gebhart/patrepeval huggingface dataset:
Single Fibre Flexibility Measurement in a Flow Cell Based Device (2009)

Single ﬁbre ﬂexibility is widely recognised as an important parameter in the papermaking process. A novel ﬂow cell based method for its measurement was developed at the Institute for Paper, Pulp and Fibre Technology at Graz University of Technology. A special ﬂow channel geometry is used to induce high shear forces in a laminar ﬂow regime. The movement of single ﬁbres passing the highly sheared region is recorded by means of a high speed image acquisition system. Based on the reactions of the ﬁbres to the ﬂuid forces a ﬂexibility parameter is determined for each evaluated ﬁbre.
Drugs Active at ATP‐sensitive K + Channels (2006)

This chapter contains sections titled: Introduction Mitochondrial KATP Channel Openers for Myocardial Ischemia Sarc-KATP Blockers for Ventricular Arrhythmia SUR1/Kir6.2 Openers for Diabetes and Hyperinsulinemia SUR2B/Kir6.2 Openers for Overactive Bladder (OAB) KATP Openers for Alopecia Conclusions
Hemodialysis (2011)

This book contains notable contributions from the well-known Vicenza course on hemodialysis and miniaturized wearable devices for renal replacement therapy. The main themes covered in this publication include cardio-renal syndromes as well as new technologies in hemodialysis, new dialysis membranes and techniques, the importance of vitamin D rece
A single amino acid polymorphism in the glycosyltransferase CpsK defines four Streptococcus suis serotypes (2017)

The capsular polysaccharide (CPS) is the major virulence factor of the emerging zoonotic pathogen Streptococcus suis. CPS differences are also the basis for serological differentiation of the species into 29 serotypes. Serotypes 2 and 1/2, which possess identical gene content in their cps loci, express CPSs that differ only by substitution of galactose (Gal) by N-acetylgalactosamine (GalNAc) in the CPS side chain. The same sugar substitution differentiates the CPS of serotypes 14 and 1, whose cps loci are also identical in gene content. Here, using mutagenesis, CPS structural analysis, and protein structure modeling, we report that a single amino acid polymorphism in the glycosyltransferase CpsK defines the enzyme substrate predilection for Gal or GalNAc and therefore determines CPS composition, structure, and strain serotype. We also show that the different CPS structures have similar antiphagocytic properties and that serotype switching has limited impact on the virulence of S. suis.
Three-dimensional measurements of the nuclear magnetic resonance chemical shift and a new analytic data transform for the shift anisotropy (2000)

Three-dimensional measurements of the C13 nuclear magnetic resonance (NMR) chemical shift in methyl-α-D-glucopyranoside are presented. One dimension measures the isotropic shift under ordinary magic angle spinning. In the remaining two dimensions, the chemical shift anisotropy (CSA) is recoupled in two complementary ways. An analytic transform is constructed which takes the time-domain data directly to the three isotropic shift parameters, which can then be read off the resulting plot. The possibility of using such an experiment to resolve chemical sites by the CSA alone in powdered samples is discussed.
Treatment of coronary stent thrombosis with rheolytic thrombectomy: Results from a multicenter experience (2002)

Abstract The objective of this study was to assess the feasibility, efficacy, and safety of rheolytic thrombectomy (RT) for treatment of coronary stent thrombosis. Stent thrombosis is an infrequent but potentially devastating complication. Conventional treatment with balloon angioplasty and/or thrombolysis has yielded suboptimal results. RT was used to treat 18 patients (mean age, 62 ± 8 years; 72% male) with in‐stent thrombosis (mean time to stent thrombosis, 2.4 ± 1.8 days). Device success, procedure success, in‐hospital and 30‐day major cardiovascular events (MACE) were assessed in the hospital and at 30 days. Device success was obtained in 94% and procedure success was achieved in 100% of patients. Following RT, 11 patients underwent balloon angioplasty and 7 patients received additional stents. TIMI 3 coronary flow was obtained in 94.4% and all (100%) patients achieved either TIMI 2 or 3 coronary flow. The angiographic thrombus area decreased from 113.7 ± 79 to 5.5 ± 5.7 mm 2 after RT, and to 0.9 ± 2.1 mm 2 ( P &lt; 0.001) after final treatment. Procedural complications were limited to transient no‐reflow in five patients. Only one patient evolved a Q‐wave MI. At 30 days of follow‐up, no patients suffered death, emergent bypass surgery, or stroke. Our data suggest that the adjunctive use of rheolytic thrombectomy offers improved outcomes compared to prior results of intervention after coronary stent thrombosis and should be strongly considered as a treatment option for this complication. Cathet Cardiovasc Intervent 2003;58:11–17. © 2003 Wiley‐Liss, Inc.
Practical and Employable Protocols for UC-Secure Circuit Evaluation over Z n . (2013)

Abstract. We present a set of new, efficient, universally composable two-party protocols for evaluating reactive arithmetic circuits modulo n, where n is a safe RSA modulus of unknown factorization. Our protocols are based on a homomorphic encryption scheme with message space Zn, zero-knowledge proofs of existence, and a novel “mixed ” trapdoor commitment scheme. Our protocols are proven secure against adaptive corruptions (assuming secure erasures) under standard assumptions in the CRS model (without random oracles). Our protocols appear to be the most efficient ones that satisfy these security requirements. In contrast to prior protocols, we provide facilities that allow for the use of our protocols as building blocks of higher-level protocols. An additional contribution of this paper is a universally composable construction of the variant of the Dodis-Yampolskiy oblivious pseudorandom function in a group of order n as originally proposed by Jarecki and Liu.
Treatment of Symptomatic Cartilage Defects of the Knee (2009)

Characterized chondrocyte implantation for the treatment of articular cartilage defects of the femoral condyles of the knee results in significantly better clinical outcome at 36 months in a randomized trial compared with MF. Time to treatment and chondrocyte quality were shown to affect outcome.
RoadSpeak (2008)

A great number of people spend one or more hours each day driving between home and the office. These daily roadway commutes are highly predictable and regular, and provide a great opportunity to form virtual mobile communities. However, even though these commuters are already physically present in the same location, they are limited in their ability to communicate with each other. This paper presents a framework for building such communities, which we call Vehicular Social Networks (VSNs), to facilitate better communication between commuters driving on roadways. As a proof of concept, we present the design of RoadSpeak, a VSN-based system which allows drivers to automatically join VSNs along popular roadways, and communicate with each other by means of voice chat messages.
Discovering New Gene Functionalities from Random Perturbations of Known Gene Ontological Annotations (2014)

Genomic annotations describing functional features of genes and proteins through controlled terminologies and ontologies are extremely valuable, especially for computational analyses aimed at inferring new biomedical knowledge. Thanks to the biology revolution led by the introduction of the novel DNA sequencing technologies, several repositories of such annotations have becoming available in the last decade; among them, the ones including Gene Ontology annotations are the most relevant. Nevertheless, the available set of genomic annotations is incomplete, and only some of the available annotations represent highly reliable human curated information. In this paper we propose a novel representation of the annotation discovery problem, so as to enable applying supervised algorithms to predict Gene Ontology annotations of different organism genes. In order to use supervised algorithms despite labeled data to train the prediction model are not available, we propose a random perturbation method of the training set, which creates a new annotation matrix to be used to train the model to recognize new annotations. We tested the effectiveness of our approach on nine Gene Ontology annotation datasets. Obtained results demonstrated that our technique is able to improve novel annotation predictions with respect to state of the art unsupervised methods.
Competitive ELISA-Based Screening of Plant Derivatives for the Inhibition of VEGF Family Members Interaction with Vascular Endothelial Growth Factor Receptor 1 (2008)

The activation of vascular endothelial growth factor receptor-1 (VEGFR-1, also known as Flt-1) is crucial in many physiological and pathological conditions, like angiogenesis, cancer, inflammation, hematopoiesis, bone marrow precursors/stem cells recruitment in tumor angiogenesis, and metastasis formation. Many recent reports indicate that molecules able to antagonize Flt-1 activity have gained a strong interest in the view of therapeutic approaches. In order to identify new compounds able to interfere in the Flt-1 recognition by VEGFs family members, we have developed a highly sensitive competitive ELISA-based screening to study plant extracts and derivatives. Several fractions of the N-butanol extract of Pteleopsis suberosa leaves and of the chloroform extract of Parinari campestris leaves demonstrated by a bioassay-guided fractionation an evident inhibition of VEGF-A or placental growth factor (PlGF) interaction with Flt-1, with an inhibition over 50 % in particular for the VEGF-A/Flt-1 interaction at a concentration of 100 microg/mL. This activity seems be due to the presence of a combination of compounds acting synergistically.
Silicate Esters of Paclitaxel and Docetaxel: Synthesis, Hydrophobicity, Hydrolytic Stability, Cytotoxicity, and Prodrug Potential (2014)

We report here the synthesis and selected properties of various silicate ester derivatives (tetraalkoxysilanes) of the taxanes paclitaxel (PTX) and docetaxel (DTX) [i.e., PTX-OSi(OR)3 and DTX-OSi(OR)3]. Both the hydrophobicity and hydrolytic lability of these silicates can be (independently) controlled by choice of the alkyl group (R). The synthesis, structural characterization, hydrolytic reactivity, and in vitro cytotoxicity against the MDA-MB-231 breast cancer cell line of most of these derivatives are described. We envision that the greater hydrophobicity of these silicates (vis-à-vis PTX or DTX itself) should be advantageous from the perspective of preparation of stable aqueous dispersions of amphiphilic block-copolymer-based nanoparticle formulations.
Age-Related Changes in Body Composition of Bovine Growth Hormone Transgenic Mice (2008)

GH has a significant impact on body composition due to distinct anabolic and catabolic effects on lean and fat mass, respectively. Several studies have assessed body composition in mice expressing a GH transgene. Whereas all studies report enhanced growth of transgenic mice as compared with littermate controls, there are inconsistencies in terms of the relative proportion of lean mass to fat mass in these animals. The purpose of this study was to characterize the accumulation of adipose and lean mass with age and according to gender in a bovine (b) GH transgenic mouse line. Weight and body composition measurements were assessed in male and female bGH mice with corresponding littermate controls in the C57BL/6J genetic background. Body composition measurements began at 6 wk and continued through 1 yr of age. At the conclusion of the study, tissue weights were determined and triglyceride content was quantified in liver and kidney. Although body weights for bGH mice were significantly greater than their corresponding littermate controls at all time points, body composition measurements revealed an unexpected transition midway through analyses. That is, younger bGH mice had relatively more fat mass than nontransgenic littermates, whereas bGH mice became significantly leaner than controls by 4 months in males and 6 months in females. These results reveal the importance in timing and gender when conducting studies related to body composition or lean and fat tissue in GH transgenic mice or in other genetically manipulated mouse strains in which body composition may be impacted.
Re: Loss of PBRM1 Rescues VHL Dependent Replication Stress to Promote Renal Carcinogenesis (2018)

No AccessJournal of UrologyUrological Survey1 Aug 2018Re: Loss of PBRM1 Rescues VHL Dependent Replication Stress to Promote Renal Carcinogenesis Anthony AtalaMD Anthony AtalaAnthony Atala More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2018.05.019AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: Loss of PBRM1 Rescues VHL Dependent Replication Stress to Promote Renal Carcinogenesis." The Journal of Urology, 200(2), p. 247 © 2018 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 200Issue 2August 2018Page: 247 Advertisement Copyright & Permissions© 2018 by American Urological Association Education and Research, Inc.MetricsAuthor Information Anthony Atala More articles by this author Expand All Advertisement PDF downloadLoading ...
Author response: Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated (2017)

Smells are simply chemicals in the air that are recognized by nerves in our nose. Each nerve has a receptor that can identify a limited number of chemicals, and the nerve then relays this information to the brain. Animals have hundreds to thousands of different types of these nerves meaning that they can detect a wide array of smells. Smell receptors are proteins, and the genes that encode these proteins can be very different in two unrelated people. This could partly explain, for example, why some people find certain odors intense and unpleasant while others do not. However, having different genes for smell receptors does not by itself completely explain why some people are more sensitive than others to particular smells. The amounts of each nerve type in the nose might also differ between people and have an effect, but to date it has not been possible to accurately count them all. Ibarra-Soria et al. have now devised a new method to essentially count the number of each nerve type in the noses of mice from different breeds. The method makes use of a technique called RNA-sequencing, which can reveal which genes are active at any one time, and thus show how many nerves are producing each type of smell receptor. Ibarra-Soria et al. learned that different breeds of mice had remarkably different compositions of nerves in their noses. Further analysis revealed that this was due to changes to the DNA code near to the genes that encode the smell receptor. Next, Ibarra-Soria et al. sought to find out how the amount of each nerve type is controlled by giving mice water with different smells for weeks and looking how this affected their noses. These experiments revealed that a small number of the nerve types became more or less common after exposure to a smell. The altered nerves were directly involved in recognizing the smells, proving that the very act of smelling can change the make-up of nerves in a mouse’s nose. These results confirm that the diversity in the nose of each individual is not only dictated by the types of receptors found in there, but also by the number of each nerve type. The next challenge is to understand better how these differences change the way people perceive smells.
Geoclimatic Influences on Invasive Aspergillosis after Hematopoietic Stem Cell Transplantation (2010)

Climatic variables differentially affect airborne spore counts and IA risk in geographically disparate centers.
Modeling type II collagenopathy skeletal dysplasia by directed conversion and induced pluripotent stem cells (2014)

Type II collagen is a major component of cartilage. Heterozygous mutations in the type II collagen gene (COL2A1) result in a group of skeletal dysplasias known as Type II collagenopathy (COL2pathy). The understanding of COL2pathy is limited by difficulties in obtaining live chondrocytes. In the present study, we converted COL2pathy patients' fibroblasts directly into induced chondrogenic (iChon) cells. The COL2pathy-iChon cells showed suppressed expression of COL2A1 and significant apoptosis. A distended endoplasmic reticulum (ER) was detected, thus suggesting the adaptation of gene expression and cell death caused by excess ER stress. Chondrogenic supplementation adversely affected the chondrogenesis due to forced elevation of COL2A1 expression, suggesting that the application of chondrogenic drugs would worsen the disease condition. The application of a chemical chaperone increased the secretion of type II collagen, and partially rescued COL2pathy-iChon cells from apoptosis, suggesting that molecular chaperons serve as therapeutic drug candidates. We next generated induced pluripotent stem cells from COL2pathy fibroblasts. Chondrogenically differentiated COL2pathy-iPS cells showed apoptosis and increased expression of ER stress-markers. Finally, we generated teratomas by transplanting COL2pathy iPS cells into immunodeficient mice. The cartilage in the teratomas showed accumulation of type II collagen within cells, a distended ER, and sparse matrix, recapitulating the patient's cartilage. These COL2pathy models will be useful for pathophysiological studies and drug screening.
Supplementary Data from Stress-Mediated Reprogramming of Prostate Cancer One-Carbon Cycle Drives Disease Progression (2023)

&lt;p&gt;Supplementary Materials and Methods&lt;/p&gt;
Fast Skeletal Muscle Troponin Activation Increases Force of Mouse Fast Skeletal Muscle and Ameliorates Weakness Due to Nebulin-Deficiency (2013)

The effect of the fast skeletal muscle troponin activator, CK-2066260, on calcium-induced force development was studied in skinned fast skeletal muscle fibers from wildtype (WT) and nebulin deficient (NEB KO) mice. Nebulin is a sarcomeric protein that when absent (NEB KO mouse) or present at low levels (nemaline myopathy (NM) patients with NEB mutations) causes muscle weakness. We studied the effect of fast skeletal troponin activation on WT muscle and tested whether it might be a therapeutic mechanism to increase muscle strength in nebulin deficient muscle. We measured tension-pCa relations with and without added CK-2066260. Maximal active tension in NEB KO tibialis cranialis fibers in the absence of CK-2066260 was ∼60% less than in WT fibers, consistent with earlier work. CK-2066260 shifted the tension-calcium relationship leftwards, with the largest relative increase (up to 8-fold) at low to intermediate calcium levels. This was a general effect that was present in both WT and NEB KO fiber bundles. At pCa levels above ∼6.0 (i.e., calcium concentrations <1 µM), CK-2066260 increased tension of NEB KO fibers to beyond that of WT fibers. Crossbridge cycling kinetics were studied by measuring k(tr) (rate constant of force redevelopment following a rapid shortening/restretch). CK-2066260 greatly increased k(tr) at submaximal activation levels in both WT and NEB KO fiber bundles. We also studied the sarcomere length (SL) dependence of the CK-2066260 effect (SL 2.1 µm and 2.6 µm) and found that in the NEB KO fibers, CK-2066260 had a larger effect on calcium sensitivity at the long SL. We conclude that fast skeletal muscle troponin activation increases force at submaximal activation in both wildtype and NEB KO fiber bundles and, importantly, that this troponin activation is a potential therapeutic mechanism for increasing force in NM and other skeletal muscle diseases with loss of muscle strength.
REMOVED: Systematic Identification of Permeance Models for Pervaporation or Vapor Permeation Membranes (2012)

This article has been removed: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been removed at the request of the Executive Publisher. This article has been removed because it was published without the permission of the author(s).
Evaluation of a surface‐sampling probe electrospray mass spectrometry system for the analysis of surface‐deposited and affinity‐captured proteins (2006)

A combined self-aspirating electrospray emitter/surfacing-sampling probe coupled with an ion trap mass spectrometer was used to sample and mass analyze proteins from surfaces. The sampling probe mass spectrometer system was used to sample and detect lysozyme that had been deposited onto a glass slide using a piezoelectric spotter or murine gamma-interferon affinity captured on a glass slide using surface-immobilized anti-gamma-interferon antibody. The detection level for surface-deposited lysozyme (spot size < or =200 microm) was approximately 1.0 fmol (approximately 100 fmol/mm2) as determined from the ability to measure accurately the protein molecular mass from the mass spectrum acquired by sampling the deposit. These detection limits may be sufficient for certain applications in which protein fractions from a separation method are collected onto a surface. Radiolabeled proteins were used to quantify the surface density of immobilized antibody and the efficiency of capture of the gamma-interferon on glass and higher surface area ceramic supports. The capture density of gamma-interferon at surface saturation ranged from about 23 to 50 fmol/mm2 depending on the capture surface. Nonetheless, mass spectrometric detection of affinity capture protein was successful in some cases, but the results were not reproducible. Thus, improvement of the sampling system, ionization efficiency and/or capture density will be necessary for practical sampling of affinity-captured proteins. The means to accomplish improved sampling system detection limits and to increase the absolute amounts of protein captured per unit area are discussed.
Blind multi-user MMSE detection of CDMA signals (2002)

The recovery of code-division multiple access (CDMA) information signals in a frequency selective fading channel is a problem of great theoretical and practical interest. This paper addresses the estimation of an optimal (within the class of linear detectors) multi-user CDMA receiver. A novel approach is introduced that enables the estimation of the minimum mean-square error (MMSE) detector in a blind setting. The MMSE detector is obtained through a double subspace projection that exploits the subspace structure associated with both the code of the desired user and the estimated signal subspace of the covariance matrix for the observed signals. The technique allows for interference rejection without requiring the knowledge of the codes for the interferers.