gebhart/patrepeval huggingface dataset:
Source-Level Linkage: Adding Semantic Information to C++ Fact-bases (2006)

Facts extracted from source code have been used to support a variety of software engineering activities, ranging from architectural understanding, through detection of design patterns, to program exploration. Several fact extractors have been developed and published in the literature, but most of them extract facts only from individual compilation units. Linking multiple fact-bases is largely overlooked. Source-level linkage is different from compilation linkage. Its goal is to assist a software engineer, not to produce an executable program. Thus a source-level linker needs to collect as many as possible facts that may be potentially helpful to a software engineer's task, many of which are not available from a compiler linker. We present the design of a source-level linker for C++. This linker has been used to analyze a dozen of Microsoft Foundation Classes (MFC) programs and over 200 C++ programs that cover an extensive subset of C++ features, including templates from the standard template library (STL). As a further validation, we design a structural constraint language, SCL, to express and machine-check a wide range of constraints on the abstract semantics graph (ASG) produced by the linker
2-Aminopurine:  A Probe of Structural Dynamics and Charge Transfer in DNA and DNA:RNA Hybrids (2002)

Spectroscopic techniques are employed to probe relationships between structural dynamics and charge transfer (CT) efficiency in DNA duplexes and DNA:RNA hybrids containing photoexcited 2-aminopurine (Ap). To better understand the variety of interactions and reactions, including CT, between Ap and DNA, the fluorescence behavior of Ap is investigated in a full series of redox-inactive as well as redox-active assemblies. Thus, Ap is developed as a dual reporter of structural dynamics and base-base CT reactions in nucleic acid duplexes. CD, NMR, and thermal denaturation profiles are consistent with the family of DNA duplexes adopting a distinct conformation versus the DNA:RNA hybrids. Fluorescence measurements establish that the d(A)-r(U) tract of the DNA:RNA hybrid exhibits enhanced structural flexibility relative to that of the d(A)-d(T) tract of the DNA duplexes. The yield of CT from either G or 7-deazaguanine (Z) to Ap in the assemblies was determined by comparing Ap emission in redox-active G- or Z-containing duplexes to otherwise identical duplexes in which the G or Z is replaced by inosine (I), the redox-inactive nucleoside analogue. Investigations of CT not only demonstrate efficient intrastrand base-base CT in the DNA:RNA hybrids but also reveal a distance dependence of CT yield that is more shallow through the d(A)-r(U) bridge of the A-form DNA:RNA hybrids than through the d(A)-d(T) bridge of the B-form DNA duplexes. The shallow distance dependence of intrastrand CT in DNA:RNA hybrids correlates with the increased conformational flexibility of bases within the hybrid duplexes. Measurements of interstrand base-base CT provide another means to distinguish between the A- and B-form helices. Significantly, in the A-form DNA:RNA hybrids, a similar distance dependence is obtained for inter- and intrastrand reactions, while, in B-DNA, a more shallow distance dependence is evident with interstrand CT reactions. These observations are consistent with evaluations of intra- and interstrand base overlap in A- versus B-form duplexes. Overall, these data underscore the sensitivity of CT chemistry to nucleic acid structure and structural dynamics.
Enhanced and preferential optical trapping in a slot-graphite photonic crystal (2017)

High-stiffness optical traps are developed for dielectric and metallic particles by exploiting the strong confinement of light in slot-graphite photonic crystal. An optical sieve is realized using the difference in growth kinetics of different nanoparticles.
Application of Organic Silicon Clusters to Pattern Transfer Process for Deep UV Lithography (2000)

A pattern transfer process using organic silicon clusters (OSCs) as bottom antireflective coating (BARC) for deep UV (DUV) lithography is introduced to realize high antireflective performance and efficient etch properties simultaneously. Unlike linear polysilanes, OSC has three-dimensional quaternary Si atoms (cluster units called Q units). It can be simply spin-coated and lowers the cost of ownership. Its refractive index at 248 nm is n =1.80 and k =0.30, and the intrinsic reflectivity is greatly reduced to 0.6%. Etch selectivity of BARC/resist is 3.3, which is much higher than that of the conventional organic BARC, namely, ∼1. OSC can also act as an adequate etch mask: etch resistance is 1.1 times greater than that of the resist and it is not denatured during substrate (dielectrics) etching. In comparison with the conventional organic BARC process, the OSC's excellent etch properties reduce resist thickness required to etch a substrate by approximately 270 nm, which enlarges the lithographic process window.
Action and therapeutic potential of oxyntomodulin (2013)

Oxyntomodulin (OXM) is a peptide hormone released from the gut in post-prandial state that activates both the glucagon-like peptide-1 receptor (GLP1R) and the glucagon receptor (GCGR) resulting in superior body weight lowering to selective GLP1R agonists. OXM reduces food intake and increases energy expenditure in humans. While activation of the GCGR increases glucose production posing a hyperglycemic risk, the simultaneous activation of the GLP1R counteracts this effect. Acute OXM infusion improves glucose tolerance in T2DM patients making dual agonists of the GCGR and GLP1R new promising treatments for diabetes and obesity with the potential for weight loss and glucose lowering superior to that of GLP1R agonists.
Glycosylation of Erythrocyte Spectrin and Its Modification in Visceral Leishmaniasis (2011)

Using a lectin, Achatinin-H, having preferential specificity for glycoproteins with terminal 9-O-acetyl sialic acid derivatives linked in α2-6 linkages to subterminal N-acetylgalactosamine, eight distinct disease-associated 9-O-acetylated sialoglycoproteins was purified from erythrocytes of visceral leishmaniaisis (VL) patients (RBC(VL)). Analyses of tryptic fragments by mass spectrometry led to the identification of two high-molecular weight 9-O-acetylated sialoglycoproteins as human erythrocytic α- and β-spectrin. Total spectrin purified from erythrocytes of VL patients (spectrin(VL)) was reactive with Achatinin-H. Interestingly, along with two high molecular weight bands corresponding to α- and β-spectrin another low molecular weight 60 kDa band was observed. Total spectrin was also purified from normal human erythrocytes (spectrin(N)) and insignificant binding with Achatinin-H was demonstrated. Additionally, this 60 kDa fragment was totally absent in spectrin(N). Although the presence of both N- and O-glycosylations was found both in spectrin(N) and spectrin(VL), enhanced sialylation was predominantly induced in spectrin(VL). Sialic acids accounted for approximately 1.25 kDa mass of the 60 kDa polypeptide. The demonstration of a few identified sialylated tryptic fragments of α- and β-spectrin(VL) confirmed the presence of terminal sialic acids. Molecular modelling studies of spectrin suggest that a sugar moiety can fit into the potential glycosylation sites. Interestingly, highly sialylated spectrin(VL) showed decreased binding with spectrin-depleted inside-out membrane vesicles of normal erythrocytes compared to spectrin(N) suggesting functional abnormality. Taken together this is the first report of glycosylated eythrocytic spectrin in normal erythrocytes and its enhanced sialylation in RBC(VL). The enhanced sialylation of this cytoskeleton protein is possibly related to the fragmentation of spectrin(VL) as evidenced by the presence of an additional 60 kDa fragment, absent in spectrin(N) which possibly affects the biology of RBC(VL) linked to both severe distortion of erythrocyte development and impairment of erythrocyte membrane integrity and may provide an explanation for their sensitivity to hemolysis and anemia in VL patients.
Type 1 Endoleak: Management following Thoracic Endovascular Aortic Repair (2022)

The best treatment option for type IA endoleak after thoracic endovascular aortic repair (TEVAR) is its avoidance by understanding the underlying disease process, having/creating adequate landing zones, as well as respecting anatomy in combination with knowledge of the capabilities and limitations of the TEVAR device used.
Low-density lipoprotein density and atherosclerosis. Unraveling the connection. (1994)

Unraveling the connection between dense LDL and atherogenesis should provide important insights into the basic mechanisms underlying atherogenesis.
On the Thermoeconomic Approach to the Diagnosis of Energy System Malfunctions - Indicators to Diagnose Malfunctions: Application of a New Indicator for the Location of Causes (2004)

Diagnosis procedures primarily aim at locating the control volumes where anomalies occurred. This is not a simple task, since the effects of anomalies generally propagate through the whole system and affect the behavior of several components. Some components may therefore present a reduced efficiency, although they are not sources of operation anomalies, due to non-flat efficiency curves. These induced effects are a big obstacle in the use of the thermoeconomic indicators for the search of the origin of the anomalies. As discussed in a brief overview of the several thermoeconomic indicators suggested in the literature, the reason for this inability is the focus on specific exergy consumptions as independent variables of the thermoeconomic model of the energy system. Instead, the real cause of the alteration of component behavior is the modification of its characteristic curve. Based on this concept, a new indicator measuring the alteration of the characteristic curve of the component affected by the operation anomaly is discussed and applied to the combined cycle power plant of the TADEUS problem.
Elastic and scalable tracing and accurate replay of non-deterministic events (2013)

SCALATRACE represents the state-of-the-art of parallel application tracing for high performance computing (HPC). This paper presents SCALATRACE II, a next generation tracer that delivers even higher trace compression capability, even when events are not always regular. In this work, we contribute a spectrum of novel compression and replay techniques that are fundamentally different from our past approaches. SCALATRACE II features a redesigned low-level encoding scheme of trace data such that data elements are elastic and self explanatory. With this new encoding scheme, trace compression is enhanced by introducing innovative intra-node and inter-node trace compression algorithms that guarantee high compression rates in a loop structure agnostic fashion. In practice, the improved compression scheme is particularly efficient for scientific codes that demonstrate inconsistent behavior across time steps and nodes. A novel approach is further contributed to probabilistically replay sequences of non-deterministic events. To assess the compression efficacy of SCALATRACE II, we conduct experiments not only with computational kernels but also a real-world application, the Parallel Ocean Program (POP). Compared to the first generation SCALATRACE, we observe key improvements on trace compression for benchmarks with inconsistent time step behavior and diverging task level behavior while retaining timing accuracy even under probabilistic replay.
Parks, Rosa (1913–2005) and the Montgomery Bus Boycott (2009)

Rosa Parks became a national symbol of the civil rights movement when on Thursday, December 1, 1955 she refused to give up her bus seat to a white passenger in Montgomery, Alabama. Her subsequent arrest sparked the beginning of the Montgomery Bus Boycott, which is widely considered to be the beginning of the modern civil rights movement. The boycott, originally meant to last only a day, continued for more than a year and resulted in a Supreme Court decision outlawing segregated seating on public buses.
Neuropsychological Correlates of the Electroencephalogram in Epileptics (1976)

In 57 male and 33 female uncontrolled adult epileptics treated solely by diphenylhydantoin, scores on a broad battery of neuropsychological tests were compared with the separate and simultaneous consideration of the topographic distribution and average rate of occurrence of their EEG epileptiform discharges. These studies were given within a median of 1.24 days of each other. In the battery of tests, it was statistically significant that the group with generalized discharges did the poorest, patients with focal epileptiform activity were intermediate, and those without discharges did the best. When the rates of occurrence of discharges were compared to the neuropsychological test scores, results were less often significantly correlated with the EEG findings. In general, however, individuals with discharges occurring at the rate of more than 1/min did worse than those with fewer discharges. When the topographic distribution and average rate variables were considered in combination, their impacts on psychological performance were cumulative. The results suggest that EEG epileptiform discharges serve as an index of brain function having a bearing upon neuropsychological performance of epileptics.
Time varying behavior of cocurrent gas-liquid flows in packed beds (1992)

The time-varying fluid mechanics of the pulse flow regime are studied by the use of continuous pressure measurements. It is found that pulses can occur either or intermittently and the time period between pulses scales inversely with a modified Reynolds number. A simple physical basis for this scaling is suggested by a one-dimentional map. The results emphasize the importance of knowing the time scale of pulses and suggest that it is worthwhile to look for similar scalings for other intermittent flow phenomena such as slugs in horizontal gas-liquid flows.
Hepatic SIRT6 deficit promotes liver tumorigenesis in the mice models (2020)

SIRT6 belongs to class III sirtuin family with NAD+-dependent histone deacetylase activities and controls multiple processes including aging, metabolism and inflammation. In recent years, increasing studies showed tumor suppressor role of SIRT6 in HCC development. We established a two-stage DEN followed CCl4 induced liver carcinogenesis in the hepatic-specific SIRT6 HKO mice models and found that hepatic SIRT6 deficit significantly promotes liver injury and liver cancer through inhibition of the ERK1/2 pathway. SIRT6 was compensatory upregulated in mice tumor tissues and human HCC cells and overexpressed SIRT6 inhibits tumor growth both <i>in vitro</i> and <i>in vivo</i>. Taken together, we provide a useful mouse model for delineating the molecular pathways involved in chronic liver diseases and primary liver cancer and suggest that SIRT6 can be a promising target for HCC therapies.
Remarkable Oxidation Stability of Glycals: Excellent Substrates for Cerium(IV)-Mediated Radical Reactions (2008)

The remarkable stability of glycals under oxidative conditions becomes apparent by their redox data in solution, computed HOMO energies, and behavior on the addition of electrophilic radicals generated in the presence of cerium(IV) ammonium nitrate. Oxidation potentials up to 2.03 V vs ferrocene were obtained, which are exceptionally high for cyclic enol ethers but correlate nicely with the reaction times of the radical reactions. Protecting groups have a strong influence on the oxidation stability and HOMO energies of glycals as E(ox) is shifted from O-silyl over O-benzyl to O-acetyl by more than 500 mV. Interestingly, this effect must be transmitted through sigma-bonds, even up to the para-position of a benzoate group, as verified by a wide variation of remote substituents in the carbohydrate. Favorable interactions of the sigma*-orbital of the adjacent C-O bond with the HOMO of the double bond are proposed as a mechanistic rationale, which might be important for the redox behavior of other allylic systems. Finally, donors and acceptors in the 1-position exert the strongest influence on the oxidation stability, shifting the potentials by almost 1 V and resulting in different follow-up reactions of the cerium(IV)-mediated additions of malonates. It is the remarkable oxidation stability of glycals that makes them valuable building blocks in carbohydrate chemistry.
Experimental feasibility of breast tumor detection and localization (2003)

Microwave breast imaging with radar-based techniques has been proposed for breast tumor detection. The feasibility study reported in this paper is designed to evaluate detection and localization of objects in three dimensions (3D). Experimental setups consisting of a PVC pipe (skin) and wood spheres (tumors) are illuminated with a resistively loaded monopole antenna. Improved image reconstruction algorithms are applied to the measured data, and the resulting images demonstrate detection and localization of smaller 3D tumor models.
Leveraging Identity to Make Learning Fun: Possible Selves and Experiential Learning in Massively Multiplayer Online Games (MMOGs) (2007)

Elizabeth Simpson (2005) believes the relevance and engagement demands of today&amp;apos;s generation of learners are largely unmet in typically didactic classrooms. Video games, she argues, can provide an opportunity to meet this challenge, since many teenagers already choose to live much of their real social lives in virtual space—exchanging instant messages, meeting friends online, and interacting with real people in virtual game worlds. Video games cross &amp;quot;all cultural and ethnic boundaries... [but] not recognizing that these shared experiences exist, public education has failed to provide for the impact of that experience on students&amp;apos; learning &amp;quot; (Simpson 2005, 17). Her argument represents the growing momentum of scholars and researchers who believe video games are the gateway to computer literacy and to better education in general (e.g., Gee 2003; Halverson 2005; Foreman 2004). Along with their intrinsically engaging properties, games have been touted for their ability to teach ill-defined problem-solving skills, elicit creativity, and develop leadership, collaboration, and other valuable interpersonal skills via constructivist/active learning and Vygotskian social scaffolding (Prensky 2001; Gee 2003). Despite researchers &amp;apos; optimism for melding gaming and education, some efforts to bolt learning onto video games—attempts to create edutainment—have been unsuccessful. Educational games frequently consist of repetitive, superficial tasks with limited transfer or poorly disguised attempts to sugar coat learning, which can
Unique Straddle Design for Placement Inside Damaged Down Hole Safety Valve Nipple Seal Area (2010)

Abstract Up until today operators have been facing a challenge on how to avoid recompletion of wells where the nipple seal area inside the TRSCSSV (Tubing Retrievable Surface Controlled Subsurface Safety Valve) is damaged due to large amount of well interventions or damaged due to corrosion. Various methods have been used for repairing a TRSCSSV with a damaged seal area. This includes standard insert WRSCSSV (Wireline Retrievable Surface Controlled Subsurface Safety Valve), with normal and oversize swell packing elements. Honing of the upper and lower seal area prior to installing an insert valve has also been performed but with variable success. To have the DHSV working properly it is vital to maintain barrier control of the well. If the DHSV nipple profile is damaged the alternatives are to repair it using one of the above mentioned methods or to secure the well for later recompletion Since all the above mentioned methods of repairing a damaged seal area for insert valve have failed, Statoil initiated a development project for a straddle design using well know element technology based on an HPHT Bridge Plug design. The straddle has solid elements, which shape according to the damage inside the seal areas. In addition each element is equipped with expanding anti-extrusion back-up rings on both sides, trapping the element so it has nowhere to go when differential pressure is applied. The straddle uses the existing nipple profile above the no-go for anchoring and is equipped with dogs to fit this profile. A standard insert safety valve is made up to the bottom of the straddle and is then operated by existing surface control line. This paper will compare the different methods used for repairing a damaged Down Hole Safety Valve nipple seal area and discuss the development process and qualification testing done for the new unique straddle system and setting tool. Case histories will also be presented from several prolific North Sea Wells.
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams (2016)

Monitoring and modeling biomedical, health care and wellness data from individuals and converging data on a population scale have tremendous potential to improve understanding of the transition to the healthy state of human physiology to disease setting. Wellness monitoring devices and companion software applications capable of generating alerts and sharing data with health care providers or social networks are now available. The accessibility and clinical utility of such data for disease or wellness research are currently limited. Designing methods for streaming data capture, real-time data aggregation, machine learning, predictive analytics and visualization solutions to integrate wellness or health monitoring data elements with the electronic medical records (EMRs) maintained by health care providers permits better utilization. Integration of population-scale biomedical, health care and wellness data would help to stratify patients for active health management and to understand clinically asymptomatic patients and underlying illness trajectories. In this article, we discuss various health-monitoring devices, their ability to capture the unique state of health represented in a patient and their application in individualized diagnostics, prognosis, clinical or wellness intervention. We also discuss examples of translational bioinformatics approaches to integrating patient-generated data with existing EMRs, personal health records, patient portals and clinical data repositories. Briefly, translational bioinformatics methods, tools and resources are at the center of these advances in implementing real-time biomedical and health care analytics in the clinical setting. Furthermore, these advances are poised to play a significant role in clinical decision-making and implementation of data-driven medicine and wellness care.