gebhart/patrepeval huggingface dataset:
An E. coli Ribonucleoprotein Containing 4.5 S RNA Resembles Mammalian Signal Recognition Particle (1990)

The signal recognition particle (SRP) plays a central role in directing the export of nascent proteins from the cytoplasm of mammalian cells. An SRP-dependent translocation machinery in bacteria has not been demonstrated in previous genetic and biochemical studies. Sequence comparisons, however, have identified (i) a gene in Escherichia coli (ffh) whose product is homologous to the 54-kilodalton subunit (SRP54) of SRP, and (ii) an RNA encoded by the ffs gene (4.5S RNA) that shares a conserved domain with the 7SL RNA of SRP. An antiserum to Ffh precipitated 4.5S RNA from E. coli extracts, implying that the two molecules reside in a complex. The 4.5S RNA can also bind to SRP54 and can replace 7SL RNA in an enzymatic assay. The product of a dominant mutation in the ffs gene (4.5S RNAdl1) is also coprecipitated by the antiserum to Ffh protein and is lethal when expressed from an inducible promoter. After induction of 4.5S RNAdl1, the earliest observed phenotype was a permanent induction of the heat shock response, suggesting that there was an accumulation of aberrant proteins in the cytoplasm. Late after induction, translocation of beta-lactamase was impaired; this may be an indirect effect of heat shock, however, because translocation of ribose binding protein or of the porin, OmpA, was unaffected. An unusual separation of the inner and outer membranes, suggestive of a defect in cell envelope, was also observed. Protein synthesis did not cease until very late, an indication that 4.5S RNA probably does not have a direct role in this process.
Helical nonracemic tubular coordination polymer gelators from simple achiral molecules (2008)

A novel class of helical nonracemic tubular coordination polymers, which can immobilize a wide range of solvents at very low concentrations, have been synthesized for the first time in the absence of chiral influences and appended groups.
Bridged polyaromatics: Synthesis and isomorphous properties of polymers and oligomers containing O, S, CH2bridges (1973)

Abstract A study of the isomorphous relationships existing among five crystalline polyaromatic polymers containing O, S, CH 2 bridges, i.e., magnified image where Ph is phenyl, is reported. Appropriate series of oligomers corresponding to these polymers have also been prepared in order to investigate how the solid‐state properties of the oligomers correlate with those of the polymers. A preliminary x‐ray analysis is reported showing that the polymers are actually isostructural.
Patient-controlled analgesia with sufentanil: A comparison of two different methods of administration (1996)

The main advantage of EPCA sufentanil in this postsurgical setting was its ability to provide a more rapid onset of analgesia than traditional i.v. PCA with morphine while offering greater safety than i.v. sufentanil.
Isolation and characterization of the receptor on human neutrophils that mediates cellular adherence. (1987)

The receptor on human neutrophils (polymorphonuclear leukocytes or PMN) that mediates cellular adherence has been purified from the peripheral blood PMN obtained from an individual with chronic myelogenous leukemia (CML). This receptor consists of two noncovalently associated subunits, designated alpha M (Mac-1 alpha, CD11b) (Mr = 170,000) and beta (Mac-1 beta, CDw18) (Mr = 100,000), respectively, which are identical on normal and CML PMN. The subunits were purified by monoclonal antibody 60.1-Sepharose (anti-alpha M) affinity chromatography and separated in 5-nmol quantities by high pressure liquid chromatography on a TSK-4000 gel filtration column. Subunits were characterized by amino acid composition, NH2-terminal amino acid sequence, and carbohydrate content. The NH2-terminal sequence of the human PMN alpha M subunit contains regions of homology with the human platelet glycoprotein IIb alpha. We conclude that nanomole amounts of individual alpha M and beta subunits of the receptor on human PMN that mediates cellular adherence can be isolated and separated using CML PMN.
Digital Microfluidics for Integration of Lab-on-a-Chip Devices (2009)

Digital microfluidics is a new technology that permits manipulation of liquid droplets on an array of electrodes. Using this technology, nanoliter to microliter size droplets of different samples and reagents can be dispensed from reservoirs, moved, split, and merged together. Digital microfluidics is poised to become an important and useful tool for biomedical applications because of its capacity to precisely and automatically carry out sequential chemical reactions. In this thesis, a set of tools is presented to accelerate the integration of digital microfluidics into Lab-on-a-Chip platforms for a wide range of applications.\nAn important contribution in this thesis is the development of three rapid prototyping techniques, including the use of laser printing to pattern flexible printed circuit board (PCB) substrates, to make the technology accessible and less expensive. Using these techniques, both digital and channel microfluidic devices can be produced in less than 30 minutes at a minimal cost. These rapid prototyping techniques led to a new method for manipulating liquid droplets on non-planar surfaces. The method, called All Terrain Droplet Actuation (ATDA), was used for several applications, including DNA enrichment by liquid-liquid extraction. ATDA has great potential for the integration of different physico-chemical environments on Lab-on-a-Chip devices.\nA second important contribution described herein is the development of a new microfluidic format, hybrid microfluidics, which combines digital and channel microfluidics on the same platform. The new hybrid device architecture was used to perform biological sample processing (e.g. enzymatic digestion and fluorescent labeling) followed by electrophoretic separation of the analytes. This new format will facilitate complete automation of Lab-on-a-Chip devices and will eliminate the need for extensive manual sample processing (e.g. pipetting) or expensive robotic stations.\nFinally, numerical modeling of droplet actuation on single-plate digital microfluidic devices, using electrodynamics, was used to evaluate the droplet actuation forces. Modeling results were verified experimentally using an innovative technique that estimates actuation forces based on resistive forces against droplet motion. The results suggested a list of design tips to produce better devices. It is hoped that the work presented in this thesis will help introduce digital microfluidics to many of the existing Lab-on-a-Chip applications and inspire the development of new ones.
Synthesis of benzocarbacephem and benzocarbapenem derivatives by copper-promoted intramolecular aromatic substitution (1987)

Copper-mediated cyclisation of 4-[2-(o-bromophenyl)ethyl] azetidinones and 4-[o-bromophenyl)methyl]azetidinones proved to be a route to benzocarbacephem and benzocarbapenem derivatives respectively. The effect of functionalities present in the alkyl part of the ring to be formed was considered with regard to cyclisation efficiency and further chemical modifications. Conversion, into halide, of the diastereoisomeric mixture (4R,6S; 4S,6R; 4R,6R; and 4S,6S) of t-butyl 2-hydroxybenzocarbacephem-4′-carboxylate (14f) afforded either the chloride (17a) as racemic diastereoisomers or the fluoride (17c) as a single racemic diastereoisomer. The corresponding free carboxylic acids (18a, c) were designed as inactivators of beta-lactamases.
Local Intramural Delivery of l -Arginine Enhances Nitric Oxide Generation and Inhibits Lesion Formation After Balloon Angioplasty (1997)

A single intramural administration of L-arginine enhances vascular NO generation and inhibits lesion formation. Local augmentation of NO production at the site of balloon angioplasty may be a novel strategy to prevent restenosis.
Acid phosphatase polypeptides in Saccharomyces cerevisiae are encoded by a differentially regulated multigene family. (1982)

Two clones from a lambda phage collection containing yeast genes regulated by inorganic phosphate were shown by low-stringency hybridization to select three mRNAs that direct the in vitro synthesis of repressible acid phosphatase (EC 3.1.3.2) polypeptides p60, p58, and p56. By higher stringency hybridization one yeast fragment [8 kilobases (kb)] selects p60 mRNA and the other (5 kb) selects p56 mRNA. These EcoRI digestion fragments were subcloned in yeast transformation vectors and hybridization selection assignments were confirmed by measuring enzyme and mRNA levels in transformants. Enzyme and mRNA levels in (8-kb) high copy number transformants grown in high inorganic phosphate medium revealed a hitherto undetected acid phosphatase protein, P57, which is believed to correspond to the constitutive enzyme encoded by PHO3. The identify of the 8-kb fragment purported to contain the PHO5/PHO3 genes was confirmed by genetic mapping of an integrated copy of this fragment. The site of integration of the 5-kb fragment was demonstrated to be unlinked to the PHO5/PHO3 genes.
Synthesis and glycosylation of the common alpha subunit of human glycoprotein hormones in mouse cells. (1984)

The synthesis and the post-translational modification of the alpha subunit of human glycoprotein hormones have been studied in a mouse cell. A full-length cDNA coding for the human alpha subunit has been expressed in mouse C127 cells under the control of mouse metallothionein regulatory sequences, using a bovine papilloma virus vector. Stable clones secreting the alpha subunit into the medium have been obtained. Two intracellular forms of 22,000 Da and 21,000 Da have been detected. Pulse-chase experiments suggest that the 22,000-Da form is exported, while the 21,000-Da form appears to remain intracellular. The secreted form of the alpha subunit migrates as a broad peak between 22,000 and 30,000 Da, suggesting further modification of the intracellular form prior to secretion. Both the secreted and the intracellular forms incorporate glucosamine label, indicating that at least a portion of the modification observed here is in the form of glycosylation.
Autologous Fibroblasts for Treatment of Facial Rhytids and Dermal Depressions (1999)

Intradermal injection of autologous fibroblasts may be an effective treatment option for facial rhytids and depressed scars.
A Truncated Intracellular HER2/neu Receptor Produced by Alternative RNA Processing Affects Growth of Human Carcinoma Cells (1993)

Cloned sequences encoding a truncated form of the HER2 receptor were obtained from cDNA libraries derived from two HER2-overexpressing human breast cancer cell lines, BT-474 and SK-BR-3. The 5' 2.1 kb of the encoded transcript is identical to that of full-length 4.6-kb HER2 transcript and would be expected to produce a secreted form of HER2 receptor containing only the extracellular ligand binding domain (ECD). The 3' end of the truncated transcript diverges 61 nucleotides before the receptor's transmembrane region, reads through a consensus splice donor site containing an in-frame stop codon, and contains a poly(A) addition site, suggesting that the truncated transcript arises by alternative RNA processing. S1 nuclease protection assays show a 40-fold variation in the abundance of the truncated 2.3-kb transcript relative to full-length 4.6-kb transcript in a panel of eight HER2-expressing tumor cell lines of gastric, ovarian, and breast cancer origin. Expression of this truncated transcript in COS-1 cells produces both secreted and intracellular forms of HER2 ECD; however, immunofluorescent labeling of HER2 ECD protein in MKN7 tumor cells that natively overexpress the 2.3-kb transcript suggests that transcriptionally generated HER2 ECD is concentrated within the perinuclear cytoplasm. Metabolic labeling and endoglycosidase studies suggest that this HER2 ECD (100 kDa) undergoes differential trafficking between the endoplasmic reticulum and Golgi compartments compared with full-length (185-kDa) HER2 receptor. Transfection studies indicate that excess production of HER2 ECD in human tumor cells overexpressing full-length HER2 receptor can result in resistance to the growth-inhibiting effects of anti-HER2 monoclonal antibodies such as muMAb4D5. These findings demonstrate alternative processing of the HER2 transcript and implicate a potentially important growth regulatory role for intracellularly sequestered HER2 ECD in HER2-amplified human tumors.
Comparative stabilities in vitro and in vivo of a recombinant mouse antibody FvCys fragment and a bisFvCys conjugate (1992)

A murine antibody FvCys fragment with a single additional cysteine residue at the C terminus of the VH domain was expressed in Escherichia coli from a modified expression plasmid containing the structural genes for the VH and VL domains derived from the anti-lysozyme hybridoma D1.3. Chemical cross-linking between the introduced sulfhydryl groups of two FvCys fragments by means of bis-maleimidohexane was used to generate a bisFvCys conjugate. The stability of the bisFvCys conjugate and an FvCys analogue that had been reacted with N-ethyl-maleimide to block the free sulfhydryl group, FvCys(BL), were compared after 125I-labeling. The bisFvCys conjugate was completely stable to incubation in solution at 37 degrees C for 24 h whereas only 60% of the FvCys(BL) fragment remained soluble. After i.v. administration to normal Wistar rats, both Fv proteins were rapidly cleared from the circulation with biphasic kinetics that were best fitted to a two-compartment open pharmacokinetic model. The alpha-phase half-life of the bisFvCys conjugate, 0.32 h, was significantly longer than that of the FvCys(BL) fragment, 0.15 h (p less than 0.001) whereas there was no significant difference between the beta-phase half-lives, 1.4 to 1.6h. No chain cleavage or covalent attachment to serum protein was detected by SDS-PAGE analysis of serum samples. However, gel permeation HPLC revealed that both Fv proteins associated with serum proteins in vivo and in vitro.
MACHINERY INVESTMENT DECISIONS: A SIMULATED ANALYSIS FOR CASH GRAIN FARMS (1988)

A combination of experimental and simulation procedures identify important factors in an Illinois cash grain farmer's machinery investment decisions. In an experiment setting, a panel of farmers based investment decisions on their own expectations, farm situations, and varying policy scenarios. In general, the results show investment levels statistically related to the tenure and leverage of operators, the economic conditions they faced, and the age of existing machinery. Alternative public policies of lower commodity price supports, tax reform, and interest rate subsidies influenced the timing of purchases but did not alter total investment amounts.
[Tissue amino acids in patients with colorectal carcinoma]. (1998)

Different catabolic conditions have their special characteristics of intracellular biochemical changes. The objective of the presented work is to assess the concentration of free amino acids in muscles of patients with colorectal carcinoma. In a group of 17 patients the free amino acid level was assessed in tissues and plasma. Material was collected on operation by biopsy of the rectus abdominis muscle, the concentration of different amino acids was assessed by the HPLCV method with fluorescent detection. For statistical evaluation the T-test was used. From the results ensues that in patients with colorectal cancer in plasma statistically significantly lower taurine, glutamine, valine, tyrosine levels were found, intracellularly significantly reduced levels of taurine, glutamic acid, methionine and ornithine were recorded. Significantly elevated intracellular levels of valine, isoleucine, leucine, tyrosine and phenylalanine were found. Assessment of the tissue aminoacidogram is the first step when attempting to influence the intracellular amino acid concentration by defined dietetic preparations.
High genetic variability of the group-specific a-determinant of hepatitis B virus surface antigen (HBsAg) and the corresponding fragment of the viral polymerase in chronic virus carriers lacking detectable HBsAg in serum (2000)

Chronic carriers of hepatitis B virus (HBV) usually show hepatitis B surface antigen (HBsAg) in their sera, which is considered the best marker for acute and chronic HBV infection. In some individuals, however, this antigen cannot be detected by routine serological assays despite the presence of virus in liver and peripheral blood. One reason for this lack of HBsAg might be mutations in the part of the molecule recognized by specific antibodies. To test this hypothesis, the HBV S gene sequences were determined of isolates from 33 virus carriers who were negative for HBsAg but showed antibodies against the virus core (anti-HBc) as the only serological marker of hepatitis B. Isolates from 36 HBsAg-positive patients served as controls. In both groups, a considerable number of novel mutations were found. In isolates from individuals with anti-HBc reactivity only, the variability of the major hydrophilic loop of HBsAg, the main target for neutralizing and diagnostic antibodies, was raised significantly when compared with the residual protein (22·6 vs 9·4 mutations per 1000 amino acids; P &lt;0·001) and with the corresponding region in the controls (22·6 vs 7·5 exchanges per 1000 residues; P &lt;0·001). A similar hypervariable spot was identified in the reverse transcriptase domain of the viral polymerase, encoded by the same nucleotide sequence in an overlapping reading frame. These findings suggest that at least some of the chronic low-level carriers of HBV, where surface antigen is not detected, could be infected by diagnostic escape mutants and/or by variants with impaired replication.
Use of B-Type Natriuretic Peptide in the Evaluation and Management of Acute Dyspnea (2004)

Used in conjunction with other clinical information, rapid measurement of B-type natriuretic peptide in the emergency department improved the evaluation and treatment of patients with acute dyspnea and thereby reduced the time to discharge and the total cost of treatment.
rgf Encodes a Novel Two-Component Signal Transduction System of Streptococcus agalactiae (2002)

The adhesion of gram-positive bacteria to extracellular matrix (ECM) proteins is regarded as an important determinant of pathogenicity. A comparison of the adhesion of Streptococcus agalactiae strain O90R to different ECM proteins showed that the most pronounced binding could be observed for immobilized fibrinogen. To investigate the genetic determinants of S. agalactiae fibrinogen binding, a pGhost9:ISS1 mutant library was screened for mutants displaying reduced agglutination of fibrinogen-coated latex beads. A putative two-component signal transduction system was identified and designated rgfBDAC. It comprises genes encoding a putative response regulator of 218 amino acids and a putative histidine kinase of 426 amino acids. Comparison of the deduced proteins with the GenBank database revealed a significant similarity to quorum-sensing systems of gram-positive pathogens. Transcription analysis of the rgf locus showed that the encoding genes are located on one transcript. To further characterize the influence of the putative histidine kinase encoded in the rgf locus on the adhesion of S. agalactiae to immobilized fibrinogen, a targeted mutant of rgfC was generated. In comparison to the wild-type strain this mutant demonstrated altered fibrinogen binding capacities depending on bacterial cell density. Transcription analysis of secreted and surface-localized S. agalactiae proteins in the wild type and the rgfC mutant strain revealed that mRNA levels of the C5a peptidase gene scpB were increased in the mutant strain while the transcription of the secreted CAMP factor gene cfb was unaffected by this mutation. Based on these results, we hypothesize that rgf regulates the expression of bacterial cell surface components.
Treprostinil for the treatment of pulmonary hypertension (2008)

Treprostinil sodium is a stable prostacyclin analogue, sharing pharmacologic actions similar to epoprostenol with comparable haemodynamic effects. Treprostinil is chemically stable at room temperature and has a long half-life (2 - 4 h), making this drug suitable for subcutaneous administration, with practical benefits in avoiding the risk of line infection and thrombosis, and cardiovascular reactions due to abrupt drug discontinuation.
Goal‐based Caustics (2011)

Abstract We propose a novel system for designing and manufacturing surfaces that produce desired caustic images when illuminated by a light source. Our system is based on a nonnegative image decomposition using a set of possibly overlapping anisotropic Gaussian kernels. We utilize this decomposition to construct an array of continuous surface patches, each of which focuses light onto one of the Gaussian kernels, either through refraction or reflection. We show how to derive the shape of each continuous patch and arrange them by performing a discrete assignment of patches to kernels in the desired caustic. Our decomposition provides for high fidelity reconstruction of natural images using a small collection of patches. We demonstrate our approach on a wide variety of caustic images by manufacturing physical surfaces with a small number of patches.
Information-agnostic flow scheduling for commodity data centers (2015)

Many existing data center network (DCN) flow scheduling schemes minimize flow completion times (FCT) based on prior knowledge of flows and custom switch functions, making them superior in performance but hard to use in practice. By contrast, we seek to minimize FCT with no prior knowledge and existing commodity switch hardware. To this end, we present PIAS1, a DCN flow scheduling mechanism that aims to minimize FCT by mimicking Shortest Job First (SJF) on the premise that flow size is not known a priori. At its heart, PIAS leverages multiple priority queues available in existing commodity switches to implement a Multiple Level Feedback Queue (MLFQ), in which a PIAS flow is gradually demoted from higher-priority queues to lower-priority queues based on the number of bytes it has sent. As a result, short flows are likely to be finished in the first few high-priority queues and thus be prioritized over long flows in general, which enables PIAS to emulate SJF without knowing flow sizes beforehand. We have implemented a PIAS prototype and evaluated PIAS through both testbed experiments and ns- 2 simulations. We show that PIAS is readily deployable with commodity switches and backward compatible with legacy TCP/IP stacks. Our evaluation results show that PIAS significantly outperforms existing information-agnostic schemes. For example, it reduces FCT by up to 50% and 40% over DCTCP [11] and L2DCT [27] respectively; and it only has a 4.9% performance gap to an ideal information-aware scheme, pFabric [13], for short flows under a production DCN workload.