gebhart/patrepeval huggingface dataset:
Role of Titanium Surface Topography and Surface Wettability on Focal Adhesion Kinase Mediated Signaling in Fibroblasts (2011)

Changes of titanium surface roughness and surface free energy may influence protein absorption that increases cell differentiation through activation of focal adhesion kinase related pathways. However, the influence of titanium surface roughness and hydrophilicity on fibroblast behavior is not well understood. The aim of this study was to investigate the influence of topography and hydrophilicity on fibroblast attachment, spreading, morphology, intracellular signaling, proliferation, and collagen I mRNA levels. Using a cellular FAK knockout (FAK<sup>-/-</sup>) model and wild-type (WT) controls, we also investigated the contribution of adhesion in fibroblasts cultured on smooth (PT), sand-blasted, large grit, acid-etched (SLA) and hydrophilic SLA topographies. Loss of FAK did not significantly affect fibroblast attachment to any surface, but SLA and hydrophilic SLA surface attenuated spreading of WT cells significantly more than FAK<sup>-/-</sup> fibroblasts. Both FAK<sup>-/-</sup> and WT cells formed numerous focal adhesions on PT surfaces, but significantly less on SLA and hydrophilic SLA surfaces. In WT cells, phosphorylation levels of FAK were lower on SLA and hydrophilic SLA in comparison with PT 24 h post seeding. Labeling of cells with antibodies to cortactin showed that FAK<sup>-/-</sup>cells contained significantly more cortactin-rich focal adhesion in comparison with WT cells on PT surfaces, but not on SLA or hydrophilic SLA. ERK 1/2 phosphorylation was highest in WT cells on all surfaces which correlated with collagen I expression levels. We conclude that fibroblasts are sensitive to changes in surface roughness and hydrophilicity, with adhesive interactions mediated through FAK, an important modulator of fibroblast response.
Redox-Sensitive Copolymer:  A Single-Component pH Sensor (2006)

A novel redox-active copolymer has been developed, capable of sensing pH. The polymer incorporates the redox-active but pH-insensitive vinylferrocene moiety as the internal reference signal, alongside the redox-active and pH-sensitive vinylanthracene moiety. The anthracene moiety undergoes a Nernstian potential shift with pH. The various monomer and homopolymer components have been examined in turn and the electrochemical response of the polymer characterized. Furthermore, the pH response was found to be stable over a wide temperature range.
A Comparative Genome Analysis Identifies Distinct Sorting Pathways in Gram-Positive Bacteria (2004)

Surface proteins in gram-positive bacteria are frequently required for virulence, and many are attached to the cell wall by sortase enzymes. Bacteria frequently encode more than one sortase enzyme and an even larger number of potential sortase substrates that possess an LPXTG-type cell wall sorting signal. In order to elucidate the sorting pathways present in gram-positive bacteria, we performed a comparative analysis of 72 sequenced microbial genomes. We show that sortase enzymes can be partitioned into five distinct subfamilies based upon their primary sequences and that most of their substrates can be predicted by making a few conservative assumptions. Most bacteria encode sortases from two or more subfamilies, which are predicted to function nonredundantly in sorting proteins to the cell surface. Only approximately 20% of sortase-related proteins are most closely related to the well-characterized Staphylococcus aureus SrtA protein, but nonetheless, these proteins are responsible for anchoring the majority of surface proteins in gram-positive bacteria. In contrast, most sortase-like proteins are predicted to play a more specialized role, with each anchoring far fewer proteins that contain unusual sequence motifs. The functional sortase-substrate linkage predictions are available online (http://www.doe-mbi.ucla.edu/Services/Sortase/) in a searchable database.
GMP-Compliant Isolation and Expansion of Bone Marrow-Derived MSCs in the Closed, Automated Device Quantum Cell Expansion System (2012)

The estimated frequency of MSCs in BM is about 0.001-0.01% of total nucleated cells. Most commonly, one applied therapeutic cell dose is about 1-5 million MSCs/kg body weight, necessitating a reliable, fast, and safe expansion system. The limited availability of MSCs demands for an extensive ex vivo amplification step to accumulate sufficient cell numbers. Human platelet lysate (PL) has proven to be a safe and feasible alternative to animal-derived serum as supplement for MSC cultivation. We have investigated the functionally closed automated cell culture hollow fiber bioreactor Quantum cell expansion system as an alternative novel tool to conventional tissue flasks for efficient clinical-scale MSC isolation and expansion from bone marrow using PL. Cells expanded in the Quantum system fulfilled MSC criteria as shown by flow cytometry and adipogenic, chondrogenic, and osteogenic differentiation capacity. Cell surface expression of a variety of chemokine receptors, adhesion molecules, and additional MSC markers was monitored for several passages by flow cytometry. The levels of critical media components like glucose and lactate were analyzed. PDGF-AA, PDGF-AB/BB, bFGF, TGF-β1, sICAM-1, sVCAM-1, RANTES, GRO, VEGF, sCD40L, and IL-6 were assessed using a LUMINEX platform. Originally optimized for the use of fetal calf serum (FCS) as supplement and fibronectin as coating reagent, we succeeded to obtain an average of more than 100×10(6) of MSCs from as little as 18.8-28.6 ml of BM aspirate using PL. We obtained similar yields of MSCs/µl BM in the FCS-containing and the xenogen-free expansion system. The Quantum system reliably produces a cellular therapeutic dose in a functionally closed system that requires minimal manipulation. Both isolation and expansion are possible using FCS or PL as supplement. Coating of the hollow fibers of the bioreactor is mandatory when loading MSCs. Fibronectin, PL, and human plasma may serve as coating reagents.
The regulation of the endosomal compartment by p53 the tumor suppressor gene (2009)

The endosomal compartment of the cell is involved in a number of functions including: (a) internalizing membrane proteins to multivesicular bodies and lysosomes; (b) producing vesicles that are secreted from the cell (exosomes); and (c) generating autophagic vesicles that, especially in times of nutrient deprivation, supply cytoplasmic components to the lysosome for degradation and recycling of nutrients. The p53 protein responds to various stress signals by initiating a transcriptional program that restores cellular homeostasis and prevents the accumulation of errors in a cell. As part of this process, p53 regulates the transcription of a set of genes encoding proteins that populate the endosomal compartment and impact upon each of these endosomal functions. Here, we demonstrate that p53 regulates transcription of the genes TSAP6 and CHMP4C, which enhance exosome production, and CAV1 and CHMP4C, which produce a more rapid endosomal clearance of the epidermal growth factor receptor from the plasma membrane. Each of these p53-regulated endosomal functions results in the slowing of cell growth and division, the utilization of catabolic resources and cell-to-cell communication by exosomes after a stress signal is detected by the p53 protein. These processes avoid errors during stress and restore homeostasis once the stress is resolved.
Imatinib-Loaded Polyelectrolyte Microcapsules for Sustained Targeting of BCR-ABL + Leukemia Stem Cells (2010)

This pilot study provides the proof-of-principle for the clinical application of biodegradable IM-loaded PMC as feasible, safe and effective ex vivo purging agents to target CML stem cells, in order to improve transplant outcome of resistant/relapsed patients or reduce IM dose escalation.
Specialized Membrane Domains for Water Transport in Glial Cells: High-Resolution Immunogold Cytochemistry of Aquaporin-4 in Rat Brain (1997)

Membrane water transport is critically involved in brain volume homeostasis and in the pathogenesis of brain edema. The cDNA encoding aquaporin-4 (AQP4) water channel protein was recently isolated from rat brain. We used immunocytochemistry and high-resolution immunogold electron microscopy to identify the cells and membrane domains that mediate water flux through AQP4. The AQP4 protein is abundant in glial cells bordering the subarachnoidal space, ventricles, and blood vessels. AQP4 is also abundant in osmosensory areas, including the supraoptic nucleus and subfornical organ. Immunogold analysis demonstrated that AQP4 is restricted to glial membranes and to subpopulations of ependymal cells. AQP4 is particularly strongly expressed in glial membranes that are in direct contact with capillaries and pia. The highly polarized AQP4 expression indicates that these cells are equipped with specific membrane domains that are specialized for water transport, thereby mediating the flow of water between glial cells and the cavities filled with CSF and the intravascular space.
Monolithically Integrated Enhancement/Depletion-Mode AlGaN/GaN HEMT Inverters and Ring Oscillators Using$hboxCF_4$Plasma Treatment (2006)

Fabrication and characterization of AlGaN/GaN HEMT inverters and ring oscillators utilizing integrated enhancement/depletion-mode (E/D-mode) AlGaN/GaN HEMTs are presented. The core technique is a <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$hboxCF_4$</tex> plasma treatment that can effectively convert a D-mode AlGaN/GaN heterostructure to an E-mode heterostructure. A significant advantage of the plasma-treated E-mode HEMTs is that the gate current is reduced in both reverse- and forward-bias regions due to the effectively enhanced barrier height induced by the negatively charged fluorine ions in the AlGaN barrier. As a result, the input voltage swing is expanded by about 1 V for the E-mode HEMT, enabling convenient input/output logic level matching for multistage logic circuits such as ring oscillators. The fabricated 17-stage direct-coupled field-effect transistor logic ring oscillator using the 1- <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$muhboxm$</tex> -gate technology can operate properly at a larger supply voltage of 3.5 V, and a minimum propagation delay of 130 ps/stage is achieved.
Network authentication tokens (2003)

Network users may be authenticated by different means and from a variety of locations. Once authenticated, the user's access should be consistent with the strength of the authentication. The author examines one possible method for determining the authentication strength and conveying this information within a distributed network. The approach discussed uses a token composed of a unique user ID and an authentication level. The token is sent along with the request for establishing a remote session. Once the token is received, the remote location determines user access based solely on the authentication token.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
BNP/NT‐ProBNP and Cardiac Pacing: A Review (2009)

Natriuretic peptide (NP) levels (B-type natriuretic peptide [BNP] and N-terminal proBNP) are now widely used in clinical practice and cardiovascular research all over the world and have been incorporated into many cardiovascular guidelines for heart failure (HF). The roles of NP levels are evolving rapidly not only in diagnosis, therapy monitoring, and risk stratification of HF, but also in differential diagnosis of acute dyspnea, predicting death and rehospitalization in HF patients. NP assays have been applied in permanent cardiac pacing in recent years, whereas it is still not well known how NP levels change and whether NP levels can predict HF in permanent cardiac pacing. Therefore, this article reviews the role of NP levels in permanent cardiac pacing, mainly including NP changes in different cardiac pacing modes and cardiac resynchronization therapy.
Optimization of 3-Pyrimidin-4-yl-oxazolidin-2-ones as Allosteric and Mutant Specific Inhibitors of IDH1 (2016)

High throughput screening and subsequent hit validation identified 4-isopropyl-3-(2-((1-phenylethyl)amino)pyrimidin-4-yl)oxazolidin-2-one as a potent inhibitor of IDH1<sup>R132H</sup>. Synthesis of the four separate stereoisomers identified the (<i>S</i>,<i>S</i>)-diastereomer (<b>IDH125</b>, <b>1f</b>) as the most potent isomer. This also showed reasonable cellular activity and excellent selectivity vs IDH1<sup>wt</sup>. Initial structure-activity relationship exploration identified the key tolerances and potential for optimization. X-ray crystallography identified a functionally relevant allosteric binding site amenable to inhibitors, which can penetrate the blood-brain barrier, and aided rational optimization. Potency improvement and modulation of the physicochemical properties identified (<i>S</i>,<i>S</i>)-oxazolidinone <b>IDH889</b> (<b>5x</b>) with good exposure and 2-HG inhibitory activity in a mutant IDH1 xenograft mouse model.
Drying of Loose and Particulate Materials (1992)

Particle properties moisture in particulate solids handling of feedstocks effects of drying moisture in gases heat transfer to particles kinetics of drying material and energy requirements in drying design and specification of a dryer process conditions in progressive dryers process conditions in non-progressive dryers hazards in drying control of dryers product collection and recovery.
Chemical cross‐linking and mass spectrometry for mapping three‐dimensional structures of proteins and protein complexes (2003)

Chemical cross-linking of proteins, an established method in protein chemistry, has gained renewed interest in combination with mass spectrometric analysis of the reaction products for elucidating low-resolution three-dimensional protein structures and interacting sequences in protein complexes. The identification of the large number of cross-linking sites from the complex mixtures generated by chemical cross-linking, however, remains a challenging task. This review describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the strategies employing intra- or intermolecular chemical cross-linking and mass spectrometry. The various approaches described in the literature to facilitate detection of cross-linking products and also computer software for data analysis are reviewed. Cross-linking techniques combined with mass spectrometry and bioinformatic methods have the potential to provide the basis for an efficient structural characterization of proteins and protein complexes.
Improving OLAP performance by multidimensional hierarchical clustering (2003)

Data warehousing applications cope with enormous data sets in the range of Gigabytes and Terabytes. Queries usually either select a very small set of this data or perform aggregations on a fairly large data set. Materialized views storing pre-computed aggregates are used to efficiently process queries with aggregations. This approach increases resource requirements in disk space and slows down updates because of the view maintenance problem. Multidimensional hierarchical clustering (MHC) of OLAP data overcomes these problems while offering more flexibility for aggregation paths. Clustering is introduced as a way to speed up aggregation queries without additional storage cost for materialization. Performance and storage cost of our access method are investigated and compared to current query processing scenarios. In addition performance measurements on real world data for a typical star schema are presented.
Intermediate-Density Lipoproteins and Progression of Carotid Arterial Wall Intima-Media Thickness (1997)

These data provide further evidence for the role of triglyceride-rich lipoproteins in the progression of atherosclerosis and support the evidence that indicates that the risk of atherosclerosis attributable to LDL-C may in part be the result of lipoproteins in the IDL fraction (Sf 12 to 20) that is included within the traditional measurements of LDL-C.
Nanobioengineered Electrospun Composite Nanofibers and Osteoblasts for Bone Regeneration (2008)

Bone defects represent a medical and socioeconomic challenge. Engineering bioartificial bone tissues may help to solve problems related to donor site morbidity and size limitations. Nanofibrous scaffolds were electrospun into a blend of synthetic biodegradable polycaprolactone (PCL) with hydroxyapatite (HA) and natural polymer gelatin (Gel) at a ratio of 1:1:2 (PCL/HA/Gel) compared to PCL (9%), PCL/HA (1:1), and PCL/Gel (1:2) nanofibers. These fiber diameters were around 411 +/- 158 to 856 +/- 157 nm, and the pore size and porosity around 5-35 microm and 76-93%, respectively. The interconnecting porous structure of the nanofibrous scaffolds provides large surface area for cell attachment and sufficient space for nutrient transportation. The tensile property of composite nanofibrous scaffold (PCL/HA/Gel) was highly flexible and allows penetrating osteoblasts inside the scaffolds for bone tissue regeneration. Fourier transform infrared analysis showed that the composite nanofiber contains an amino group, a phosphate group, and carboxyl groups for inducing proliferation and mineralization of osteoblasts for in vitro bone formation. The cell proliferation (88%), alkaline phosphatase activity (77%), and mineralization (66%) of osteoblasts were significantly (P < 0.001) increased in composite nanofibrous scaffold compared to PCL nanofibrous scaffolds. Field emission scanning electron microscopic images showed that the composite nanofibers supported the proliferation and mineralization of osteoblast cells. These results show that the fabrication of electrospun PCL/HA/Gel composite nanofibrous scaffolds has potential for the proliferation and mineralization of osteoblasts for bone regeneration.
Diameter Credit-Control Application (2005)

This document specifies a Diameter application that can be used to implement real-time credit-control for a variety of end user services such as network access, Session Initiation Protocol (SIP) services, messaging services, and download services.
The Effect of Elevated Triglycerides on the Onset and Progression of Coronary Artery Disease: A Retrospective Chart Review (2015)

Background. The American College of Cardiology and American Heart Association did not indicate a correlation between treating hypertriglyceridemia and reducing cardiovascular events. Objective. This study investigated whether patients with hypertriglyceridemia were more prone to worse outcomes during cardiac catheterization. Methods. Data collected over a one-year period analyzed lipid panels obtained at the time of cardiac catheterization. Triglyceride levels were categorized into three groups: <150 mg/dL, 150 mg/dL-300 mg/dL, and >300 mg/dL. Controlled variables included age, gender, the presence of hypertension, diabetes, hyperlipidemia, and history of coronary artery disease. Results. Subjects with a triglyceride level <150 mg/dL have a 54% likelihood of being treated medically compared to 38% and 41% in the 150 mg/dL-300 mg/dL and >300 mg/dL groups, respectively (p < 0.01). Subjects with a triglyceride level >300 mg/dL have a 20% percent chance of being treated with a coronary artery bypass graft compared to 12% and 15% in the <150 mg/dL and 150 mg/dL-300 mg/dL groups, respectively (p < 0.01). Subjects with a triglyceride level between 150 and 300 mg/dL have a 44% percent of being treated with a percutaneous coronary intervention compared to 34% and 43% in the <150 mg/dL and >300 mg/dL groups, respectively (p < 0.01). Conclusion. Hypertriglyceridemia was associated with worse outcomes in percutaneous coronary intervention or surgery.
Use of atrial and bifocal cardiac pacemakers for treating resistant dysrhythmias. (1975)

Several permanent cardiac pacing techniques have been utilized to control resistant cardiac arrhythmias. SA block, sinus arrest and intermittent ventricular tachycardia was controlled by the use of an atrial 'J' catheter and a rate programmable demand pacemaker. When these arrhythmias were associated with AV conduction delay they were managed with an AV sequential pacemaker with the additional insertion of a ventricular pacing lead. Appropriate adjustment of the AV sequential interval inhibited reciprocal AV or VA reentry thus controlling reciprocal tachycardia. Frequent ventricular premature systoles or intermittent ventricular tachycardia with in appropriately delayed sinus or subsidiary escape cycle lengths appear best managed by an AV sequential pacemaker by adjusting the atrial return cycle. Intractable atrial reentry tachycardias appear best managed by paired or rapid atrial stimulating pacemakers. Development of variable atrial rate, AV sequential and atrial return cycle activating pacemakers offer an effective control of resistant cardiac arrhythmias.
Peptidoglycan recognition proteins: on and off switches for innate immunity (2004)

Insects rely on innate immune mechanisms to defend themselves against microbes. The inducible anti-microbial peptides constitute an important arm of this defense. In Drosophila, the Toll and the Imd pathways are the major routes to induce the peptides, and it has become clear that to a certain extent, these pathways can discriminate between different microbes and mount an appropriate response to eliminate the intruder. This review discusses the proteins responsible for this discriminatory recognition, the peptidoglycan recognition proteins (PGRPs). The serum protein PGRP-SA triggers a humoral cascade of proteases upon infection by certain gram-positive bacteria to activate the Toll pathway. The membrane-bound receptor PGRP-LC activates the Imd pathway in response to certain gram-negative bacteria or their peptidoglycans. Other PGRPs have enzymatic activity, cleaving lactylamide bonds in peptidoglycan to eliminate its immunogenicity, thus turning off the immune response. The PGRP family is conserved from insects to man. Short mammalian PGRP variants are synthesized in neutrophils and stored in granules. These PGRPs seem to influence the survival of phagocytosed non-pathogenic bacteria. Long PGRP variants are expressed in the liver and secreted into the bloodstream where their peptidoglycan-degrading activity might serve scavenger functions.
Cataract, Alzheimer??s disease, and other conformational diseases (1998)

Unfolding of proteins was shown to occur in human cataract more than 25 years ago. Recently, the term conformational diseases was applied to a whole group of diseases in which unfolded or misfolded proteins accumulate. In this article, common features in the biochemistry and epidemiology of cataract, Alzheimer's disease, and other conformational diseases are explored.
BlinkFill (2016)

The recent Programming By Example (PBE) techniques such as FlashFill have shown great promise for enabling end-users to perform data transformation tasks using input-output examples. Since examples are inherently an under-specification, there are typically a large number of hypotheses conforming to the examples, and the PBE techniques suffer from scalability issues for finding the intended program amongst the large space. We present a semi-supervised learning technique to significantly reduce this ambiguity by using the logical information present in the input data to guide the synthesis algorithm. We develop a data structure InputDataGraph to succinctly represent a large set of logical patterns that are shared across the input data, and use this graph to efficiently learn substring expressions in a new PBE system B link F ill . We evaluate B link F ill on 207 real-world benchmarks and show that B link F ill is significantly faster (on average 41x) and requires fewer input-output examples (1.27 vs 1.53) to learn the desired transformations in comparison to F lash F ill .