Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance Modeling, Optimization, and Characterization on Heterogeneous Architectures

(ABSTRACT) Today, heterogeneous computing has truly reshaped the way scientists think and approach high-performance computing (HPC). Hardware accelerators such as general-purpose graphics processing units (GPUs) and Intel Many Integrated Core (MIC) architecture continue to make inroads in accelerating large-scale scientific applications. These advancements, however, introduce new sets of challenges to the scientific community such as: selection of best processor for an application, effective performance optimization strategies, maintaining performance portability across architectures etc. In this thesis, we present our techniques and approach to address some of these significant issues. Firstly, we present a fully automated approach to project the relative performance of an OpenCL program over different GPUs. Performance projections can be made within a small amount of time, and the projection overhead stays relatively constant with the input data size. As a result, the technique can help runtime tools make dynamic decisions about which GPU would run faster for a given kernel. Usage cases of this technique include scheduling or migrating GPU workloads over a heterogeneous cluster with different types of GPUs. We then present our approach to accelerate a seismology modeling application that is based on the finite difference method (FDM), using MPI and CUDA over a hybrid CPU+GPU cluster. We describe the generic computational complexities involved in porting such applications to the GPUs and present our strategy of efficient performance optimization and characterization. We also show how performance modeling can be used to reason and drive the hardware-specific optimizations on the GPU. The performance evaluation of our approach delivers a maximum speedup of 23-fold with a single GPU and 33-fold with dual GPUs per node over the serial version of the application, which in turn results in a many-fold speedup when coupled with the MPI distribution of the computation across the cluster. We also study the efficacy of GPU-integrated MPI, with MPI-ACC as an example implementation, on a seismology modeling application and discuss the lessons learned. Dedication I dedicate this thesis to my mom, dad, and sister. iii Acknowledgments I would like to express my heartfelt gratitude to my advisor Dr. Wu-chun Feng, foremost, for his invaluable guidance and support throughout my M.S. studies. His belief in his students and encouragement to think independently to develop solutions to the research problems made the overall research experience greatly rewarding. His diligent work-ethic and dynamic personality had been a wonderful source of inspiration to me. It has been a pleasure …
Patients Administered Neoadjuvant Chemotherapy Could be Enrolled into an Enhanced Recovery after Surgery Program for Locally Advanced Gastric Cancer

Background: Most studies on enhanced recovery after surgery (ERAS) for gastric cancer exclude patients who received neoadjuvant chemotherapy. Here, we aimed to evaluate whether patients who received neoadjuvant chemotherapy can be enrolled into the ERAS program for locally advanced gastric cancer. Methods: From April 2015 to July 2017, 114 patients who received neoadjuvant chemotherapy for locally advanced gastric cancer were randomized into ERAS and standard care (SC) groups. Postoperative length of stay, complications, bowel function, and nutritional status were recorded. Results: The postoperative length of stay of the ERAS group was shorter compared with that of the SC group (5.9 ± 5.6 vs. 8.1 ± 5.3 days, P = 0.037). The postoperative complication rate was 9.3% in the ERAS group and 11.5% in the SC group (P = 0.700). The time to first flatus (2.7 ± 2.0 vs. 4.5 ± 4.6 days, P = 0.010) and time to a semi-liquid diet (3.2 ± 2.1 vs. 6.3 ± 4.9 days, P < 0.001) in the ERAS group were shorter compared with those in the SC group. On the 10th day after surgery, the values of weight, total protein, albumin, and prealbumin of the ERAS group were lower compared with those of the SC group. Conclusions: Patients who received neoadjuvant chemotherapy could be enrolled into ERAS programs for locally advanced gastric cancer. The nutritional status of these patients was not adversely affected.
Local Signature Quantization by Sparse Coding

In 3D object retrieval it is very important to define reliable shape descriptors, which compactly characterize geometric properties of the underlying surface. To this aim two main approaches are considered: global, and local ones. Global approaches are effective in describing the whole object, while local ones are more suitable to characterize small parts of the shape. Some strategies to combine these two approaches have been proposed recently but still no consolidate work is available in this field. With this paper we address this problem and propose a new method based on sparse coding techniques. A set of local shape descriptors are collected from the shape. Then a dictionary is trained as generative model. In this fashion the dictionary is used as global shape descriptor for shape retrieval purposes. Preliminary experiments are performed on a standard dataset by showing a drastic improvement of the proposed method in comparison with well known local-to-global and global approaches.
Kinematic Differences During Single‐Leg Step‐Down Between Individuals With Femoroacetabular Impingement Syndrome and Individuals Without Hip Pain

•STUDY DESIGN: Controlled laboratory study, case‐control design. •BACKGROUND: Despite recognition that femoroacetabular impingement syndrome (FAIS) is a movement‐related disorder, few studies have examined dynamic unilateral tasks in individuals with FAIS. •OBJECTIVES: To determine whether movements of the pelvis and lower extremities in individuals with FAIS differ from those in individuals without hip pain during a single‐leg step‐down, and to analyze kinematic differences between male and female participants within groups. •METHODS: Individuals with FAIS and individuals without hip pain performed a single‐leg step‐down while kinematic data were collected. Kinematics were evaluated at 60° of knee flexion. A linear regression analysis assessed the main effects of group, sex, and side, and the interaction of sex by group. •RESULTS: Twenty individuals with FAIS and 40 individuals without hip pain participated. Individuals with FAIS performed the step‐down with greater hip flexion (4.9°; 95% confidence interval [CI]: 0.5°, 9.2°) and anterior pelvic tilt (4.1°; 95% CI: 0.9°, 7.3°) than individuals without hip pain. Across groups, female participants performed the task with more hip flexion (6.1°; 95% CI: 1.7°, 10.4°), hip adduction (4.8°; 95% CI: 2.2°, 7.4°), anterior pelvic tilt (5.8°; 95% CI: 2.6°, 9.0°), pelvic drop (1.4°; 95% CI: 0.3°, 2.5°), and thigh adduction (2.7°; 95% CI: 1.3°, 4.2°) than male participants. •CONCLUSION: The results of this study suggest that individuals with FAIS have alterations in pelvic motion during a dynamic unilateral task. The noted altered movement patterns in the FAIS group may contribute to the development of hip pain and may be due to impairments that are modifiable through rehabilitation.
Opposite Effects of Early Maternal Deprivation on Neurogenesis in Male versus Female Rats

Background Major depression is more prevalent in women than in men. The underlying neurobiological mechanisms are not well understood, but recent data shows that hippocampal volume reductions in depressed women occur only when depression is preceded by an early life stressor. This underlines the potential importance of early life stress, at least in women, for the vulnerability to develop depression. Perinatal stress exposure in rodents affects critical periods of brain development that persistently alter structural, emotional and neuroendocrine parameters in adult offspring. Moreover, stress inhibits adult hippocampal neurogenesis, a form of structural plasticity that has been implicated a.o. in antidepressant action and is highly abundant early postnatally. We here tested the hypothesis that early life stress differentially affects hippocampal structural plasticity in female versus male offspring. Principal Findings We show that 24 h of maternal deprivation (MD) at PND3 affects hippocampal structural plasticity at PND21 in a sex-dependent manner. Neurogenesis was significantly increased in male but decreased in female offspring after MD. Since no other structural changes were found in granule cell layer volume, newborn cell survival or proliferation rate, astrocyte number or gliogenesis, this indicates that MD elicits specific changes in subsets of differentiating cells and differentially affects immature neurons. The MD induced sex-specific effects on neurogenesis cannot be explained by differences in maternal care. Conclusions Our data shows that early environment has a critical influence on establishing sex differences in neural plasticity and supports the concept that the setpoint for neurogenesis may be determined during perinatal life. It is tempting to speculate that a reduced level of neurogenesis, secondary to early stress exposure, may contribute to maladaptation of the HPA axis and possibly to the increased vulnerability of women to stress-related disorders.
Aspirin locally disrupts the liquid-ordered phase

Local structure and dynamics of lipid membranes play an important role in membrane function. The diffusion of small molecules, the curvature of lipids around a protein and the existence of cholesterol-rich lipid domains (rafts) are examples for the membrane to serve as a functional interface. The collective fluctuations of lipid tails, in particular, are relevant for diffusion of membrane constituents and small molecules in and across membranes, and for structure and formation of membrane domains. We studied the effect of aspirin (acetylsalicylic acid, ASA) on local structure and dynamics of membranes composed of dimyristoylphosphocholine (DMPC) and cholesterol. Aspirin is a common analgesic, but is also used in the treatment of cholesterol. Using coherent inelastic neutron scattering experiments and molecular dynamics (MD) simulations, we present evidence that ASA binds to liquid-ordered, raft-like domains and disturbs domain organization and dampens collective fluctuations. By hydrogen-bonding to lipid molecules, ASA forms ‘superfluid’ complexes with lipid molecules that can organize laterally in superlattices and suppress cholesterol’s ordering effect.
Geographical, seasonal, and depth variation in sinking particle speeds in the North Atlantic

Particle sinking velocity is considered to be a controlling factor for carbon transport to the deep sea and thus carbon sequestration in the oceans. The velocities of the material exported to depth are considered to be high in high‐latitude productive systems and low in oligotrophic distributions. We use a recently developed method based on the measurement of the radioactive pair 210Po‐210Pb to calculate particle sinking velocities in the temperate and oligotrophic North Atlantic during different bloom stages. Our estimates of average sinking velocities (ASVs) show that slowly sinking particles (<100 m d−1) contribute significantly to carbon flux at all the locations except in the temperate regions during the bloom. ASVs appear to vary strongly with season, which we propose is caused by changes in the epipelagic community structure. Our results are the first field data to confirm the long‐standing theory that particle sinking velocities increase with depth, with increases of up to 90% between 50 and 150 m depth.
Fast Fog Detection for De-Fogging of Road Driving Images

SUMMARY Advanced driver assistance system (ADAS) can recognize tra ﬃ c signals, vehicles, pedestrians, and so on all over the vehicle. However, because the ADAS is based on images taken in an outdoor environment, it is susceptible to ambient weather such as fog. So, preprocessing such as de-fog and de-hazing techniques is required to prevent degradation of object recognition performance due to decreased visibility. But, if such a fog removal technique is applied in an environment where there is little or no fog, the visual quality may be deteriorated due to excessive contrast improvement. And in foggy road environments, typical fog removal algorithms su ﬀ er from color distortion. In this paper, we propose a temporal ﬁlter-based fog detection algorithm to selectively apply de-fogging method only in the presence of fog. We also propose a method to avoid color distortion by detecting the sky region and applying di ﬀ erent methods to the sky region and the non-sky region. Experimental results show that in the actual images, the proposed algorithm shows an average of more than 97% fog detection accuracy, and improves subjective image quality of existing de-fogging algorithms. In addition, the proposed algorithm shows very fast computation time of less than 0.1ms per frame.
SOLID LIPID NANOPARTICLES AS NOVEL DRUG DELIVERY SYSTEM: AN OVERVIEW

Solid lipid nanoparticles are at the vanguard of the rapidly growing field of nanotechnology with numerous prospective applications in drug delivery, clinical research, Biotechnology, Cosmetology and in addition to other diverse sciences. Solid lipid nanoparticle offers great advantages over a traditional drug delivery system. A solid lipid nanoparticle (SLN) is a typically colloidal spherical with an average diameter between 10 to 1000 nm. Solid lipid nanoparticles hold a solid lipid core matrix that can solubilize lipophilic molecules as well as hydrophilic drugs. The lipid core of SLNs is stabilized by the surfactants (emulsifiers). Due to their inimitable size-dependent properties, lipid nanoparticles offer the possibility to develop new therapeutics. The potential to incorporate drugs into nanocarriers offers a new archetype in drug delivery that could hold an immense promise in accomplishing the bioavailability enhancement accompanied by controlled and site specific drug delivery. Solid lipid nanoparticles offers enhance bioavailability by improving drug dissolution and permeability across intestinal cell wall by incorporation of drug in solid lipid nanoparticle . This review presents a discussion on the introduction, advantages, disadvantages, Nano structured lipid carrier, lipid drug conjugate, production procedures, Principle of drug release from SLN, pharmaceutical applications, characterization studies, and evaluation of SLNs.
A Picture is Worth a Thousand Words : Visual Model Evaluation in Data Science Applications

Besides programming and mathematical or statistical skills, domain knowledge about the investigated problem is an important factor in data science. In practical applications, however, there often exist a gap between data scientists who have the technical skills in advanced analytics methods and the domain experts like managers and decision makers with substantial knowledge in their field. Less participation of domain experts during the complex model building and evaluation process of the data science pipeline can lead to acceptance problems and prejudices against the results. Moreover, data scientists depend on the domain knowledge of experts when it comes to evaluation and problem identification of their models. In this paper we address this issue by introducing an easy-to-understand heat map visualization technique for model evaluation. It enables all parties to discuss the analysis on the same level of complexity. The benefits are demonstrated based on a real world business example.
Chinese spoken language understanding across domain

A robust parsing model for spontaneous Chinese based on semantic constituent spotting and concept assembling model (SCAM) had been successfully developed in our “LOADSTAR ” dialog system[1]. It is a travel information accessing system and the SCAM is rule based. Considering the domain portability, a statistical model for spoken language understanding is adopted. The statistical spoken language understanding model is developed in the domain of hotel reservation. Then the statistical model was ported to the domain of travel information accessing within four weeks.
Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation

In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element. Here, we show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of the full-length transcripts is static: it exclusively populates the functional off-state but cannot switch to the on-state, regardless of the presence or absence of ligand. We show that only the combined matching of transcription rates and ligand binding enables transcription intermediates to undergo ligand-dependent conformational refolding. DOI: http://dx.doi. org/10.7554/eLife.21297. 001
PASTASpark: multiple sequence alignment meets Big Data

Motivation: One basic step in many bioinformatics analyses is the multiple sequence alignment. One of the state‐of‐the‐art tools to perform multiple sequence alignment is PASTA (Practical Alignments using SATé and TrAnsitivity). PASTA supports multithreading but it is limited to process datasets on shared memory systems. In this work we introduce PASTASpark, a tool that uses the Big Data engine Apache Spark to boost the performance of the alignment phase of PASTA, which is the most expensive task in terms of time consumption. Results: Speedups up to 10× with respect to single‐threaded PASTA were observed, which allows to process an ultra‐large dataset of 200 000 sequences within the 24‐h limit. Availability and implementation: PASTASpark is an Open Source tool available at https://github.com/citiususc/pastaspark Contact: josemanuel.abuin@usc.es Supplementary information: Supplementary data are available at Bioinformatics online.
A pilot study with flow mediated skin fluorescence: A novel device to assess microvascular endothelial function in coronary artery disease.

BACKGROUND Endothelial dysfunction is one of the earliest vascular manifestations in the pathogen-esis of cardiovascular disease. Noninvasive, simple, and inexpensive methods of endothelial function assessment are therefore needed. METHODS Microvascular endothelial function was assessed in coronary artery disease (CAD) patients by flow mediated skin fluorescence (FMSF), based on measurements of reduced form of nicotinamide adenine dinucleotide (NADH) fluorescence intensity during brachial artery occlusion (ischemic re-sponse [IRmax]) and immediately after occlusion (hyperemic response [HRmax]). Additionally, plasma levels of asymmetric dimethylarginine (ADMA) and endothelin-1 (ET-1) were measured to assess the association between biochemical markers and microvascular function evaluated in vivo by FMSF. RESULTS A significant inverse correlation was found between ADMA levels and hyperemic response (r = -0.534, p = 0.003), while ET-1 levels were inversely related to the ischemic response (r= -0.575, p = 0.001). Both IR and HR were found lowest in patients with advanced CAD and diabetes. When the repeatability of the method was tested, the intraclass correlation coefficient for IRmax and HRmax were 0.985 (p < 0.001) and 0.914 (p < 0.001), respectively. Moreover, in Bland and Altman analysis, both variables IRmax and HRmax showed good agreement in repeated measurements. CONCLUSIONS In this pilot study, it was demonstrated that NADH fluorescence measured by FMSF device in CAD patients was associated with established plasma endothelial markers, and that both ischemic and hyperemic response were blunted in patients with advanced disease and diabetes. Fur-thermore, FMSF device showed excellent repeatability and good agreement for repeated measurements. However, further study is warranted to confirm these results in a larger patient cohort. (Cardiol J 2018; 25, 1: 120-127).
Interior Micro-structure and Mechanical Performance Anisotropy of Gun Propellants

In view of the mechanical performance anisotropy caused by adopting gel-diractional-pressing-elongation technics in the process of manufacturing propellant,the cause,differential degree and possible solutions to the anisotropy are studied in this paper.The axial and radial anti-tensile intensities of homemade flat propellant sticks are tested at different temperatures.The interior micro-structure of propellants is studied through SEM testing.The analysis of the reason of causing the mechanical performance anisotropy of propellants shows that: when the radial intensity has only 1/3～1/4 of the axial intensity,the anisotropy occurs.Several possible solutions to improving mechanical intensity anisotropy of propellants are proposed.
Atorvastatin Calcium Inhibits PDGF-ββ-Induced Proliferation and Migration of VSMCs Through the G0/G1 Cell Cycle Arrest and Suppression of Activated PDGFRβ-PI3K-Akt Signaling Cascade

Background/Aims: Abnormal proliferation of vascular smooth muscle cells (VSMCs) is a hallmark of vascular lesions, such as atherosclerosis and restenosis. PDGF-ββ, an isoform of PDGF (platelet-derived growth factor), has been demonstrated to induce proliferation and migration of VSMCs. Atorvastatin calcium, a selective inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, has favorable protective effects on VSMCs. This study examined the effects of atorvastatin calcium on the proliferation and migration of PDGF-ββ-treated VSMCs, as well as its underlying mechanisms. Methods: MTT assays, Edu imaging, cell cycle analysis, wound healing assays, transwell migration assays, and western blot analysis were performed. Results: Atorvastatin calcium significantly inhibited cell proliferation, DNA synthesis and cell migration of PDGF-ββ-treated VSMCs. We demonstrated that atorvastatin calcium induced cell cycle arrest in the G0/G1 phase in response to PDGF-ββ stimulation and decreased the expression of G0/G1-specific regulatory proteins, including proliferating cell nuclear antigen (PCNA), CDK2, cyclin D1, cyclin E and CDK4 in PDGF-ββ-treated VSMCs. Moreover, pretreatment with atorvastatin calcium inhibited the PDGF-ββ-treated phosphorylation of PDGFRβ and Akt, whereas atorvastatin calcium did not affect the phosphorylation of PLC-γ1 or (ERK) 1/2. Conclusion: Our data suggested that atorvastatin calcium inhibited abnormal proliferation and migration of VSMCs through G0/G1 cell cycle arrest and suppression of the PDGFRβ-Akt signaling cascade.