gebhart/patrepeval huggingface dataset:
Genomewide Function Conservation and Phylogeny in the Herpesviridae (2001)

The Herpesviridae are a large group of well-characterized double-stranded DNA viruses for which many complete genome sequences have been determined. We have extracted protein sequences from all predicted open reading frames of 19 herpesvirus genomes. Sequence comparison and protein sequence clustering methods have been used to construct herpesvirus protein homologous families. This resulted in 1692 proteins being clustered into 243 multiprotein families and 196 singleton proteins. Predicted functions were assigned to each homologous family based on genome annotation and published data and each family classified into seven broad functional groups. Phylogenetic profiles were constructed for each herpesvirus from the homologous protein families and used to determine conserved functions and genomewide phylogenetic trees. These trees agreed with molecular-sequence-derived trees and allowed greater insight into the phylogeny of ungulate and murine gammaherpesviruses.
Construction and characterization of a potent HIV-2 Tat transdominant mutant protein. (1994)

The human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) Tat proteins Tat-1 and Tat-2 stimulate transcription of the viral long terminal repeat (LTR) sequences and are required for efficient viral replication. A class of mutant Tat proteins, termed "transdominant mutants," has been described that possesses relatively low transactivation activity, yet is able to inhibit the function of wild-type Tat. These mutant proteins contain a nonfunctional TAR RNA-binding domain but apparently retain a functional activation domain. A potential limitation for therapeutic use of transdominant mutants described to date is their low but significant basal level of transactivation for the HIV-1 or HIV-2 LTRs. In order to make an improved transdominant mutant, we have constructed Tat-2 proteins that contain mutations in four contiguous arginines at residues 81 to 84 in the RNA-binding domain. Using purified proteins and in vitro RNA-binding assays, we verified that these mutant Tat-2 proteins are defective for TAR RNA binding. We also verified that these mutant Tat-2 proteins bind to a cellular protein kinase in vitro that we have previously shown to bind specifically to the Tat-1 and Tat-2 activation domain. Using plasmid cotransfection assays, we compared the phenotypes of these mutant Tat-2 proteins with the most potent Tat-1 transdominant mutant described to date. One Tat-2 mutant, named "R81-84A," was found to be equivalent to the Tat-1 mutant in ability to inhibit wild-type Tat transactivation of HIV-1 and HIV-2 LTRs. Moreover, the R81-84A mutant possessed a significantly lower basal level of transactivation than the Tat-1 mutant. The R81-84A Tat-2 mutant is therefore a promising reagent for future development as an anti-HIV agent. Additionally, our results suggest that wild-type Tat-2 transactivation of the HIV-2 LTR is especially sensitive to inhibition by transdominant mutants.
Nuclear waste policy and politics (1989)

This article illustrates our approach for modeling the solid matrix of biological tissues using reactive constrained mixtures. Several examples are presented to highlight the potential benefits of this approach, showing that seemingly disparate fields of mechanics and chemical kinetics are actually closely interrelated and may be elegantly expressed in a unified framework. Thus, constrained mixture models recover classical theories for fibrous materials with bundles oriented in different directions or having different reference configurations, that produce characteristic fiber recruitment patterns under loading. Reactions that exchange mass among various constituents of a mixture may be used to describe tissue growth and remodeling, which may also alter the material's anisotropy. Similarly, reactions that describe the breaking and reforming of bonds may be used to model free energy dissipation in a viscoelastic material. Therefore, this framework is particularly well suited for modeling biological tissues.
Avermectins and milbemycins (1986)

H. G. Davies and R. H. Green, Nat. Prod. Rep., 1986, 3, 87 DOI: 10.1039/NP9860300087
Obesity and depression or anxiety (2009)

Clinicians should be aware that the association can occur in both directions

Obesity and common mental disorders, such as anxiety and depression, independently account for a substantial proportion of the global burden of disease and its associated economic costs, so it is important to determine the interaction between the two conditions. In the linked prospective cohort study (British Whitehall Study II; doi:10.1136/bmj.b3765), Kivimaki and colleagues looked for a bidirectional association between obesity and common mental disorders.1 Between 1985 and 1988, they recruited civil servants who were aged 35-55 years at baseline and studied them in three waves over 19 years. They found that common mental disorders were associated with an increased risk of obesity, and that the risk of obesity increased with the number of episodes of depression or anxiety. In contrast, they found weaker non-significant associations between obesity and the risk of common mental disorders.

Kivimaki and colleagues’ findings are consistent with previous cohort studies showing that baseline depression or anxiety predict obesity,2 3 4 but …
Ehk-1 and Ehk-2: two novel members of the Eph receptor-like tyrosine kinase family with distinctive structures and neuronal expression. (1993)

We have identified two novel members of the Eph RTK family, termed Ehk (eph homology kinase) -1 and -2. Compared to the amino acid sequences of various Eph family members, Ehk-1 and Ehk-2 are closest to the Sek and Cek-4/Mek-4/Hek kinases, and both are more similar to the Elk kinase than they are to the Eck or Eph kinases. Analysis of Ehk-1 cDNAs from various brain libraries reveals alternatively spliced transcripts that can encode five different forms of Ehk-1 transmembrane proteins. By contrast, Ehk-2 cDNAs revealed only a single form of protein coding region. However, the structure of Ehk-2 differs from all known members of the Eph family based on a 42 amino acid insert positioned between homology regions IV and V in the kinase domain. Ehk-1 and Ehk-2 are almost exclusively expressed in the nervous system. RNA in situ hybridization analyses on adult brain show that the Ehks are predominantly expressed in neurons and display overlapping, but distinct patterns of expression in various neuronal populations.
Further Resolution of the Low-sulphurS-Carboxymethylkerateine Fraction from Wool by Acrylamide-gel Electrophoresis (1972)

Click to increase image sizeClick to decrease image sizeKEY WORDS (SPECIFIC TERMS): FRACTIONATIONACRYLAMIDE-GEL ELECTROPHORESISSTARCH-GEL ELECTROPHORESISLINCOLN WOOLMERINO WOOLMOHAIRPORCUPINE QUILLLOW-SULPHUR PROTEINSS-CARBOXYMETHYL KERATEINECOMPONENT 7COMPONENT 8KEY WORDS (BROADER TERMS): ELECTROPHORESISWOOLHAIRKERATIN FIBRES
[Pathological features of hepatocellular carcinoma carrying hepatitis C virus antigen]. (1997)

HCCs carrying only HCAg have different pathological features and clinical characteristics from which carrying HBV marker(s). The results of image cytometry are in accordance with the biological behaviour of HCC.
Ambient ionization mass spectrometry: current understanding of mechanistic theory; analytical performance and application areas (2010)

Ambient ionization mass spectrometry allows the rapid analysis of samples or objects in their native state in the open environment with no prior preparation. Over the past six years, the ability of these techniques to provide selective analyte desorption and ionization, in combination with mass spectrometry (MS), has provided a growing number of powerful analytical alternatives across broad application areas, both quantitative and qualitative in nature, including pharmaceutical analysis, process chemistry, biological imaging, in vivo analysis, proteomics, metabolomics, forensics, and explosives detection. With the emergence of new ambient ionization methods, and the complementary nature of existing desorption and/or ionization techniques, additional hyphenated methods have been devised, which pushes the total number of documented methods to almost thirty. To cover all current ambient ionization techniques in detail would be too complex and detract from the main objective of this review. Rather, an overview of the field of ambient ionization MS will be given, followed by broad classification to allow detailed discussion of theory and common mechanistic factors underpinning a number of key techniques. Consideration will be given to experimental design, ease of implementation and analytical performance, detailing subsequent impact on a number of application areas, both established and emerging.
Layered expression scanning: rapid molecular profiling of tumor samples. (2000)

Layered expression scanning is a new approach to comprehensive molecular analysis of tumor samples that uses a layered array of capture membranes coupled to antibodies or DNA sequences to perform multiplex protein or mRNA analysis. Cell or tissue samples are transferred through a series of individual capture layers, each linked to a separate antibody or DNA sequence. As the biomolecules traverse the membrane set, each targeted protein or mRNA is specifically captured by the layer containing its antibody or cDNA sequence. The two-dimensional relationship of the cell populations is maintained during the transfer process, thereby producing a molecular profile of each cell type present. Reduction-to-practice of the technique is demonstrated by analysis of prostate-specific antigen (PSA) protein, gelatinase A protein, and POV1 (PB39) cDNA. As layered expression scanning technology progresses, we envision a laboratory method that will have multiple applications for high-throughput molecular profiling of normal and tumor samples.
ChemInform Abstract: Reactions of Titanium Derivatives of Some CH‐Acids with Carbonyl Compounds. Part 4. Synthesis and Some Transformations of (2‐ Alkenylidene)malonic Acid Derivatives. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Membrane Repair Defects in Muscular Dystrophy Are Linked to Altered Interaction between MG53, Caveolin-3, and Dysferlin (2009)

Defective membrane repair can contribute to the progression of muscular dystrophy. Although mutations in caveolin-3 (Cav3) and dysferlin are linked to muscular dystrophy in human patients, the molecular mechanism underlying the functional interplay between Cav3 and dysferlin in membrane repair of muscle physiology and disease has not been fully resolved. We recently discovered that mitsugumin 53 (MG53), a muscle-specific TRIM (Tri-partite motif) family protein (TRIM72), contributes to intracellular vesicle trafficking and is an essential component of the membrane repair machinery in striated muscle. Here we show that MG53 interacts with dysferlin and Cav3 to regulate membrane repair in skeletal muscle. MG53 mediates active trafficking of intracellular vesicles to the sarcolemma and is required for movement of dysferlin to sites of cell injury during repair patch formation. Mutations in Cav3 (P104L, R26Q) that cause retention of Cav3 in Golgi apparatus result in aberrant localization of MG53 and dysferlin in a dominant-negative fashion, leading to defective membrane repair. Our data reveal that a molecular complex formed by MG53, dysferlin, and Cav3 is essential for repair of muscle membrane damage and also provide a therapeutic target for treatment of muscular and cardiovascular diseases that are linked to compromised membrane repair.
The serum albumin‐binding domain of streptococcal protein G is a three‐helical bundle: a heteronuclear NMR study (1996)

Streptococcal protein G (SPG) is a cell surface receptor protein with a multiple domain structure containing tandem repeats of serum albumin-binding domains (ABD) and immunoglobulin-binding domains (IgBD). In this paper, we have analysed the fold of ABD. Far-UV circular dichroism analysis of ABD indicates high helical content (56%). Based on an analysis of nuclear magnetic resonance 13C secondary chemical shifts, sequential and short-range NOEs, and a few key nuclear Overhauser effects, we conclude that the ABD is a three-helix bundle. The structure of the ABD is, thus, quite different from the IgBD of protein G [Gronenborn, A.M. et al. (1991) Science 253, 657-661]. This strongly suggests that the ABD and the IgBD of SPG have evolved independently from each other. However, the fold of ABD is similar to that of the IgBD of staphylococcal protein A, possibly indicating a common evolutionary ancestor, despite the lack of sequence homology.
Expression of a gp33/27,000 MW activation inducer molecule (AIM) on human lymphoid tissues. Induction of cell proliferation on thymocytes and B lymphocytes by anti-AIM antibodies. (1989)

We have recently described several monoclonal antibodies (mAb) that recognize a heterodimeric structure (gp33/27,000 MW) expressed on the surface of human peripheral blood T lymphocytes upon activation with different mitogenic stimuli. Such mAb, when used in combination with submitogenic doses of phorbol ester, were capable of triggering T-cell proliferation. The antigen has been designated as activation inducer molecule (AIM). In the present study we have investigated the expression of the AIM in different lymphoid and non-lymphoid tissues. In addition, we have analysed the ability of lymphocyte subsets derived from thymus and tonsil to proliferate in response to anti-AIM mAb. The presence of AIM on subpopulations of lymphoid cells from thymus, tonsil, lymph node and spleen has been demonstrated by immunoprecipitation, flow cytometry and immunoperoxidase staining of tissue sections. By contrast, non-lymphoid cells from tissue such as brain, kidney, liver, lung or skin did not react with anti-AIM mAb. In thymus, the AIM expression was restricted to a subset of CD3+ medullary thymocytes, whereas CD1+ CD3- cortical thymocytes did not express this antigen. Nevertheless, the majority of both purified CD1- and CD3- thymocytes expressed AIM antigen after treatment with PMA. In tonsil and lymph node, a strong staining of a subset of CD3+ T lymphocytes located in the germinal centre was observed by immunohistochemical labelling with anti-AIM mAb. Certain T cells from the paracortical zone and CD19+ B lymphocytes from mantle region were also reactive. Both purified tonsillar T and B lymphocytes strongly expressed AIM after activation with PMA. The anti-AIM mAb was able to induce a strong proliferative response on purified CD1- thymocytes as well as on both purified tonsillar T and B lymphocytes in the presence of submitogenic doses of PMA. By contrast, no proliferative response was induced through the AIM in the CD3- immature thymocyte subset.
The history of live bacterial vaccines. (1995)

Recent developments have made it possible to construct non-reverting live bacterial vaccine candidates with defined deletions of two or more genes. Such vaccines have proven safe and immunogenic in human volunteers. Since the virulent parent strains are only pathogenic to man (S. typhi, S. flexneri, and V. cholerae), they pose no threat to the environment. Besides holding promise as efficacious vaccines for protection against typhoid fever, bacillary dysentery and cholera, the attenuated strains are well suited as vectors for delivery of heterologous antigenic epitopes from micro-organisms such as Helicobacter pylori, Neisseira gonorrhoeae, rotavirus, HIV and many others. Instead of using a virulent parent bacterium as the starting organism for making a vector, attempts have recently been made to employ non-pathogenic bacteria of the normal human flora, such as Streptococcus gordonii for delivery of foreign antigens. At present, the feasibility of this approach for human beings remains to be proven.
Myelodysplastic Syndromes (2009)

This review gives an account of the clinical and hematologic features of the myelodysplastic syndromes. It supplies the latest classification of these disorders, discusses the cytogenetic and molecular genetic changes that occur, and analyzes how some of these conditions convert to acute myeloid leukemia.
Manifestations of Sepsis (1987)

The clinical manifestations of sepsis may be flagrant or subtle. Awareness of the signs and symptoms of sepsis allows early recognition and prompt, appropriate management. The clinical presentation, relative frequency, and current pathophysiologic understanding of the manifestations of sepsis are reviewed. Special emphasis is placed on the cardiopulmonary manifestations, which are examined in a temporal sequence of preshock, early shock, and late shock states. While therapy for the underlying infection (such as antibiotics and drainage of abscesses) is often sufficient, therapy for the specific manifestations of sepsis may also be necessary. Guidelines for therapy for these manifestations of sepsis are given.
Tranilast, an antifibrogenic agent, ameliorates a dietary rat model of nonalcoholic steatohepatitis† (2008)

Our findings suggest that targeting TGF-beta with tranilast represents a new mode of therapy for NASH.
Pyrosequencing Sheds Light on DNA Sequencing (2001)

DNA sequencing is one of the most important platforms for the study of biological systems today. Sequence determination is most commonly performed using dideoxy chain termination technology. Recently, pyrosequencing has emerged as a new sequencing methodology. This technique is a widely applicable, alternative technology for the detailed characterization of nucleic acids. Pyrosequencing has the potential advantages of accuracy, flexibility, parallel processing, and can be easily automated. Furthermore, the technique dispenses with the need for labeled primers, labeled nucleotides, and gel-electrophoresis. This article considers key features regarding different aspects of pyrosequencing technology, including the general principles, enzyme properties, sequencing modes, instrumentation, and potential applications.
Electrostimulation Effects of the Vagus Nerve on Balance in Epilepsy (1992)

Preliminary results of selected postural measures in quiet standing indicate that stimulation of the vagus nerve appears not to be producing adverse effects. With this specific sample size, more testing is needed to determine long-term effects and future data analyses will examine correlations between electroencephalogram results, drug levels, and seizure frequency. In the present study three subjects have had old injuries to hips and ankles. Two subjects had normal values for postural control prior to stimulation, while other subjects were severely abnormal. In future, studies should include larger homogeneous sample sizes, as the current subjects show marked variability in age and premorbid health backgrounds. Future work should also control more vigorously for variables such as visual input (i.e., blindfolding subjects instead of simply closing the eyes). Evaluation of postural control mechanisms will be continued to assess stability changes in these patients as seizure frequency continues to subside.
The MHC-Binding and gp120-Binding Functions of CD4 Are Separable (1989)

CD4 is a cell surface glycoprotein that is thought to interact with nonpolymorphic determinants of class II major histocompatibility (MHC) molecules. CD4 is also the receptor for the human immunodeficiency virus (HIV), binding with high affinity to the HIV-1 envelope glycoprotein, gp120. Homolog-scanning mutagenesis was used to identify CD4 regions that are important in class II MHC binding and to determine whether the gp120 and class II MHC binding sites of CD4 are related. Class II MHC binding was abolished by mutations in each of the first three immunoglobulin-like domains of CD4. The gp120 binding could be abolished without affecting class II MHC binding and vice versa, although at least one mutation examined reduced both functions significantly. These findings indicate that, while there may be overlap between the gp120 and class II MHC binding sites of CD4, these sites are distinct and can be separated. Thus it should be possible to design CD4 analogs that can block HIV infectivity but intrinsically lack the ability to affect the normal immune response by binding to class II MHC molecules.
Signal stability-based adaptive routing (SSA) for ad hoc mobile networks (1997)

Ad hoc networks have no spatial hierarchy and suffer from frequent link failures which prevent mobile hosts from using traditional routing schemes. Under these conditions, mobile hosts must find routes to destinations without the use of designated routers and also must dynamically adapt the routes to the current link conditions. This article proposes a distributed adaptive routing protocol for finding and maintaining stable routes based on signal strength and location stability in an ad hoc network and presents an architecture for its implementation. Interoperability with mobile IP (Internet protocol) is discussed.
Electrical Communication between Glucose Oxidase and Electrodes Based on Poly(Vinyl Imidazole) Complex of Os(bpy)2Cl2 (1994)

Glucose oxidase was electrically wired to glassy carbon electrodes by redox hydrogels based on poly(N-vinyl imidazole) (PVI) complexed with Os(bpY) 2C12(PVI-Os). The hydrogels were formed by crosslinking PVI-Os and glucose oxidase with poly(ethylene glycol) diglycidyl ether (PEGDGE). Glucose was electrooxidized on the PVI-Os based wired enzyme electrodes at 350 mV vs SCE. The dependence of the electrooxidation current on pH, ionic strength, film thickness, weight fraction of the enzyme in the redox hydrogel and oxygen partial pressure for electrodes rotating at 1000 rpm is described.
5‐Hydroxytryptamine and functional bowel disorders (1996)

The possibility that 5-hydroxytryptamine (5-HT) acts as a key sensitising agent in the aetiology of irritable bowel syndrome (IBS) is reviewed. The strategic locations of 5-HT and its receptors are described, the most dominant being the 5-HT3 and 5-HT4 type. 5-HT, acting mostly at 5-HT3 or 5-HT3-like receptors, enhances the sensitivity of visceral neurones projecting between the gut and the central nervous systems. 5-HT, acting at 5-HT4 receptors promotes the sensitivity of enteric neurones that react to luminal stimuli. 5-HT4 and 5-HT3 receptors also mediate, respectively, sensitising and physiological actions of 5-HT on gastro-intestinal motor and secretory functions. This distribution implies that some 5-HT3 receptor antagonists might reduce certain symptoms of IBS, such as pain, by reducing the reactivity of the visceral afferent neurones linking the gut with the brain and spinal cord. However, such antagonists are not likely to find widespread clinical acceptance because they can also affect normal lower bowel function and promote constipation. 5-HT4 receptor antagonists, by contrast, reduce 5-HT-induced enteric nerve hypersensitivity without notably affecting the function of the normal bowel. Accordingly, these agents may reduce the symptoms of IBS directly, by reducing the incidence of defecation and diarrhoea and indirectly, by reducing both 'rebound' constipation and the post-prandial discomfort and pain associated with gastrointestinal hyper-reactivity.
Information-Theoretically Secure Regenerating Codes for Distributed Storage (2011)

Regenerating codes are a class of codes for distributed storage networks that provide reliability and availability of data, and also perform efficient node repair. Another important aspect of a distributed storage network is its security. In this paper, we consider a threat model where an eavesdropper may gain access to the data stored in a subset of the storage nodes, and possibly also, to the data downloaded during repair of some nodes. We provide explicit constructions of regenerating codes that achieve information-theoretic secrecy capacity in this setting.