Miracle-dz/UniFAR-FTUs huggingface dataset:
SimGrid VM: Virtual Machine Support for a Simulation Framework of Distributed Systems

As real systems become larger and more complex, the use of simulator frameworks grows in our research community. By leveraging them, users can focus on the major aspects of their algorithm, run in-siclo experiments (i.e., simulations), and thoroughly analyze results, even for a large-scale environment without facing the complexity of conducting in-vivo studies (i.e., on real testbeds). Since nowadays the virtual machine (VM) technology has become a fundamental building block of distributed computing environments, in particular in cloud infrastructures, our community needs a full-fledged simulation framework that enables us to investigate large-scale virtualized environments through accurate simulations. To be adopted, such a framework should provide easy-to-use APIs as well as accurate simulation results. In this paper, we present a highly-scalable and versatile simulation framework supporting VM environments. By leveraging SimGrid, a widely-used open-source simulation toolkit, our simulation framework allows users to launch hundreds of thousands of VMs on their simulation programs and control VMs in the same manner as in the real world (e.g., suspend/resume and migrate). Users can execute computation and communication tasks on physical machines (PMs) and VMs through the same SimGrid API, which will provide a seamless migration path to IaaS simulations for hundreds of SimGrid users. Moreover, SimGrid VM includes a live migration model implementing the precopy migration algorithm. This model correctly calculates the migration time as well as the migration traffic, taking account of resource contention caused by other computations and data exchanges within the whole system. This allows user to obtain accurate results of dynamic virtualized systems. We confirmed accuracy of both the VM and the live migration models by conducting several micro-benchmarks under various conditions. Finally, we conclude the article by presenting a first use-case of one consolidation algorithm dealing with a significant number of VMs/PMs. In addition to confirming the accuracy and scalability of our framework, this first scenario illustrates the main interest of SimGrid VM: investigating through in-siclo experiments pros/cons of new algorithms in order to limit expensive in-vivo experiments only to the most promising ones.
Remaining Useful Life Prediction and State of Health Diagnosis for Lithium-Ion Batteries Using Particle Filter and Support Vector Regression

Accurate remaining useful life (RUL) prediction and state-of-health (SOH) diagnosis are of extreme importance for safety, durability, and cost of energy storage systems based on lithium-ion batteries. It is also a crucial challenge for energy storage systems to predict RUL and diagnose SOH of batteries due to the complicated aging mechanism. In this paper, a novel method for battery RUL prediction and SOH estimation is proposed. First, a novel support vector regression-based battery SOH state-space model is established to simulate the battery aging mechanism, which takes the capacity as the state variable and takes the representative features during a constant-current and constant-voltage protocol as the input variables. The estimated impedance variables are taken as the output due to the correlation between battery capacity and the sum of charge transfer resistance and electrolyte resistance. Second, in order to suppress the measurement noises of current and voltage, a particle filter is employed to estimate the impedance degradation parameters. Furthermore, experiments are conducted to validate the proposed method. The results show that the proposed SOH estimation method can provide an accurate and robustness result. The proposed RUL prediction framework can also ensure an accurate RUL prediction result.
Myogenic regulatory transcription factors regulate growth in rhabdomyosarcoma

Rhabdomyosarcoma (RMS) is a pediatric malignacy of muscle with myogenic regulatory transcription factors MYOD and MYF5 being expressed in this disease. Consensus in the field has been that expression of these factors likely reflects the target cell of transformation rather than being required for continued tumor growth. Here, we used a transgenic zebrafish model to show that Myf5 is sufficient to confer tumor-propagating potential to RMS cells and caused tumors to initiate earlier and have higher penetrance. Analysis of human RMS revealed that MYF5 and MYOD are mutually-exclusively expressed and each is required for sustained tumor growth. ChIP-seq and mechanistic studies in human RMS uncovered that MYF5 and MYOD bind common DNA regulatory elements to alter transcription of genes that regulate muscle development and cell cycle progression. Our data support unappreciated and dominant oncogenic roles for MYF5 and MYOD convergence on common transcriptional targets to regulate human RMS growth. DOI: http://dx.doi. org/10.7554/eLife.19214. 001
The advanced lung cancer inflammation index is an independent prognostic factor after surgical resection in patients with non-small-cell lung cancer.

OBJECTIVES The usefulness of a recently developed advanced lung cancer inflammation index (ALI) has been reported in advanced non-small-cell lung cancer (NSCLC) and small-cell lung cancer. However, no previous studies have examined the prognostic significance of ALI in patients with operable NSCLC. Therefore, the aim of this study was to explore the relationship between ALI and the prognosis of resected NSCLC. METHODS Three hundred and forty-three patients with NSCLC who underwent surgery at our institution between 2008 and 2012 were included. The ALI score was calculated as body mass index × serum albumin/neutrophil to lymphocyte ratio. A Web-based software programme [Cutoff Finder (http://molpath.charite.de/cutoff/)] was used to determine the optimal cut-off value for ALI. The Kaplan-Meier methods and a multivariable Cox proportional hazards model were used to evaluate the potential prognostic factors. RESULTS The optimal cut-off value of ALI was defined as 37.66. The low-ALI group (ALI < 37.66) displayed more adverse clinical characteristics. Furthermore, compared with patients in the high-ALI group (ALI > 37.66), those in the low-ALI group had significantly poorer survival rates. On multivariable analysis, gender, histological diagnosis, pN status, serum carcinoembryonic antigen level, serum C-reactive protein level and ALI were associated independently with cancer-specific survival. CONCLUSIONS This study is the first to investigate whether ALI is useful for predicting postoperative survival in patients with NSCLC. Preoperative ALI might serve as a potentially clinically valuable marker of the prognosis for patients with operable NSCLC.
Diagnostic index of 3D osteoarthritic changes in TMJ condylar morphology

The aim of this study was to investigate imaging statistical approaches for classifying 3D osteoarthritic morphological variations among 169 Temporomandibular Joint (TMJ) condyles. Cone beam Computed Tomography (CBCT) scans were acquired from 69 patients with long-term TMJ Osteoarthritis (OA) (39.1 ± 15.7 years), 15 patients at initial diagnosis of OA (44.9 ± 14.8 years) and 7 healthy controls (43 ± 12.4 years). 3D surface models of the condyles were constructed and Shape Correspondence was used to establish correspondent points on each model. The statistical framework included a multivariate analysis of covariance (MANCOVA) and Direction-Projection- Permutation (DiProPerm) for testing statistical significance of the differences between healthy control and the OA group determined by clinical and radiographic diagnoses. Unsupervised classification using hierarchical agglomerative clustering (HAC) was then conducted. Condylar morphology in OA and healthy subjects varied widely. Compared with healthy controls, OA average condyle was statistically significantly smaller in all dimensions except its anterior surface. Significant flattening of the lateral pole was noticed at initial diagnosis (p < 0.05). It was observed areas of 3.88 mm bone resorption at the superior surface and 3.10 mm bone apposition at the anterior aspect of the long-term OA average model. 1000 permutation statistics of DiProPerm supported a significant difference between the healthy control group and OA group (t = 6.7, empirical p-value = 0.001). Clinically meaningful unsupervised classification of TMJ condylar morphology determined a preliminary diagnostic index of 3D osteoarthritic changes, which may be the first step towards a more targeted diagnosis of this condition.
Force Modeling, Identification, and Feedback Control of Robot-Assisted Needle Insertion: A Survey of the Literature

Robot-assisted surgery is of growing interest in the surgical and engineering communities. The use of robots allows surgery to be performed with precision using smaller instruments and incisions, resulting in shorter healing times. However, using current technology, an operator cannot directly feel the operation because the surgeon-instrument and instrument-tissue interaction force feedbacks are lost during needle insertion. Advancements in force feedback and control not only help reduce tissue deformation and needle deflection but also provide the surgeon with better control over the surgical instruments. The goal of this review is to summarize the key components surrounding the force feedback and control during robot-assisted needle insertion. The literature search was conducted during the middle months of 2017 using mainstream academic search engines with a combination of keywords relevant to the field. In total, 166 articles with valuable contents were analyzed and grouped into five related topics. This survey systemically summarizes the state-of-the-art force control technologies for robot-assisted needle insertion, such as force modeling, measurement, the factors that influence the interaction force, parameter identification, and force control algorithms. All studies show force control is still at its initial stage. The influence factors, needle deflection or planning remain open for investigation in future.
Costing of three feeding regimens for home-based management of children with uncomplicated severe acute malnutrition from a randomised trial in India

Trial design Three feeding regimens—centrally produced ready-to-use therapeutic food, locally produced ready-to-use therapeutic food, and augmented, energy-dense, home-prepared food—were provided in a community setting for children with severe acute malnutrition (SAM) in the age group of 6–59 months in an individually randomised multicentre trial that enrolled 906 children. Foods, counselling, feeding support and treatment for mild illnesses were provided until recovery or 16 weeks. Methods Costs were estimated for 371 children enrolled in Delhi in a semiurban location after active survey and identification, enrolment, diagnosis and treatment for mild illnesses, and finally treatment with one of the three regimens, both under the research and government setting. Direct costs were estimated for human resources using a price times quantity approach, based on their salaries and average time taken for each activity. The cost per week per child for food, medicines and other consumables was estimated based on the total expenditure over the period and children covered. Indirect costs for programme management including training, transport, non-consumables, infrastructure and equipment were estimated per week per child based on total expenditures for research study and making suitable adjustments for estimations under government setting. Results No significant difference in costs was found across the three regimens per covered or per treated child. The average cost per treated child in the government setting was estimated at US$56 (<3500 rupees). Conclusion Home-based management of SAM with a locally produced ready-to-use therapeutic food is feasible, acceptable, affordable and very cost-effective in terms of the disability-adjusted life years saved and gross national income per capita of the country. The treatment of SAM at home needs serious attention and integration into the existing health system, along with actions to prevent SAM. Trial registration number NCT01705769; Pre-results.
Synthea: An approach, method, and software mechanism for generating synthetic patients and the synthetic electronic health care record

Abstract Objective Our objective is to create a source of synthetic electronic health records that is readily available; suited to industrial, innovation, research, and educational uses; and free of legal, privacy, security, and intellectual property restrictions. Materials and Methods We developed Synthea, an open-source software package that simulates the lifespans of synthetic patients, modeling the 10 most frequent reasons for primary care encounters and the 10 chronic conditions with the highest morbidity in the United States. Results Synthea adheres to a previously developed conceptual framework, scales via open-source deployment on the Internet, and may be extended with additional disease and treatment modules developed by its user community. One million synthetic patient records are now freely available online, encoded in standard formats (eg, Health Level-7 [HL7] Fast Healthcare Interoperability Resources [FHIR] and Consolidated-Clinical Document Architecture), and accessible through an HL7 FHIR application program interface. Discussion Health care lags other industries in information technology, data exchange, and interoperability. The lack of freely distributable health records has long hindered innovation in health care. Approaches and tools are available to inexpensively generate synthetic health records at scale without accidental disclosure risk, lowering current barriers to entry for promising early-stage developments. By engaging a growing community of users, the synthetic data generated will become increasingly comprehensive, detailed, and realistic over time. Conclusion Synthetic patients can be simulated with models of disease progression and corresponding standards of care to produce risk-free realistic synthetic health care records at scale.
The role of primary lymph node sites in survival and mortality prediction in Hodgkin lymphoma: a SEER population‐based retrospective study

As diagnostic and therapeutic modalities for Hodgkin's Lymphoma (HL) continue to improve, patient‐related factors affecting survival become more difficult to identify. Very little is known about the relationship between the primary site of lymph node (LN) involvement and survival of HL patients. We retrospectively analyzed the United States Surveillance, Epidemiology and End Results (SEER) database for 12,658 HL patients reported between 1973 and 2010 using survival analysis and time‐interval multiple logistic regression (MLR) to disclose that relationship. The effect of all primary LN sites on the survival of HL patients was supported. The intra‐abdominal (IAB) primary LN site was significantly associated with the worst survival. The pelvic (P) LN sites were significantly and independently associated with nearly 2 times and 2.5 times the probability of having 1‐year overall mortality (OM) and 1‐year cancer‐specific mortality (CSM), respectively. Head, face and neck (HFN) primary LN sites were significant and independent predictors of better overall and HL‐specific survival. A worse survival with the intra‐abdominal primary LN site was probably related to their association with higher age, or advanced stages of HL. The biological basis behind the aggressiveness of intra‐abdominal and pelvic LN sites is yet to be investigated.
Victimization and HIV Risks Among Croatian Female Sex Workers

To assess the association between victimization and HIV vulnerability among Croatian female sex workers (FSWs), a survey involving 157 FSWs recruited from Croatia’s two largest urban areas was conducted in 2014. A majority of participants reported direct and indirect victimization, which was found to be significantly associated with condom use at most recent noncommercial sexual intercourse and sexually transmitted infection (STI) diagnosis in the past 12 months. The association between victimization and STI diagnosis was partially mediated by depressiveness and moderated by social support. The buffering role of social support points to the importance of including counseling services in HIV prevention programs in Croatia.
Demography of Rusty Grain Beetle in Stored Bulk Wheat: Part II. Mathematical Modeling to Characterize and Predict Population Dynamics

Abstract Data collected in Part I of this study were further analyzed by using mathematical modeling methods. Out of the nine unstructured population models tested, no model could fit the insect numbers under all of the tested conditions. This analysis showed that Cryptolestes ferrugineus (Stephens) (Coleoptera: Laemophloeidae) inside small patches (50 ml volume) had different characterization of population dynamics from that inside large patches (18 liter volume) and had different population demography when the insect number at the previous time was different.The key factor analysis showed that the first two main factors influencing the population dynamics were the temperature and the previous insect numbers.The total numbers of insects increased with the increase of sum of degree days. However, the degree day model developed based on the constant temperatures could not predict insect numbers under fluctuating temperatures. A newly developed model, which used the result of the unstructured population models, key factor analysis, and the degree day model, could explain about 66% of the insect numbers under fluctuating temperature conditions.
SIRT4 accelerates Ang II-induced pathological cardiac hypertrophy by inhibiting manganese superoxide dismutase activity

Aims Oxidative stress contributes to the development of cardiac hypertrophy and heart failure. One of the mitochondrial sirtuins, Sirt4, is highly expressed in the heart, but its function remains unknown. The aim of the present study was to investigate the role of Sirt4 in the pathogenesis of pathological cardiac hypertrophy and the molecular mechanism by which Sirt4 regulates mitochondrial oxidative stress. Methods and results Male C57BL/6 Sirt4 knockout mice, transgenic (Tg) mice exhibiting cardiac-specific overexpression of Sirt4 (Sirt4-Tg) and their respective controls were treated with angiotensin II (Ang II, 1.1 mg/kg/day). At 4 weeks, hypertrophic growth of cardiomyocytes, fibrosis and cardiac function were analysed. Sirt4 deficiency conferred resistance to Ang II infusion by significantly suppressing hypertrophic growth, and the deposition of fibrosis. In Sirt4-Tg mice, aggravated hypertrophy and reduced cardiac function were observed compared with non-Tg mice following Ang II treatment. Mechanistically, Sirt4 inhibited the binding of manganese superoxide dismutase (MnSOD) to Sirt3, another member of the mitochondrial sirtuins, and increased MnSOD acetylation levels to reduce its activity, resulting in elevated reactive oxygen species (ROS) accumulation upon Ang II stimulation. Furthermore, inhibition of ROS with manganese 5, 10, 15, 20-tetrakis-(4-benzoic acid) porphyrin, a mimetic of SOD, blocked the Sirt4-mediated aggravation of the hypertrophic response in Ang II-treated Sirt4-Tg mice. Conclusions Sirt4 promotes hypertrophic growth, the generation of fibrosis and cardiac dysfunction by increasing ROS levels upon pathological stimulation. These findings reveal a role of Sirt4 in pathological cardiac hypertrophy, providing a new potential therapeutic strategy for this disease.
Moonlight Makes Owls More Chatty

Background Lunar cycles seem to affect many of the rhythms, temporal patterns and behaviors of living things on Earth. Ambient light is known to affect visual communication in animals, with the conspicuousness of visual signals being largely determined by the light available for reflection by the sender. Although most previous studies in this context have focused on diurnal light, moonlight should not be neglected from the perspective of visual communication among nocturnal species. We recently discovered that eagle owls Bubo bubo communicate with conspecifics using a patch of white throat plumage that is repeatedly exposed during each call and is only visible during vocal displays. Methodology/Principal Findings Here we provide evidence that this species uses moonlight to increase the conspicuousness of this visual signal during call displays. We found that call displays are directly influenced by the amount of moonlight, with silent nights being more frequent during periods with no-moonlight than moonlight. Furthermore, high numbers of calling bouts were more frequent at moonlight. Finally, call posts were located on higher positions on moonlit nights. Conclusions/Significance Our results support the idea that moon phase affects the visual signaling behavior of this species, and provide a starting point for examination of this method of communication by nocturnal species.
Determination of diffusion and partition coefficients of model migrants by direct contact and vapour phase transfer from low-density polyethylene films into cake

ABSTRACT The aim of the present study was to determine the migration kinetics of one photoinitiator, benzophenone, and two optical brighteners, Uvitex OB and 1,4-diphenyl-1,3-butadiene (DPBD), from low-density polyethylene (LDPE) films into cake. Transfer was assessed by both direct contact and also the vapour phase. To perform the migration tests by direct contact, plastic films enriched with the additives were placed between two cake slices. To evaluate the migration through the gas phase, cake and the fortified LDPE film were placed with no direct contact in a glass container that was hermetically closed. Samples were stored at different time–temperature conditions. Target compounds were extracted from the films with ethanol (70°C, 24 h) and analysed by HPLC-DAD. Relevant parameters such as partition and diffusion coefficients between food and plastic film were calculated. The Arrhenius equation was applied to estimate the diffusion coefficient at any temperature. The data indicate that migration of benzophenone occurs in a significant extent into cake by both direct contact and through the gas phase (no direct contact). Conversely, very little migration occurred for Uvitex OB by direct contact and none through the gas phase. Results for benzophenone suggest that migration through the gas phase should be considered when evaluating migration from food packaging materials into food. Graphical Abstract
Second Generation Small Pixel Technology Using Hybrid Bond Stacking †

In this work, OmniVision’s second generation (Gen2) of small-pixel BSI stacking technologies is reviewed. The key features of this technology are hybrid-bond stacking, deeper back-side, deep-trench isolation, new back-side composite metal-oxide grid, and improved gate oxide quality. This Gen2 technology achieves state-of-the-art low-light image-sensor performance for 1.1, 1.0, and 0.9 µm pixel products. Additional improvements on this technology include less than 100 ppm white-pixel process and a high near-infrared (NIR) QE technology.