gebhart/patrepeval huggingface dataset:
Towards an Ecosystem for Reproducible Research in Computer Networking (2017)

Reproducibility is key to rigorous scientific progress. However, many publications in the computer networks community lack support for reproducibility. In this paper, we argue that the lack is mainly rooted in the additional effort that authors need to spend, without expecting sufficient benefits. Based on our experience in both authoring reproducible research and reproducing publications, we propose an ecosystem that incentivizes authors and reproducers to invest additional effort. This ecosystem consists of various building blocks, which can be combined into venue-specific profiles. A key building block is the Reproducibility Challenge, which we suggest to co-locate with the annual SIGCOMM conference to leverage reproducibility research in practice.
Endocrinopathies, Bone Health, and Insulin Resistance in Patients with Fanconi Anemia after Hematopoietic Cell Transplantation (2016)

A number of endocrinopathies have been described after hematopoietic cell transplantation (HCT), but data are limited in patients with Fanconi anemia (FA). We report several endocrine-based disorders in a cohort of 44 patients with FA after HCT compared with both 74 patients who received HCT for hematologic malignancies and with 275 healthy controls. Endocrinopathies assessed included hypothyroidism, hypogonadism, short stature, dyslipidemia, insulin resistance, abnormalities in body composition, and bone health. Most (86%) patients with FA had at least 1 endocrinopathy, with 11% having 3 or more. Hypothyroidism was seen in 57%, hypogonadism in 27%, short stature in 50%, and reduced total body and lumbar spine bone mineral density (BMD) (height adjusted Z-score < -1) in 57% and 21%, respectively. Vitamin D deficiency was seen in 71%. Short stature was associated with younger age at HCT and gonadal failure was associated with older age at HCT. Insulin resistance was associated with increased percent fat mass and increased android/gynoid ratio by dual energy X-ray absorptiometry. Hypothyroidism, short stature, and reduced total body BMD were more prevalent in patients with FA compared with patients with hematologic malignancies. We recommend an assessment before transplantation and close follow-up afterwards to ensure proper clinical management. Future studies should continue to explore the impact of HCT on endocrinopathies in FA patients.
Modified Powder Processing as a Green Method for Ferrite Synthesis (2011)

This chapter contains sections titled: Introduction Experimental Results and Discussion Conclusions
Final design of a compact sweeper magnet for nuclear physics (2002)

A superconducting dipole, designed for use as a sweeper magnet for nuclear physics experiments, is being constructed by the NHMFL for operation at the NSCL. The magnet operates at a peak mid-plane field of 3.8 T in a 140 mm gap. A multi-particle beam enters the magnet from the upstream side. The neutrons continue straight through to a neutron detector. The charged particles are swept 43 degrees on a one meter radius into a mass spectrometer. Extensive model-based computer analysis (MBA) have been applied for optimizing the coils and the stainless steel bobbin with regard to its shape while keeping the strain and the fraction of actual to critical current within reasonable limits. The structural FEM analysis had to address a variety of complex physical phenomena (composites with orthotropic material properties, cool down, surface-to-surface contacts, etc.) and the loads due to operation (Lorentz forces) had to be obtained from a parallel/coupled magnetic field analysis. One of the challenges magnet designers face in optimizing magnet systems is that the detail required to obtain reasonable accuracy is not well known. This paper presents results of the structural design optimization for the sweeper project and evaluates the adequacy of alternative modeling approaches. Also the final magnetic design of the system is summarized and progress toward fabrication is presented.
ChemInform Abstract: Patchwork Protein Chemistry: A Practitioner′s Treatise on the Advances in Synthetic Peptide Stitchery (2013)

Abstract Review: 240 refs.
Abstract P212: Reduced High-Density Lipoprotein Efflux in Psoriasis Relates to Increased Coronary Plaque Burden by Quantitative CT Angiography (2015)

INTRODUCTION: Psoriasis is known to increase cardiovascular risk, possibly due to the presence of inflammatory, lipid-rich, non-calcified plaques in the coronary arteries. Psoriasis is also known to decrease HDL activity. However, whether having abnormal or low-functioning HDL increases arterial disease is currently unknown.

HYPOTHESIS: We aimed to test our hypothesis that coronary plaque burden assessed by quantitative CT angiography is related to HDL efflux capacity and other cardiometabolic parameters in a well-phenotyped psoriasis cohort (NCT# 01778569).

METHODS: Psoriasis patients (N=67) underwent coronary CT angiography (Toshiba 320 slice). Coronary plaque was assessed using QAngio CT (Medis, The Netherlands). Total (TB), dense calcium (DCB), and non-calcified burden (NCB) plaque indices were calculated by dividing total vessel plaque volume by total vessel length. We also performed deep phenotyping for lipid markers including HDL efflux capacity and other cardiometabolic parameters.

RESULTS: The study population was middle aged (52.2 ± 12.4 yr), had relatively low Framingham Risk Score (median 4%, IQR 2-7%), and had normal Apo A1 (156 ± 26.3 mg/dL) and HDL levels (54 ± 17 mg/dL). However, HDL efflux capacity was similar to that in coronary artery disease (0.95 ± 0.17). In univariate regression, NCB increased as HDL efflux capacity decreased (β= -0.84, p=0.01) and was robust to adjustment for cardiometabolic risk factors (β= -0.67, p=0.03). Furthermore, when stratified by median HDL efflux (0.94), patients having lower HDL efflux capacity had higher TB and NCB (TB 3.80 ± 0.82, 4.17 ± 0.97 mm2, p=0.003; NCB 3.59 ± 0.68, 3.94 ± 0.75 mm2, p=0.001 in the low and high HDL efflux groups, respectively). Additional biologic relations in univariate regression are shown in Table 1.

CONCLUSIONS: We show that HDL efflux is negatively associated with coronary plaque burden measured by quantitative CT angiography. Low HDL efflux may therefore be a strong biomarker for subclinical coronary atherosclerosis.

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Fretting Wear Behavior of Laser Peened Ti-6Al-4V (2012)

Abstract This work deals with the influence of laser peening on the fretting wear behavior of Ti-6Al-4V. Laser peening was carried out on Ti-6Al-4V. The laser-peened surface was characterized by transmission electron microscopy. Surface roughness, nanoindentation hardness, residual stress, and tensile properties of the material in both laser-peened and unpeened conditions were determined. Fretting wear tests were conducted at different normal loads using a ball-on-flat contact geometry. Laser peening resulted in the formation of nanocrystallites on the surface and near-surface regions, increased hardness, and compressive residual stress. Laser peening did not affect the tensile properties and surface roughness significantly. There was no considerable difference between the values of the tangential force coefficient of laser-peened and unpeened samples. The fretting scar size, wear volume, and wear rate of laser-peened specimens were lower than those of unpeened samples. This may be attributed to an increase in surface hardness due to strain hardening and grain refinement at the surface and near-surface regions, higher compressive residual stress, and higher resistance to plastic deformation of laser-peened samples. KEY WORDS: Surface ModificationLaser PeeningFrettingHardnessTi-6Al-4VTEM Acknowledgments Review led by Richard Ney
<i>Tupaia Belangeri</i> as an Experimental Animal Model for Viral Infection (2014)

Tupaias, or tree shrews, are small mammals that are similar in appearance to squirrels. The morphological and behavioral characteristics of the group have been extensively characterized, and despite previously being classified as primates, recent studies have placed the group in its own family, the Tupaiidae. Genomic analysis has revealed that the genus Tupaia is closer to humans than it is to rodents. In addition, tupaias are susceptible to hepatitis B virus and hepatitis C virus. The only other experimental animal that has been demonstrated to be sensitive to both of these viruses is the chimpanzee, but restrictions on animal testing have meant that experiments using chimpanzees have become almost impossible. Consequently, the development of the tupaia for use as an animal infection model could become a powerful tool for hepatitis virus research and in preclinical studies on drug development.
Strategies for improving GDE performance by a uniform dispersion of catalyst nanoparticles and an optimal Nafion content (2021)

In the context of the strategies needed to mitigate CO<sub>2</sub> emissions and combat climate change, the electrochemical CO<sub>2</sub> reduction represents a promising alternative. Among the different reactors, GDE-based ones are widely studied systems: here, the limitations shown by configurations with CO<sub>2</sub> dissolved in electrolyte solutions can be overcome by feeding CO<sub>2</sub> directly in gaseous form. In this work, the manufacturing process of the Cu-based gas diffusion electrode, namely the catalytic ink deposition on a porous carbon paper support, was carried out both by airbrushing (manual) and by spray-coating (automated) techniques. The characterization of the electrodes was performed by using X-ray Diffraction (XRD) and Field Emission Scanning Electron Microscopy (FESEM) techniques. To assess electrodes behavior, cyclic and linear sweep voltammetry techniques were conducted. When comparing the achieved current densities at the highest applied potential, the electrode obtained with the spray coater displayed a better electrocatalytic activity (~10 mA/cm<sup>2</sup> higher at about -2.25 V vs Ag/AgCl), with respect to that fabricated with the airbrush. A thorough study of the GDEs performance was accomplished, testing the so obtained electrodes and thereby evaluating the effect of a variation of Nafion content in the productivity and selectivity results toward the desired products. The catalyst layer dispersion is a critical aspect of electrochemical CO<sub>2</sub> reduction and, confirming previous studies on the different deposition methods, a more uniform distribution of the catalyst particles enabled the spray coated GDEs to outperform the hand-made ones. Furthermore, the variation of Nafion content on the GDE structure had a relevant effect on the electrode performance, allowing to considerably reduce the side-production of hydrogen and increasing at the same time the CO generation.
Adaptive negative cycle detection in dynamic graphs (2001)

We examine the problem of detecting negative cycles in a dynamic graph, which is a fundamental problem that arises in electronic design automation and systems theory. We introduce the concept of adaptive negative cycle detection, in which a graph changes over time, and negative cycle detection needs to be done periodically, but not necessarily after every individual change. Such scenarios arise, for example, during iterative design space exploration for hardware and software synthesis. We present an algorithm for this problem, called the Adaptive Bellman-Ford (ABF) algorithm, based on a novel extension of the well known Bellman-Ford algorithm. The ABF algorithm allows us to systematically adapt information for a given graph to a modified version of the graph. We show that the ABF algorithm significantly outperforms previously available approaches for dynamic graphs, which either recompute negative cycle information from scratch whenever a graph is modified, or process the modifications one at a time ("incrementally"). As an application of the ABF technique, we show that it can be used to obtain a very fast implementation of Lawler's technique for the computation of the maximum-cycle mean (MCM) of a graph, especially for a certain important kind of sparse graph. We further illustrate the application of the ABF technique to design-space exploration by developing automated search techniques for scheduling iterative data-flow graphs.
Language and memory abilities of internationally adopted children from China: evidence for early age effects (2013)

The goal of the present study was to examine if internationally adopted (IA) children from China (M = 10;8) adopted by French-speaking families exhibit lags in verbal memory in addition to lags in verbal abilities documented in previous studies (Gauthier & Genesee, 2011). Tests assessing verbal and non-verbal memory, language, non-verbal cognitive ability, and socio-emotional development were administered to thirty adoptees. Their results were compared to those of thirty non-adopted monolingual French-speaking children matched on age, gender, and socioeconomic status. The IA children scored significantly lower than the controls on language, verbal short-term memory, verbal working memory, and verbal long-term memory. No group differences were found on non-verbal memory, non-verbal cognitive ability, and socio-emotional development, suggesting language-specific difficulties. Despite extended exposure to French, adoptees may experience language difficulties due to limitations in verbal memory, possibly as a result of their delayed exposure to that language and/or attrition of the birth language.
Computational Analyses of YY1 and Its Target RKIP Reveal Their Diagnostic and Prognostic Roles in Lung Cancer (2022)

Lung cancer (LC) represents a global threat, being the tumor with the highest mortality rate. Despite the introduction of novel therapies (e.g., targeted inhibitors, immune-checkpoint inhibitors), relapses are still very frequent. Accordingly, there is an urgent need for reliable predictive biomarkers and therapeutically druggable targets. Yin-Yang 1 (YY1) is a transcription factor that may work either as an oncogene or a tumor suppressor, depending on the genotype and the phenotype of the tumor. The Raf Kinase Inhibitory Protein (RKIP), is a tumor suppressor and immune enhancer often found downregulated in the majority of the examined cancers. In the present report, the role of both YY1 and RKIP in LC is thoroughly explored through the analysis of several deposited RNA and protein expression datasets. The computational analyses revealed that YY1 negatively regulates <i>RKIP</i> expression in LC, as corroborated by the deposited YY1-ChIP-Seq experiments and validated by their robust negative correlation. Additionally, YY1 expression is significantly higher in LC samples compared to normal matching ones, whereas RKIP expression is lower in LC and high in normal matching tissues. These observed differences, unlike many current biomarkers, bear a diagnostic significance, as proven by the ROC analyses. Finally, the survival data support the notion that both YY1 and RKIP might represent strong prognostic biomarkers. Overall, the reported findings indicate that YY1 and RKIP expression levels may play a role in LC as potential biomarkers and therapeutic targets. However, further studies will be necessary to validate the in silico results.
Low-temperature ordering caused by exchange interaction in the Si:P impurity system near the insulator - Metal phase transition (2014)

Behavior of the paramagnetic susceptibility in Si:P at low temperatures was investigated by Electron Spin Resonance in order to detect the antiferromagnetic and ferromagnetic ordering in the vicinity of the insulator-metal phase transition. A procedure was developed to operate sufficiently smooth changes of the spin density, by proton irradiated.
Bio-Microfluidics Real-Time Monitoring Using CNN Technology (2008)

A new non-invasive real-time system for the monitoring and control of microfluidodynamic phenomena involving transport of particles and two phase fluids is proposed. The general purpose design of such system is suitable for in vitro and in vivo experimental setup and, therefore, for microfluidic applications in the biomedical field, such as lab-on-chip and for research studies in the field of microcirculation. The system consists of an ad hoc optical setup for image magnification providing images suitable for acquisition and processing. The main feature of the optical system is the accessibility of the information at any point of the optical path. It was designed and developed using discrete opto-mechanic components mounted on a breadboard. The optical sensing, acquisition, and processing were all performed using an integrated vision system based on cellular nonlinear networks (CNNs) analogic (analog plus logic) technology called focal plane processor (FPP, Eye-RIS, Anafocus) that was inserted in the optical path. Ad hoc algorithms were implemented for the real-time analysis and extraction of fluidodynamic parameters in micro-channels. They were firstly tested on sequences of images recorded during in vivo microcirculation experiments on hamsters and then applied on images acquired and processed in real-time during in vitro experiments on two-phase fluid flow in a continuous microfluidic device (serpentine mixer, ThinXXS).
Short-Term Effects of Microstructured Surfaces: Role in Cell Differentiation toward a Contractile Phenotype (2014)

Cell adhesion plays a key role in cell behavior, in terms of migration, proliferation, differentiation and apoptosis. All of these events concur with tissue regeneration and remodeling mechanisms, integrating a complex network of intracellular signaling modules. Morphogenetic responses, which involve changes in cell shape, proliferation and differentiation, are thought to be controlled by both biochemical and biophysical cues. Indeed, the extracellular matrix not only displays adhesive ligands necessary for cell adhesion but also plays an essential biomechanical role - responsible, for instance, for the acquisition of the contractile phenotype. The substrate topography around the forming tissues and the associated mechanical stresses that are generated regulate cellular morphology, proliferation and differentiation. Thus, the ability to tailor topographical features around cells can be a crucial design parameter in tissue engineering applications, inducing cells to exhibit the required performances.In this work, we designed micropillared substrates using highly spaced arrays (interspacing equal to 25 µm) to evaluate the effects of topography on C2C12 myoblasts' adhesion and differentiation. Optical and fluorescence microscopy images were used to observe cell adhesion, together with Western blot analysis on vinculin and focal adhesion kinase (FAK) expression, a protein highly involved in adhesive processes. Differentiation marker (Myf5, myogenin and myosin heavy chain [MHC]) expression was also studied, in relation to the effect of different substrate topographies on the enhancement of a contractile phenotype. Our results demonstrated that microstructured surfaces may play a key role in the regeneration of functional tissues.
Pathophysiology of the urothelium and detrusor (2011)

Conventional wisdom now agrees that symptoms of overactive bladder (OAB) seem to emanate from an aberration in the voiding reflex, leading to involuntary detrusor contractions of either neurogenic or myogenic origin. Furthermore, emerging evidence also encourages us to adopt a new paradigm, in which bladder urothelium is not just a simple barrier but an active contributor to bladder function. In this paradigm, aberration in sensory mechanisms emanating from the urothelium can also contribute to OAB symptoms through altered excitability of afferents in the bladder leading to increased bladder sensation. The high density of muscarinic receptors expressed on urothelium can not only mediate release of urothelium-derived inhibitory factor, but can also be seen as an alternative site of action for antimuscarinic drugs. Urothelium also expresses a host of other receptors such as TRPV1 and TRPM8, whose functional role is yet to be confirmed.
Development of a high-resolution digital tomosynthesis system and its clinical application. (1991)

Conventional tomography has been criticized for its low contrast caused by scattered radiation and tomographic blur. The authors developed a digital tomosynthesis system as a substitute for conventional tomography. With the image processor in the system, two types of postprocessing can be performed to improve the quality of synthesized tomograms. One-dimensional spatial frequency filtering effectively reduces linear tomographic blur and enhances image information when an appropriate filter is used. Correction of structure mottle helps enhance the image clarity. The system allows reconstruction of tomograms at any desired depth and performance of tomosynthetic angiography and dual-energy subtraction. The system solves some of the problems associated with plain tomography and dual-energy subtraction and provides diagnostic clinical images.
Synthese des α‐Anomeren von ara‐7‐Desazaguanosin durch Phasentransferglycosylierung — Steuerung des Anomerenverhältnisses durch das quartäre Ammoniumsalz (1982)

Abstract 2‐Amino‐7‐(α‐D‐arabinofuranosyl)‐3,7‐dihydro‐4 H ‐pyrrolo[2,3‐ d ]pyrimidin‐4‐on ( 1 ), das α‐Anomer von ara ‐7‐Desazaguanosin ( 2 ), wurde durch Phasentransferglycosylierung von 4‐Methoxy‐2‐methylthio‐7 H ‐pyrrolo[2,3‐ d ]pyrimidin ( 3 ) mit 2,3,5‐Tri‐ O ‐benzyl‐1‐bromarabinofuranose ( 5a/5b ) dargestellt. Eine Anomerensteuerung kann über die äquilibrierung der α‐Halogenose 5a zur β‐Verbindung 5b durch das quartäre Ammoniumsalz erreicht werden. Das reaktivere 5b führt dann in einem S N 2‐Mechanismus bevorzugt zum α‐Nucleosid 6b . Säurehydrolyse führt zur Etherspaltung bei 6b unter Bildung von 7a ; anschließende Methoxymethylierung gibt 7b. Nucleophile Substitution des Methylthiorestes in einer Natriumhydrid/Acetamidschmelze führt zu 7c , das zu 7d deacetyliert wird. Simultane Abspaltung der Methoxymethylgruppe und der Benzylreste mit Bortrichlorid bei — 78°C führt zum kristallinen α‐Nucleosid 1.
[Fractures of the tuberculum intercondyloideum laterale in children]. (1983)

Thirty-one fractures of the tibial spine in children have been treated, two of them being old fractures. They were reviewed after a minimum follow-up of six months and a maximum of seven years. Ten were treated conservatively, 21 operatively. The mechanism is discussed. The trauma is described as either a posterior displacement of the femoral condyle or rotation and abduction of the leg with the knee flexed. The importance of testing stability under general anaesthesia is stressed. Sixteen cases had an anterior drawer sign. The medical meniscus was only injured in one case. The indications for treatment are: Conservative treatment should be given in fractures without displacement and without instability. All other types should be treated surgically with fixation of the anterior cruciate ligament made through a tunnel in the tibia. Whichever type of treatment is used, the length of immobilisation in plaster should not exceed 30 days. Twenty-seven cases were available for study. Twenty-three had excellent results, three good results and one poor result.
Une variante des tests de sphéricité pour l'adéquation de données transcriptomiques à un graphe de régulations génétiques (2009)

When analyzing genomic data, the researcher often encounters the situation where different genetic regulation graphs can be determined on the same dataset with several genetic regulation graph inference methods. One graph is very often compared to another with the help of databases gathering already known interactions between genes: the more known interactions an inferred graph contains, the better it is considered as. We propose a different approach, adapted from the theory of tests, to determine whether a graph fits the dataset.