Miracle-dz/UniFAR-FTUs huggingface dataset:
BScout: Direct Whole Patch Presence Test for Java Executables

To protect end-users and software from known vulnerabilities, it is crucial to apply security patches to affected executables timely. To this end, patch presence tests are proposed with the capability of independently investigating patch application status on a target without source code. Existing work on patch presence testing adopts a signature-based approach. To make a trade-off between the uniqueness and the stability of the signature, existing work is limited to use a small and localized patch snippet (instead of the whole patch) for signature generation, so they are inherently unreliable. In light of this, we present BSCOUT, which directly checks the presence of a whole patch in Java executables without generating signatures. BSCOUT features several new techniques to bridge the semantic gap between source code and bytecode instructions during the testing, and accurately checks the fine-grained patch semantics in the whole target executable. We evaluate BScout with 194 CVEs from the Android framework and third-party libraries. The results show that it achieves remarkable accuracy with and without line number information (i.e., debug information) presented in a target executable. We further apply BSCOUT to perform a large-scale patch application practice study with 2,506 Android system images from 7 vendors. Our study reveals many findings that have not yet been reported.
Donky: Domain Keys - Efficient In-Process Isolation for RISC-V and x86

Efﬁcient and secure in-process isolation is in great demand, as evidenced in the shift towards JavaScript and the recent re-vival of memory protection keys. Yet, state-of-the-art systems do not offer strong security or struggle with frequent domain crossings and oftentimes intrusive kernel modiﬁcations. We propose Donky, an efﬁcient hardware-software co-design for strong in-process isolation based on dynamic memory protection domains. The two components of our design are a secure software framework and a non-intrusive hardware extension. We facilitate domain switches entirely in userspace, thus minimizing switching overhead as well as kernel complexity. We show the versatility of Donky in three realistic use cases, secure V8 sandboxing, software vaults, and untrusted third-party libraries. We provide an open-source implementation on a RISC-V Ariane CPU and an Intel-MPK-based emulation mode for x86. We evaluate the security and performance of our implementation for RISC-V synthesized on an FPGA. We also evaluate the performance on x86 and show why our new design is more secure than Intel MPK. Donky does not impede the runtime of in-domain computation. Cross-domain switches are 16–116x faster than regular process context switches. Fully protecting the mbedTLS cryptographic operations has a 4 % overhead.
Computarized analysis of phonographic registers for the detection of heart murmurs

The aim of this work is to present some arguments that during the last years have generated interest in the development of digital phonocardiography research, for supporting the diagnosis of heart murmurs. In addition, a methodology for the detection of heart murmurs caused by valvulopathies by means of computerized phonographic register analysis is exposed, using specifically acoustic algorhythms analysis and non-linear dynamic techniques. The separation between normal (heart sounds) and pathologic (murmurs) is compared through the measurements obtained by the already mentioned techniques and making the detection by means of a classifying algorhythm both in conditions where these acoustic perturbations are diminished as in those where these kind of perturbations remain.
Interpretable biomanufacturing process risk and sensitivity analyses for quality‐by‐design and stability control

While biomanufacturing plays a significant role in supporting the economy and ensuring public health, it faces critical challenges, including complexity, high variability, lengthy lead time, and very limited process data, especially for personalized new cell and gene biotherapeutics. Driven by these challenges, we propose an interpretable semantic bioprocess probabilistic knowledge graph and develop a game theory based risk and sensitivity analyses for production process to facilitate quality‐by‐design and stability control. Specifically, by exploring the causal relationships and interactions of critical process parameters and product quality attributes, we create a Bayesian network based probabilistic knowledge graph characterizing the complex causal interdependencies of all factors. Then, we introduce a Shapley value based sensitivity analysis, which can correctly quantify the variation contribution from each input factor on the outputs (i.e., productivity, product quality). Since the bioprocess model coefficients are learned from limited process observations, we derive the Bayesian posterior distribution to quantify model uncertainty and further develop the Shapley value based sensitivity analysis to evaluate the impact of estimation uncertainty from each set of model coefficients. Therefore, the proposed bioprocess risk and sensitivity analyses can identify the bottlenecks, guide the reliable process specifications and the most informative data collection, and improve production stability.
Finite time stabilization for nonlinear systems with unknown control directions and unstructured uncertainties (Extended version)

This paper investigates the finite time stabilization problem for a class of nonlinear systems with unknown control directions and unstructured uncertainties. The unstructured uncertainties indicate that not only the parameters but also the structure of the system nonlinearities are uncertain. The contributions are mainly in the following two aspects: First, a new adaptive control method is proposed for the considered system. Logic-based switching rule is utilized to tune the controller parameters online to stabilize the system in finite time. Different from the existing adaptive controllers for structured/parametric uncertainties, a new switching barrier Lyapunov method and supervisory functions are introduced to overcome the obstacles caused by unstructured uncertainties and unknown control directions. Second, based on a time-varying backstepping scheme, an extension is made to the proposed method such that all the system states can be regulated to zero in prescribed finite time. Moreover, a new analysis tool is presented to show the boundedness of the control signals. Simulations are conducted to verify the effectiveness of the proposed methods.
Vigorous exercise and birth outcomes in a sample of recreational exercisers : A prospective study across pregnancy

An estimated 10% of Australian women of childbearing age exercise vigorously on a regular basis. This prospective study sought to determine whether this practice is associated with low infant birth weight or low gestational age at birth. Participating in the study were 148 pregnant women whose exercise frequency and intensity were monitored at baseline; at 16 to 23, 24 to 31, and 32 to 38 weeks gestation; and 1 to 2 weeks postpartum. Two definitions of vigorous exercise were used, one formulated by Bell et al (at least 30 minutes of running, swimming, or other aerobic activity at no less than 50% of maximal heart rate) and the other based on American College of Obstetricians and Gynecologists (ACOG) recommendations (up to 15 minutes of exercise at a heart rate of 140 or less at least 3 times each week). More than 85% of women exercised vigorously according to the Bell criteria, and approximately 60% of exercising women exceeded the ACOG criteria. Neither birth weight nor gestational age at birth could be related to the level of exercise, regardless of which set of criteria for exercise intensity was applied. Exercise level could not be implicated in the delivery of 4 low-birth-weight infants. This prospective study yielded no evidence that the intensity, duration, and/or frequency of vigorous exercise performed by pregnant women are associated with significantly adverse pregnancy outcomes. The investigators point out, however, that no conclusions should be drawn before replicating these findings in a large and more diverse group of pregnant women.
Bioengineering and Biophysical Aspects of Electromagnetic Fields

BIOENGINEERING AND BIOPHYSICAL ASPECTS OF ELECTROMAGNETIC FIELDS Environmental and Occupationally Encountered Electromagnetic Fields K.H. Mild and B. Greenebaum Endogenous Electric Fields in Animals R. Nuccitelli Dielectric and Magnetic Properties of Biological Materials C. Gabriel Magnetic Properties of Biological Material J. Dobson Interaction of Direct Current and Extremely Low Frequency Electric Fields with Biological Materials and Systems F. Barnes Magnetic Field Effects on Free Radical Reactions in Biology S. Engstrom Signals, Noise, and Thresholds J.C. Weaver and M. Bier Biological Effects of Static Magnetic Field S. Ueno and T. Shigemitsu The Ion Cyclotron Resonance Hypothesis A.R. Liboff Computational Methods for Predicting Field Intensity and Temperature Change J.C. Lin and P. Bernardi Experimental EMF Exposure Assessment S. Kuhn and N. Kuster Electromagnetic Imaging of Biological Systems W.T. Joines, Q.H. Liu, and G. Ybarra
Differential selection in sexes, genetic drift, and stable coexistence of identical species

The competitive exclusion principle states that identical species cannot coexist indefinitely. It is shown that this principle is extremely fragile with biological deviations from the implicit assumption of genetic homogeneity. Assuming female demographic dominance and differential selection in sexes, we argue that there is a wide variety of conditions under which the rate oe population growth is not maximized by evolution. Population growth rate may be higher near the unstable allelic fixation boundaries than in the internal polymorphic equilibria, which implies that there may exist a negative correlation between population growth rate and heterozygosity. Since random genetic drift manifested in small populations generally results in a significant loss of heterozygosity, a species at low density may gain an advantage in per capita population growth, making stable coexistence of identical species possible
Stomach contents of a sperm whale (Physeter macrocephalus) stranded in Italy (Ligurian Sea, north-western Mediterranean)

The stomach contents of a male sperm whale, Physeter macrocephalus, stranded on Forte dei Marmi beach (Italy, Ligurian Sea) were examined. Food items consisted exclusively of cephalopod hard parts: 233 upper and 291 lower beaks and one fish eye lens. The majority of the identified cephalopod beaks belonged to Histioteuthis bonnellii, but a few beaks of Galiteuthis armata and Octopoteuthis sp. were also found. A new beak size–cephalopod size regression was created for H. bonnellii with specimens caught in the study area. Reconstructed prey weight for the species was much higher when applying this new regression instead of Clarke's, highlighting the need for area- and species-specific regressions for dietary studies. Our analysis represents the second report on the stomach contents of sperm whales from the Mediterranean and the first available information for the Western basin.
Effects of phosphorus deficiency stress on protective enzyme activities, MDA content and chromosome of wheat substitution lines.

The effects of phosphorus deficiency stress on physiological characteristic and chromosome response in wheat was studied by determining protective enzyme activities and MDA content and locating the gene controlling protective enzyme activity and MDA content at different developing stages using wheat substitution lines between Chinese Spring(CS) and Synthetic 6x.The results showed that SOD and POD activities,and MDA content increased under phosphorus deficiency stress.The genes promoting SOD activity might be located on 2A,3B,2D and 7D chromosome of Synthetic 6x;and the genes promoting POD activity might be located on 2A,5A,6A,7B and 7D chromosome,while the genes inhibiting MDA content might be located on 5A,2D,5D and 7D chromosome of Synthetic 6x.
Wind-Blown Soil in the Epidemiology of Bacterial Leaf Spot of Alfalfa and Common Blight of Bean

Potted, healthy alfalfa and bean plants were placed in a laboratory wind tunnel and exposed to naturally infested dry field soil blown at regulated air speeds. The plants were then kept on a greenhouse bench for 10-14 days, and the resulting incidence of bacterial leaf spot of alfalfa and common blight of bean was determined. Disease incidence increased as wind speed and exposure time increased and was greater in the row nearest the wind source. Lesions were mostly contined to the lower 10-cm of plant shoots where the blowing particles were most concentrated. Lesions on stems were confined to their windward side. Bacterial leaf spot incidence increased from 6% after 3-min exposure to soil blown 9.4 m/sec to 26% after 5-min exposure at 13.9 m/sec. Blight incidence in 2-week-old bean plants from exposure to soil blown 13.9 a/sec for 3 and 5 min was 25 and 55%, respectively. Phytopathology 63: 1417-1419 Additional key words: wind, Xanthomonas alfalfae, Xanthomonas phaseoli. Researchers (1, 6, 8) have suggested that wind-blown soil and debris not only disseminate bacterial plant pathogens but wound host tissue and permit bacterial penetration. Vakili (7) reported wind-blown, naturally infested soil t o be important in the epidemiology of bacterial spot of tomatoes in the field. Plant injury caused by wind-blown sand or soil is well documented. Wind speeds of 17.9 mlsec (40 mph) without abrasive flux slightly damaged green bean plants but adding 6 g/cm widthlmin of sand into the wind-stream greatly increased injury and reduced yields up to 53% (5). The average yield reduction of alfalfa exposed to sand blown at 7 wind velocities between 8.9 m/sec (20 mph) and 13.9 m/sec (31 mph) for 12 min was 55% (4). In Kansas, summer prevailing winds are from the south, and most stem lesions of common blight of beans and bacterial leaf spot of alfalfa occur on their south side, frequently during hot, dry periods. This suggests that wind-blown soil could be an inoculating agent. The effects on the incidence of bacterial leaf spot of alfalfa and common blight of bean from exposing healthy plants to naturally infested soil or artificially infested sand blown at different speeds and durations in a wind tunnel are reported in this
A Yoga-Based Program Decreases Physician Burnout in Neonatologists and Obstetricians at an Academic Medical Center

Background Nearly half of U.S. pediatricians have symptoms of burnout. This pilot study examined the feasibility of a 6-week yoga-based program (RISE) for neonatologists and obstetricians at Brigham and Women’s Hospital and studied the effects on burnout, professional fulfillment, and psychological health. Methods Participants were recruited via email to participate either in both program and research study, or exclusively the program. RISE was delivered 1 hour/week during the workday for 6 consecutive weeks either in-person or remotely; 18 physicians participated, 12 completed post-program, and 11 completed 2-month follow-up. The questionnaires assessed burnout and measures of psychological health, professional fulfillment, work exhaustion, interpersonal disengagement/burnout (PFI), mindfulness (FFMQ), perceived stress (PSS), positive/negative affect (PANAS), resilience (RS), anxiety/depression/sleep disturbances (PROMIS), at baseline, post-program, and 2 months after RISE. Findings Average attendance in-person was 2.8 sessions and remotely 1.4 sessions (4.2/6 sessions). Participants demonstrating total burnout reduced from 50.0% at baseline to 9.1% post-program. Participants demonstrating professional fulfillment were 8.3% at baseline and 27.3% post-program. Paired samples t-tests revealed statistically significant improvements in burnout, professional fulfillment, interpersonal disengagement, stress, resilience, anxiety, and depression at post-program compared with baseline (N = 12, all ps < .05). At 2-month follow-up, statistically significant improvements in interpersonal disengagement, resilience, and mindfulness (N = 11, all ps < .05) compared with baseline were reported. Conclusions/Application to Practice RISE is feasible within a workday and may address burnout and other psychological health measures in physicians with effects potentially sustainable over 2 months. Occupational health practitioners in health care should consider this type of intervention for their workers.
Growth Profile of Crown Gall Cells of Tobacco in Suspension Culture

In order to obtain a basic information of plant cell suspension culture as a step toward the development of large scale culture, culture conditions of crown gall cells (auxin non-requiring cells) were investigated. Addition of yeast extract to culture medium was significantly effective for the growth and cell dispersion.In experiments on the ability of the cultured cells to utilize sugars as the carbon source, it was observed that galactose, added to the culture medium, markedly inhibited the cell growth.Pasteurization of the medium containing fructose as carbon source made it brownish by Maillard reaction and the medium apparently restrained the cell growth. However, the fructose medium sterilized by filtration was excellent for the cell growth as well as sucrose or glucose medium. In a jar fermentor, even the glucose medium became brownish by heat sterilization and the brown colored medium restrained the cell growth. Under optimum conditions, the doubling time was 1.1 day in exponential phase and 2.0 g .
WhatsApp as an Emergency Teleradiology Application for Cranial CT Assessment in Emergency Services.

OBJECTIVE To evaluate the diagnostic agreement of transmitted images of cranial CT due to trauma, through WhatsApp software compared to workstation image-based diagnosis. STUDY DESIGN Observational study. PLACE AND DURATION OF STUDY Department of Emergency Medicine, Adiyaman University Training and Research Hospital, from January 2017 to May 2018. METHODOLOGY A total of 94 cases that presented to the Emergency Department and underwent cranial CT were included in the study. CT images were video-recorded by the emergency physician using an Apple iPhone 7. The images were evaluated by two different radiologists using Samsung Galaxy Edge 7 and Samsung Note 8 mobile phones. Later, the radiological images were reviewed by two different radiologists at the PACS workstation. Then, the WhatsApp-mediated and final diagnoses were compared for various lesions to evaluate the interobserver agreement and diagnostic success of the use of WhatsApp software. RESULTS In the assessment of the interobserver agreement, the kappa values were found to be 0.89 for normal findings, 0.84 for subdural hematoma, 0.73 for subarachnoid hemorrhage, 0.81 for epidural hematoma, 0.85 for fractures, 1 for parenchymal hematoma, and 0.68 for parenchymal contusion. CONCLUSION Although WhatsApp can be used in the evaluation of emergency cranial CT images, it is essential to note that some findings, especially those indicating fractures, subdural hematoma, and parenchymal contusion, can be overlooked. Key Words: Teleradiology, PACS, Medical software, Computed tomography, WhatsApp, Instant Messenger.
Trifluoperazine induces cellular apoptosis by inhibiting autophagy and targeting NUPR1 in multiple myeloma

Multiple myeloma (MM) is the second most common hematologic malignancy of immunoglobulin‐secreting plasma cells. Recent modern combination therapies have improved survival rates, but many patients develop resistance to novel drugs, leading to relapse. Trifluoperazine (TFP), a typical antipsychotic drug, has been reported to exert antitumor effects by targeting various pathways. Thus far, the role of TFP in MM has not been elucidated. In the current study, we demonstrated that TFP inhibited cell growth and autophagy activity but induced apoptosis of U266 and RPMI 8226 MM cells. Furthermore, cotreatment of these cell lines with TFP and rapamycin, a potent autophagy inducer, reduced cell apoptosis compared with TFP treatment alone. We also found that TFP inhibited nuclear protein 1 (NUPR1) expression. In the presence of TFP, cells stably overexpressing NUPR1 showed a higher viability than cells treated with the nonspecific control. Autophagy suppression and apoptosis induction caused by TFP were also reversed in MM cells upon NUPR1 overexpression. Overall, our results indicate that in the context of MM, TFP targets NUPR1, inhibiting cell growth and inducing apoptosis by autophagy inhibition. Our results could contribute toward efforts for the development of more effective therapies for MM to be tested in future clinical trials.
The Integrated Analyses of Driver Genes Identify Key Biomarkers in Thyroid Cancer

Aim: Thyroid cancer is the most common endocrine cancer, the incidence rate has continuously increased worldwide. However, there are still lack of effective molecular biomarkers for the diagnosis and treatment of the disease. The study was conducted to identify driver genes that may serve as potential biomarkers for the disease. Methods: The computational tools oncodriveCLUST, oncodriveFM, icages and drgap were used to detect driver genes in thyroid cancer using somatic mutations from The Cancer Genome Atlas database. Integrated analyses were performed on the driver genes using multiomics data from the TCGA database. Results: A set of 291 driver genes were identified in thyroid cancer. BRAF, NRAS, HRAS, OTUD4, EIF1AX were the top 5 frequently mutated genes in thyroid cancer. The weighted gene co-expression network analysis identified 4 coexpression modules. The modules 1-3 were significantly associated with patients’ tumor size, residual tumor, cancer stage, distant metastasis and multifocality. SEC24B, MET and ITGAL were the hub genes in the modules 1-3 respectively. Hierarchical clustering analysis of the 20 driver genes with the most frequent copy number changes revealed 3 clusters of PRAD patients. Cluster 1 tumors exhibited significantly older age, tumor size, cancer stages, and poorer prognosis than cluster 2 and 3 tumors. 16 genes were significantly associated with number of lymph nodes, tumor size and pathologic stage, such as IL7 R, IRS1, PTK2B, MAP3K3 and FGFR2. Conclusions: The set of cancer genes and subgroups of patients shed insight on the tumorigenesis of thyroid cancer and open up avenues for developing prognostic biomarkers and driver gene-targeted therapies in thyroid cancer.