gebhart/patrepeval huggingface dataset:
FAST TCP: Motivation, Architecture, Algorithms, Performance (2006)

We describe FAST TCP, a new TCP congestion control algorithm for high-speed long-latency networks, from design to implementation. We highlight the approach taken by FAST TCP to address the four difficulties which the current TCP implementation has at large windows. We describe the architecture and summarize some of the algorithms implemented in our prototype. We characterize its equilibrium and stability properties. We evaluate it experimentally in terms of throughput, fairness, stability, and responsiveness
The T84 human colonic adenocarcinoma cell line produces mucin in culture and releases it in response to various secretagogues (1990)

The T84 colonic adenocarcinoma cell line, which has been used extensively as a model for studies of epithelial chloride secretion, also produces mucin and secretes it in culture. Electron microscopy of fixed sections of cultured cells, along with Immunogold labelling with an antibody to human small intestine (SI) mucin, revealed the presence of goblet-like cells with mucin-containing secretory granules. The mucin was of high molecular mass, had an amino acid composition similar to that of purified human SI and colonic mucins, and competed effectively with SI mucin for binding to the anti-(SI mucin) antibody. A sensitive solid-phase immunoassay specific for intestinal mucins was developed and used to measure mucin secretion by T84 cells. Cultures were treated for 30 min at 37 degrees C with a number of agents known to cause chloride secretion by T84 cell monolayers and the amount of mucin appearing in the medium was measured. Carbachol (1 mM), A23187 (10 microM), prostaglandin E1 (PGE1) (1 microM) and vasoactive intestinal polypeptide (VIP) (0.1 microM) all stimulated mucin release, but histamine (1 mM) had no effect. Whereas VIP is reported to stimulate chloride secretion more strongly than carbachol, it was less effective than carbachol in stimulating mucin secretion. Phorbol 12-myristate 13-acetate (PMA) (0.1-10 microM) also stimulated mucin release strongly, implicating a responsive protein-kinase C-dependent pathway. Additive secretory responses were obtained with combined stimulation by VIP (10 nM-1 microM) and carbachol (1 mM). Responses to stimulation with A23187 (1-10 microM) together with PMA (10 nM-10 microM) suggest that cytosolic Ca2+ concentration is a modulator of PMA activity.
Spherotoric bag-in-the-lens intraocular lens: Power calculation and predictive misalignment nomogram (2011)

Drs. Gobin and Mathysen have no financial or proprietary interest in any material or method mentioned. Additional disclosures are found in the footnotes.
Respiratory Syncytical Virus–induced Chemokine Expression in the Lower Airways: Eosinophil Recruitment and Degranulation (1999)

Characterization of chemokine expression patterns in virus-infected epithelial cells provides important clues to the pathophysiology of such infections. The aim of this study was to determine the chemokine response pattern of respiratory epithelium when infected with respiratory syncytial virus (RSV). Macrophage inflammatory protein-1-alpha (MIP-1-alpha), interleukin-8 (IL-8), and RANTES concentrations were measured from RSV-infected HEp-2, MRC-5, and WI-38 cell culture supernatants daily following infection. Additionally, MIP-1-alpha, IL-8, and RANTES concentrations were measured from lower respiratory secretions obtained from 10 intubated infants (0-24 mo) with RSV bronchiolitis, and from 10 control subjects. Our results indicate that respiratory epithelial cells respond to RSV infection by producing MIP-1-alpha, IL-8, and RANTES. Production of MIP-1-alpha required ongoing viral replication, whereas RANTES and IL-8 could be elicited by inactivated forms of the virus. MIP-1-alpha, RANTES, and IL-8 were also present in lower airway secretions obtained from patients with RSV bronchiolitis. Eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN), the eosinophil secretory ribonucleases, were detected in lower airway secretions from RSV-infected patients; ECP concentrations correlated with MIP-1-alpha concentrations (r = 0.93). We conclude that MIP-1-alpha is present in the lower airways during severe RSV disease. The correlation between MIP-1-alpha and ECP concentrations suggests a role for eosinophil degranulation products in the pathogenesis of RSV bronchiolitis.
Discovery of Indoline-Based, Natural-Product-like Compounds as Probes of Focal Adhesion Kinase Signaling Pathways (2009)

With the goal of identifying small molecule modulators of protein-protein interactions, we developed a solid-phase synthesis method, which was then successfully utilized in a library generation of 164 aminoindoline-derived, natural-product-like compounds. This library and several other related intermediates synthesized during this project were then subjected to different biological assays in search of small molecule modulators of focal adhesion kinase (FAK)-mediated signaling pathways. This study included (i) an in vitro, full length FAK inhibition assay, (ii) a cell proliferation assay, and (iii) a wound healing assay. In FAK inhibition assay, eight library members (5-12) and three aminoindoline derivatives (13, 14, and 2) were identified as promising candidates. Compounds 13 and 2 inhibited the FAK activity by 25-45% at 10 microM. These two lead compounds also showed activity in a wound healing assay. To our knowledge, these aminoindoline-derived small molecules belong to a new family of FAK inhibitors.
Oxygen vacancy formation characteristics in the bulk and across different surface terminations of La(1−x)SrxFe(1−y)CoyO(3−δ) perovskite oxides for CO2 conversion (2016)

Oxygen vacancy formation energies and CO<sub>2</sub> adsorption strengths on La<sub>0.5</sub>Sr<sub>0.5</sub>BO<sub>3</sub> (B = Fe or Co) type of perovskite oxides.
Nucleotide sequence of theEscherichia coliuridine phosphorylase (udp) gene (1989)

Journal Article Nucleotide sequence of the Escherichia coli uridine phosphorylase (udp) gene Get access Leslie Walton, Leslie Walton Search for other works by this author on: Oxford Academic PubMed Google Scholar Cynthia A. Richards, Cynthia A. Richards 1Experimental Therapy, Burroughs Wellcome Co.Research Triangle Park, NC 27709, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Lynn P. Elwell Lynn P. Elwell Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 16, 25 August 1989, Page 6741, https://doi.org/10.1093/nar/17.16.6741 Published: 25 August 1989 Article history Received: 05 July 1989 Published: 25 August 1989
Histone deacetylase inhibitor suberoylanilide hydroxamic acid reduces acute graft-versus-host disease and preserves graft-versus-leukemia effect (2004)

Acute graft-versus-host disease (GVHD) and leukemic relapse are the two major obstacles to successful outcomes after allogeneic bone marrow transplantation (BMT), an effective therapy for hematological malignancies. Several studies have demonstrated that the dysregulation of proinflammatory cytokines and the loss of gastrointestinal tract integrity contribute to GVHD, whereas the donor cytotoxic responses are critical for graft-versus-leukemia (GVL) preservation. Suberoylanilide hydroxamic acid (SAHA) is currently in clinical trials as an antitumor agent; it inhibits the activity of histone deacetylases and at low doses exhibits antiinflammatory effects by reducing the production of proinflammatory cytokines. Using two well characterized mouse models of BMT, we have studied the effects of SAHA on GVHD severity and GVL activity. Administration of SAHA from day +3 to day +7 after BMT reduced serum levels of the proinflammatory cytokines and decreased intestinal histopathology, clinical severity, and mortality from acute GVHD compared with vehicle-treated animals. However, SAHA had no effect on donor T cell proliferative and cytotoxic responses to host antigens in vivo or in vitro. When mice received lethal doses of tumor cells at the time of BMT, administration of SAHA did not impair GVL activity and resulted in significantly improved leukemia-free survival by using two different tumor and donor/recipient combinations. These findings reveal a critical role for histone deacetylase inhibition in the proinflammatory events contributing to GVHD and suggest that this class of pharmacologic agents may provide a strategy to reduce GVHD while preserving cytotoxic T cell responses to host antigens and maintaining beneficial GVL effects.
Transient Facial Nerve Paralysis (Bell's Palsy) following Intranasal Delivery of a Genetically Detoxified Mutant of Escherichia coli Heat Labile Toxin (2009)

While the unique anatomical predisposition of the facial nerve to compression suggests nasal delivery of neuronal-binding LT-derived adjuvants is inadvisable, their continued investigation as topical or mucosal adjuvants and antigens appears warranted on the basis of longstanding safety via oral, percutaneous, and other mucosal routes.
Chemical structure of the lipid A component of the lipopolysaccharide from a Proteus mirabilis Re‐mutant (1983)

The chemical structure of the lipid A component from the lipopolysaccharide of a Proteus mirabilis Re-mutant (strain R45) was analysed. It consists of a beta(1-6)-linked D-glucosamine disaccharide which carries two phosphate groups, one being ester-linked to position 4' of the nonreducing glucosaminyl residue and the other being bound to the glycosidic hydroxyl group of the reducing glucosaminyl residue. The ester-bound phosphate group is quantitatively substituted by a 4-amino-4-deoxy-L-arabinopyranosyl residue, the glycosidic phosphoryl group appears to be unsubstituted. Two available hydroxyl groups of the disaccharadide (probably at positions 3 and 3') are acylated by approximately 1 mol each of (R)-3-tetradecanoyloxytetradecanoic and (R)-3-hydroxytetradecanoic acid/mol. The amino group of the nonreducing glucosaminyl residue carries (R)-3-tetradecanoyloxytetradecanoic and that of the reducing residue (R)-3-hydroxytetradecanoic acid. In addition smaller amounts of (R)-3-hexadecanoyloxytetradecanoic acid are present in amide linkage. The attachment site of the oligosaccharide portion to lipid A was also investigated. It was found that the hydroxyl group at position 6' of the nonreducing glucosaminyl residue carries 3-deoxy-D-manno-octulosonic acid. This indicates that the saccharide portion in this Proteus lipopolysaccharide is linked to lipid A via the primary hydroxyl group in position 6'.
Local grayvalue invariants for image retrieval (1997)

This paper addresses the problem of retrieving images from large image databases. The method is based on local grayvalue invariants which are computed at automatically detected interest points. A voting algorithm and semilocal constraints make retrieval possible. Indexing allows for efficient retrieval from a database of more than 1,000 images. Experimental results show correct retrieval in the case of partial visibility, similarity transformations, extraneous features, and small perspective deformations.
Differentiation Pathways in Human Embryonic Stem Cell‐Derived Cardiomyocytes (2005)

Human embryonic stem (hES) cells are pluripotent cell lines derived from the inner cell mass of the blastocyst-stage embryo. These unique cell lines can be propagated in the undifferentiated state in culture, while retaining the capacity to differentiate into derivatives of all three germ layers, including cardiomyocytes. The derivation of the hES cell lines presents a powerful tool to explore the early events of cardiac progenitor cell specification and differentiation, and it also provides a novel cell source for the emerging field of cardiovascular regenerative medicine. A spontaneous differentiation system of these stem cells to cardiomyocytes was established and the generated myocytes displayed molecular, structural, and functional properties of early-stage heart cells. In order to follow the in vitro differentiation process, the temporal expression of signaling molecules and transcription factors governing early cardiac differentiation was examined throughout the process. A characteristic pattern was noted recapitulating the normal in vivo cardiac differentiation scheme observed in other model systems. This review discusses the known pathways involved in cardiac specification and the possible factors that may be used to enhance cardiac differentiation of hES cells, as well as the steps required to fully harness the enormous potential of these unique cells.
Expression of bcl-2 mRNA and protein in leukemia-lymphoma cell lines. (1995)

The expression of the proto-oncogene bcl-2 was examined in a panel of 75 continuous human leukemia-lymphoma cell lines originated from different hematopoietic cell types. The presence of the bcl-2 protein, as evidenced by Western blotting, and its mRNA, as determined by Northern blotting, were not restricted to cells with the chromosomal translocation t(14;18)(q32;q21), but were also detected in a large number of cell lines without t(14;18). The amount of the bcl-2 protein and mRNA in the cell lines with t(14;18) was in the same order of magnitude as in other bcl-2 expressing cell lines of the same lineage, but without the translocation. Bcl-2 was found in all types of hematopoietic cell lines which were assigned to the following lineages based on their phenotypical characteristics: pre-B, B, plasma, T, myeloid, monocytic, erythroid-megakaryocytic and Hodgkin's lymphoma derived cell lines. The levels of accumulated mRNA and protein corresponded fairly well in most of the cell lines examined. Our results suggest the notion that bcl-2 expression is widely present in hematopoietic cell lines without restriction to single lineages and, in fact, clearly independent of the chromosomal aberration t(14;18). It is conceivable that bcl-2 expression is a common feature in established hematopoietic cell lines and may contribute to their unlimited growth in vitro.
Theoretical Aspects of LC with Packed and Open Small-Bore Columns (1980)

The performance characteristics of LC in three types of narrow bore columns are compared: (A) small bore packed columns, (B) packed capillary columns, and (C) open tubular columns. The available experimental data confirm that reduced plate height/reduced velocity curves (h, ν curves) for types A and B are similar to those for conventional wide-bore packed columns, that the permeability of type A columns is the same as conventional packed columns, but that type B columns are about three times more permeable. Experimental data for open tubular columns confirm that with 50 μm bore tubes the Golay equation gives a good approximation to actual behaviour. Theoretical analysis indicates that while it is possible to operate type A columns of 10,000 plates upwards under optimum conditions with an injector/detector having an effective volume of 0.1 mm3, there are no practical circumstances under which type B and C columns can be so operated. It is further shown that even though type B columns are three times more permeable than type A columns, it is still not possible with feasible injector/detector systems for them to compete In terms of performance with type A columns. Open tubular columns, on the other hand, because of their 100 times lower separation impedance under optimum conditions, can compete with type A columns if a very large number of plates is required. Foradetector volume of 0.1 mm3 the cross-over occurs at N ∼ 500,000 with a 27.5 μ m bore column 120 m in length and a time for the unretained peak of about 8 hr. Consideration of the optimum ratio of stationary to mobile zone indicates that the wall layer in an open tubular column for LC should be about 25% of the diameter of the bore, giving a stationary to mobile zone ratio of about 55 to 45.
Small Molecule Inhibition of GDC-0449 Refractory Smoothened Mutants and Downstream Mechanisms of Drug Resistance (2010)

Inappropriate Hedgehog (Hh) signaling has been directly linked to medulloblastoma (MB), a common malignant brain tumor in children. GDC-0449 is an Hh pathway inhibitor (HPI) currently under clinical investigation as an anticancer agent. Treatment of a MB patient with GDC-0449 initially regressed tumors, but this individual ultimately relapsed with a D473H resistance mutation in Smoothened (SMO), the molecular target of GDC-0449. To explore the role of the mutated aspartic acid residue in SMO function, we substituted D473 with every amino acid and found that all functional mutants were resistant to GDC-0449, with positively charged residues conferring potential oncogenic properties. Alanine scan mutagenesis of SMO further identified E518 as a novel prospective mutation site for GDC-0449 resistance. To overcome this form of acquired resistance, we screened a panel of chemically diverse HPIs and identified several antagonists with potent in vitro activity against these GDC-0449-resistant SMO mutants. The bis-amide compound 5 was of particular interest, as it was able to inhibit tumor growth mediated by drug resistant SMO in a murine allograft model of MB. However, focal amplifications of the Hh pathway transcription factor Gli2 and the Hh target gene cyclin D1 (Ccnd1) were observed in two additional resistant models, indicating that resistance may also occur downstream of SMO. Importantly, these HPI resistant MB allografts retained their sensitivity to PI3K inhibition, presenting additional opportunities for the treatment of such tumors.
Cyanogenic Glucosides: The Biosynthetic Pathway and the Enzyme System Involved (2007)

In vitro studies with a microsomal system obtained from etiolated sorghum seedlings have indicated a biosynthetic pathway for cyanogenic glucosides involving amino acids, N-hydroxyamino acids, aldoximes, nitriles and cyanohydrins. NADPH is an essential cofactor. Simultaneous measurements of tyrosine metabolism and oxygen consumption show that three molecules of oxygen are consumed for each molecule of p-hydroxymandelonitrile produced. This indicates the operation of three monooxygenases in the pathway and implies the involvement of one hitherto undetected intermediate in the pathway. The nature of this intermediate is unknown. Gel filtration and sucrose gradient centrifugation of the microsomal system resulted in a more than tenfold increase in specific activity. Attempts to further purify the system did not produce preparations of higher specific activity because of a simultaneous partial loss of essential components as demonstrated by reconstitution experiments.
Preoperative Percutaneous Cranial Nerve Mapping in Head and Neck Surgery (2003)

Preoperative percutaneous nerve mapping is a new method of identifying the location of the peripheral branches of the cranial nerves. Identifying and mapping the course of peripheral branches of the cranial nerves safely assists the head and neck surgeon in the placement of incisions in a favorable location and in the dissection of the area involving the nerves. Mapping alerts the surgeon to an area containing a nerve and allows the surgeon to avoid just the specific area where a nerve is present, preventing large-scale abandonment of unmapped areas for fear of potential nerve damage.
The Effects of Gold-Containing Compounds on Pregnant Rabbits and Their Fetuses (1978)

The test compounds were: SK&F 369 14, SK&F D-39 162, and gold sodium thiomalate. Their formulas appear on page 2. New Zealand White rabbits were acclimated and randomly assigned to control and treatment groups. The animals were housed in air-conditioned rooms at 72'F f 2' and 50% f 5% relative humidity. Alternate 12-hour periods of light and darkness were maintained daily. The animals received PurinaB Rabbit Chow@. Drinking water was constantly available. The females were sequentially mated to males of the same stock (2 consecutive matings, approximately 6 hours apart). Day of mating was designated day 0 of pregnancy. SK&F 36914 and SK&F D-39162 were administered to female rabbits by intubation in volumes of 5 ml/kg of body weight from day 6 through 18 of pregnancy. Gold sodium thiomalate was administered to female rabbits of the same stock by subcutaneous injection in volumes of 2 ml/kg of body weight from day 6 through 18 of pregnancy. Control females received equal volumes of the vehicle during the same period. Body weight records were maintained. All females were killed prior to term and Caesarean section was performed. The uterine horns were examined for implantation, resorption, and placement of fetuses. All fetuses were removed, weighed, and examined for external malformations. Approximately one-half of the live fetuses from each litter were placed in an incubator for observation of their 24-hour survival. Thereafter, every third fetus in each litter was futed in Bouin's solution and examined for visceral abnormalities according to the method of Wilson'. The viscera of the remaining fetuses were excised and examined for gross malformations. About 2/3 of the fetuses from each litter were cleared in a KOH solution containing alizarin red S dye and examined for skeletal abnormalities.
Effects of Flow–Pipe Interaction on Drill Pipe Buckling and Dynamics (2005)

A theoretical study has been performed on the buckling and lateral vibration of drillpipe interacted with incompressible fluid in vertical holes. Particular attention is paid to the flow–pipe interaction near drillpipe neutral zone. A new theoretical model has been established. The flow–pipe interaction forces are characterized in this model. Dimensional analysis has been conducted to generalize this model. An innovative numerical method has been developed to solve the eigensystem. Several numerical examples are provided to show the effects of flow–pipe interaction on drillpipe buckling and dynamics. Results show that drilling fluid has significant hydrodynamic influence on drillpipe statics and dynamics.
Crystallization and Precipitation (2003)

Abstract The article contains sections titled: 1. Introduction 2. System Properties 2.1. Solutions and Solubility 2.2. Saturation and Supersaturation 2.3. Crystal Size and Solubility 2.4. Effect of Impurities 3. Phase Equilibria 3.1. One‐Component Systems 3.2. Two‐Component Systems 3.2.1. Eutectics 3.2.2. Solid Solutions 3.2.3. Compound Formation 3.3. Three‐Component Systems 3.4. Multicomponent Systems 3.5. Phase Transformations 4. Kinetics and Mechanisms of Crystallization 4.1. Crystal Nucleation 4.1.1. Primary Nucleation 4.1.2. Secondary Nucleation 4.1.3. Nucleation Measurements 4.1.4. Induction Periods 4.2. Crystal Growth 4.2.1. Measurement of Growth Rate 4.2.2. Expression of Growth Rate 4.2.3. Dependence of Growth Rate on Crystal Size 4.3. Growth ‐ Nucleation Interactions 4.4. Crystal Habit Modification 4.5. Inclusions in Crystals 4.6. Caking of Crystals 5. Crystallization from Solutions 5.1. Cooling Crystallizers 5.1.1. Nonagitated Vessels 5.1.2. Agitated Vessels 5.1.3. Direct‐Contact Cooling 5.2. Evaporating Crystallizers 5.3. Vacuum (Adiabatic Cooling) Crystallizers 5.4. Continuous Crystallizers 5.5. Crystal Yield 5.6. Controlled Crystallization 5.7. Comparison of Batch and Continuous Crystallization 5.8. Crystallizer Modeling and Design 5.8.1. Population Balance 5.8.2. Design and Scaleup Problems 6. Crystallization from Melts 6.1. Single Stage Processes 6.2. Multistage Processes 6.3. Column Crystallizers 6.4. High‐Pressure Crystallization 6.5. Prilling and Granulation 7. Crystallization from Vapors 8. Precipitation 8.1. Solubility Products 8.2. Ostwald's Rule of Stages 8.3. Development of Precipitates 8.3.1. Ripening 8.3.2. Agglomeration 8.3.3. Precipitate Morphology 8.3.4. <jats:styled-con