Miracle-dz/UniFAR-FTUs huggingface dataset:
Counterexample-based Refinement for Powerset Domains

Counterexample-based Refinement for Powerset Domains R. Manevich, J. Field , T. A. Henzinger, G. Ramalingam, and M. Sagiv 1 Tel Aviv University, {rumster,msagiv}@tau.ac. il 2 IBM T.J. Watson Research Center, jfield@watson.ibm. com 3 EPFL, tah@epfl.ch 4 Microsoft Research India, grama@microsoft.com Abstract. Counterexample-guided abstraction refinement (CEGAR) is a powerful technique to scale automatic program analysis techniques to large programs. However, so far it has been used primarily for model checking in the context of predicate abstraction. We formalize CEGAR for general powerset domains. If a spurious abstract counterexample needs to be removed through abstraction refinement, there are often several choices, such as which program location(s) to refine, which abstract domain(s) to use at different locations, and which abstract values to compute. We define several plausible preference orderings on abstracCounterexample-guided abstraction refinement (CEGAR) is a powerful technique to scale automatic program analysis techniques to large programs. However, so far it has been used primarily for model checking in the context of predicate abstraction. We formalize CEGAR for general powerset domains. If a spurious abstract counterexample needs to be removed through abstraction refinement, there are often several choices, such as which program location(s) to refine, which abstract domain(s) to use at different locations, and which abstract values to compute. We define several plausible preference orderings on abstraction refinements, such as refining as “late” as possible and as “coarse” as possible. We present generic algorithms for finding refinements that are optimal with respect to the different preference orderings. We also compare the different orderings with respect to desirable properties, including the property if locally optimal refinements compose to a global optimum. Finally, we point out some difficulties with CEGAR for nonpowerset domains.
Cryopreservation of chicken blastodermal cells and their quality assessment by flow cytometry and transmission electron microscopy

The goal of this study was to evaluate effect of slow freezing and vitrification methods on the viability of chicken blastodermal cells (BCs). Proper aliquot of isolated BCs were diluted in the freezing medium composed of 10% DMSO and frozen in the freezing vessel BICELL to reach desired temperature up to −80°C. Then samples were immersed in liquid nitrogen. Other cell aliquot was vitrified in solution containing 10% DMSO and samples were immediately immersed in the liquid nitrogen. The viability of fresh and frozen/thawed BCs was evaluated using Trypan blue method and flow cytometry. Flow cytometry analysis was provided by DRAQ5 dye in combination with Live‐Dead kit. Overall, this technique provides both quantitative and qualitative information about BCs. Results obtained from Trypan blue method showed significant differences (P < 0.05) between control (8.37 ± 1.04%) slow freezing (83.73 ± 2.72%) and vitrification group (84.39 ± 1.77%) in the percentage of Trypan blue positive (necrotic) BCs. Moreover, differences (P < 0.05) between control and slow freezing (5.08 ± 1.94%, 73.31 ± 3.90%) and control and vitrification group (2.97 ± 0.30%, 79.02 ± 1.56%) in results on portion of necrotic cells (DRAQ5+/LD+) analyzed by flow cytometry were also observed. The large percentage of necrotic BCs was found in all freezing methods. However, based on ultrastructural analysis, our study showed, that BCs contain lipid granules which prevent successful freezing even though different methods of cryopreservation were used. Thus, freezing of BCs probably required subsequent culture to eliminate lipid droples and yolk granules in the cells, which could possibly improve the success. © 2018 American Institute of Chemical Engineers Biotechnol. Prog. , 34:778–783, 2018
Clinical outcomes of patients with symptomatic acetabular rim fractures after arthroscopic FAI treatment

ABSTRACT This study aims to investigate the influence of the acetabular rim fractures on outcomes of hip arthroscopy at minimum 2-year follow-up. Between January 2009 and August 2012, data were prospectively collected on all patients undergoing hip arthroscopy. Anatomic findings, including presence of rim fractures, were recorded intraoperatively. Patients were assessed preoperatively and at 3 months, 1 year and minimum 2 years postoperatively with four patient-reported outcome measures: modified Harris Hip Score, Non-Arthritic Hip Score, Hip Outcome Score-Activities of Daily Living and Hip Outcome Score-Sport Specific Subscales. Pain was estimated using a visual analog scale. Satisfaction was measured on a scale from 0 to 10. Patients with rim fractures were identified and retrospectively matched to a control group based on gender, BMI category, and age at surgery within 3 years and compared in terms of demographic factors, intraoperative findings, procedures and outcomes. Twenty-one patients with rim fractures were matched to a control group of 21 patients with symptomatic femoroacetabular impingement without rim fractures. No significant differences were detected with respect to demographic characteristics, surgical procedures (besides the removal of rim fractures), or in terms of preoperative, postoperative, or improvement in patient-reported outcome scores and satisfaction. The presence or absence of an acetabular rim fracture does not significantly influence clinical outcomes at minimum 2-year follow-up after hip arthroscopy. Case–control study design is used in this study.
Genetic algorithm for solving minimal exposure path in mobile sensor networks

The Minimal Exposure Path (MEP) is a fundamental factor to measure quality of service in Wireless Sensor Networks (WSNs). The MEP not only improves the performance of WSNs but also guides the action of agents in the sensing field. Up to now, MEP has been focusing on solving problems in stationary sensor networks. MEP with both high dimensionality and non-linear property in stationary WSNs is NP-hard problem. This paper formulated a problem of finding the MEP in Mobile Sensor Networks (MSNs), in which sensors' mobility plays an important role in the execution of application, and then proposed a genetic algorithm to solve it. Our methodology is not only to calculate upper and lower bounds of exposure value, but also to determine the MEP trajectory. The proposed algorithm was experimented on 30 random instances with various numbers of mobile sensors and different velocities of intruder which are proportional to the velocity of sensors. We also compared the minimal exposure value obtained from MSNs model with the one obtained from static sensor network model. Experimental results showed that our genetic algorithm is stable, convergent and effective when applying in both mobile and static models of WSNs.
DECENTRALISED ACTIVE VIBRATION CONTROL USING A REMOTE SENSING STRATEGY

In many applications it is desirable to use a decentralised control strategy, in which multiple sensor-actuator pairs are utilised to control the response of a structure. This avoids the need for connections between multiple sensors and actuators and allows the system to be easily scaled to different applications. However, because the individual control loops, consisting of a single sensor-actuator pair, only have a direct measurement of the local vibration signal it is not straightforward to guarantee global reduction of the kinetic energy of the structure. In this paper a novel decentralised control strategy is proposed in which the vibration at remote locations is estimated utilising the local error sensor signal and the local control loop is then adapted to minimise the sum of both the squared local and the estimated remote error signals. When multiple loops are employed, it is also necessary for each local control loop to predict the global effect of the remote control signals and use this information in the adaptation of the local control loop. This paper describes the proposed control strategy, including the calibration of the algorithm and the estimation of the error and control signals. The proposed control strategy is evaluated through simulation of an acoustically excited flat panel and its performance is compared to both standard centralised and decentralised control strategies.
Overexpression of the Receptor Tyrosine Kinase Tie-1 Intracellular Domain in Breast Cancer

Objective: Tyrosine kinase with immunoglobulin and epidermal growth factor homology domains (Tie-1) is a receptor tyrosine kinase that regulates angiogenesis and antiapoptotic survival signaling. Tie-1 expression is generally associated with endothelial cells and neovascularization. We previously identified Tie-1 in human breast tumor samples using a PCR-based screen for protein kinases expressed in breast tumors. The purpose of this study was to determine the cell types expressing Tie-1, whether Tie-1 is expressed in tumor cells, and to examine the regulation of Tie-1 in breast cancer. Methods: Tie-1 expression was analyzed by Western blot and immunohistochemistry using an antibody to the carboxy terminus of Tie-1. Tie-1 expression was determined in a variety of cancer cell lines, clinical breast and colon tumor samples, and in corresponding benign tissue from the same patient. Tie-1 expression and distribution in breast tumors was scored by immunohistochemistry. Results: Tie-1 was overexpressed in 14/23 breast tumors compared with 0/9 corresponding normal tissues from the same patients. Immunohistochemistry revealed that Tie-1 was overexpressed in epithelial breast cancer cells and ductal carcinoma in situ. In all breast tumor samples, Tie-1 was expressed as a truncated 40- to 43-kD doublet consisting of the intracellular portion of the protein, which contains the tyrosine kinase catalytic domain. The 40- to 43-kD Tie-1 doublet was expressed in a broad variety of cell lines. Conclusions: We have shown that breast cancer cells overexpress a cleaved form of the Tie-1 protein. Our results implicate the intracellular domain of Tie-1, which includes the catalytic kinase domain, in breast cancer progression.
Clinical significance of cerebral microbleeds on MRI: A comprehensive meta-analysis of risk of intracerebral hemorrhage, ischemic stroke, mortality, and dementia in cohort studies (v1)

Background Cerebral microbleeds can confer a high risk of intracerebral hemorrhage, ischemic stroke, death and dementia, but estimated risks remain imprecise and often conflicting. We investigated the association between cerebral microbleeds presence and these outcomes in a large meta-analysis of all published cohorts including: ischemic stroke/TIA, memory clinic, “high risk” elderly populations, and healthy individuals in population-based studies. Methods Cohorts (with > 100 participants) that assessed cerebral microbleeds presence on MRI, with subsequent follow-up (≥3 months) were identified. The association between cerebral microbleeds and each of the outcomes (ischemic stroke, intracerebral hemorrhage, death, and dementia) was quantified using random effects models of (a) unadjusted crude odds ratios and (b) covariate-adjusted hazard rations. Results We identified 31 cohorts (n = 20,368): 19 ischemic stroke/TIA (n = 7672), 4 memory clinic (n = 1957), 3 high risk elderly (n = 1458) and 5 population-based cohorts (n = 11,722). Cerebral microbleeds were associated with an increased risk of ischemic stroke (OR: 2.14; 95% CI: 1.58–2.89 and adj-HR: 2.09; 95% CI: 1.71–2.57), but the relative increase in future intracerebral hemorrhage risk was greater (OR: 4.65; 95% CI: 2.68–8.08 and adj-HR: 3.93; 95% CI: 2.71–5.69). Cerebral microbleeds were an independent predictor of all-cause mortality (adj-HR: 1.36; 95% CI: 1.24–1.48). In three population-based studies, cerebral microbleeds were independently associated with incident dementia (adj-HR: 1.35; 95% CI: 1.00–1.82). Results were overall consistent in analyses stratified by different populations, but with different degrees of heterogeneity. Conclusions Our meta-analysis shows that cerebral microbleeds predict an increased risk of stroke, death, and dementia and provides up-to-date effect sizes across different clinical settings. These pooled estimates can inform clinical decisions and trials, further supporting cerebral microbleeds role as biomarkers of underlying subclinical brain pathology in research and clinical settings.
Predicting the presence of pulmonary function impairment in adult respiratory distress syndrome survivors.

Varying degrees of impairment in pulmonary function in survivors of adult respiratory distress syndrome (ARDS) have been reported. Physiologic indices of the severity of disease have been associated with impaired pulmonary function after ARDS, including duration of exposure to FIO2 > 0.6, AaDO2, maximal mean pulmonary artery pressure, lowest total static thoracic compliance, and peak airway pressure. Prediction of impairment following ARDS is difficult because clinical observations may reflect reversible lung injury (e.g. lung edema) and clinical features of ARDS do not predict subsequent function reliably. We developed a severity score to predict the presence of impairment of pulmonary function in 51 ARDS survivors, by examining the following clinical variables: (1) predisposing factor for ARDS; (2) age; (3) sex; (4) severity of hypoxemia; (5) smoking history; (6) number of days of positive pressure ventilation; (7) lowest total static thoracic compliance; (8) maximal mean pulmonary artery pressure, and (9) presence of barotrauma. Pulmonary function studies were performed at least 1 year after ARDS onset. The ARDSscore developed required only two variables: ARDSscorce = duration of positive pressure ventilation (days) minus lowest static thoracic compliance (ml/cm H2O). Significant correlations (p < 0.001) were found between linear regressions of percent predicted FEV1, FVC, TLC and DLCO against ARDSscore. ARDSscore > +20 predicted an 82% probability of impaired FEV1, FVC or TLC and a 100% probability of an impaired DLCO. We conclude that a score based upon duration of positive pressure ventilation and lowest static thoracic compliance predicts impaired pulmonary function more than 1 year after ARDS.
Malnutrition, Growth Response and Metabolic Changes Within the First 24 Months After ART Initiation in HIV-infected Children Treated Before the Age of 2 Years in West Africa

Background: There is limited information about malnutrition, growth evolution and metabolic changes among children initiated early on lopinavir-based antiretroviral therapy (ART) in Africa. Methods: HIV-1-infected children, age <2 years were initiated on ART, as part of the MONOD ANRS 12206 project, conducted in Burkina Faso and Côte d’Ivoire. Weight-for-age, height-for-age and weight-for-height Z scores defined malnutrition [Z score less than −2 standard deviations (SDs)] using World Health Organization growth references. Biologic data were collected every 6 months. Factors associated with baseline malnutrition were evaluated using multivariate logistic regression, and with growth evolution in the first 24 months on ART using linear mixed models. Results: Between 2011 and 2013, 161 children were enrolled: 64% were from Abidjan, 54% were girls. At ART initiation, median age was 13.7 months (interquartile range 7.7; 18.4), 52% were underweight (weight-for-age), 52% were stunted (height-for-age) and 36% were wasted (weight-for-height). Overall, baseline malnutrition was more likely for children living in Burkina Faso, with low birth weight, never breastfed and older age (12–24 months). Growth improved on ART, mainly within the first 6 months for weight, and was greater for the most severely malnourished children at baseline, but 8%–32% remained malnourished after 24 months. Over the 24-month period of ART, there was a significant increase of hypercholesterolemia and decrease of anemia and hypoalbuminemia. Conclusions: Prevalence of malnutrition was high before ART initiation. Even though growth improved on ART, some children remained malnourished even after 2 years of ART, highlighting the need for more active nutritional support.
RSF: A recommendation system for farmers

In this paper, we present a recommendation system named as RSF for farmers, which can recommend farmers most suitable crops to produce in different areas. The system first detects a user's location and works with different agro-ecological and agro-climatic data in upazila level to calculate similarity between upazilas using Pearson co-relation similarity algorithm. Then it selects top-n similar upazilas. Finally, utilizing the seasonal information and crop production rates of each crop of the similar upazilas, it recommends top-fc crops to a user of a upazila. The system has been evaluated with real data and we have found a reasonable and satisfactory accuracy. The system can help farmers in producing appropriate crops. As a result, they can increase their lifestyle and can contribute more to the society. We provided the system layout both in Bangla and English so that the farmers as well as the people who works with farmers can get help easily from this.
Long-Term Effects of the Substituted Benzamide Derivative Amisulpride on Baseline and Stimulated Prolactin Levels

In the present study, we investigated the long-term effects of treatment with amisulpride, a substituted benzamide derivative, as compared with the effects of treatment with flupenthixol, a thioxanthene, on the prolactin levels in schizophrenic patients. After completing 6 weeks of medication with either amisulpride or flupenthixol, the patients entered a long-term maintenance treatment with amisulpride 200–600 mg/day or flupenthixol 5–15 mg/day for a maximum of 12 months with a subsequent drug-free follow-up until month 15. Eighteen initially included patients were still participating in the study at month 6. In the flupenthixol group, only 1 patient treated reached month 12, and none of the patients reached month 15. For the amisulpride treatment group, months 12 and 15 were completed by 9 and 6 patients, respectively. After 1, 3, 6, and 12 months of treatment, and finally 3 months after cessation of treatment, the basal and thyrotropin-releasing hormone-stimulated secretions of prolactin were investigated. The prolactin plasma levels were elevated in both treatment groups during the course of maintenance treatment with a maximum effect at month 1. Flupenthixol treatment initially raised the prolactin levels about two- or threefold, and a subsequent decline during months 3 and 6 occurred. However, only the changes for month 1 reached the level of a statistical trend. The prolactin secretion was initially increased over tenfold by amisulpride. The prolactin levels at months 1, 3, 6, and 12 were significantly elevated as compared with the baseline values. A continuous decline of prolactin levels in both treatment groups occurred over the course of the next months. The prolactin response after the thyrotropin-releasing hormone challenge was not significantly changed over the long-term course. Notably, in the amisulpride group, 3 months after cessation of treatment at month 12, the elevated levels of prolactin returned to baseline at month 15. In summary, amisulpride demonstrated more pronounced effects than flupenthixol on the prolactin levels. However, the findings indicate also that treatment with amisulpride at clinically effective doses can be achieved at significantly lower prolactin levels during the long-term maintenance phase than during the prior acute phase.
Control of cell number in the bed nucleus of the stria terminalis of mice: role of testosterone metabolites and estrogen receptor subtypes.

INTRODUCTION The bed nucleus of the stria terminalis (BNST) exhibits several sex differences that may be related to male sexual behavior and gender identity. In mice and rats, sex differences in the principal nucleus of the BNST (BNSTp) are due to sexually dimorphic cell death during perinatal life. Although testosterone treatment of newborn female rats increases BNSTp cell number, the relevant hormone metabolite(s) are not known, and the effect of testosterone on the development of BNSTp cell number in mice has not been examined. AIM To identify the sex hormone metabolites and receptors controlling cell number, volume, and cell size in the BNSTp of mice. METHODS In the first experiment, C57BL/6J male mice were injected on the day of birth with peanut oil; females were injected with testosterone propionate (TP), estradiol benzoate (EB), dihydrotestosterone propionate (DHTP), or oil alone, and the BNSTp of all animals was examined in adulthood. In the second experiment, to compare effects of EB to the effects of estrogen receptor subtype specific agonists, newborn female mice were injected with EB, propyl-pyrazole-triol (PPT, a selective estrogen receptor alpha [ERalpha] agonist), or diarylpropionitrile (DPN, a selective estrogen receptor beta [ERbeta] agonist). MAIN OUTCOME MEASURES Nuclear volume measurements and stereological cell counts in the BNSTp in adulthood. RESULTS TP treatment of newborn females completely masculinized both BNSTp volume and cell number. EB masculinized neuron number, whereas DHTP had no effect on volume or cell number. In the second experiment, EB again fully masculinized neuron number in the BNSTp and in this study also masculinized BNSTp volume. PPT and DPN each significantly increased cell number, but neither completely mimicked the effects of EB. CONCLUSIONS We conclude that estrogenic metabolites of testosterone control sexually dimorphic cell survival in the BNSTp and that activation of both ERalpha and ERbeta may be required for complete masculinization of this brain region.
Microcystin-LR degradation utilizing a novel effective indigenous bacterial community YFMCD1 from Lake Taihu

ABSTRACT Microcystins (MC) produced by species of cyanobacteria including Microcystis, Anabaena, and Aphanizomenon are a group of monocyclic hepatotoxins posing serious threat to public health. Microcystin-LR (MC-LR) is the most toxic and frequently encountered microcystin variant in the environment, and thus removal of this toxin using bacteria was shown to be a reliable, efficient, and cost-effective method that avoids utilization of chemicals that may produce potentially harmful by-products. The aim of this study was to determine whether a novel indigenous bacterial community designated YFMCD1 was effective in destroying MC. In addition, the influence of environmental factors such as temperature, MC concentration, and pH was examined on the effectiveness of YFMCD1 to degrade MC-LR. MC-degradation products were identified by high performance liquid chromatography coupled with an ultra-high resolution LTQ Orbitrap Velos Pro ETD mass spectrometry equipped with electrospray ionization interface (HPLC-ESI-MS). MC-LR underwent maximal degradation at rate of 0.5 µg/ml/hr with YFMCD1 containing Klebsiella sp. termed YFMCD1-1 or Stenotrophomonas sp. termed YFMCD1-2. Moreover, Adda (3-amino-9-methoxy-2, 6, 8-trimethyl-10-phenyldeca-4, 6-dienoic acid) is a constituent within the MC-LR molecule found to be responsible for biological activity expression and critical for MC-induced toxicity, which is also degraded by YFMCD1. The results showed that YFMCD1 effectively degraded MC-LR. The degradation rate was significantly affected by temperature, pH, and MC-LR concentrations. Data indicate that this bacterial community may prove beneficial in bioremediation of lakes containing MC.