gebhart/patrepeval huggingface dataset:
Refining data flow information using infeasible paths (1997)

Abstract. Experimental evidence indicates that large programs exhibit significant amount of branch correlation amenable to compile-time de-tection. Branch correlation gives rise to infeasible paths, which in turn make data flow information overly conservative. For example, def-use pairs that always span infeasible paths cannot be tested by any program input, preventing 100 % defuse, testing coverage. We present an algo-rithm for identifying infeasible program paths and a data flow analysis technique that improves the precision of traditional def-use pair analysis by incorporating the information about infeasible paths into the analysis. Infeasible paths are computed using branch correlation analysis, which can be performed either intra- or inter-procedurally. The efficiency of our technique is achieved through demand-driven formulation of both the infeasible paths detection and the defuse pair analysis. Our experi-ments indicate that even when a simple form of intraprocedural branch correlation is considered, more than 2 % of defuse pairs in the SPEC95 benchmark programs can be found infeasible. 1
Strontium‐containing hydroxyapatite (Sr‐HA) bioactive cement for primary hip replacement: An in vivo study (2005)

The purpose of this study was to evaluate the strontium-containing hydroxyapatite (Sr-HA) cement in primary hip replacement, using a rabbit model, and to investigate the histological findings at the cement-implant and bone-cement interfaces under weight-bearing conditions. Unilateral hip replacement was performed with Sr-HA cement or polymethylmethacrylate (PMMA) cement in rabbits and observations were made after 6 months. Good fixation between the Sr-HA cement and implant was observed. Osseointegration of the Sr-HA cement with cancellous bone was widespread. Many multinucleus cells covered the surface of the cement, and resorbed the superficial layer of the cement. By scanning electron microscopy (SEM) and energy-dispersive X-ray (EDX) analysis, high calcium and phosphorus levels were detected at the interface with a thickness of about 10 microm. Intimate contact was also observed between the Sr-HA cement and cortical bone without fibrous layer intervening. The overall affinity index of bone on Sr-HA cement was (85.06 +/- 5.40)%, which is significantly higher than that on PMMA cement (2.77%+/- 0.49%). On the contrary, a fibrous layer was consistently observed between PMMA cement and bone, and PMMA cement evoked an inflammatory response and foreign body reaction in the surrounding bony tissues. Results suggested good bioactivity and bone-bonding ability of the Sr-HA cement under weight-bearing conditions.
Frequency-dependent harmonic-distortion analysis of a linearized cross-coupled CMOS OTA and its application to OTA-C filters (2006)

Recent progress of wide-band communication systems demands high-frequency circuits. Conventionally, the linearity of the operational transconductance amplifier and capacitor (OTA-C) has been analyzed using Taylor series expansion. Unfortunately, this approach does not predict the frequency-dependent linearity degradation. Thus, to properly design linearized OTAs, the frequency dependence of these coefficients must be determined. In this paper, we present a frequency-dependent harmonic-distortion analytical method applied to a linear-enhanced OTA. This OTA, which is suitable for high-frequency operation, uses three linearization techniques simultaneously: 1) attenuation through floating-gate MOS transistors; 2) source degeneration; and 3) polynomial cancellation techniques. By using the harmonic-distortion analysis, some properties on the performance of OTA are used to improve the performance of OTA-C based circuits at high frequencies. A 0.5-/spl mu/m CMOS OTA simulation and experimental results are shown to verify the harmonic-distortion analytical method.
CNS-directed gene therapy for the treatment of neurologic and somatic mucopolysaccharidosis type II (Hunter syndrome) (2016)

Mucopolysaccharidosis type II (MPSII) is an X-linked lysosomal storage disease characterized by severe neurologic and somatic disease caused by deficiency of iduronate-2-sulfatase (IDS), an enzyme that catabolizes the glycosaminoglycans heparan and dermatan sulphate. Intravenous enzyme replacement therapy (ERT) currently constitutes the only approved therapeutic option for MPSII. However, the inability of recombinant IDS to efficiently cross the blood-brain barrier (BBB) limits ERT efficacy in treating neurological symptoms. Here, we report a gene therapy approach for MPSII through direct delivery of vectors to the CNS. Through a minimally invasive procedure, we administered adeno-associated virus vectors encoding IDS (AAV9-<i>Ids</i>) to the cerebrospinal fluid of MPSII mice with already established disease. Treated mice showed a significant increase in IDS activity throughout the encephalon, with full resolution of lysosomal storage lesions, reversal of lysosomal dysfunction, normalization of brain transcriptomic signature, and disappearance of neuroinflammation. Moreover, our vector also transduced the liver, providing a peripheral source of therapeutic protein that corrected storage pathology in visceral organs, with evidence of cross-correction of nontransduced organs by circulating enzyme. Importantly, AAV9-<i>Ids</i>-treated MPSII mice showed normalization of behavioral deficits and considerably prolonged survival. These results provide a strong proof of concept for the clinical translation of our approach for the treatment of Hunter syndrome patients with cognitive impairment.
Coat Protein Properties Indicate That Maize Dwarf Mosaic Virus-KS1 Is a Strain of Johnsongrass Mosaic Virus (1990)

It has recently been shown that 17 potyvirus isolates infecting maize, sorghum, and sugarcane in Australia and the United States, and previously classified as strains of sugarcane mosaic virus (SCMV), belong to four distinct potyviruses. However, the taxonomic status of other SCMV strains is uncertain at present. Using amino acid composition, high-performance liquid chromatographic peptide profiling of tryptic digests, partial amino acid sequence data, and electro-blot immunoassay of coat proteins, we confirm that the oat-infecting strain of maize dwarf mosaic virus (MDMV-O) from the United States is structurally and serologically closely related to the Australian johnsongrass strain of johnsongrass mosaic virus (JGMV-JG) (...)
Learning to Show You're Listening: A Back-Channel Trainer for Arabic (2007)

100 word abstract Good listeners generally produce back-channel feedback, and do so in a language-appropriate way. Second language learners often lack this skill. This paper presents a training sequence which enables the acquisition of basic Arabic back-channel skill, namely, that of producing feedback immediately after the speaker produces a sharp pitch downslope. This training sequence includes software that provides feedback on learners' attempts to produce the cue themselves and feedback on learners' performance as they play the role of an attentive listener in response to one side of a pre-recorded dialog. Preliminary experiments indicate that this is effective.
Salivary Digestion Extends the Range of Sugar-Aversions in the German Cockroach (2021)

Saliva has diverse functions in feeding behavior of animals. However, the impact of salivary digestion of food on insect gustatory information processing is poorly documented. Glucose-aversion (GA) in the German cockroach, <i>Blattella germanica</i>, is a highly adaptive heritable behavioral resistance trait that protects the cockroach from ingesting glucose-containing-insecticide-baits. In this study, we confirmed that GA cockroaches rejected glucose, but they accepted oligosaccharides. However, whereas wild-type cockroaches that accepted glucose also satiated on oligosaccharides, GA cockroaches ceased ingesting the oligosaccharides within seconds, resulting in significantly lower consumption. We hypothesized that saliva might hydrolyze oligosaccharides, releasing glucose and terminating feeding. By mixing artificially collected cockroach saliva with various oligosaccharides, we demonstrated oligosaccharide-aversion in GA cockroaches. Acarbose, an alpha-glucosidase inhibitor, prevented the accumulation of glucose and rescued the phagostimulatory response and ingestion of oligosaccharides. Our results indicate that pre-oral and oral hydrolysis of oligosaccharides by salivary alpha-glucosidases released glucose, which was then processed by the gustatory system of GA cockroaches as a deterrent and caused the rejection of food. We suggest that the genetic mechanism of glucose-aversion support an extended aversion phenotype that includes glucose-containing oligosaccharides. Salivary digestion protects the cockroach from ingesting toxic chemicals and thus could support the rapid evolution of behavioral and physiological resistance in cockroach populations.
Supplementary Figure 5 from Reducing TNF Receptor 2<sup>+</sup> Regulatory T Cells via the Combined Action of Azacitidine and the HDAC Inhibitor, Panobinostat for Clinical Benefit in Acute Myeloid Leukemia Patients (2023)

&lt;p&gt;PDF file - 1448K, The proportion of TNFR2- and TNFR2+ effector T cells between healthy and AML patients.&lt;/p&gt;
Virtual Synchronous Machine-based Power Control in Active Rectifiers for Micro Grids (2012)

The concept of micro grid interfaced with an active rectifier is an emerging technology for smart integration of dc distributed generation units to the ac grid where active rectifier plays the role of inverting dc to ac with appropriate control strategies. Having the operation of a synchronous generator in a micro grid introduces several advantages in terms of stability and reliability in the power system due the inherent damping and inertia properties of the machine. These advantages motivate the question if an active rectifier of a micro grid can imitate the behaviour of those inherent properties, can such stability and reliability be emulated in a micro grid. With the above intention, under the scope of the master thesis, firstly, a research should be carried on the state-of-the-art for uninterruptible power supplies (UPS) to mainly identify the active rectifier control strategies. Secondly, the concept of virtual synchronous machine (VSM) has to be further extended with the pre-studies from the fall project to observe the effects of virtual inertia and damping properties. Incorporating the above studies and simulations based on UPS and VSM, a model of an active rectifier should be developed making the choices from available control strategies. The model should be operable alone and in parallel with several active rectifiers in a micro grid both in grid-tied and island modes. Also the active rectifier model needs to emulate the inertia, damping and power sharing properties.
Multispectral imaging – a new tool in seed quality assessment? (2018)

Abstract Multispectral imaging is a new technology that is being deployed to assess seed quality parameters. Examples of applications in the detection and identification of fungi on seeds are presented, together with an example of the technology used for maturity determination in sugar beet seed. Results from multispectral imaging are compared with reference methods, and a high correlation is found. Applications of the technique for varietal discrimination and insect damage are also presented. There is a need for non-destructive, reliable and fast techniques, and it is concluded that multispectral imaging has potential for seed quality assessment, in particular for those components associated with surface structure and chemical composition, seed colour, morphology and size.
Spanning high-dimensional expression space using ribosome-binding site combinatorics (2013)

Protein levels are a dominant factor shaping natural and synthetic biological systems. Although proper functioning of metabolic pathways relies on precise control of enzyme levels, the experimental ability to balance the levels of many genes in parallel is a major outstanding challenge. Here, we introduce a rapid and modular method to span the expression space of several proteins in parallel. By combinatorially pairing genes with a compact set of ribosome-binding sites, we modulate protein abundance by several orders of magnitude. We demonstrate our strategy by using a synthetic operon containing fluorescent proteins to span a 3D color space. Using the same approach, we modulate a recombinant carotenoid biosynthesis pathway in Escherichia coli to reveal a diversity of phenotypes, each characterized by a distinct carotenoid accumulation profile. In a single combinatorial assembly, we achieve a yield of the industrially valuable compound astaxanthin 4-fold higher than previously reported. The methodology presented here provides an efficient tool for exploring a high-dimensional expression space to locate desirable phenotypes.
Electrophile-Promoted Carbon−Sulfur Bond Cleavage in η2-Thiophene Complexes of Pentaammineosmium(II) (1997)

Several S-alkylthiophenium complexes of the type [Os(NH3)5(4,5-η2-L)](OTf)3 (where L = S-alkylthiophenium, S-methylbenzo[b]thiophenium) are prepared by alkylation of the corresponding thiophene complexes. The S-alkylthiophenium species are proposed to undergo rapid and reversible cleavage of the C5−S bond, forming highly electrophilic metallacyclopropene intermediates. Although not directly observable, these vinyl cation intermediates may be trapped with both anionic and neutral nucleophiles affording η2-4-(alkylthio)-1,3-butadiene complexes. Treatment of selected 4-(alkylthio)-1,3-butadiene complexes with an oxidant (e.g., DDQ) affords the organic ligand in good yield.
Effect of rapid alteration in glucose concentration and insulin on thymidine uptake in bovine retinal capillary endothelium. (1991)

The effect of insulin and rapid changes in glucose concentration on bovine retinal capillary endothelium (BRCE) was examined by use of tissue culture and 3H-thymidine incorporation. In the absence of insulin, no effect on thymidine uptake by BRCE was observed when glucose concentration was rapidly altered, either increased or decreased. The stimulating effect of insulin on retinal capillary endothelin was more pronounced in log-phase cells than in stationary-phase cells. The extent of stimulation by insulin decreased with increasing glucose concentrations. This effect was not observed when osmotic pressure was increased by mannitol. The results of our experiments make it unlikely that altered osmotic stress, rapidly changing or abnormal glucose levels would be primarily responsible for altered endothelial activity.
AlGaAsSb–InGaAsSb HPTs With High Optical Gain and Wide Dynamic Range (2004)

Novel heterojunction phototransistors based on AlGaAsSb-InGaAsSb material systems are fabricated and their characteristics are demonstrated. Responsivity of a phototransistor is measured with applied bias voltage at four different wavelengths. The maximum responsivity around 1400 A/W and minimum noise equivalent power of 1.83/spl times/10/sup -14/ W/Hz/sup 1/2/ from this phototransistor with bias of 4.0 V at a wavelength of 2.05 /spl mu/m were measured at 20/spl deg/C and -20/spl deg/C, respectively. Noise equivalent power of the phototransistor is considerably lower compared with commercially available InGaAs p-i-n photodiodes. Collector current measurements with applied incident power are performed for two phototransistors. Currents of 400 nA at low intensity of 0.425 /spl mu/W/cm/sup 2/ and of 30 mA at high intensity of 100 mW/cm/sup 2/ are determined. Collector current increases nearly by five orders of magnitude between these two input intensities. High and constant optical gain of 500 in the 0.46-nW to 40-/spl mu/W input power range is achieved, which demonstrates high dynamic range for such devices at these power levels.
Temporal Characteristics of Electron Bunch in a Laser Plasma Electron Acceleration (2009)

We have measured and evaluated the femtosecond bunch duration of electron bunches produced by a 12 TW 40 fs laser pulse focused into a He gas jet. Well reproducible electron bunches can be generated with a low-emittance and high-charge, which are very important characteristics for future time-resolved applications. The bunch duration of such electron bunches was determinded to be less than 2 ps (FWHM) at 340 mm downstream from the gas jet by spectral analysis of the coherent transition radiation. The effects of bunch elongation due to both the energy spread and the space charge of electron bunches were estimated, and this estimation is in good agreement with the experimental results. The feasibility for time-resolved applications is also discussed.
Diet-Quality Scores and the Risk of Type 2 Diabetes in Men (2011)

Several diet-quality scores were associated with a lower risk of type 2 diabetes and reflect a common dietary pattern characterized by high intakes of plant-based foods such as whole grains; moderate alcohol; and low intakes of red and processed meat, sodium, sugar-sweetened beverages, and trans fat. High-quality diets may yield the greatest reduction in diabetes cases when followed by those with a high BMI.
Towards Optimal Strategy for Adaptive Probing in Incomplete Networks (2017)

We investigate a graph probing problem in which an agent has only an incomplete view $G' \subsetneq G$ of the network and wishes to explore the network with least effort. In each step, the agent selects a node $u$ in $G'$ to probe. After probing $u$, the agent gains the information about $u$ and its neighbors. All the neighbors of $u$ become \emph{observed} and are \emph{probable} in the subsequent steps (if they have not been probed). What is the best probing strategy to maximize the number of nodes explored in $k$ probes? This problem serves as a fundamental component for other decision-making problems in incomplete networks such as information harvesting in social networks, network crawling, network security, and viral marketing with incomplete information. While there are a few methods proposed for the problem, none can perform consistently well across different network types. In this paper, we establish a strong (in)approximability for the problem, proving that no algorithm can guarantees finite approximation ratio unless P=NP. On the bright side, we design learning frameworks to capture the best probing strategies for individual network. Our extensive experiments suggest that our framework can learn efficient probing strategies that \emph{consistently} outperform previous heuristics and metric-based approaches.
Post-translational modification patterns on β-myosin heavy chain are altered in ischemic and non-ischemic human hearts (2021)

Abstract Phosphorylation and acetylation of sarcomeric proteins are important for fine-tuning myocardial contractility. Here, we used bottom-up proteomics and label-free quantification to identify novel post-translational modifications (PTMs) on beta-myosin heavy chain ( β -MHC) in normal and failing human heart tissues. We report six acetylated lysines and two phosphorylated residues: K34-Ac, K58-Ac, S210-P, K213-Ac, T215-P, K429-Ac, K951-Ac, and K1195-Ac. K951-Ac was significantly reduced in both ischemic and non-ischemic failing hearts compared to non-diseased hearts. Molecular dynamics simulations show that K951-Ac may impact stability of thick filament tail interactions and ultimately myosin head positioning. K58-Ac altered the solvent exposed SH3 domain surface – known for protein-protein interactions – but did not appreciably change motor domain conformation or dynamics under conditions studied. Together, K213-Ac/T215-P altered loop 1’s structure and dynamics – known to regulate ADP-release, ATPase activity, and sliding velocity. Our study suggests that β-MHC acetylation levels may be influenced more by the PTM location than the type of heart disease since less protected acetylation sites are reduced in both heart failure groups. Additionally, these PTMs have potential to modulate interactions between β-MHC and other regulatory sarcomeric proteins, ADP-release rate of myosin, flexibility of the S2 region, and cardiac myofilament contractility in normal and heart failure hearts.
Algorithm Instance Games (2014)

This paper introduces algorithm instance games (AIGs) as a conceptual classification applying to games in which outcomes are resolved from joint strategies algorithmically. For such games, a fundamental question asks: How do the details of the algorithm's description influence agents' strategic behavior? We analyze two versions of an AIG based on the set-cover optimization problem. In these games, joint strategies correspond to instances of the set-cover problem, with each subset (of a given universe of elements) representing the strategy of a single agent. Outcomes are covers computed from the joint strategies by a set-cover algorithm. In one variant of this game, outcomes are computed by a deterministic greedy algorithm, and the other variant utilizes a non-deterministic form of the greedy algorithm. We characterize Nash equilibrium strategies for both versions of the game, finding that agents' strategies can vary considerably between the two settings. In particular, we find that the version of the game based on the deterministic algorithm only admits Nash equilibrium in which agents choose strategies (i.e., subsets) containing at most one element, with no two agents picking the same element. On the other hand, in the version of the game based on the non-deterministic algorithm, Nash equilibrium strategies can include agents with zero, one, or every element, and the same element can appear in the strategies of multiple agents.
Understanding Disconnection and Stabilization of Chord (2010)

Previous analytical work on the resilience of P2P networks has been restricted to disconnection arising from simultaneous failure of all neighbors in routing tables of participating users. In this paper, we focus on a different technique for maintaining consistent graphs-Chord's successor sets and periodic stabilizations-under both static and dynamic node failure. We derive closed-form models for the probability that Chord remains connected under both types of node failure and show the effect of using different stabilization interval lengths (i.e., exponential, uniform, and constant) on the probability of partitioning in Chord.
Quantification of In Situ Tremor in Microscopic Surgery (2019)

While the ophthalmic surgeon’s forearm during retinal surgeries is supported using a standard symmetric wrist rest when operating on the patients’ same side as the dominant hand (SSD), the surgeon’s hand is typically placed on the forehead when operating on the contralateral side of the dominant hand (CSD). It was hypothesized that more tremor occurs during CSD than SSD surgeries. Fifty-one surgical microscope videos recorded from three surgeons were analyzed using marker-less motion tracking with tremor acceleration, frequency, and magnitude measured. After 34 surgeries using a symmetric wrist support, an experimental asymmetric wrist rest was used. There was 0.12 mm/s2 (24%) greater ( p=.04) average tremor acceleration magnitude for CSD surgeries (0.62 mm/s2, SD=0.08) than SSD surgeries (0.50 mm/s2, SD=0.10) for the symmetric wrist rest, while no significant (p&gt;.05) differences were observed for the asymmetric wrist rest. This suggests that supporting the forearms rather than the hands, reduces surgeon hand tremor.