Miracle-dz/UniFAR-FTUs huggingface dataset:
Graphite

In this paper, we propose a new parallelism model denoted as MPI * X and suggest a linear algebra-based graph analytics system, namely, Graphite, which effectively employs it. MPI * X promotes thread-based partitioning to distribute computation and communication across threads on a cluster of machines, while eliminating the need for unnecessary thread synchronizations. Consequently, it contrasts with the traditional MPI + X parallelism model, which utilizes process-based partitioning to distribute data among processes as a way to scale out on a cluster of machines (the MPI part), then splits each partition into subpartitions among the threads of each process as a method to scale up within a machine (the X part). Besides adopting MPI * X, Graphite is NUMA-aware. In particular, it assigns threads to partitions in a way that exploits CPU and memory affinity, alongside leveraging faster MPI shared memory transport. Moreover, it adopts a variant of the popular GAS (Gather, Apply, and Scatter) computing model, thus decoupling the computation of partitions from the communication of partial results. Lastly, it supports thread-level asynchrony, which does not only overlap the computation with communication, but further interleaves multiple communications. We compared Graphite against GraphPad, Gemini, and LA3 graph analytics systems in an HPC environment using different graph applications. Results show that Graphite is roughly up to 3X faster than these state-of-the-art systems.
A General Arbitration Model for Robust Human-Robot Shared Control with Multi-Source Uncertainty Modeling

Shared control in teleoperation leverages both human and robot's strengths and has demonstrated great advantages of reducing the difficulties in teleoperating a robot and increasing the task performance. One fundamental question in shared control is how to effectively allocate the control power to the human and robot. Researchers have been subjectively defining the arbitrate policies following conflicting principles, which resulted in great inconsistency in the policies. We attribute this inconsistency to the inconsiderateness of the multi-resource uncertainty in the human-robot system. To fill the gap, we developed a multi-source uncertainty model that was applicable to various types of uncertainty in real world, and then a general arbitration model was developed to comprehensively fuse the uncertainty and regulate the arbitration weight assigned to the robotic agent. Beside traditional macro performance metrics, we introduced objective and quantitative metrics of robotic helpfulness and friendliness that evaluated the assistive robot's cooperation at micro and macro levels. Results from simulations and experiments showed the new arbitration model was more effective and friendly over the existing policies and was robust to coping with multi-source uncertainty. With this new arbitration model, we expect the increased adoption of human-robot shared control in practical and complex teleoperation tasks.
A clinical study of prognostic significance of left atrial volume index in patients with acute coronary syndrome

Background: The aim of the study is to determine the relationship of left atrial volume index (LAVI) with the clinical presentation, comorbidities, and adverse events in acute coronary syndrome (ACS) patients at admission and during their follow-up. Methods: A total of 160 ACS patients enrolled have been divided into Group A (LAVI > 34 ml/m2) and Group B ( LAVI ≤ 34 ml/m2). The symptoms and the LAVI have been assessed at 1, 6, and 12 months of follow-up. The primary end point was cardiovascular (CV) mortality. The secondary end point is the occurrence of major adverse CV events, i.e., repeat hospitalization postdischarge for heart failure, reinfarction, atrial fibrillation, or ischemic stroke. Results: Overall, the median age at presentation was 55 years. There was no sex predilection for increased LAVI or an association with conventional risk factors. The echocardiographic E wave velocity divided by propagation velocity had a positive correlation with the LAVI (r = 0.321, P = 0.0036). The relative risk of morbidity with an increased LAVI was 2.74. The hazard ratio for adverse events in patients with increased LAVI was 2.81. The total number of deaths was 21 (16 and 5 in Group A and B). The LAVI was found to be the independent predictor of mortality than left ventricular ejection fraction on multivariate regression analysis. The receiver operating characteristic curve analysis had an area under the curve of 0.801 for increased LAVI. Conclusion: The LAVI is an independent predictor of adverse events and mortality during the initial hospital stay and at follow-up in ACS patients.
Tumor-Infiltrating T Cells From Clear Cell Renal Cell Carcinoma Patients Recognize Neoepitopes Derived From Point and Frameshift Mutations

Mutation-derived neoantigens are important targets for T cell-mediated reactivity toward tumors and, due to their unique tumor expression, an attractive target for immunotherapy. Neoepitope-specific T cells have been detected across a number of solid cancers with high mutational burden tumors, but neoepitopes have been mostly selected from single nucleotide variations (SNVs), and little focus has been given to neoepitopes derived from in-frame and frameshift indels, which might be equally important and potentially highly immunogenic. Clear cell renal cell carcinomas (ccRCCs) are medium-range mutational burden tumors with a high pan-cancer proportion of frameshift mutations. In this study, the mutational landscape of tumors from six RCC patients was analyzed by whole-exome sequencing (WES) of DNA from tumor fragments (TFs), autologous tumor cell lines (TCLs), and tumor-infiltrating lymphocytes (TILs, germline reference). Neopeptides were predicted using MuPeXI, and patient-specific peptide–MHC (pMHC) libraries were created for all neopeptides with a rank score < 2 for binding to the patient's HLAs. T cell recognition toward neoepitopes in TILs was evaluated using the high-throughput technology of DNA barcode-labeled pMHC multimers. The patient-specific libraries consisted of, on average, 258 putative neopeptides (range, 103–397, n = 6). In four patients, WES was performed on two different sources (TF and TCL), whereas in two patients, WES was performed only on TF. Most of the peptides were predicted from both sources. However, a fraction was predicted from one source only. Among the total predicted neopeptides, 16% were derived from frameshift indels. T cell recognition of 52 neoepitopes was detected across all patients (range, 4–18, n = 6) and spanning two to five HLA restrictions per patient. On average, 21% of the recognized neoepitopes were derived from frameshift indels (range, 0–43%, n = 6). Thus, frameshift indels are equally represented in the pool of immunogenic neoepitopes as SNV-derived neoepitopes. This suggests the importance of a broad neopeptide prediction strategy covering multiple sources of tumor material, and including different genetic alterations. This study, for the first time, describes the T cell recognition of frameshift-derived neoepitopes in RCC and determines their immunogenic profile.
Prevalence of coexisting autoimmune thyroidal diseases in coeliac disease is decreasing

Background Coeliac disease (CD) is associated with an increased risk of other immune-mediated conditions. Aim: To investigate the prevalence of coexistent immune-mediated diseases in CD patients, and changes in the prevalence of autoimmune thyroidal diseases over the last 50 years. Methods Medical record data were collected retrospectively from 749 CD patients in Ireland. Prevalence of autoimmune diseases was compared with previously published results from general populations. Patients were divided into four groups based on the year of diagnosis to analyse changes in the prevalence of autoimmune thyroidal disease over time. Results Median age at the time of CD diagnosis was 56 years (range 18–91 years). A total of 233 (31.1%) patients had a coexistent immune-mediated condition (IMC). Autoimmune thyroidal diseases were seen in 149 (19.9%) patients, hypothyroidism in 110 (14.7%), type 1 diabetes in 27 (3.6%), psoriasis in 20 (2.7%), inflammatory bowel disease in 14 (1.9%) and rheumatoid arthritis in 12 (1.6%). All conditions were more common in CD patients than in the general population. Type 1 diabetes was diagnosed mainly before CD, whereas there was no such trend in other conditions. Autoimmune thyroidal diseases became less common in female CD patients over time. Conclusions Prevalence of autoimmune diseases is increased in adult CD patients compared with the general population. However, concomitant autoimmune thyroidal diseases became less common over time in women.
GASP! Generating Abstracts of Scientific Papers from Abstracts of Cited Papers

Creativity is one of the driving forces of human kind as it allows to break current understanding to envision new ideas, which may revolutionize entire fields of knowledge. Scientific research offers a challenging environment where to learn a model for the creative process. In fact, scientific research is a creative act in the formal settings of the scientific method and this creative act is described in articles. In this paper, we dare to introduce the novel, scientifically and philosophically challenging task of Generating Abstracts of Scientific Papers from abstracts of cited papers (GASP) as a text-to-text task to investigate scientific creativity, To foster research in this novel, challenging task, we prepared a dataset by using services where that solve the problem of copyright and, hence, the dataset is public available with its standard split. Finally, we experimented with two vanilla summarization systems to start the analysis of the complexity of the GASP task.
Targeting bedaquiline mycobacterial efflux pump to potentially enhance therapy in Mycobacterium abscessus

Background: Mycobacterium abscessus is notorious for being intrinsically resistant to most antibiotics. Antibiotic efflux is one of the mechanisms used by M. abscessus to pump out antibiotics from their cells. Inhibiting efflux pumps (EPs) can be an attractive strategy to enhance the activity of drugs. The objective of this study is to determine the activity of EP inhibitors (EPIs) to enhance the efficacy of the new drug bedaquiline against M. abscessus clinical isolates. Methods: A total of 31 phenotypically and genotypically identified M. abscessus subsp. abscessus, M. abscesss subsp. massiliense, and M. abscessus subsp. bolletii clinical isolates were studied. The contribution of EPs was determined by investigating the minimum inhibitory concentration (MIC) levels of bedaquiline reduction in the absence and presence of EPIs verapamil and reserpine using the resazurin microtiter assay. Results: The observed bedaquiline MIC reduction by verapamil was observed in 100% isolates and by reserpine in 54.8% isolates. Bedaquiline MIC was 4–32-fold using verapamil with M. abscessus subsp. bolletii showing the highest fold change and between 2- and 4-fold using reserpine. Conclusions: The results obtained in this study confirm that bedaquiline MIC decreased in the presence of EPIs verapamil and reserpine in clinical isolates of M. abscessus. Verapamil was the most effective EPI. As shown in previous studies, verapamil may have clinical potential as adjunctive therapy to enhance the effect of bedaquiline.
Energy-aware Goal Selection and Path Planning of UAV Systems via Reinforcement Learning.

Smart data collection via UAV systems is an attractive topic in various disciplines. Disturbances such as intense wind can significantly hinder the operational time of drones. This work demonstrates a reinforcement learning approach for the optimization of power consumption in a UAV system for data collection in sparse locations. Two common reinforcement learning algorithms, Q-learning and SARSA, are implemented in a simulation environment, utilizing a combination of robot operating system (ROS) and Gazebo. The effect of time-varying wind fields and time-dependency of the tasks were simulated and the developed framework showed reliable adaptability in various scenarios. This framework can result in 30% power consumption improvement for intense wind conditions in comparison to na\"ive control algorithms.
The prevalence of malocclusion among 10–12-year-old schoolchildren in Khammam district, Telangana: An epidemiological study

Aim: The study aimed to determine the prevalence of malocclusion among 10–12-year-old school-going children in Khammam district of Telangana state. Materials and Methods: A descriptive cross-sectional study was conducted among 2550 schoolchildren aged 10–12 years old in the Department of Pedodontics and Preventive Dentistry, Mamata Dental College and Hospital, Khammam, Telangana, India, to assess the prevalence of malocclusion. An oral examination was conducted by a single trained examiner using a mouth mirror and probe. Occlusal characteristics such as molar relation, overjet, overbite, open bite, crossbite, midline deviations, midline diastema, and rotation were recorded. The data were tabulated and analyzed using the Chi-square test. Results: The results revealed that the overall prevalence of malocclusion was 76.6%. Of this, 65.9% of the children had Angle's Class I malocclusion, 9.25% had Class II malocclusion, and 1.37% had Class III malocclusion. About 15.4% showed an increased overjet (>3 mm), 0.2% had reverse overjet, 43.6% had increased overbite (>3 mm), 2% had open bite, 14.01% had crossbite, 46.23% had deviation of midline, 2.07% had midline diastema, and 2.98% had rotated tooth. Conclusion: There is a high prevalence of malocclusion among schoolchildren in Khammam district of Telangana. Problems of a functional nature that arise from these morphological changes may become more complex skeletal problems in future with serious psychosocial consequences for the developing individual.
Sophorolipid Biosurfactant Can Control Cutaneous Dermatophytosis Caused by Trichophyton mentagrophytes

Trichophyton mentagrophytes, a zoophilic species, is one of the most frequently isolated dermatophytes in many parts of the world. This study investigated the efficacy of a sophorolipid (SL-YS3) produced by Rhodotorula babjevae YS3 against dermatophytosis caused by T. mentagrophytes. SL-YS3 was characterized by gas chromatography–mass spectrometry (GC–MS) and ultra-performance liquid chromatography, coupled with electrospray mass spectrometry (UPLC-ESI-MS). SL-YS3 comprised of six different fatty acids as the hydrophobic components of constituent congeners and sophorose as the hydrophilic component. Inhibitory effects of purified SL-YS3 against hyphal growth was found to be 85% at a 2 mg ml–1 concentration, and MIC was 1 mg ml–1. Microscopic examination with scanning electron microscopy (SEM), atomic force microscopy, and confocal laser scanning microscopy (CLSM) revealed that SL-YS3 exerts its effect by disrupting cell membrane integrity causing cell death. SL-YS3 was also effective in reducing the biofilms formed by T. mentagrophytes, which was observed spectrophotometrically with crystal-violet staining and further validated with SEM and CLSM studies of treated biofilms. In vivo studies in a mouse model of cutaneous dermatophytosis involving macroscopic observations, percent culture recovery from skin samples, and histopathological studies showed that SL-YS3 could effectively cure the infected mice after 21 days of topical treatment. Terbinafine (TRB) was used as a standard drug in the experiments. We demonstrate, for the first time, the antidermatophytic activity of a sophorolipid biosurfactant. The findings are suggestive that SL-YS3 can be formulated as a novel antifungal compound to treat cutaneous mycoses caused by T. mentagrophytes.
An exact method for optimizing two linear fractional functions over the efficient set of a Multiobjective Integer Linear Fractional Program

In this paper, an exact method is proposed to optimize two fractional linear functions over the efficient set of a fractional multiobjective linear problem (MOILFP). This type of problems is encountered when there are two decision makers and each has his own utility function that he wants to optimize over the efficient set of multiobjective problem. The proposed method uses Branch and Bound method combined with a cutting plane technique to find the efficient solutions for both utility functions and (MOILFP) without going through all the efficient solutions of the two problems. An illustrative example and a computational study are reported.
Understanding the Downstream Instability of Word Embeddings

Many industrial machine learning (ML) systems require frequent retraining to keep up-to-date with constantly changing data. This retraining exacerbates a large challenge facing ML systems today: model training is unstable, i.e., small changes in training data can cause significant changes in the model's predictions. In this paper, we work on developing a deeper understanding of this instability, with a focus on how a core building block of modern natural language processing (NLP) pipelines---pre-trained word embeddings---affects the instability of downstream NLP models. We first empirically reveal a tradeoff between stability and memory: increasing the embedding memory 2x can reduce the disagreement in predictions due to small changes in training data by 5% to 37% (relative). To theoretically explain this tradeoff, we introduce a new measure of embedding instability---the eigenspace instability measure---which we prove bounds the disagreement in downstream predictions introduced by the change in word embeddings. Practically, we show that the eigenspace instability measure can be a cost-effective way to choose embedding parameters to minimize instability without training downstream models, outperforming other embedding distance measures and performing competitively with a nearest neighbor-based measure. Finally, we demonstrate that the observed stability-memory tradeoffs extend to other types of embeddings as well, including knowledge graph and contextual word embeddings.
Female predominant coronary tortuosity is related to significant coronary artery disease. A prospective observational study

Background: Coronary tortuosity (CT), quantified by our new tortuosity severity index (TSI), strongly predicts anginal pain in patients with normal coronary angiography (CA). The connection between CT and coronary arteriosclerosis is still imprecise. Objectives: The objective was to study CT in patients with coronary artery disease (CAD). Patients and Methods: This is a prospective study at university hospitals between May 2016 and January 2017. We included 331 consecutive patients who underwent CA due to typical chest pain and showed CAD with a lesion >30%. Patients were prospectively divided into two groups based on the presence (n = 186) or absence (n = 145) of significant CAD (≥70%) and compared for clinical, echocardiographic, and CA characteristics. The TSI was either significant (mild/moderate CT with >4 curvatures in total or severe/extreme CT with any number of curvatures) or not significant TSI (mild/moderate CT with curvatures ≤4 curvatures in total). Results: Patients with significant CAD had the highest rate of CT (66% vs. 17%, P ≤ 0.001) and significant TSI (69% vs. 20%, P < 0.001) compared to those without. CT affects the left anterior descending coronary artery in middle and distal segments as a single vessel in 80% of patients. Patients with CT were more commonly females and hypertensives with small body surface area. Multivariate logistic regression analysis identified female gender (odds ratio [OR] = 4.7, confidence interval [CI] = 2.4–8.9) and CT as the main predictors of significant CAD (OR = 6.7, CI = 3.2–14.2). Conclusions: CT with significant TSI is positively related with significant CAD. This finding is more pronounced among hypertensive females with small body surface area.
Heart Dosimetric Parameters Were Associated With Cardiac Events and Overall Survival for Patients With Locally Advanced Esophageal Cancer Receiving Definitive Radiotherapy

Objectives: The aim of this study was to assess the association between heart dosimetric parameters and cardiac events or overall survival (OS) for patients with stage III esophageal cancer receiving definitive radiotherapy. Materials and Methods: Patients with stage III esophageal cancer receiving definitive radiotherapy at our hospital from 2011 to 2013 were enrolled retrospectively. The primary endpoint was grade ≥ 2 cardiac events, and the second endpoint was 5-year OS. Competing risk analysis and Cox regressions analysis were performed to evaluate the association between heart dose and cardiac events or OS. Results: Three hundred forty-six patients were analyzed. Median follow-up was 30 months. Median prescribed dose was 60 Gy. Seventy-eight patients (22.5%) had 91 grade ≥ 2 cardiac events, at a median of 14 months to first event. Thirty-three patients (9.5%) had 42 grade ≥ 3 cardiac events. Of the 78 patients with grade ≥ 2 cardiac events, 70 (89.7%) had the first cardiac events that occurred within first 3 years after radiotherapy. Multivariable analysis showed that preexisting ischemic heart disease [hazard ratio (HR), 2.26; 95% confidence interval (CI), 1.26–4.06; p = 0.006] and mean heart dose (HR, 1.12; 95% CI, 1.04–1.20; p = 0.002) were significantly associated with increased risk of grade ≥ 2 cardiac events. Disease progression (HR, 2.60; 95% CI, 1.82–3.70; p < 0.001), Eastern Cooperative Oncology Group (ECOG) performance status (HR, 0.71; 95% CI, 0.56–0.91; p = 0.007), heart volume receiving ≥ 5 Gy (V5, HR, 1.01; 95% CI, 1.00–1.03; p = 0.035), and gross tumor volume (GTV; HR, 1.00; 95% CI, 1.00–1.00; p = 0.020) were significant predictors of 5-year OS on multivariable analysis. Conclusion: Higher heart dose was significantly associated with an increased cardiac event rate and a worse OS outcome for patients with stage III esophageal cancer treated with definitive radiotherapy. Most of the first cardiac events occurred within first 3 years after treatment.