gebhart/patrepeval huggingface dataset:
NEZHA: Efficient Domain-Independent Differential Testing (2017)

Differential testing uses similar programs as cross-referencing oracles to find semantic bugs that do not exhibit explicit erroneous behaviors like crashes or assertion failures. Unfortunately, existing differential testing tools are domain-specific and inefficient, requiring large numbers of test inputs to find a single bug. In this paper, we address these issues by designing and implementing NEZHA, an efficient input-format-agnostic differential testing framework. The key insight behind NEZHA's design is that current tools generate inputs by simply borrowing techniques designed for finding crash or memory corruption bugs in individual programs (e.g., maximizing code coverage). By contrast, NEZHA exploits the behavioral asymmetries between multiple test programs to focus on inputs that are more likely to trigger semantic bugs. We introduce the notion of δ-diversity, which summarizes the observed asymmetries between the behaviors of multiple test applications. Based on δ-diversity, we design two efficient domain-independent input generation mechanisms for differential testing, one gray-box and one black-box. We demonstrate that both of these input generation schemes are significantly more efficient than existing tools at finding semantic bugs in real-world, complex software. NEZHA's average rate of finding differences is 52 times and 27 times higher than that of Frankencerts and Mucerts, two popular domain-specific differential testing tools that check SSL/TLS certificate validation implementations, respectively. Moreover, performing differential testing with NEZHA results in 6 times more semantic bugs per tested input, compared to adapting state-of-the-art general-purpose fuzzers like American Fuzzy Lop (AFL) to differential testing by running them on individual test programs for input generation. NEZHA discovered 778 unique, previously unknown discrepancies across a wide variety of applications (ELF and XZ parsers, PDF viewers and SSL/TLS libraries), many of which constitute previously unknown critical security vulnerabilities. In particular, we found two critical evasion attacks against ClamAV, allowing arbitrary malicious ELF/XZ files to evade detection. The discrepancies NEZHA found in the X.509 certificate validation implementations of the tested SSL/TLS libraries range from mishandling certain types of KeyUsage extensions, to incorrect acceptance of specially crafted expired certificates, enabling man-in-the-middle attacks. All of our reported vulnerabilities have been confirmed and fixed within a week from the date of reporting.
Design, Fabrication and Testing of Fixed-Valve Micro-Pumps (1995)

Abstract Micro-fluidic systems rely on positive displacement pumps to move fluid due to the low Reynolds numbers encountered at flow rates that are typically in a range around 100 μl/min. These pumps are usually reciprocating devices due to limitations of rotating machinery at small scales. Valves for micro-pumps are not necessarily scaled-down macro-valve designs. Existing designs range from passive membranes to complex thermally-controlled active devices. A simpler idea and one that may be more applicable to particulate-laden fluids is a valve that is fixed in shape. Such a valve operates solely by the differential pressure characteristics in each flow direction, which are caused by the flow through it. Such fixed or no-moving-parts (NMP) valves are attractive due to their simplicity of fabrication but have not been studied in enough detail to determine optimal designs. We present design and testing techniques for use in developing efficient NMP valves and for comparing various designs. These techniques were applied to diffuser and valvular conduit designs etched on silicon. Valve performance was characterized by flow resistance and by diodicity, which is the ratio of pressure losses in the reverse to forward direction. Techniques for measuring diodicity in steady and transient flow were developed, and both viscous and dynamic loss contributions to valve performance were analyzed. Computational techniques were used to demonstrate their use in the design of efficient valves.
On-demand device discovery enhancement of IEEE802.15.3 MAC for 60GHz WPAN system (2008)

Because of the unknown position of devices in ad-hoc network, it is difficult for the MAC to discover other devices by using directional antenna. This device discovery procedure needs extra signaling and costs considerable time, especially if there are a lot of devices. In this paper, on top of IEEE 802.15.3 MAC, we introduce the ultra superframe concept and propose an on-demand device discovery mechanism that significantly reduces signaling overhead, therefore speeds up the device discovery process and increases channel efficiency. Computer simulations show that, assuming up to 64 uniformly distributed devices, this MAC enhancement accomplishes device discovery procedure within 200 ms while keeping channel efficiency over 70% under 60 GHz channel environment.
A reliable, adaptive network protocol for video transport (2002)

We present an adaptive network layer protocol for VBR video transport. It: (1) minimizes the buffer requirement in the network while guaranteeing that packets of VBR encoded video flows will not be lost, and (2) minimizes the end-to-end delay and jitter of frames. To achieve the former objective, we utilize a receiver-oriented adaptive credit-based flow control algorithm, and derive the necessary and sufficient number of buffers that should be reserved for ensuring its reliability. To minimize the end-to-end delay and jitter for VBR encoded video streams, we: (1) present bandwidth estimation techniques which exploit the structure of the video traffic, and (2) define a new fairness criteria for buffer allocation and then present a fair buffer/bandwidth allocation algorithm. We experimentally evaluate this protocol for a wide range of parameters and many network configurations, and demonstrate its adaptability. We also compare the performance of the protocol with numerous other schemes and demonstrate its suitability for video transport.
The VVV Templates Project Towards an automated classification of VVV light-curves (2014)

Context. The Vista Variables in the Vía Láctea (VVV) ESO Public Survey is a variability survey of the Milky Way bulge and an adjacent section of the disk carried out from 2010 on ESO Visible and Infrared Survey Telescope for Astronomy (VISTA). The VVV survey will eventually deliver a deep near-IR atlas with photometry and positions in five passbands (ZYJHKS) and a catalogue of 1−10 million variable point sources – mostly unknown – that require classifications.
Identification of Missing Proteins in Human Olfactory Epithelial Tissue by Liquid Chromatography–Tandem Mass Spectrometry (2018)

We performed proteomic analyses of human olfactory epithelial tissue to identify missing proteins using liquid chromatography-tandem mass spectrometry. Using a next-generation proteomic pipeline with a < 1.0% false discovery rate at the peptide and protein levels, we identified 3731 proteins, among which five were missing proteins (P0C7M7, P46721, P59826, Q658L1, and Q8N434). We validated the identified missing proteins using the corresponding synthetic peptides. No olfactory receptor (OR) proteins were detected in olfactory tissue, suggesting that detection of ORs would be very difficult. We also identified 49 and 50 alternative splicing variants mapped at the neXtProt and GENCODE databases, respectively, and 2000 additional single amino acid variants. This data set is available at the ProteomeXchange consortium via PRIDE repository (PXD010025).
Phase and transmission error study for the alternating-element (Levenson) phase-shifting mask (1992)

Despite the potential of phase shifting masks to extend projection optical imaging to higher resolution or lower ki, several issues remain to be investigated before the technology can be fully used. This paper addresses the effects of phase and transmission errors on the alternating-element phase shifting method, otherwise known as the Levenson technique, for printing closely packed lines and spaces. Aerial image simulation is used to generate exposure-defocus trees and the normalized depth of focus k2 is used as the criteria based on given assumptions of linewidth tolerance and exposure allowance. Response surfaces are generated to define the tolerance limit for the phase and the transmission errors which affect both the depth of focus and the center focus. The dependency of these errors on ki, A, and NA are discussed.
Excessive Growth Hormone Expression in Male GH Transgenic Mice Adversely Alters Bone Architecture and Mechanical Strength (2015)

Patients with acromegaly have a higher prevalence of vertebral fractures despite normal bone mineral density (BMD), suggesting that GH overexpression has adverse effects on skeletal architecture and strength. We used giant bovine GH (bGH) transgenic mice to analyze the effects of high serum GH levels on BMD, architecture, and mechanical strength. Five-month-old hemizygous male bGH mice were compared with age- and sex-matched nontransgenic littermates controls (NT; n=16/group). Bone architecture and BMD were analyzed in tibia and lumbar vertebrae using microcomputed tomography. Femora were tested to failure using three-point bending and bone cellular activity determined by bone histomorphometry. bGH transgenic mice displayed significant increases in body weight and bone lengths. bGH tibia showed decreases in trabecular bone volume fraction, thickness, and number compared with NT ones, whereas trabecular pattern factor and structure model index were significantly increased, indicating deterioration in bone structure. Although cortical tissue perimeter was increased in transgenic mice, cortical thickness was reduced. bGH mice showed similar trabecular BMD but reduced trabecular thickness in lumbar vertebra relative to controls. Cortical BMD and thickness were significantly reduced in bGH lumbar vertebra. Mechanical testing of femora confirmed that bGH femora have decreased intrinsic mechanical properties compared with NT ones. Bone turnover is increased in favor of bone resorption in bGH tibia and vertebra compared with controls, and serum PTH levels is also enhanced in bGH mice. These data collectively suggest that high serum GH levels negatively affect bone architecture and quality at multiple skeletal sites.
Transmission Line Security Monitor: Final Report (2011)

The Electric Power Transmission Line Security Monitor System Operational Test is a project funded by the Technical Support Working Group (TSWG). TSWG operates under the Combating Terrorism Technical Support Office that functions under the Department of Defense. The Transmission Line Security Monitor System is based on technology developed by Idaho National Laboratory. The technology provides a means for real-time monitoring of physical threats and/or damage to electrical transmission line towers and conductors as well as providing operational parameters to transmission line operators to optimize transmission line operation. The end use is for monitoring long stretches of transmission lines that deliver electrical power from remote generating stations to cities and industry. These transmission lines are generally located in remote transmission line corridors where security infrastructure may not exist. Security and operational sensors in the sensor platform on the conductors take power from the transmission line and relay security and operational information to operations personnel hundreds of miles away without relying on existing infrastructure. Initiated on May 25, 2007, this project resulted in pre-production units tested in realistic operational environments during 2010. A technology licensee, Lindsey Manufacturing of Azusa California, is assisting in design, testing, and ultimately production. The platform was originally designed for a security monitoring mission, but it has been enhanced to include important operational features desired by electrical utilities.
Use of cement kiln dust in blended cement concretes (2010)

This paper reports results of a study conducted to evaluate certain mechanical properties and durability characteristics of blended cement concretes, such as silica fume, fly ash and blastfurnace slag, incorporating up to 15% cement kiln dust. The results indicate that the compressive strength of silica fume and fly ash cement concretes with up to 10% kiln dust was marginally less than that of type I cement concrete. The compressive strength of slag cement concrete incorporating kiln dust was lower than that of other blended and type I cement concretes. A significant increase in the drying shrinkage was noted in the blended cement concretes. The electrical resistivity of blended cement concretes was, however, generally more than that of type I cement concrete. It is recommended to use 5% silica fume plus 10% kiln dust or 10% fly ash plus 10% kiln dust as a replacement of type I cement. Such usage would lead to technical, economic, and environmental benefits in terms of a reduction in the quantity of cement and utilisation of waste industrial by-products. As the electrical resistivity of blended cement concretes incorporating kiln dust is more than that of type I cement without kiln dust, it is expected that the useful service-life of the former would be more than that of the latter. As the compressive strength of slag cement concretes, incorporating up to 10% kiln dust, is low, it may be used in low-strength applications. It should, however, be noted that blended cement concretes require good curing to minimise drying shrinkage cracks.
[Effect of local estriol therapy on the urethral pressure profile in the postmenopausal period]. (1986)

Measurements of the pressure in the urethra were performed under standardized conditions with the aid of perfused catheters in 20 fertile and 20 postmenopausal women, from it 12 women after local estrogen therapy by means of Ostriol-Ovula. Hormone-cytological swabs from the urethra, vagina and from the urinary cells were done. Proliferation of the urogenital epithelialia under the estriol-therapy and an ascent of the MUP and MUCP in the urethra pressure profile under resting conditions could be achieved. The maximum of the pressure profile could be displaced proximaly. In the urethra pressure profile the distal pressure transmission increased. Estriol therapy was without secondary effects and is suitable for the conservative therapy of the stress incontinence type I to III.
Silicon Diffusion Engineering in Rapid Melt Growth of Silicon-Germanium on Insulator (2014)

In this paper we focus on developing an efficient method to obtain a crystalline SiGe layer on top of an insulator. The method is aimed at enabling the fabrication of different concentration of crystalline SiGe alloy through structure engineering. This technique could enable the alloy composition to be different by design across a single wafer by using a single Germanium deposition step.
A Two Degree of Freedom Kinematic Model for Predicting the Deformations of Deep Beams (2016)

Abstract: In modern construction, it is not unusual to require a short span member to carry a very large load such as with a transfer girder. These members generally have high shear strengths with strut-and-tie models being able to predict these strengths generally in a conservative manner. For serviceability checks, cracked stiffness estimates, and seismic design, however, it is also important to be able to predict the deformations of the member accurately. In this paper a set of eight large and heavily instrumented reinforced concrete deep beams subjected to monotonic or cyclic loading are summarized. The displacements of these tests are explained in detail with particular attention paid to the development of deformations over the full load history. From these deformations, the paper notes that a simple 2 degree of freedom (DOF) kinematic model can be developed to predict the entire displacement field for a beam after diagonal cracking has occurred. These two degrees of freedom are the average longitudinal strain in the flexural reinforcement, and the vertical distortion of the critical loading zone near the applied load. When the results of the measured displacements of the beam tests are compared to the pattern of deformations from the 2 DOF model, excellent agreement is obtained. In addition, it is shown that the width of the main diagonal crack can also be explained well using the same 2 DOF model once these parameters are known. A forthcoming paper will explain how these parameters themselves can be predicted. 1.
Bilateral Renal Parenchymal Malacoplakia Presenting as Fever of Unknown Origin: Case Report and Review (1994)

Malacoplakia is a rare inflammatory disorder seen most often in the urinary tract, where it is highly associated with coliform infection. Although first recognized by pathologists in 1902, it has received little attention from the infectious disease community. While there remains much uncertainty regarding the specific cause of malacoplakia, it appears to be associated with a defect in intracellular killing of ingested microorganisms by macrophages. We report a case of bilateral renal parenchymal malacoplakia that presented as fever of unknown origin, and we review 33 previously identified cases. Renal malacoplakia has traditionally been associated with high morbidity and mortality. More recently, treatment with antimicrobial agents such as trimethoprim or ciprofloxacin has yielded a better outcome than had been documented with other therapy. Malacoplakia should be considered in the evaluation of fever of unknown origin or of relapsing or refractory urinary tract infection. Therapy with antimicrobial agents capable of intracellular penetration is recommended.
Analysis of new type III effectors from Xanthomonas uncovers XopB and XopS as suppressors of plant immunity (2012)

The pathogenicity of the Gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv) is dependent on type III effectors (T3Es) that are injected into plant cells by a type III secretion system and interfere with cellular processes to the benefit of the pathogen. In this study, we analyzed eight T3Es from Xcv strain 85-10, six of which were newly identified effectors. Genetic studies and protoplast expression assays revealed that XopB and XopS contribute to disease symptoms and bacterial growth, and suppress pathogen-associated molecular pattern (PAMP)-triggered plant defense gene expression. In addition, XopB inhibits cell death reactions induced by different T3Es, thus suppressing defense responses related to both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI). XopB localizes to the Golgi apparatus and cytoplasm of the plant cell and interferes with eukaryotic vesicle trafficking. Interestingly, a XopB point mutant derivative was defective in the suppression of ETI-related responses, but still interfered with vesicle trafficking and was only slightly affected with regard to the suppression of defense gene induction. This suggests that XopB-mediated suppression of PTI and ETI is dependent on different mechanisms that can be functionally separated.
Scaling-up fermentation of Escherichia coli for production of recombinant P64k protein from Neisseria meningitidis (2018)

P64k is a Neisseria meningitidis high molecular weight protein present in meningococcal vaccine preparations. The lpdA gene, which encodes for this protein, was cloned in Escherichia coli and the P64k recombinant protein was expressed in E. coli K12 GC366 cells under the control of a tryptophan promoter. P64k was expressed as an intracellular soluble protein about 28% of the total cellular protein. Several scale-up criteria of fermentation processes were studied to obtain the recombinant P64k protein at the pilot production scale. The best operational conditions at a larger scale production of P64k recombinant protein were studied and compared using the four following criteria: Constant Reynold's number (Re constant), Constant impeller tip speed (n di constant), Constant power consumption per unit liquid volume (P/V constant) and Constant volumetric oxygen transfer coefficients (KLa/k constant). The highest production of the recombinant protein was achieved based on the constant KLa/k scale-up fermentation criterion, calculating the aeration rate (Q) and the impeller agitation speed (n) by iterative process, keeping constant the KLa/k value from bench scale. The P64k protein total production at the 50 l culture scale was 546 mg l-1 in comparison with the 284 mg l-1 obtained at 1.5 l bench scale. The methodology described herein, for the KLa/k scale-up fermentation criterion, allowed us to obtain the P64k protein at 50 l scale. A fermentation process for the production of P64k protein from N. meningitidis was established, a protein to be used in future vaccine formulations in humans. How to cite: Espinosa R, García J, Narciandi E, et al. Scaling-up fermentation of Escherichia coli for production of recombinant P64k protein from Neisseria meningitidis. Electron J Biotechnol 2018;33. https://doi.org/10.1016/j.ejbt.2018.03.004.
Transcranial LED therapy for cognitive dysfunction in chronic, mild traumatic brain injury: two case reports (2010)

Two chronic, traumatic brain injury (TBI) cases are presented, where cognitive function improved following treatment with transcranial light emitting diodes (LEDs). At age 59, P1 had closed-head injury from a motor vehicle accident (MVA) without loss of consciousness and normal MRI, but unable to return to work as development specialist in internet marketing, due to cognitive dysfunction. At 7 years post-MVA, she began transcranial LED treatments with cluster heads (2.1" diameter with 61 diodes each - 9x633nm, 52x870nm; 12-15mW per diode; total power, 500mW; 22.2 mW/cm2) on bilateral frontal, temporal, parietal, occipital and midline sagittal areas (13.3 J/cm2 at scalp, estimated 0.4 J/cm2 to brain cortex per area). Prior to transcranial LED, focused time on computer was 20 minutes. After 2 months of weekly, transcranial LED treatments, increased to 3 hours on computer. Performs nightly home treatments (now, 5 years, age 72); if stops treating &gt;2 weeks, regresses. P2 (age 52F) had history of closed-head injuries related to sports/military training and recent fall. MRI shows fronto-parietal cortical atrophy. Pre-LED, was not able to work for 6 months and scored below average on attention, memory and executive function. Performed nightly transcranial LED treatments at home (9 months) with similar LED device, on frontal and parietal areas. After 4 months of LED treatments, returned to work as executive consultant, international technology consulting firm. Neuropsychological testing (post- 9 months of transcranial LED) showed significant improvement in memory and executive functioning (range, +1 to +2 SD improvement). Case 2 reported reduction in PTSD symptoms.