gebhart/patrepeval huggingface dataset:
MIPS: a database for genomes and protein sequences (2000)

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried near Munich, Germany, develops and maintains genome oriented databases. It is commonplace that the amount of sequence data available increases rapidly, but not the capacity of qualified manual annotation at the sequence databases. Therefore, our strategy aims to cope with the data stream by the comprehensive application of analysis tools to sequences of complete genomes, the systematic classification of protein sequences and the active support of sequence analysis and functional genomics projects. This report describes the systematic and up-to-date analysis of genomes (PEDANT), a comprehensive database of the yeast genome (MYGD), a database reflecting the progress in sequencing the Arabidopsis thaliana genome (MATD), the database of assembled, annotated human EST clusters (MEST), and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). MIPS provides access through its WWW server (http://www.mips.biochem.mpg.de) to a spectrum of generic databases, including the above mentioned as well as a database of protein families (PROTFAM), the MITOP database, and the all-against-all FASTA database.
A New Softmax Operator for Reinforcement Learning. (2016)

A softmax operator applied to a set of values acts somewhat like the
maximization function and somewhat like an average. In sequential decision
making, softmax is often used in settings where it is necessary to maximize
utility but also to hedge against problems that arise from putting all of one's
weight behind a single maximum utility decision. The Boltzmann softmax operator
is the most commonly used softmax operator in this setting, but we show that
this operator is prone to misbehavior. In this work, we study an alternative
softmax operator that, among other properties, is both a non-expansion
(ensuring convergent behavior in learning and planning) and differentiable
(making it possible to improve decisions via gradient descent methods). We
provide proofs of these properties and present empirical comparisons between
various softmax operators.
Influence of silicone surface roughness and hydrophobicity on adhesion and colonization of <i>Staphylococcus epidermidis</i> (2008)

Bacterial adhesion and colonization are complicated processes that depend on many factors, including surface chemistry, hydrophobicity, and surface roughness. The contribution of each of these factors has not been fully elucidated because most previous studies used different polymeric surfaces to achieve differences in properties. The objective of this study was to modify hydrophobicity and roughness on one polymeric surface, eliminating the confounding contribution of surface chemistry. Mechanically assembled monolayer (MAM) preparation methods (both one- and two-dimensional) were used to impart different degrees of hydrophobicity on fluoroalkylsilane (FAS)-coated silicone. Surface roughness was varied by casting the silicone to templates prepared with different abrasives. Surface hydrophobicity was determined by contact angle measurement, whereas surface roughness was determined by scanning electron microscopy (SEM) and atomic force microscopy (AFM). Bacterial adhesion and colonization were analyzed using a direct colony-counting method and SEM images. Hydrophobicity increased as a function of stretched length or width (Deltax or Deltay); it reached a maximum at Deltax = 60% with one-dimensional MAM and decreased as Deltax further increased to 80 and 100%. The same trend was observed for the two-dimensional MAM. After 12-h incubation, all the FAS/silicone surfaces had significantly reduced adherence of Staphylococcus epidermidis by 42-89%, compared to untreated silicone, and the degree of which is inversely related to surface hydrophobicity. On the other hand, surface roughness had a significant effect on bacterial adhesion and colonization only when the root-mean-square roughness was higher than 200 nm.
Helicopter optimal descent and landing after power loss (1977)

An optimal control solution is obtained for the descent and landing of a helicopter after the loss of power in level flight. The model considers the helicopter vertical velocity, horizontal velocity, and rotor speed; and it includes representations of ground effect, rotor inflow time lag, pilot reaction time, rotor stall, and the induced velocity curve in the vortex ring state. The control (rotor thrust magnitude and direction) required to minimize the vertical and horizontal velocity at contact with the ground is obtained using nonlinear optimal control theory. It is found that the optimal descent after power loss in hover is a purely vertical flight path. Good correlation, even quantitatively, is found between the calculations and (non-optimal) flight test results.
Selective Inhibition of Trypsin by (2R,4R)-4-Phenyl-1-[N α-(7- methoxy-2-naphthalenesulfonyl)-l-arginyl]-2-piperidinecarboxylic Acid (2000)

Evidence is accumulating indicating that trypsin stimulates divergent cellular reactions through the proteinase-activated receptor, in addition to its role as the digestive enzyme. In this report, we introduce (2R,4R)- 4-phenyl-1-[N(alpha)-(7-methoxy-2-naphthalenesulfonyl)-l-arginyl]- 2-p iperidinecarboxylic acid as a potent and selective trypsin inhibitor. The agent inhibited trypsin competitively with the K(i) value of 0. 1 micrometer. It inhibited thrombin weakly (K(i) = 2 micrometer) and did not inhibit plasmin, plasma kallikrein, urokinase, and mast cell tryptase (K(i) values for these enzymes are >60 micrometer). Comparative studies with several established proteinase inhibitors revealed that the compound was the first small molecular weight trypsin inhibitor without tryptase inhibitory activity. A docking study has provided a plausible explanation for the molecular mechanism of the selective inhibition showing that the agent fits into the active site of trypsin without any severe collision but that it comes into clash at the 4-phenyl group of piperidine ring against the "60-insertion loop" of thrombin and at the 7-methoxy-2-naphthalenesulfonyl group against Gln(98) of tryptase.
GM-CSF Production by Glioblastoma Cells Has a Functional Role in Eosinophil Survival, Activation, and Growth Factor Production for Enhanced Tumor Cell Proliferation (2011)

Medicinal interventions of limited efficacy are currently available for the treatment of glioblastoma multiforme (GBM), the most common and lethal primary brain tumor in adults. The eosinophil is a pivotal immune cell in the pathobiology of atopic disease that is also found to accumulate in certain tumor tissues. Inverse associations between atopy and GBM risk suggest that the eosinophil may play a functional role in certain tumor immune responses. To assess the potential interactions between eosinophils and GBM, we cultured human primary blood eosinophils with two separate human GBM-derived cell lines (A172, U87-MG) or conditioned media generated in the presence or absence of TNF-α. Results demonstrated differential eosinophil adhesion and increased survival in response to coculture with GBM cell lines. Eosinophil responses to GBM cell line-conditioned media included increased survival, activation, CD11b expression, and S100A9 release. Addition of GM-CSF neutralizing Abs to GBM cell cultures or conditioned media reduced eosinophil adhesion, survival, and activation, linking tumor cell-derived GM-CSF to the functions of eosinophils in the tumor microenvironment. Dexamethasone, which has been reported to inhibit eosinophil recruitment and shrink GBM lesions on contrast-enhanced scans, reduced the production of tumor cell-derived GM-CSF. Furthermore, culture of GBM cells in eosinophil-conditioned media increased tumor cell viability, and generation of eosinophil-conditioned media in the presence of GM-CSF enhanced the effect. These data support the idea of a paracrine loop between GM-CSF-producing tumors and eosinophil-derived growth factors in tumor promotion/progression.
Compressing relations and indexes (2002)

We propose a new compression algorithm that is tailored to database applications. It can be applied to a collection of records, and is especially effective for records with many low to medium cardinality fields and numeric fields. In addition, this new technique supports very fast decompression. Promising application domains include decision support systems (DSS), since fact tables, which are by far the largest tables in these applications, contain many low and medium cardinality fields and typically no text fields. Further, our decompression rates are faster than typical disk throughputs for sequential scans; in contrast, gzip is slower. This is important in DSS applications, which often scan large ranges of records. An important distinguishing characteristic of our algorithm, in contrast to compression algorithms proposed earlier, is that we can decompress individual tuples (even individual fields), rather than a full page (or an entire relation) at a time. Also, all the information needed for tuple decompression resides on the same page with the tuple. This means that a page can be stored in the buffer pool and used in compressed form, simplifying the job of the buffer manager and improving memory utilization. Our compression algorithm also improves index structures such as B-trees and R-trees significantly by reducing the number of leaf pages and compressing index entries, which greatly increases the fan-out. We can also use lossy compression on the internal nodes of an index.
Han et al 2018 Cell Reports (2018)

The data are the original, uncropped western blots in the paper entitiled "FXR Inhibits Endoplasmic Reticulum Stress-Induced NLRP3 Inflammasome in Hepatocytes and Ameliorates Liver Injury".
Expression, regulation and clinical significance of soluble and membrane CD14 receptors in pediatric inflammatory lung diseases (2010)

This study demonstrates for the first time the expression, regulation and clinical significance of soluble and membrane CD14 receptors in pediatric inflammatory lung diseases and suggests sCD14 as potential marker for pneumonia in children.
Automatic shimming for localized spectroscopy (1988)

Localized in vivo nuclear magnetic resonance studies often require a high spectral resolution not achievable with the basic shim of a whole-body magnetic resonance magnet. Therefore, the magnetic field homogeneity needs to be optimized in the selected volume of interest within a reasonable time. For this purpose, a method of automatic shimming was developed and tested on phantoms and volunteers. The volume selection is performed by means of a surface coil or by using a localization method which generates a stimulated echo from the volume of interest. The optimization procedure uses the time integral over the magnitude of the free induction decay or echo signal as homogeneity criterion. A complete shimming process generally requires only 80 transients. Test experiments were conducted on various volume sizes ranging from 2 X 2 X 2 cm3 to 15 X 15 X 15 cm3 inside a large phantom. The resulting linewidth in small volumes at the magnet center compared well with the natural linewidth determined by means of the Carr-Purcell-Meiboom-Gill sequence. As expected, shimming in selected volumes at off center positions led to somewhat broader lines. Results obtained on volunteers demonstrate the practical value of this rapid, automatic shimming method for in vivo studies.
EGF cell surface receptor quantitation on ocular cells by an immunocytochemical flow cytometry technique. (1992)

A method is presented for the rapid flow cytometric determination of epidermal growth factor (EGF) receptor densities on the surface of cultured ocular cells. The technique uses a biotinylated monoclonal antibody directed against the EGF receptor in conjunction with a streptavidin-bound fluorochrome and requires the specific fluorescence per cell to be measured as a function of ligand and receptor concentration. Because the measurement is noninvasive and restricted to cell surface-bound material, the cells can be kept in a physiologic environment, even at the moment of assay. Calculated receptor densities ranged from 5142/cell (infant human corneal endothelium) to 35,678/cell (infant human keratocytes) to greater than 5 x 10(5)/cell for an A431 control cell line. Species and donor age differences were noted, as was transient receptor downregulation after EGF administration. Flow cytometry represents a valuable time saving procedure for large scale applications while providing the same level of sensitivity as standard radioimmunoassays. This technique is applicable to quantitation of other growth factor cell surface receptors and could greatly expand the use of flow cytometry in the research laboratory.
A High Speed Schottky 4 k-Bit PROM Using Diffused Eutectic Aluminum Process (Deap) (1980)

To achieve higher packing density for larger integration, various undesirable parasitic effects which degrade performance of each element must be primarily taken into account. This paper will describe a high speed 4096 bit bipolar shorted-junction type Schottky TTL PROM fabricated by the use of passive isolation techniques named “Shallow V Groove” (SVG) and “Isolation by Oxide and Polysilicon” (IOP). These two techniques have suppressed the undesirable parasitic effects and accomplished drastic improvement especially in both of cell size and speed by the factor of 1/2 and 2, respectively, as compared to those of our current gold doped device.
Adventures in group theory: Rubik's Cube, Merlin's machine, and other mathematical toys (2003)

Group theory deals with symmetry, in the most abstract form possible. It is a core part of the undergraduate math curriculum, and forms part of the training of theoretical physicists and chemical crystallographers. In this book, David Joyner uses mathematical toys (primarily the Rubik's Cube and its more modern cousins, the Megaminx, the Pyraminx, and so on) as well as other mathematical examples (for example, bell-ringing) to breathe new life into a time-honoured, and usually dry, subject. Why, asks the author, two such different topics, mechanical puzzles and abstract group theory, be related? This book takes the reader on an intellectual trip to answer this curiosity. The book should not only appeal to maths enthusiasts and interested general readers but should also find use in the classroom as a supplementary text in any abstract algebra or group theory course.
Cone beam volumetric tomography vs. medical CT scanners. (2005)

This article describes the benefits and dental applications of a three-dimensional imaging technique known as cone beam volumetric tomography (CBVT). When compared to conventional medical CT scanners, CBVT is more accurate, requires less radiation, captures the maxilla and mandible in a single rotation of the X-ray source, and is cost-effective for patients. Here we describe the dental applications of CBVT and its advantages when placing dental implants.
TIME RESOLVED IMAGE MICROSCOPY (1992)

Time Resolved Image Microscopy" integrates temporally resolved dynamic properties with the spatial resolution of the light microscope.Fast kinetic and luminescence decay parameters are measured simultaneously at every pixel of a CCD image.We are developing time resolved methods that can be applied conveniently and routinely to biological material in the microscope over a large time domain.In addition to the augmented purely spectroscopic and reaction kinetic information, simultaneous spatial and temporal resolution of an image in a microscope provides significant improvement in image contrast, probe identification and differentiation.For instance, the ability to separate phosphorescence and prompt fluorescence furnishes a new parameter, the ratio of delayed to prompt luminescence at every pixel of the picture, emphasizing particular objects.The time resolution makes it possible to recover structures in an image that are concealed by faster decaying intense luminescence.Examples of these procedures for both delayed luminescence and prompt fluorescence will be given, and the instrumentation required for data acquisition and analysis will be discussed.A normal fluorescence microscope is used; phase-locked coordination between the modulation and image recording is used.
Adjuvant‐induced inflammation of rat paw is associated with altered calcitonin gene‐related peptide immunoreactivity within cell bodies and peripheral endings of primary afferent neurons (1994)

Local inflammation is associated with profound changes in the biochemistry and physiology of primary afferent nerve fibers and the central neurons responding to their signals. In some tissues, the neural changes accompanying inflammation include sprouting and cytochemical changes that are delayed several days after the initial injury. In the present study, we have analyzed the effect of complete Freund's adjuvant (CFA)-induced inflammation in the rat paw on calcitonin gene-related peptide (CGRP) immunoreactivity (IR) in dorsal root ganglia and within tissue of the inflamed paw. We quantified the CGRP-IR within the L1, L4, and L6 ganglia, and in ankle, midpaw, joint and toe tissues. Analysis of the processed tissue revealed a significant increase in the percentage of CGRP-positive cells within L4 dorsal root ganglia ipsilateral to an inflamed hindpaw six days after administration of CFA. There was a parallel increase in the number and staining density of detectable CGRP-immunoreactive fibers in periarticular and perivascular tissues of the inflamed digits and inflamed ankle. The other tissues of the paw, including epidermis and the regions surrounding the abcesses, did not have detectable changes in CGRP-immunoreactive fibers, despite tissue swelling and dystrophic changes in the foot that included loss of mast cell staining. These data demonstrate that local inflammation of the rat paw has delayed influences on the peripheral nervous system, in addition to a number of previously characterized acute effects. The alterations of CGRP-IR were focused around specific tissue types, such as joints and subdermal blood vessels, and absent from others, such as epidermis or in the areas surrounding abscesses. This suggests production of local factors within reactive tissues that selectively interact with nerve fibers to induce changes in CGRP-IR within the fibers.
Codon Optimization of<i>Candida rugosa lip</i>1 Gene for Improving Expression in<i>Pichia pastoris</i>and Biochemical Characterization of the Purified Recombinant LIP1 Lipase (2006)

An important industrial enzyme, Candida rugosa lipase (CRL) possesses several different isoforms encoded by the lip gene family (lip1-lip7), in which the recombinant LIP1 is the major form of the CRL multigene family. Previously, 19 of the nonuniversal serine codons (CTG) of the lip1 gene hav been successfully converted into universal serine codons (TCT) by overlap extension PCR-based multiple-site-directed mutagenesis to express an active recombinant LIP1 in the yeast Pichia pastoris. To improve the expression efficiency of recombinant LIP1 in P. pastoris, a regional synthetic gene fragment of lip1 near the 5' end of a transcript has been constructed to match P. pastoris-preferred codon usage for simple scale-up fermentation. The present results show that the production level (152 mg/L) of coLIP1 (codon-optimized LIP1) has an overall improvement of 4.6-fold relative to that (33 mg/L) of non-codon-optimized LIP1 with only half the cultivation time of P. pastoris. This finding demonstrates that the regional codon optimization the lip1 gene fragment at the 5' end can greatly increase the expression level of recombinant LIP1 in the P. pastoris system. More distinct biochemical properties of the purified recombinant LIP1 for further industrial applications are also determined and discussed in detail.
Clinical applications of breath testing (2010)

Breath testing has the potential to benefit the medical field as a cost-effective, non-invasive diagnostic tool for diseases of the lung and beyond. With growing evidence of clinical worth, standardization of methods, and new sensor and detection technologies the stage is set for breath testing to gain considerable attention and wider application in upcoming years.
Reactivity of the Human Thioltransferase (Glutaredoxin) C7S, C25S, C78S, C82S Mutant and NMR Solution Structure of Its Glutathionyl Mixed Disulfide Intermediate Reflect Catalytic Specificity<sup>,</sup> (1998)

Human thioltransferase (TTase) is a 12 kDa thiol-disulfide oxidoreductase that appears to play a critical role in maintaining the redox environment of the cell. TTase acts as a potent and specific reducing agent for protein-S-S-glutathione mixed disulfides (protein-SSG) likely formed during oxidative stress or as redox intermediates in signal transduction pathways. Accordingly, the catalytic cycle of thioltransferase itself involves a covalent glutathionyl enzyme disulfide intermediate (TTase-C22-SSG). To understand the molecular basis of TTase specificity for the glutathione moiety, we engineered a quadruple Cys to Ser mutant of human TTase (C7S, C25S, C78S, and C82S) which retains only the active site cysteine residue (C22), and we solved its high-resolution NMR solution structure in the mixed disulfide intermediate with glutathione (QM-TTase-SSG). This mutant which cannot form a C22-S-S-C25 intramolecular disulfide displays the same catalytic efficiency (Vmax/KM) and specificity for glutathionyl mixed disulfide substrates as wild-type TTase, indicating that the Cys-25-SH moiety is not required for catalysis or glutathionyl specificity. The structure of human thioltransferase is characterized by a thioredoxin-like fold which comprises a four-stranded central beta-sheet flanked on each side by alpha-helices. The disulfide-adducted glutathione in the TTase-SSG complex has an extended conformation and is localized in a cleft near the protein surface encompassing the residues from helices-alpha2,alpha3, the active site loop, and the loop connecting helix-alpha3 and strand-beta3. Numerous van der Waals and electrostatic interactions between the protein and the glutathione moiety are identified as contributing to stabilization of the complex and confering the substrate specificity. Comparison of the human thioltransferase with other thiol-disulfide oxidoreductases reveals structural and functional differences.
Studies on ketene and its derivatives. XCII. Reaction of diketene with benzaldehyde, cinnamaldehyde, and .BETA.-phenylcinnamaldehyde. (1978)

Reaction of diketene with benzaldehyde (1) in the presence of sulfuric acid gives α-benzylideneacetoacetic acid (5). Similarly, reaction of diketene with cinnamaldehyde (2) and β-phenylcinnamaldehyde (3) gives 2-acetyl-5-phenyl-2, 4-pentadienoic acid (6) and 2-acetyl-5, 5-diphenyl-2, 4-pentadienoic acid (7), respectively.