gebhart/patrepeval huggingface dataset:
8 The Function and Regulation of Heat Shock Proteins in Escherichia coli (1990)

I. INTRODUCTION The heat shock response in E. coli was first identified by monitoring the response of individual proteins to temperature upshift (Lemaux et al. 1978; Yamamori et al. 1978; for review, see Neidhardt and VanBogelen 1987). Most E. coli proteins do not change their rate of synthesis significantly when the temperature is suddenly increased. However, a small group of proteins show a large but transient increase in their rate of synthesis. These proteins have been called the heat shock proteins (hsps). hsps are induced by several stimuli other than heat, including DNA-damaging agents, coumermycin, amino acid analogs, starvation for amino acids, bacteriophage λ infection, and ethanol. hsps may serve to protect the cell against a variety of adverse conditions. The heat shock regulon includes about 20 of the approximately 2000 proteins that E. coli synthesizes (Neidhardt and VanBogelen 1987). Two of the major E. coli hsps are homologous to eukaryotic hsps. DnaK is homologous to the eukaryotic hsp70 family (Bardwell and Craig 1984), and GroEL is related to eukaryotic mitochondrial hsps (McMullin and Hallberg 1988), as well as the plant RuBisCO binding protein (Hemmingsen et al. 1988). HptG, another E. coli hsp, is homologous to hsp83 (Bardwell and Craig 1987). This conservation of hsps suggests that the functions required to protect the cell from thermal stress are evolutionarily conserved among nearly all organisms. Thus, a study of the function of the E. coli hsps will not only contribute to an understanding of the physiology of eubacteria, but will also...
The UCSC Genome Browser Database: update 2009 (2008)

The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.
Biological applications for small solenoids: NMR spectroscopy of microliter volumes at high fields (1993)

In this paper we describe features of an NMR probe designed for the study of small, superfused muscles. We also present the results of an empirical study of the performance characteristics of several configurations of small solenoid coils, ca 2 mm diameter. Our data show that optimal use of the available volume of sample becomes the prime consideration in coil design at this scale. In contrast to large biological samples, for such small coils the equivalent resistance associated with the sample is minor relative to the resistance of the RF coil itself. Thus, substantial improvements in the S/N ratio can be obtained by adopting coil configurations that are inferior electrically, but which can sample a greater volume of tissue.
Extending 2-D Convolutional Neural Networks to 3-D for Advancing Deep Learning Cancer Classification With Application to MRI Liver Tumor Differentiation (2018)

Deep learning (DL) architectures have opened new horizons in medical image analysis attaining unprecedented performance in tasks such as tissue classification and segmentation as well as prediction of several clinical outcomes. In this paper, we propose and evaluate a novel three-dimensional (3-D) convolutional neural network (CNN) designed for tissue classification in medical imaging and applied for discriminating between primary and metastatic liver tumors from diffusion weighted MRI (DW-MRI) data. The proposed network consists of four consecutive strided 3-D convolutional layers with 3 × 3 × 3 kernel size and rectified linear unit (ReLU) as activation function, followed by a fully connected layer with 2048 neurons and a Softmax layer for binary classification. A dataset comprising 130 DW-MRI scans was used for the training and validation of the network. To the best of our knowledge this is the first DL solution for the specific clinical problem and the first 3-D CNN for cancer classification operating directly on whole 3-D tomographic data without the need of any preprocessing step such as region cropping, annotating, or detecting regions of interest. The classification performance results, 83% (3-D) versus 69.6% and 65.2% (2-D), demonstrated significant tissue classification accuracy improvement compared to two 2-D CNNs of different architectures also designed for the specific clinical problem with the same dataset. These results suggest that the proposed 3-D CNN architecture can bring significant benefit in DW-MRI liver discrimination and potentially, in numerous other tissue classification problems based on tomographic data, especially in size-limited, disease-specific clinical datasets.
An object-oriented framework for dynamically configuring extensible distributed systems (1994)

Developing extensible, robust and efficient distributed systems is a complex task. To help alleviate this complexity, we have developed the ADAPTIVE Service eXecutive (ASX) framework. ASX is an object-oriented framework composed of automated tools and reusable components. These tools and components help to simplify the development, configuration and reconfiguration of applications in a distributed environment. Using the ASX framework, the services in the applications may be updated and extended without modifying, recompiling, relinking or restarting the applications at run-time. This paper describes the features and object-oriented architecture of the ASX framework. It also describes how the ASX framework has been used to develop a highly modular, reusable and dynamically reconfigurable family of distributed system management applications.
Localization of the Fusobacterium nucleatum T18 adhesin activity mediating coaggregation with Porphyromonas gingivalis T22 (1993)

Adherence of pathogenic bacteria is often an essential first step in the infectious process. The ability of bacteria to adhere to one another, or to coaggregate, may be an important factor in their ability to colonize and function as pathogens in the periodontal pocket. Previously, a strong and specific coaggregation was demonstrated between two putative periodontal pathogens, Fusobacterium nucleatum and Porphyromonas gingivalis. The interaction appeared to be mediated by a protein adhesin on the F. nucleatum cells and a carbohydrate receptor on the P. gingivalis cells. In this investigation, we have localized the adhesin activity of F. nucleatum T18 to the outer membrane on the basis of the ability of F. nucleatum T18 vesicles to coaggregate with whole cells of P. gingivalis T22 and the ability of the outer membrane fraction of F. nucleatum T18 to inhibit coaggregation between whole cells of F. nucleatum T18 and P. gingivalis T22. Proteolytic pretreatment of the F. nucleatum T18 outer membrane fraction resulted in a loss of coaggregation inhibition, confirming the proteinaceous nature of the adhesin. The F. nucleatum T18 outer membrane fraction was found to be enriched for several proteins, including a 42-kDa major outer membrane protein which appeared to be exposed on the bacterial cell surface. Fab fragments prepared from antiserum raised to the 42-kDa outer membrane protein were found to partially but specifically block coaggregation. These data support the conclusion that the 42-kDa major outer membrane protein of F. nucleatum T18 plays a role in mediating coaggregation with P. gingivalis T22.
Baboon Mesenchymal Stem Cells Can Be Genetically Modified to Secrete Human Erythropoietin <i>In Vivo</i> (2001)

Human mesenchymal stem cells (MSCs) are capable of differentiating into multiple mesenchymal lineages including chondrocytes, osteocytes, adipocytes, and marrow stromal cells. Using a nonhuman primate model, we evaluated nonhuman primate MSCs as targets for gene therapy. Baboon MSCs (bMSCs) cultured from bone marrow aspirates appeared as a homogeneous population of spindle-shaped cells. bMSCs were capable of differentiating into adipocytes and osteocytes in vitro and chondrocytes in vivo. bMSCs were genetically modified with a bicistronic vector encoding the human erythropoietin (hEPO) gene and the green fluorescent protein (GFP) gene. Transduction efficiencies ranged from 72 to 99% after incubation of MSCs with retroviral supernatant. Transduced cells produced from 1.83 x 10(5) to 7.12 x 10(5) mIU of hEPO per 10(6) cells per 24 hr in vitro before implantation. To determine the capacity of bMSCs to express hEPO in vivo, transduced bMSCs were injected intramuscularly in NOD/SCID mice. In a separate experiment, transduced bMSCs were loaded into immunoisolatory devices (IIDs) and surgically implanted into either autologous or allogeneic baboon recipients. Human EPO was detected in the serum of NOD/SCID mice for up to 28 days and in the serum of five baboons for between 9 and 137 days. NOD/SCID mice experienced sharp rises in hematocrit after intramuscular injection of hEPO-transduced bMSCs. The baboon that expressed hEPO for 137 days experienced a statistically significant (p < 0.04) rise in its hematocrit. These data demonstrate that nonhuman primate MSCs can be engineered to deliver a secreted and biologically active gene product. Therefore, human MSCs may be an effective target for future human gene therapy trials.
A case of biopsy-proven leptomeningeal amyloidosis and intravenous Ig-responsive polyneuropathy associated with the Ala25Thr transthyretin gene mutation (2006)

A growing body of literature has described familial leptomeningeal amyloidosis, a rare phenotype resulting from deposition of transthyretin (TTR) amyloid within the leptomeninges. We report herein the case of a patient with leptomeningeal amyloidosis presenting with hearing loss, asymmetrical polyneuropathy and sensory ataxia. This is the first Japanese case displaying TTR mutation at codon 25, replacing alanine with threonine. Neurophysiological examinations suggested demyelinating polyradiculoneuropathy, which improved dramatically after high-dose intravenous immunoglobulin treatment. Demyelinating polyneuropathy in our patient may be attributable to massive leptomeningeal amyloidosis, and no systemic organ involvement was identified. These characteristic clinical manifestations may have resulted from the Ala25Thr TTR gene mutation.
Phase stepping in projected-fringe fibre-based moiré interferometry (1993)

An optical fibre based moiré interferometer for surface shape measurement is described. The technique uses an optical fibre interferometer to project interference fringes and is readily phase stepped without mechanical movement of components.
Insomnia and Psychiatric Disorders (2008)

CME Educational Objectives 1. Discuss the biological mechanisms shard by sleep and mood disorders. 2. Summarize the nature of sleep abnormalities in different psychiatric disorders. 3. Describe the relation of insomnia and psychiatric disorders
NCIH services, architecture, and implementation (1994)

The telecommunications planners for the North Carolina State Government recognising the potential of asynchronous transfer mode and synchronous optical network, asked BellSouth, Carolina Telephone, and GTE to develop a proposal for a network based on ATM and SONET to enable a multitude of high-speed data and video applications throughout the state. This B-ISDN, now known as the North Carolina Information Highway (NCIH), has become widely recognized as a model for the National Information Infrastructure (NII). The services provided by the NCIH are designed to be able to support numerous emerging applications that are expected to provide significant benefits in the areas of education, health care, crime control, economic development, and government.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Effect of Hydrophobic Modification of a Nonionic Cellulose Derivative on the Interaction with Surfactants. Phase Behavior and Association (1997)

Phase separation studies have been carried out concerning the addition of different surfactants to systems containing either ethyl(hydroxyethyl)cellulose (EHEC) or the hydrophobically modified analogue (HM-EHEC). The polymer concentration was kept constant at 1 g polymer/100 g of water (1 w/w%), while the surfactant concentration was varied. In the polymer/sodium dodecyl sulfate (SDS) systems, which were studied in more detail, phase diagrams were obtained in the presence of various concentrations of inert salt. Moreover, the phase behavior of the HM-EHEC/SDS system showed no marked changes by purification of the surfactant or by contamination with decanol. It was shown that the SDS binding to EHEC was cooperative and could be described in the framework of a closed association model, while for HM-EHEC a two-step binding model had to be used to get a proper description of the binding. In the noncooperative part of the HM-EHEC binding isotherm, the binding showed similarities to the adsorption of SDS on a hydrophobic surface and could be described by a Langmuir adsorption model. From the binding isotherms for SDS, binding isotherms for ionic surfactants with varying chain length could be calculated from simple assumptions. These isotherms give a basis for the interpretation of the phase diagrams. For the ionic surfactants, the phase behavior could be rationalized by considering the polymer/surfactant complex to possess polyelectrolyte characteristics. The observations were discussed in terms of an attractive hydrophobic interaction and a repulsive electrostatic force. Addition of nonionic surfactants was discussed by observing that generally a pair of a nonionic polymer and a nonionic surfactant segregates. However, with HM-EHEC there is an extra attractive hydrophobic interaction due to the presence of polymer hydrophobic tails which can serve as nucleation sites for the surfactants.
Applications of Microwave in Organic Synthesis: An Improved One-step Synthesis of Metallophthalocyanines and a New Modified Microwave Oven for Dry Reactions (2001)

Metallophthalocyanine complexes are obtained quickly and efficiently by the reaction of phthalodinitrile with hydrated metallic salts without solvent and under microwave irradiation. The use of a modified commercial microwave oven to perform this type of reactions under dry conditions is described. Metallophthalocyanines and metallododecachlorophthalocyanines of some divalent metals can be also obtained from phthalic or tetrachlorophthalic anhydrides with hydrated metallic salt and urea under microwave irradiation and without solvent.
Targeting Organic Anion Transporter 3 with Probenecid as a Novel Anti-Influenza A Virus Strategy (2012)

Influenza A virus infection is a major global health concern causing significant mortality, morbidity, and economic loss. Antiviral chemotherapeutics that target influenza A virus are available; however, rapid emergence of drug-resistant strains has been reported. Consequently, there is a burgeoning need to identify novel anti-influenza A drugs, particularly those that target host gene products required for virus replication, to reduce the likelihood of drug resistance. In this study, a small interfering RNA (siRNA) screen was performed to identify host druggable gene targets for anti-influenza A virus therapy. The host organic anion transporter-3 gene (OAT3), a member of the SLC22 family of transporters, was validated as being required to support influenza A virus replication. Probenecid, a prototypical uricosuric agent and chemical inhibitor of organic anion transporters known to target OAT3, was shown to be effective in limiting influenza A virus infection in vitro (50% inhibitory concentration [IC(50)] of 5.0 × 10(-5) to 5.0 × 10(-4) μM; P < 0.005) and in vivo (P < 0.05). Probenecid is widely used for treatment of gout and related hyperuricemic disorders, has been extensively studied for pharmacokinetics and safety, and represents an excellent candidate for drug repositioning as a novel anti-influenza A chemotherapeutic.
Reconfigurable audio output stage in 45nm process for single speaker mobile application (2009)

This paper presents a fully integrated solution for single speaker mobile application which can be embedded in today' market codecs. It makes use of a capacitor-free low-dropout regulator (LDO) which shares the pass device with the output audio power stage, allowing high quality performances for both hands-free and receiver modes and high power for hands-free. The system is capable of delivering 1 W in hands-free operation, and 80 mW in receive with 118 dB of PSRR and 0.06% of THD. The whole design has been implemented using TSMC 45 nm technology.
Raster Analysis of Urban Form (2004)

A new paradigm for investigating the environment consequences of urban texture is proposed. Using raster-based models and software algorithms derived from image processing the authors develop efficient methods of measuring geometric parameters and predicting radiation exchange. The possibilities of generating synthetic urban textures and of integrating cellular automata are explored. Results suggest the possibility of a raster-based urban model to inform planning and design.
Helmet and Shoulder Pad Removal From a Player With Suspected Cervical Spine Injury (1998)

Helmet and shoulder pad removal in the unstable cervical spine is a complex maneuver. In the unstable C1-C2 segment, helmet removal causes more angulation in flexion, more distraction, and more narrowing of the space available for the cord. In the lower cervical spine (C5-C6), helmet removal causes flexion of 9.32 degrees, and during shoulder pad removal the neck extends 8.95 degrees, a total of approximately 18 degrees. Disc height changes from 1.24 mm of distraction to 1.06 mm of compression during helmet removal and shoulder pad removal for a total 2.3-mm change. Translation, which correlates with the change in the space available for the cord, is greater at C5-C6 during shoulder pad removal. Because most of the cadavers had C5 anteriorly displaced on C6 to begin with, the extension force during shoulder pad removal caused a 3.87-mm change in reduction of C5 on C6. Because of the motion observed in the unstable spine, helmet and shoulder pad removal should be performed in a carefully monitored setting. They should be removed together by at least three, preferably four, trained people.
Finansiering van vee met vee (2012)

Die finansiering van vee het die laaste jaar toenemend onder die soeklig gekom. In werklikheid kan ons nie se dit was die finansiering van vee wat die omstredenheid veroorsaak het nie, maar eerder die feit dat vee nou as sekuriteit aangebied kan word om finansiering te bekom.
Delayed graft function in renal transplantation (2004)

This review discusses the current literature on several recent findings of pathophysiologic mechanisms of, and possible therapeutic interventions in, delayed graft function.
Substitution and pooling in visual crowding induced by similar and dissimilar distractors (2015)

Visual crowding refers to a phenomenon whereby objects that appear in the periphery of the visual field are more difficult to identify when embedded within clutter. Pooling models assert that crowding results from an obligatory averaging or other combination of target and distractor features that occurs prior to awareness. One well-known manifestation of pooling is feature averaging, with which the features of target and nontarget stimuli are combined at an early stage of visual processing. Conversely, substitution models assert that crowding results from binding a target and nearby distractors to incorrect spatial locations. Recent evidence suggests that substitution predominates when target-flanker feature similarity is low, but it is unclear whether averaging or substitution best explains crowding when similarity is high. Here, we examined participants' orientation report errors for targets crowded by similar or dissimilar flankers. In two experiments, we found evidence inconsistent with feature averaging regardless of target-flanker similarity. However, the observed data could be accommodated by a probabilistic substitution model in which participants occasionally "swap" a target for a distractor. Thus, we conclude that-at least for the displays used here-crowding likely results from a probabilistic substitution of targets and distractors, regardless of target-distractor feature similarity.
TGF-β-Mediated Epithelial-Mesenchymal Transition and Cancer Metastasis (2019)

Transforming growth factor β (TGF-β) is a secreted cytokine that regulates cell proliferation, migration, and the differentiation of a plethora of different cell types. Consistent with these findings, TGF-β plays a key role in controlling embryogenic development, inflammation, and tissue repair, as well as in maintaining adult tissue homeostasis. TGF-β elicits a broad range of context-dependent cellular responses, and consequently, alterations in TGF-β signaling have been implicated in many diseases, including cancer. During the early stages of tumorigenesis, TGF-β acts as a tumor suppressor by inducing cytostasis and the apoptosis of normal and premalignant cells. However, at later stages, when cancer cells have acquired oncogenic mutations and/or have lost tumor suppressor gene function, cells are resistant to TGF-β-induced growth arrest, and TGF-β functions as a tumor promotor by stimulating tumor cells to undergo the so-called epithelial-mesenchymal transition (EMT). The latter leads to metastasis and chemotherapy resistance. TGF-β further supports cancer growth and progression by activating tumor angiogenesis and cancer-associated fibroblasts and enabling the tumor to evade inhibitory immune responses. In this review, we will consider the role of TGF-β signaling in cell cycle arrest, apoptosis, EMT and cancer cell metastasis. In particular, we will highlight recent insights into the multistep and dynamically controlled process of TGF-β-induced EMT and the functions of miRNAs and long noncoding RNAs in this process. Finally, we will discuss how these new mechanistic insights might be exploited to develop novel therapeutic interventions.