gebhart/patrepeval huggingface dataset:
Real time dynamic fracture with volumetric approximate convex decompositions (2013)

We propose a new fast, robust and controllable method to simulate the dynamic destruction of large and complex objects in real time. The common method for fracture simulation in computer games is to pre-fracture models and replace objects by their pre-computed parts at run-time. This popular method is computationally cheap but has the disadvantages that the fracture pattern does not align with the impact location and that the number of hierarchical fracture levels is fixed. Our method allows dynamic fracturing of large objects into an unlimited number of pieces fast enough to be used in computer games. We represent visual meshes by volumetric approximate convex decompositions (VACD) and apply user-defined fracture patterns dependent on the impact location. The method supports partial fracturing meaning that fracture patterns can be applied locally at multiple locations of an object. We propose new methods for computing a VACD, for approximate convex hull construction and for detecting islands in the convex decomposition after partial destruction in order to determine support structures.
Stanniocalcin-1: a novel molecular blood and bone marrow marker for human breast cancer. (2003)

STC-1 is proposed as a novel, specific, and clinically useful molecular marker for detecting occult breast cancer cells in the BM and blood.
Physiological role for cholecystokinin in reducing postprandial hyperglycemia in humans. (1988)

It is known that the ingestion of glucose alone causes a greater increase in plasma glucose levels than ingestion of the same amount of glucose given with other nutrients. Since physiological plasma concentrations of cholecystokinin (CCK) prolong gastric emptying, it is proposed that after a meal, CCK may modify plasma glucose levels by delaying glucose delivery to the duodenum. To evaluate the effect of CCK on oral glucose tolerance, plasma CCK, insulin, and glucose levels and gastric emptying rates were measured in eight normal males before and after the ingestion of 60 g glucose with the simultaneous infusion of either saline or one of two doses of CCK-8 (12 or 24 pmol/kg per h). Gastric emptying rates were measured by gamma camera scintigraphy of technetium 99m sulfur colloid and plasma CCK levels were measured by a sensitive and specific bioassay. Basal CCK levels averaged 1.0 +/- 0.1 pM (mean +/- SEM, n = 8) and increased to 7.1 +/- 1.1 pM after a mixed liquid meal. After glucose ingestion, but without CCK infusion, CCK levels did not change from basal, and the gastric emptying t1/2 was 68 +/- 3 min. Plasma glucose levels increased from basal levels of 91 +/- 3.9 mg/dl to peak levels of 162 +/- 11 mg/dl and insulin levels increased from 10.7 +/- 1.8 microU/ml to peak levels of 58 +/- 11 microU/ml. After glucose ingestion, with CCK infused at 24 pmol/kg per h, plasma CCK levels increased to 8 pM and the gastric emptying t1/2 increased to 148 +/- 16 min. In concert with this delay in gastric emptying, peak glucose levels rose to only 129 +/- 17 mg% and peak insulin levels rose to only 24.2 +/- 4.2 microU/ml. With CCK at 12 pmol/kg per h, similar but less dramatic changes were seen. To demonstrate that endogenous CCK could modify the plasma glucose and insulin responses to oral glucose, oral glucose was given with 50 g of lipid containing long-chain triglycerides. This lipid increased peak CCK levels to 3.7 +/- 0.9 pM. Concomitant with this rise in CCK was a delay in gastric emptying and a lowering of plasma glucose and insulin values. To confirm that CCK reduced hyperglycemia by its effect on gastric motility, 36 g glucose was perfused directly into the duodenum through a nasal-duodenal feeding tube in four subjects. With duodenal perfusion of glucose, there was no change in plasma CCK levels, but plasma glucose levels increased from basal levels of 93+/-5 to 148+/-6 mg/dl and insulin levels rose from 10.6+/-3.5 to 29.5+/-5.2 microU/ml. When CCK was infused at 24 pmol/kg per h, neither the plasma glucose nor insulin responses to the duodenal administration of glucose were modified. Thus we conclude that CCK, in physiological concentrations, delays gastric emptying, slows the delivery of glucose to the duodenum, and reduces postprandial hyperglycemia. These data indicate, therefore, that CCK has a significant role in regulating glucose homeostasis in human.
Stereochemistry and curvature effects in supramolecular organization and separation processes of micellar N-alkylaldonamide mixtures (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemistry and curvature effects in supramolecular organization and separation processes of micellar N-alkylaldonamide mixturesJuergen Hinrich Fuhrhop and Christoph BoettcherCite this: J. Am. Chem. Soc. 1990, 112, 5, 1768–1776Publication Date (Print):February 1, 1990Publication History Published online1 May 2002Published inissue 1 February 1990https://pubs.acs.org/doi/10.1021/ja00161a018https://doi.org/10.1021/ja00161a018research-articleACS PublicationsRequest reuse permissionsArticle Views783Altmetric-Citations106LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Multirate filter designs using comb filters (1984)

Results on multistage multirate digital filter design indicate most of the stages can be designed to control aliasing with only slight regard for the passband which is controlled by a single stage compensator. Because of this, the aliasing controlling stages can be made very simple. This paper considers comb filter structures for decimators and interpolators in multistage structures. Design procedures are developed and examples shown that have a very low multiplication rate, very few filter coefficients, low storage requirements, and a simple structure.
Characterization of the Promoter of Rice Plastid <italic>psaA-psaB-rps14</italic> Operon and the DNA-Specific Binding Proteins (1993)

Transcriptional analysis of the promoter of rice psaA-psaB-rps14 operon was performed with Bal 31 deleted mutants in spinach chloroplast extracts. Two functional promoters in this operon (denoted as "-175" and "-129" promoters) were revealed to be utilized by the spinach transcription machinery; however only the "-175" promoter is utilized in vivo. The existence of psaA promoter-specific binding factors in the chloroplast extracts was indicated by competitive gel retardation assay and exonuclease III protection analysis. After ammonium sulfate fractionation of the extracts followed by heparin-agarose column chromatography, the sequence-specific binding factors were characterized to be 66-kDa and 31-kDa polypeptides. Southwestern analysis demonstrated that the two protein factors interact independently with the psaA promoter-containing DNA fragment.
Evolution of ibrutinib resistance in chronic lymphocytic leukemia (CLL) (2014)

The Bruton tyrosine kinase inhibitor (BTKi) ibrutinib is a new targeted therapy for patients with chronic lymphocytic leukemia (CLL). Ibrutinib is given orally on a continuous schedule and induces durable remissions in the majority of CLL patients. However, a small proportion of patients initially responds to the BTKi and then develops resistance. Estimating the frequency, timing, and individual risk of developing resistance to ibrutinib, therefore, would be valuable for long-term management of patients. Computational evolutionary models, based on measured kinetic parameters of patients, allow us to approach these questions and to develop a roadmap for personalized prognosis and treatment management. Our kinetic models predict that BTKi-resistant mutants exist before initiation of ibrutinib therapy, although they only comprise a minority of the overall tumor burden. Furthermore, we can estimate the time required for resistant cells to grow to detectable levels. We predict that this can be highly variable, depending mostly on growth and death rates of the individual CLL cell clone. For a specific patient, this time can be predicted with a high degree of certainty. Our model can thus be used to predict for how long ibrutinib can suppress the disease in individual patients. Furthermore, the model can suggest whether prior debulking of the tumor with chemo-immunotherapy can prolong progression-free survival under ibrutinib. Finally, by applying the models to data that document progression during ibrutinib therapy, we estimated that resistant mutants might have a small (<2%) mean fitness advantage in the absence of treatment, compared with sensitive cells.
Proteomic Profiling Identifies Dysregulated Pathways in Small Cell Lung Cancer and Novel Therapeutic Targets Including PARP1 (2012)

SCLC is a highly lethal cancer with a 5-year survival rate of less than 10%. To date, no molecularly targeted agents have prolonged survival in patients with SCLCs. As a step toward identifying new targets, we systematically profiled SCLCs with a focus on therapeutically relevant signaling pathways. Our data reveal fundamental differences in the patterns of pathway activation in SCLCs and NSCLCs and identify several potential therapeutic targets for SCLCs, including PARP1 and EZH2. On the basis of these results, clinical studies evaluating PARP and EZH2 inhibition, together with chemotherapy or other agents, warrant further investigation.
Efficient region tracking with parametric models of geometry and illumination (1998)

As an object moves through the field of view of a camera, the images of the object may change dramatically. This is not simply due to the translation of the object across the image plane; complications arise due to the fact that the object undergoes changes in pose relative to the viewing camera, in illumination relative to light sources, and may even become partially or fully occluded. We develop an efficient general framework for object tracking, which addresses each of these complications. We first develop a computationally efficient method for handling the geometric distortions produced by changes in pose. We then combine geometry and illumination into an algorithm that tracks large image regions using no more computation than would be required to track with no accommodation for illumination changes. Finally, we augment these methods with techniques from robust statistics and treat occluded regions on the object as statistical outliers. Experimental results are given to demonstrate the effectiveness of our methods.
Inhibition of FKBP Rotamase Activity by Immunosuppressant FK506: Twisted Amide Surrogate (1990)

The immunosuppressive agents cyclosporin A and FK506 inhibit the transcription of early T cell activation genes. The binding proteins for cyclosporin A and FK506, cyclophilin and FKBP, respectively, are peptidyl-prolyl-cis-trans isomerases, or rotamases. One proposed mechanism for rotamase catalysis by cyclophilin involves a tetrahedral adduct of an amide carbonyl and an enzyme-bound nucleophile. The potent FKBP rotamase inhibitor FK506 has a highly electrophilic carbonyl that is adjacent to an acyl-pipicolinyl (homoprolyl) amide bond. Such a functional group would be expected to form a stabilized, enzyme-bound tetrahedral adduct. Spectroscopic and chemical evidence reveals that the drug interacts noncovalently with its receptor, suggesting that the alpha-keto amid of FK506 serves as a surrogate for the twisted amide of a bound peptide substrate.
Increased adipose tissue in male and female estrogen receptor-α knockout mice (2000)

Estrogen regulates the amount of white adipose tissue (WAT) in females, but its role in males and whether WAT effects involve estrogen receptor-α (ERα) or ERβ were unclear. We analyzed the role of ERα in WAT and brown adipose tissue by comparing these tissues in wild-type (WT) and ERα-knockout (αERKO) male and female mice. Brown adipose tissue weight was similar in αERKO and WT males at all ages. Progressive increases in WAT were seen in αERKO males with advancing age. Epididymal, perirenal, and inguinal WAT weighed 139–185% more in αERKO than in WT males by 270–360 days of age. Epididymal and perirenal adipocyte size was increased 20% in αERKO males. Adipocyte number was 82–168% greater in fat pads of αERKO vs. WT males. Compared with WT, 90-day-old αERKO females had increases in fat pad weights (54–103%), adipocyte size, and number. Both αERKO males and females had insulin resistance and impaired glucose tolerance, similar to humans lacking ERα or aromatase. Energy intake was equal in WT and αERKO males, indicating that obesity was not induced by hyperphagia. In contrast, energy expenditure was reduced by 11% in αERKO compared with WT males, indicating that altered energy expenditure may be important for the observed obesity. In summary, ERα absence causes adipocyte hyperplasia and hypertrophy, insulin resistance, and glucose intolerance in both sexes. These results are evidence that estrogen/ERα signaling is critical in female and male WAT; obesity in αERKO males involves a mechanism of reduced energy expenditure rather than increased energy intake.
Factors that Determine the Protein Resistance of Oligoether Self-Assembled Monolayers − Internal Hydrophilicity, Terminal Hydrophilicity, and Lateral Packing Density (2003)

Protein resistance of oligoether self-assembled monolayers (SAMs) on gold and silver surfaces has been investigated systematically to elucidate structural factors that determine whether a SAM will be able to resist protein adsorption. Oligo(ethylene glycol) (OEG)-, oligo(propylene glycol)-, and oligo(trimethylene glycol)-terminated alkanethiols with different chain lengths and alkyl termination were synthesized as monolayer constituents. The packing density and chemical composition of the SAMs were examined by XPS spectroscopy; the terminal hydrophilicity was characterized by contact angle measurements. IRRAS spectroscopy gave information about the chain conformation of specific monolayers; the amount of adsorbed protein as compared to alkanethiol monolayers was determined by ellipsometry. We found several factors that in combination or by themselves suppress the protein resistance of oligoether monolayers. Monolayers with a hydrophobic interior, such as those containing oligo(propylene glycol), show no protein resistance. The lateral compression of oligo(ethylene glycol) monolayers on silver generates more highly ordered monolayers and may cause decreased protein resistance, but does not necessarily lead to an all-trans chain conformation of the OEG moieties. Water contact angles higher than 70 degrees on gold or 65 degrees on silver reduce full protein resistance. We conclude that both internal and terminal hydrophilicity favor the protein resistance of an oligoether monolayer. It is suggested that the penetration of water molecules in the interior of the SAM is a necessary prerequisite for protein resistance. We discuss and summarize the various factors which are critical for the functionality of "inert" organic films.
Abstract 18099: Heart Rate and AV Delay Modify Left Ventricular Filling Vortex Properties (2012)

Background: Intraventricular flow generates vortex structures during rapid filling which grow during diastole and vanish during ejection. Vorticity has been proposed to increase global chamber efficiency by optimizing filling flow transportation and coupling kinetic energy to ejection. It also improves blood mixing avoiding stasis. Vorticity has been related to chamber geometrical properties, but the effects of electrical events have never been characterized. We have recently developed and validated a new method that allows measuring vortex properties by processing conventional transthoracic color-Doppler sequences. Methods: 27 patients carrying an implantable CRT device were studied after AV optimization (AVOPT - iterative method), longest AV (AVLONG), shortest AV (AVSHORT), CRT off (CRToff), and DDD AVOPT at 100 beats per minute (100BPM). Two-dimensional B-mode and conventional color-Doppler sequences of the full LV were obtained from an apical long-axis (Lax) view during each phase. Time-resolved maps of the 2D velocity fields were generated at high temporal resolution (> 100 Hz) using custom software by computing the optimal solution to the continuity equation that minimizes numerical errors. Circulation, energy, position, and radius of the main (antero-septal) and secondary (infero-lateral) vortices were estimated along the cardiac cycle. Results: Compared to AVOPT, the main vortex component remained closer to the base during 100BPM (difference = -20% of Lax length, p Conclusions: Heart rate and AV synchronicity influence vortex dynamics. These novel aspects of diastolic function can be studied by fluid dynamic quantitative analysis of color-Doppler echocardiograms.
Uniqueness of 3D pose under weak perspective: a geometrical proof (1995)

We present a purely geometrical proof that under the weak perspective model, the 3D pose of a 3-point configuration is determined uniquely up to a reflection by its 2D projection.
scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation (2019)

In conclusion, we present robust protocols for tissue preservation for up to 24 h prior to scRNA-seq analysis. This greatly facilitates the logistics of sample collection for Human Cell Atlas or clinical studies since it increases the time frames for sample processing.
The Impact of Obesity on US Mortality Levels: The Importance of Age and Cohort Factors in Population Estimates (2013)

Previous research has likely underestimated obesity's impact on US mortality. Methods attentive to cohort variation in obesity prevalence and age variation in obesity's effect on mortality risk suggest that obesity significantly shapes US mortality levels, placing it at the forefront of concern for public health action.
Cofilin Phosphorylation and Actin Reorganization Activities of Testicular Protein Kinase 2 and Its Predominant Expression in Testicular Sertoli Cells (2001)

We previously identified testicular protein kinase 1 (TESK1), which phosphorylates cofilin and induces actin cytoskeletal reorganization. We now report identification and characterization of another member of a TESK family, testicular protein kinase 2 (TESK2), with 48% amino acid identity with TESK1. Like TESK1, TESK2 phosphorylated cofilin specifically at Ser-3 and induced formation of actin stress fibers and focal adhesions. Both TESK1 and TESK2 are highly expressed in the testis, but in contrast to TESK1, which is predominantly expressed in testicular germ cells, TESK2 is expressed predominantly in nongerminal Sertoli cells. Thus, TESK1 and TESK2 seem to play distinct roles in spermatogenesis. In HeLa cells, TESK1 was localized mainly in the cytoplasm, whereas TESK2 was localized mainly in the nucleus, which means that TESK1 and TESK2 likely have distinct cellular functions. Because the kinase-inactive mutant of TESK2 was localized in the cytoplasm, nuclear/cytoplasmic localization of TESK2 depends on its kinase activity. A TESK2 mutant lacking the C-terminal noncatalytic region had about a 10-fold higher kinase activity in vitro and, when expressed in HeLa cells, induced punctate actin aggregates in the cytoplasm and unusual condensation and fragmentation of nuclei, followed by apoptosis. Thus, we propose that the C-terminal region plays important roles in regulating the kinase activity and cellular functions of TESK2.
Plasma Natriuretic Peptide Levels and the Risk of Cardiovascular Events and Death (2004)

The natriuretic peptides are counterregulatory hormones involved in volume homeostasis and cardiovascular remodeling. The prognostic significance of plasma natriuretic peptide levels in apparently asymptomatic persons has not been established.
Range Detection based on Ultrasonic Principle (2014)

The proposed system „The Ultrasonic Range Detector‟ employs an ultrasonic module that consists of an ultrasonic transmitter and receiver along with anATmega16a microcontroller. It works by transmitting a short pulse of sound at a frequency inaudible to the ear (ultrasonic sound or ultrasound). Afterwards the microcontroller listens for an echo. The time elapsed during transmission to echo reception gives information on the distance to the object. We aimed at designing rangefinder free from the conventional problems arising from the undesirable direct waves, wherein a signal level for detecting a right signal due to the reflection waves from a ranging object is automatically varied and the detection of the right signal is made inaccurate by the time-dependent signal level.
Antibacterial Activity of Povidone Iodine towards Non‐sporing Bacteria (1979)

The antibacterial activity of povidone iodine was examined in vitro in saline, in nutrient broth, in simulated ulcer experiments and in the presence of blood components. Minimum inhibitory and minimum bactericidal concentrations were within a narrow concentration range. Nutrient broth and plasma had little inactivating activity but 1 g haemoglobin inactivated 50 mg of free iodine: experiments with 125 I showed that uptake of iodine by red cells occurred rapidly. Optimal antimicrobial effects in clinical use should be achieved in relatively blood‐free situations. Povidone iodine produced a potent, and sometimes persistent bactericidal effect towards bacteria on healthy skin. It is suggested that antiseptics such as povidone iodine should continue to replace topical antibiotics for prevention and treatment of wound infection.
Antigen delivery by attenuated Bacillus anthracis: new prospects in veterinary vaccines (1999)

This report summarizes the recent investigations on the use of Bacillus anthracis as a live vector for delivery of antigens. Recombinant strains were constructed by engineering the current live Sterne vaccine. This vaccine, used to prevent anthrax in cattle, causes side-effects due to anthrax toxin activities. Bacteria producing a genetically detoxified toxin factor were devoid of lethal effects and were as protective as the Sterne strain against experimental anthrax. Moreover, B. anthracis expressing a foreign antigen controlled by an in vivo inducible promoter were able to generate either antibody or cellular protective responses against heterologous diseases.
A tool for RNA sequencing sample identity check (2013)

Supplementary data are available at Bioinformatics online.
<title>Efficient SIMD evaluation of image processing programs</title> (1997)

SIMD parallel systems have been employed for image processing and computer vision applications since their inception. This paper describes a system in which parallel programs are implemented using a machine-independent, retargetable object library that provides SIMD execution on the Lockheed Martin PAL-I SIMD parallel processor. Programs' performance on this machine is improved through on-the-fly execution analysis and scheduling. We describe the relevant elements of the system structure, the general scheme for execution analysis, and the current cost model for scheduling.