gebhart/patrepeval huggingface dataset:
Structural Correlates of Antibodies Associated with Acute Reversal of Amyloid β-related Behavioral Deficits in a Mouse Model of Alzheimer Disease (2009)

Immunotherapy targeting of amyloid beta (Abeta) peptide in transgenic mouse models of Alzheimer disease (AD) has been widely demonstrated to resolve amyloid deposition as well as associated neuronal, glial, and inflammatory pathologies. These successes have provided the basis for ongoing clinical trials of immunotherapy for treatment of AD in humans. Acute as well as chronic Abeta-targeted immunotherapy has also been demonstrated to reverse Abeta-related behavioral deficits assessing memory in AD transgenic mouse models. We observe that three antibodies targeting the same linear epitope of Abeta, Abeta(3-7), differ in their ability to reverse contextual fear deficits in Tg2576 mice in an acute testing paradigm. Reversal of contextual fear deficit by the antibodies does not correlate with in vitro recognition of Abeta in a consistent or correlative manner. To better define differences in antigen recognition at the atomic level, we determined crystal structures of Fab fragments in complex with Abeta. The conformation of the Abeta peptide recognized by all three antibodies was highly related and is also remarkably similar to that observed in independently reported Abeta:antibody crystal structures. Sequence and structural differences between the antibodies, particularly in CDR3 of the heavy chain variable region, are proposed to account for differing in vivo properties of the antibodies under study. These findings provide a structural basis for immunotherapeutic strategies targeting Abeta species postulated to underlie cognitive deficits in AD.
A randomized clinical trial onn-3 polyunsaturated fatty acids supplementation and all-cause mortality in elderly men at high cardiovascular risk (2010)

We observed a tendency toward reduction in all-cause mortality in the n-3 PUFA groups that, despite a low number of participants, reached borderline statistical significance. The magnitude of risk-reduction suggests that a larger trial should be considered in similar populations.
Specific Interaction of Hepatitis C Virus Protease/Helicase NS3 with the 3′-Terminal Sequences of Viral Positive- and Negative-Strand RNA (2001)

The hepatitis C virus (HCV)-encoded protease/helicase NS3 is likely to be involved in viral RNA replication. We have expressed and purified recombinant NS3 (protease and helicase domains) and Delta pNS3 (helicase domain only) and examined their abilities to interact with the 3'-terminal sequence of both positive and negative strands of HCV RNA. These regions of RNA were chosen because initiation of RNA synthesis is likely to occur at or near the 3' untranslated region (UTR). The results presented here demonstrate that NS3 (and Delta pNS3) interacts efficiently and specifically with the 3'-terminal sequences of both positive- and negative-strand RNA but not with the corresponding complementary 5'-terminal RNA sequences. The interaction of NS3 with the 3'-terminal negative strand [called 3'(-) UTR(127)] was specific in that only homologous (and not heterologous) RNA competed efficiently in the binding reaction. A predicted stem-loop structure present at the 3' terminus (nucleotides 5 to 20 from the 3' end) of the negative-strand RNA appears to be important for NS3 binding to the negative-strand UTR. Deletion of the stem-loop structure almost totally impaired NS3 (and Delta pNS3) binding. Additional mutagenesis showed that three G-C pairs within the stem were critical for helicase-RNA interaction. The data presented here also suggested that both a double-stranded structure and the 3'-proximal guanosine residues in the stem were important determinants of protein binding. In contrast to the relatively stringent requirement for 3'(-) UTR binding, specific interaction of NS3 (or Delta pNS3) with the 3'-terminal sequences of the positive-strand RNA [3'(+) UTR] appears to require the entire 3'(+) UTR of HCV. Deletion of either the 98-nucleotide 3'-terminal conserved region or the 5' half sequence containing the variable region and the poly(U) and/or poly(UC) stretch significantly impaired RNA-protein interaction. The implication of NS3 binding to the 3'-terminal sequences of viral positive- and negative-strand RNA in viral replication is discussed.
Regulation of amylase gene expression in diabetic mice is mediated by a cis-acting upstream element close to the pancreas-specific enhancer. (1990)

We localized the cis-acting sequences that mediate the regulation of a pancreatic amylase gene, Amy-2.2, in diabetic mice. We constructed three hybrid genes containing sequences from the 5'-flanking region of the amylase gene upstream of the heterologous elastase promoter linked to the CAT structural gene. These constructs were transferred to the germ line of transgenic mice by microinjection of fertilized eggs. The amylase sequences had two effects on expression of the elastase promoter: Basal expression was increased, and expression in diabetic animals was reduced to approximately 2% of basal levels. A 30-bp amylase fragment was sufficient to transfer both of these regulatory functions to the elastase promoter. Sequences within this 30-bp fragment are included in the binding site for the pancreatic nuclear protein PTF1. The close association of the PTF1-binding site and the regulatory functions is consistent with a mechanism based on interference with activation by PTF1 in diabetic pancreas. PTF1-binding activity is not reduced in diabetic pancreas. The data presented here demonstrate that the 5'-flanking region of the pancreatic amylase gene contains a novel insulin-dependent element (IDE) that mediates the loss of expression in diabetic animals.
Intermediary Metabolism in Clostridium acetobutylicum : Levels of Enzymes Involved in the Formation of Acetate and Butyrate (1984)

The levels of seven intermediary enzymes involved in acetate and butyrate formation from acetyl coenzyme A in the saccharolytic anaerobe Clostridium acetobutylicum were investigated as a function of time in solvent-producing batch fermentations. Phosphate acetyltransferase and acetate kinase, which are known to form acetate from acetyl coenzyme A, both showed a decrease in specific activity when the organism reached the solvent formation stage. The three consecutive enzymes thiolase, beta-hydroxybutyrylcoenzyme A dehydrogenase, and crotonase exhibited a coordinate expression and a maximal activity after growth had ceased. Only low levels of butyryl coenzyme A dehydrogenase activity were found. Phosphate butyryltransferase activity rapidly decreased after 20 h from 5 to 11 U/mg of protein to below the detection limit (1 mU/mg). Butyrate no longer can be formed, and the metabolic flux may be diverted to butanol. Butyrate kinase showed a 2.5- to 10-fold increase in specific activity after phosphate butyryltransferase activity no longer could be detected. These results suggest that the uptake of acetate and butyrate during solvent formation can not proceed via a complete reversal of the phosphate transferase and kinase reactions. The activities of all enzymes investigated as a function of time in vitro are much higher than the metabolic fluxes through them in vivo. This indicates that none of the maximal activities of the enzymes assayed is rate limiting in C. acetobutylicum.
Protection of Nonhuman Primates against Two Species of Ebola Virus Infection with a Single Complex Adenovirus Vector (2010)

Ebola viruses are highly pathogenic viruses that cause outbreaks of hemorrhagic fever in humans and other primates. To meet the need for a vaccine against the several types of Ebola viruses that cause human diseases, we developed a multivalent vaccine candidate (EBO7) that expresses the glycoproteins of Zaire ebolavirus (ZEBOV) and Sudan ebolavirus (SEBOV) in a single complex adenovirus-based vector (CAdVax). We evaluated our vaccine in nonhuman primates against the parenteral and aerosol routes of lethal challenge. EBO7 vaccine provided protection against both Ebola viruses by either route of infection. Significantly, protection against SEBOV given as an aerosol challenge, which has not previously been shown, could be achieved with a boosting vaccination. These results demonstrate the feasibility of creating a robust, multivalent Ebola virus vaccine that would be effective in the event of a natural virus outbreak or biological threat.
Nucleotide sequence and over-expression of morphine dehydrogenase, a plasmid-encoded gene from Pseudomonas putida M10 (1993)

Pseudomonas putida M10 was originally isolated from factory waste liquors by selection for growth on morphine. The NADP(+)-dependent morphine dehydrogenase that initiates morphine catabolism is encoded by a large plasmid of 165 kb. Treatment of P. putida M10 with ethidium bromide led to the isolation of a putative plasmid-free strain that was incapable of growth on morphine. The structural gene for morphine dehydrogenase, morA, has been located on the plasmid by oligonucleotide hybridization, by coupled transcription-translation of cloned restriction fragments and by nucleotide sequence analysis and is contained within a 1.7 kb SphI fragment that has been cloned into Escherichia coli. The cloned dehydrogenase enzyme is expressed at high levels in E. coli resulting in a 65-fold increase in morphine dehydrogenase activity in cell-free extracts compared with P. putida M10. Morphine dehydrogenase was rapidly purified to homogeneity, as judged by SDS/PAGE, by a one-step affinity chromatography procedure on Mimetic Orange 3 A6XL. The properties of the purified enzyme were identical with those previously reported for P. putida M10 morphine dehydrogenase. The morA gene was sequenced and the deduced amino acid sequence confirmed by N-terminal amino acid sequencing of the over-expressed protein. The predicted amino acid sequence of morA, deduced from the nucleotide sequence, indicated that morphine dehydrogenase did not belong to the non-metal-requiring short-chain class of dehydrogenases, but was more closely related to the aldo-ketoreductases.
Pop III Objects and their Relationship with Dwarf Galaxies (1998)

In this paper we briefly review some of the most recent developments concerning the formation of the first luminous objects in the universe, to which we refer to as Pop III objects, and their observable effects. In particular, we try to critically discuss the possible connection between them and dwarf spheroidal galaxies. We come to the conclusion that, if the properties of Pop IIIs are correctly predicted by hierarchical cosmological models, their identification with present day dwarf galaxies presents several difficulties.
soxR, a locus governing a superoxide response regulon in Escherichia coli K-12 (1990)

The nfo (endonuclease IV) gene of Escherichia coli is induced by superoxide generators such as paraquat (methyl viologen). An nfo'-lacZ operon fusion was used to isolate extragenic mutations affecting its expression. The mutations also affected the expression of glucose 6-phosphate dehydrogenase, Mn2(+)-superoxide dismutase (sodA), and three lacZ fusions to soi (superoxide-inducible) genes of unknown function. The mutations were located 2 kilobases clockwise of ssb at 92 min on the current linkage map. One set of mutations, in a new gene designated soxR, caused constitutive overexpression of nfo and the other genes. It included insertions or deletions affecting the carboxyl end of a 17-kilodalton polypeptide. In a soxR mutant, the expression of sodA, unlike that of nfo, was also regulated independently by oxygen tension. Two other mutants were isolated in which the target genes were noninducible; they had an increased sensitivity to killing by superoxide-generating compounds. One had a Tn10 insertion in or near soxR; the other had a multigene deletion encompassing soxR. Therefore, the region functions as a positive regulator because it encodes one or more products needed for the induction of nfo. Regulation is likely to be at the level of transcription because the mutations were able to affect the expression of an nfo'-lac operon fusion that contained the ribosome-binding site for lacZ. Some mutant plasmids that failed to suppress (or complement) constitutivity in trans had insertion mutations several hundred nucleotides upstream of soxR in the general region of a gene for a 13-kilodalton protein encoded by the opposite strand, raising the possibility of a second regulatory gene in this region. The result define a new regulon, controlled by soxR, mediating at least part of the global response to superoxide in E. coli.
Azithromycin Resistance and Decreased Ceftriaxone Susceptibility in Neisseria gonorrhoeae, Hawaii, USA (2017)

During 2016, eight Neisseria gonorrhoeae isolates from 7 patients in Hawaii were resistant to azithromycin; 5 had decreased in vitro susceptibility to ceftriaxone. Genomic analysis demonstrated a distinct phylogenetic clade when compared with local contemporary strains. Continued evolution and widespread transmission of these strains might challenge the effectiveness of current therapeutic options.
The effects of Doppler spreads in OFDM(A) mobile radio systems (1999)

We analyze the effects of Doppler spread in mobile channels on orthogonal frequency division multiplex (OFDM) systems. This is important, since channel variations during one OFDM symbol cause inter sub-carrier interference (ICI) in OFDM systems, which degrades the performance, since ICI can be seen as additional near-Gaussian noise. The analysis is outlined, and closed-form results given for numerous important practical Doppler spread encountered in mobile channels. We also show that for the case of asymmetrical Doppler spreads, the frequency correction of the receiver can be adjusted so as to minimize the ICI. To extend our work to OFDM(A) mobile radio systems in the uplink case where many users' contributions to the ICI overlap, we have introduced the concept of an equivalent single-user which causes the total ICI, in order to use the same analytical framework. For some channel examples, we simulated the Doppler spread of this equivalent user. Simulation results confirm our analysis and show the importance of the analytical tool to perform realistic system analysis without having to resort to time consuming time-domain simulations.
Immunologic Relationship between Blood Group Substances and a Fucose-Containing Glycolipid of Human Adenocarcinoma (1967)

Summary A fucose-containing glycolipid isolated from human adenocarcinoma tissue was found to lack blood group A or B activity regardless of the blood type of the tissue donor. The tumor glycolipid had weak H and moderate Lea activity. Tumor glycolipid was precipitated by type XIV pneumococcal polysaccharide antiserum only after mild acid hydrolysis. Antisera to tumor glycolipid agglutinated erythrocytes of type A more strongly than erythrocyte of type B, AB, or O. Furthermore, tumor glycolipid and type A glycolipid inhibited the agglutination of tumor cells by a certain phytoagglutinin more strongly than other glycolipids tested. Thus blood group A substance or erythrocytes appear to contain increased amounts of a hapten structure similar to or identical with the carbohydrate moiety of tumor glycolipid. It is suggested that tumor glycolipid results from an aberration in synthesis of glycolipids possessing blood group activity.
Trophoblast cell activation by trophinin ligation is implicated in human embryo implantation (2007)

During human embryo implantation, trophectoderm mediates adhesion of the blastocyst to the uterine epithelium. The rapid growth of the embryo and invasion of the maternal tissue suggest adhesion-induced activation of the embryonal cells. We show here that ligation of trophinin, a homophilic cell adhesion molecule expressed on trophoblastic cells, induces tyrosine phosphorylation in trophinin-expressing trophoblastic HT-H cells. The phosphorylation could be induced in HT-H cells with the binding of trophinin-expressing cells or anti trophinin antibodies. Trophinin-dependent tyrosine phosphorylation was associated with actin reorganization. We also isolated trophinin-binding peptides from phage libraries. These peptides exhibited the consensus sequence GWRQ and seemed to reproduce the effects of trophinin-mediated cell adhesion. Upon binding of a GWRQ peptide, HT-H cells became highly proliferative and motile. HT-H cells expressed ErbB family receptors and bound EGF and heparin-binding EGF-like growth factor (HB-EGF), but ErbB family receptor phosphorylation in these cells required GWRQ. In the absence of GWRQ, trophinin interacted with the cytoplasmic protein bystin, which binds to ErbB4 and blocks its autophosphorylation. In HT-H cells, GWRQ peptide dissociated trophinin from bystin, and ErbB4 was activated. Culturing monkey blastocysts in the presence of the peptide increased total number and motility of the trophectoderm cells. These results suggest that trophinin-mediated cell adhesion functions as a molecular switch for trophectoderm activation in human embryo implantation.
Relationships between Obesity and Cardiovascular Diseases in Four Southern States and Colorado (2011)

Obesity is among the leading causes of elevated cardiovascular disease (CVD) mortality and morbidity. In the present study, the associations between the increase in body mass index (BMI) and the increase rates of CVD and high blood pressure (HBP) in the states of Mississippi, Alabama, Louisiana, Tennessee, and Colorado are examined using regression analysis and by means of neural network models for obesity and HBP. Data from Behavioral Risk Factor Surveillance System were obtained and analyzed for obesity rates, percent of myocardial infarction, stroke, and HBP from 2005-2009. Results of this study showed a low association between obesity and myocardial infarction rates (R2=0.067); a moderate association with stroke rates ((R2=0.462); and a strong association with HBP rates ((R2=0.811). The highest rates of obesity, CVD, and HBP were found in Mississippi, while Colorado had the lowest rates. Maintaining healthy weight helps reduce the risks of developing CVD.
A possible central mechanism in autism spectrum disorders, part 2: immunoexcitotoxicity. (2009)

In this section, I explore the effects of mercury and inflammation on transsulfuration reactions, which can lead to elevations in androgens, and how this might relate to the male preponderance of autism spectrum disorders (ASD). It is known that mercury interferes with these biochemical reactions and that chronically elevated androgen levels also enhance the neurodevelopmental effects of excitotoxins. Both androgens and glutamate alter neuronal and glial calcium oscillations, which are known to regulate cell migration, maturation, and final brain cytoarchitectural structure. Studies have also shown high levels of DHEA and low levels of DHEA-S in ASD, which can result from both mercury toxicity and chronic inflammation. Chronic microglial activation appears to be a hallmark of ASD. Peripheral immune stimulation, mercury, and elevated levels of androgens can all stimulate microglial activation. Linked to both transsulfuration problems and chronic mercury toxicity are elevations in homocysteine levels in ASD patients. Homocysteine and especially its metabolic products are powerful excitotoxins. Intimately linked to elevations in DHEA, excitotoxicity and mercury toxicity are abnormalities in mitochondrial function. A number of studies have shown that reduced energy production by mitochondria greatly enhances excitotoxicity. Finally, I discuss the effects of chronic inflammation and elevated mercury levels on glutathione and metallothionein.
Sortase‐Mediated Ligation: A Gift from Gram‐Positive Bacteria to Protein Engineering (2009)

Abstract A new enzymatic protein ligation tool , sortase, has recently emerged from Gram‐positive bacteria. This article outlines the technique, sortase‐mediated ligation, and its applications in protein engineering, which include the introduction of unnatural molecules into proteins, protein immobilization, protein–protein conjugation, protein cyclization, as a self‐cleavable tag for protein expression, protein–PNA hybrids, neoglycoconjugates, and cell‐surface protein labeling, etc. magnified image
Synthesis of Functionalized Pentacenes from Isobenzofurans Derived from C−H Bond Activation (2010)

The synthesis of unsymmetric functionalized pentacenes from 1,4-anthraquinones and functionalized isobenzofurans, which were prepared by transformation via C-H bond activation, was successfully accomplished. Examples of the synthesis of pentacenes with functional groups at the 5-position are still rare. These obtained functionalized pentacenes are highly soluble in hexane, toluene, and THF.
Fast Bayesian Uncertainty Estimation of Batch Normalized Single Image Super-Resolution Network. (2019)

In recent years, deep convolutional neural network (CNN) has achieved unprecedented success in image super-resolution (SR) task. But the black-box nature of the neural network and due to its lack of transparency, it is hard to trust the outcome. In this regards, we introduce a Bayesian approach for uncertainty estimation in super-resolution network. We generate Monte Carlo (MC) samples from a posterior distribution by using batch mean and variance as a stochastic parameter in the batch-normalization layer during test time. Those MC samples not only reconstruct the image from its low-resolution counterpart but also provides a confidence map of reconstruction which will be very impactful for practical use. We also introduce a faster approach for estimating the uncertainty, and it can be useful for real-time applications. We validate our results using standard datasets for performance analysis and also for different domain-specific super-resolution task. We also estimate uncertainty quality using standard statistical metrics and also provides a qualitative evaluation of uncertainty for SR applications.
Asymmetric Total Synthesis of Taxol\R (1999)

A new method for the total asymmetric synthesis of antitumor agent Taxol is described. Baccatin III, a complex carbon framework, is synthesized by way of B to BC to ABC ring construction. Further, a method of forming Taxol from baccatin III and a β-amino acid is also demonstrated.
Patterning and Composition Arrays of Supported Lipid Bilayers by Microcontact Printing (2001)

Fluid-supported lipid bilayers self-assemble on glass and SiO2 surfaces. We have found that it is also possible to assemble fluid bilayers on plasma-oxidized polydimethyl siloxane (PDMS) surfaces. Furthermore, it is possible to transfer or print the supported bilayer from raised PDMS surfaces, such as are typically used for microcontact printing, to fresh glass surfaces creating a supported bilayer membrane replica of the patterned PDMS surface on glass. These patterned islands of bilayer are fully fluid and indefinitely stable under water. The pattern is erased upon addition of more vesicles leaving a continuous bilayer surface. By printing membrane islands of various sizes onto a glass surface that is prepatterned with a material that forms permanent barriers to lateral diffusion and then backfilling the open region with vesicles, it is possible to create arbitrary concentration or composition arrays of membrane-associated components. These arrays may be useful for studies of membrane biophysics, for high throughput screening of compounds that target membrane components, and for probing and possibly controlling living cell−synthetic membrane interactions.