gebhart/patrepeval huggingface dataset:
Adeno‐associated virus‐mediated gene transfer (2008)

Although the remarkable versatility and efficacy of recombinant adeno-associated virus 2 (AAV2) vectors in transducing a wide variety of cells and tissues in vitro, and in numerous pre-clinical animal models of human diseases in vivo, have been well established, the published literature is replete with controversies with regard to the efficacy of AAV2 vectors in hematopoietic stem cell (HSC) transduction. A number of factors have contributed to these controversies, the molecular bases of which have begun to come to light in recent years. With the availability of several novel serotypes (AAV1 through AAV12), rational design of AAV capsid mutants, and strategies (self-complementary vector genomes, hematopoietic cell-specific promoters), it is indeed becoming feasible to achieve efficient transduction of HSC by AAV vectors. Using a murine serial bone marrow transplantation model in vivo, we have recently documented stable integration of the proviral AAV genome into mouse chromosomes, which does not lead to any overt hematological abnormalities. Thus, a better understanding of the AAV-HSC interactions, and the availability of a vast repertoire of novel serotype and capsid mutant vectors, are likely to have significant implications in the use of AAV vectors in high-efficiency transduction of HSCs as well as in gene therapy applications involving the hematopoietic system.
Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19 (2020)

The novel coronavirus disease COVID-19 that emerged in 2019 is caused by the virus SARS CoV-2 and named for its close genetic similarity to SARS CoV-1 that caused severe acute respiratory syndrome (SARS) in 2002. Both SARS coronavirus genomes encode two overlapping large polyproteins, which are cleaved at specific sites by a 3C-like cysteine protease (3CL<sup>pro</sup>) in a post-translational processing step that is critical for coronavirus replication. The 3CL<sup>pro</sup> sequences for CoV-1 and CoV-2 viruses are 100% identical in the catalytic domain that carries out protein cleavage. A research effort that focused on the discovery of reversible and irreversible ketone-based inhibitors of SARS CoV-1 3CL<sup>pro</sup> employing ligand-protease structures solved by X-ray crystallography led to the identification of <b>3</b> and <b>4</b>. Preclinical experiments reveal <b>4</b> (<b>PF-00835231</b>) as a potent inhibitor of CoV-2 3CL<sup>pro</sup> with suitable pharmaceutical properties to warrant further development as an intravenous treatment for COVID-19.
Correspondence of the brain's functional architecture during activation and rest (2009)

Neural connections, providing the substrate for functional networks, exist whether or not they are functionally active at any given moment. However, it is not known to what extent brain regions are continuously interacting when the brain is "at rest." In this work, we identify the major explicit activation networks by carrying out an image-based activation network analysis of thousands of separate activation maps derived from the BrainMap database of functional imaging studies, involving nearly 30,000 human subjects. Independently, we extract the major covarying networks in the resting brain, as imaged with functional magnetic resonance imaging in 36 subjects at rest. The sets of major brain networks, and their decompositions into subnetworks, show close correspondence between the independent analyses of resting and activation brain dynamics. We conclude that the full repertoire of functional networks utilized by the brain in action is continuously and dynamically "active" even when at "rest."
DNA sequence analysis with droplet-based microfluidics (2013)

Droplet-based microfluidic techniques can form and process micrometer scale droplets at thousands per second. Each droplet can house an individual biochemical reaction, allowing millions of reactions to be performed in minutes with small amounts of total reagent. This versatile approach has been used for engineering enzymes, quantifying concentrations of DNA in solution, and screening protein crystallization conditions. Here, we use it to read the sequences of DNA molecules with a FRET-based assay. Using probes of different sequences, we interrogate a target DNA molecule for polymorphisms. With a larger probe set, additional polymorphisms can be interrogated as well as targets of arbitrary sequence.
Nanoparticle Therapy for Allergic and Inflammatory Disease (2010)

Allergic and auto-immune inflammatory diseases are a worldwide medical concern. Present therapeutics are effective in disease maintenance, allowing relief of symptoms, but are frequently accompanied by unacceptable side effects when given chronically for long periods. Immunotherapy for allergies is effective at inducing anergy to some allergens clinically, but for others it is either ineffective or has a risk of an adverse response. Similarly glucocorticoids, and nonsteroidal anti-inflammatory drugs, which are widely used to treat inflammatory auto immune diseases, are associated with debilitating side effects. Nanoparticles, derived from a variety of different molecular approaches, provide a means to deliver drugs to target organs and cells, lowering the dose requirement and potentially overcoming problems associated with systemic drug delivery. Novel therapeutics in the form of small molecules, proteins, DNA or small inhibitory RNAs, are advancing at a rapid rate toward the clinic and may suffer similar problems to those of current therapeutics. A large body of evidence using nanoparticles for delivery in both allergy and auto-immune disease models demonstrates improvement in alleviating disease. Delivery of current anti-inflammatory drugs, as well as novel therapeutics via nanoparticles also show improved attenuation of disease. The several chemically distinct nanoparticle structures, combined with the currently used drugs, the new wave of drug targets, and novel gene targeted approaches may provide the opportunity to discover optimal combinations for treating allergic and inflammatory disease.
Importance of p12 protein in Mason-Pfizer monkey virus assembly and infectivity (1992)

Mason-Pfizer monkey virus (M-PMV) represents the prototype type D retrovirus, characterized by the assembly of intracytoplasmic A-type particles within the infected-cell cytoplasm. These immature particles migrate to the plasma membrane, where they are released by budding. The gag gene of M-PMV encodes a novel protein, p12, just 5' of the major capsid protein (CA) p27 on the polyprotein precursor. The function of p12 is not known, but an equivalent protein is found in mouse mammary tumor virus and is absent from the type C retroviruses. In order to determine whether the p12 protein plays a role in the intracytoplasmic assembly of capsids, a series of in-frame deletion mutations were constructed in the p12 coding domain. The mutant gag genes were expressed by a recombinant vaccinia virus-T7 polymerase-based system in CV-1 cells or in the context of the viral genome in COS-1 cells. In both of these high-level expression systems, mutant Gag precursors were competent to assemble but were not infectious. In contrast, when stable transfectant HeLa cell lines were established, assembly of the mutant precursors into capsids was drastically reduced. Instead, the polyprotein precursors remained predominantly soluble in the cytoplasm. These results show that while p12 is not required for the intracytoplasmic assembly of M-PMV capsids, under the conditions of low-level protein biosynthesis seen in virus-infected cells, it may assist in the stable association of polyprotein precursors for capsid assembly. Moreover, the presence of the p12 coding domain is absolutely required for the infectivity of M-PMV virions.
Expression of recombinant transmembrane CD59 in paroxysmal nocturnal hemoglobinuria B cells confers resistance to human complement (1994)

Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired hematopoietic disorder characterized by complement-mediated hemolytic anemia, pancytopenia, and venous thrombosis. These clinical manifestations arise from an underlying molecular defect of bone marrow stem cells. Specifically, somatic mutations in the phosphatidylinositol glycan class A gene result in the ability of blood cells to anchor complement- regulatory proteins (CD59 and DAF) to the cell surface via glycosyl phosphatidylinositol (GPI). In an attempt to circumvent the functional defect in PNH cells, a recombinant transmembrane form of CD59 (CD59-TM) was analyzed for the ability to regulate complement activity. Balb/3T3 stable transfectants expressing similar levels of either CD59-TM or native CD59 (CD59-GPI) were equally protected against human complement- mediated membrane damage. Treatment of these cells with phosphatidylinositol-specific phospholipase C failed to release CD59-TM from the cell surface. Retroviral transduction of GPI-anchoring deficient mouse L cells with CD59-TM resulted in surface expression of the protein and rendered these cells resistant to human complement- mediated membrane damage. Conversely, L cells transduced with CD59-GPI failed to express this protein on the cell surface. A GPI-anchoring deficient complement-sensitive B-cell line derived from a PNH patient was successfully transduced with CD59-TM, resulting in surface expression of the protein. The PNH B cells expressing CD59-TM were protected against classical complement-mediated membrane damage by human serum. Taken together, these data establish that a functional recombinant transmembrane form of CD59 can be expressed on the surface of GPI-anchoring deficient PNH cells and suggest that retroviral gene therapy with this molecule could provide a treatment for PNH patients.
A Low-Noise, Non-Contact EEG/ECG Sensor (2007)

Typical electroencephalogram (EEG) and electrocardiogram (ECG) sensors require conductive gel to ensure low-impedance electrical contact between the sensor and skin, making set-up time-consuming and long-term recording problematic. We present a gel-free, non-contact EEG/ECG sensor with on-board electrode that capacitively couples to the skin. Active shielding of the high-impedance input significantly reduces noise pickup, and reduces variations in gain as a function of gap distance. The integrated sensor combines amplification, bandpass filtering, and analog-to-digital conversion within a 1 inch diameter enclosure. The measured input-referred noise, over 1-100 Hz frequency range, is 2μVrms at 0.2 mm sensor distance, and 17μVrms at 3.2 mm distance. Experiments coupling the sensor to human scalp through hair and to chest through clothing produce clear EEG and ECG recorded signals.
Acinetobacter baumannii Utilizes a Type VI Secretion System for Bacterial Competition (2013)

Type VI secretion systems (T6SS) are a class of macromolecular secretion machines that are utilized by a number of bacteria for inter-bacterial competition or to elicit responses in eukaryotic cells. Acinetobacter baumannii is an opportunistic pathogen that causes severe infections in humans. These infections, including pneumonia and bacteremia, are important, as they are often associated with hospitals and medical-settings where they disproportionally affect critically ill patients like those residing in intensive care units. While it is known that A. baumannii genomes carry genes whose predicted products have homology with T6SS-associated gene products from other bacteria, and secretion of a major T6SS structural protein Hcp has been demonstrated, no additional work on an A. baumannii T6SS has been reported. Herein, we demonstrated that A. baumannii strain M2 secretes Hcp and this secretion was dependent upon TssB, an ortholog of a bacteriophage contractile sheath protein, confirming that strain M2 produces a functional T6SS. Additionally, we demonstrated that the ability of strain M2 to out-compete Escherichia coli was reliant upon the products of tssB and hcp. Collectively, our data have provided the first evidence demonstrating function in inter-bacterial competition, for a T6SS produced by A. baumannii.
Maintenance of superior learning and memory function in NR2B transgenic mice during ageing (2007)

Brain ageing represents a general and evolutionarily conserved phenomenon and is marked by gradual declines in cognitive functions such as learning and memory. As a synaptic coincidence detector, the N-methyl-d-aspartate (NMDA) receptor is known to be essential for the induction of synaptic plasticity and memory formation. Here, we test the hypothesis that up-regulation of NR2B expression is beneficial for learning and memory in the aged animals. Our in vitro recordings show that the aged transgenic mice with the forebrain-specific overexpression of the NR2B subunit indeed exhibit more robust hippocampal long-term potentiation (LTP) induced by either high-frequency stimulation or theta-stimulation protocol. Furthermore, those aged NR2B transgenic mice consistently outperform their wild-type littermates in five different learning and memory tests, namely, novel object recognition, contextual and cued fear conditioning, spatial reference memory, and spatial working memory T-maze task. Thus, we conclude that increased expression of NR2B in the forebrain improves learning and memory function in the aged brain.
Corynebacterium glutamicumUtilizes both Transsulfuration and Direct Sulfhydrylation Pathways for Methionine Biosynthesis (2002)

A direct sulfhydrylation pathway for methionine biosynthesis in Corynebacterium glutamicum was found. The pathway was catalyzed by metY encoding O-acetylhomoserine sulfhydrylase. The gene metY, located immediately upstream of metA, was found to encode a protein of 437 amino acids with a deduced molecular mass of 46,751 Da. In accordance with DNA and protein sequence data, the introduction of metY into C. glutamicum resulted in the accumulation of a 47-kDa protein in the cells and a 30-fold increase in O-acetylhomoserine sulfhydrylase activity, showing the efficient expression of the cloned gene. Although disruption of the metB gene, which encodes cystathionine gamma-synthase catalyzing the transsulfuration pathway of methionine biosynthesis, or the metY gene was not enough to lead to methionine auxotrophy, an additional mutation in the metY or the metB gene resulted in methionine auxotrophy. The growth pattern of the metY mutant strain was identical to that of the metB mutant strain, suggesting that both methionine biosynthetic pathways function equally well. In addition, an Escherichia coli metB mutant could be complemented by transformation of the strain with a DNA fragment carrying corynebacterial metY and metA genes. These data clearly show that C. glutamicum utilizes both transsulfuration and direct sulfhydrylation pathways for methionine biosynthesis. Although metY and metA are in close proximity to one another, separated by 143 bp on the chromosome, deletion analysis suggests that they are expressed independently. As with metA, methionine could also repress the expression of metY. The repression was also observed with metB, but the degree of repression was more severe with metY, which shows almost complete repression at 0.5 mM methionine in minimal medium. The data suggest a physiologically distinctive role of the direct sulfhydrylation pathway in C. glutamicum.
Synthesis of 6,3'-methanocytidine,6,3'-methanouridine, and their 2'-deoxyribonucleosides (nucleosides and nucleotides. LXXVII). (1988)

Condensation of 5-O-tert-butyldimethylsilyl-1, 2-O-isopropylidene-α-D-erythro-3-pentulo-furanose (4) with 2, 4-dimethoxypyrimidin-6-ylmethyllithium (5) afforded a 3-pyrimidinylmethyl-ribose derivative (6). The protecting groups of 6 were changed to give the 5-O-benzoyl-1, 2-di-O-acetyl derivative (8). The intramolecular glycosylation of 8 by treatment with stannic chloride furnished the 6, 3'-methanol-O4-methyluridine derivative (9), which was further converted to 6, 3'-methanouridine (10) and 6, 3'-methanocytidine (11). The 2'-deoxygenation of 9 by way of the 2'-imidazolylthiocarbonyl dericative gave, after appropriate derivatization, 2'-deoxy-6, 3'-methanocytidine (16) and -uridine (17).
Immobilization of Rhodium Complexes at Thiolate Monolayers on Gold Surfaces:  Catalytic and Structural Studies (2005)

Chiral rhodium-diphosphine complexes have been incorporated into self-assembled thiolate monolayers (SAMs) on gold colloids. Catalysts of this type are of interest because they combine properties of homogeneous and heterogeneous systems. In addition, it should be possible to influence the catalytic properties of the metal center by the neighboring thiolate molecules. Colloids with a diameter of ca. 3 nm, coated with a mixed monolayer of n-octanethiolates and thiolates with chiral rhodium-PYRPHOS end groups, were studied as hydrogenation catalysts. With methyl alpha-acetamido-cinnamate as substrate, virtually the same enantioselectivities (up to 93% ee) and full conversion were obtained as with the corresponding homogeneous [Rh(COD)(PYRPHOS)]BAr(F) catalyst. The colloids were easily recovered by filtration and reused as catalysts three times without loss of enantioselectivity. STM studies of analogous SAMs on Au(111) gave a detailed picture of the structure and dynamics of mixed monolayers of this type. The STM images showed that the catalyst-bearing thiolates are distributed statistically on the surface and that the ordered structure of the n-octanethiolate SAM can be retained during incorporation of the catalyst-bearing thiols using the place-exchange methodology.
Prediction of residues in discontinuous B‐cell epitopes using protein 3D structures (2006)

Discovery of discontinuous B-cell epitopes is a major challenge in vaccine design. Previous epitope prediction methods have mostly been based on protein sequences and are not very effective. Here, we present DiscoTope, a novel method for discontinuous epitope prediction that uses protein three-dimensional structural data. The method is based on amino acid statistics, spatial information, and surface accessibility in a compiled data set of discontinuous epitopes determined by X-ray crystallography of antibody/antigen protein complexes. DiscoTope is the first method to focus explicitly on discontinuous epitopes. We show that the new structure-based method has a better performance for predicting residues of discontinuous epitopes than methods based solely on sequence information, and that it can successfully predict epitope residues that have been identified by different techniques. DiscoTope detects 15.5% of residues located in discontinuous epitopes with a specificity of 95%. At this level of specificity, the conventional Parker hydrophilicity scale for predicting linear B-cell epitopes identifies only 11.0% of residues located in discontinuous epitopes. Predictions by the DiscoTope method can guide experimental epitope mapping in both rational vaccine design and development of diagnostic tools, and may lead to more efficient epitope identification.
Suppression of the modulatory effects of the antileukemic and anti-human immunodeficiency virus compound avarol on gene expression by tryptophan. (1989)

The amino acid L-tryptophan is known to be a modulator of many processes of cell metabolism. In this contribution we show that L-tryptophan interferes with some biological effects of the antileukemic and anti-human immunodeficiency virus agent avarol, possibly by different mechanisms. Avarol has been shown to be able to modulate posttranscriptional events of mRNA synthesis, resulting in an increase of the base-sequence complexities of the nonabundant and rare mRNA classes. Here it is demonstrated that this change in mRNA abundancy distribution is accompanied by an increase in the level of some specific, low abundant mRNAs (ras and c-myc). Addition of L-tryptophan was found to abolish avarol-caused gene relaxation in L1210 mouse leukemia cells. In addition, L-tryptophan suppressed the induction of gamma-interferon mRNA production in human peripheral blood lymphocytes. At the level of DNA, L-tryptophan inhibited the production of strand breaks by cytotoxic avarol concentrations in Friend erythroleukemia cells in vitro. Moreover, it competed with avarol for binding to the nuclear envelope binding site; this effect was not shown by other amino acids.
Approaches to rheumatoid arthritis in 2000 (2001)

The year 2000 was characterized by euphoria among clinicians based on the continued and consolidated success of tumor necrosis factor (TNF) inhibition but also by problems caused by the high cost of this therapy. Looking at the risks and adverse effects has only begun, and there is so far a remarkable lack of publications dealing with this topic. Leflunomide also emerges as an established disease-modifying antirheumatic drug (DMARD). Other therapies include the cyclooxygenase-2 (Cox-2) inhibitors, which are tolerated better by the gastrointestinal system but raise concerns regarding thromboembolism in patients at risk. The enthusiasm regarding Cox-2 inhibitors is somewhat tempered by recent reports of thromboembolic complications, although those have been rare. The advances in research regarding mechanisms of inflammation and pathogenesis continue to generate new therapeutic approaches, which, however, remain mostly experimental. The complexity of genetics has been emphasized by reports on susceptibility and severity relation to TNF, mannose-binding lectin, and gamma-interferon polymorphism. Epidemiologic studies focusing on prevalence, incidence and outcome continue to deliver conflicting messages. One major worry relates to chronic inflammation in RA and other rheumatic diseases as putative cause of accelerated atherosclerosis.
Nucleotide Discrimination with DNA Immobilized in the MspA Nanopore (2011)

Nanopore sequencing has the potential to become a fast and low-cost DNA sequencing platform. An ionic current passing through a small pore would directly map the sequence of single stranded DNA (ssDNA) driven through the constriction. The pore protein, MspA, derived from Mycobacterium smegmatis, has a short and narrow channel constriction ideally suited for nanopore sequencing. To study MspA's ability to resolve nucleotides, we held ssDNA within the pore using a biotin-NeutrAvidin complex. We show that homopolymers of adenine, cytosine, thymine, and guanine in MspA exhibit much larger current differences than in α-hemolysin. Additionally, methylated cytosine is distinguishable from unmethylated cytosine. We establish that single nucleotide substitutions within homopolymer ssDNA can be detected when held in MspA's constriction. Using genomic single nucleotide polymorphisms, we demonstrate that single nucleotides within random DNA can be identified. Our results indicate that MspA has high signal-to-noise ratio and the single nucleotide sensitivity desired for nanopore sequencing devices.
A broadband differential cascode power amplifier in 45 nm CMOS for high-speed 60 GHz system-on-chip (2010)

A compact two-stage differential cascode power amplifier is designed and fabricated in 45 nm standard LP CMOS. The cascode configuration, with the common gate device placed in a separate P-well, provides reliable operating condition for the devices. The amplifier shows 20 dB small-signal gain centered at 60 GHz with a flat frequency response and 1-dB bandwidth of 10 GHz. The broadband large-signal operation is also ensured by providing constant load resistance to both stages over the entire band and coupling them with a dual resonance matching network. The chip delivers 11.2 dBm output power at 1-dB compression and up to 14.5 dBm power in saturation. The power amplifier operates with 2 V supply and draws 90 mA total current which results in 14.4% maximum PAE. The output third order intercept point is measured to be 18 dBm for two-tone measurement at 60 GHz with 0.5 GHz, 1 GHz and 2 GHz frequency separations.