gebhart/patrepeval huggingface dataset:
Integrating Traceability Within the IDE to Prevent Requirements Documentation Debt (2018)

Documentation issues in software projects have been recently classified as a type of technical debt (TD), a concept that express-es how shortcuts during software development result in additional maintenance and evolution effort. The specific type of TD is termed documentation debt, and is among the most prevalent ones in practice and research. In this study we propose a tool-based approach for preventing documentation TD during requirements engineering, by: (a) integrating requirements specifications into the IDE, and (b) enabling the real-time creation of traces between requirements and code. To this end, we collaborated with a small/medium software company and conducted a qualitative case study to: (a) analyze the current process and identify existing TD types, (b) collect the requirements and implement a tool that aims at preventing the accumulation of documentation TD, and (c) investigate whether the tool successfully meets its goal. The results of the study suggest that the developers are motivated to use the developed tool, since they feel that they can develop, maintain and utilize requirements specifications and traces as part of their daily routine.
Energetics of the structure of the four-alpha-helix bundle in proteins. (1988)

The main features of the four-alpha-helix bundle, one of the characteristic structural elements of many proteins, can be explained in terms of noncovalent interactions between the constituent helices. Conformational energy computations have been carried out on four types of four-alpha-helix bundles, each consisting of four CH3CO-(L-Ala)10-NHCH3 polypeptide chains, with various combinations of parallel and antiparallel orientations of the helices. In the bundle with the most favorable energy, all pairs of neighboring helices are oriented antiparallel--i.e., in the orientation that is favored by electrostatic interactions between the helices. In this structure, the orientation angle between neighboring helix axes is -168 degrees, within +/- 7 degrees, in close agreement with the orientation angles observed in proteins and with the value that we computed earlier for the most favorable packing of pairs of interacting alpha-helices. This orientation corresponds to a left-handed twisting of the helical bundle. The preferred handedness of this twisting arises as a result of favorable nonbonded interactions between the alpha-helices.
Integrated fourth-order Sigma Delta convertor with stable self-tuning continuous-time noise shaper (1994)

A fourth-order monolithic Sigma Delta convertor is presented. The circuit shows how it is possible to use a completely continuous-time noise shaper with integrated passive components, moving the sampling function to the output of the filter. The associated uncertainty in the fabricated time constants, which is a serious problem in such a high-order design, is made negligible by means of a self tuning circuit. The convertor is unconditionally stable and recovers immediately from gross overload. The chip is fabricated in 1.6 µm CMOS, and operates from a single 5 V supply.
SRT2379, a small-molecule SIRT1 activator, fails to reduce cytokine release in a human endotoxemia model (2013)

Background: Reliable surveillance methods are indispensable for benchmarking of healthcare-associated infection rates. The National Healthcare Safety Network (NHSN) recently introduced surveillance of ventilator-associated events (VAE), including ventilator-associated conditions (VAC) [1]. This new algorithm is amenable to automated implementation and strives for more consistent interpretation. We assess the feasibility and reliability of automated implementation. Materials and methods: Retrospective analysis of an ICU cohort with prospective assessment of ventilator-associated pneumonia (VAP) in two academic medical centers (January 2011 to June 2012). The algorithm was electronically implemented as specified by the NHSN using minuteto-minute ventilator data. Two minor modifications were developed to improve stability and comparability with manual surveillance (10th percentile and intermittent ventilation). Concordance was assessed between the algorithms and prospective surveillance. Attributable mortality of VAC was estimated by multivariable competing-risk survival analysis. Results: Two thousand and eighty patients contributed 2,296 episodes of mechanical ventilation (MV). VAC incidence was 10.0/1,000 MV days. Prospective surveillance identified 8 VAP cases/1,000 MV days. The original VAC algorithm detected 32% (38/115) of patients affected by VAP; positive predictive value was 25% (38/152). Using the 10th percentile identified the same number of VAC cases, but only 116 were identical. VAC incidence was 24.9/1,000 MV days with the intermittent ventilation modification. Concordance between the original algorithm and the modified versions was suboptimal. Estimates of attributable mortality varied by implementation: original VAC subdistribution hazard ratio (sdHR) = 4.33, 10th percentile sdHR = 6.26 and intermittent ventilation sdHR = 2.40. Conclusions: Concordance between manual VAP surveillance and the VAE algorithm was poor. Although electronic implementation of the VAE algorithm was feasible, small variations considerably altered the events detected and their effect on mortality. Using the current specifications, comparability across institutions using different electronic or manual implementations remains questionable.
Novel Antidiabetic and Hypolipidemic Agents. 3. Benzofuran-Containing Thiazolidinediones (1999)

Several thiazolidinedione derivatives having 5-hydroxy-2,3-dihydro-2, 2,4,6,7-pentamethylbenzofuran moieties and their 5-benzyloxy derivatives and 5-hydroxy-2,4,6,7-tetramethylbenzofuran moieties were synthesized and evaluated in db/db mice. Insertion of an N-Me group into the linker between thiazolidinedione and substituted benzofuran pharmacophores showed considerable improvement in their euglycemic activity. Further improvement has been observed when a pyrrolidine moiety is introduced in the structure to give 5-[4-[N-[3(R/S)-5-benzyloxy-2,3-dihydro-2,2,4,6, 7-pentamethylbenzofuran-3-ylmethyl]-(2S)-pyrrolidin-2- ylmethoxy]pheny lene]thiazolidine-2,4-dione (21a). At a 100 mg/kg/day dose of the maleate salt, compound 21a reduced the plasma glucose and triglyceride to the level of lean littermate, i.e. 8 +/- 1 mM, and is the most potent and efficacious compound reported in this series.
Novel oxidative photochemical aporphine synthesis. Total synthesis of corunnine and nandazurine (1973)

S. M. Kupchan and P. F. O'Brien, J. Chem. Soc., Chem. Commun., 1973, 915 DOI: 10.1039/C39730000915
Design, synthesis and solution structure of a helix–loop–helix dimer—a template for the rational design of catalytically active polypeptides (1995)

A ploypeptide with 42 amino acids, SA-42, has been designed to fold into a ‘hairpin’ helix–loop–helix motif. Its intended use is to serve as a template for the rational design of catalytically active polypeptides. SA-42 is made up of two amphiphilic helices, that are designed to interact through the hydrophobic effect and are connected by a short loop. Evidence is presented that it does adopt the intended motif and that it dimerises in an antiparallel mode at concentrations between 2 µmol dm–3 and 5.6 mmol dm–3. The structural evidence was obtained from NMR and CD spectroscopy and the state of aggregation was determined with equilibrium sedimentation ultracentrifugation and CD spectroscopy. Special attention was paid to the design of SA-42 with respect to the expected NMR spectrum. The mean residue ellipticity at 222 nm of SA-42, –25000 deg cm2 dmol–1, compares well with that of other published helix–loop–helices. Two polypeptides that were developed from SA-42 by the replacement of three and five residues, respectively, were recently shown to have catalytical activity.
Quantum Hall states in graphene from strain-induced nonuniform magnetic fields (2012)

We examine strain-induced quantized Landau levels in graphene. Specifically, arc-bend strains are found to cause nonuniform pseudomagnetic fields. Using an effective Dirac model which describes the low-energy physics around the nodal points, we show that several of the key qualitative properties of graphene in a strain-induced pseudomagnetic field are different compared to the case of an externally applied physical magnetic field. We discuss how using different strain strengths allows us to spatially separate the two components of the pseudospinor on the different sublattices of graphene. These results are checked against a tight-binding calculation on the graphene honeycomb lattice, which is found to exhibit all the features described. Furthermore, we find that introducing a Hubbard repulsion on the mean-field level induces a measurable polarization difference between the $A$ and the $B$ sublattices, which provides an independent experimental test of the theory presented here.
Mashup Advisor: A Recommendation Tool for Mashup Development (2008)

Mashup editors, like Yahoo Pipes and IBM Lotus Mashup Maker, allow non-programmer end-users to ldquomash-uprdquo information sources and services to meet their information needs. However, with the increasing number of services, information sources and complex operations like filtering and joining, even an easy to use editor is not sufficient. MashupAdvisor aims to assist mashup creators to build higher quality mashups in less time. Based on the current state of a mashup, the MashupAdvisor quietly suggests outputs (goals) that the user might want to include in the final mashup. MashupAdvisor exploits a repository of mashups to estimate the popularity of specific outputs, and makes suggestions using the conditional probability that an output will be included, given the current state of the mashup. When a suggestion is accepted, MashupAdvisor uses a semantic matching algorithm and a metric planner to modify the mashup to produce the suggested output. Our prototype was implemented on top of IBM Lotus MashupMaker and our initial results show that it is effective.
Supplementary Figure 1 from A Cell Proliferation and Chromosomal Instability Signature in Anaplastic Thyroid Carcinoma (2023)

Supplementary Figure 1 from A Cell Proliferation and Chromosomal Instability Signature in Anaplastic Thyroid Carcinoma
Mechanisms of Hebbian‐like plasticity in the ventral premotor – primary motor network (2022)

The functional connection between ventral premotor cortex (PMv) and primary motor cortex (M1) is critical for the organization of goal-directed actions. Repeated activation of this connection by means of cortico-cortical paired associative stimulation (cc-PAS), a transcranial magnetic stimulation (TMS) protocol, may induce Hebbian-like plasticity. However, the physiological modifications produced by Hebbian-like plasticity in the PMv-M1 network are poorly understood. To fill this gap, we investigated the effects of cc-PAS on PMv-M1 circuits. We hypothesized that specific interactions would occur with I<sub>2</sub> -wave interneurons as measured by the short intracortical facilitation protocol (SICF). We used different paired-pulse TMS protocols to examine the effects of PMv-M1 cc-PAS on SICF, on GABAergic circuits as measured by short (SICI) and long (LICI) intracortical inhibition protocols, and varied the current direction in M1 to target different M1 neuronal populations. Finally, we examined the effects of cc-PAS on PMv-M1 connectivity using a dual coil approach. We found that PMv-M1 cc-PAS induces both a long-term potentiation (LTP)- or long-term depression (LTD)-like after-effect in M1 neuronal activity that is strongly associated with a bidirectional-specific change in I<sub>2</sub> -wave activity (SICF = 2.5 ms ISI). Moreover, cc-PAS induces a specific modulation of the LICI circuit and separately modulates PMv-M1 connectivity. We suggest that plasticity within the PMv-M1 circuit is mediated by a selective mechanism exerted by PMv on M1 by targeting I<sub>2</sub> -wave interneurons. These results provide new mechanistic insights into how PMv modulates M1 activity that are relevant for the design of brain stimulation protocols in health and disease. KEY POINTS: The I<sub>2</sub> -wave is specifically modulated by the induction of ventral premotor cortex - primary motor cortex (PMv-M1) plasticity. After PMv-M1 cortico-cortical paired associative stimulation (cc-PAS), corticospinal excitability correlates negatively with I<sub>2</sub> -wave amplitude. Different cc-PAS coil orientations can lead to a long-term potentiation- or long-term depression-like after-effect in M1.
Pierwsze eksperymenty na zwierzętach robota chirurgicznego Robin Heart (2010)

A study is presented of the molecular dynamics and of the viscosity in pure [Aliquat][Cl] ionic liquid and in a mixture of [Aliquat][Cl] with 1% (v/v) of [Aliquat][FeCl4]. The (1)H spin-lattice relaxation rate, R1, was measured by NMR relaxometry between 8 and 300 MHz. In addition, the translation self-diffusion, D, was measured by pulse field gradient NMR. The ILs' viscosity was measured as a function of an applied magnetic field, B, and it was found that the IL mixture's viscosity decreased with increasing B, whereas the [Aliquat][Cl] viscosity is independent of B. All experimental results were analyzed taking into account the viscosity's magnetic field dependence, assuming a modified Stokes-Einstein diffusion/viscosity relation. The main difference between the relaxation mechanisms responsible for R1 in the two IL systems is related to the additional paramagnetic relaxation contribution associated with the (1)H spins-[FeCl4] paramagnetic moments' interactions. Cross-relaxation cusps in the R1 dispersion, associated with (35)Cl and (1)H nuclear spins in the IL systems, were detected. The R1 model considered was successfully fitted to the experimental results, and it was possible to estimate the value of D at zero field in the case of the IL mixture which was consistent with the values of D measured at 7 and 14.1 T and with the magnetic field dependence estimated from the viscosity measurements. It was observed that a small concentration of [Aliquat][FeCl4] in the [Aliquat][Cl] was enough to produce a "superparamagnetic"-like effect and to change the IL mixture's molecular dynamics and viscosity and to allow for their control with an external magnetic field.
Supplementary Data from Urokinase Receptor Promotes Skin Tumor Formation by Preventing Epithelial Cell Activation of Notch1 (2023)

&lt;p&gt;This file include more detailed Material and Methods&lt;/p&gt;
Functional Genetic and Biophysical Analyses of Membrane Disruption by Human Adenovirus (2011)

The identification of the adenovirus (AdV) protein that mediates endosome penetration during infection has remained elusive. Several lines of evidence from previous studies suggest that the membrane lytic factor of AdV is the internal capsid protein VI. While these earlier results imply a role for protein VI in endosome disruption, direct evidence during cell entry has not been demonstrated. To acquire more definitive proof, we engineered random mutations in a critical N-terminal amphipathic α-helix of VI in an attempt to generate AdV mutants that lack efficient membrane penetration and infection. Random mutagenesis within the context of the AdV genome was achieved via the development of a novel technique that incorporates both error-prone PCR and recombineering. Using this system, we identified a single mutation, L40Q, that significantly reduced infectivity and selectively impaired endosome penetration. Furthermore, we obtained biophysical data showing that the lack of efficient endosomalysis is associated with reduced insertion of the L40Q mutation in protein VI (VI-L40Q) into membranes. Our studies indicate that protein VI is the critical membrane lytic factor of AdV during cellular entry and reveal the biochemical basis for its membrane interactions.
Recovery of Gold from Thiourea, Thiocyanate, or Thiosulfate Solutions by Reduction-Precipitation with a Stabilized Form of Sodium Borohydride (1991)

Abstract Sodium borohydride can be used as an efficient agent for reducing gold and silver in acidic solutions of thiourea, thiocyanate, thiosulfate, acid chloride, and acid nitrate. The Au(I) ion is reduced to metallic gold in the form of very fine crystals, as indicated by XRD and SEM analysis. The reduction reaction is carried out at ambient temperature for a very short period of time (30 s). The reduction of Au(I) in such solutions can be performed for a wide range of gold concentrations (2 mg/L-2 g/L). Different parameters controlling the rate of the reaction and the efficiency of borohydride were studied, namely: acidity, stoichiometry, thiourea concentration, the presence of foreign ions, and temperature. Gold reduction by sodium borohydride is more favorable in the presence of Ag+ and/or Zn2+ ions, while the presence of Fe2+, Co2+, Ni2+, and Cu2+ ions decreases the efficiency of borohydride. The reduction reaction is selective for gold and silver over base metals in a solution mixture since the reaction is carried out in acidic medium. High recovery is obtained (>99%) and the product is pure. Thiourea does not undergo any degradation reaction during the course of reduction, and it can be recycled. The process appears promising for the gold industry due to its simplicity, speed, and low capital investment requirements.
Surfactant ionic liquid-based microemulsions for polymerization (2006)

Surfactants based on imidazolium ionic liquids (ILs), including polymerizable surfactant ILs, have been synthesized and used to stabilize polymerizable microemulsions useful for producing polymer nanoparticles, gels, and open-cell porous materials.
Differential prognostic impact of hypoxia induced and diffuse HIF-1α expression in invasive breast cancer (2005)

Different regulation pathways of HIF-1alpha overexpression exist in breast cancer: (1) hypoxia induced, perinecrotic HIF-1alpha overexpression with strong expression of hypoxia associated genes (CA IX and GLUT-1), which is associated with a poor prognosis; and (2) diffuse HIF-1alpha overexpression lacking major hypoxia associated downstream effects, resulting in a more favourable prognosis.
Friendly Viruses (2009)

Endogenous retroviruses (ERVs) are present in the genome of all vertebrates and have coevolved with their hosts for millions of years. Some ERVs play a critical role in placental development, contribute to genome plasticity, and protect the host against infection of related pathogenic and exogenous retroviruses, thus some ERVs have been positively selected and maintained in the host genome. The sheep genome contains 27 endogenous retroviruses (enJSRVs) related to the pathogenic Jaagsiekte sheep retrovirus (JSRV), the causative agent of a transmissible lung cancer in sheep. enJSRVs are able to protect their host against JSRV infection by blocking different steps of the viral replication cycle. In addition, enJSRVs are absolutely required for sheep placental development. Thus, enJSRVs-JSRV provides a unique and interesting model to study the symbiotic relationship and interplay between host ERVs and evolution. This review will provide some examples of the biological functions of ERVs. In particular, the role of ERVs in reproductive biology and in protecting the host against pathogenic retrovirus infections will be emphasized using enJSRVs/JSRV and the sheep as a model.
Deep eutectic solvent based gas‐assisted dispersive liquid‐phase microextraction combined with gas chromatography and flame ionization detection for the determination of some pesticide residues in fruit and vegetable samples (2017)

In this study, a gas-assisted dispersive liquid-phase microextraction method using a deep eutectic solvent as the extraction solvent combined with gas chromatography and flame ionization detection was developed for the extraction and determination of some pesticide residues in vegetable and fruit juice samples. In this method, choline chloride and 4-chlorophenol at a molar ratio of 1:2 were mixed. By heating and vortexing, a clear, water-immiscible, and homogeneous liquid was formed. The obtained deep eutectic solvent was added to an aqueous solution of the analytes in a conical test tube. Air was bubbled into the aqueous solution and a cloudy solution was obtained. During this step, the analytes were extracted into the fine droplets of the extraction solvent. After centrifugation, an aliquot of the settled phase was injected into the separation system. Under the optimum extraction conditions, enrichment factors, and extraction recoveries were obtained in the ranges of 247-355 and 49-71%, respectively. The obtained values for the limits of detection and quantification were in the ranges of 0.24-1.4 and 0.71-4.2 μg/L, respectively. The proposed method is simple, fast, efficient, and inexpensive.
Small‐Angle X‐ray Scattering Study of Gelling Silica–Organic Polymer Solution: Systems Containing Poly(Sodium Styrenesulfonate) (1992)

Phase separations which result in micrometer‐range interconnected porous morphologies in a silica sol–gel system have been investigated using tetraethoxysilane and poly(sodium styrenesulfonate) (NaPSS) as starting materials. The dependence of domain size of interconnected structure on several important reaction variables such as solution composition and temperature is reported. Small‐angle X‐ray scattering measurements were performed to detect the effect of coexisting NaPSS on the polymerization behavior of silica in situ. The amount of NaPSS was found to play a key role in determining the micrometer‐range gel morphology by affecting the aggregation process and phase separation behavior of hydrolyzed silica.
Secondary ion yield matrix effects in SIMS depth profiles of Si/Ge multilayers (1989)

Abstract Thin multilayer samples of Si/Ge, with individual layer thicknesses of 4–33 nm, have been analyzed by secondary ion mass spectrometry (SIMS) using Ar + , O 2 + and Cs + primary ion beams. Bombardment with both Ar + and O 2 + produced positive secondary ion depth profiles in which pronounced distortions were observed. Similar effects were found in negative secondary ion depth profiles with Cs + bombardment. In each case, the SIMS depth profiles were characterized by abrupt interfacial secondary ion signal variations and a shift in the secondary ion signal maxima indicating that the layers were superposed, a condition that was not consistent with sample preparation, as verified by Auger electron spectroscopy. Auger electron spectroscopy depth profiling was also used to quantify the level of oxygen in the films. From these data it was concluded that the distortions in the positive secondary ion depth profiles under Ar + bombardment were the result of secondary ion yield variations induced by enhanced incorporation of ambient oxygen, during sample preparation, into the stronger oxide‐forming silicon layers. Under O 2 + and Cs + bombardment, the profile distortions were introduced by differential incorporation of the implanted primary species into the lower‐sputter‐yield silicon layers.