gebhart/patrepeval huggingface dataset:
Mea culpa: How developers fix their own simple bugs differently from other developers (2021)

In this work, we study how the authorship of code affects bug-fixing commits using the SStuBs dataset, a collection of single-statement bug fix changes in popular Java Maven projects. More specifically, we study the differences in characteristics between simple bug fixes by the original author - that is, the developer who submitted the bug-inducing commit - and by different developers (i.e., non-authors). Our study shows that nearly half (i.e., 44.3%) of simple bugs are fixed by a different developer. We found that bug fixes by the original author and by different developers differed qualitatively and quantitatively. We observed that bug-fixing time by authors is much shorter than that of other developers. We also found that bug-fixing commits by authors tended to be larger in size and scope, and address multiple issues, whereas bug-fixing commits by other developers tended to be smaller and more focused on the bug itself. Future research can further study the different patterns in bug-fixing and create more tailored tools based on the developer's needs.
Synthesis of a High-Coercivity FePt–Ag Nanocomposite Magnet via Block Copolymer-Templated Self-Assembly (2017)

Magnetic recording media are composed of magnetic thin films consisting of magnetically isolated crystallites. For practical use of magnetic particles as recording media, it will be necessary to realize high coercivity by fabricating nanocrystalline grains and forming grain boundaries with the nonmagnetic phase. In this study, a high-coercivity FePt–Ag nanocomposite magnet was synthesized by means of block copolymer-templated self-assembly. Precursors of Fe, Pt, and Ag were introduced into a polymer block, and the resulting material was oxidized and then reduced to form a nanocomposite consisting of FePt nanoparticles surrounded by a matrix of Ag. X-ray diffraction analysis revealed that the introduction of Ag did not significantly affect the crystalline ordering of the FePt. The addition of Ag increased the coercivity by 53% (from 11.1 to 17.0 kOe). Our results suggest that the grain boundaries of the nonmagnetic Ag metal acted as pinning sites, disrupting magnetic coupling between individual FePt nanocrystallites and hindering domain wall motion at an external magnetic field.
Rectification of Perspective Document Image Captured by Digital Camera (2007)

A rectification method of perspective document image captured by the digital camera was proposed.The potential text margin in the perspective document image is a convex quadrilateral and in the oringinal document is a rectangle.The relation between the convex quadrilateral and the rectangle was used to determine a homographic matrix.The perspective document image was rectified by the homographic matrix.The efficiency is shown by experimental results.
An LO Frequency Tripler with Phase Shifter and Detector in 28nm FD-SOI CMOS for 28-GHz Transceivers (2021)

This paper presents an LO frequency multiplier and phase shifter for the 28-GHz band, implemented in 28nm FD-SOI CMOS technology. The phase control is introduced in an injection-locked oscillator, followed by an injection-locked frequency tripler. The phase of the output signal is compared with that of the input signal using a phase detector based on third harmonic mixing, enabling automatic phase tuning using low frequency detector outputs. Additionally, the phase detector can be used to detect locking of the oscillators, supporting automatic frequency tuning. A 24-30GHz sliding-IF receiver is also implemented to test the LO circuitry. Simulations show that the phase shifter achieves >360° tuning range over the full 24-30GHz span, with a gain variation of 0.11 dB or less, and that the phase detector has an rms phase error of <2.5°. The entire chip, including pads, measures 1080µm x 1080µm and consumes 27–29 mW from a 1 V supply.
Robust ASV Navigation Through Ground to Water Cross-Domain Deep Reinforcement Learning (2021)

This paper presents a framework to alleviate the Deep Reinforcement Learning (DRL) training data sparsity problem that is present in challenging domains by creating a DRL agent training and vehicle integration methodology. The methodology leverages accessible domains to train an agent to solve navigational problems such as obstacle avoidance and allows the agent to generalize to challenging and inaccessible domains such as those present in marine environments with minimal further training. This is done by integrating a DRL agent at a high level of vehicle control and leveraging existing path planning and proven low-level control methodologies that are utilized in multiple domains. An autonomy package with a tertiary multilevel controller is developed to enable the DRL agent to interface at the prescribed high control level and thus be separated from vehicle dynamics and environmental constraints. An example Deep Q Network (DQN) employing this methodology for obstacle avoidance is trained in a simulated ground environment, and then its ability to generalize across domains is experimentally validated. Experimental validation utilized a simulated water surface environment and real-world deployment of ground and water robotic platforms. This methodology, when used, shows that it is possible to leverage accessible and data rich domains, such as ground, to effectively develop marine DRL agents for use on Autonomous Surface Vehicle (ASV) navigation. This will allow rapid and iterative agent development without the risk of ASV loss, the cost and logistic overhead of marine deployment, and allow landlocked institutions to develop agents for marine applications.
Economic burden of diabetic foot ulcers and amputations: Data Points #3 (2011)

Beneficiaries with a diabetic foot ulcer are seen by their outpatient health care provider about 14 times per year and are hospitalized about 1.5 times per year. The cost of care for these beneficiaries is substantial, at about $33,000 for total reimbursement of all Medicare services per year.Beneficiaries with a lower extremity amputation are seen by their outpatient health care provider about 12 times per year and are hospitalized about 2 times per year. The cost of care for these beneficiaries is substantial, at about $52,000 for total reimbursement of all Medicare services per year.
Carbon Nanotubes with Small and Tunable Diameters from Poly(ferrocenylsilane)-block-polysiloxane Diblock Copolymers (2006)

Iron-containing nanostructures produced from various self-assembled poly(ferrocenylsilane)-block-polysiloxane thin films are catalytically active for the initiation and growth of high density, small diameter carbon nanotubes (CNTs). Moreover, the tube diameter and density can be tuned by adjusting the chain lengths of the block copolymer. Iron-containing nanostructures from poly(ferrocenylmethylethylsilane)-b-poly(methylvinylsiloxane) polymer with 25 repeat units of an iron-containing segment and 265 repeat units of a non-iron-containing segment are able to produce CNTs with diameters around or less than 1 nm. Lithographically selective growth of CNTs across a large surface area has been demonstrated using this polymer system. Under the same growth condition, it has been found that the yield of defect-free CNTs varies with the size of the catalytically active nanostructures, which are dictated by the chain lengths of the two blocks. This result indicates that, for a specific-sized catalyst nanocluster, a unique set of growth conditions is required for synthesizing high yield, defect-free CNTs. This finding further addresses the importance of using uniform-sized catalyst-containing nanostructures for consistently achieving high-yield and high-quality CNTs with a minimum number of defects and amount of amorphous carbon.
Synthesis and Properties of an Overcrowded Silabenzene Stable at Ambient Temperature (2000)

Solid-state, room-temperature stability for silabenzene 1 is granted by the bulky silane rendering kinetic inertness. Silabenzene 1 is synthesized in good yield from the crowded chlorosilane 2 with tert-butyllithium. The delocalized, aromatic nature of 1 was confirmed by NMR spectroscopy and the 1JSi−C value, as well as calculations on an analogous silabenzene.
Biological Sequence Kernels with Guaranteed Flexibility (2023)

Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning methods are ineffective or unreliable in this problem domain. We study these challenges theoretically, through the lens of kernels. Methods based on kernels are ubiquitous: they are used to predict molecular phenotypes, design novel proteins, compare sequence distributions, and more. Many methods that do not use kernels explicitly still rely on them implicitly, including a wide variety of both deep learning and physics-based techniques. While kernels for other types of data are well-studied theoretically, the structure of biological sequence space (discrete, variable length sequences), as well as biological notions of sequence similarity, present unique mathematical challenges. We formally analyze how well kernels for biological sequences can approximate arbitrary functions on sequence space and how well they can distinguish different sequence distributions. In particular, we establish conditions under which biological sequence kernels are universal, characteristic and metrize the space of distributions. We show that a large number of existing kernel-based machine learning methods for biological sequences fail to meet our conditions and can as a consequence fail severely. We develop straightforward and computationally tractable ways of modifying existing kernels to satisfy our conditions, imbuing them with strong guarantees on accuracy and reliability. Our proof techniques build on and extend the theory of kernels with discrete masses. We illustrate our theoretical results in simulation and on real biological data sets.
A new approach to detect the contact of two‐dimensional elliptical particles (2001)

Abstract The objective of this paper is to introduce a new algorithm to calculate analytically the overlap of two‐dimensional ellipses. The algorithm may be applied for the direct numerical simulation of granular material dynamics by the discrete element method (DEM). The stability of the algorithm is analysed. Moreover, optimization for possible iterative methods is dealt with. Copyright © 2001 John Wiley &amp; Sons, Ltd.
Opto-thermally Excited Fabry-Perot Resonance Frequency Behaviors of Clamped Circular Graphene Membrane (2019)

An opto-thermally excited optical fiber Fabry-Perot (F-P) resonant probe with suspended clamped circular graphene diaphragm is presented in this paper. Then, the dependence of resonance frequency behaviors of graphene diaphragm upon opto-mechanical factors including membrane properties, laser excitation parameters and film boundary conditions are investigated via COMSOL Multiphysics simulation. The results show that the radius and thickness of membrane will linearly affect the optical fiber light-induced temperature distribution, thus resulting in rapidly decreasing resonance frequency changes with the radius-to-thickness ratio. Moreover, the prestress can be regulated in the range of 10<sup>8</sup> Pa to 10⁸ Pa by altering the environmental temperature with a scale factor of 14.2 MPa/K. It is important to note that the availability of F-P resonant probe with a defective clamped circular graphene membrane can be improved notably by fabricating the defected circular membrane to a double-end clamped beam, which gives a broader perspective to characterize the resonance performance of opto-thermally excited F-P resonators.
Single Wall Carbon Nanotube Aerogels (2006)

Novel aerogels made from single wall carbon nanotubes were created by freeze drying and critical point drying of aqueous SWNT suspensions. The electrical and physical properties of the aerogels are explored.
AquaCrop—The FAO Crop Model to Simulate Yield Response to Water: I. Concepts and Underlying Principles (2009)

This article introduces the FAO crop model AquaCrop. It simulates attainable yields of major herbaceous crops as a function of water consumption under rainfed, supplemental, deficit, and full irrigation conditions. The growth engine of AquaCrop is water‐driven , in that transpiration is calculated first and translated into biomass using a conservative, crop‐specific parameter: the biomass water productivity, normalized for atmospheric evaporative demand and air CO 2 concentration. The normalization is to make AquaCrop applicable to diverse locations and seasons. Simulations are performed on thermal time, but can be on calendar time, in daily time‐steps. The model uses canopy ground cover instead of leaf area index (LAI) as the basis to calculate transpiration and to separate out soil evaporation from transpiration. Crop yield is calculated as the product of biomass and harvest index (HI). At the start of yield formation period, HI increases linearly with time after a lag phase, until near physiological maturity. Other than for the yield, there is no biomass partitioning into the various organs. Crop responses to water deficits are simulated with four modifiers that are functions of fractional available soil water modulated by evaporative demand, based on the differential sensitivity to water stress of four key plant processes: canopy expansion, stomatal control of transpiration, canopy senescence, and HI. The HI can be modified negatively or positively, depending on stress level, timing, and canopy duration. AquaCrop uses a relatively small number of parameters (explicit and mostly intuitive) and attempts to balance simplicity, accuracy, and robustness. The model is aimed mainly at practitioner‐type end‐users such as those working for extension services, consulting engineers, governmental agencies, nongovernmental organizations, and various kinds of farmers associations. It is also designed to fit the need of economists and policy specialists who use simple models for planning and scenario analysis.
Mesenchymal Stem Cells (MSCs) Treatment Alleviates Smoke Inhalation and Burn-Induced Acute Respiratory Distress Syndrome (ARDS) by Inhibiting HMGB1-TLR4 Signal (2023)

Abstract ARDS is one of the leading causes of high morbidity and mortality in trauma patients. Previously our data demonstrated autologous MSCs treatment improved survival in a swine model of smoke inhalation and burn injury. However, the pathophysiological mechanisms are still largely unknown. Twenty anesthetized female swine underwent smoke inhalation injury and 40% TBSA burns, were then randomly assigned to either mock treatment (IC, n=10), or autologous MSCs treatment (MSCs, n=10), followed by ICU care up to 72 hours except in case of early death. Three doses of MSCs collected by bone marrow aspiration and concentrated using a bedside cell concentrator device were applied at 2, 24, and 48 hours of post-injury (PI). Blood and tissue samples were collected for ELISA and IHC analyses. In IC group, 10/10 injured pigs developed ARDS, but only 6/10 pigs in MSCs group developed ARDS. Serum analysis revealed that the HMGB1 level gradually increased after injury and reached a peak at 48h PI (5.7-fold increase vs. baseline). The SDC-1 and C3a levels also increased after injury but reached a peak at 24h (2.9-fold) and 72h PI (2.2-fold), respectively. The MSCs treatment significantly reduced the HMGB1 level in the serum, especially at 6h and 12h PI compared to the IC group but failed to inhibit the SDC-1 and C3a increases. IHC analyses showed that injury triggered a significantly higher expressions of HMGB1 and TLR4, as well as co-localization of HMGB1 and TLR4 in the lung; while MSCs treatment was able to disrupt the HMGB1-TLR4 interaction and significantly reduce their expressions. Our data indicate that the way MSCs treatment mitigates ARDS might be by reducing HMGB1 release and inhibiting the HMGB1-TLR4 signal pathway activation in pigs after smoke and burn injury. This work was supported by the US Army Medical Research and Development Command (USAMRDC) under Grant No. W81XWH-13-2-0005.
Syntaxin 4 Expression in Pancreatic β-Cells Promotes Islet Function and Protects Functional β-Cell Mass (2018)

Syntaxin 4 (Stx4) enrichment in human and mouse islet grafts improves the success of transplants in reversing streptozotocin (STZ)-induced diabetes in mice, although the underlying molecular mechanisms remain elusive. Toward a further understanding of this, human islets and inducible transgenic mice that selectively overexpress Stx4 in islet β-cells (βTG-Stx4) were challenged with proinflammatory stressors in vitro and in vivo. Remarkably, βTG-Stx4 mice resisted the loss of β-cell mass and the glucose intolerance that multiple low doses of STZ induce. Under standard conditions, glucose tolerance was enhanced and mice maintained normal fasting glycemia and insulinemia. Conversely, Stx4 heterozygous knockout mice succumbed rapidly to STZ-induced glucose intolerance compared with their wild-type littermates. Human islet β-cells overexpressing Stx4 exhibited enhanced insulin secretory capability; resilience against proinflammatory cytokine-induced apoptosis; and reduced expression of the <i>CXCL9</i>, <i>CXCL10</i>, and <i>CXCL11</i> genes coordinate with decreased activation/nuclear localization of nuclear factor-κB. Finding ways to boost Stx4 expression presents a novel potential therapeutic avenue for promoting islet function and preserving β-cell mass.
The effect of bile acids and piroxicam on MHC antigen expression in rat colonocytes during colon cancer development. (1994)

The effect of bile acids and piroxicam on the expression of major histocompatibility complex (MHC) antigens in colonocytes was evaluated in rats treated with the colonic carcinogen azoxymethane (AOM). Male Fischer-344 rats were fed a basal diet (AIN-76) supplemented with 0.4% cholic acid, 0.4% ursodeoxycholic acid, 0.2% ursodeoxycholic acid plus 0.2% cholic acid, or 75 p.p.m. piroxicam. Rats were injected subcutaneously once a week for 2 weeks with AOM (15 mg/kg body weight/week) or vehicle, after being fed their respective diets for two weeks. The rats were killed at 16 weeks, while parallel identical groups of rats were killed at 28 weeks, and colon tumours were counted. None of the rats treated with AOM-vehicle developed tumours at 28 weeks, while in the AOM-treated rats the frequency of colonic tumours was as follows: AOM alone 50%, cholic acid 74%, ursodeoxycholic acid 17%, piroxicam 28%, ursodeoxycholic plus cholic acid 46%. The expression of RT1A, RT1B and RT1D was determined in isolated colonocytes by immune fluocytometry. Normal rat colonocytes express all three MHC antigens strongly. Neither the bile acids nor piroxicam affected MHC antigen expression in AOM-vehicle-treated rats. AOM did not effect MHC antigen expression compared to normal controls. Cholic acid had no significant effect on the expression of MHC antigens in AOM-treated rats. Ursodeoxycholic acid alone or in combination with cholic acid increased the expression of RT1A compared to normal controls, of RT1B compared to AOM-treated rats, and of RT1D compared to controls or AOM-treated rats. Piroxicam increased the expression of all three antigens compared to either control or AOM-treated rats. These findings indicate that (1) ursodeoxycholic acid and piroxicam up-regulate colonic MHC antigen expression in the AOM model of colonic carcinogenesis; (2) the colon of rats exposed to AOM responds differently than the normal colon with respect to MHC regulation; and (3) the protective effect of ursodeoxycholic acid and piroxicam on colon tumour formation seems to be paralleled by an increase in MHC antigen expression.
Chondrogenic differentiation of human adipose-derived stem cells using microcarrier and bioreactor combination technique (2014)

The aim of the current study was to explore the application of microcarrier technology in the rapid amplification and chondrogenic differentiation of human adipose‑derived stem cells (ADSCs) in a rotating bioreactor. Human ADSCs were cultivated with Cytodex 3 microcarriers in a rotary cell culture system (RCCS), and using inverted and scanning electron microscopes, the ADSCs were observed on the surface of the microcarriers. The harvested ADSCs were stained with safranin‑O or toluidine blue histochemical stains, and type II collagen immunohistochemical stain. ADSCs were adherent to the surface of Cytodex 3 microcarriers by 24 h. They became short and spindle‑shaped, and as time progressed, the adherence of the cells to the microcarriers gradually improved. By the end of the culture period, the cell densities were ~19 times that of the initial cell density. The harvested cells on microcarriers were safranin-O and toluidine blue staining and collagen Ⅱ‑positive staining, which were stronger than the control group. The application of microcarrier technology is able to rapidly amplify human ADSC proliferation and successfully implement chondrogenic differentiation in vitro.
Alternating donor–acceptor indigo-cyclopentadithiophene copolymers: competition between excited state conformational relaxation, energy transfer and excited state proton transfer (2017)

In a copolymer with indigo and CPDT, fast ESPT and/or intrachain energy transfer are observed whereas conformational relaxation is absent.
A SPEEDUP METHOD OF A HIGH-SPEED DIRECT-COUPLED JOSEPHSON LOG1 (1993)

The switching mechanism of a direct-coupled Josephson logic gate, a four-junction logic (4JL) gate, has been investigated. It was found that a high-speed input signal current is wasted in an input-output separation resistance mi). We have developed a speedup method in which an inductance is connected to Ri in series. The value of the inductance was found to be five times larger than the effective inductance of the input junction. 40 % speedup of the gate switching was demonstrated by a logic delay experiment using submicron NbN/MgO/NbN junction technology. The minimum logic delay of 3.0 ps/gate was obtained with fan-out 1.
Effects of Prostacyclin During Cardiopulmonary Bypass in Man (1981)

AbstractEffects of prostacyclin infusion were studied in adult patients operated on for acquired heart disease during the period November 1979-June 1980. In group A. 10 patients received prostacyclin 50 ng × kg b.w.−1 x min−1 for the first 30 min of cardiopulmonary bypass (CPB). Twelve patients served as controls. In group B, 14 patients received prostacyclin 100 ng × kg b.w.−1 x min−1 throughout CPB apart from the last 5-20 min. Nine patients served as controls. CPB was by roller pump and bubble oxygenator primed with a crystalloid solution. Hypothermia to 25-28°C was induced. All patients were given heparin 3 mg/kg b.w. before cannulation + 50-75 mg added to the pump prime.There were 3 deaths in the control groups and 1 death in the prostacyclin groups. One control and 2 prostacyclin patients were re-operated on for bleeding. There was no difference between control and prostacyclin patients in regard to intra- or postoperative bleeding. One prostacyclin patient operated on for calcific aortic stenosis suffered hemiplegia. There were no other instances of cerebral damage in prostacyclin patients, whereas 2 control patients with prolonged CPB showed severe damage. Infusion of prostacyclin reduced aortic blood pressure (often to less than 30 mmHg) and systemic vascular resistance was decreased by approximately 50% during infusion.The platelet count corrected for haematocrit was significantly (p < 0.01) better preserved in prostacyclin patients than in control patients both during and after CPB. After 90 min of CPB, the platelet count in control patients was (X ± S.D.) 71±19% and in prostacyclin patients 100±22% of pre-CPB value. Platelet aggregation induced by ADP and collagen was abolished in group B patients during prostacyclin infusion and they showed a tendency to better ADP induced platelet aggregation after bypass in comparison with control patients.