gebhart/patrepeval huggingface dataset:
Structural characterizations of nonpeptidic thiadiazole inhibitors of matrix metalloproteinases reveal the basis for stromelysin selectivity (1998)

The binding of two 5-substituted-1,3,4-thiadiazole-2-thione inhibitors to the matrix metalloproteinase stromelysin (MMP-3) have been characterized by protein crystallography. Both inhibitors coordinate to the catalytic zinc cation via an exocyclic sulfur and lay in an unusual position across the unprimed (P1-P3) side of the proteinase active site. Nitrogen atoms in the thiadiazole moiety make specific hydrogen bond interactions with enzyme structural elements that are conserved across all enzymes in the matrix metalloproteinase class. Strong hydrophobic interactions between the inhibitors and the side chain of tyrosine-155 appear to be responsible for the very high selectivity of these inhibitors for stromelysin. In these enzyme/inhibitor complexes, the S1' enzyme subsite is unoccupied. A conformational rearrangement of the catalytic domain occurs that reveals an inherent flexibility of the substrate binding region leading to speculation about a possible mechanism for modulation of stromelysin activity and selectivity.
Collision detection: A survey (2007)

A process of determining whether two or more bodies are making contact at one or more points is called collision detection or intersection detection. Collision detection is inseparable part of the computer graphics, surgical simulations, and robotics. There are varieties of methods for collision detection. We will review some of the most common ones. Algorithms for contact determination can be grouped into two general parts: broad-phase and narrow-phase. This paper provides a comprehensive classification of a collision detection literature into the two phases. Moreover, we have attempted to explain some of the existing algorithms which are not easy to interpret. Also, we have tried to keep sections self-explanatory without sacrificing depth of coverage.
Tissue biomechanics during cranial neural tube closure measured by Brillouin microscopy and optical coherence tomography (2018)

We demonstrated the capability of OCT-guided Brillouin microscopy to quantify tissue longitudinal modulus of mouse embryos in situ, and observed distinct change in the modulus during the closure of cranial neural tube. Although this preliminary work cannot provide definitive conclusions on biomechanics of neural tube closure yet as a result of the limited number of samples, it provides an approach of quantifying the tissue mechanics during embryo development in situ, thus could be helpful in investigating the role of tissue biomechanics in the regulation of embryonic development. Our next study involving more embryo samples will investigate systematic changes in tissue mechanics during embryonic development.
Ticking Fast or Ticking Slow, Through Shc Must You Go? (2004)

Circumstantial evidence places the p66 isoform of the adapter protein Shc in a position to mediate the accelerated aging phenotype displayed by mice expressing shortened forms of the tumor suppressor protein p53. We present a model in which p66(shc) may be responsible for integrating signals from the p53 pathway with signals from the insulin-like growth factor-1/Daf pathway in mammals. A full understanding of how interactions between p53 and p66(shc) affect longevity will require the production of animals with mutations in the genes encoding both proteins.
Application of artificial neural networks to the real time operation of water treatment plants (2002)

The water industry is facing increased pressure to produce higher quality treated water at a lower cost. The efficiency of a treatment process closely relates to the operation of the plant. To improve the operating performance, an artificial neural network (ANN) paradigm has been applied to a water treatment plant. An ANN which is able to learn the non-linear performance relationships of historical data of a plant, has been proved to be capable of providing operational guidance for plant operators. A backpropagation network is used to determine the alum and polymer dosages. The results show that the ANN model is most promising. The correlation coefficients (r) between the actual and predicted values for the alum and polymer dosages were both 0.97 and the average absolute percentage errors were 4.09% and 8.76% for the alum and polymer dosages respectively. The application of the ANN model is illustrated using data from Wyong Shire Council's Wyong Water Treatment Plant on the Central Coast of NSW.
Meta-Analysis of Genome-Wide Association Studies in >80 000 Subjects Identifies Multiple Loci for C-Reactive Protein Levels (2011)

We identified 18 loci that were associated with CRP levels. Our study highlights immune response and metabolic regulatory pathways involved in the regulation of chronic inflammation.
The anther‐specific protein encoded by the <i>Brassica napus</i> and <i>Arabidopsis thaliana</i> A6 gene displays similarity to β‐1,3‐glucanases (1993)

An anther-specific Brassica napus cDNA, A6, and two corresponding Arabidopsis thaliana genes have been isolated. Sequence analyses of A6 revealed similarity to beta-1,3-glucanases. The deduced A6 protein differs from other beta-1,3-glucanases in the possession of a long C-terminus. Immunoblotting using an antibody raised to the A6 protein detects a temporal 60 kDa protein in B. napus buds, suggesting that the long C-terminal region is present in the mature protein. A6 promoter-GUS and RNase fusions demonstrate that the A6 gene is tapetum-specific and temporally expressed with a peak in activity when the plant normally expresses callase (a complex of endo- and exo-beta-1,3-glucanase activities). The sequence similarity of A6 to other beta-1,3-glucanases, coupled with the temporal and spatial expression data, suggests that A6 may be part of the callase enzyme complex.
Second malignancies in patients with essential thrombocythaemia treated with busulphan and hydroxyurea: long‐term follow‐up of a randomized clinical trial (2000)

We have previously demonstrated that hydroxyurea (HU) reduces the rate of vascular complications in patients with essential thrombocythaemia (ET) at high risk of thrombosis. However, the relatively short follow-up (median 27 months) did not enable the evaluation of the risk of developing secondary malignancies. In this study, we report the long-term outcome of the 114 patients included in the trial: 56 patients randomized to receive HU and 58 patients to receive no cytoreductive therapy. Before randomization, 15 patients had been treated with busulphan. During the observation period, 29 patients (50%) shifted from the control to the HU group mainly because of thrombosis. Median follow-up was 73 months (range 3-94). Analysis was by intention to treat and, when indicated, by treatment. When analysed by intention to treat, 46 out of 54 patients (85%) originally randomized in the HU group are alive, compared with 49 of 58 patients (84%) in the control group [not significant (n.s.)]. Five patients (9%) in the HU group and 26 patients (45%) in the control group had thrombosis (P < 0.0001). Seven patients (13%) in the HU group developed secondary acute leukaemia, myelodysplastic syndromes or solid tumours, compared with only one of the control group patients (1.7%) (P = 0.032). The occurrence of secondary malignancies was also analysed by treatment: none of the 20 patients who had never been treated with chemotherapy developed neoplasia vs. three of the 77 patients given HU only (3.9% n.s.) and five of the 15 patients given busulphan plus HU (33% P < 0. 0001). This study showed that: (a) HU reduced the risk of thrombosis in ET patients; (b) the sequential use of busulphan and HU significantly increased the risk of second malignancies; and (c) overall survival was not affected by HU therapy.
Lack of Association Between Juvenile Myoclonic Epilepsy and HLA‐DR13 (1999)

Unlike previously reported positive association, in this population, there is no evidence that susceptibility to juvenile myoclonic epilepsy is associated with HLA-DR13.
Apical root resorption in upper anterior teeth (1983)

The incidence and extent of apical root resorption in maxillary incisors were studied radiographically in 719 consecutively treated orthodontic patients. Mean age at start of treatment was 12.8 years and mean observation time 3.6 years in both sexes. Root lengths were measured to the nearest 1/10 mm on standardized intra-oral radiographs taken before and after treatment. Mean root shortening for the four incisors were 0.73 mm and 0.67 mm for girls and boys respectively. When using the most severe single root resorption per patient as a parameter the mean was 1.34 mm for both sexes. A statistical search for clinical risk factors in apical root resorption indicated that patients starting treatment after 11 years of age experienced significantly more root resorption than patients starting earlier, even when taking residual root growth into account. Highly significant risk factors were: previous trauma, the correction of impacted maxillary canines, the use of rectangular archwires and Class II elastics. Fixed appliances caused significantly more apical root resorption than removable appliances. Sex, overbite, overjet and the length of time with bands on the teeth were not closely related to the amount of apical root resorption.
Bulk Superconductivity of Y-Ba-Cu-O and Er-Ba-Cu-O (1987)

High T c superconductivity in Y-Ba-Cu-O prepared with the improved conditions are investigated by both elctrical resistivity and magnetic susceptibility measurements. The results provide a clear evidence for the bulk superconductivity in this oxide material. A discovery of new supercoducting oxide Er-Ba-Cu-O with transition temperature as high as 90 K is also reported. It is found that these two compound shows very similar X-ray diffraction patterns and, thus, it is likely that the high T c superconductivity is realized in the common crystal structure.
Tuberculosis Treatment in HIV Infected Ugandans with CD4 Counts >350 Cells/mm3 Reduces Immune Activation with No Effect on HIV Load or CD4 Count (2010)

TB therapy leads to measurable decreases in immune activation in persons with HIV/TB co-infection and CD4 counts>350 cells/mm3.
<i>Japanese Government and Politics</i>. By Harold S. Quigley. New York: The Century Co., 1932. pp. xii, 442. Index. $3.75. (1934)

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Examining the Relationship between FindBugs Warnings and App Ratings (2015)

In the mobile-app ecosystem, user ratings of apps (a measure of user perception) are extremely important because they correlate strongly with downloads and hence revenue. A case study examined the relationship between ratings (and the associated review comments) and static-analysis warnings (collected using FindBugs) for 10,000 free-to-download Android apps. Three warning categories - bad practice, internationalization, and performance - were more frequent in low-rated apps and corresponded to the review comment complaints. Thus, these categories were closely related to the user experience. These results suggest that app developers could use static-analysis tools to identify the bugs behind the issues that users complain about, before releasing an app.
HDAC4 controls histone methylation in response to elevated cardiac load (2013)

In patients with heart failure, reactivation of a fetal gene program, including atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP), is a hallmark for maladaptive remodeling of the LV. The mechanisms that regulate this reactivation are incompletely understood. Histone acetylation and methylation affect the conformation of chromatin, which in turn governs the accessibility of DNA for transcription factors. Using human LV myocardium, we found that, despite nuclear export of histone deacetylase 4 (HDAC4), upregulation of ANP and BNP in failing hearts did not require increased histone acetylation in the promoter regions of these genes. In contrast, di- and trimethylation of lysine 9 of histone 3 (H3K9) and binding of heterochromatin protein 1 (HP1) in the promoter regions of these genes were substantially reduced. In isolated working murine hearts, an acute increase of cardiac preload induced HDAC4 nuclear export, H3K9 demethylation, HP1 dissociation from the promoter region, and activation of the ANP gene. These processes were reversed in hearts with myocyte-specific deletion of Hdac4. We conclude that HDAC4 plays a central role for rapid modifications of histone methylation in response to variations in cardiac load and may represent a target for pharmacological interventions to prevent maladaptive remodeling in patients with heart failure.
Compounds R1R2EMMe3 (E = P, As; M = Si, Sn) - Convenient and Versatile Reagents for the Syntheses of Tertiary (Fluoroaryl)phosphanes and -arsanes (2008)

Synthetic and mechanistic aspects of nucleophilic replacement of fluorine in fluorobenzenes, fluoropyridines and fluoroquinolines by phosphanyl and arsanyl groups via their reactions with R 1 R 2 EMMe 3 (E = P, As; M = Si, Sn; R 1 , R 2 = Me, i -Pr, t -Bu, Ph, etc.) reagents are considered.
Mitochondrial DNA Damage and Dysfunction Associated With Oxidative Stress in Failing Hearts After Myocardial Infarction (2001)

Mitochondria are one of the enzymatic sources of reactive oxygen species (ROS) and could also be a major target for ROS-mediated damage. We hypothesized that ROS may induce mitochondrial DNA (mtDNA) damage, which leads to defects of mtDNA-encoded gene expression and respiratory chain complex enzymes and thus may contribute to the progression of left ventricular (LV) remodeling and failure after myocardial infarction (MI). In a murine model of MI and remodeling created by the left anterior descending coronary artery ligation for 4 weeks, the LV was dilated and contractility was diminished. Hydroxyl radicals, which originated from the superoxide anion, and lipid peroxide formation in the mitochondria were both increased in the noninfarcted LV from MI mice. The mtDNA copy number relative to the nuclear gene (18S rRNA) preferentially decreased by 44% in MI by a Southern blot analysis, associated with a parallel decrease (30% to 50% of sham) in the mtDNA-encoded gene transcripts, including the subunits of complex I (ND1, 2, 3, 4, 4L, and 5), complex III (cytochrome b), complex IV (cytochrome c oxidase), and rRNA (12S and 16S). Consistent with these molecular changes, the enzymatic activity of complexes I, III, and IV decreased in MI, whereas, in contrast, complex II and citrate synthase, encoded only by nuclear DNA, both remained at normal levels. An intimate link among ROS, mtDNA damage, and defects in the electron transport function, which may lead to an additional generation of ROS, might play an important role in the development and progression of LV remodeling and failure.
Diffusive Resistances at, and Transpiration Rates from Leaves in Situ Within the Vegetative Canopy of a Corn Crop (1967)

At several heights and times of day within a crop of Zea mays, internal leaf diffusion resistance (r(i)) and external boundary layer diffusion resistance (r(a)) were evaluated by measuring the temperature of a transpiring and a non-transpiring leaf (simulated by covering both sides of a normal leaf with strips of poly-ethylene tape), and by measuring the immediate air temperature, humidity and windspeed.Both r(a) and r(i) increased with depth into the crop. However, r(a) generally was less than 10% of r(i).Profiles of latent-heat flux density and source intensity of transpiration showed that transpiration corresponded roughly to foliage distribution (with an upward shift) and were not similar to the profile of radiation absorption.The data were compared with heat budget data. The 2 approaches yielded quite similar height distributions of transpiration per unit leaf area and total transpiration resistance.The total crop resistance to transpiration was computed as 0.027 min cm(-1). This compares to Monteith's values of 0.017 to 0.040 min cm(-1) for beans (Phaseolus vulgaris L.), and Linacre's values of 0.015 to 0.020 min cm(-1) for turf.
Management of hypertension in chronic kidney disease: The Italian multicentric study (2005)

BP target was not reached in most CKD patients routinely seen in the renal clinics. The main barrier to guideline implementation is possibly the inadequate treatment of extracellular volume expansion despite the large prevalence of factors, such as older age and diabetes, which further enhance the intrinsic BP salt sensitivity of CKD.
Physical activity and type 2 diabetes : therapeutic effects and mechanisms of action (2008)

Chapter 1. The Increasing Burden of Type 2 Diabetes: Magnitude, Causes, and Implications of the Epidemic Chapter 2. Waging War on Type 2 Diabetes: Primary Prevention Through Exercise Biology Chapter 3. Fatty Acid Uptake and Insulin Resistance Chapter 4. Lipid Metabolism and Insulin Signaling Chapter 5. Metabolic Inflexibility and Insulin Resistance Chapter 6. Nutrient Sensor Links Obesity With Diabetes Risk Chapter 7. Inflammation-induced Insulin Resistance in Obesity: When immunity Impacts on Metabolic Control Chapter 8. Transcription Factors Regulating Exercise Adaptation Chapter 9. Exercise and Calorie Restriction Use Different Mechanisms to Improve Insulin Sensitivity Chapter 10. Mitochondrial Oxidative Capacity and Insulin Resistance Chapter 11. Effects of Acute Exercise and Exercise Training on Insulin Action in Skeletal Muscle Chapter 12. Resistance Exercise Training and the Management of Diabetes Chapter 13. AMPK: The Master Switch for Type 2 Diabetes? Chapter 14. Protein Kinase C and Insulin Resistance Chapter 15. Evidence for the Prescription of Exercise as a Therapy.
An efficient test vector compression scheme using selective huffman coding (2003)

This paper presents a compression/decompression scheme based on selective Huffman coding for reducing the amount of test data that must be stored on a tester and transferred to each core in a system-on-a-chip (SOC) during manufacturing test. The test data bandwidth between the tester and the SOC is a bottleneck that can result in long test times when testing complex SOCs that contain many cores. In the proposed scheme, the test vectors for the SOC are stored in compressed form in the tester memory and transferred to the chip where they are decompressed and applied to the cores. A small amount of on-chip circuitry is used to decompress the test vectors. Given the set of test vectors for a core, a modified Huffman code is carefully selected so that it satisfies certain properties. These properties guarantee that the codewords can be decoded by a simple pipelined decoder (placed at the serial input of the core's scan chain) that requires very small area. Results indicate that the proposed scheme can provide test data compression nearly equal to that of an optimum Huffman code with much less area overhead for the decoder.
Catfacing of Tomato Fruits as Influenced by Pruning1 (1976)

Abstract Catfacing on tomato fruit ( Lycopersicon esculentum mill. cv. Manapal) was affected more by time of pruning than amount of pruning. Results indicated that a 2 stem, delayed pruning system produced a lower percentage of catfaced fruit than either 1 or 2 stem early pruning system. Catfacing rates in an unpruned system were equal to that of the delayed pruning system, but early marketable yields were depressed with the unpruned plants. Differences noted in vegetative characteristics, treatment response, and the nature of the deformity suggest that growth regulator balance may influence the formation of catfaced fruit
Haptic Rendering of Surface-to-Surface Sculpted Model Interaction (1999)

Abstract Previous work in haptics surface tracing for virtual prototyping and surface design applications has used a point model for virtual finger-surface interaction. We extend this tracing method for surface-to-surface interactions. A straightforward extension of the point-surface formulation to surface-surface can yield extraneous, undesirable solutions, although we rework the formulation to yield more satisfactory solutions. Additionally, we derive an alternative novel velocity formulation for use in a surface-surface tracing paradigm that exhibits additional stability beyond the Newton methods. Both methods require evaluating the surface point and first and second surface partial derivatives for both surfaces, an efficient kilohertz rate computation. These methods are integrated into a three step tracking process that uses a global minimum distance method, the local Newton formulation, and the new velocity formulation.
Therapeutic potential of neuropeptide Y (NPY) receptor ligands (2010)

Neuropeptide Y (NPY) is widely distributed in the human body and contributes to a vast number of physiological processes. Since its discovery, NPY has been implicated in metabolic regulation and, although interest in its role in central mechanisms related to food intake and obesity has somewhat diminished, the topic remains a strong focus of research concerning NPY signalling. In addition, a number of other uses for modulators of NPY receptors have been implied in a range of diseases, although the development of NPY receptor ligands has been slow, with no clinically approved receptor therapeutics currently available. Nevertheless, several interesting small molecule compounds, notably Y2 receptor antagonists, have been published recently, fueling optimism in the field. Herein we review the role of NPY in the pathophysiology of a number of diseases and highlight instances where NPY receptor signalling systems are attractive therapeutic targets.
Thalocsessine, a New C20-Diterpenoid Alkaloid from Thalictrum sessile Hayata (1987)

The structure of thalicsessine, a new C20-diterpenoid alkaloid isolated from Thalictrum sessile Hayata (Ranunculaceael, together with a
Active Reprioritization of the Reading Worklist Using Artificial Intelligence Has a Beneficial Effect on the Turnaround Time for Interpretation of Head CT with Intracranial Hemorrhage (2020)

The approach used to present flags from artificial intelligence and machine learning algorithms to the radiologist can reduce image wait time and turnaround times.© RSNA, 2021See also the commentary by O'Connor and Bhalla in this issue.
On the Electrochemical Reactivity Mechanism of CoSb[sub 3] vs. Lithium (2003)

The electrochemical reactivity of vs. lithium has been studied. This phase reacts with more than 9.5 lithium in a two-step process, consisting of the uptake of 9 Li at a constant voltage close to 0.6 V, and of about one lithium over the final voltage decay to 0.01 V. Upon recharge, only 8 lithium can be extracted. From in situ X-ray diffraction, microscopy, and magnetic measurements, we provide evidence that the constant voltage process is rooted in the decomposition of leading to the formation of a composite made of Co and nanograins. We also illustrate that the mechanism by which the internal nanostructured electrode, formed during reduction, converts back to is quite unusual. It involves, concomitant with the dealloying reaction, a chemical reaction between Co and Sb nanograins. The extra capacity, measured at low potential, appears to be nested in a decomposition-type reaction catalyzed by the cobalt nanoparticles, in a manner similar to that previously reported for CoO. Although these materials can reversibly uptake about 8 lithium, they are of negligible value, since their capacity rapidly decays with cycling, independent of the electrode processing. © 2003 The Electrochemical Society. All rights reserved.