gebhart/patrepeval huggingface dataset:
Prediction and identification of a T cell epitope in the fusion protein of measles virus immunodominant in mice and humans (1990)

Amino acid residues 288 to 302 of the fusion protein of measles virus were predicted by a variety of methods to represent a putative T cell epitope. This sequence was synthesized and the peptide was injected into mice of six inbred strains to test this possibility. Lymphocytes from peptide-immunized mice from all six H-2 disparate strains were able to mount a proliferative response following in vitro culture with the peptide. In addition, lymphocytes from three strains also proliferated in the presence of live measles virus. The peptide also behaved as a B cell epitope in that immunization with free peptide in adjuvant resulted in anti-peptide antibody production in all mouse strains. However, these antibodies did not react with the virus in either a solid-phase immunoassay or a virus neutralization assay. Peripheral blood lymphocytes from 10 laboratory personnel with a prior history of exposure to measles virus were tested in a proliferation assay with the peptide and with the virus. Lymphocytes from all 10 individuals proliferated in response to culture with the virus and those from eight responded to the peptide. These results give further support to the concept of permissive interaction of antigenic peptides with a wide range of class II major histocompatibility complex molecules both in mice and man and indicate the possibility of designing peptides that could be used as components of a synthetic vaccine for use in man.
Perfil del profesor universitario (2005)

El rol que debe desempenar el profesor en el ambito universitario es un tema muy controvertido. En este texto se defiende la figura del profesor como mediador, experto en su area de conocimiento pero a la vez ilusionado con su papel como docente. Se le concibe como estimulador de la perplejidad intelectual, facilitador del aprendizaje significativo, impulsor del trabajo en equipo, critico, comprometido y transmisor de cultura. Para que esto sea posible es necesario que los docentes reciban una formacion adecuada que les permita desarrollarse equilibradamente como profesores y como investigadores, asi como crear recursos de apoyo efectivo a la docencia en la Universidad que favorezcan la mejora de la practica docente.
The Preparation of Solid-Supported Peptide Boronic Acids Derived from 4-Borono-l-phenylalanine and their Affinity for Alizarin (2007)

A library of solid-supported pentapeptide diboronic acids, a ‘lysine series’ and an ‘arginine series’, has been efficiently prepared using N-Fmoc-4-pinacolatoborono-l-phenylalanine and standard solid phase peptide synthesis methods. A technique for measuring the affinity of the chromophoric diol, alizarin, to the solid-supported peptide boronic acids has been developed. Considerable variation in alizarin binding strengths, both within and between arginine and lysine series was observed, with association constants in the range 200–1100 M–1 being recorded. The selective binding characteristics of these boronic acid–peptide hybrids suggest their potential use in carbohydrate sensors and cell-specific diagnostics and therapeutics.
A 1.25 Gb/s, 460 mW CMOS transceiver for serial data communication (2002)

To improve I/O performance in computer systems and networks, many new serial data communication standards have been recently proposed with data rates in the gigabit per second range. For example, the proposed IEEE Gigabit Ethernet standard has an encoded baud rate of 1.25Gb/s. Similarly, the IEEE 1394.2 Serial Express proposal requires a baud rate of 1.25Gb/s. Although not yet finalized, it is likely that the physical layers of both the Gigabit Ethernet and the Serial Express will be based upon the ANSI Fibre Channel standard. It is possible to design a single transceiver for all three applications. A single-chip CMOS transceiver is fully compliant with the ANSI Fibre Channel standard at 1.0625Gb/s. It is capable of running at 1.2 or 1.25Gb/s and, therefore, can potentially be used for Gigabit Ethernet and Serial Express.
Prevalence of Prostate Cancer among Men with a Prostate-Specific Antigen Level ≤4.0 ng per Milliliter (2004)

Biopsy-detected prostate cancer, including high-grade cancers, is not rare among men with PSA levels of 4.0 ng per milliliter or less--levels generally thought to be in the normal range.
Abelson virus abrogation of interleukin-3 dependence in a lymphoid cell line. (1986)

Among several tyrosine-protein kinases, only v-abl could abrogate interleukin 3 dependence of a lymphoblastoid cell line; v-src and v-fps proteins gave partial or no interleukin 3 independence, respectively. Lymphokine independence was achieved via a nonautocrine mechanism. Direct involvement of c-myc in this process was not evident.
Water Intensity of Transportation (2008)

As the need for alternative transportation fuels increases, it is important to understand the many effects of introducing fuels based upon feedstocks other than petroleum. Water intensity in "gallons of water per mile traveled" is one method to measure these effects on the consumer level. In this paper we investigate the water intensity for light duty vehicle (LDV) travel using selected fuels based upon petroleum, natural gas, unconventional fossil fuels, hydrogen, electricity, and two biofuels (ethanol from corn and biodiesel from soy). Fuels more directly derived from fossil fuels are less water intensive than those derived either indirectly from fossil fuels (e.g., through electricity generation) or directly from biomass. The lowest water consumptive (<0.15 gal H20/mile) and withdrawal (<1 gal H2O/mile) rates are for LDVs using conventional petroleum-based gasoline and diesel, nonirrigated biofuels, hydrogen derived from methane or electrolysis via nonthermal renewable electricity, and electricity derived from nonthermal renewable sources. LDVs running on electricity and hydrogen derived from the aggregate U.S. grid (heavily based upon fossil fuel and nuclear steam-electric power generation) withdraw 5-20 times and consume nearly 2-5 times more water than by using petroleum gasoline. The water intensities (gal H20/mile) of LDVs operating on biofuels derived from crops irrigated in the United States at average rates is 28 and 36 for corn ethanol (E85) for consumption and withdrawal, respectively. For soy-derived biodiesel the average consumption and withdrawal rates are 8 and 10 gal H2O/mile.
Mode of resistance to respiration inhibitors at the cytochrome bc1 enzyme complex of Mycosphaerella fijiensis field isolates (2000)

Field isolates of Mycosphaerella fijiensis, causing black Sigatoka of banana, were characterised for their sensitivity to different inhibitors of the cytochrome bc1 enzyme complex (Qo respiration inhibitors, strobilurin fungicides), using physiological, biochemical and molecular genetic methods. Strobilurin-resistant isolates exhibited very high resistance factors both in mycelial growth inhibition and NADH consumption assays. Cross-resistance was observed among all Qo inhibitors, including trifloxystrobin, azoxystrobin, famoxadone, strobilurin B and myxothiazol. However, the Qi and the cytochrome aa3 inhibitors, antimycin A and potassium cyanide, respectively, were not cross-resistant to Qo inhibitors. In sensitive but not in resistant isolates, mixtures of Qo inhibitors and SHAM, an inhibitor of the alternative oxidase (AOX), were more active than the components alone, indicating that the alternative pathway is essential in metabolism, but not causal for resistance. In the cell-free NADH-consumption assay, the Qo inhibitors affected the sensitive but not the resistant isolates, suggesting that AOX was not active in sub-mitochondrial particles. In whole cells, however, the AOX has a basic expression level and is probably not inducible by trifloxystrobin. Sequencing of the cytochrome b gene of sensitive and resistant M fijiensis isolates revealed a difference in the nucleotide sequence leading to a single amino acid change from glycine to alanine at position 143 in the resistant isolate. This change is known to occur also in the naturally tolerant basidiomycete Mycena galopoda. It is suggested that the field isolates of M fijiensis can acquire resistance to Qo inhibitors due to a target site alteration with a single base pair change. Resistant isolates do not seem to contain a mixture of mutated and non-mutated DNA, indicating a complete selection of resistant mitochondria and a maternally donated mode of resistance. © 2000 Society of Chemical Industry
Theory of the soliton self-frequency shift (1986)

Raman effects cause a continuous downshift of the mean frequency of pulses propagating in optical fibers. For solitons in silica fibers, the effect varies roughly with the inverse fourth power of the pulse width. At 1.5-microm wavelength in a fiber with 15 psec/nm/km time-of-flight dispersion, a soliton of 250-fsec duration is predicted to shift by its own spectral width after about l00m of propagation. The theory agrees well with recent measurements.
Promising Personalized Therapeutic Options for Diffuse Large B-cell Lymphoma Subtypes with Oncogene Addictions (2012)

Currently, two major classification systems segregate diffuse large B-cell lymphoma (DLBCL) into subtypes based on gene expression profiles and provide great insights about the oncogenic mechanisms that may be crucial for lymphomagenesis as well as prognostic information regarding response to current therapies. However, these current classification systems primarily look at expression and not dependency and are thus limited to inductive or probabilistic reasoning when evaluating alternative therapeutic options. The development of a deductive classification system that identifies subtypes in which all patients with a given phenotype require the same oncogenic drivers, and would therefore have a similar response to a rational therapy targeting the essential drivers, would significantly advance the treatment of DLBCL. This review highlights the putative drivers identified as well as the work done to identify potentially dependent populations. These studies integrated genomic analysis and functional screens to provide a rationale for targeted therapies within defined populations. Personalizing treatments by identifying patients with oncogenic dependencies via genotyping and specifically targeting the responsible drivers may constitute a novel approach for the treatment of DLBCL.
Fluorescence imaging of cancer tissue based on metal-free polymeric nanoparticles – a review (2013)

The utilization of fluorescent nanoparticles (FNPs), which consist of organic fluorophores embedded into a polymer matrix, seems to be a promising concept for in vivo cancer imaging showing good biocompatibility, biodegradability, and low toxicity of the agents. Polymeric nanoparticles as fluorescent nanocarriers can be systematically designed with regard to the requested task, i.e., specific accumulation in the tumor tissue. Versatile organic fluorophores can be entrapped into polymers with fine-tuned properties, which were synthesized via polymerization techniques. Moreover, the formulation of the nanoparticles can be adjusted, and passive as well as active targeting strategies can be employed. Despite their evident benefits, fluorescent polymeric nanoparticles are still not in clinical application for cancer detection due to a still existing lack of understanding of their in vivo interactions as well as their reproducible production. This review focuses on cancer imaging based on organic dyes and metal-free polymeric fluorescent nanoparticles highlighting recent interesting reports about their design and application as well as their limitations.
Human mucosal addressin cell adhesion molecule-1 is preferentially expressed in intestinal tract and associated lymphoid tissue. (1997)

Lymphocyte homing to normal tissues and recruitment to inflammatory tissue sites are controlled, in part, by the selective expression of chemokines, pro-inflammatory cytokines and mediators, and various adhesion proteins and molecules. In the mouse, mucosal addressin cell adhesion molecule-1 (MAdCAM-1) is selectively expressed on endothelium of high endothelial venules in gut and gut-associated lymphoid tissue. By interaction with its integrin ligand, alpha 4 beta 7, lymphocytes presumed to be involved in mucosal immunity are selectively recruited to these intestinal sites. After generating monoclonal antibodies against a murine cell line expressing recombinant human MAdCAM-1, we qualitatively and semiquantitatively assessed MAdCAM-1 expression in human tissue sections from various normal and inflammatory disorders. We found that human MAdCAM-1, as in the mouse, is expressed in a tissue-selective manner. In normal tissues, MAdCAM-1 is constitutively expressed to endothelium of venules of intestinal lamina propria. Interestingly, using computer-assisted morphometric analysis, the proportion of venular endothelium within lamina propria that expresses MAdCAM-1 is increased, compared with normal tissues, at inflammatory foci associated with ulcerative colitis and Crohn's disease. Moreover, for the most part, MAdCAM-1 is not detected in the majority of normal or inflamed extra-intestinal tissues, including those with mucosal surfaces. These results are consistent with a role, as originally defined in the mouse, for human MAdCAM-1 in the localization of alpha 4 beta 7+ lymphocytes in the gastrointestinal tract and associated lymphoid tissue. As such, the pathway defined by MAdCAM-1/alpha 4 beta 7 may be a relevant tissue-specific therapeutic target for the modulation of inflammatory bowel disease activity.
Split intein mediated ultra‐rapid purification of tagless protein (SIRP) (2013)

Rapid and efficient tag removal remains a significant problem in recombinant protein purification. Using an engineered DnaE intein from Nostoc punctiforme, we developed a split intein mediated ultra-rapid purification (SIRP) method for the purification of tagless recombinant protein from E. coli lysate in less than 1 h. This system exhibits extraordinarily rapid thio-induced C-terminal cleavage with about 50% completion within 30 s at both 22°C and 6°C. This is the fastest C-terminal cleavage activity reported to date for inteins. Although the reaction kinetics slow down after the first minute, >90% cleavage completion is achieved within 30 min at 22°C, or within 3 h at 6°C. The ultra-rapid cleavage kinetics are made possible by the positioning of the purification tag at the split junction to the C-terminus of the intein N-fragment, thus avoiding potential steric hindrance of the critical interaction between the N- and C-extein. Target proteins are cleaved to >72% completion after 1 h of intein reaction regardless of the identity of the N-terminal amino acid except in the cases of threonine (50% cleavage) and proline. The C-terminal cleavage reaction can be effectively inhibited by divalent Zn(2+) under non-reducing conditions. Importantly, the association of the intein N- and C-fragments is reversible, enabling the column-bound intein N-fragment bait protein to be regenerated for multiple usages and further reducing the cost of protein purification. SIRP technology should provide a useful tool for the purification of tagless proteins and peptides.
Programmable shaping of femtosecond optical pulses by use of 128-element liquid crystal phase modulator (1992)

Programmable shaping of femtosecond pulses by using a 128-element liquid crystal modulator to manipulate the phases of optical frequency components which are spatially dispersed within a grating-and-lens pulse shaping apparatus is described. This apparatus makes possible gray-level control of the spectral phases and allows modification of the pulse shape on a millisecond time scale under electronic control. Refinements in the design of the multielement modulator result in pulse shaping fidelity comparable to that which can be achieved with microlithographically fabricated masks. Several examples of pulse shaping operation, including pulse position modulation, programmable pulse compression, and adjustable cubic phase distortion, are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of the PspA Sequence fromStreptococcus pneumoniaeEF5668 to the Previously Identified PspA Sequence from Strain Rx1 and Ability of PspA from EF5668 To Elicit Protection against Pneumococci of Different Capsular Types (1998)

PspA (pneumococcal surface protein A) is a serologically varied virulence factor of Streptococcus pneumoniae. In mice, PspA has been shown to elicit an antibody response that protects against fatal challenge with encapsulated S. pneumoniae, and the protection-eliciting residues have been mapped to the alpha-helical N-terminal half of the protein. To date, a published DNA sequence for pspA is available only for S. pneumoniae Rx1, a laboratory strain. PspA/EF5668 (EF5668 indicates the strain of origin of the PspA) is serologically distinct from PspA/Rx1. Sequencing of the gene encoding PspA/EF5668 revealed 71% identity with that of PspA/Rx1. The greatest amount of divergence between the two proteins was seen in their alpha-helical portions, which are surface exposed and probably under selective pressure to diversify serologically. In spite of the diversity within the alpha-helical regions of PspAs, we have observed that recombinant PspA (rPspA)/EF5668, like rPspA/Rx1, can elicit cross-protection against pneumococci of different capsular and PspA serological types.
Effect of Direct-Fed Microbials on Performance, Diet Digestibility, and Rumen Characteristics of Holstein Dairy Cows (2007)

The objective of this study was to determine the effect of feeding direct-fed microbial (DFM) products containing Lactobacillus acidophilus and Propionibacteria freudenreichii on the performance, nutrient digestibility, and rumen fermentation of Holstein dairy cows in midlactation. Experiments were conducted from February to May 2003. Cows were fed 1 of 3 dietary treatments: 1) 1 x 10(9) colony-forming units (cfu)/d of live L. acidophilus strain LA747 and 2 x 10(9) cfu/d of live P. freudenreichii strain PF24 (DFM1); 2) 1 x 10(9) cfu/d of live L. acidophilus strain LA747, 2 x 10(9) cfu/d of live P. freudenreichii strain PF24, and 5 x 10(8) cfu/d of L. acidophilus strain LA45 (DFM2); or 3) lactose (control). Treatments were administered by mixing 45 g of finely ground corn with 5 g of DFM products or lactose and top dressing on the total mixed rations once daily. All cows received the same total mixed ration: 12.7% alfalfa hay, 46.2% corn silage, and 41.1% concentrate on a dry matter (DM) basis. In study 1 (lactation study), 39 multiparous and 18 primiparous Holstein cows were blocked by parity and randomly assigned to treatments for 84 d. Starting on d 35, fecal grab samples were collected from each cow at 5- to 8-h intervals over 48 h for digestibility measurements. A rumen fermentation study (study 2) was conducted concurrently with the lactation study. Three rumenfistulated, multiparous Holstein cows were randomly assigned to dietary treatments DFM1, DFM2, and control in a 3 x 3 Latin square design with 28-d periods. In study 1, there was no difference in average DM intake (23.9, 23.6, and 24.2 kg/d) or 4% fat-corrected milk (36.8, 35.3, and 36.2 kg/d) for treatments DFM1, DFM2, and control. Percentage or yield of milk components also did not differ among treatments. Feed efficiency averaged 1.52 kg of 4% fat-corrected milk/kg of DM intake and did not differ among treatments. There were no differences in apparent DM, crude protein, neutral detergent fiber, or starch digestibility among treatments. In study 2, there was no difference in rumen pH and concentrations of ammonia or total volatile fatty acids measured at 0, 1, 3, and 6 h after feeding. Under the conditions of these studies, supplementing midlactation cows with DFM products containing L. acidophilus and P. freudenreichii did not affect cow performance, diet digestibility, or rumen fermentation.
A PCR differential screening method for rapid isolation of clones from a cDNA library. (1994)

We have developed a new two-step differential screening method that allows the rapid isolation of induced or suppressed pure gene clones from a lambda phage cDNA library. This method involves a primary differential screening step and a PCR differential screening step. From the primary screening step, impure pools of positive cDNA clones are obtained. Each pool of clones is then amplified directly by PCR using two primers flanking the cloning site in the vector. The PCR products are run on two duplicate agarose gels and blotted onto two filter strips. These two filters are then subjected to differential Southern hybridization with different cDNA probes. Each pure positive cDNA band on the gel is identified and selected for further subcloning. This method has three advantages over the traditional differential screening method. First, several rounds of plaque rescreening are replaced by a single PCR screening. Second, plaque hybridization is replaced by a more reliable and accurate PCR DNA Southern hybridization. Third, the time-consuming and tedious phage DNA isolation step is eliminated, and subcloning is facilitated by direct cloning of the pure PCR product to a plasmid vector. We have successfully used this method to isolate ozone-responsive genes from a cDNA library of monkey respiratory airways.
Complex effects of nucleotide variants in a mammalian cis -regulatory element (2012)

Cis -regulatory elements (CREs) control gene expression by recruiting transcription factors (TFs) and other DNA binding proteins. We aim to understand how individual nucleotides contribute to the function of CREs. Here we introduce CRE analysis by sequencing (CRE-seq), a high-throughput method for producing and testing large numbers of reporter genes in mammalian cells. We used CRE-seq to assay &gt;1,000 single and double nucleotide mutations in a 52-bp CRE in the Rhodopsin promoter that drives strong and specific expression in mammalian photoreceptors. We find that this particular CRE is remarkably complex. The majority (86%) of single nucleotide substitutions in this sequence exert significant effects on regulatory activity. Although changes in the affinity of known TF binding sites explain some of these expression changes, we present evidence for complex phenomena, including binding site turnover and TF competition. Analysis of double mutants revealed complex, nucleotide-specific interactions between residues in different TF binding sites. We conclude that some mammalian CREs are finely tuned by evolution and function through complex, nonadditive interactions between bound TFs. CRE-seq will be an important tool to uncover the rules that govern these interactions.