Miracle-dz/UniFAR-FTUs huggingface dataset:
Work‐efficient parallel union‐find

The incremental graph connectivity (IGC) problem is to maintain a data structure that can quickly answer whether two given vertices in a graph are connected, while allowing more edges to be added to the graph. IGC is a fundamental problem and can be solved efficiently in the sequential setting using a solution to the classical union‐find problem. However, sequential solutions are not sufficient to handle modern‐day large, rapidly‐changing graphs where edge updates arrive at a very high rate. We present the first shared‐memory parallel data structure for union‐find (equivalently, IGC) that is both provably work‐efficient (ie, performs no more work than the best sequential counterpart) and has polylogarithmic parallel depth. We also present a simpler algorithm with slightly worse theoretical properties, but which is easier to implement and has good practical performance. Our experiments on large graph streams with various degree distributions show that it has good practical performance, capable of processing hundreds of millions of edges per second using a 20‐core machine.
Prediction of next career moves from scientific profiles

Changing institution is a scientist's key career decision, which plays an important role in education, scientific productivity, and the generation of scientific knowledge. Yet, our understanding of the factors influencing a relocation decision is very limited. In this paper we investigate how the scientific profile of a scientist determines their decision to move (i.e., change institution). To this aim, we describe a scientist's profile by three main aspects: the scientist's recent scientific career, the quality of their scientific environment and the structure of their scientific collaboration network. We then design and implement a two-stage predictive model: first, we use data mining to predict which researcher will move in the next year on the basis of their scientific profile; second we predict which institution they will choose by using a novel social-gravity model, an adaptation of the traditional gravity model of human mobility. Experiments on a massive dataset of scientific publications show that our approach performs well in both the stages, resulting in a 85% reduction of the prediction error with respect to the state-of-the-art approaches.
Beneficial Effect of Renal Denervation on Ventricular Premature Complex Induced Cardiomyopathy

Background Frequent ventricular premature complexes (VPCs) can lead to the development of dilated cardiomyopathy and sudden cardiac death. Renal artery sympathetic denervation (RDN) may protect the heart from remodeling. This study aimed to investigate the effect of frequent VPCs on structural and electrical properties and whether RDN can protect the heart from remodeling. Methods and Results Eighteen rabbits were randomized to control (n=6), VPC (n=6), and VPC‐RDN (n=6) groups. Surgical and chemical RDNs were approached through bilateral retroperitoneal flank incisions in the VPC‐RDN group. Pacemakers were implanted to the left ventricular apex to produce 50% VPC burden for 5 weeks in the VPC and VPC‐RDN groups. In addition, ventricular myocardium was harvested for western blot and trichrome stain. Echocardiographic results showed left ventricular enlargement after 5‐week pacing in the VPC group, but not in the VPC‐RDN group, when compared to baseline. In biventricles, ion channel protein expressions of Nav1.5, Cav1.2, Kir2.1, and SERCA2 were similar among 3 groups. However, the degree of biventricular fibrosis was extensive in the VPC group, compared to the control and VPC‐RDN groups. Importantly, ventricular fibrillation inducibility was higher in the VPC group (41%) when comparing to the control (13%; P<0.05) and VPC‐RDN groups (13%; P<0.05), respectively. Conclusions Frequent VPCs are associated with the development of cardiac structural remodeling and high ventricular fibrillation inducibility. RDN prevents cardiac remodeling and the occurrence of ventricular arrhythmia through antifibrosis.
A pilot evaluation of an educational program that offers visualizations of cervical spine injuries: medical students’ self-efficacy increases by training

In this pilot study, a new method for visualization through imaging and simulation (VIS-Ed) for teaching diagnosis and treatment of cervical spine trauma was formatively evaluated. The aims were to examine if medical students’ self-efficacy would change by training using VIS-Ed, and if so these changes were related to how they evaluated the session, and the user interface (UI) of this program. Using a one-group, pre–post course test design 43 Swedish medical students (4th year, 17 males, 26 females) practiced in groups of three participants. Overall the practice and the UI were considered as positive experiences. They judged VIS-Ed as a good interactive scenario-based educational tool. All students’ self-efficacy increased significantly by training (p < 0.001). Spearman’s rank correlation tests revealed that increased self-efficacy was only associated with: how the session was compared to as expected (p < 0.007). Students’ self-efficacy increased significantly by training, but replication studies should determine if this training effect is gender-related.
Multi-Task Structured Prediction for Entity Analysis: Search-Based Learning Algorithms

Entity analysis in natural language processing involves solving multiple structured prediction problems such as mention detection, coreference resolution, and entity linking. We explore the space of search-based learning approaches to solve the problem of multi-task structured prediction (MTSP) in the context of entity analysis. In this paper, we study three different search architectures to solve MTSP problems that make different tradeoffs between speed and accuracy of training and inference. In all three architectures, we learn one or more scoring functions that employ both intra-task and inter-task features. In the “pipeline” architecture, which is the fastest, we solve different tasks one after another in a pipelined fashion. In the “joint” architecture, which is the most expensive, we formulate MTSP as a single-task structured prediction, and search the joint space of multi-task structured outputs. To improve the speed of joint architecture, we introduce two different pruning methods and associated learning techniques. In the intermediate “cyclic” architecture, we cycle through the tasks multiple times in sequence until there is no performance improvement. Results on two benchmark domains show that the joint architecture improves over the pipeline approach as well as the previous state-of-the-art approach based on graphical models. The cyclic architecture is faster than the joint approach and achieves competitive performance.
ACQR: acoustic quick response codes for content sharing on low end phones with no internet connectivity

In this paper we introduce Acoustic Quick Response codes to facilitate sharing between Interactive Voice Response (IVR) service users. IVRs are telephone-based, and similar to the world wide web in many aspects, but currently lack support for content sharing. Our approach uses 'audio codes' to let people share their call positions, and allows callers to hold their normal (low-end) handsets together to synchronise. The technique uses remote generation and recognition of audio codes to ensure that sharing is possible on any type of phone without the need for textual literacy or an internet connection. We begin by exploring existing user needs for sharing, then evaluate the technical robustness of our audio-based design. We demonstrate the value of the approach for voice service users over several separate studies--including an eight-month extended field deployment--then conclude with a discussion of future possibilities for such scenarios.
Global transcriptome-wide analysis of the function of GDDR in acute gastric lesions

Acute gastric lesions induced by stress are frequent occurrences in medical establishments. The gastric dramatic downrelated gene (GDDR) is a secreted protein, which is abundantly expressed in normal gastric epithelia and is significantly decreased in gastric cancer. In our previous study, it was found that GDDR aggravated stress-induced acute gastric lesions. However, the role of GDDR in acute gastric lesions remains to be fully elucidated. In the present study, RNA sequencing was performed in order to examine the gene expression profile regulated by GDDR in acute gastric lesions. The dataset comprised four stomach samples from wild-type (WT) mice and four stomach samples from GDDR-knockout mice. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to analyze the differentially-expressed genes (DEGs). Weighted correlation network analysis was used to identify clusters of highly correlated genes. Cytoscape was used to construct a protein-protein interaction network (PPI) of the DEGs. Based on the GO analysis, the upregulated DEGs were distinctly enriched in muscle contraction and response to wounding; and the downregulated DEGs were significantly enriched in the regulation of nitrogen compound metabolic process and regulation of RNA metabolic process. The results of the KEGG pathway analysis showed that the upregulated DEGs were enriched in ECM-receptor interaction and the signaling pathway of cGMP-PKG, and the downregulated DEGs were enriched in the renin-angiotensin system and glycerolipid metabolism. The co-expression network revealed a group of genes, which were associated with increased wound healing in the WT mice. Significant pathways were identified through the PPI network, including negative regulation of the signaling pathway of glucocorticoid receptor, regulation of cellular stress response, and regulation of hormone secretion. In conclusion, the present study improves current understanding of the molecular mechanism underlying acute gastric lesions and may assist in the treatment of gastric lesions.
Oxygen availability in the corrosion of reinforcements

The rate of steel corrosion in concrete structures is believed to be mainly controlled by the diffusion of dissolved oxygen through the concrete cover. Different techniques have been employed to measure the diffusion rate of this gas: either utilizing mechanical driving forces, natural diffusion or electrochemical forces. The Paper discusses results of oxygen flow through paste, mortar and concrete without admixtures, related to rebar corrosion and concrete resistivity. The results give information on the reliability of cathodic polarization to detect the O2 availability at the rebar surface, and confirm that the controlling variable is the humidity content in pores, which also influences the corrosion rate.
FindPrimaryPairs: An efficient algorithm for predicting element-transferring reactant/product pairs in metabolic networks

The metabolism of individual organisms and biological communities can be viewed as a network of metabolites connected to each other through chemical reactions. In metabolic networks, chemical reactions transform reactants into products, thereby transferring elements between these metabolites. Knowledge of how elements are transferred through reactant/product pairs allows for the identification of primary compound connections through a metabolic network. However, such information is not readily available and is often challenging to obtain for large reaction databases or genome-scale metabolic models. In this study, a new algorithm was developed for automatically predicting the element-transferring reactant/product pairs using the limited information available in the standard representation of metabolic networks. The algorithm demonstrated high efficiency in analyzing large datasets and provided accurate predictions when benchmarked with manually curated data. Applying the algorithm to the visualization of metabolic networks highlighted pathways of primary reactant/product connections and provided an organized view of element-transferring biochemical transformations. The algorithm was implemented as a new function in the open source software package PSAMM in the release v0.30 (https://zhanglab.github.io/psamm/).
A heterogeneous ensemble of trees

Decision Tree is a simple but popular machine learning algorithm. Although a single decision tree is not as accurate as other state-of-the-art classifiers, the performance can be significantly improved by combining the predictions of several decision trees i.e. by creating an ensemble of trees. In this paper, we study decision trees and their ensembles viz. Bagged Decision Trees, Random Forest, Extremely Randomized Trees, Rotation Forest, Gradient Boosted Trees and AdaBoosted Trees, and assess their performance on several UCI datasets. In addition, we propose a new ensemble method, Heterogeneous Ensemble of trees, and compare its performance with existing tree based classifiers. The heterogeneous ensemble is built with three different ensemble of trees (Random Forest, Rotation Forest, and Extremely Randomized Trees) with equal proportions to boost the diversity of the trees in the ensemble. A weightage scheme based on out-of-bag error is employed to combine the prediction of various trees for the final output prediction. Based on the experiments performed on several UCI datasets, the Heterogeneous Ensemble of trees obtains the best rank compared with other tree based classifiers.
A Requirement for Dimerization of HP1Hsα in Suppression of Breast Cancer Invasion*

The development and progression of cancer is controlled by gene expression, often regulated through chromatin packaging. Heterochromatin protein 1Hsα (HP1Hsα), one of three human HP1 family members, participates in heterochromatin formation and gene regulation. HP1Hsα possesses an amino-terminal chromodomain, which binds methylated lysine 9 of histone H3 (meK9 H3), and a carboxyl-terminal chromoshadow domain (CSD) that is required for dimerization and interaction with partner proteins. HP1Hsα is down-regulated in invasive metastatic breast cancer cells compared with poorly invasive nonmetastatic breast cancer cells. Expression of EGFP-HP1Hsα in highly invasive MDA-MB-231 cells causes a reduction in in vitro invasion, without affecting cell growth. Conversely, knock-down of HP1Hsα levels in the poorly invasive breast cancer cell line MCF-7 increased invasion, without affecting cell growth. To determine whether functions of the CSD were required for the regulation of invasion, mutant forms of HP1Hsα were expressed in MDA-MB-231 cells. A W174A mutation that disrupts interactions between HP1Hsα and PXVXL-containing partner proteins reduced invasion similar to that of the wild type protein. In contrast, an I165E mutation that disrupts dimerization of HP1Hsα did not decrease invasion. No gross changes in localization and abundance of HP1Hsβ, HP1Hsγ, and meK9 H3 were observed upon expression of wild type and mutant forms of HP1Hsα in MDA-MB-231 cells. Taken together, these data demonstrate that modulation of HP1Hsα alters the invasive potential of breast cancer cells through mechanisms requiring HP1 dimerization, but not interactions with PXVXL-containing proteins.
Evaluation of a Community-Based Intervention to Promote Physical Activity in Youth: Lessons from Active Winners

Purpose. To test the effects of a community-based physical activity intervention designed to increase physical activity and to conduct an extensive process evaluation of the intervention. Design. Quasi-experimental. Setting. Two rural communities in South Carolina. One community received the intervention, and the other served as the comparison. Subjects. Public school students who were in fifth grade at the start of the study (558 at baseline) were eligible to participate. A total of 436 students participated over the course of the study. Intervention. The intervention included after-school and summer physical activity programs and home, school, and community components designed to increase physical activity in youth. The intervention took place over an 18-month period. Measures. Students reported after-school physical activity at three data collection points (prior to, during, and following the intervention) using the Previous Day Physical Activity Recall (PDPAR). They also completed a questionnaire designed to measure hypothesized psychosocial and environmental determinants of physical activity behavior. The process evaluation used meeting records, documentation of program activities, interviews, focus groups, and heart rate monitoring to evaluate the planning and implementation of the intervention. Results. There were no significant differences in the physical activity variables and few significant differences in the psychosocial variables between the intervention and comparison groups. The process evaluation indicated that the after-school and summer physical activity component of the intervention was implemented as planned, but because of resource and time limitations, the home, school, and community components were not implemented as planned. Conclusions. The intervention did not have a significant effect on physical activity in the target population of children in the intervention community. This outcome is similar to that reported in other studies of community-based physical activity intervention.
Orbital-Angular-Momentum Embedded Massive MIMO: Achieving Multiplicative Spectrum-Efficiency for mmWave Communications

By enabling very high bandwidth for radio communications, the millimeter-wave (mmWave), which can easily be integrated with massive-multiple-input-multiple-output (massive-MIMO) due to small antenna size, has been attracting growing attention as a candidate for the fifth-generation (5G) and 5G-beyond wireless communications networks. On the other hand, the communication over the orthogonal states/modes of orbital angular momentum (OAM) is a subset of the solutions offered by massive-MIMO communications. Traditional massive-MIMO-based mmWave communications did not concern the potential spectrum-efficiency-gain (SE-gain) offered by the orthogonal states of OAM. However, the highly expected maximum SE-gain for OAM and massive-MIMO communications is the product of SE-gains offered by OAM and multiplexing-MIMO. In this paper, we propose the OAM-embedded-MIMO (OEM) communication framework to obtain the multiplicative SE-gain for joint OAM and massive-MIMO-based mmWave wireless communications. We design the parabolic antenna for each uniform circular array antenna to converge OAM signals. Then, we develop the mode-decomposition and multiplexing-detection scheme to obtain the transmit signal on each OAM-mode of each transmit antenna. Also, we develop the OEM-water-filling power allocation policy to achieve the maximum multiplicative SE-gain for OEM communications. The extensive simulations obtained validate and evaluate our developed a parabolic antenna-based converging method, a mode-decomposition and multiplexing-detection scheme, and an OEM-water-filling policy, showing that our proposed OEM mmWave communications can significantly increase the SE as compared with the traditional massive-MIMO-based mmWave communications.
DESIGN OF A SAMPLE RECOVERY ASSEMBLY FOR MAGNETIC RAMP‐WAVE LOADING

In order to generate new properties of metals exposed to high pressure states, it is desirable to study samples loaded in one‐dimensional strain. Previous work to obtain these ideal conditions, involve a technique where the sample was recovered at late times to examine its microstructure. In those experiments, the shock‐loading was produced by impacting the sample with a flyer plate. In the present work, we modified the sample recovery assembly and optimized it for ramp wave loading. We describe the 2‐D calculations performed with the ALEGRA MHD code that led to improved recovery assembly efficiency. Preliminary comparisons of the simulations with measurements of the sample deformation from an experiment indicate excellent agreement.
Adjuvant intraoperative photodynamic therapy in head and neck cancer.

IMPORTANCE There is an immediate need to develop local intraoperative adjuvant treatment strategies to improve outcomes in patients with cancer who undergo head and neck surgery. OBJECTIVES To determine the safety of photodynamic therapy with 2-(1-hexyloxyethyl)-2-devinyl pyropheophorbide-a (HPPH) in combination with surgery in patients with head and neck squamous cell carcinoma. DESIGN, SETTING, AND PARTICIPANTS Nonrandomized, single-arm, single-site, phase 1 study at a comprehensive cancer center among 16 adult patients (median age, 65 years) with biopsy-proved primary or recurrent resectable head and neck squamous cell carcinoma. INTERVENTIONS Intravenous injection of HPPH (4.0 mg/m2), followed by activation with 665-nm laser light in the surgical bed immediately after tumor resection. MAIN OUTCOMES AND MEASURES Adverse events and highest laser light dose. RESULTS Fifteen patients received the full course of treatment, and 1 patient received HPPH without intraoperative laser light because of an unrelated myocardial infarction. Disease sites included larynx (7 patients), oral cavity (6 patients), skin (1 patient), ear canal (1 patient), and oropharynx (1 patient, who received HPPH only). The most frequent adverse events related to photodynamic therapy were mild to moderate edema (9 patients) and pain (3 patients). One patient developed a grade 3 fistula after salvage laryngectomy, and another patient developed a grade 3 wound infection and mandibular fracture. Phototoxicity reactions included 1 moderate photophobia and 2 mild to moderate skin burns (2 due to operating room spotlights and 1 due to the pulse oximeter). The highest laser light dose was 75 J/cm2. CONCLUSIONS AND RELEVANCE The adjuvant use of HPPH-photodynamic therapy and surgery for head and neck squamous cell carcinoma seems safe and deserves further study. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00470496.
Cultivable anaerobic and aerobic bacterial communities in the fermentation chambers of Holotrichia parallela (coleoptera: scarabaeidae) larvae

As important pests, scarab beetle larvae survive on plant biomass and the microbiota of the fermentation chamber play an important role in the digestion of lignocellulose-rich diets. However, the cultivable microbes, especially the anaerobic cultivable microbes, are still largely unknown. Here, both cultivable anaerobic and aerobic bacterial communities associated with the fermentation chamber of Holotrichia parallela larvae were investigated. In total bacteria cells directly enumerated by the 4’, 6-diamidino-2-phenylindole (DAPI) staining method, the viable plate counts of cultivable bacteria in the fermentation chamber accounted for 0.92% of proportion. These cultivable bacteria were prone to attach to the fermentation chamber wall (88.41%) compared to the chamber contents. Anaerobic bacteria were dominant in the cultivable bacteria attaching to the fermentation chamber wall (70.20%), while the quantities of anaerobes and aerobes were similar in the chamber contents. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), fingerprinting and sequence analysis of isolated colonies revealed that the cultivable bacteria are affiliated with class γ-Proteobacteria, Bacteroidia, Actinobacteria, Clostridia and β-Proteobacteria. γ-Proteobacteria was the major type of anaerobic cultivable bacteria and even the only one type of aerobic cultivable bacteria. Taken together, our results suggest, for the first time, that anaerobic microbiota are dominant in cultivable bacteria in the special anoxia niche of the fermentation chamber from H. parallela larvae. These bacterial isolates could be a treasure trove for screening lignocellulytic microbes which are essential for the plant biomass digestion of this scarab species.