gebhart/patrepeval huggingface dataset:
Intratumoral heterogeneity analysis reveals hidden associations between protein expression losses and patient survival in clear cell renal cell carcinoma (2017)

Intratumoral heterogeneity (ITH) is a prominent feature of kidney cancer. It is not known whether it has utility in finding associations between protein expression and clinical parameters. We used ITH that is detected by immunohistochemistry (IHC) to aid the association analysis between the loss of SWI/SNF components and clinical parameters.160 ccRCC tumors (40 per tumor stage) were used to generate tissue microarray (TMA). Four foci from different regions of each tumor were selected. IHC was performed against PBRM1, ARID1A, SETD2, SMARCA4, and SMARCA2. Statistical analyses were performed to correlate biomarker losses with patho-clinical parameters. Categorical variables were compared between groups using Fisher's exact tests. Univariate and multivariable analyses were used to correlate biomarker changes and patient survivals. Multivariable analyses were performed by constructing decision trees using the classification and regression trees (CART) methodology. IHC detected widespread ITH in ccRCC tumors. The statistical analysis of the "Truncal loss" (root loss) found additional correlations between biomarker losses and tumor stages than the traditional "Loss in tumor (total)". Losses of SMARCA4 or SMARCA2 significantly improved prognosis for overall survival (OS). Losses of PBRM1, ARID1A or SETD2 had the opposite effect. Thus "Truncal Loss" analysis revealed hidden links between protein losses and patient survival in ccRCC.
Panoramic viewfinder: providing a real-time preview to help users avoid flaws in panoramic pictures (2005)

Image stitching allows users to combine multiple regular-sized photographs into a single wide-angle picture, often referred to as a panoramic picture. To create such a panoramic picture, users traditionally first take all the photographs, then upload them to a PC and stitch. During stitching, however, users often discover that the produced panorama contains artifacts or is incomplete. Fixing these flaws requires retaking individual images, which is often difficult by this time. In this paper, we present Panoramic Viewfinder, an interactive system for panorama construction that offers a real-time preview of the panorama while shooting. As the user swipes the camera across the scene, each photo is immediately added to the preview. By making ghosting and stitching failures apparent, the system allows users to immediately retake necessary images. The system also provides a preview of the cropped panorama. When this preview includes all desired scene elements, users know that the panorama will be complete. Unlike earlier work in the field of real-time stitching, this paper focuses on the user interface aspects of real-time stitching. We describe our prototype, individual shooting modes, and an implementation overview.
Interrupting Sitting With Short Walks Or Repeated Chair Stands Improves Glycemic Control In Healthy Adults (2020)

Uninterrupted sedentary time is an independent risk factor for the development of metabolic diseases. Interrupting prolonged sitting with brief, intermittent walks can improve postprandial glucose metabolism; however, the efficacy of other types of exercise that do not require equipment nor space beyond one’s immediate sedentary area remain to be investigated. PURPOSE: To determine the impact of interrupting prolonged sitting with practical ‘activity snacks’ on postprandial glycemia and insulinemia in healthy adults. METHODS: Fourteen participants (7 males,7 females; 23±5yr; 24±5kg/m2; 40±8ml/kg/min; 4587±1231steps/d) completed three 7.5hr trials in a randomized order consisting of uninterrupted sitting (SIT), sitting with intermittent (every 30 min) walking (WLK; 2min at 3.1mph) or sitting with intermittent squats (SQT; 15 ‘chair stands with calf raise’). Mixed-macronutrient liquid meals (~55:30:15% carbohydrate:fat:protein) provided 20% (‘breakfast’; 406±87kcal) and 30% (‘lunch’; 609±130kcal) of daily energy needs to mimic traditional Western meal patterns. Blood was obtained every 30min and analyzed for plasma glucose and insulin concentration. Positive incremental area under the curve (iAUC) for glucose, insulin and insulin:glucose ratio were calculated 1 and 3h postprandially using the trapezoidal rule. RESULTS: Postprandial glucose and insulin did not differ across conditions following breakfast. After lunch, peak insulin concentration was lower in SQT (51.6±26.7, p<0.001) and WLK (62.2±34.9, p<0.05) compared to SIT (78.9±43.0μIU/ml). The insulin:glucose iAUC 3h following lunch was also reduced by the activity snacks (SQT: 489±300; WLK: 541±401) compared to SIT (700±398, p<0.05). Insulin iAUC 1h following lunch was lower in SQT (1412±902, p<0.01) and WLK (1575±1145, p<0.05) relative to SIT (2231±1540μIU/ml x 1h, p<0.01), however 3h insulin iAUC was only reduced in SQT (SQT: 2992±1735 vs. SIT: 3954±2261μIU/ml x 3h; p<0.05). CONCLUSION: Interrupting prolonged sitting with short walks or repeated chair stands reduces postprandial insulinemia following lunch in healthy adults. Our results add to the evidence suggesting that short ‘activity snacks’ can help mitigate cardiometabolic risk factors associated with prolonged sitting. Supported by ACSM Research Endowment Grant.
Enzyme-linked immunosorbent assay (ELISA) for detection of antibodies againstPityrosporum orbiculare (1990)

IgG antibodies to Pityrosporum orbiculare were detected by an enzyme-linked immunosorbent assay (ELISA) in sera from 10 healthy adults and five healthy 6-month-old children. The ELISA showed 17-80 times higher antibody levels in adults than were found by an indirect immunofluorescence technique (IIF) used in earlier studies. Low titres of antibody were detected in the children.
Sensitivity Analysis of Transient‐MIM HYDRUS‐1D: Case Study Related to Pesticide Fate in Soils (2009)

A sensitivity analysis of the HYDRUS‐1D model was performed based on scenarios that represented the fate of a nonvolatile pesticide in three soils. We used the latest dual‐porosity, transient mobile–immobile (MIM) version of HYDRUS‐1D that includes water and solute transfers between mobile and immobile domains. We considered flat bare soils under atmospheric boundary conditions with identical initial pressure head profiles. We targeted instantaneous and mean annual pesticide concentration values at 1‐m depth as relevant output variables. Reference values for most of the parameters were obtained from in situ or laboratory measurements. Automation of parameter set generation and input formatting was achieved using SENSAN. We used a one‐group‐at‐a‐time sensitivity analysis to isolate and identify the effect of single parameter variations whose ranges were potentially different between topsoil layers (Group 1) and deep layers (Group 2). Sensitivity was analyzed by calculating the time‐dependent ratio of variation, i.e., the ratio of relative variation in output concentration to relative variation in parameter input values. As found for other single‐ or dual‐ permeability models, transient‐MIM HYDRUS‐1D was highly sensitive to parameters related to pesticide degradation and sorption, especially the Freundlich exponent associated with nonlinear sorption. Variations in the parameter n of the Mualem–van Genuchten functions had also a very significant impact. Among the MIM parameters, only saturated immobile and mobile water contents were very sensitive parameters, especially those of the topsoil layers. Parameter sensitivities hardly varied among the three soils, but this could be due to their limited contrast.
Developments in MALDI Mass Spectrometry: The Quest for the Perfect Matrix (2008)

Abstract The topic of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry has received much attention over the past several years and with the award of the Nobel Prize to Tanaka based on his landmark paper in 1988, has received even more recent attention. This review focuses on the search for an ideal matrix and generally covers the period from the mid 1990's to the present. There have been a number of excellent and comprehensive reviews on MALDI ion formation and a brief summary of some of the most important conclusions is given here. With respect to the applications of MALDI, the present review focuses primarily on polymer analysis, although in this area too, excellent reviews have been published that include consideration of the MALDI method. Although we make some mention of other uses of MALDI (e.g., to proteins and peptides) and other biological applications, we emphasize the polymer uses in the present review. Keywords: MALDImatrixpolymersionizationsolventless
Criteria for emerging telecom and data center powering architectures (2012)

Against a global backdrop of green energy initiatives, competitive pressures on Telcos and the changing communications landscape the convergence of telecoms and data centers continues unabated. In Australia the National Broadband Network project is bringing unprecedented change to telecommunications. Brought on by increasingly obscure differences in telecommunications and the Internet, mission critical power is now poised for a major transformation. In recent years a higher voltage DC (380V) has been pursued as an adjunct to the long-established and reliable -48V work horse. By contrast data centers are almost universally powered by AC UPS. The latter have come under considerable criticism against claims of inefficiency due to multiple conversion stages and lower reliability. The industry has responded with a dizzying array of new technology high-efficiency alternatives. Among the contenders vying for succession include a range of rotary, battery-less flywheel alternatives which are gaining popularity in large power applications. Are these alternative technologies capable of delivering the traditionally high reliability levels to mission critical assets? Also, with batteryless solutions being adopted which use less than a minute of energy storage, increasingly the need for traditional long battery reserves is under scrutiny.
Approaches to calculating AAPM TG-43 brachytherapy dosimetry parameters for Cs137, I125, Ir192, Pd103, and Yb169 sources (2006)

Underlying characteristics in brachytherapy dosimetry parameters for medical radionuclides 137Cs, 125I, 192Ir, 103Pd, and 169Yb were examined using Monte Carlo methods. Sources were modeled as unencapsulated point or line sources in liquid water to negate variations due to materials and construction. Importance of phantom size, mode of radiation transport physics--i.e., photon transport only or coupled photon:electron transport, phantom material, volume averaging, and Monte Carlo tally type were studied. For noninfinite media, g(r) was found to degrade as r approached R, the phantom radius. MCNP5 results were in agreement with those published using GEANT4. Brachytherapy dosimetry parameters calculated using coupled photon:electron radiation transport simulations did not differ significantly from those using photon transport only. Dose distributions from low-energy photon-emitting radionuclides 125I and 103Pd were sensitive to phantom material by upto a factor of 1.4 and 2.0, respectively, between tissue-equivalent materials and water at r =9 cm. In comparison, high-energy photons from 137Cs, 192Ir, and 169Yb demonstrated +/- 5% differences in dose distributions between water and tissue substitutes at r=20 cm. Similarly, volume-averaging effects were found to be more significant for low-energy radionuclides. When modeling line sources with L < or = 0.5 cm, the two-dimensional anisotropy function was largely within +/- 0.5% of unity for 137Cs, 125I, and 192Ir. However, an energy and geometry effect was noted for 103Pd and 169Yb, with Pd-103F(0.5,0 degrees)=l.05 and yb-169F(0.5,0 degrees)=0.98 for L=0.5 cm. Simulations of monoenergetic photons for L=0.5 cm produced energy-dependent variations in F(r, theta) having a maximum value at 10 keV, minimum at 50 keV, and approximately 1.0 for higher-energy photons up to 750 keV. Both the F6 cell heating and *F4 track-length estimators were employed to determine brachytherapy dosimetry parameters. F6 was found to be necessary for g(r), while both tallies provided equivalent results for F(r, theta).
Anthropometry and high-speed resistive exercise performance by male athletes (2015)

BACKGROUND: High-speed exercise is an essential training component to prepare athletes for competition. To date correlations between anthropometry and high-speed exercise performance are mixed. OBJECTIVE: To assess anthropometry as a correlate to performance from workouts comprised exclusively of tonic or phasic repetitions done on a high-speed resistive exercise device (Impulse Training Systems; Newnan, GA). METHODS: Male athletes (n = 31) did two workouts that involved performance of a standing unilateral rowing motion with their left arm for two 60-second sets. Each workout was comprised solely of tonic or phasic repetitions. Anthropometric measurements included: height, mass, body fat percentage, shoulder width, upper and lower arm lengths as well as torso length. Mean force and total work values from each type of workout served as criterion variables. RESULTS: Anthropometry predicted significant amounts of variance for both mean force and total work values (r 2 ∼ 0.21) from tonic workouts. However anthropometry failed to predict a significant amount of performance variance from phasic workouts. CONCLUSIONS: Anthropometry acts as a better correlate to high-speed resistive exercise performance for repetitions that do not terminate with impact forces and are inherently less ballistic, as the latter likely utilizes less momentum.
Staging and Treatment of Primary Spine Tumors (2000)

LEARNING OBJECTIVES— After reading this article, physicians should be able to: Classify tumors according to the oncologic staging system devised by Enneking et al. Describe the Weinstein-Boriani-Biagini surgical staging system for spinal tumors. Apply these systems in the planning of tumor excision surgeries
Unexpected roles for ADH1 and SORD in catalyzing the final step of erythritol biosynthesis (2019)

The low-calorie sweetener erythritol is endogenously produced from glucose through the pentose phosphate pathway in humans. Erythritol is of medical interest because elevated plasma levels of this polyol are predictive for visceral adiposity gain and development of type 2 diabetes. However, the mechanisms behind these associations remain unknown because the erythritol biosynthesis pathway, particularly the enzyme catalyzing the final step of erythritol synthesis (reduction of erythrose to erythritol), is not characterized. In this study, we purified two enzymes from rabbit liver capable of catalyzing the conversion of erythrose to erythritol: alcohol dehydrogenase 1 (ADH1) and sorbitol dehydrogenase (SORD). Both recombinant human ADH1 and SORD reduce erythrose to erythritol, using NADPH as a co-factor, and cell culture studies indicate that this activity is primarily NADPH-dependent. We found that <i>ADH1</i> variants vary markedly in both their affinity for erythrose and their catalytic capacity (turnover number). Interestingly, the recombinant protein produced from the <i>ADH1B2</i> variant, common in Asian populations, is not active when NADPH is used as a co-factor <i>in vitro</i> We also confirmed SORD contributes to intracellular erythritol production in human A549 lung cancer cells, where ADH1 is minimally expressed. In summary, human ADH1 and SORD catalyze the conversion of erythrose to erythritol, pointing to novel roles for two dehydrogenase proteins in human glucose metabolism that may contribute to individual responses to diet. Proteomics data are available via ProteomeXchange with identifier PXD015178.
Growth rate anisotropy and kinetic coefficients of vicinal faces at LPE garnet films. II. Kinetic coefficients (1978)

Kinetic coefficients of vicinal faces are determined in dependence on the vicinal angle 0.1° ⪅ α ⪅ 2° at (YSm)3(FeGa)5O12 LPE films oriented about in <110>. Dissolution striations in garnet single crystals marked by induced striations are less suitable for determination of kinetic coefficients. The driving force for volume diffusion and interfacial kinetic are presented in dependence on hydrodynamical conditions and vicinal angle. Using a model developed by Chernov, which well describes the anisotropy of kinetic coefficients of vicinal faces, the kinetic coefficients of steps, kst = (1.5 ± 0.3) × 10−2 cm/s, as well as currents of growth units to and off the interface are estimated. Es werden kinetische Koeffizienten von Vizinalflächen in Abhängigkeit vom Vizinalwinkel 0,1° ⪅ α ⪅ 2° an etwa <110>-orientierten (YSm)3(FeGa)5O12-Flüssigphasen-Epitaxieschichten ermittelt. Anlösungsstreifen in Granateinkristallen, die mit induzierten Streifen (HRISM) dekoriert wurden, sind zur Bestimmung von kinetischen Koeffizienten weniger geeignet. Die treibende Kraft für die Volumendiffusion und die Grenzflächenkinetik wird in Abhängigkeit von den hydrodynamischen Bedingungen und vom Vizinalwinkel angegeben. Auf der Grundlage eines Modells von Chernov, das die Anisotropie der kinetischen Koeffizienten der Vizinalflächen gut beschreibt, werden der kinetische Koeffizient der Stufen, kst = (1,5 ± 0,3) × 10−2 cm/s, sowie Ströme von Wachstumseinheiten zu und von der Phasengrenzfläche abgeschätzt.
CMOS Active Pixel Sensors as energy-range detectors for proton Computed Tomography (2015)

Since the first proof of concept in the early 70s, a number of technologies has been proposed to perform proton CT (pCT), as a means of mapping tissue stopping power for accurate treatment planning in proton therapy. Previous prototypes of energy-range detectors for pCT have been mainly based on the use of scintillator-based calorimeters, to measure proton residual energy after passing through the patient. However, such an approach is limited by the need for only a single proton passing through the energy-range detector in a read-out cycle. A novel approach to this problem could be the use of pixelated detectors, where the independent read-out of each pixel allows to measure simultaneously the residual energy of a number of protons in the same read-out cycle, facilitating a faster and more efficient pCT scan. This paper investigates the suitability of CMOS Active Pixel Sensors (APSs) to track individual protons as they go through a number of CMOS layers, forming an energy-range telescope. Measurements performed at the iThemba Laboratories will be presented and analysed in terms of correlation, to confirm capability of proton tracking for CMOS APSs.
Bis(diethylamino)pentafluorophenylphosphane as Valuable Precursor for the Design of Tetrafluorophenylphosphanes, Tetrafluorophenylphosphinic and ‐phosphonic Acids (2018)

Facile replacement of the p ‐fluorine atom in bis(diethylamino)pentafluorophenylphosphane [(Et 2 N) 2 PC 6 F 5 ] by organolithium derivatives LiR (R = CH 3 , n ‐Bu, Ph), lithium alkoxides (R = OMe, OEt) and amides (NMe 2 , NEt 2 ) is described. The obtained phosphanes p ‐R‐C 6 F 4 ‐P(NEt 2 ) 2 are fully characterized. Their acid‐catalyzed hydrolysis affords the corresponding phosphinic acids p ‐R‐C 6 F 4 ‐P(O)(H)OH, which are smoothly oxidized by treatment with a mixture of DMSO/I 2 to phosphonic acids p ‐R‐C 6 F 4 ‐P(O)(OH) 2 .
Vagal modulation of heart rate during exercise: effects of age and physical fitness (1998)

This study was designed to assess the effects of age and physical fitness on vagal modulation of heart rate (HR) during exercise by analyzing the instantaneous R-R interval variability from Poincaré plots (SD1) at rest and at different phases of a bicycle exercise test in a population of healthy males. SD1 normalized for the average R-R interval (SD1n), a measure of vagal activity, was compared at rest and during exercise among subjects of ages 24-34 (young, n = 25), 35-46 (middle-aged, n = 30), and 47-64 yr (old, n = 25) matched for peak O2 consumption (VO2 peak) and among subjects with VO2 peak of 28-37 (poor, n = 25), 38-45 (average, n = 36), and 46-60 ml.kg-1.min-1 (good, n = 25) matched for age. SD1n was higher at rest in the young subjects than in the middle-aged or old subjects (39 +/- 14, 27 +/- 16, and 21 +/- 8, respectively; P < 0.001), but the age-related differences in SD1n were smaller during exercise [e.g., 11 +/- 5, 9 +/- 5, and 8 +/- 4 at the level of 100 W; P = not significant (NS)]. The age-matched subjects with good, average, and poor VO2 peak showed no difference in SD1n at rest (32 +/- 17, 28 +/- 13, and 26 +/- 11, respectively; P = NS), but SD1n differed significantly among the groups from a low to a moderate exercise intensity level (e.g., 13 +/- 6, 10 +/- 5, and 6 +/- 3 for good, average, and poor fitness groups, respectively; P < 0.001, 100 W). These data show that poor physical fitness is associated with an impairment of cardiac vagal function during exercise, whereas aging itself results in more evident impairment of vagal function at rest.
A new section: Image of the month # (2008)

Anew feature entitled Image of the Month was introduced in the January 2009 issue of HEPATOLOGY. This section, which occurs following our Hepatology Elsewhere section, is intended to provide a forum for demonstration of interesting hepatic histopathology accompanied by a brief discussion of the conditions shown within the image. This section is edited by Drs. M. Isabel Fiel of the Department of Pathology, Mount Sinai School of Medicine, New York, NY, and Dr. Thomas Schiano from Adult Liver Transplantation at Mount Sinai Medical Center, New York, NY. Submissions for this section are invited, and instructions can be found in the Instructions to Authors. The journal's editors also invite comments, suggestions, and submissions regarding this new section which we hope will be of broad appeal to our readership.
Urinary Glycosaminoglycan Excretion and Microalbuminuria in Diabetes (1986)

<h3>To the Editor.—</h3> In a previous study we found a higher than normal glycosaminoglycan (GAG) excretion in patients with insulin-dependent diabetes (IDD), who have daily albumin excretion levels less than 25 mg (17 μg/min),<sup>1</sup>a value that borders on the normal range for albuminuria. This abnormality was paralleled by a higher urinary activity of lysosomal glycohydrolases involved in GAG metabolism, as well as a normal excretion of brush border enzymes not related to GAG turnover. We therefore proposed a renal origin for GAG, perhaps due to a derangement in GAG turnover in the renal basement membrane.<sup>2</sup>Since GAG is the major determinant of the anion layer of the glomerular basement membrane,<sup>3,4</sup>this finding might mirror an early decrease in membrane selectivity, which could underlie the appearance of microalbuminuria. <h3>Report of a Study.—</h3> To test this hypothesis, we evaluated urinary GAG excretion during a 24-hour period in 25
Evidence for a low-penetrant extended phenotype of RTPS1 from a kindred with gain of SMARCB1 exon 6 (2021)

We report on a long-term survivor of an atypical teratoid/rhabdoid tumor (ATRT-TYR) as an index patient, who carries a SMARCB1 exon 6 gain inherited from his father. The father was diagnosed with an unusual sequence of a myxopapillary INI1-negative ependymoma and a relapsing BRAF V600 wild type hairy-cell leukemia. He has two yet healthy sisters aged 33 and 38 years carrying the same variant, from which one had lost an infant to a malignant brain tumor. This family highlights the existence of RTPS1-associated SMARCB1 germline alterations with reduced penetrance and extends the spectrum of involved diseases