.github. io/.
Limiting Interconnect Heating in Power-Driven Physical Synthesis

Current technology trend of VLSI chips includes sub-10 nm nodes and 3D ICs. Unfortunately, due to significantly increased Joule heating in these technologies, interconnect reliability has become a significant casualty. In this paper, we explore how interconnect power dissipation (of CV2/2 per logic transition) and thus heating can be effectively constrained during a power-optimizing physical synthesis (PS) flow that applies three different PS transformations: cell sizing, Vth assignment and cell replication; the latter is particularly useful for limiting interconnect heating. Other constraints considered are timing, slew and cell fanout load. To address this multi-constraint power-optimization problem effectively, we consider the application of the aforementioned three transforms simultaneously (as opposed to sequentially in some order) as well as simultaneously across all cells of the circuit using a novel discrete optimization technique called discretized network flow (DNF). We applied our algorithm to ISPD-13 benchmark circuits: the ISPD-13 competition was for power optimization for cell-sizing and Vth assignment transforms under timing, slew and cell fanout load constraints; to these we added the interconnect heating constraint and the cell replication transform---a much harder transform to engineer in a simultaneous-consideration framework than the other two. Results show the significant efficacy of our techniques.