Miracle-dz/UniFAR-FTUs huggingface dataset:
Model Checking MDPs with a Unique Compact Invariant Set of Distributions

The semantics of Markov Decision Processes (MDPs), when viewed as transformers of probability distributions, can described as a labeled transition system over the probability distributions over the states of the MDP. The MDP can be seen as defining a set of executions, where each execution is a sequence of probability distributions. Reasoning about sequences of distributions allows one to express properties not expressible in logics like PCTL, examples include expressing bounds on transient rewards and expected values of random variables, as well as comparing the probability of being in one set of states at a given time with another set of states. With respect to such a semantics, the problem of checking that the MDP never reaches a bad distribution is undecidable~\cite{qest10}. In this paper, we identify a special class of MDPs called \emph{semi-regular} MDPs that have a unique non-empty, compact, invariant set of distributions, for which we show that checking any $\omega$-regular property is decidable. Our decidability result also implies that for semi-regular probabilistic finite automata with isolated cut-points, the emptiness problem is decidable.
Sigma factor selectivity in Borrelia burgdorferi: RpoS recognition of the ospE/ospF/elp promoters is dependent on the sequence of the −10 region

Members of the ospE/ospF/elp lipoprotein gene families of Borrelia burgdorferi, the Lyme disease agent, are transcriptionally upregulated in response to the influx of blood into the midgut of an infected tick. We recently have demonstrated that despite the high degree of similarity between the promoters of the ospF (PospF) and ospE (PospE) genes of B. burgdorferi strain 297, the differential expression of ospF is RpoS‐dependent, while ospE is controlled by σ70. Herein we used wild‐type and RpoS‐deficient strains of B. burgdorferi and Escherichia coli to analyse transcriptional reporters consisting of a green fluorescent protein (gfp) gene fused to PospF, PospE, or two hybrid promoters in which the −10 regions of PospF and PospE were switched [PospF (E − 10) and PospE (F − 10) respectively]. We found that the PospF−10 region is both necessary and sufficient for RpoS‐dependent recognition in B. burgdorferi, while σ70 specificity for PospE is dependent on elements outside of the −10 region. In E. coli, sigma factor selectivity for these promoters was much more permissive, with expression of each being primarily due to σ70. Alignment of the sequences upstream of each of the ospE/ospF/elp genes from B. burgdorferi strains 297 and B31 revealed that two B31 ospF paralogues [erpK (BBM38) and erpL (BBO39)] have −10 regions virtually identical to that of PospF. Correspondingly, expression of gfp reporters based on the erpK and erpL promoters was RpoS‐dependent. Thus, the sequence of the PospF−10 region appears to serve as a motif for RpoS recognition, the first described for any B. burgdorferi promoter. Taken together, our data support the notion that B. burgdorferi utilizes sequence differences at the −10 region as one mechanism for maintaining the transcriptional integrity of RpoS‐dependent and ‐independent genes activated at the onset of tick feeding.
Presence of Viral RNA and Proteins in Exosomes from Cellular Clones Resistant to Rift Valley Fever Virus Infection

Rift Valley Fever Virus (RVFV) is a RNA virus that belongs to the genus Phlebovirus, family Bunyaviridae. It infects humans and livestock and causes Rift Valley fever. RVFV is considered an agricultural pathogen by the USDA, as it can cause up to 100% abortion in cattle and extensive death of newborns. In addition, it is designated as Category A pathogen by the CDC and the NIAID. In some human cases of RVFV infection, the virus causes fever, ocular damage, liver damage, hemorrhagic fever, and death. There are currently limited options for vaccine candidates, which include the MP-12 and clone 13 versions of RVFV. Viral infections often deregulate multiple cellular pathways that contribute to replication and host pathology. We have previously shown that latent human immunodeficiency virus-1 (HIV-1) and human T-cell lymphotropic virus-1 (HTLV-1) infected cells secrete exosomes that contain short viral RNAs, limited number of genomic RNAs, and viral proteins. These exosomes largely target neighboring cells and activate the NF-κB pathway, leading to cell proliferation, and overall better viral replication. In this manuscript, we studied the effects of exosome formation from RVFV infected cells and their function on recipient cells. We initially infected cells, isolated resistant clones, and further purified using dilution cloning. We then characterized these cells as resistant to new RVFV infection, but sensitive to other viral infections, including Venezuelan Equine Encephalitis Virus (VEEV). These clones contained normal markers (i.e., CD63) for exosomes and were able to activate the TLR pathway in recipient reporter cells. Interestingly, the exosome rich preparations, much like their host cell, contained viral RNA (L, M, and S genome). The RNAs were detected using qRT-PCR in both parental and exosomal preparations as well as in CD63 immunoprecipitates. Viral proteins such as N and a modified form of NSs were present in some of these exosomes. Finally, treatment of recipient cells (T-cells and monocytic cells) showed drastic rate of apoptosis through PARP cleavage and caspase 3 activation from some but not all exosome enriched preparations. Collectively, these data suggest that exosomes from RVFV infected cells alter the dynamics of the immune cells and may contribute to pathology of the viral infection.
Computational Modeling of Interactions between Multiple Myeloma and the Bone Microenvironment

Multiple Myeloma (MM) is a B-cell malignancy that is characterized by osteolytic bone lesions. It has been postulated that positive feedback loops in the interactions between MM cells and the bone microenvironment form reinforcing ‘vicious cycles’, resulting in more bone resorption and MM cell population growth in the bone microenvironment. Despite many identified MM-bone interactions, the combined effect of these interactions and their relative importance are unknown. In this paper, we develop a computational model of MM-bone interactions and clarify whether the intercellular signaling mechanisms implemented in this model appropriately drive MM disease progression. This new computational model is based on the previous bone remodeling model of Pivonka et al. [1], and explicitly considers IL-6 and MM-BMSC (bone marrow stromal cell) adhesion related pathways, leading to formation of two positive feedback cycles in this model. The progression of MM disease is simulated numerically, from normal bone physiology to a well established MM disease state. Our simulations are consistent with known behaviors and data reported for both normal bone physiology and for MM disease. The model results suggest that the two positive feedback cycles identified for this model are sufficient to jointly drive the MM disease progression. Furthermore, quantitative analysis performed on the two positive feedback cycles clarifies the relative importance of the two positive feedback cycles, and identifies the dominant processes that govern the behavior of the two positive feedback cycles. Using our proposed quantitative criteria, we identify which of the positive feedback cycles in this model may be considered to be ‘vicious cycles’. Finally, key points at which to block the positive feedback cycles in MM-bone interactions are identified, suggesting potential drug targets.
Scintillography of Infantile Subdural Effusions and its Clinical Application

Progress in the treatment of persistent subdural collections of fluid in infancy must be based on further knowledge ofvarious pathogenetic factors influencing the course of this disease. The most common neurosurgical therapy is excision of the subdural membranes when present to eliminate the presumably restrictive effects of these membranes on the developing brain (5). It has also been suggested that removal of subdural membranes and their abnormally permeable blood vessels could prevent recollections of fluid (4, 7). Usually, a conventional centrolateral craniotomy is done if subdural membranes are found by exploratory burr holes. Recently, persistent reaccumulations of subdural fluid and the eventual clinical outcome have been related more to the disproportion between a contracted, poorly expansile brain and a larger skull than to the postulated effects of retained subdural membranes (8, 11). The role of neuroradiology in the study and management of subdural effusions in infancy has not been established clearly. Since a definitive diagnosis can be made in these cases by a needle puncture, contrast procedures such as lumbar encephalography and ventriculography have not been found necessary as a rule, or even desirable (5). Subdural air encephalography can visualize
Reproductive health service integration in south africa.

Background Health care in national and international settings is undergoing extensive change. In South Africa, efforts to integrate services at clinic level and increase accessibility are under way. This study explored nurses' views on reproductive health service integration, its effects on clients and nurses, and supervisory support. Face-to-face interviews were conducted with 32 nurses from four clinics. Results Nurses perceived integration to be beneficial. The process of integration was seen by some nurses as unstructured, difficult and slow, while others viewed it as necessary and well planned. Most nurses perceived supervisory visits as useful, but wanted managers to be prompt in solving problems and giving feedback about the clinic. Conclusion Health managers wishing to develop and implement effective policies should engage and support their staff throughout the process of change.
Raising Graphs From Randomness to Reveal Information Networks

We analyze the fine-grained connections between the average degree and the power-law degree distribution exponent in growing information networks. Our starting observation is a power-law degree distribution with a decreasing exponent and increasing average degree as a function of the network size. Our experiments are based on three Twitter at-mention networks and three more from the Koblenz Network Collection. We observe that popular network models cannot explain decreasing power-law degree distribution exponent and increasing average degree at the same time. We propose a model that is the combination of exponential growth, and a power-law developing network, in which new "homophily" edges are continuously added to nodes proportional to their current homophily degree. Parameters of the average degree growth and the power-law degree distribution exponent functions depend on the ratio of the network growth exponent parameters. Specifically, we connect the growth of the average degree to the decreasing exponent of the power-law degree distribution. Prior to our work, only one of the two cases were handled. Existing models and even their combinations can only reproduce some of our key new observations in growing information networks.
Quality of Life Assessment in Multiple Sclerosis: Different Perception between Patients and Neurologists

Background In recent years, neurologists are noticing that evaluation of multiple sclerosis (MS) patients based on combining relapses, disability progression, and magnetic resonance imaging activity may be insufficient to adequately assess suboptimal responses to available therapy. Inclusion of quality of life (QoL) parameters may contribute to breach this gap. Objective To evaluate agreement levels between doctor and patient perception of QoL in MS. Methods A total of 700 MS patients and 300 neurologists were invited to participate in a cross-sectional study by answering an e-mail questionnaire. The survey collected information on demographical data and included the Short Form questionnaire (SF-36). After completing the questionnaire, patients were given a standard written description of each of the subdomains assessed by SF-36 and asked to identify which three were the most important determinants of their overall health-related QoL. Results A total of 135 neurologists and 380 MS patients responded the survey. Study population mean age was 42.1 ± 10.5 years, with 61% presenting relapsing-remitting MS. SF-36 results were physical function 68.4 ± 30, physical role limitation 56.8 ± 41.7, vitality 47.6 ± 21.4, pain 71.2 ± 26.1, social function 72.6 ± 28.6, emotional role limitation 63.2 ± 39.8, mental health 60 ± 14.1, and general health 55.8 ± 22. Doctors considered physical function (75%) and physical role limitation (70%) as the most important QoL determinants in MS, followed by emotional role limitation (52%). Patients however, assigned significantly different levels of importance to physical function (58%), and physical role limitation (46%) and considered vitality (52%) more important than their physicians (p < 0.001). Important to note, the results of SF-36 questionnaire were highly correlated with the perception gap between patients and neurologists (r = 0.89; p = 0.0004). Conclusion Concerns on QoL in MS are different for patients and physicians. It is essential to enhance communication in order to better understand actual patient needs.
Noncoding RNAs in human saliva as potential disease biomarkers

Human saliva emerged as a research material in as early as the 17th century when investigators sought to understand the basis for salivary secretion (Garrett, 1975). Over the centuries, the focus of salivary research has evolved greatly and a wide range of topics has been examined (Garrett, 1975; Schipper et al., 2007). It is now known that the functions of saliva include at least lubrication, digestion of food, remineralization, prevention of demineralization, protection against microbial and viral infection, speech facilitation, and maintenance of oral and general health (Schipper et al., 2007; Malathi et al., 2014).
A Novel and Fast Approach for Population Structure Inference Using Kernel-PCA and Optimization

Population structure is a confounding factor in genome-wide association studies, increasing the rate of false positive associations. To correct for it, several model-based algorithms such as ADMIXTURE and STRUCTURE have been proposed. These tend to suffer from the fact that they have a considerable computational burden, limiting their applicability when used with large datasets, such as those produced by next generation sequencing techniques. To address this, nonmodel based approaches such as sparse nonnegative matrix factorization (sNMF) and EIGENSTRAT have been proposed, which scale better with larger data. Here we present a novel nonmodel-based approach, population structure inference using kernel-PCA and optimization (PSIKO), which is based on a unique combination of linear kernel-PCA and least-squares optimization and allows for the inference of admixture coefficients, principal components, and number of founder populations of a dataset. PSIKO has been compared against existing leading methods on a variety of simulation scenarios, as well as on real biological data. We found that in addition to producing results of the same quality as other tested methods, PSIKO scales extremely well with dataset size, being considerably (up to 30 times) faster for longer sequences than even state-of-the-art methods such as sNMF. PSIKO and accompanying manual are freely available at https://www.uea. ac.uk/computing/psiko.
Motion recognition using spatio-temporal random walks in sequence of 2D motion-related measurements

This paper describes an original approach for non parametric motion analysis in image sequences. It relies on a statistical modeling of distributions of local motion-related measurements, computed over image sequences, resulting from spatio-temporal random walks. It handles in a single probabilistic framework both spatial and temporal properties of motion content. The important feature of our method is to make feasible the exact computation of conditional likelihood functions. We have carried out motion recognition experiments over a large set of real image sequences comprising various motion types.
Effect of sludge age on methanogenic and glycogen accumulating organisms in an aerobic granular sludge process fed with methanol and acetate

The influence of sludge age on granular sludge formation and microbial population dynamics in a methanol‐ and acetate‐fed aerobic granular sludge system operated at 35°C was investigated. During anaerobic feeding of the reactor, methanol was initially converted to methane by methylotrophic methanogens. These methanogens were able to withstand the relatively long aeration periods. Lowering the anaerobic solid retention time (SRT) from 17 to 8 days enabled selective removal of the methanogens and prevented unwanted methane formation. In absence of methanogens, methanol was converted aerobically, while granule formation remained stable. At high SRT values (51 days), γ‐Proteobacteria were responsible for acetate removal through anaerobic uptake and subsequent aerobic growth on storage polymers formed [so called metabolism of glycogen‐accumulating organisms (GAO)]. When lowering the SRT (24 days), Defluviicoccus‐related organisms (cluster II) belonging to the α‐Proteobacteria outcompeted acetate consuming γ‐Proteobacteria at 35°C. DNA from the Defluviicoccus‐related organisms in cluster II was not extracted by the standard DNA extraction method but with liquid nitrogen, which showed to be more effective. Remarkably, the two GAO types of organisms grew separately in two clearly different types of granules. This work further highlights the potential of aerobic granular sludge systems to effectively influence the microbial communities through sludge age control in order to optimize the wastewater treatment processes.
Glucose-stimulated Protein Synthesis in Pancreatic β-Cells Parallels an Increase in the Availability of the Translational Ternary Complex (eIF2-GTP·Met-tRNAi) and the Dephosphorylation of eIF2α*

In pancreatic β-cells, glucose causes a rapid increase in the rate of protein synthesis. However, the mechanism by which this occurs is poorly understood. In this report, we demonstrate, in the pancreatic β-cell line MIN6, that glucose stimulates the recruitment of ribosomes onto the mRNA, indicative of an increase in the rate of the initiation step of protein synthesis. This increase in the rate of initiation is not mediated through an increase in the availability of the initiation complex eIF4F, because glucose is unable to stimulate eIF4F assembly or, in the absence of amino acids, modulate the phosphorylation status of 4E-BP1. Moreover, in MIN6 cells and isolated islets of Langerhans, rapamycin, an inhibitor of the mammalian target of rapamycin, only partially inhibited glucose-stimulated protein synthesis. However, we show that glucose stimulates the dephosphorylation of eIF2α in MIN6 cells and the assembly of the translational ternary complex, eIF2-GTP·Met-tRNAi, in both MIN6 cells and islets of Langerhans. The changes in the phosphorylation of eIF2α are not mediated by the PKR-like endoplasmic reticulum eIF2α kinase (PERK), because PERK is not phosphorylated at low glucose concentrations and overexpression of a dominant negative form of PERK has no significant effect on either glucose-stimulated protein synthesis or the phosphorylation of eIF2α. Taken together, these results indicate that glucose-stimulated protein synthesis in pancreatic β-cells is regulated by a mechanism largely independent of the activity of mammalian target of rapamycin, but which is likely to be dependent on the availability of the translational ternary complex, regulated by the phosphorylation status of eIF2α.
Trusted Analog/Mixed- Signal/RF ICs: A Survey and a Perspective

Editor’s note: The trustworthiness of integrated circuits is now an essential technical and business challenge for the semiconductor industry. In the digital domain, there has been extensive activity in understanding and counteracting the threats of hardware Trojans, piracy and counterfeiting. However, this research area is largely nascent and understudied for analog/mixed-signal (AMS) and radio frequency (RF) circuits, which are widely used in contemporary systems. This survey summarizes the state-of-art for trusted hardware design in AMS/RF IC’s, and highlights directions towards advancing the field. –Steven Nowick, Columbia University
Stable and Fast Fluid–Solid Coupling for Incompressible SPH

The solid boundary handling has been a research focus in physically based fluid animation. In this paper, we propose a novel stable and fast particle method to couple predictive–corrective incompressible smoothed particle hydrodynamics and geometric lattice shape matching (LSM), which animates the visually realistic interaction of fluids and deformable solids allowing larger time steps or velocity differences. By combining the boundary particles sampled from solids with a momentum‐conserving velocity‐position correction scheme, our approach can alleviate the particle deficiency issues and prevent the penetration artefacts at the fluid–solid interfaces simultaneously. We further simulate the stable deformation and melting of solid objects coupled to smoothed particle hydrodynamics fluids based on a highly extended LSM model. In order to improve the time performance of each time step, we entirely implement the unified particle framework on GPUs using compute unified device architecture. The advantages of our two‐way fluid–solid coupling method in computer animation are demonstrated via several virtual scenarios.
Resistive training can reduce coronary risk factors without altering VO2max or percent body fat.

Eleven healthy, untrained males (age = 44 +/- 1 yr; range = 40 to 55 yr) were studied to determine the effects of 16 wk of high-intensity resistive training on risk factors for coronary artery disease. Lipoprotein-lipid profiles, plasma glucose and insulin responses during an oral glucose tolerance test, and blood pressure at rest were determined before and after training. The training program resulted in a 13% increase in high-density lipoprotein-cholesterol (39 +/- 2 vs 44 +/- 3 mg.dl-1, P less than 0.05), a 43% increase in high-density lipoprotein-cholesterol (7 +/- 2 vs 10 +/- 2 mg.dl-1, P less than 0.05), a 5% reduction in low-density lipoprotein cholesterol (129 +/- 5 vs 122 +/- 5 mg.dl-1, P less than 0.05), and an 8% decrease in the total cholesterol/high-density lipoprotein-cholesterol ratio (5.1 +/- 0.3 vs 4.7 +/- 0.3, P less than 0.01), despite no changes in VO2max, body weight, or percent body fat. Glucose-stimulated plasma insulin concentrations during oral glucose tolerance testing were significantly lower, and supine diastolic blood pressure was reduced (P less than 0.05) as a result of the training program. No changes in any of these variables occurred in a sedentary control group. These findings indicate that resistive training can lower risk factors for coronary artery disease independent of changes in VO2max, body weight, or body composition.