gebhart/patrepeval huggingface dataset:
Glycophorin A dimerization is driven by specific interactions between transmembrane alpha-helices. (1992)

Specific side-by-side interactions between transmembrane alpha-helices may be important in the assembly and function of integral membrane proteins. We describe a system for the genetic and biophysical analysis of these interactions. The transmembrane alpha-helical domain of interest is fused to the C-terminus of staphylococcal nuclease. The resulting chimera can be expressed at high levels in Escherichia coli and is readily purified. In our initial application we study the single transmembrane alpha-helix of human glycophorin A (GpA), thought to mediate the SDS-stable dimerization of this protein. The resulting chimera forms a dimer in SDS, which is disrupted upon addition of a peptide corresponding to the transmembrane domain of GpA. Deletion mutagenesis has been used to delineate the minimum transmembrane domain sufficient for this behavior. Site-specific mutagenesis shows that a methionine residue, previously implicated as a potential interfacial residue, can be replaced with other hydrophobic residues without disrupting dimerization. By contrast, rather conservative substitutions at a valine on a different face of the alpha-helix disrupt dimerization, suggesting a high degree of specificity in the helix-helix interactions. This approach allows the interface between interacting helices to be defined.
Fabrication and Evaluation of Three-Dimensional Optically Coupled Common Memory (1995)

A three-dimensional optically coupled common memory (3D-OCC memory) test chip, on which GaAs LEDs are integrated using the microbonding technique, has been fabricated using a 2 µ m complementary metal-oxide-semiconductor (CMOS) technology. Static memory cell circuits with photodiodes were formed on the chip. Optical writing and electrical reading operations of the 3D-OCC memory test chip have been demonstrated.
Second- and third-generation aromatase inhibitors as first-line endocrine therapy in postmenopausal metastatic breast cancer patients: a pooled analysis of the randomised trials (2006)

The purpose of this study was to estimate in all randomised trials the relative risk of overall response rate (ORR), clinical benefit (CB), time to progression (TTP), overall survival (OS), and toxicity of aromatase inhibitors (AI), compared with tamoxifen (Tam) as first-line endocrine therapy in postmenopausal metastatic breast cancer (PMBC) women. Prospective randomised studies were searched through computerised queries of MEDLINE, EMBASE, and the American Society of Clinical Oncology (ASCO) abstract database. Relative risk, 95% confidence interval, and heterogeneity were derived according to the inverse variance and Mantel-Haenszel method and Q statistics. Six phase III prospective randomised trials including 2787 women were gathered. A significant advantage in ORR (P = 0.042), TTP (P = 0.007), and CB (P = 0.001) in favour of AI over Tam was detected at the fixed effects model. These results were not significant at the random effects model, owing to the significant heterogeneity. On the contrary, no difference was registered for OS (P = 0.743) with no significant heterogeneity. Regarding toxicity, Tam caused more frequently thromboembolic events (P = 0.005) and vaginal bleeding (P = 0.001) compared with AI. Aromatase inhibitors appear to be superior to Tam as first-line endocrine option in PMBC women. Owing to a component of variability between the six studies analysed, the random effects estimates differed from corresponding fixed ones. Investigators should assess heterogeneity of trial results before deriving summary estimates of treatment effect.
Adaptive circadian rhythm estimator and its application to locomotor activity (2012)

Disruption of the circadian rhythm is detrimental to human well being, with consequences ranging from lower productivity, sleep disorder, to more serious health problems. Accurate estimation of circadian rhythm is critical to the assessment and treatment of circadian disruption. Circadian estimate is also essential for light-based circadian entrainment. Direct measurements of circadian rhythm markers such as dim light melatonin onset are inconvenient and acquired at best at low rate. Wearable continuous measurements such as actigraph and body temperature are convenient but masked by many other factors. In this paper, we present a new circadian rhythm estimation scheme based on adaptive notch filter (ANF) which is commonly used in signal processing. The ANF is designed to track the gain and phase of a single sinusoid from noisy data. We extend the classic ANF to multiple harmonics with non-zero bias needed in circadian rhythm tracking. The modified ANF is tested on rat and Drosophila locomotor activity data to extract circadian argument. The estimation results are compared with linear regression and gliding cosinor. The ability to generate circadian estimate opens up the tantalizing possibility of personalized circadian rhythm estimator and light therapy.
Automatic Image Alignment And Stitching Of Medical Images With Seam Blending (2010)

This paper proposes an algorithm which automatically aligns and stitches the component medical images (fluoroscopic) with varying degrees of overlap into a single composite image. The alignment method is based on similarity measure between the component images. As applied here the technique is intensity based rather than feature based. It works well in domains where feature based methods have difficulty, yet more robust than traditional correlation. Component images are stitched together using the new triangular averaging based blending algorithm. The quality of the resultant image is tested for photometric inconsistencies and geometric misalignments. This method cannot correct rotational, scale and perspective artifacts.
Experimental Study of Portland Cement/Rock Interface In Relation to Wellbore Stability For Carbon Capture And Storage (CCS) (2012)

Primary cementing is carried out during the drilling and completions of wells and the main objective is to provide zonal isolation. For effective cementing, the cement should completely displace the drilling mud (water-clay mixture). In practice, this is never achieved as some of the mud is not displaced and remains in the wellbore. This study investigates the effect of the residual mud on the hydraulic conductivity of the cement-formation interface. Flow-through experiments were conducted at 14.48 MPa (2100 psi) overburden pressure with cement-rock composite cores and brine at a flow rate of 1 ml/min. The cement-rock composite cores had 0% and 10% clay-rich fluid contamination respectively. The pressure drop across the composite cores was recorded throughout the flow-through experiments. Extensive micro-structural characterization of the cement-rock interface was carried out before and after the flow-through experiments. Higher pH values were recorded for the effluent brine from the mud contaminated core and the higher values indicate increased leaching of Ca . Micro-CT imaging revealed that the contaminated composite core possessed higher porosity at the interface zone. This shows that clay contamination of cement-rock interface degrades the interface zone and can provide a pathway for injected CO to escape from the intended storage zone. Copyright 2012 ARMA, American Rock Mechanics Association. 2+ 2
Equipping GPS Satellites with Accelerometers and Satellite-to-Satellite Observables (2002)

Millimeter-level accuracy applications of terrestrial Global Positioning System (GPS) phase tracking can be done more robustly with global rather than regional accuracy if the GPS satellites are equipped with (1) accelerometers to measure rather than model nongravitational accelerations, (2) satellite-to-satellite phase tracking as well as ranging cross links to work around inadequately modeled atmospheric propagation effects, and (3) gyroscopes for better satellite attitude control. More complete general relativity modeling is also needed in the orbit fitting and site coordinate estimation process, for which it could be advantageous to employ a combination of Kalman filtering on the orbital motions and maximum likelihood estimation on the site coordinates, accelerometer biases, and other parameters.
Immunohistochemical detection of p53 protein overexpression in primary human osteosarcomas. (1997)

Detection of p53 expression has been reported to be associated with poor prognosis in a variety of human malignancies. The aim of the current study was to utilize immunocytochemical antigen detection techniques to search for evidence of altered p53 protein overexpression in 43 primary osteosarcomas (OS). The study was carried out on formalin fixed, paraffin-wax embedded 3 to 4 microns, previously decalcified OS tissue sections. A four step biotin-streptavidin based method was employed with peroxidase conjugation as the enzymatic label. Presence of a frequent level of p53 protein expression was detected in all 43 primary osteosarcomas, suggesting a frequent p53 gene mutation. p53 protein alterations were also associated with all grades of cell microenvironment heterogeneity in the observed OSs. Overexpression of the p53 protein was detected in 31/43 (72%) primary OS cases. Formalin fixed and paraffin-wax embedded human breast carcinoma tissue sections were employed as positive control tissue. p53 protein absence was demonstrated in normal postnatal thymus, serving as the negative control tissue. Our results lead us to the following conclusions: a) the altered p53 gene product is detectable employing the chosen mouse anti-human MoAB in decalcified, formalin fixed, paraffin-wax embedded, routine tissue sections of OSs and breast carcinomas which provides an opportunity for numerous retrospective studies and comparison with additional immunodiagnostic indicators; b) primary OSs with similar cell differentiation may be genetically heterogeneous; c) p53 gene or protein alterations represent early, immunodiagnostic markers of a malignant immunophenotype (IP) in various human neoplasms, including OSs; and d) immunomorphological techniques and in situ hybridization should be employed as methods to collect data for computerized, quantitative image analysis (IA) of the cellular accumulation and localization of the altered p53 protein.
Phase contrast microscopy of living cells within the whole lens: spatial correlations and morphological dynamics. (2012)

This method opens a new window for observing lens cells in their physiologic location, and it can be readily applied in studies on lens physiology and pathology.
Efficacy of supra-choroidal, bipolar, electrical stimulation in a vision prosthesis (2008)

The key to successful, clinical application of therapeutic neurostimulators lies primarily with the safety and efficacy of their electrode-tissue interfaces. The authors posit that for electrical stimulation of the visual system, supra-choroidal electrode placement provides a safe, stable and readily-accessible site for implantation and the provision of electrical stimulation. The present paper explores the efficacy of supra-choroidal electrical stimulation of retinal neurons. Based upon recordings made with surface electrodes placed on the primary visual cortex, areas of activation in the cortex were shown to change when different areas on the supra-choroidal space were stimulated. Finally, the threshold to elicit a response from neurons in the visual cortex, was found to be 77.55 +/- 29.85 nC.
The Biology and Mechanism of Action of Nerve Growth Factor (1982)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
A Comprehensive Study of Automatic Program Repair on the QuixBugs Benchmark (2019)

Automatic program repair papers tend to repeatedly use the same benchmarks. This poses a threat to the external validity of the findings of the program repair research community. In this paper, we perform an automatic repair experiment on a benchmark called QuixBugs that has never been studied in the context of program repair. In this study, we report on the characteristics of QuixBugs, and study five repair systems, Arja, Astor, Nopol, NPEfix and RSRepair, which are representatives of generate-and-validate repair techniques and synthesis repair techniques. We propose three patch correctness assessment techniques to comprehensively study overfitting and incorrect patches. Our key results are: 1) 15/40 buggy programs in the QuixBugs can be repaired with a test-suite adequate patch; 2) a total of 64 plausible patches for those 15 buggy programs in the QuixBugs are present in the search space of the considered tools; 3) the three patch assessment techniques discard in total 33/64 patches that are overfitting. This sets a baseline for future research of automatic repair on QuixBugs. Our experiment also highlights the major properties and challenges of how to perform automated correctness assessment of program repair patches. All experimental results are publicly available on Github in order to facilitate future research on automatic program repair.
The UV–visible absorption and fluorescence of some substituted 1,8-naphthalimides and naphthalic anhydrides (1990)

A number of substituted 1,8-naphthalimides and naphthalic anhydrides have been prepared and their absorption and fluorescence properties in absolute ethanol have been determined. In the absence of an alkylamino substituent in the naphthalene ring, the compounds are colourless and weakly fluorescent. In the presence of such a substituent they become yellow and frequently fluoresce strongly with quantum yields of the order of 0.8.
Redesign of a spherical corona shield for UHV substation connectors (2013)

When dealing with extra- and ultra-high voltage transmission systems special considerations must be taken into account to minimize corona activity. To minimize its harmful effects often corona shields are required. Depending on the device to protect, corona shields may have different geometries; the most usual are corona caps, toroids and spheres. This work analyzes by means three-dimensional finite elements method simulations the behavior of two spherical shields, i.e. a continuous flat sphere (or standard sphere) and a tubes sphere. Results presented here show that the bar shells allows reducing greatly the weight and ventilates better than the standard solution while ensuring an adequate shielding effect.
Application of hydroxypropyl cellulose to peroral controlled release dosage forms. (1978)

Since 1991 Virtual Reality has been used in student projects in the Building Information Technology group. It started as an experimental tool to assess the impact of VR technology in design, using the environment of the associated Calibre Institute. The technology was further developed in Calibre to become an important presentation tool for assessing design variants and final design solutions. However, it was only sporadically used in student projects. A major shift occurred in 1997 with a number of student projects in which various computer technologies including VR were used in the whole of the design process. In 1998, the new Design Systems group started a design studio with the explicit aim to integrate VR in the whole design process. The teaching effort was combined with the research program that investigates VR as a design support environment. This has lead to increasing number of innovative student projects.\nThe paper describes the context and history of VR in Eindhoven and presents the current set-up of the studio. It discusses the impact of the technology on the design process and outlines pedagogical issues in the studio work.
Combining Wave Field Synthesis and Multi-Viewer Stereo Displays (2006)

We present our experiences of combining wave field synthesis audio with a projection-based multi-viewer stereo display. Wave field synthesis is able to simulate spatial sound sources of various kinds without the need for headphones or user tracking. Multi-viewer systems support multiple tracked users with individual perspectively correct stereoscopic images. The combination of both approaches allows the consistent display of virtual objects and spatial audio sources for multiple participants. First impressions with two application scenarios confirm that sound sources can be quite well located in space by each user. The system allows the creation of sound sources attached to virtual objects, which can be moved around in real-time without perceivable latency. In addition users appreciated the possibility of natural communication while they were exploring the audio-visual scenarios.
Chemoreception of oviposition inhibiting terpenoids in the diamondback moth <i>Plutella xylostella</i> (1998)

Abstract The effects of six terpenoids and two terpenoid containing extracts of the neem tree ( Azadirachta indica A. Juss.) on oviposition by the diamondback moth ( Plutella xylostella L., Yponomeutidae: Lepidoptera) were tested. Two drimane terpenoids, the sesquiterpenoid polygodial and the neem extract Margosan‐O exerted significant inhibitory effects at the dosages tested. Ablation experiments showed that both antennae and fore‐tarsi contributed to mediation of the inhibition by a drimane. Location of chemosensilla on prothoracic tarsi and ovipositor was examined by scanning electronmicroscopy. Electrophysiological recordings from ovipositor and tarsal taste sensilla showed that distilled water produced distinct responses from one neuron. In tarsal sensilla, ethanol and drimane solutions produced responses from two neurons, one of which might be the water cell that fired at a reduced rate. A drimane significantly decreased the responses of tarsal chemoreceptors to a cabbage leaf extract, which is a possible sensory mechanism leading to behavioural avoidance of this compound.
Buspirone effect on tobacco withdrawal symptoms: a pilot study. (1991)

Tobacco withdrawal symptoms hamper smoking cessation. This was a pilot study of buspirone, a new azapirone anxiolytic, for tobacco withdrawal. Thirteen smokers entered an open clinical trial. Smokers were titrated to 30 mg/day of oral buspirone for 2 weeks prior to cessation. Tobacco withdrawal and Spielberger state-anxiety scales were used at baseline, on the quit date, and then at 24 hours, 48 hours, 1 week, and 2 weeks after abrupt cessation. At the final visit, smokers compared their withdrawal experience with previous cessation attempts. Two patients (15 percent) could not tolerate the medication and did not attempt smoking cessation. Of the remaining 11 smokers, 3 (27 percent) rated withdrawal relief "very definite," 6 (55 percent) "moderate," and 2 (18 percent) "slight." More than two-thirds of the smokers believed that their difficulty concentrating, craving, restlessness, and anxiety were improved compared with earlier tobacco withdrawal attempts. Five patients (46 percent) reported decreased smoking urges during the 2-week medication titration period. Tobacco withdrawal symptoms and state-anxiety scores changed significantly during the study (P less than 0.05). These results are encouraging, but they should be interpreted with caution because of the small sample size and lack of placebo control. Buspirone effect on tobacco withdrawal symptoms should be studied in a randomized, controlled clinical trial.
Weed Seedbanks and Seedling Emergence in a Two and Three Crop Narrow Strip Intercropping/Rotation System (2000)

Weed populations in agronomic settings are, in part, a reflection of the cropping system utilized. The goal of this project was to gain an understanding of the weed population dynamics in a narrow strip intercropping (NSI) rotation by assessing the weed seedbank, weed emergence, and seedling establishment over the growing season for a corn-soybean (two-crop), and a corn-soybean-oat+berseem clover (three-crop) system. Field research was conducted in 1994 and 1995, near Nashua, IA, and each crop was grown m 4.6 m wide strips. Giant foxtail and total weed seed densities were significantly lower in the three-crop NSI rotation system than in the two-crop system. NSI rotation system affected total preplant weed emergence. Preplant density ranged from 103 to 433 weeds m-2 in the two-crop system, while density ranged from 3 to 99 weeds m-2 in the three-crop system. There were no consistently significant differences in weed seedling emergence after crop planting due to NSI rotation system when individual species were examined. Changes in Iowa cropping systems may result from a better understanding of these system dynamics.
Discrete spectral peak estimation in incoherent backscatter heterodyne lidar. I. Spectral accumulation and the Cramer-Rao lower bound (1993)

The theory of the Cramer-Rao lower bound (CRLB) and maximum-likelihood (ML) estimators is summarized in the context of a heterodyne lidar. Numerical experiments are described that indicate the scaling of this CRLB with parameters such as the signal bandwidth and the level of noise. This CRLB is also compared with the CRLB of a highly idealized noiseless direct detection system using photon counting. It is found that the asymptotic bounds developed in the radar literature for the heterodyne CRLB should not be used as approximations for the correct expression in lidar applications at intermediate signal levels. Moreover, the variance of the ML estimator may be greater or even less than the heterodyne CRLB, depending on the mechanism leading to the departure from the bound.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<i>Fasciola hepatica</i>Suppresses a Protective Th1 Response against<i>Bordetella pertussis</i> (1999)

Fasciolosis, like other helminth infections, is associated with the induction of T-cell responses polarized to the Th2 subtype. Respiratory infection with Bordetella pertussis or immunization with a pertussis whole-cell vaccine (Pw) induces a potent Th1 response, which confers a high level of protection against bacterial challenge. We have used these two pathogens to examine bystander cross-regulation of Th1 and Th2 cells in vivo and provide evidence of immunomodulation of host T-cell responses to B. pertussis by a concomitant infection with Fasciola hepatica. Mice with a coinfection of F. hepatica and B. pertussis exhibited a Th2 cytokine profile in response to F. hepatica antigens, similar to those infected with F. hepatica alone. By contrast, the Th1 response to B. pertussis antigens was markedly suppressed and the bacterial infection was exacerbated following infection with F. hepatica. Furthermore, an established Th1 response induced in mice by infection with B. pertussis or by parenteral immunization with Pw was also suppressed following infection with F. hepatica. This immunomodulatory effect of B. pertussis-induced responses by F. hepatica infection is significantly reduced, but not completely abrogated, in IL-4 knockout mice. Our findings demonstrate that Th2-inducing parasites can exert bystander suppression of protective Th1 responses to infection or vaccination with a bacterial pathogen and that the modulation is mediated in part by IL-4 and, significantly, is effective at both the induction and effector stages of the Th1 response.
mobileVision: A Face-mounted, Voice-activated, Non-mydriatic “Lucky” Ophthalmoscope (2014)

We present mobileVision, a portable, smartphone-based ophthalmoscopy system intended to reduce the barriers to ocular pathology screening in developing regions.