gebhart/patrepeval huggingface dataset:
A hands-on Java Pathfinder tutorial (2013)

Java Pathfinder (JPF) is an open source analysis system that automatically verifies Java programs. The JPF tutorial provides an opportunity to software engineering researchers and practitioners to learn about JPF, be able to install and run JPF, and understand the concepts required to extend JPF. The hands-on tutorial will expose the attendees to the basic architecture framework of JPF, demonstrate the ways to use it for analyzing their artifacts, and illustrate how they can extend JPF to implement their own analyses. One of the defining qualities of JPF is its extensibility. JPF has been extended to support symbolic execution, directed automated random testing, different choice generation, configurable state abstractions, various heuristics for enabling bug detection, configurable search strategies, checking temporal properties and many more. JPF supports these extensions at the design level through a set of stable well defined interfaces. The interfaces are designed to not require changes to the core, yet enable the development of various JPF extensions. In this tutorial we provide attendees a hands on experience of developing different interfaces in order to extend JPF. The tutorial is targeted toward a general software engineering audience-software engineering researchers and practitioners. The attendees need to have a good understanding of the Java programming language and be fairly comfortable with Java program development. The attendees are not required to have any background in Java Pathfinder, software model checking or any other formal verification techniques. The tutorial will be self-contained.
Hot topics in Evolutionary Computation (2011)

We introduce the special issue on Evolutionary Computation (EC) reporting a non-exhaustive list of topics which have recently attracted much interest from the EC community, with particular regard to the ones dealt with by the papers included in this issue: EC research, hybrid neuro-evolutionary systems and synergies between EC and complex systems. In addition, we introduce a more technological emerging topic: the parallel implementation of evolutionary and Swarm Intelligence algorithms on graphics processor units (GPUs), by which new applications of evolutionary algorithms have been made possible, even in real-time environments.
Endovascular therapy or conventional vascular surgery? A complex choice. (2003)

Endovascular therapy and open vascular surgery have advantages and disadvantages. A single therapeutic option is rarely ideal for all patients. Rather, the two options are tools that are best used selectively; their availability allows for therapy to be tailored to optimize patient care.
Rhinovirus Species–Specific Antibodies Differentially Reflect Clinical Outcomes in Health and Asthma (2018)

<b>Rationale:</b> Rhinoviruses (RVs) are major triggers of common cold and acute asthma exacerbations. RV species A, B, and C may have distinct clinical impact; however, little is known regarding RV species-specific antibody responses in health and asthma.<b>Objectives:</b> To describe and compare total and RV species-specific antibody levels in healthy children and children with asthma, away from an acute event.<b>Methods:</b> Serum samples from 163 preschool children with mild to moderate asthma and 72 healthy control subjects from the multinational Predicta cohort were analyzed using the recently developed PreDicta RV antibody chip.<b>Measurements and Main Results:</b> RV antibody levels varied, with RV-C and RV-A being higher than RV-B in both groups. Compared with control subjects, asthma was characterized by significantly higher levels of antibodies to RV-A and RV-C, but not RV-B. RV antibody levels positively correlated with the number of common colds over the previous year in healthy children, and wheeze episodes in children with asthma. Antibody levels also positively correlated with asthma severity but not with current asthma control.<b>Conclusions:</b> The variable humoral response to RV species in both groups suggests a differential infectivity pattern between RV species. In healthy preschoolers, RV antibodies accumulate with colds. In asthma, RV-A and RV-C antibodies are much higher and further increase with disease severity and wheeze episodes. Higher antibody levels in asthma may be caused by a compromised innate immune response, leading to increased exposure of the adaptive immune response to the virus. Importantly, there is no apparent protection with increasing levels of antibodies.
Topological Mapping of the Cysteine Residues of N-Carbamyl-D-amino-acid Amidohydrolase and Their Role in Enzymatic Activity (1996)

The N-carbamyl-D-amino-acid amidohydrolase from Agrobacterium radiobacter NRRL B11291, the enzyme used for the industrial production Of D-amino acids, was cloned, sequenced, and expressed in Escherichia coli. The protein, a dimer constituted by two identical subunits of 34,000 Da with five cysteines each, was susceptible to aggregation under oxidizing conditions and highly sensitive to hydrogen peroxide. To investigate the role of the cysteines in enzyme stability and activity, mutant proteins were constructed by site-directed mutagenesis in which the five residues were substituted by either Ala or Ser. Only the mutant carrying the Cys172 substitution was catalytically inactive, and the other mutants maintained the same specific activity as the wild type enzyme. The crucial role of Cys172 in enzymatic activity was also confirmed by chemical derivatization of the protein with iodoacetate. Furthermore, chemical derivatizations using both acrylamide and Ellman's reagent revealed that (i) none of the five cysteines is engaged in disulfide bridges, (ii) Cys172 is easily accessible to the solvent, (iii) Cys193 and Cys250 appear to be buried in the protein core, and (iv) Cys243 and Cys279 seem to be located within or in proximity of external loops and are derivatized under mild denaturing conditions. These data are discussed in light of the possible mechanisms of enzyme inactivation and catalytic reaction.
Supplementary Figure 2 from Genome-Wide CpG Island Profiling of Intraductal Papillary Mucinous Neoplasms of the Pancreas (2023)

&lt;p&gt;PDF file - 76K&lt;/p&gt;
Performance Evaluation of the Active-set Algorithm for Peak to Average Ratio Reduction in Wireless OFDM Communication Systems (2006)

For high speed data transmission over multipath fading channels orthogonal frequency division multiplexing (OFDM) can be a spectrally efficient multicarrier modulation technique. All OFDM systems suffer from large peak-to-average-power ratio (PAR), which can lead to power inefficiency and nonlinear distortion at the RF portion of the transmitter. Tone reservation method uses reserved tones to generate a peak-canceling signal to lower the PAR of a transmit OFDM block. This paper investigates the recently proposed active-set tone reservation method, for complex-baseband signals, to reduce the PAR in wireless and broadcast systems. When PAR reduction is applied on an OFDM symbol and its PAR level still exceeds the target PAR after reduction this OFDM symbol suffers clipping. In frequency domain clipping energy spreads across all tones and acts as error power. Simulations are performed to investigate the error power on data tones after active-set method
Deciphering protein signatures using color, morphological, and topological analysis of immunohistochemically stained human tissues (2016)

Images of tissue specimens enable evidence-based study of disease susceptibility and stratification. Moreover, staining technologies empower the evidencing of molecular expression patterns by multicolor visualization, thus enabling personalized disease treatment and prevention. However, translating molecular expression imaging into direct health benefits has been slow. Two major factors contribute to that. On the one hand, disease susceptibility and progression is a complex, multifactorial molecular process. Diseases, such as cancer, exhibit cellular heterogeneity, impeding the differentiation between diverse grades or types of cell formations. On the other hand, the relative quantification of the stained tissue selected features is ambiguous, tedious and time consuming, prone to clerical error, leading to intra- and inter-observer variability and low throughput. Image analysis of digital histopathology images is a fast-developing and exciting area of disease research that aims to address the above limitations. We have developed a computational framework that extracts unique signatures using color, morphological and topological information and allows the combination thereof. The integration of the above information enables diagnosis of disease with AUC as high as 0.97. Multiple staining show significant improvement with respect to most proteins, and an AUC as high as 0.99.
Large signal compensation network design for VRM transient response improvement (2005)

Most of the compensation network designs in power supplies are based on the small signal model methods, which can not apply to the transient periods because it goes into the saturation region. The large signal response is determined by error amplifier dv/dt and main converter di/dt, a trade off between the stability and transient response. This paper presents one new control circuit to improve large signal transient response. Finally, experimental prototype was carried out in VRM with current injection converter to verify the theoretical analysis.
Early childhood linear growth faltering in low- and middle-income countries (2020)

Summary Globally 149 million children under five are estimated to be stunted (length more than 2 standard deviations below international growth standards). Stunting, a form of linear growth faltering, increases risk of illness, impaired cognitive development, and mortality. Global stunting estimates rely on cross-sectional surveys, which cannot provide direct information about the timing of onset or persistence of growth faltering— a key consideration for defining critical windows to deliver preventive interventions. We performed the largest pooled analysis of longitudinal studies in low- and middle-income countries to date (n=32 cohorts, 52,640 children, ages 0-24 months), allowing us to identify the typical age of linear growth faltering onset and to investigate recurrent faltering in early life. The highest incidence of stunting onset occurred from birth to age 3 months. From 0 to 15 months, less than 5% of children per month reversed their stunting status, and among those who did, stunting relapse was common. Early timing and low reversal rates emphasize the importance of preventive intervention delivery within the prenatal and early postnatal phases coupled with continued delivery of postnatal interventions through the first 1000 days of life.
Subunit structure of thymus leukemia antigens (1975)

EDTA-containing buffer solubilizes thymus leukemia antigens (TLa) from crude thymocyte membrane fractions. The TL antigens consist mainly of molecules of a size similar to immunoglobulin G when gel chromatography analyses were performed under physiological conditions. A single component of TLa was apparent on sucrose density gradient ultracentrifugation of solubilized thymocyte membrane macromolecules as monitored by indirect immunoprecipitation. The sedimentation constant for the TL antigens (5.8 S) was considerably less than that for immunoglobulin G. The gel chromatography and ultracentrifugation data suggest an apparent molecular weight for TLa of about 120000. TLa isolated by indirect immunoprecipitation is composed of two types of polypeptide chains. The smaller subunit was identified as beta2-microglobulin. The larger polypeptide chain carried the alloantigenic determinants and displayed a molecular weight of about 50000 after reduction and alkylation. TLa subjected to molecular weight determination under denaturing conditions was composed of two components. The smaller component was beta2-microglobulin which evidently is linked to the larger polypeptide chain by noncovalent interactions only. The larger component had a size greater than reduced and alkylated immunoglobulin G heavy chains. Upon reduction and alkylation of the latter component its size was reduced and it appeared to have a molecular weight of about 50000. Consequently, TLa is composed of two disulfide linked heavy polypeptide chains and two beta2-microglobulin molecules. TLa solubilized by papain digestion comprises two polypeptide chains, one of which is beta2-microglobulin. The larger 37000-dalton subunit is a fragment of the heavy polypeptide chain. This was demonstrated by digesting solubilized 120000-dalton TLa with papain. The proteolytic fragments obtained were indistinguishable from those directly released from the cell surface by proteolysis. The papain-derived TLa fragment exhibited most if not all the alloantigenic determinants.
Cellular modeling: insight into oral minimal models of insulin secretion (2009)

The oral glucose tolerance test and meal tolerance test are common clinical tests of the glucose-insulin system. Several mathematical models have been suggested as means to extract information about beta-cell function from data from oral tolerance tests. Any such model needs to be fairly simple but should at the same time be linked to the underlying biology of the insulin-secreting beta-cells. The scope of the present work is to present a way to make such a connection using a recent model describing intracellular mechanisms. We show how the three main components of oral minimal secretion models, derivative control, proportional control, and delay, are related to subcellular events, thus providing mechanistic underpinning of the assumptions of the minimal models.
A transcriptomic analysis of the effects of macrophage polarization and endotoxin tolerance on the response to Salmonella (2022)

Salmonella is an intracellular pathogen causing significant morbidity and mortality. Its ability to grow inside macrophages is important to virulence, and is dependent on the activation state of the macrophages. Classically activated M1 macrophages are non-permissive for Salmonella growth, while alternatively activated M2 macrophages are permissive for Salmonella growth. Here we showed that endotoxin-primed macrophages (MEP), such as those associated with sepsis, showed similar levels of Salmonella resistance to M1 macrophages after 2 hr of intracellular infection, but at the 4 hr and 24 hr time points were susceptible like M2 macrophages. To understand this mechanistically, transcriptomic sequencing, RNA-Seq, was performed. This showed that M1 and MEP macrophages that had not been exposed to Salmonella, demonstrated a process termed here as primed activation, in expressing relatively higher levels of particular anti-infective genes and pathways, including the JAK-STAT (Janus kinase-signal transducer and activator of transcription) pathway. In contrast, in M2 macrophages these genes and pathways were largely expressed only in response to infection. Conversely, in response to infection, M1 macrophages, but not MEP macrophages, modulated additional genes known to be associated with susceptibility to Salmonella infection, possibly contributing to the differences in resistance at later time points. Application of the JAK inhibitor Ruxolitinib before infection reduced resistance in M1 macrophages, supporting the importance of early JAK-STAT signalling in M1 resistance to Salmonella.
Activity of acyclic 6-(phenylselenenyl)pyrimidine nucleosides against human immunodeficiency viruses in primary lymphocytes (1991)

Several 6-phenylselenenyl-substituted acyclouridine derivatives were prepared for evaluation as antiviral agents. Lithiation of the tert-butyldimethylsilyl-protected acyclonucleosides 4a-f with lithium diisopropylamide at -78 degrees C, followed by reaction with diphenyl diselenide as an electrophile, and subsequent removal of the protecting group with tetra n-butylammonium fluoride gave 1-[(2-hydroxyethoxy)methyl]-6-(phenylselenenyl)uracils 6a-f in 50-70% overall yield. The potency and spectrum of activity of compounds 6a-f against HIV-1 in vitro was similar to HEPT (1), a related 6-phenylthio acyclonucleoside. However, whereas HEPT inhibited HIV-1 reverse transcriptase, the selenium-containing derivatives were ineffective, suggesting a different mechanism of action. Of significance was the finding that the 6-phenylselenenyl acyclonucleosides inhibited also HIV-2 in primary human lymphocytes.
Microorganisms in High‐Temperature Sulfur Environments (2020)

Abstract Sulfur‐rich high‐temperature environments such as solfataric fields, hot springs and ‘black smokers’ provide habitats for microbial life at the upper temperature border. Such regions have yielded extremely and hyperthermophilic bacteria and archaea that grow optimally at temperatures above 70 °C, some even above 100 °C. Key Concepts Hyperthermophilic and extremely thermophilic bacteria and archaea thrive at high temperature, up to boiling point of water. They are phylogenetically and metabolically diverse. They represent deepest phylogenetic linages in prokaryotes. They perform closed sulfur cycle in thermal environments. The highest growth temperature is the capacity of microorganisms inhabiting deep‐sea hot vents.
A Data-Driven Multiobjective Optimization Framework for Hyperdense 5G Network Planning (2020)

The trials and rollout of the fifth generation (5G) network technologies are gradually intensifying as 5G is positioned as a platform that not only accommodates exploding data traffic but also unlocks a multitude use cases, services and deployment scenarios. However, the need for hyperdense 5G deployments is revealing some of the limitations of planning approaches that hitherto proved adequate for pre-5G systems. The hyperdensification envisioned in 5G networks not only adds complexity to network planning and optimization problems, but underlines need for more realistic data-driven approaches that consider cost, varying demands and other contextual attributes to produce feasible topologies. Furthermore, the quest for network programmability and automation including the 5G radio access network (RAN), as manifested by network slicing technologies and more flexible RAN architectures, are also among other factors that influence planning and optimization frameworks. Collectively, these deployment trends, technological developments and evolving (and diverse) service demands point towards the need for more holistic frameworks. This article proposes a data-driven multiobjective optimization framework for hyperdense 5G network planning with practical case studies used to illustrate added value compared to contemporary network planning and optimization approaches. Comparative results from the case study with real network data reveal potential performance and cost improvements of hyperdense optimized networks produced by the proposed framework due to increased use of contextual data of planning area and focus on objectives that target demand satisfaction.
Diesel exhaust particles induce NF-kappa B activation in human bronchial epithelial cells in vitro: importance in cytokine transcription. (1999)

Fine particles derived from diesel engines (diesel exhaust particles, DEP) have attracted attention, since their density in industrial countries seems related to the increased prevalence of pulmonary diseases. Previous studies have suggested that DEP have a potential to directly activate airway epithelial cells to produce and release inflammatory cytokines and mediators, and thus facilitate inflammatory responses in the lung. To elucidate the molecular mechanisms of their action, we studied here IL-8 gene expression, one of the important cytokines in inflammatory responses, by Northern blot analysis and run-on transcription assay. Suspended DEP (1-50 microgram/ml) increased the steady state levels of IL-8 mRNA, which was suggested to be largely due to increased transcriptional rates. Electrophoretic mobility shift assay demonstrated that DEP induced increased binding to the specific motif of NF-kappa B, but not of transcription factor AP-1. The luciferase reporter gene assay using wild-type and mutated NF-kappa B-binding sequences showed that DEP-induced NF-kappa B activation was involved in IL-8 transcription. Finally, both N-acetylcysteine and pyrrolidine dithiocarbamate attenuated the action of DEP on IL-8 mRNA expression, suggesting that oxidant-mediated pathway might be involved in its processes. These results suggested that DEP activate NF-kappa B, which might be an important mechanism of its potential to increase the expression of inflammatory cytokines in vitro.
Phosphorylation-Specific Peptidyl-Prolyl Isomerization of Neuronal Cytoskeletal Proteins by Pin1: Implications for Therapeutics in Neurodegeneration (2010)

Pin1 [Protein Interacting with NIMA (never in mitosis A)] is a peptidyl prolyl cis-trans isomerase that isomerizes phospho-Serine/Threonine-Proline [p(S/T)-P] motifs of its target proteins. Pin1 functions in concert with proline directed kinases such as cyclin-dependent protein kinases, extracellular signal-regulated kinases, and c-Jun N- terminal kinase, and protein phosphatases such as protein phosphatase 2A (PP2A) and PP2B, in the regulation of a wide range of cellular processes including cell division, DNA damage response, and gene transcription, and in susceptibility to cancer and neurodegenerative diseases. This review focuses on the roles of Pin1 in neurodegenerative disorders including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Frontotemporal dementia associated with parkinsonism linked to chromosome 17. Pin1 interacts with neuronal cytoskeletal proteins such as tau, amyloid-beta protein precursor, alpha-synuclein, and neurofilaments, often in association with phosphorylation events that influence their functions in the neuronal cytoskeleton. Overexpression of Pin1 reduces WT tau stability but increases P301L mutant tau stability. Pin1 associates with neurofilament H (NF-H) and modulates excitotoxic and oxidative stress induced perikaryal phosphorylation of NF-H. Pin1 mediates the neural specific apoptosis machinery. The specific inhibitors of Pin1 may have potential therapeutic implications in neurodegeneration.