gebhart/patrepeval huggingface dataset:
Mycobacterial mistranslation is necessary and sufficient for rifampicin phenotypic resistance (2014)

Errors are inherent in all biological systems. Errors in protein translation are particularly frequent giving rise to a collection of protein quasi-species, the diversity of which will vary according to the error rate. As mistranslation rates rise, these new proteins could produce new phenotypes, although none have been identified to date. Here, we find that mycobacteria substitute glutamate for glutamine and aspartate for asparagine at high rates under specific growth conditions. Increasing the substitution rate results in remarkable phenotypic resistance to rifampicin, whereas decreasing mistranslation produces increased susceptibility to the antibiotic. These phenotypic changes are reflected in differential susceptibility of RNA polymerase to the drug. We propose that altering translational fidelity represents a unique form of environmental adaptation.
Cellular control of membrane permeability. Implications for a bioartificial renal tubule. (1989)

A hemofiltrate processor, which consists of a cultured monolayer of renal epithelial cells on a permeable membrane, displayed transport functions that mimicked the renal tubule. Two cell lines, LLC-PK1 (a proximal tubule-like cell) and MDCK (a distal tubule-like cell), were cultured on microporous cellulose nitrate membranes and studied in a diffusion chamber. Dual-label tracer experiments revealed that inulin, glucose, and para-aminohippurate (PAH) moved across unseeded membranes with similar rates in either direction. Solute concentrations in both compartments reached equilibrium in less than 12 hours. MDCK cell-covered membranes were impermeable to all three solutes, as expected from a distal tubule-like cell. LLC-PK1 cell-covered membranes were impermeable to inulin and PAH, but demonstrated a net apical to basal glucose flux of 150 to 350 ng/cm2/min, depending on the conditions. This led within 72 hours to a zero glucose concentration in the compartment on the apical side of the cells, versus 4.6 mg/ml on the basal side. This glucose transport function was inhibited by 0.5 mmol/L phlorizin. Highest glucose flux was obtained using extracellular matrix as the cell attachment substrate on the membrane, suggesting the highest degree of cell differentiation. Based on estimates of the surface area of the normal kidney, the glucose reabsorption capacity of the LLC-PK1 cell line was about 20% that of the normal tubule. The absence of PAH secretion may have been due to the heterogeneity of cells derived from the proximal tubule. Different cell types, culture conditions, and attachment substrates may enhance the transport capacity of the bioartificial renal tubule.
Synthesis of 1,2,3,4‐Tetrahydro‐4‐oxothieno[3,2‐d]pyrimidine and Perhydropyrimidine Derivates from Alkyl Dicyanoacetates (1991)

Abstract Nucleophilic addition of methyl 3‐aminothiophene‐2‐carboxylate ( 2 ) as well as of β‐alanine ethyl ester ( 11 ) to one CN group of the salts 1 of alkyl dicyanoacetates, followed by cyclization, yielded 1,2,3,4‐tetrahydro‐4‐oxothieno[3,2‐ d ]pyridimine derivatives 6 – 10 ( Scheme 1 ) and perhydropyrimidine derivatives 17 – 19 ( Scheme 2 ), respectively.
Integration of IC Industry Feature Sizes with University Back-End-of-Line Post Processing: Example Using a Phase-Change Memory Test Chip (2009)

We have demonstrated that back-end-of-line (BEOL) processing can successfully be performed in a university environment on die that have been fabricated at a foundry. This processing option enables universities to integrate state-of-the-art feature sizes with low resolution photolithography capabilities, such as achieved with a contact aligner, typically available at universities. With this capability, new device technologies and materials can be explored at the university level, where the basic research on the technology can occur without the timelines and expectations that are placed on product development in an industrial setting. By incorporating state-of-the-art feature sizes with these research efforts, the research results will be more applicable and more easily transferable to an industrial environment. In our project, we have demonstrated the integration of a foundry processed chip with the BEOL university processing through the fabrication of a small phase-change memory array with CMOS access transistors and addressing circuitry wherein the phase-change memory material was processed BEOL at Boise State University.
Cytotoxic T Lymphocyte and Helper T Cell Responses following HIV Polynucleotide Vaccination (1995)

Expression vectors encoding either HIV-1 gp160/rev, gp120, or rev alone were used for direct vaccination of mice and nonhuman primates. Each vaccine elicited long-lived (> 7 months) helper T cell responses in mice and monkeys as measured by in vitro proliferation of splenocytes following recombinant antigen treatment. Cytokine assays of the cell supernatants showed that approximately 100-fold more gamma-interferon than IL-4 was secreted during culture indicating that these vaccines elicited TH1-like responses. CD8+ CTL activities were also observed both in mice and rhesus. The gp120 and gp160/rev vaccines elicited antigen-specific antibodies, although these responses were more variable and lower magnitude for gp160/rev, and gp120 DNA-vaccinated African green monkeys had moderate levels of neutralizing antibodies. No antibodies were found against rev (an intracellular protein) with either rev vaccine. Similar antibody titers were obtained for gp120 by either intramuscular or intradermal injection although T cell responses were generally lower by intradermal route. These results indicate that DNA vaccines may provide a powerful means to elicit cellular and humoral immune responses against HIV.
Moisture-Dependent Crystallization of Amorphous Lamotrigine Mesylate (1996)

A commercially available computer-controlled vacuum moisture balance was used for determining moisture sorption isotherms of freeze-dried and spray-dried lamotrigine mesylate drug substance and freeze dried drug product containing mannitol. The presence or absence of desorption hysteresis and the characteristics of the weight-versus-time profile as a sample was exposed to a defined relative humidity ramp were sensitive indicators of moisture-induced crystallization. Combination of the moisture sorption data with polarized light microscopy, differential scanning calorimetry, and X-ray powder diffraction provided qualitative verification of the crystallization with < 50 mg of sample. The normalized water loss during crystallization was used to detect as little as 2% amorphous content in physical mixtures of amorphous and crystalline lamotrigine mesylate. Moisture sorption, water plasticization, and crystallization properties of amorphous forms prepared by spray drying and freeze drying were nearly identical. Cofreeze-drying lamotrigine mesylate with D-mannitol resulted in a mixture of amorphous lamotrigine mesylate with properties similar to those of spray-dried or freeze-dried materials and crystalline D-mannitol. The amount of water needed for crystallization over a time scale observable in the moisture balance was considerably more than the amount needed to lower the glass transition temperature of the sample to the operating temperature of the instrument. This result illustrated the importance of time scale effects in determining critical moisture levels for crystallization from the amorphous state.
Polarization of the fluorescence of macromolecules. 2. Fluorescent conjugates of ovalbumin and bovine serum albumin (1952)

Research Article| May 01 1952 Polarization of the fluorescence of macromolecules. 2. Fluorescent conjugates of ovalbumin and bovine serum albumin G. Weber G. Weber ∗ 1Biochemical Laboratory, University of Cambridge Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1952) 51 (2): 155–167. https://doi.org/10.1042/bj0510155 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation G. Weber; Polarization of the fluorescence of macromolecules. 2. Fluorescent conjugates of ovalbumin and bovine serum albumin. Biochem J 1 May 1952; 51 (2): 155–167. doi: https://doi.org/10.1042/bj0510155 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1952 CAMBRIDGE UNIVERSITY PRESS1952 Article PDF first page preview Close Modal You do not currently have access to this content.
Role of the adhesion molecule ICAM‐1 (CD54) in staphylococcal enterotoxin‐mediated cytotoxicity (1991)

Abstract Staphylococcal enterotoxin A (SEA) binds to major histocompatibility complex (MHC) class II molecules on target cells and directs human cytotoxic T lymphocytes (CTL) of irrelevant nominal specificity to mediate strong cytotoxicity against target cells. In this report we describe the importance of ICAM‐1(CD54) expression on the target cell in SEA‐dependent cell‐mediated cytotoxicity (SDCC), utilizing murine L cells co‐transfected with HLA‐DR and ICAM‐1. Human CTL mediated a low but significant cytotoxicity against HLA‐DR2‐and HLA‐DR7‐transfected cells after preincubation with SEA, but no reactivity towards uncoated HLA‐DR2 and HLA‐DR7 cells or SEA‐coated ICAM‐1‐transfected and untransfected L cells. In contrast, a strong cytotoxic response was mediated by CTL against L cells co‐transfected with HLA‐DR/ICAM‐1 and HLA‐DR7/ICAM‐1. Similar cytotoxic activity of the CTL was seen at a 30‐fold lower effector‐to‐target cell ratio when comparing the HLA‐DR2/ICAM‐1‐expressing cells with the HLA‐DR2‐expressing cells. SEA dose‐response analysis demonstrated that the HLA‐DR2/ICAM‐1‐expressing target cells enabled the CTL to respond to a 1000‐fold lower concentration of SEA in comparison to the HLA‐DR2‐expressing cells. CD3 + CD4 + and CD3 + CD8 + cytotoxic T cell lines were equally dependent on the expression of ICAM‐1 on the target cell. The strong CTL activity against HLA‐DR2/ICAM‐1‐transfected cells could be blocked by anti‐CD11a or anti‐CD18 monoclonal antibodies (mAb), but not by anti‐CD11b, anti‐CD11c, anti‐CD2 or unrelated control mAb. The great sensitivity of HLA‐DR2/ICAM‐1 expressing target cells to SDCC was strongly reduced by preincubation with various anti‐ICAM‐1 mAb but not by mAb against monomorphic HLA‐DR or murine MHC class I determinants. The result in this study clearly demonstrates that efficient re‐targeting of human CTL by SE is dependent on a proper interaction with the heterodimer CD11a/CD18 (Leu‐CAMa, LFA‐1) on the CTL and its target cell ligand ICAM‐1.
Total Synthesis of (+)-Astrophylline (2003)

The first total synthesis of (+)-astrophylline (2) has been achieved, starting from readily available enantiomerically pure (+)-(1R,4S)-4-hydroxycyclopent-2-enyl acetate (11). A novel ruthenium-catalyzed ring-closing ring-opening ring-closing metathesis of carbocyclic olefins of general type 5 was the key step, providing the stereochemically well-defined bis-piperidyl skeleton of the target molecule. A [2,3]-Wittig-Still rearrangement of 9 was also employed as the critical transformation in the stereocontrolled generation of the 1,2-trans configuration of the cyclopentene intermediate 6c. Our early synthetic efforts toward 1,2-trans cyclopentene derivatives of type 6, as well as the synthetic pathway to an optimized 13-step total synthesis of 2 (12% overall yield), are reported.
Common phrases and minimum-space text storage (1973)

A method for saving storage space for text strings, such as compiler diagnostic messages, is described. The method relies on hand selection of a set of text strings which are common to one or more messages. These phrases are then stored only once. The storage technique gives rise to a mathematical optimization problem: determine how each message should use the available phrases to minimize its storage requirement. This problem is nontrivial when phrases which overlap exist. However, a dynamic programming algorithm is presented which solves the problem in time which grows linearly with the number of characters in the text. Algorithm 444 applies to this paper.
A user-programmable vertex engine (2001)

In this paper we describe the design, programming interface, and implementation of a very efficient user-programmable vertex engine. The vertex engine of NVIDIA's GeForce3 GPU evolved from a highly tuned fixed-function pipeline requiring considerable knowledge to program. Programs operate only on a stream of independent vertices traversing the pipe. Embedded in the broader fixed function pipeline, our approach preserves parallelism sacrificed by previous approaches. The programmer is presented with a straightforward programming model, which is supported by transparent multi-threading and bypassing to preserve parallelism and performance.
Distribution, Organization, and Ecology of Bacteria in Chronic Wounds (2008)

Between 1 and 2% of the population in the developed world experiences a nonhealing or chronic wound characterized by an apparent arrest in a stage dominated by inflammatory processes. Lately, research groups have proposed that bacteria might be involved in and contribute to the lack of healing of these wounds. To investigate this, we collected and examined samples from chronic wounds obtained from 22 different patients, all selected because of suspicion of Pseudomonas aeruginosa colonization. These wound samples were investigated by standard culturing methods and peptide nucleic acid-based fluorescence in situ hybridization (PNA FISH) for direct identification of bacteria. By means of the culturing methods, Staphylococcus aureus was detected in the majority of the wounds, whereas P. aeruginosa was observed less frequently. In contrast, using PNA FISH, we found that a large fraction of the wounds contained P. aeruginosa. Furthermore, PNA FISH revealed the structural organization of bacteria in the samples. It appeared that P. aeruginosa aggregated as microcolonies imbedded in the matrix component alginate, which is a characteristic hallmark of the biofilm mode of growth. The present investigation suggests that bacteria present within these wounds tend to be aggregated in microcolonies imbedded in a self-produced matrix, characteristic of the biofilm mode of growth. Additionally, we must conclude that there exists no good correlation between bacteria detected by standard culturing methods and those detected by direct detection methods such as PNA FISH. This strongly supports the development of new diagnostic and treatment strategies for chronic wounds.
Representation Learning: A Review and New Perspectives (2013)

The success of machine learning algorithms generally depends on data representation, and we hypothesize that this is because different representations can entangle and hide more or less the different explanatory factors of variation behind the data. Although specific domain knowledge can be used to help design representations, learning with generic priors can also be used, and the quest for AI is motivating the design of more powerful representation-learning algorithms implementing such priors. This paper reviews recent work in the area of unsupervised feature learning and deep learning, covering advances in probabilistic models, autoencoders, manifold learning, and deep networks. This motivates longer term unanswered questions about the appropriate objectives for learning good representations, for computing representations (i.e., inference), and the geometrical connections between representation learning, density estimation, and manifold learning.
Real-time adaptive regulation of a visual camera for automatic investigation of changing environments (2002)

An adaptive strategy for regulating the intrinsic parameters of a CCD visual camera is proposed. The parameter regulation procedure is based on the computation of the "quality" of an acquired signal by means of a set of functions which estimate the goodness of the datum. Each function performs a quantitative evaluation by computing several features derived from the high-frequency content of an image and from the histogram analysis. The regulation strategy uses such values to compute the actual values of the camera parameters, i.e., focusing distance, aperture diameter, electronic gain, and black level. Moreover, the same strategy can be applied both to the whole image and to smaller subareas, so providing a focus-of-attention mechanism. This is useful for the automatic investigation and control of environments subject to dynamically changing conditions (e.g., the illumination and the structure of a scene), whenever it is not possible to interact directly with such environments. The system has been implemented on a Sun Spark Station II linked with a CCD camera (with the capability of computer-controlled parameters) and with an image-acquisition system, which permits real time performances.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bacterial attachment to stainless steel welds: Significance of substratum microstructure (2001)

AISI Type 304 L stainless steel (SS) is a widely used material in industry due to its strength and resistance to corrosion. However, corrosion on SS is reported largely at welds or adjacent areas. Bacteria were observed to colonize preferentially near welds as a result of surface roughness. In the present study, the influence of another important metal surface condition on bacterial adhesion has been evaluated, i.e. substratum microstructure. Type 304 L SS weld samples were prepared and machined to separate weld metal, the heat affected zone (HAZ) and base metal regions. The coupons were molded in resin so that only the surfaces polished to a 3 p.m finish were exposed to the experimental medium with Pseudomonas sp. isolated from a corrosive environment in Japan. The coupons were exposed for varying durations. The area of bacterial attachment showed significant differences with time of exposure and; the type of coupons. Generally, the weld metal samples showed more attachment whilst the base metal showed the least. The area of attachment was inversely proportional to the average grain size of the three samples. As the bacteria started colonizing, attachment mainly occurred on the grain boundaries of the base metal (after 8h, 84.62% and 15.38% of the total number of bacteria attached in the field of view (FOV) at the grain boundary and matrix, respectively) and on the austenite‐ferrite interface in the weld metal (after 8h, 88.33% and 11.77% of the total number of bacteria attached in the FOV at the boundary and matrix, respectively). The weld area had more grains and hence more grain boundary/ unit area than the base metal, resulting in more bacterial attachment. SEM observations showed this increased attachment of Pseudomonas sp. resulted in the initiation of microbiologically influenced corrosion (MIC) on the weld coupons by 16 d. Therefore, the results provide data to support the fact that substratum microstructure influences bacterial attachment, which in turn leads to corrosion. Key words: stainless steel welds Pseudomonas sp.bacterial attachmentmicrobiologically influenced corrosionsubstratum microstructure Notes Corresponding author; fax: +81–66879–8689; e‐mail: kikuchi@jwri.osaka‐u.ac.jp
The effect of purified aminoaldehydes produced by polyamine oxidation on the development in vitro of Plasmodium falciparum in normal and glucose-6-phosphate-dehydrogenase-deficient erythrocytes (1986)

Purified aminoaldehydes produced by polyamine oxidation were toxic to the malarial parasite, Plasmodium falciparum, cultured in human erythrocytes. There was a profound effect on young ring forms, and, during maturation, parasites became more sensitive to the aldehydes. Oxidation of the aldehydes abolished the lethal effect. The plasmodia within glucose-6-phosphate-dehydrogenase (G6PD)-deficient erythrocytes were more sensitive to mono- and di-aldehydes than were parasites in normal erythrocytes. G6PD-deficient erythrocytes were also more sensitive to pretreatment with the dialdehyde produced by the oxidation of spermine. Pretreatment prevented further invasion by the parasites.
Analysis of the human VH gene repertoire. Differential effects of selection and somatic hypermutation on human peripheral CD5(+)/IgM+ and CD5(-)/IgM+ B cells. (1997)

To analyze the immunoglobulin repertoire of human IgM+ B cells and the CD5(+) and CD5(-) subsets, individual CD19(+)/ IgM+/CD5(+) or CD5(-) B cells were sorted and non-productive as well as productive VH gene rearrangements were amplified from genomic DNA and sequenced. In both subsets, the VH3 family was overrepresented largely as a result of preferential usage of a small number of specific individual family members. In the CD5(+) B cell subset, all other VH families were found at a frequency expected from random usage, whereas in the CD5(-) population, VH4 appeared to be overrepresented in the nonproductive repertoire, and also negatively selected since it was found significantly less often in the productive compared to the nonproductive repertoire; the VH1 family was significantly diminished in the productive rearrangements of CD5(-) B cells. 3-23/DP-47 was the most frequently used VH gene segment and was found significantly more often than expected from random usage in productive rearrangements of both CD5(+) and CD5(-) B cells. Evidence for selection based on the D segment and the JH gene usage was noted in CD5(+) B cells. No differences were found between the B cell subsets in CDR3 length, the number of N-nucleotides or evidence of exonuclease activity. Somatically hypermutated VHDJH rearrangements were significantly more frequent and extensive in CD5(-) compared to CD5(+) IgM+ B cells, indicating that IgM+ memory B cells were more frequent in the CD5(-) B cell population. Of note, the frequency of specific VH genes in the mutated population differed from that in the nonmutated population, suggesting that antigen stimulation imposed additional biases on the repertoire of IgM+ B cells. These results indicate that the expressed repertoire of IgM+ B cell subsets is shaped by recombinational bias, as well as selection before and after antigen exposure. Moreover, the influences on the repertoires of CD5(+) and CD5(-) B cells are significantly different, suggesting that human peripheral blood CD5(+) and CD5(-) B cells represent different B cell lineages, with similarities to murine B-1a and B-2 subsets, respectively.
Nanopillar array structures for enhancing biosensing performance (2006)

Fabrication of metallic nanopillar array structures and their application as electrodes in electrochemical-based biosensors are discussed in this report. Vertically standing nanopillar array structures were fabricated using an electrodeposition technique and their electrochemical characteristics were evaluated. For possible use in biosensing applications, these standing nanopillars should have sufficient mechanical stability to sustain the capillary forces caused by the nanopillar-liquid interactions in aqueous environment and should provide increased signal response in an electrochemical process. Our results showed that the developed nanopillar arrays were mechanically stable in aqueous environments and the nanostructured electrodes exhibited increased electrochemical response compared with flat electrodes.
Antigenic structure, evolution and immunobiology of human respiratory syncytial virus attachment (G) protein. (1997)

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