gebhart/patrepeval huggingface dataset:
Toward a defect prediction model of exception handling method call structures (2014)

The ability to predict where faults are likely to arise in the source code can help guide test plans, reduce effort and cost, narrow the test space, and improve software quality. Our preliminary results show that exception handling code can be more risky than normal code. Therefore, in order to support more efficient testing of exception handling code, this extended abstract proposes a framework to predict faults from annotated exception handling method call structures. This framework will generate annotated exception call graphs of the whole system and calculate property-based software engineering measurement values. The framework will then predict the high risk area of the system by applying statistical modeling techniques to perform fault prediction.
Mechanical and Chemical Properties of Cysteine-Modified Kinesin Molecules (1999)

To probe the structural changes within kinesin molecules, we made the mutants of motor domains of two-headed kinesin (4-411 aa) in which either all the five cysteines or all except Cys45 were mutated. A residual cysteine (Cys45) of the kinesin mutant was labeled with an environment-sensitive fluorescent probe, acrylodan. ATPase activity, mechanical properties, and fluorescence intensity of the mutants were measured. Upon acrylodan-labeled kinesin binding to microtubules in the presence of 1 mM AMPPNP, the peak intensity was enhanced by 3.4-fold, indicating the structural change of the kinesin head by the binding. Substitution of cysteines decreased both the maximum microtubule-activated ATPase and the sliding velocity to the same extent. However, the maximum force and the step size were not affected; the force produced by a single molecule was 6-6.5 pN, and a step size due to the hydrolysis of one ATP molecule by kinesin molecules was about 10 nm for all kinesins. This step size was close to a unitary step size of 8 nm. Thus, the mechanical events of kinesin are tightly coupled with the chemical events.
MAV Propulsion System Using the Coanda Effect (2009)

In an effort to to fill the micro aerial vehicle (MAV) performance gap between efficient cruise (fixed wing) and hover (rotary), a Coandǎ type propulsive platform is proposed. A jet, deflected by a curved surface is used for hover, while the curved surface can also be used as a wing for efficient cruise. The principles allowing the attachment of the flow are not clear and therefore efficient sizing of the surface and jet is difficult. For this purpose design rules are proposed and validated by Reynolds averaged Navier-Stokes and latticeBoltzmann models. The efficiency of converting the jet into thrust was in the order of 60 to 80 percent with respect to the predicted ideal thrust for the tested configurations. The correspondence in predicted and calculated pressure coefficient for circular surfaces was adequate, with the exception of the expansion of the jet and the stagnation point at separation. Measurements are, therefore, still needed for further validation of the computations.
IgG rheumatoid factors and staphylococcal protein A bind to a common molecular site on IgG. (1985)

The antigenic determinant on the Fc region of human IgG for two IgG rheumatoid factors (IgG-RF) from patients with rheumatoid arthritis were investigated in detail. The RF did not interact with IgG fragments that contained the C gamma 2 or C gamma 3 region alone, but required the presence of both regions for binding. The RF binding to solid-phase IgG were poorly inhibited by the IgG3 subclass and strongly inhibited by staphylococcal protein A (SPA) (42 kD), and fragment D of SPA (7 kD), indicating that the binding site is most likely the same as the Ga antigenic determinant described for IgM-RF, and is in the same location as the site on IgG that binds SPA. pH titration studies of the RF binding to IgG indicated the involvement of histidine and lysine or tyrosine side chains. Chemical modification studies showed the histidines were involved on the Fc side of the interactions, and tyrosines were involved on both the antigenic and antibody sides of the interactions. Lysines were not involved. The above information, and the knowledge of the number and position in space of the amino acid residues involved in the C gamma 2-C gamma 3 interface region of IgG, the binding site for SPA, and the amino acid substitutions in IgG3 that account for its inability to bind protein A, allowed the identification of the site on IgG that bind IgG-RF. This binding site involves some of the same amino acid side chains, His 435, Tyr 436, and one or both His 433 and 310, and is in the same location as the site that binds SPA. The same site is likely to be a common antigenic determinant for other RF. Furthermore, the described molecular mimicry suggests a biological relationship between bacterial Fc-binding proteins and the production of RF in rheumatoid arthritis.
Modeling of linear objects considering bend, twist, and extensional deformations (2002)

Various deformable objects are manipulated in many manufacturing processes. Deformation of these objects is often utilized in order to manipulate them successfully while the manipulation sometimes fails because of unexpected deformation of the objects. Modeling of deformable objects is thus required so that the shape of the objects can be evaluated on a computer in advance. In this paper, we develop an analytical method to model the shape of a deformable linear object such as cords and tubes. First, a geometric representation to describe the shape of a linear object with bending and torsional deformation is introduced. The potential energy of the object and the geometric constraints imposed on it are then formulated. The shape of the object in the stable state can be derived by minimizing the potential energy under the geometric constraints. Next, procedure to compute the deformed shape is developed by applying a nonlinear programming technique. Finally, some numerical examples are shown in order to demonstrate how deformed shapes of linear objects are computed using the proposed approach.
Clinical experience with Andriol® Testocaps®– The first Austrian surveillance study on the treatment of late-onset hypogonadism (2007)

Short-term treatment with oral testosterone undecanoate in a clinical practice setting improved late-onset hypogonadism symptoms in aging men with low testosterone levels.
The status of differentiation therapy of cancer (1988)

This book contains the proceedings on the status of differentiation therapy of cancer. Topics covered include: Strategies for modifying gene expression during differentiation; Growth factors and differentiation therapy; Design of combination differentiation therapy; and Clinical traits of differentiation therapy.
Beta-glucuronidase in physiology and disease. (2003)

beta-glucoronidase (EC 3.2.1.31) is a lysosomal enzyme catylysing the decomposition of beta-D-glucoronides--compounds arising as a result of the combination of beta-D-glucoronic acid and a number of compounds both exo- and endogenous, containing hydroxylic, carboxylic, amine, imine or thiol groups. The most common test evaluating the activity of the enzyme is that using phenolphtalein glucoronide as a biosynthetic substrate. The freed aglycons are colorimetrically assayed. The activity of beta-glucoronidase increases in many pathological conditions: liver infammations, cirrhosis of the liver, inflammations of other organs, cholestatic jaundice, tuberculosis, sarcoidosis and also in neoplasms. Many authors point to beta-glucoronidase as a sensitive indicator signalling cell damage.
DNA-Binding Ligands from Peptide Libraries Containing Unnatural Amino Acids (1998)

Combinatorial chemistry with a newly-developed screening procedure using complementary fluorescein- and rhodamine-labelled oligonucleotides (below) has been used to select peptide dsDNA binding ligands. A high structure–affinity relationship of the dsDNA-binding unnatural peptide was observed.
Three‐dimensional ultrasound‐guided robotic needle placement: an experimental evaluation (2008)

A 3D US-guided robot can eliminate error bias and reduce invasiveness (the number of insertions required) compared to manual needle insertion. Remaining future challenges include target motion compensation.
British applied linguistics: impacts of and impacts on (2012)

Abstract This article critically examines the demand that academic research should be assessed by its impact, and universities' compliance with that demand. Although the discussion centres mainly on the UK, it will have relevance to any academic context where government and/or business seek to control academics. The article begins by briefly examining the meaning of impact. It next considers the role of applied linguistics in shaping language-teaching revolutions, and suggests it was commercial and political interests which had the greatest impact. Moving on to the current wider scope of applied linguistics, it suggests that while the discipline has had positive influence in some areas, it has failed to influence government policy, but that this failure is not a measure of its worth. In the second part of the article, the focus changes to a consideration of impacts on applied linguistics by public relations (PR) models of language, and government interference in academic affairs. It notes the growth and power of PR units within British universities, and wonders why applied linguistics fails to challenge the vapid and often incorrect assertions made by these communication ‘experts’ about language use. It links this ‘PR turn’ in universities, and the vague language which surrounds it, to the tightening stranglehold of current and recent UK governments on university activity, comparing this briefly to the more open recruitment of applied linguistics to serve national security interests in the USA. The overall conclusions of the article are that impact is not necessarily a measure of academic worth, and that informed critique of establishment values should remain one of the main roles of academics. While these conclusions are relevant to all academic disciplines they are of particular poignancy for applied linguistics, given the role of language in establishing control and undermining academic freedoms.
Chemical pathology of homocysteine. IV. Excitotoxicity, oxidative stress, endothelial dysfunction, and inflammation. (2009)

This review considers recent advances in the chemical pathology of homocysteine in atherogenesis, oxidative metabolism, and carcinogenesis. Homocysteine is a potent excitatory neurotransmitter that binds to the N-methyl-D-aspartate (NMDA) receptor and leads to oxidative stress, cytoplasmic calcium influx, cellular apoptosis, and endothelial dysfunction. According to the adsorption-induction theory, cytoplasmic calcium influx leads to depletion of cellular adenosine triphosphate (ATP) by reaction with cytoplasmic phosphate, leading to calcium apatite deposition. Oxidative stress is caused by failure of ATP synthesis and accumulation of reactive oxygen radicals, theoretically because of inhibition of thioretinaco ozonide function within mitochondria and endoplasmic reticulum. The toxicity of oxygen difluoride is theoretically explained by the displacement of ozone from thioretinaco ozonide, leading to inhibition of cellular respiration. Depletion of thioretinaco ozonide from cellular membranes is suggested to underlie the carcinogenic and atherogenic effects of fluoride and other electrophilic carcinogens. In atherogenesis the acute inflammatory response is related to cellular apoptosis and necrosis, autoantibodies to proteins containing peptide-bound homocysteine and oxidized low-density lipoprotein (Ox-LDL), and microbial products and antigens originating from homocysteinylated LDL aggregates trapped within vasa vasorum of developing atherosclerotic plaques. The trapping of lipoprotein aggregates and obstruction of the lumen of vasa vasorum are enhanced by high tissue pressure and by endothelial dysfunction because of narrowing of the lumen by swollen and hyperplastic endothelial cells, leading to the creation of vulnerable plaques.
Lifetime History of Sexual Abuse, Clinical Presentation, and Outcome in a Clinical Trial for Adolescent Depression (2004)

Sexual abuse is a negative predictor of long-term outcome in adolescent depression. CBT for depression may not be as efficacious for those depressed adolescents with a history of sexual abuse. These findings suggest that a history of sexual abuse should be assessed not only in clinical practice, but also in research studies of depressive outcome. Further work is indicated to understand the relationship between sexual abuse and poor outcome in order to help restore these high-risk youths to an optimal developmental trajectory.
Interfacing the PACS and the HIS: Results of a 5-year Implementation (2000)

An interface was created between the Department of Defense's hospital information system (HIS) and its two picture archiving and communication system (PACS)-based radiology information systems (RISs). The HIS is called the Composite Healthcare Computer System (CHCS), and the RISs are called the Medical Diagnostic Imaging System (MDIS) and the Digital Imaging Network (DIN)-PACS. Extensive mapping between dissimilar data protocols was required to translate data from the HIS into both RISs. The CHCS uses a Health Level 7 (HL7) protocol, whereas the MDIS uses the American College of Radiology-National Electrical Manufacturers Association 2.0 protocol and the DIN-PACS uses the Digital Imaging and Communications in Medicine (DICOM) 3.0 protocol. An interface engine was required to change some data formats, as well as to address some nonstandard HL7 data being output from the CHCS. In addition, there are differences in terminology between fields and segments in all three protocols. This interface is in use at 20 military facilities throughout the world. The interface reduces the amount of manual entry into more than one automated system to the smallest level possible. Data mapping during installation saved time, improved productivity, and increased user acceptance during PACS implementation. It also resulted in more standardized database entries in both the HIS (CHCS) and the RIS (PACS).
Changes in gene order and gene expression. (1982)

Studies on changes in gene position in germ line and somatic cell chromosomes during evolution and differentiation have led biologists to abandon the static view of chromosomes as invariant linear arrays of hereditary information. Prokaryotic cells contain several classes of DNA insertion elements which move from place to place in the genome and mediate chromosome rearrangements. Similar elements exist in a wide variety of eukaryotic organisms (yeasts, insects, plants, and vertebrates). In addition, both reversible and irreversible changes of chromosome primary structure provide developmental controls on gene activity in bacteria, bacteriophages, yeasts, trypanosomes, and mammalian lymphocytes. At least five recombination mechanisms are known to catalyze chromosome changes: 1) general homologous, 2) site-specific reciprocal, 3) illegitimate, 4) DNA splicing, and 5) replicative. Various combinations of these mechanisms can explain many different chromosome rearrangements and changes in gene dosage. Changes in gene position can alter gene expression in many ways, some of which we understand (such as insertional mutation and inversion of coding and regulatory sequences) and some of which are still unexplained. The activities of DNA insertion elements and somatic rearrangement systems are subjects to controls at several levels by specific regulatory systems, natural selection, and connection to cell lineage. Despite the recent increase in knowledge about the biological importance of changes in gene order on chromosomes, there are far more questions than answers, particularly about the mechanisms that coordinate recombination events and cell division in higher organisms.
Protective and curative potential of vaccination with interleukin-2-gene-transfected cells from a spontaneous mouse mammary adenocarcinoma. (1993)

The potential of interleukin 2-gene-transfected tumor cells to prevent tumor growth and cure established tumors was evaluated using cells from a spontaneous, invasive, and metastasizing mouse mammary adenocarcinoma. Tumor cells engineered to secrete interleukin 2 initially trigger a local inflammatory reaction that leads to inhibition of established parental adenocarcinomas, as well as an antigenically unrelated fibrosarcoma. The ensuing systemic immunity selectively inhibits subsequent parental cell challenges and cures established parental adenocarcinomas and their lung metastases, although less effectively as the neoplastic mass increases. Multiple injections of interleukin 2-gene-transfected tumor cells may thus be considered a new form of vaccination in the management of minimal residual disease and incipient metastases.
Platelet transfusions irradiated with ultraviolet-B light may have a role in reducing recipient alloimmunization (1991)

The recipients of multiple platelet transfusions frequently develop alloantibodies directed against the human leucocyte antigens (HLA) present on both leucocytes and platelets. Such alloimmunization (AI) may result in refractoriness to further platelet transfusions. Contaminating leucocytes bearing Class II HLA and present in platelet concentrates (PC) are responsible for the formation of HLA antibodies and their removal by filtration reduces the rate of recipient AI. Ultraviolet irradiation (UVR) of PC at an appropriate dose inactivates the contaminating mononuclear leucocytes so that responses in vitro to mitogens and alloantigens are abrogated. It seems likely that UV-irradiation of donor dendritic cells (DC) is important in preventing in vitro responses to alloantigens and in vivo allosensitization. At the same time, satisfactory platelet function and structure is retained when measured by in vitro tests. In vivo assessments of platelet recovery and survival in healthy subjects and the ability to correct the bleeding time in thrombocytopenic patients are comparable to non-irradiated PC. Prospective studies are now in progress to determine if UVR will reduce recipient AI to HLA in multiply-transfused patients with leukaemia and lymphoma.
Imatinib Mesylate Enhances Therapeutic Effects of Gemcitabine in Human Malignant Mesothelioma Xenografts (2008)

Imatinib mesylate enhances the therapeutic response to gemcitabine, in accordance with our previous in vitro data. These in vivo results validate imatinib mesylate and gemcitabine as a combination treatment of malignant mesothelioma, also in view of its known positive effects on tumor drug uptake. These evidences provide the rationale for the currently ongoing clinical trials.
New Developments in Understanding the Complexity of Human Speech Production (2016)

Speech is one of the most unique features of human communication. Our ability to articulate our thoughts by means of speech production depends critically on the integrity of the motor cortex. Long thought to be a low-order brain region, exciting work in the past years is overturning this notion. Here, we highlight some of major experimental advances in speech motor control research and discuss the emerging findings about the complexity of speech motocortical organization and its large-scale networks. This review summarizes the talks presented at a symposium at the Annual Meeting of the Society of Neuroscience; it does not represent a comprehensive review of contemporary literature in the broader field of speech motor control.
Endosialin (TEM1, CD248) is a marker of stromal fibroblasts and is not selectively expressed on tumour endothelium (2005)

Fibroblasts are a diverse cell type and display clear topographic differentiation and positional memory. In a screen for fibroblast specific markers we have characterized four monoclonal antibodies to endosialin (TEM1/CD248). Previous studies have reported that endosialin is a tumour endothelium marker and is localized intracellularly. We demonstrate conclusively that endosialin is a cell surface glycoprotein and is predominantly expressed by fibroblasts and a subset of pericytes associated with tumour vessels but not by tumour endothelium. These novel antibodies will facilitate the isolation and classification of fibroblast and pericyte lineages as well as the further functional analysis of endosialin.
Effect of temperature, carbon dioxide enrichment, nitrogen form and rate of nitrogen fertiliser on the yield and nitrate content of two varieties of glasshouse lettuce (1992)

Abstract Head weight of winter glasshouse lettuce was increased slightly by higher temperature (7°C day/4°C night and 10°C day/7°C night) and carbon dioxide enrichment (350 and 1000 μl litre −1 ) but, despite faster growth, plant nitrate concentration was unaffected. Addition at the lowest rate (138 kg ha −1 N) of ammonium nitrate, calcium nitrate and urea increased plant nitrate by a similar amount compared with nil fertilizer nitrogen, but addition of more fertilizer (276 kg ha −1 N) had no further effect. Urea produced a lower yield than the other two N sources. Coated controlled‐release nitrogen produced both low yields and low plant nitrate concentrations because its nitrogen release rate was too slow to keep pace with plant growth. The most effective material in terms of high yield and low plant nitrate was one containing a nitrification inhibitor within the fertiliser granules.
Murine Noroviruses Bind Glycolipid and Glycoprotein Attachment Receptors in a Strain-Dependent Manner (2012)

Human norovirus infections are the most common cause of acute nonbacterial gastroenteritis in humans worldwide, and glycan binding plays an important role in the susceptibility to these infections. However, due to the lack of an efficient cell culture system or small animal model for human noroviruses, little is known about the biological role of glycan binding during infection. Murine noroviruses (MNV) are also enteric viruses that bind to cell surface glycans, but in contrast to their human counterparts, they can be grown in tissue culture and a small animal host. In this study, we determined glycan-binding specificities of the MNV strains MNV-1 and CR3 in vitro, identified molecular determinants of glycan binding, and analyzed infection in vivo. We showed that unlike MNV-1, CR3 binding to murine macrophages was resistant to neuraminidase treatment and glycosphingolipid depletion. Both strains depended on N-linked glycoproteins for binding, while only MNV-1 attachment to macrophages was sensitive to O-linked glycoprotein depletion. In vivo, CR3 showed differences in tissue tropism compared to MNV-1 by replicating in the large intestine. Mapping of a glycan-binding site in the MNV-1 capsid by reverse genetics identified a region topologically similar to the histo-blood group antigen (HBGA)-binding sites of the human norovirus strain VA387. The recombinant virus showed distinct changes in tissue tropism compared to wild-type virus. Taken together, our data demonstrate that MNV strains evolved multiple strategies to bind different glycan receptors on the surface of murine macrophages and that glycan binding contributes to tissue tropism in vivo.