gebhart/patrepeval huggingface dataset:
The Protein Information Resource: an integrated public resource of functional annotation of proteins (2002)

The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases).
Reversible Performance of Dodecyl Tetramethyl Guanidine Solution Induced by CO2 Trigger (2009)

Abstract Dodecyl tetramethyl guanidine (DTMG) were synthesized and characterized, and its reversible performance was studied. The results showed that DTMG could form bicarbonate ionic adduct after exposed to CO 2 , so it could be used as CO 2 switchable surfactants. By bubbling CO 2 through DTMG solution or heating CO 2 saturated DTMG solution, the alkali and surface active properties of solution was changed reversibly. Emulsion and foam stabilized by DTMG could be controlled between stable and unstable state by CO 2 . In addition, the state of DTMG solution was easy to be distinguished by naked eye through a simple indicator, phenolphthalein. Pink indicated it was inactive, and colorless indicated it was active.
The Transmembrane Aspartates in Presenilin 1 and 2 Are Obligatory for γ-Secretase Activity and Amyloid β-Protein Generation (2000)

The discovery that a deficiency of presenilin 1 (PS1) decreases the production of amyloid beta-protein (Abeta) identified the presenilins as important mediators of the gamma-secretase cleavage of beta-amyloid precursor protein (APP). Recently, we found that two conserved transmembrane (TM) aspartates in PS1 are critical for Abeta production, providing evidence that PS1 either functions as a required diaspartyl cofactor for gamma-secretase or is itself gamma-secretase. Presenilin 2 (PS2) shares substantial sequence and possibly functional homology with PS1. Here, we show that the two TM aspartates in PS2 are also critical for gamma-secretase activity, providing further evidence that PS2 is functionally homologous to PS1. Cells stably co-expressing TM Asp --> Ala mutations in both PS1 and PS2 show further accumulation of the APP-derived gamma-secretase substrates, C83 and C99. The production of Abeta is reduced to undetectable levels in the conditioned media of these cells. Furthermore, endoproteolysis of the exogenous Asp mutant PS2 is absent, and endogenous PS1 C-terminal fragments are diminished to undetectable levels. Therefore, the co-expression of PS1 and PS2 TM Asp --> Ala mutants suppresses the formation of any detectable PS1 or PS2 heterodimeric fragments and essentially abolishes the production of Abeta. These results explain the residual Abeta production seen in PS1-deficient cells and demonstrate the absolute requirement of functional presenilins for Abeta generation. We conclude that presenilins, and their TM aspartates in particular, are attractive targets for lowering Abeta therapeutically to prevent Alzheimer's disease.
Immunogenicity and Tolerogenicity of Hepatitis B Virus Structural and Nonstructural Proteins: Implications for Immunotherapy of Persistent Viral Infections (2002)

Persistent hepatitis B virus (HBV) infection is characterized by a weak and narrowly focused CD8+ T-cell response to HBV that is thought to reflect the induction of central and/or peripheral tolerance to HBV proteins in neonatal and adult onset infections, respectively. Immunotherapeutic strategies that overcome tolerance and boost these suboptimal responses may lead to viral clearance in chronically infected individuals. The present study was performed to compare the relative immunogenicities and tolerogenicities of HBV structural (envelope [ENV]) and nonstructural (polymerase [POL]) proteins at the CD8+ cytotoxic T lymphocyte (CTL) level in transgenic mice that replicate HBV in the liver and secrete infectious virus into the blood, thus representing an excellent model of persistent HBV infection. Interestingly, the mice were tolerant to the ENV but not to the POL proteins at the CTL level. Furthermore, the POL-specific CTLs had no impact on HBV replication or liver function in vivo, even though they were readily induced and reached the liver after DNA immunization, reflecting their relatively low avidity and the low level at which the POL protein is expressed by the hepatocyte. Collectively, these results suggest that the factors that make POL less tolerogenic also make POL-specific CTLs relatively inefficient effector cells when they reach the target organ. Immunotherapeutic strategies to control HBV infection by inducing virus-specific CTL responses in chronically infected subjects should be evaluated in light of this observation.
Eye Position Signal Modulates a Human Parietal Pointing Region during Memory-Guided Movements (2000)

Using functional magnetic resonance imaging, we examined the signal in parietal regions that were selectively activated during delayed pointing to flashed visual targets and determined whether this signal was dependent on the fixation position of the eyes. Delayed pointing activated a bilateral parietal area in the intraparietal sulcus (rIPS), rostral/anterior to areas activated by saccades. During right-hand pointing to centrally located targets, the left rIPS region showed a significant increase in activation when the eye position was rightward compared with leftward. As expected, activation in motor cortex showed no modulation when only eye position changed. During pointing to retinotopically identical targets, the left rIPS region again showed a significant increased signal when the eye position was rightward compared with leftward. Conversely, when pointing with the left arm, the right rIPS showed an increase in signal when eye position was leftward compared with rightward. The results suggest that the human parietal hand/arm movement region (rIPS), like monkey parietal areas (Andersen et al., 1985), exhibits an eye position modulation of its activity; modulation that may be used to transform the coordinates of the retinotopically coded target position into a motor error command appropriate for the wrist.
An Architecture for Describing Simple Network Management Protocol (SNMP) Management Frameworks (2002)

standardization state and status of this protocol. Distribution of this memo is unlimited.
The Role of the Intestinal Tract as a Reservoir and Source for Transmission of Nosocomial Pathogens (2004)

The intestinal tract provides an important reservoir for many nosocomial pathogens, including Enterococcus species, Enterobacteriaciae, Clostridium difficile, and Candida species. These organisms share several common risk factors and often coexist in the intestinal tract. Disruption of normal barriers, such as gastric acidity and the indigenous microflora of the colon, facilitates overgrowth of pathogens. Factors such as fecal incontinence and diarrhea contribute to the subsequent dissemination of pathogens into the health care environment. Selective pressure exerted by antibiotics plays a particularly important role in pathogen colonization, and adverse effects associated with these agents often persist beyond the period of treatment. Infection-control measures that are implemented to control individual pathogens may have a positive or negative impact on efforts to control other pathogens that colonize the intestinal tract.
Strategies to optimize capsid protein expression and single-stranded DNA formation of adeno-associated virus inSaccharomyces cerevisiae (2017)

New manufacturing strategies for AAV-based gene therapy vectors (rAAV) are needed to reduce costs and time of production. Our study explores the feasibility of yeast as alternative system for rAAV production.
Evaluation of germline sequence variants within the promoter region of RANTES gene in a cohort of women with endometriosis from Spain (2003)

The RANTES (regulated upon activation normal T cells expressed and secreted) chemokine, is known to be expressed in endometriotic lesions in a concentration correlating with the severity of endometriosis. Since it has been widely demonstrated that endometriosis has a genetic basis, we postulated that the gene encoding RANTES could be a good candidate gene for the disease. We have used fluorescence resonance energy transfer (FRET) technology to genotype and evaluate the role of the variants -403G-->A and -28C-->G, located within the promoter region of the gene, as susceptibility factors in a cohort of Spanish women with endometriosis. No differences have been found in the allelic frequencies of both variants nor in the haplotype/ genotype distribution between patients and controls. These data are consistent with the lack of association between these polymorphisms and endometriosis in our population. They do not exclude completely a possible role of other variants within RANTES gene in this pathology.
Homologous catalytic domains in a rumen fungal xylanase: evidence for gene duplication and prokaryotic origin (1992)

A cDNA (xynA), encoding xylanase A (XYLA), was isolated from a cDNA library, derived from mRNA extracted from the rumen anaerobic fungus, Neocallimastix patriciarum. Recombinant XYLA, purified from Escherichia coli harbouring xynA, had a M(r) of 53,000 and hydrolysed oat-spelt xylan to xylobiose and xylose. The enzyme did not hydrolyse any cellulosic substrates. The nucleotide sequence of xynA revealed a single open reading frame of 1821 bp coding for a protein of M(r) 66,192. The predicted primary structure of XYLA comprised an N-terminal signal peptide followed by a 225-amino-acid repeated sequence, which was separated from a tandem 40-residue C-terminal repeat by a threonine/proline linker sequence. The large N-terminal reiterated regions consisted of distinct catalytic domains which displayed similar substrate specificities to the full-length enzyme. The reiterated structure of XYLA suggests that the enzyme was derived from an ancestral gene which underwent two discrete duplications. Sequence comparison analysis revealed significant homology between XYLA and bacterial xylanases belonging to cellulase/xylanase family G. One of these homologous enzymes is derived from the rumen bacterium Ruminococcus flavefaciens. The homology observed between XYLA and a rumen prokaryote xylanase could be a consequence of the horizontal transfer of genes between rumen prokaryotes and lower eukaryotes, either when the organisms were resident in the rumen, or prior to their colonization of the ruminant. It should also be noted that Neocallimastix XYLA is the first example of a xylanase which consists of reiterated sequences. It remains to be established whether this is a common phenomenon in other rumen fungal plant cell wall hydrolases.
Enhancement of bone ingrowth by transforming growth factor-beta. (1995)

Enhancement of bone ingrowth with transforming growth factor-beta was evaluated in a canine model. Ten dogs had bilateral implantation of a titanium-fiber-metal-coated rod in the proximal part of the humerus. A three-millimeter gap between the outer surface of the porous coating and the surrounding cancellous bone was created to impair bone ingrowth. All of the implants were plasma-flame-sprayed with hydroxyapatite and tricalcium phosphate. In each animal, one implant was also treated with recombinant transforming growth factor-beta 1 while the other implant, which was not so treated, served as a paired control. Two doses of transforming growth factor-beta 1 were used: 335 micrograms in five animals and 120 micrograms in the other five. At four weeks, the amount of bone ingrowth in the implants that had been treated with 120 micrograms of transforming growth factor-beta 1 was threefold higher than that in the paired controls (p = 0.009), but with the numbers available there was no significant increase in bone ingrowth with the higher dose. The amount of new-bone formation in the three-millimeter gaps adjacent to the treated implants was twice that in the gaps of the paired controls, regardless of the dose. The differences between the treated and control implants with regard to the architecture of the new bone in the gap indicate that the mechanism of action of transforming growth factor-beta 1 may include both proliferation of osteoprogenitor cells and production of matrix by committed osteoblasts. Compared with the findings in a previous study in which this canine model was used, the data from the present investigation indicate that enhancement of bone ingrowth in implants that have been treated with a combination of a hydroxyapatite-tricalcium phosphate coating and transforming growth factor-beta 1 may exceed that obtainable with grafting of the gap with autogenous cancellous bone.
Antibody-forming cell response to virus challenge in mice immunized with DNA encoding the influenza virus hemagglutinin (1995)

Immunization of mice with DNA encoding the influenza virus hemagglutinin (HA) affords complete protection against lethal influenza virus infection and the means to investigate the mechanisms of B-cell responsiveness to virus challenge. Using a single-cell enzyme-linked immunospot assay, we sought to determine the localization of HA-specific antibody-forming cells (AFCs) during the development of humoral immunity in mice given HA DNA vaccine by gene gun. At 33 days postvaccination, populations of AFCs were maintained in the spleen and bone marrow. In response to lethal challenge with influenza virus, the AFCs became localized at the site of antigenic challenge, i.e., within the draining lymph nodes of the lung compartment. Immunoglobulin G (IgG)- and IgA-producing AFCs were detected in lymph nodes of the upper and lower respiratory tracts, underscoring their importance in clearing virus from the lungs. Response to challenge required competent CD4+ T cells, without which no AFCs were generated, even those producing IgM. By contrast, in mice vaccinated with an HA-containing subunit vaccine, fewer AFCs were generated in response to challenge, and these animals were less capable of resisting infection. Our findings demonstrate the comparable localization of AFCs in response to challenge in mice vaccinated with either HA DNA or live virus. Moreover, the former strategy generates both IgG- and IgA-producing plasma cells.
Synthesis of Bi2S3 Nanostructures from Bismuth(III) Thiourea and Thiosemicarbazide Complexes (2009)

Rod-shaped nanostructures of Bi2S3 were synthesized by the solution decomposition of the two new bismuth(III) complexes [Bi6(pydc)8(Hpydc)2(tu)8] (1) and {[Bi2(pydc)3(tsc)(H2O)2]·H2O}∞ (2) (H2pydc = 2,6-pyridinedicarboxylic acid also known as dipicolinic acid; tu = thiourea, tsc = thiosemicarbazide). They were obtained by treatment of Bi2O3 with dipicolinic acid in the presence of the sulfur-containing ligands. The complexes were characterized with the aid of elemental analysis, IR spectroscopy, and single-crystal X-ray diffraction. The dipicolinate anions behave as tridentate ligands toward Bi(III), but two modes of coordination are found. In both cases the ligand serves as a pincer ligand O,N,O-bonded to one bismuth(III) center, but it can also function as a bridging ligand through one carboxylate group that assembles into hexanuclear molecules (1) or a polymeric chain (2). The air-stable complexes 1 and 2 have been used as starting materials in the preparation of bismuth sulfide nanoparticles (NPs) in the presence of different surfactants. Decomposition of 1 and 2 gave Bi2S3 in all cases, but addition of a small amount of 1-dodecanethiol (DT) or 1-octadecanethiol (OT) at 120 °C resulted in better crystallite growth with the observation of nanorods up to several hundreds of nanometers in length. These were examined by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The influence of various reaction conditions on the shape and size of the nanocrystals is discussed. The high resolution (HR) TEM images reveal a number of linear and planar crystal defects and atomic distortions that account for the splitting of bismuth sulfide nanocrystals as observed previously. The growth mechanism is believed to involve decomposition of the precursors and formation of Bi2S3 seeds, followed by the preferential [001] growth of larger particles. Crystal splitting caused by defects and atomic distortions as well as Ostwald ripening processes play important roles in shaping the morphologies of the final Bi2S3 nanostructures.
Rate-Adaptive Coding for Optical Fiber Transmission Systems (2011)

We propose a rate-adaptive transmission scheme using variable-rate forward error correction (FEC) codes with a fixed signal constellation and a fixed symbol rate, quantifying how achievable bit rates vary with distance in a long-haul fiber system. The FEC scheme uses serially concatenated Reed-Solomon (RS) codes with hard-decision decoding, using shortening and puncturing to vary the code rate. An inner repetition code with soft combining provides further rate variation. While suboptimal, repetition coding allows operation at very low signal-to-noise ratio (SNR) with minimal increase in complexity. A rate adaptation algorithm uses the SNR or the FEC decoder input bit-error ratio (BER) estimated by a receiver to determine the combination of RS-RS and repetition codes that maximizes the information bit rate while satisfying a target FEC decoder output BER and providing a specified SNR margin. This FEC scheme is combined here with single-carrier polarization-multiplexed quadrature phase-shift keying (PM-QPSK) and digital coherent detection, achieving 100-Gbit/s peak information bit rate in a nominal 50-GHz channel bandwidth. We simulate variable-rate single-channel transmission through a long-haul system incorporating numerous optical switches, evaluating the impact of fiber nonlinearity and bandwidth narrowing. With zero SNR margin, achievable information bit rates vary from 100 Gbit/s at 2000 km, to about 60 Gbit/s at 3000 km, to about 35 Gbit/s at 4000 km. Compared to an ideal coding scheme achieving information-theoretic limits on an AWGN channel, the proposed coding scheme exhibits a performance gap ranging from about 5.9 dB at 2000 km to about 7.5 dB at 5000 km. Much of the increase in the gap arises from the inefficiency of the repetition coding used beyond 3280 km. Rate-adaptive transmission can extend reach when regeneration sites are not available, helping networks adapt to changing traffic demands. It is likely to become more important with the continued evolution toward optically switched mesh networks, which make signal quality more variable.
Nitrile Oxides, Nitrones and Nitronates in Organic Synthesis: Novel Strategies in Synthesis (1988)

Data were pooled from 3 studies of recently resolved community-dwelling problem drinkers to determine whether a behavioral economic index of the value of rewards available over different time horizons distinguished among moderation (n = 30), abstinent (n = 95), and unresolved (n = 77) outcomes. Moderation over 1- to 2-year prospective follow-up intervals was hypothesized to involve longer term behavior regulation processes than abstinence or relapse and to be predicted by more balanced preresolution monetary allocations between short-term and longer term objectives (i.e., drinking and saving for the future). Standardized odds ratios (ORs) based on changes in standard deviation units from a multinomial logistic regression indicated that increases on this "Alcohol-Savings Discretionary Expenditure" index predicted higher rates of abstinence (OR = 1.93, p = .004) and relapse (OR = 2.89, p < .0001) compared with moderation outcomes. The index had incremental utility in predicting moderation in complex models that included other established predictors. The study adds to evidence supporting a behavioral economic analysis of drinking resolutions and shows that a systematic analysis of preresolution spending patterns aids in predicting moderation.
Genetic Mapping in Human Disease (2008)

Genetic mapping provides a powerful approach to identify genes and biological processes underlying any trait influenced by inheritance, including human diseases. We discuss the intellectual foundations of genetic mapping of Mendelian and complex traits in humans, examine lessons emerging from linkage analysis of Mendelian diseases and genome-wide association studies of common diseases, and discuss questions and challenges that lie ahead.
Timing and patterns of astrocyte migration from xenogeneic transplants of the cortex and corpus callosum (1990)

The timing, pattern, and pathway of astrocyte migration were investigated in vivo by transplantation of CD-1 mouse cerebral cortex (E13-14) or corpus callosum (P2-3) into neonatal rat cortex. A monoclonal antibody specific for a mouse astrocyte surface antigen (M2) was used to identify the location of the grafts and the migrated donor astrocytes. Within the host cortex, astrocytes from cortical grafts began migration at post-transplantation day (PTD) 7. Over the next 4 days, the most distant displaced donor cells were found progressively further away from the grafts, migrating at a rate of about 220 microns/day. After PTD 11, the migration rate for the farthest displaced donor cells slowed to 25 microns/day, and the cells appeared to stop at about PTD 16 at a distance of 1,100 microns from the edge of the graft. Astrocytes had a faster migration speed in the white matter and covered a longer distance (5 mm) than those in the gray matter, extending on occasion into the contralateral hemisphere. The patterns of astrocyte migration differed depending on local cues around the transplant. Donor astrocytes that had been implanted into the host cortex migrated toward the host cortical surface, sometimes in several radial lines. Astrocytes from grafts, especially callosal grafts, placed in the subcortical white matter migrated along the host fiber tracts. Many astrocytes transplanted into the hippocampus formed laminar patterns close to the hippocampal neuronal layers. These results suggest that the direction, pattern, and speed of astrocyte migration are influenced by local substrates in the host brain.