gebhart/patrepeval huggingface dataset:
Human Embryonic Stem Cells Derived in Xeno-Free Conditions (2012)

In this chapter, we describe the derivation and characterization of nine hIn this chapter, we describe the derivation and characterization of nine human embryonic stem cells (hESC) (VAL-3 to -11B) from different developmental embryo stages (inner cell mass from a blastocyst, morula, and blastomere from a 3-day embryo) under xeno-free conditions providing the necessary protocols and techniques to carry out their derivation, characterization, and propagation.
Does immune suppression after moderate stressors occur to free resources in the house sparrow (Passer domesticus) (2011)

Stressors affect immune functions, but exactly why has yet to be discerned entirely. Two non-exclusive hypotheses have been proposed to explain this phenomenon: (i) immunosuppression abates the autoimmune response to self-antigens exposed by the rigors of a stressor, and (ii) immunosuppression allows allocation of resources to functions more valuable than protection against infection during a stressful event, (e.g., physical performance augments predator evasion). In this experiment, the second hypothesis was tested in wild house sparrows (Passer domesticus) by comparing rates of change in vertical flight performance versus antibacterial capacity of blood over a six week period of captivity. I predicted that if the latter hypothesis was true, immune function would decline over time, while physical capability would remain relatively stable, or even increase due to the reallocation of resources. Body mass, vertical hover duration, and antibacterial blood capacity all decreased over time in captivity. However, immune function did not decline more rapidly than physical performance, lending no support to the idea that resources are scavenged from immune function for physical activities. However, the possibility that demands other than vertical flight are traded-off against immune function cannot be dismissed.
High concordance of BAP1 and PBRM1 expression in patient-matched primary and metastatic ccRCC tumors. (2015)

507 Background: Clear cell renal cell carcinoma (ccRCC) is a well-described molecularly heterogeneous tumor. Herein, we assessed the concordance of two of the most commonly mutated genes in ccRCC, PBRM1 (~50%), and BAP1 (~15%), in patient-matched primary and metastatic tumors. Methods: One pathologist (PK) assessed PBRM1 and BAP1 protein expression using immunohistochemistry (IHC) in 99 patients with a primary and at least one metastatic ccRCC tumor available for analysis. All available metastatic tumors were analyzed. Results: A total of 99 patients (48 M0 and 51 M1) had both a primary tumor and at least one metastatic tumor available for analysis. There were a total of 158 metastases with one patient having up to 7 metastases available for analysis. The concordance between primary and patient-matched metastasis was 87% for PBRM1 and 99% for BAP1. We observed a similar concordance between patients with M0 versus M1 disease. Conclusions: While ccRCC is molecularly heterogeneous, PRBM1, and BAP1 are largely concordant between primary and metastatic lesions suggesting that PBRM1 and BAP1 are genetically truncal events in the molecular pathogenesis of ccRCC.
BRCA1 Expression Restores Radiation Resistance in BRCA1-defective Cancer Cells through Enhancement of Transcription-coupled DNA Repair (1999)

The breast cancer predisposition genes, BRCA1 and BRCA2, are responsible for the vast majority of hereditary breast cancer. Although BRCA2 functions to help the cell repair double-stranded DNA breaks, the function of BRCA1 remains enigmatic. Here, we develop a human genetic system to study the role of BRCA1 in oxidative DNA damage. We show that human cancer cells containing mutated BRCA1 are hypersensitive to ionizing radiation. This hypersensitivity can be reversed by the expression of forms of BRCA1 that are not growth suppressing. Reversal of hypersensitivity requires the ring finger of BRCA1, its transactivation domain, and its BRCT domain. Lastly, we show that unlike BRCA2, BRCA1 does not function in the repair of double-stranded DNA breaks. Instead, it functions in transcription-coupled DNA repair (TCR). TCR ability correlated with radioresistance as cells containing BRCA1 showed both increased TCR and radioresistance, whereas cells without BRCA1 showed decreased TCR and radiosensitivity. These findings give physiologic significance to the interaction of BRCA1 with the basal transcription machinery.
Review of recent non-hyperbaric oxygen interventions for mild traumatic brain injury. (2017)

Traumatic brain injury (TBI) affects 3.2 to 5.3 million persons in the United States (U.S.), and the impact in the U.S. military is proportionally higher. Consensus is lacking regarding an accepted outcome to measure the effectiveness of interventions to improve the symptoms associated with TBI, and no standard-of-care treatment exists for mild TBI (mTBI). A recent literature review evaluated hyperbaric oxygen therapy (HBO₂) interventions, and findings were mixed. We conducted a systematic review of non-HBO₂ mTBI interventional trials published in 2005-2015 in military and civilian populations. A total of 154 abstracts, seven randomized controlled trials (RCTs) and five pilot studies were reviewed. RCTs were evaluated using Consolidated Standards of Reporting Trials criteria. Results indicated that studies published within the period of review were small pilot studies for rehabilitation therapy and motion capture or virtual reality gaming interventions. Neuropsychological assessments were commonly specified outcomes, and most studies included a combination of symptom and neuropsychological assessments. Findings indicated a lack of large-scale, well-controlled trials to address the symptoms and sequelae of this condition, but results of small exploratory studies show evidence of potentially promising interventions.
Aedes notoscriptus(Diptera: Culicidae) Survival and Dispersal Estimated by Mark-Release-Recapture in Brisbane, Queensland, Australia (2000)

The survival and dispersal of adult Aedes notoscriptus (Skuse) were estimated in Brisbane, Queensland, Australia, where this species has been identified as a vector of Ross River and Barmah Forest viruses and shown to be orally susceptible to dengue virus types 1-4. Standard mark-release-recapture methods were used. Before the field study, laboratory trials showed that marking Ae. notoscriptus with fluorescent powder had no effect on survivorship. Female recapture rates of 10.6 and 2.3% over an 8-d period were achieved for two cohorts of marked Ae. notoscriptus released at the same field site. No males were recaptured over the 8-d period. The probability of daily survival was calculated using the Saul model as 0.77 and 0.79 for blue- and pink-marked females, respectively. For blue- and pink-marked females, the mean distance traveled was 105.2 and 179.9 m, and the maximum distance traveled was 195 and 238 m, respectively. The results indicate that protected harborage sites and shade influenced the distribution of Ae. notoscriptus within the study site.
P2‐174: NUMB PREVENTS NEURODEGENERATION BY REGULATING INTRANEURONAL TAU LEVELS IN AN ISOFORM‐SPECIFIC MANNER (2019)

Intraneuronal accumulation of the microtubule associated protein Tau is largely recognized as an important toxic factor linked to neuronal cell death in Alzheimer's disease (AD) and tauopathies. While there has been progress uncovering the mechanisms that lead to the formation of toxic Tau tangles, less is known about how intraneuronal Tau levels are regulated in health and disease. Based on various studies, including our own, which identified the endocytic adaptor protein Numb as a key regulator of intracellular protein trafficking in neurons, we hypothesized that Numb might control Tau levels. To explore this possibility, we studied retinal ganglion cells (RGCs), which express Numb and were shown to accumulate Tau in models of AD and tauopathies. Conditional inactivation of Numb (cKO) in RGCs caused a sharp increase in monomeric and oligomeric Tau levels and increased axonal blebbing in optic nerves, followed by significant neuronal cell loss in older mice. Interestingly, siRNA-mediated knock-down of Tau in Numb cKO RGCs rescued neuronal cell death in culture, suggesting that increased Tau levels renders cKO RGCs more susceptible to degeneration. While all four isoforms of Numb physically interact with Tau, only one could decrease intracellular Tau levels when overexpressed in a Tau reporter cell line, identifying this isoform as a potential neuroprotective agent for AD and tauopathies. To test this idea, we overexpressed Numb in RGCs of Tau P301S and 3Tg AD mouse models in vitro and in vivo. Remarkably, we found that Numb reduces the number of axonal blebs in mutant RGCs in culture. In vivo, three days after NMDA injury, Numb-treated P301S and 3Tg mice had 50% more RGCs than control-treated mutant mice and were not significantly different than non-transgenic control mice. Taken together, these results uncover Numb as a novel regulator of Tau protein homeostasis in neurons and as a potential neuroprotective agent for AD and tauopathies. As the relative levels of the different Numb isoforms are altered in the cortex of AD patients, these results also suggest that Numb might be involved in the pathophysiology of AD, representing de facto a novel therapeutic target.
Who buys logistics services? Organisational and occupational issues (2017)

Recent literature focuses on the question, why or how to select logistics service providers. There is little knowledge regarding the organisational units and the individuals involved in the buying process. This research investigates organisational and occupational issues of logistics service buying based on a survey. The results provide evidence that depending on the stage of the logistics service buying process, various organisational divisions are involved. While early stages show the coexistence and cooperation of purchasing and logistics departments, logistics is dominant in supporting the relationship. The chief logistics officer is of central importance. Nevertheless, other general groups of actors participate.
Epitaxial heterojunction InAs<inf>1-x</inf>Sb<inf>x</inf>photodiodes (1976)

Heterojunction p-InAs <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">.95</inf> Sb <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">.05</inf> /n-InSb photodiodes have been fabricated using gas phase epitaxially grown material. The major differences between the performance of homojunction InSb and these devices will be discussed. It will be shown that detectors produced from this epitaxial material exhibit background-limited performance, excellent uniformity and enhanced blue response. Characteristics such as detectivity, responsivity, dynamic range and noise figures will be presented. Applications of these detectors in infrared optical systems will be pointed out.
Development of Intelligent Digital Certificate Fuzzer Tool (2017)

Present day software testing demands effective ways to find software vulnerabilities through testing. This is especially true in case of network security that employ digital certificates for authentication. Digital certificates are the de-facto standard for verification of users and an integral part of public key infrastructure used to secure channels of communication within networks. An effective approach to testing digital certificates is to implement protocol based fuzzing. Fuzzing in general terms is the process of inserting high volume of invalid or random inputs into a program with the aim of obtaining unexpected results, thus identifying errors and potential vulnerabilities. This paper aims to introduce a protocol aware, user friendly graphical user interface (GUI) based digital certificate fuzzing tool. The tool aims to provide an effective means of black box testing through the use of mutation based fuzzing and OpenSSL to create digital certificates with user provided test-case specific fields. The fuzzed certificates are used as inputs in order to expose defects in digital certificate validation systems.
Identification of Structural–Kinetic and Structural–Thermodynamic Relationships for Thrombin Inhibitors (2013)

To improve our understanding of drug-target interactions, we explored the effect of introducing substituted amine residues with increased chain length in the P3 residue of the thrombin inhibitor melagatran. Inhibition, kinetic, and thermodynamic data obtained via stopped-flow spectroscopy (SF), isothermal microcalorimetry (ITC), and surface plasmon resonance (SPR) biosensor analysis were interpreted with the help of X-ray crystal structures of the enzyme-inhibitor complexes. The association rate became faster when the lipophilicity of the inhibitors was increased. This was coupled to an increased enthalpic component and a corresponding decreased entropic component. The dissociation rates were reduced with an increase in chain length, with only a smaller increase and a decrease in the enthalpic and entropic components, respectively. Overall, the affinity increased with an increase in chain length, with similar changes in the enthalpic and entropic components. ITC analysis confirmed the equilibrium data from SPR analysis, showing that the interaction of melagatran was the most enthalpy-driven interaction. Structural analysis of the thrombin-inhibitor complex showed that the orientation of the P1 and P2 parts of the molecules was very similar, but that there were significant differences in the interaction between the terminal part of the P3 side chain and the binding pocket. A combination of charge repulsion, H-bonds, and hydrophobic interactions could be used to explain the observed kinetic and thermodynamic profiles for the ligands. In conclusion, changes in the structure of a lead compound can have significant effects on its interaction with the target that translate directly into kinetic and thermodynamic effects. In contrast to what may be intuitively expected, hydrogen bond formation and breakage are not necessarily reflected in enthalpy gains and losses, respectively.
High-Performance Liquid Chromatographic Enantioseparation of Flavanones on 2-Hydroxy-3-Methacryloyloxypropyl -Cyclodextrin Copolymer Coated Silica Phase (2005)

Chromatographic resolution of four flavanones is achieved by reversed-phase high-performance liquid chromatography (HPLC) on a chiral stationary phase based on silica coated with a (2-hydroxy-3-methacryloyloxypropyl beta-cyclodextrin-co-N-vinylpyrrolidone) copolymer. The influence of the mobile phase water content and the nature of the organic modifier on the retention and resolution is evaluated. Monosubstituted flavanones are better resolved than the unsubstituted one. Nevertheless, the 6- and 7-methoxy substituents enhance retention and chiral recognition to polymeric beta-cyclodextrin stationary phase less than the 6-hydroxy group.
Concave or convex π-dimers: the role of the pancake bond in substituted phenalenyl radical dimers (2015)

π-stacking in dimers of phenalenyl represents the prototypical pancake bonding between radicals. This type of π-stacking aggregate is a key structural motif in conducting organic and multifunctional materials. It is driven by the bonding combination of the singly occupied molecular orbitals (SOMOs) of the monomers resulting in π-stacking contacts that are significantly shorter than the sum of the van der Waals (vdW) radii. Analysis of 56 structures from the literature (mostly from the Cambridge Structural Database) coupled with DFT computations shows that the central CC contact in derivatives of phenalenyl does not contribute directly to the π-stacking pancake bonding in accordance with the fact that the SOMO coefficient is zero at the central carbon. This central CC contact is typically longer than the contacts between the SOMO bearing α-carbons with a convex dimer shape with one known exception of a complex containing bulky tert-butyl groups. This unusual case of a concave shaped dimer with a significantly shorter central CC contact is due to the steric repulsions at the periphery of the molecule pushing the central atoms closer together relative to the α-α-contacts which provide the attractive driving force for the multicenter pancake bonding. The diradical character of the pancake bonding is revealed by the analysis of the unpaired electron density based on high-level multireference theory.
Generation of Single Isolated 67-Attosecond Pulses (2012)

Matching negative dispersion of materials with positive atto-chirp of short trajectories is critical for generating transform-limited attosecond pulses. We produced isolated 67 as pulses by removing XUV spectrum from the positive dispersion region of metal filters.
Automated cardiac MR image segmentation: theory and measurement evaluation (2002)

We present a new approach to magnetic resonance image segmentation with a Gradient-Vector-Flow-based snake applied to selective smoothing filtered images. The system also allows automated image segmentation in the presence of grey scale inhomogeneity, as in cardiac Magnetic Resonance imaging. Removal of such inhomogeneities is a difficult task, but we proved that using non-linear anisotropic diffusion filtering, myocardium edges are selectively preserved. The approach allowed medical data to be automatically segmented in order to track not only endocardium, which is usually a less difficult task, but also epicardium in anatomic and perfusion studies with Magnetic Resonance. The method developed proceeds in three distinct phases: (a) an anisotropic diffusion filtering tool is used to reduce grey scale inhomogeneity and to selectively preserve edges; (b) a Gradient-Vector-Flow-based snake is applied on filtered images to allow capturing a snake from a long range and to move into concave boundary regions; and (c) an automatic procedure based on a snake is used to fit both endocardium and epicardium borders in a multiphase, multislice examination. A good agreement (P<0.001) between manual and automatic data analysis, based on the mean difference+/-SD, was assessed in a pool of 907 cardiac function and perfusion images.
Indium(III) Triflate (2015)

[128008-30-0] C3F9O9S3In (MW 562.02) InChI = 1S/3CHF3O3S.In/c3*2-1(3,4)8(5,6)7;/h3*(H,5,6,7);/q;;;+3/p-3 InChIKey = UCYRAEIHXSVXPV-UHFFFAOYSA-K (reagent used a Lewis acid catalyst in organic synthesis and as a co-catalyst in organometallic catalysis) Physical Data: mp no data, decomposes; bp no data. Solubility: insoluble in water; sparingly soluble in hydrocarbons, diethyl ether; widely used in dichloromethane, acetonitrile, nitromethane. Form Supplied in: available in powdered form. dry in a vacuum dessicator prior to use. Handling, Storage, and Precautions: hygroscopic. Store material in a tightly sealed bottle away from moisture. May be irritating to skin and eyes. Inhalation of dust may lead to irritation in the respiratory tract. Forms acidic solutions in water.
Supplementary Data from Modulation of the Human Pancreatic Ductal Adenocarcinoma Immune Microenvironment by Stereotactic Body Radiotherapy (2023)

Supplementary Data from Modulation of the Human Pancreatic Ductal Adenocarcinoma Immune Microenvironment by Stereotactic Body Radiotherapy
Rate-Dependent Modeling of a Highly Filled Vulcanizate (2000)

Abstract Many filled elastomers exhibit characteristic types of non-linear and weakly rate-dependent behavior not well represented by viscoelasticity. Previous attempts to overcome these problems are discussed. Recently, there has been particular interest in rate-independent “frictional”, such as triboelastic, models. In the current paper rate-dependent variants of triboelastic models are described. Essential aspects of the behavior of these models are discussed. Predictions for the models are compared with experimental data for sinusoidal deformation histories and stress relaxation tests.
Thermodynamic Analysis of the Self‐Assembly of Pseudo Isocyanine Chloride in the Presence of Crowding Agents (2021)

Abstract Pseudo isocyanine chloride (PIC) is a water‐soluble cationic dyestuff, which self‐assembles to fiber‐like aggregates below a characteristic temperature threshold. The threshold temperature decreases with decreasing PIC concentration. Macromolecular cosolutes affect this self‐assembly of PIC, similar to the impact macromolecular crowding has on the aggregation of proteins in living systems. The present study analyses the impact of triethylene glycol (TEG), polyethylene glycol (PEG), and Ficoll 400 as synthetic macromolecular crowding agents on the self‐assembly of PIC. A drastic change in the absorption behavior of visible light by PIC, which accompanies the transformation of monomeric PIC to the aggregate state of PIC, allows to analyze the temperature‐dependent self‐assembly in detail. Assisted by calorimetric measurements and by an analogy between self‐assembly and chemical polymerization, the thermodynamic analysis allowed to interpret the observed tendency of TEG and PEG to suppress and of Ficoll 400 to promote self‐assembly of PIC. Whereas the suppression by TEG and PEG can be attributed to preferential interactions between TEG or PEG and PIC, the promoting effect induced by Ficoll 400 is caused by excluded volume effects exerted by Ficoll. The results are in support of PIC as a cheap substitute of proteins in test tube studies of self‐assembly and as sensor for crowding effects on self‐assembly processes in cells.
The Antioxidant α-Lipoic Acid Enhances Insulin-Stimulated Glucose Metabolism in Insulin-Resistant Rat Skeletal Muscle (1996)

Insulin resistance of muscle glucose metabolism is a hallmark of NIDDM. The obese Zucker (fa/fa) rat--an animal model of muscle insulin resistance--was used to test whether acute (100 mg/kg body wt for 1 h) and chronic (5-100 mg/kg for 10 days) parenteral treatments with a racemic mixture of the antioxidant alpha-lipoic acid (ALA) could improve glucose metabolism in insulin-resistant skeletal muscle. Glucose transport activity (assessed by net 2-deoxyglucose [2-DG] uptake), net glycogen synthesis, and glucose oxidation were determined in the isolated epitrochlearis muscles in the absence or presence of insulin (13.3 nmol/l). Severe insulin resistance of 2-DG uptake, glycogen synthesis, and glucose oxidation was observed in muscle from the vehicle-treated obese rats compared with muscle from vehicle-treated lean (Fa/-) rats. Acute and chronic treatments (30 mg.kg-1.day-1, a maximally effective dose) with ALA significantly (P < 0.05) improved insulin-mediated 2-DG uptake in epitrochlearis muscles from the obese rats by 62 and 64%, respectively. Chronic ALA treatment increased both insulin-stimulated glucose oxidation (33%) and glycogen synthesis (38%) and was associated with a significantly greater (21%) in vivo muscle glycogen concentration. These adaptive responses after chronic ALA administration were also associated with significantly lower (15-17%) plasma levels of insulin and free fatty acids. No significant effects on glucose transporter (GLUT4) protein level or on the activities of hexokinase and citrate synthase were observed. Collectively, these findings indicate that parenteral administration of the antioxidant ALA significantly enhances the capacity of the insulin-stimulatable glucose transport system and of both oxidative and nonoxidative pathways of glucose metabolism in insulin-resistant rat skeletal muscle.
Residual effects of intra‐articular betamethasone and triamcinolone acetonide in an equine acute synovitis model (2022)

Current regulatory guidelines may be insufficient if the concern is residual anti-inflammatory effects. Additionally, intra-articular corticosteroid administration is not without risk, as evidenced by a significant suppression of serum cortisol concentration and, as such, the benefits of their administration should be weighed against those risks.