gebhart/patrepeval huggingface dataset:
Gene Selection for the Identiﬁcation of Biomarkers in High- Throughput Data (2010)

Jaesik Jeong, Marina Vannucci, Kim-Anh Do, Bradley Broom, Sinae Kim, Naijun Sha, Mahlet Tadesse, Kai Yan, and Lajos Pusztai Indiana University, Indianapolis, IN; Rice University, Houston, TX; UT Texas MD Anderson Cancer Center, Houston, TX; University of Michigan, Ann Arbor, MI; University of Texas at El Paso, TX and Georgetown University, Washington, DCIn this chapter we review our contribution to the development of Bayesian methods for variable selection. In particular, we review linear regression settings where the response variable is either continuous, categorical or a survival time. We also brieﬂy describe how some of the key ideas of the variable selection method can be used in a diﬀerent modeling context, i.e. model-based sample clustering. In the linear settings, we use a latent variable selection indicator to induce mixture priors on the regression coeﬃcients. In the clustering setting, the group structure in the data is uncovered by specifying mixture models. In both the linear and the clustering settings, we specify conjugate priors and integrate out some of the parameters to accelerate the model ﬁtting. We use Markov chain Monte Carlo (MCMC) techniques to identify the high probability models. The methods we describe are particularly relevant for the analysis of genomic studies, where high-throughput technologies allow thousands of variables to be measured on individual samples. The amount of measured variables in such data is in fact often substantially larger than the sample size. A typical example with this characteristic, and one that we useto illustrate our methodologies, is DNA microarray data. The practical utility of variable selection is well recognized and this topichas been the focus of much research. Variable selection can help assess the importance of explanatory variables, improve prediction accuracy, provide a better understanding of the underlying mechanisms generating data, and reduce the cost of measurement and storage for future data. A comprehensive account of widely used classical methods, such as stepwise regression with forward and backward selection can be found in Miller.22 In recent years, procedures that speciﬁcally deal with very large number of variables have been proposed. One such approach is the least absolute shrinkage and selection operator (lasso) method of Tibshirani,36 which uses a penalized likelihood approach to shrink to zero coeﬃcient estimates associated with unimportant covariates. For Bayesian variable selection methods, pioneering work in the univariate linear model setting was done by Mitchell & Beauchamp,23 and George & McCulloch,15 and in the multivariate setting by Brown et al..6 The key idea of the Bayesian approach is to introduce a latent binary vector to index possible subsets of variables. This indicator is used to induce a mixture prior on the regression coeﬃcients, and the variable selection is performed based on the posterior model probabilities.
Radiological Evaluation of Isolated Ventricular Septal Defects Before and After Surgical Closure (1959)

The remarkable and often spectacular accomplishments in the field of cardiac surgery are familiar to each of us who has been in a position to follow the radiographic course of these patients. Whereas a short time ago only those radiologists associated with large teaching hospitals had this opportunity, many institutions now have their own “cardiac team” and are successfully diagnosing and correcting surgical defects of the heart. Consequently whether we are associated with a large teaching institution or a smaller hospital, or are even following the postoperative cardiac patient in office practice, it behooves us as radiologists to be familiar with the radiologic aspects of congenital heart disease and the changes to be expected following surgery. With the development and improvement of the pump-oxygenator, the surgical correction of many forms of congenital heart disease has become a common procedure. Although an isolated ventricular septal defect reportedly represents only about 8 per cent of all forms of congenital heart disease (1), in our series it was the most common defect for which open heart surgery was performed (2). At the time of this writing, approximately 150 ventricular septal defect closures have been performed at The Texas Children's Hospital. Each of these surgical procedures was done by Dr. Denton Cooley and his associates. Because of the accumulation of this number of cases, and because there is little reported information concerning the radiologic aspects following surgery, the present evaluation seems appropriate. Isolated ventricular septal defects are usually considered to be of two general types (3): the “simple” defect which occurs in the lower portion of the ventricular septum and the more disabling defect located at a higher level, near the aortic root. Regardless of the location of the defect, the clinical course and the radio-graphic findings depend more on its size than on its position. In the present study consideration is given only to the ventricular septal defects unassociated with other cardiac abnormalities. Preceding the preparation of this paper, a review of a large number of patients with isolated ventricular septal defects led to the clinical impression that there were distinct variations within the group of patients with this malformation (4). It further appeared that the heart size, the symptomatology, and the response to surgery varied with the degree of pulmonary hypertension and the magnitude and direction of the intracardiac shunt. An effort was made to assess the accuracy of this clinical impression by considering all the patients with isolated ventricular septal defects for whom complete physiologic studies (5) were available. For many of the patients who had presurgical evaluation elsewhere catheterization data were incomplete, and the series was thus narrowed from approximately 300 to 144.
Spermidine synthesis by Pseudomonas sp. strain Kim, previously reported to lack this polyamine (1989)

Pseudomonas sp. strain Kim has previously been reported to be the only known naturally occurring organism lacking spermidine. We now show that it synthesizes this polyamine. The apparent lack of intracellular levels of spermidine results from an efficient conversion of spermidine to putrescine and hydroxyputrescine.
The loudspeaker as a measurement sweep generator for the derivation of the acoustical impulse response of a concert hall (2008)

Precision digital technology has made the measurement of an accurate and representative acoustical impulse response function (AIRF) difficult. In using the exponential sine-sweep technique to record the acoustical parameters of a concert hall, there are several measurement issues that need to be resolved in order to determine an appropriate set of international standards. One of the issues is the type of the loudspeaker to be used as the source generator for a signal sweep. This paper presents a discussion on the role of the loudspeaker in the AIRF measurement process. Two high-quality loudspeaker systems are used and evaluated: one a direct-radiator-type near-field studio monitor, and the other a high-frequency (HF) compression driver and horn-loaded sound reinforcement system. Through an analysis of specific loudspeaker characteristics and measurement results, it is shown that the HF horn-loaded system is a suitable reference monitor for acoustic measurement of concert halls.
Closure to “Discussion of ‘The Unsteady Aerodynamics of a Finite Supersonic Cascade With Subsonic Axial Flow’” (1974, ASME J. Appl. Mech., 41, pp. 539–540) (1974)

theoretical objection concerning convergence of finite cascade predictions. However, this procedure appears to be the only analytical approach presently available to the compressor designer, which can provide flutter information over the range of blade motion frequencies of practical interest.
Analysis of the metabolic deterioration of ex vivo skin from ischemic necrosis through the imaging of intracellular NAD(P)H by multiphoton tomography and fluorescence lifetime imaging microscopy (2010)

Ex vivo human skin has been used extensively for cosmeceutical and drug delivery studies, transplantable skin allografts, or skin flaps. However, it has a half-life of a few days due to ischemic necrosis. Traditional methods of assessing viability can be time-consuming and provide limited metabolic information. Using multiphoton tomography and fluorescence lifetime imaging (MPT-FLIM) we assess ischemic necrosis of ex vivo skin by NAD(P)H autofluorescence intensity and fluorescence lifetime. Ex vivo skin is stored in the presence and absence of nutrient media (Dulbecco Modified Eagle Medium) at -20, 4, and 37 degrees C and room temperature over a 7-day time course to establish different rates of metabolic deterioration. At higher temperatures we observe a decrease in NAD(P)H autofluorescence, higher image noise, and a significant increase in the average fluorescence lifetime (tau(m)) from approximately 1000 to 2000 ps. Additionally, significant distortions in NAD(P)H fluorescence lifetime histograms correspond to the reduction in autofluorescence. Skin kept at 4 degrees C, with or without media, showed the least change. Our findings suggest that MPT-FLIM enables useful noninvasive optical biopsies to monitor the metabolic state and deterioration of human skin for research and clinical purposes.
35 Years of Pietro Torasso’s work on diagnosis (2018)

The paper describes Pietro Torasso’s contribution to the area of diagnostic problem solving, starting from the early 80’s and recalling the work carried on by Pietro and by the research group he started at the Department of Computer Science of the University of Torino.
Researches on Chemotherapeutic Drugs against Viruses. V (1952)

(1) Sodium 3-phenylazonaphthionate shows a remarkable. effect on the Japanese encephalitis virus in vitro and in vivo. The compound possesse virucidal, protective and curative effects against neurotropic virus and a low toxity.(2) It is assumed that the antiviral activity of sodium 3-phenylazonaphthionate might be caused by direct interaction of the compound and the virus.(3) Sodium 3-phenylazonaphthionate is of promise for treatments of diseases caused by small neurotropic viruses.
ChemInform Abstract: Super‐Acid Catalysed Addition of Allylsilanes to Carbonyl Compounds; Synthetic and Mechanistic Aspects. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Homogeneous time-resolved fluoroimmunoassay of thyroxin in serum. (1988)

We describe a rapid, simple nonseparation fluoroimmunoassay for determination of thyroxin in serum. The assay is based on the labeling of thyroxin directly with a fluorescent europium chelate, the fluorescence of which is quenched on binding to an antithyroxin antibody. With the assay buffer we used, maximum quenching is 90%. The rapid achievement of equilibrium in the assay solution, regardless of the sequence of reagent additions, allows fast measurement of thyroxin. Precision was good (CV less than 5%) within the clinical range for total thyroxin (50-300 nmol/L), and results correlated well with those by a commercial radioimmunoassay.
Flexible CdTe/CdS solar cells on thin glass substrates (2015)

We demonstrate flexible CdTe/CdS thin-film solar cells in a superstrate configuration with a cell conversion efficiency as high as 10.9%. We deposit a CdS window layer and a CdTe absorber layer on a flexible glass substrate using the chemical bath deposition method and close-spaced sublimation method, respectively. The thin and flexible glass substrates were able to tolerate a high growth temperature and post-growth processes. We repeatedly apply a strain of 0.15% to the fabricated CdTe/CdS solar cells, and this was shown to have a negligible effect on their performances. Our proposed thin films-on-compliant substrate structure, which was prepared by replacing a rigid glass with a bendable one, demonstrated flexible CdTe/CdS p-n junction thin-film solar cells without compromising the cell performance.
What are the shapes of response time distributions in visual search? (2010)

Many visual search experiments measure response time (RT) as their primary dependent variable. Analyses typically focus on mean (or median) RT. However, given enough data, the RT distribution can be a rich source of information. For this paper, we collected about 500 trials per cell per observer for both target-present and target-absent displays in each of three classic search tasks: feature search, with the target defined by color; conjunction search, with the target defined by both color and orientation; and spatial configuration search for a 2 among distractor 5s. This large data set allows us to characterize the RT distributions in detail. We present the raw RT distributions and fit several psychologically motivated functions (ex-Gaussian, ex-Wald, Gamma, and Weibull) to the data. We analyze and interpret parameter trends from these four functions within the context of theories of visual search.
72. CONTACT AREA, CONTACT PRESSURE AND LOAD-FAILURE OF 3 ROTATOR CUFF REPAIR METHOD: A BIOMECHANICAL ANALYSIS (2011)

Purpose: Comparer la technique de reparation de la coiffe des rotateurs par haubanage tendineux en simple rangee aux techniques transosseuse et double-rangee par rapport a la surface et la pression de contact a l’interface tendon-os, et la force de rupture. Method: Pour tester la pression et la surface de contact, les techniques de reparation ont ete faite sur 2 specimens cadaveriques (tete humerale et sus-epineux) chaque. Un film Prescale pressure-sensing a ete interpose entre les tendons et l’os pendant 2 minutes avec une tension de 120N sur les tendons. Les films ont ete numerises pour l’analyse avec le logiciel ImageJ. La force de rupture a ete teste sur un modele Sawbones d’humerus proximal. Des tendons synthetiques en fibre de nylon et polyesther dans du silicone ont ete crees pour les proprietes d’un tendon proportionnellement a la rigidite du Sawbones. La force a ete appliquee a 135° jusqu’a rupture sur 2 montages par technique de reparation. La suture transosseuse utilisait 2 fils Orthocord dans 2 tunnels transosseux. La suture double range a ete faite avec 2 ancres Spiralok medialement et 2 ancres Versalok lateralement avec des fils Orthocord. Le haubanage tendineux a ete fait avec 2 ancres Panalok RC lateralement dans la zone corticale. Results: La surface de contact du haubanage de 17mm2 etait significativement plus basse que de la suture transosseuse a 48mm2 (p=0.002) et double-rangee a 86mm2 (p=0.001). La difference entre transosseux et double rangee etait significative (p=0.029). La pression de contact du haubanage de 0.353MPa etait significativement plus basse que de la suture transosseuse a 0.441MPa (p=0.002) et double-rangee a 0.567MPa (p=0.003). La difference entre transosseux et double rangee etait significative (p-0.029). La force de rupture du haubanage de 106N etait significativement plus basse que de la suture transosseuse a 249N (p=0.03) et double-rangee a 316N (p=0.04). La difference entre transosseux et double rangee n’etait pas significative. Conclusion: Le haubanage tendineux ne reproduit pas l’empreinte anatomique du sus-epineux sur la grande tuberosite ni une pression de contact adequate en plus d’avoir une force de rupture plus faible. Malgre son cout plus eleve, la suture par double rangee est superieure a la technique transosseuse ou simple rangee.
HEPATOCYTE GROWTH FACTOR BECOMES ELEVATED AFTER DONOR NEPHRECTOMY AND RENAL TRANSPLANTATION (1999)

294 Purpose: Hepatocyte growth factor (HGF) is a 90 kD molecule synthesized in renal epithelial cells in response to injury and in normal development. Urinary excretion reflects renal synthesis. Urinary HGF is elevated after 3/4 nephrectomy or acute tubular necrosis in animal models. We hypothesized that urinary levels of HGF would increase due to compensatory growth after donor nephrectomy and in response to ischemia-reperfusion injury following renal transplantation. Methods: Urine was collected daily following donor nephrectomy and renal transplantation (live donor and cadaver) during the initial hospitalization and stored at −80°C. Monthly urine samples are being collected in long-term follow-up. Urinary HGF was measured by ELISA and urine creatinine was determined using an autoanalyzer. Urinary HGF to creatinine ratios (HGF/Cr) were calculated for donors (n=5) and recipients (n= 10). Data from the hospital course are presented as mean ± standard deviation. Results: All transplants functioned without delayed function. The perioperative course for all donors was uneventful. HGF/Cr (ng/mg) peaked on the first or second day after donor nephrectomy and then returned to baseline as shown in the table below. HGF/Cr peaked later in the recipient group and remained elevated for several days. In contrast, HGF/Cr averaged < 5.0 ng/mg in control subjects and patients with chronic renal failure (prior studies from our laboratory).TableConclusion: Compensatory changes in the remaining kidney after donor nephrectomy and recovery from ischemia-reperfusion injury after renal transplantation were associated with renal production of HGF. These preliminary results, the first reported in man, provide further support for the role of the cytokine HGF in the regeneration and repair of the kidney.
Theoretical Study of Effects of Impurities on High Temperature Cuprate Superconductors (2004)

We theoretically investigate the effects of nonmagnetic impurities on the properties of high-Tc cuprate superconductors, on the basis of the d-p model, within the fluctuation-exchange approximation and the coherent potential approximation. The obtained reduction of Tc is consistent with the experimental values. We find a large reduction in the Tc at the low doping concentrations corresponding to the optimum regime.
Identification of Hot Spots in the Variola Virus Complement Inhibitor (SPICE) for Human Complement Regulation (2008)

Variola virus, the causative agent of smallpox, encodes a soluble complement regulator named SPICE. Previously, SPICE has been shown to be much more potent in inactivating human complement than the vaccinia virus complement control protein (VCP), although they differ only in 11 amino acid residues. In the present study, we have expressed SPICE, VCP, and mutants of VCP by substituting each or more of the 11 non-variant VCP residues with the corresponding residue of SPICE to identify hot spots that impart functional advantage to SPICE over VCP. Our data indicate that (i) SPICE is approximately 90-fold more potent than VCP in inactivating human C3b, and the residues Y98, Y103, K108 and K120 are predominantly responsible for its enhanced activity; (ii) SPICE is 5.4-fold more potent in inactivating human C4b, and residues Y98, Y103, K108, K120 and L193 mainly dictate this increase; (iii) the classical pathway decay-accelerating activity of activity is only twofold higher than that of VCP, and the 11 mutations in SPICE do not significantly affect this activity; (iv) SPICE possesses significantly greater binding ability to human C3b compared to VCP, although its binding to human C4b is lower than that of VCP; (v) residue N144 is largely responsible for the increased binding of SPICE to human C3b; and (vi) the human specificity of SPICE is dictated primarily by residues Y98, Y103, K108, and K120 since these are enough to formulate VCP as potent as SPICE. Together, these results suggest that principally 4 of the 11 residues that differ between SPICE and VCP partake in its enhanced function against human complement.
1041 Anti-Slipping Control System for Drive Wheels of Electric Wheelchair (2007)

Wheelchairs improve mobility for people for whom walking is difficult or impossible, due to illness or disabilities. However, the road condition influence the driving ability of the wheelchairs. In the snowy region during winter, slipping often occurs because the grip between the wheel and the road cannot be secured enough when driving on the frozen road or the slope. In this study, the control mechanism that detects slipping and reflects it in driving power was developed so that the slipping actively decreased. This control mechanism was developed for existing electric wheelchairs. To develop the system that controls slipping, a miniature model was produced, and the design and confirming the operation of the control mechanism were done. the experiment machine that equipped the electric wheelchair was produced based on the mechanism of the miniature model. From the experiment in the room and outdoor it was confirmed that slipping is decreased by the developed control mechanism.
Average Heat Transfer Coefficient for Pool Boiling of R-134a and R-123 on Smooth and Enhanced Tubes (RP-1316) (2010)

Abstract This paper presents information about nucleate pool boiling of R-134a and R-123 on TBIIHP and TBIILP tubes, respectively, as well as on smooth tubes. This is the first phase of ASHRAE project RP-1316, Experimental Evaluation of Heat Transfer Impacts of Tube Pitch in a Highly Enhanced Surface Tube Bundle. Data were taken at a saturation temperature of 4.44°C (40°F). The test tubes' outer diameter was 19.05 mm (0.75 in.) and had lengths of 1 m (39.37 in.). Tubes were water heated with an insert in the water passage. A new analytical method known as enthalpy-based heat transfer analysis (EBHT) was introduced and used to determine the refrigerant heat transfer coefficient. The heat flux range was 4–135 kW/m2 (1269–42,823 Btu/h·ft2) for R-134a on TBIIHP and 5–60 kW/m2 (1586–19,033 Btu/h·ft2) for R-123 on TBIILP. The resulting heat transfer coefficient range for R-134a on TBIIHP was 6270–23,268 W/m2·°C (1105–4100 Btu/h·ft2·°F) and 6748–23,338 W/m2·°C (1189–4113 Btu/h·ft2·°F) for R-123 on TBIILP. The present study provided one of the widest heat flux ranges studied with this type of tubes and showed significant structure to the pool boiling curve, which had not been traditionally observed. The experimental data of the smooth tubes were compared against the Cooper and Stephan-Abdelsalam correlations. The Cooper correlation provided a better fit with the experimental data, with an average uncertainty of 27% for R-123 and 16% for R-134a.
Efficient translational frameshifting occurs within a conserved sequence of the overlap between the two genes of a yeast Ty1 transposon. (1988)

The Ty (transposon yeast) family of retroviral-like transposons include two genes, TYA and TYB, analogous to the gag and pol genes of metazoan retroviruses. TYB lies downstream of TYA, the two genes overlapping by 38 base pairs. The primary translation product of TYB is a TYA/TYB fusion protein whose expression has been inferred to occur by translational frameshifting within the overlap region. We show that the event leading to expression of TYB is very efficient, resulting in 20% read-through into TYB from TYA. We demonstrate that the Ty mRNA is colinear with the DNA sequence of the element, eliminating any pretranslational model for TYB expression. Frameshifting requires no particular sequence of the upstream TYA gene, nor any global RNA structure. Surprisingly, it can be promoted by a 14-base-pair oligonucleotide of the overlap region. The ability of this oligonucleotide to function is inhibited when it is positioned immediately downstream of an initiator AUG. We conclude that the TYB gene is expressed by an efficient ribosomal frameshifting event requiring a small oligonucleotide sequence derived from the TYA/TYB overlap region.