gebhart/patrepeval huggingface dataset:
Asymmetric Baeyer−Villiger Oxidations of 4-Mono- and 4,4-Disubstituted Cyclohexanones by Whole Cells of EngineeredEscherichiacoli (2001)

Whole cells of an Escherichia coli strain that overexpresses Acinetobacter sp. NCIB 9871 cyclohexanone monooxygenase have been used for the Baeyer-Villiger oxidations of a variety of 4-mono- and 4,4-disubstituted cyclohexanones. In cases where comparisons were possible, this new biocatalytic reagent provided lactones with chemical yields and optical purities that were comparable to those obtained from the purified enzyme or a strain of bakers' yeast that expresses the same enzyme. The efficient production of cyclohexanone monooxygenase in the E. coli expression system (ca. 30% of total soluble protein) allowed these oxidations to reach completion in approximately half the time required for the engineered bakers' yeast strain. Surprisingly, 4,4-disubstituted cyclohexanones were also accepted by the enzyme, and the enantioselectivities of these oxidations could be rationalized by considering the conformational energies of bound substrates along with the enzyme's intrinsic enantioselectivity. The enzyme expressed in E. coli cells also oxidized several 4-substituted cyclohexanones bearing polar substituents, often with high enantioselectivities. In the case of 4-iodocyclohexanone, the lactone was obtained in > 98% ee and its absolute configuration was assigned by X-ray crystallography. The crystal belongs to the monoclinic P2(1) space group with a = 5.7400(10), b = 6.1650(10), c = 11.377(2) A, b = 99.98(2) degrees, and Z = 2. Taken together, these results demonstrate the utility of an engineered bacterial strain in delivering useful chiral building blocks in an experimentally simple manner.
The role of Adhesion Molecules in the Pathogenesis of Rheumatoid Arthritis (1993)

Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by infiltration of mononuclear cells, mainly T lymphocytes, into the synovial membrane (SM). The interaction of peripheral blood T cells with the different components of the rheumatoid synovium is mediated by cell surface proteins such as selectins, integrins, members of the immunoglobulin superfamily and homing receptors. T lymphocytes infiltrating the rheumatoid SM show an activated phenotype and display an increased avidity of their adhesion receptors that results in an enhanced interaction of these cells with both extracellular matrix proteins (ECM) and cellular ligands (VCAM-1, ICAMs). The interaction of T cell integrins with their ligands, besides an additional antigenic stimulus, could trigger a mitogenic response on these cells, a phenomenon that can contribute to increased cellularity observed into the rheumatoid SM. Moreover, cell attachment to ECM through integrins induces the secretion of several proteases that can contribute to the tissue damage observed in RA. The increased knowledge about the role of adhesion receptors in the pathogenesis of RA and other inflammatory diseases will allow the introduction of a new therapeutic approach by: the use of specific blocking reagents designed to interfere with the function of adhesion molecules.
Quantified flow characteristics in a model cardiac assist device (1997)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1997.
HHV‐8 subtypes in South Africa: Identification of a case suggesting a novel B variant (2001)

Human herpesvirus 8 (HHV-8) has been identified as the causative agent for all forms of Kaposi's sarcoma and is also associated with the development of body cavity-based B-cell lymphomas and multicentric Castleman's disease. HHV-8 genomes are now classified into five major subtypes (A-E) that reflect sequence heterogeneity in the highly variable open reading frame (ORF) K1. To identify HHV-8 subtypes associated with different forms of Kaposi's sarcoma, we compared the ORF 26 and ORF-K1 gene sequences from South African patients with the prototype strains of the major subtypes, as well as published sequences from other African strains. DNA prepared from Kaposi's sarcoma biopsies and/or peripheral blood lymphocytes were available from 14 patients with postrenal transplant (iatrogenic) Kaposi's sarcoma, six patients with the African endemic form, and one patient with AIDS-related body cavity-based B-cell lymphoma. We identified a B2 subtype in six patients, four of whom also had a novel B5 type ORF 26 polymorphism. Two patients had B2 type patterns for both the ORF 26 and ORF-K1 genes. The ORF-K1 subtype A5 was identified in samples from three patients with a B3/C2 type polymorphism in the ORF 26 gene. A novel ORF-K1 B variant strain was identified in a patient with African endemic Kaposi's sarcoma, who also had a B3/C2 class ORF 26 pattern. In 58.3% of iatrogenic Kaposi's sarcoma patients, a B5-type ORF 26 gene sequence pattern was identified. No association was found among particular subtypes, geographical origin of patients, or clinical presentation.
Unconventional nucleotide analogues. Part X. Synthesis of N-substituted 3-(adenin-9-yl)pyrrolidin-2-ones (1973)

3-(Adenin-9-yl)-N-2-hydroxyethylpyrrolidin-2-one (1) was synthesized by constructing the purine base on the amino-group of 3-amino-N-2-hydroxyethylpyrrolidin-2-one (3), itself obtained from 2-dibenzylaminobutyro-lactone by aminolysis, followed by chlorination of the product and recyclization. Attempts to obtain compound (3) from acylated 2-aminobutyrolactones (4a and b) led to side reactions, the mechanisms of which are discussed. 3-(6-Chloropurin-9-yl)-N-2-hydroxyethylpyrrolidin-2-one (18b) was converted into the AMP analogue (2) by a phosphorylation–amination–debenzylation sequence, lodination of compound (1), followed by dehydrohalogen-ation of the product led to the N-vinyl derivative (21 ), a monomer for a poly-A model.
A Double-blind Clinical Trial in Weight Control (1984)

We performed a double-blind, controlled clinical trial comparing phentermine resin (30 mg in the morning), fenfluramine hydrochloride (20 mg three times a day), and a combination of phentermine resin (15 mg in the morning) and fenfluramine hydrochloride (30 mg before the evening meal), and placebo. We combined low doses of the two drugs to maintain efficacy while diminishing adverse effects. Eighty-one people with simple obesity (130% to 180% of ideal body weight) participated. Individualized diets were prescribed and discussed again during the 24-week study period. Weight loss in those receiving the combination (8.4 +/- 1.1 kg; mean +/- SEM) was significantly greater than in those receiving placebo (4.4 +/- 0.9 kg; Scheff é's test) and equivalent to that of those receiving fenfluramine (7.5 +/- 1.2 kg) or phentermine (10.0 +/- 1.2 kg) alone. Adverse effects were less frequent with the combination regimen than with other active treatments. Thirty-seven participants dropped out of the study, 18 for reasons related to drug treatment. Combining fenfluramine and phentermine capitalized on their pharmacodynamic differences, resulting in equivalent weight loss, fewer adverse effects, and better appetite control.
Mir_Eval: A Transparent Implementation Of Common Mir Metrics. (2014)

[TODO] Add abstract here.
Techniques for Evaluating Insect Resistance in Crop Plants (1994)

Introduction. Evaluation of Plants for Insect Resistance. Techniques to Determine Categories of Plant Resistance. Techniques and Methods to Evaluate the Allelochemical Bases of Insect Resistance. Evaluation of the Morphological Bases of Insect Resistance. Techniques for Identifying Insect Biotypes. Use of Tissue Culture and Artificial Diets for Evaluating Insect Resistance. Index.
THE ROUTE OF ENTERIC INFECTION IN NORMAL MICE (1974)

This study followed the early pathogenesis of orally induced murine typhoid fever. Intragastrically administered Salmonella enteritidis moves quickly through the normal undisturbed gut so that only a small residuum remains in the cecum and large intestine after the first few hours. Dye injection of the gut wall was used to show that lymph from discrete portions of the gastrointestinal tract drains to separate lymph nodes, probably via the regional Peyer's patches. Plating techniques capable of detecting a single colony-forming unit of S. enteritidis within the different Peyer's patches and draining lymph nodes indicate that, although the cecum and large intestine are exposed to large numbers of Salmonella for longer time periods than the small intestine, the primary site of bacterial penetration involves the distal ileum. This area of the small intestine as well as the cecum are both drained by the distal mesenteric lymph nodes, and were the only nodes which contained detectable numbers of viable Salmonella over the first 24 h of infection. Neither the pyloric nor the proximal mesenteric lymph nodes (which drain the stomach and duodenum) nor the pancreatic and caudal lymph nodes (which drain the transverse and descending colon) contained viable Salmonella. Salmonella were observed to infect the ileal mucosa and its Peyer's patches. With time, this infection progresses to the draining lymph node and ultimately reaches the liver and spleen. Some of the implications of these findings relative to the development of acquired resistance to enteric disease are discussed.
Effect of Temperature on a Complementary  WO 3 ‐ Prussian Blue Electrochromic System (1992)

An electrochromic device consisting of a cathodically coloring tungsten trioxide film and an anodically coloring Prussian blue (PB) film may find use in automotive "smart windows." These windows have prospects for reduction of solar heat load on air conditioning systems and privacy applications in automobiles. Such windows must have good stability at elevated temperatures. The thermal stability and electrochromic switching performance of a complementary device is reported over the temperature range of 25 to 80°C. The device showed good thermal stability up to 80°C. Electrochromic switching was found to be faster at elevated temperatures.
Universal Mobility-Field Curves for Electrons and Holes in MOS Inversion Layers (1987)

The mobility of carriers in a silicon surface inversion layer is one of the most important parameters required to accurately model and predict MOSFET device and circuit performance. It has been found that electron mobility follows a universal curve when plotted as a function of an effective normal field regardless of substrate bias, substrate doping (≤ 1017 cm−3) and nominal process variations [1]. Although accurate modeling of p-channel MOS devices has become important due to the prevalence of CMOS technology, the existence of a universal hole mobility-field relationship has not been demonstrated. Furthermore, the effect on mobility of low-temperature and rapid high-temperature processing, which are commonly used in modern VLSI technology to control impurity diffusion, is unknown.
The protection of information in computer systems (1975)

This tutorial paper explores the mechanics of protecting computer-stored information from unauthorized use or modification. It concentrates on those architectural structures-whether hardware or software-that are necessary to support information protection. The paper develops in three main sections. Section I describes desired functions, design principles, and examples of elementary protection and authentication mechanisms. Any reader familiar with computers should find the first section to be reasonably accessible. Section II requires some familiarity with descriptor-based computer architecture. It examines in depth the principles of modern protection architectures and the relation between capability systems and access control list systems, and ends with a brief analysts of protected subsystems and protected objects. The reader who is dismayed by either the prerequisites or the level of detail in the second section may wish to skip to Section III, which reviews the state of the art and current research projects and provides suggestions for further reading.
Food Composition Table for Retort-packaged Baby Foods (2008)

A food composition table was prepared for estimating the dietary composition of retort-packaged baby food to use in surveys on the dietary intake of infants. The food composition table was based on estimates by several registered dietitians of the ingredients and weight of food in retort-packaged baby food according to product photographs and the nutritional facts label on the packages. The data were prepared from 124 baby food products with high market share according to a point of sale database. The estimated weights of ingredients per 100g of baby food were 16-26g of rice or noodles, 6-9g of meat, fish, or hen's egg, and 19-32g of vegetables. These weights were less than those empirically recognized by the dietitians. This suggests that dietitians tend to over-estimate the weights of protein foods and vegetables which are the main ingredients in baby food. The estimated food composition of retort-pack-aged baby food was statistically classified into six types to provide a standardized tool for surveying the energy and 42 nutrients in infant food.
BAFF is involved in macrophage-induced bortezomib resistance in myeloma (2017)

We aimed to characterize the role of B-cell activating factor (BAFF) in macrophage-mediated resistance of multiple myeloma (MM) cells to bortezomib (bort), and to further understand the molecular mechanisms involved in the process. First, we detected BAFF and its three receptors on myeloma cells and macrophages using the quantitative reverse transcriptase-polymerase chain reaction and flow cytometry. The secretion of BAFF was tested in patients with MM, MM cell lines, and macrophages. The ability of macrophages to protect MM cells from bort-induced apoptosis was significantly attenuated using BAFF-neutralizing antibody in the co-culture system or knocking down the expression of BAFF in macrophages with small interfering RNA. We also showed that the MM-macrophage interaction through BAFF and its receptors was primarily mediated by the activation of Src, Erk1/2, Akt, and nuclear factor kappa B signaling and the suppression of caspase activation induced by bort. Our data demonstrated that BAFF played a functional role in the macrophage-mediated resistance of MM cells to bort, suggesting that targeting BAFF may provide a basis for the molecular- and immune-targeted therapeutic approach.
Device mismatch and tradeoffs in the design of analog circuits (2005)

Random device mismatch plays an important role in the design of accurate analog circuits. Models for the matching of MOS and bipolar devices from open literature show that matching improves with increasing device area. As a result, accuracy requirements impose a minimal device area and this paper explores the impact of this constraint on the performance of general analog circuits. It results in a fixed bandwidth-accuracy-power tradeoff which is set by technology constants. This tradeoff is independent of bias point for bipolar circuits whereas for MOS circuits some bias point optimizations are possible. The performance limitations imposed by matching are compared to the limits imposed by thermal noise. For MOS circuits the power constraints due to matching are several orders of magnitude higher than for thermal noise. For the bipolar case the constraints due to noise and matching are of comparable order of magnitude. The impact of technology scaling on the conclusions of this work are briefly explored.
Control of Staphylococcal Adhesion to Polymethylmethacrylate and Enhancement of Susceptibility to Antibiotics by Poloxamer 407 (2000)

We studied the antiadhesive effect of Poloxamer 407 (P407), together with modifications in the antimicrobial susceptibility of residual adherent staphylococci. Bacterial adherence was markedly inhibited (77% to more than 99.9%) whether polymethylmethacrylate was exposed to P407 before or during the adherence assay. Furthermore, residual adherent staphylococci appeared to be more susceptible to antibiotic activity, suggesting that combination of P407 with antibiotics could be a promising approach to the prevention of infection of foreign material.
Bayesian representation learning with oracle constraints (2015)

Representation learning systems typically rely on massive amounts of labeled data in order to be trained to high accuracy. Recently, high-dimensional parametric models like neural networks have succeeded in building rich representations using either compressive, reconstructive or supervised criteria. However, the semantic structure inherent in observations is oftentimes lost in the process. Human perception excels at understanding semantics but cannot always be expressed in terms of labels. Thus, \emph{oracles} or \emph{human-in-the-loop systems}, for example crowdsourcing, are often employed to generate similarity constraints using an implicit similarity function encoded in human perception. In this work we propose to combine \emph{generative unsupervised feature learning} with a \emph{probabilistic treatment of oracle information like triplets} in order to transfer implicit privileged oracle knowledge into explicit nonlinear Bayesian latent factor models of the observations. We use a fast variational algorithm to learn the joint model and demonstrate applicability to a well-known image dataset. We show how implicit triplet information can provide rich information to learn representations that outperform previous metric learning approaches as well as generative models without this side-information in a variety of predictive tasks. In addition, we illustrate that the proposed approach compartmentalizes the latent spaces semantically which allows interpretation of the latent variables.
Muscle-tendon interaction and elastic energy usage in human walking (2005)

The present study was designed to explore how the interaction between the fascicles and tendinous tissues is involved in storage and utilization of elastic energy during human walking. Eight male subjects walked with a natural cadence (1.4 +/- 0.1 m/s) on a 10-m-long force plate system. In vivo techniques were employed to record the Achilles tendon force and to scan real-time fascicle lengths for two muscles (medial gastrocnemius and soleus). The results showed that tendinous tissues of both medial gastrocnemius and soleus muscles lengthened slowly throughout the single-stance phase and then recoiled rapidly close to the end of the ground contact. However, the fascicle length changes demonstrated different patterns and amplitudes between two muscles. The medial gastrocnemius fascicles were stretched during the early single-stance phase and then remained isometrically during the late-stance phase. In contrast, the soleus fascicles were lengthened until the end of the single-stance phase. These findings suggest that the elastic recoil takes place not as a spring-like bouncing but as a catapult action in natural human walking. The interaction between the muscle fascicles and tendinous tissues plays an important role in the process of release of elastic energy, although the leg muscles, which are commonly accepted as synergists, do not have similar mechanical behavior of fascicles in this catapult action.
Regulation of phosphatidylserine synthase from Saccharomyces cerevisiae by phospholipid precursors (1986)

The addition of ethanolamine or choline to inositol-containing growth medium of Saccharomyces cerevisiae wild-type cells resulted in a reduction of membrane-associated phosphatidylserine synthase (CDPdiacylglycerol:L-serine O-phosphatidyltransferase, EC 2.7.8.8) activity in cell extracts. The reduction of activity did not occur when inositol was absent from the growth medium. Under the growth conditions where a reduction of enzyme activity occurred, there was a corresponding qualitative reduction of enzyme subunit as determined by immunoblotting with antiserum raised against purified phosphatidylserine synthase. Water-soluble phospholipid precursors did not effect purified phosphatidylserine synthase activity. Phosphatidylserine synthase (activity and enzyme subunit) was not regulated by the availability of water-soluble phospholipid precursors in S. cerevisiae VAL2C(YEp CHO1) and the opi1 mutant. VAL2C(YEp CHO1) is a plasmid-bearing strain that over produces phosphatidylserine synthase activity, and the opi1 mutant is an inositol biosynthesis regulatory mutant. The results of this study suggest that the regulation of phosphatidylserine synthase by the availability of phospholipid precursors occurs at the level of enzyme formation and not at the enzyme activity level. Furthermore, the regulation of phosphatidylserine synthase is coupled to inositol synthesis.
Diverse Amino Acid Residues Function within the Type 1 Peroxisomal Targeting Signal (Implications for the Role of Accessory Residues Upstream of the Type 1 Peroxisomal Targeting Signal) (1997)

The purpose of this study was to determine whether the plant type 1 peroxisomal targeting signal (PTS1) utilizes amino acid residues that do not strictly adhere to the serine-lysine-leucine (SKL) motif (small-basic-hydrophobic residues). Selected residues were appended to the C terminus of chloramphenicol acetyltransferase (CAT) and were tested for their ability to target CAT fusion proteins to glyoxysomes in tobacco (Nicotiana tabacum L.) cv Bright Yellow 2 suspension-cultured cells. CAT was redirected from the cytosol into glyoxysomes by a wide range of residues, i.e. A/C/G/S/T-H/K/ L/N/R-I/L/M/Y. Although L and N at the -2 position (-SLL, -ANL) do not conform to the SKL motif, both functioned, but in a temporally less-efficient manner. Other SKL divergent residues, however, did not target CAT to glyoxysomes, i.e. F or P at the -3 position (-FKL, -PKL), S or T at the -2 position (-SSI, STL), or D at the -1 position (-SKD). The targeting inefficiency of CAT-ANL could be ameliorated when K was included at the -4 position (-KANL). In summary, the plant PTS1 mostly conforms to the SKL motif. For those PTS1s that possess nonconforming residue(s), other residues upstream of the PTS1 appear to function as accessory sequences that enhance the temporal efficiency of peroxisomal targeting.
Industry-Community-Regulator Consultation in Improving Environmental Performance in Victoria (2001)

Company Environment Improvement Plans created under Victoria's Environment Protection Act often involve the formation of ongoing Community Liaison Committees (CLCs) at industrial sites. Industry, community and Environment Protection Authority (EPA) CLC participants were interviewed to assess the value of local community participation in environmental protection decisions. Almost all respondents reported that the benefits of consultation exceeded its costs. Each group was better informed due to consultation: industry participants reported knowing more about community beliefs and the identities of those affected by pollution; community participants, about plant operations and firms' behaviour, and EPA staff, about community beliefs and firms' abilities to and costs of reducing emissions. Judging by the opinions of those directly involved, local community consultation can be a valuable additional instrument for local environmental protection because, with consultation, each of the parties is better informed about and more understanding of the concerns and problems of the others.