gebhart/patrepeval huggingface dataset:
Alignment of Conduits for the Nascent Polypeptide Chain in the Ribosome-Sec61 Complex (1997)

An oligomer of the Sec61 trimeric complex is thought to form the protein-conducting channel for protein transport across the endoplasmic reticulum. A purified yeast Sec61 complex bound to monomeric yeast ribosomes as an oligomer in a saturable fashion. Cryo-electron microscopy of the ribosome-Sec61 complex and a three-dimensional reconstruction showed that the Sec61 oligomer is attached to the large ribosomal subunit by a single connection. Moreover, a funnel-shaped pore in the Sec61 oligomer aligned with the exit of a tunnel traversing the large ribosomal subunit, strongly suggesting that both structures function together in the translocation of proteins across the endoplasmic reticulum membrane.
Vaccinia Virus Recombinant Expressing Herpes Simplex Virus Type 1 Glycoprotein D Prevents Latent Herpes in Mice (1985)

In humans, herpes simplex virus causes a primary infection and then often a latent ganglionic infection that persists for life. Because these latent infections can recur periodically, vaccines are needed that can protect against both primary and latent herpes simplex infections. Infectious vaccinia virus recombinants that contain the herpes simplex virus type 1 (HSV-1) glycoprotein D gene under control of defined early or late vaccinia virus promoters were constructed. Tissue culture cells infected with these recombinant viruses synthesized a glycosylated protein that had the same mass (60,000 daltons) as the glycoprotein D produced by HSV-1. Immunization of mice with one of these recombinant viruses by intradermal, subcutaneous, or intraperitoneal routes resulted in the production of antibodies that neutralized HSV-1 and protected the mice against subsequent lethal challenge with HSV-1 or HSV-2. Immunization with the recombinant virus also protected the majority of the mice against the development of a latent HSV-1 infection of the trigeminal ganglia. This is the first demonstration that a genetically engineered vaccine can prevent the development of latency.
Sorting of β-Actin mRNA and Protein to Neurites and Growth Cones in Culture (1998)

The transport of mRNAs into developing dendrites and axons may be a basic mechanism to localize cytoskeletal proteins to growth cones and influence microfilament organization. Using isoform-specific antibodies and probes for in situ hybridization, we observed distinct localization patterns for beta- and gamma-actin within cultured cerebrocortical neurons. beta-Actin protein was highly enriched within growth cones and filopodia, in contrast to gamma-actin protein, which was distributed uniformly throughout the cell. beta-Actin protein also was shown to be peripherally localized after transfection of beta-actin cDNA bearing an epitope tag. beta-Actin mRNAs were localized more frequently to neuronal processes and growth cones, unlike gamma-actin mRNAs, which were restricted to the cell body. The rapid localization of beta-actin mRNA, but not gamma-actin mRNA, into processes and growth cones could be induced by dibutyryl cAMP treatment. Using high-resolution in situ hybridization and image-processing methods, we showed that the distribution of beta-actin mRNA within growth cones was statistically nonrandom and demonstrated an association with microtubules. beta-Actin mRNAs were detected within minor neurites, axonal processes, and growth cones in the form of spatially distinct granules that colocalized with translational components. Ultrastructural analysis revealed polyribosomes within growth cones that colocalized with cytoskeletal filaments. The transport of beta-actin mRNA into developing neurites may be a sequence-specific mechanism to synthesize cytoskeletal proteins directly within processes and growth cones and would provide an additional means to deliver cytoskeletal proteins over long distances.
Recent-secure authentication: enforcing revocation in distributed systems (2002)

A general method is described for formally specifying and reasoning about distributed systems with any desired degree of immediacy for revoking authentication. To effect revocation, 'authenticating entities' impose freshness constraints on credentials or authenticated statements made by trusted intermediaries. If fresh statements are not presented, then the authentication is questionable. Freshness constraints are derived from initial policy assumptions and authentic statements made by trusted intermediaries. By adjusting freshness constraints, the delay for certain revocation can be arbitrarily bounded. We illustrate how the inclusion of freshness policies within certificates enables the design of a secure and highly available revocation service. We illustrate the application of the method and new techniques in an example.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Recombinant Modified Vaccinia Virus Ankara Expressing the Hemagglutinin Gene Confers Protection against Homologous and Heterologous H5N1 Influenza Virus Infections in Macaques (2008)

Therefore, MVA-HA-VN/04 is a promising vaccine candidate for the induction of protective immunity against highly pathogenic H5N1 avian influenza viruses in humans.
Clone-specific T cell receptor antagonists of major histocompatibility complex class I-restricted cytotoxic T cells. (1993)

A previous report showed that the proliferative response of helper T cells to class II major histocompatibility complex (MHC)-restricted antigens can be inhibited by analogues of the antigen, which act as T cell receptor (TCR) antagonists. Here we define and analyze peptide variants that antagonize various functions of class I MHC-restricted cytotoxic T lymphocyte (CTL) clones. Of 64 variants at individual TCR contact sites of the Kb-restricted octamer peptide ovalbumin257-264 (OVAp), a very high proportion (40%) antagonized lysis by three OVAp-specific CTL clones. This effect was highly clone specific, since many antagonists for one T cell clone have differential effects on another. We show that this inhibition of CTL function is not a result of T cell-T cell interaction, precluding veto-like phenomena as a mechanism for antagonism. Moreover, we present evidence for direct interaction between the TCR and antagonist-MHC complexes. In further analysis of the T cell response, we found that serine esterase release and cytokine production are susceptible to TCR antagonism similarly to lysis. Ca2+ flux, an early event in signaling, is also inhibited by antagonists but may be more resistant to the antagonist effect than downstream responses.
Effect of Thin Gold Interstitial-layer on the Photovoltaic Properties of Tandem Organic Solar Cell (1990)

Abstract Tandem type organic solar cell consisting of two combined unit cells was fabricated. Each unit cell was two-layer organic solar cell composed of metal-free phthalocyanine and perylene tetracarboxylic derivative. When ultra-thin Au layer was inserted between unit cells, photovoltage increased about 2 times, while photocurrent density was much dependent on the thickness of the inserted Au layer.
Mood, Sexuality, Hormones, and the Menstrual Cycle. III. Sexuality and the Role of Androgens (1983)

Sexual interest and activity at different stages of the menstrual cycle was recorded by 55 women with normal ovulatory cycles. In women with marked cyclical mood change, there was an associated cyclical pattern of sexual feelings. Subjective sexuality independent of mood change, was maximal in the mid-follicular (i.e., postmenstrual) and late luteal (i.e., premenstrual) phases. Sexual activity was maximal in the mid-follicular phase. There was no evidence of a periovulatory increase in sexual interest or activity. Mean testosterone levels were correlated with masturbation frequency but not with sexuality involving the partner. A weak association between testosterone and life style (i.e., in full-time work or a housewife) was also evident.
Object-oriented units of measurement (2004)

Programs that manipulate physical quantities typically represent these quantities as raw numbers corresponding to the quantities' measurements in particular units (e.g., a length represented as a number of meters). This approach eliminates the possibility of catching errors resulting from adding or comparing quantities expressed in different units (as in the Mars Climate Orbiter error [11]), and does not support the safe comparison and addition of quantities of the same dimension. We show how to formulate dimensions and units as classes in a nominally typed object-oriented language through the use of statically typed metaclasses. Our formulation allows both parametric and inheritance poly-morphism with respect to both dimension and unit types. It also allows for integration of encapsulated measurement systems, dynamic conversion factors, declarations of scales (including nonlinear scales) with defined zeros, and nonconstant exponents on dimension types. We also show how to encapsulate most of the "magic machinery" that handles the algebraic nature of dimensions and units in a single meta-class that allows us to treat select static types as generators of a free abelian group.
Neuropsychiatric sequelae of head injury (2005)

Almost half of people suffering head injury may later be diagnosed with neuropsychiatric disorders. Psychiatric disturbances associated with head injury are reviewed. Authors highlight the close link between head injury and psychiatry and provide an overview of the epidemiology, risk factors, and mechanisms of psychiatric sequelae including cognitive deficits, substance abuse, psychoses, mood disorders, suicide, anxiety disorders, dissociative disorders, post-concussion syndrome and personality changes following head injury. Various neuropsychiatric sequelae are briefly discussed and the respective treatments are outlined with emphasis on a multidisciplinary approach.
Thermochemical Properties of Nicotine Salts (2001)

Abstract The thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC) results presented in this report clearly show that the thermal stability and the endothermic peak nicotine release temperatures are different for different nicotine salts and these temperatures appear to be linked to the general microstructural details of the salt itself. In addition, the peak nicotine release temperatures are highly dependent upon the sample size used. The heat of vaporization for neat (non-protonated) nicotine is also sample-size dependent. The TGA data showed that the least stable of the salts tested at elevated temperatures was the liquid salt nicotine triacetate followed by the crystalline materials (e.g., nicotine gallate) and finally, the amorphous salts (e.g., nicotine alginate). The DSC results revealed that the liquid and crystalline salts exhibit nicotine release endotherms that are strongly related to the sample weight being tested. The amorphous salts show nicotine endotherm peak temperatures that are nearly independent of the sample weight. The range of peak nicotine release temperatures varied depending upon the specific salts and the sample size from 83 oC to well over 200 oC. Based on these results, the evolution of nicotine from the nicotine salt should be expected to vary based on the composition of the salt, the details of its microstructure, and the amount of nicotine salt tested.
Regression of Coronary Artery Disease as a Result of Intensive Lipid-Lowering Therapy in Men with High Levels of Apolipoprotein B (1990)

In men with coronary artery disease who were at high risk for cardiovascular events, intensive lipid-lowering therapy reduced the frequency of progression of coronary lesions, increased the frequency of regression, and reduced the incidence of cardiovascular events.
mRNA polyadenylate-binding protein: gene isolation and sequencing and identification of a ribonucleoprotein consensus sequence. (1986)

We identified and produced antibodies to the major proteins that interact with poly(A)+ RNAs in the yeast Saccharomyces cerevisiae. The major proteins which were cross-linked by UV light to poly(A)+ RNA in intact yeast cells had apparent molecular weights of 72,000, 60,000, and 50,000. The poly(A) segment of the RNA was selectively cross-linked to the 72,000-molecular-weight protein (72K protein). Mice immunized with purified UV-cross-linked RNA-protein (RNP) complexes produced antibodies to the three major RNP proteins. A yeast genomic DNA library constructed in the lambda gt11 expression vector was screened with the anti-RNP serum, and recombinant bacteriophage clones were isolated. One recombinant phage, lambda YPA72.1, bearing a 2.5-kilobase insert, produced a large beta-galactosidase-RNP fusion protein. Affinity-selected antibodies from the anti-RNP serum on this fusion protein recognized a single 72K protein which was cross-linked to the poly(A) segment of RNA in the intact cell. Furthermore, the fusion protein of lambda YPA72.1 had specific poly(A)-binding activity. Therefore, lambda YPA72.1 encodes the 72K poly(A)-binding protein. Immunofluorescence microscopy showed that this protein was localized in the cytoplasm. Hybrid-selected mRNA translated in vitro produced the 72K poly(A)-binding protein, and mRNA blot analysis detected a single 2.1-kilobase mRNA. DNA blot analysis suggested a single gene for the poly(A)-binding protein. DNA sequence analysis of genomic clones spanning the entire gene revealed a long open reading frame encoding a 64,272-molecular-weight protein with several distinct domains and repeating structural elements. A sequence of 11 to 13 amino acids is repeated three times in this protein. Strikingly, this repeated sequence (RNP consensus sequence) is highly homologous to a sequence that is repeated twice in a major mammalian heterogeneous nuclear RNP protein, A1. The conservation of the repetitive RNP consensus sequence suggests an important function and a common evolutionary origin for messenger RNP and heterogeneous nuclear RNP proteins.
Transcription factor ATF cDNA clones: an extensive family of leucine zipper proteins able to selectively form DNA-binding heterodimers. (1989)

An activating transcription factor (ATF)-binding site (consensus sequence 5'-GTGACGTACAG-3') is a promoter element present in a wide variety of viral and cellular genes. The two best-characterized classes of genes that contain ATF sites are E1A-inducible adenoviral genes and cAMP-inducible cellular genes. Here, we report the isolation of eight ATF cDNA clones, each of which is derived from a separate gene. All ATF cDNA clones examined contain a leucine zipper motif and are significantly similar to one another only within this region. The leucine zipper region of ATF proteins is also similar to that of the AP-1/c-jun family of transcription factors, whose DNA-binding site differs from the ATF-binding site at a single position. DNA binding studies reveal two mechanisms for generating further diversity from the ATF proteins. First, some, but not all, combinations of ATF proteins form heterodimers that efficiently bind to DNA. Second, although all ATF proteins bind to the ATF site, their precise interactions with DNA differ from one another, as evidenced by methylation interference analysis. Our results help to explain how a single promoter element, an ATF site, can be present in a wide variety of promoters.
Traffic Management of Special Events in Small Communities (2009)

Planned special events (PSE), such as sporting events and concerts, produce nonrecurring congestion as attendees simultaneously attempt to exit the event and overload the local transportation network. These types of events can have a significant impact on traffic operations, particularly in small urban and rural environments, where limited infrastructure is available to access and egress the PSE venue. The research presented here applied a variety of traffic management strategies to manage congestion resulting from football games at Montana State University in Bozeman, Montana, in fall 2007. These strategies included the provision of real-time travel information, road closures, traffic signal retiming, and real-time traffic monitoring. Results indicated that these strategies could be successfully applied in a rural community to manage the congestion arising from PSEs. For example, results indicated that signal retiming and manual traffic control strategies allowed for improvements in traffic flow on approaches that served game traffic.
Specific interaction of CCR5 amino-terminal domain peptides containing sulfotyrosines with HIV-1 envelope glycoprotein gp120 (2000)

The HIV-1 envelope glycoprotein gp120 interacts consecutively with CD4 and the CCR5 coreceptor to mediate the entry of certain HIV-1 strains into target cells. Acidic residues and sulfotyrosines in the amino-terminal domain (Nt) of CCR5 are crucial for viral fusion and entry. We tested the binding of a panel of CCR5 Nt peptides to different soluble gp120/CD4 complexes and anti-CCR5 mAbs. The tyrosine residues in the peptides were sulfated, phosphorylated, or unmodified. None of the gp120/CD4 complexes associated with peptides containing unmodified or phosphorylated tyrosines. The gp120/CD4 complexes containing envelope glycoproteins from isolates that use CCR5 as a coreceptor associated with Nt peptides containing sulfotyrosines but not with peptides containing sulfotyrosines in scrambled Nt sequences. Finally, only peptides containing sulfotyrosines inhibited the entry of an R5 isolate. Our data show that proper posttranslational modification of the CCR5 Nt is required for gp120 binding and viral entry. More importantly, the Nt domain determines the specificity of the interaction between CCR5 and gp120s from isolates that use this coreceptor.
Hepatocytes and Epithelial Cells of Donor Origin in Recipients of Peripheral-Blood Stem Cells (2002)

Circulating stem cells can differentiate into mature hepatocytes and epithelial cells of the skin and gastrointestinal tract.
Using Soluble Polymers in Latent Biphasic Systems (2003)

A new strategy for carrying out reactions with a soluble polymer-bound reagent or catalyst is described. In this latent biphasic process, a solvent mixture at the cusp of immiscibility is prepared and used to carry out a reaction under homogeneous conditions. Then, after the reaction is complete, this mixture is perturbed by the addition of solvent or some other perturbing agent to produce a biphasic mixture. The product-containing phase is then separated under liquid/liquid conditions from the polymer-containing phase. The generality of this process is demonstrated using both dye-labeled polymers as surrogates for polymer-bound catalysts and with various polymer-bound organic and transition metal catalysts or reagents. In cases where a polymeric catalyst is used, the addition of fresh solvent and substrate reforms the original mixture allowing facile reuse of the catalyst.
Expression of the c-Kit receptor and its ligand SCF in non-small-cell lung carcinomas (1998)

Increasing experimental evidence indicates that stem-cell factor (SCF) and its cognate receptor c-Kit may participate in the growth control of various solid human malignancies. In the present study, we have extended this analysis to non-small-cell lung carcinomas (NSCLC). The results of an immunohistochemical analysis demonstrated that c-Kit/SCF are expressed by 30%/58% of adenocarcinomas, 15%/37% of squamous-cell carcinomas and by 40%/30% of undifferentiated carcinomas respectively. In 15% of primary and 18% of metastatic tumors, co-expression of the receptor and its ligand was documented. Western-blot assays of tumor extracts demonstrated that both molecules exhibit features of the normal receptor and ligand. Since biologically active SCF is physiologically present in the bloodstream, our data indicate that SCF is available to c-kit-expressing NSCLC cells via autocrine, paracrine or endocrine mechanisms. Thus activation of c-Kit in these tumors may contribute critically to their progression.
Fc receptor signaling and trafficking: a connection for antigen processing (1999)

Most hematopoietic cells express a wide variety of receptors for the Fc portion of immunoglobulins (FcR) belonging to the immunoreceptor family. FcRs are multichain complexes composed of ligand-binding alpha chains, which determine Ig binding, and signal tranduction subunits, bearing a conserved immunoreceptor tyrosine-based activation motif (ITAM). Besides signaling, most Fc gamma Rs also efficiently internalize antigen-antibodies complexes and thus induce efficient processing of antigens into peptides presented by major histocompatibility complex (MHC) class II molecules. Importantly, ITAMs and cytosolic effectors of cell signaling also determine Fc gamma R's endocytic transport and antigen presentation capacities.
Chromosomal rearrangements and microRNAs: a new cancer link with clinical implications (2007)

There is widespread aberrant expression of mature and/or precursor microRNAs in cancer cells, as microRNAs are deregulated consequent to chromosomal alterations and other genomic abnormalities. The identification of such abnormalities has a clear diagnostic and prognostic significance, and there are ever increasing examples of links between certain human cancers and modifications at microRNA loci.