gebhart/patrepeval huggingface dataset:
A PHASE I TRIAL OF IMMUNOSUPPRESSION WITH ANTIIC AM-1 (CD54) mAb IN RENAL ALLOGRAFT RECIPIENTS (1993)

Several adhesion molecules contribute to the interaction between T cells and antigen presenting cells or target cells. Leukocyte function-associated molecule-1 (LFA-1[CD11a/CD18]) and intercellular adhesion molecule-1 (ICAM-1 [CD54]) are one such critical adhesive receptor-counter-receptor combination. The importance of ICAM-1 dependent adhesion in the rejection response was initially demonstrated in cynomolgus renal allograft recipients treated with the anti-ICAM-1 murine monoclonal antibody BIRR1. BIRR1 also appeared to limit ischemic damage in these animals. A Phase I clinical trial has subsequently been completed in 18 patients who received cadaver donor renal allografts at high risk for delayed graft function (prolonged preservation time, highly-sensitized recipient). An adequate BIRR1 serum level was associated with significantly less delayed graft function (P < .01) and rejection (P < .01). In 1-hr biopsies, mouse IgG was detected along the endothelium of the vessels and glomeruli in the graft. There were no instances of primary non-function (PNF), and current allograft survival (followup: 16-30 months) in these "high-risk" mAb-treated patients is 78%. There were 3 instances of PNF and a graft survival rate of 56% in the recipients of the contralateral kidney allografts treated with conventional immunosuppression. No significant "first-dose" effect was associated with BIRR1 administration. These results establish a dosing schedule and the clinical safety of BIRR1. They also suggest that inhibition of leukocyte adhesion by mAb therapy may be useful in controlling allograft rejection and possibly in limiting reperfusion injury. Thus, these observations support the clinical importance of accessory molecules in T cell function. We hypothesize that anti-CD54 mAb acts by blocking leukocyte adhesion to the endothelium, thereby interfering with sensitization or target cell interaction.
Therapeutic rAAVrh10 Mediated SOD1 Silencing in Adult SOD1 G93A Mice and Nonhuman Primates (2015)

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease; survival in ALS is typically 3-5 years. No treatment extends patient survival by more than three months. Approximately 20% of familial ALS and 1-3% of sporadic ALS patients carry a mutation in the gene encoding superoxide dismutase 1 (SOD1). In a transgenic ALS mouse model expressing the mutant SOD1(G93A) protein, silencing the SOD1 gene prolongs survival. One study reports a therapeutic effect of silencing the SOD1 gene in systemically treated adult ALS mice; this was achieved with a short hairpin RNA, a silencing molecule that has raised multiple safety concerns, and recombinant adeno-associated virus (rAAV) 9. We report here a silencing method based on an artificial microRNA termed miR-SOD1 systemically delivered using adeno-associated virus rAAVrh10, a serotype with a demonstrated safety profile in CNS clinical trials. Silencing of SOD1 in adult SOD1(G93A) transgenic mice with this construct profoundly delayed both disease onset and death in the SOD1(G93A) mice, and significantly preserved muscle strength and motor and respiratory functions. We also document that intrathecal delivery of the same rAAVrh10-miR-SOD1 in nonhuman primates significantly and safely silences SOD1 in lower motor neurons. This study supports the view that rAAVrh10-miR-SOD1 merits further development for the treatment of SOD1-linked ALS in humans.
Amplification of the put genes and identification of the put gene products in Escherichia coli K12 (1980)

The utilization of L-proline as carbon or nitrogen source for the growth of Escherichia coli K12 requires the activities of an L-proline porter (PP-I) and a bifunctional L-proline dehydrogenase-delta1-pyrroline carboxylate dehydrogenase. PP-I is inactivated by mutations at putP and the bifunctional dehydrogenase is encoded in the adjacent locus, putA, at 22 min on the chromosome map. Two additional loci, proP (at 92 min) and proT (at 82 min), have also been implicated in L-proline transport. We have studied four ColE1/E. coli K12 hybrid plasmids from the plasmid bank prepared by Clarke and Carbon. Each of these plasmids was shown previously to complement an L-proline transport defect in E. coli. Genetic complementation analysis and biochemical assays of L-proline transport and L-proline dehydrogenase activity show that three of these hybrid plasmids bear the putPA region of the E. coli chromosome (plasmids pLC4-45, pLC10-29, and pLC43-41). The fourth plasmid, pLC35-38, specifically enhances the L-proline transport activity of its host bacteria but not their L-proline dehydrogenase activity. It probably encodes putP. We have used these plasmids in an E. coli minicell system to identify the putA and putP gene products.
Nociception in Persistent Pancreatitis in Rats (2003)

These results indicate that animals with the dibutyltin dichloride-induced experimental pancreatitis expressed serum, histologic, and behavioral characteristics similar in duration to those present during acute attacks experienced by patients with chronic pancreatitis. These findings and responsivity to morphine suggest the utility of this model developed in a commercially available strain of rats for study of persistent visceral pain.
Use of phoA gene fusions to identify a pilus colonization factor coordinately regulated with cholera toxin. (1987)

The transposon TnphoA was used to generate fusions between phoA, the gene for alkaline phosphatase (PhoA), and genes encoding proteins that are secreted by Vibrio cholerae. One of the PhoA+ mutants isolated showed a dramatic reduction in its ability to colonize the intestines of suckling mice. This mutant no longer produced a 20.5-kDa protein (TcpA) that we show is the major subunit of a V. cholerae pilus. Amino-terminal sequence analysis of the TcpA pilus subunit showed that it shares amino acid homology with the pilins produced by several other pathogenic bacteria. The TcpA pilus was coordinately expressed with cholera toxin under various culture conditions, and this effect appeared to be dependent on the transcriptional activator encoded by the toxR gene. We conclude that the toxR gene plays a central role in the transcriptional regulation of multiple virulence genes of V. cholerae.
Improving Recoverability in Multi-tier Storage Systems (2007)

Enterprise storage systems typically contain multiple storage tiers, each having its own performance, reliability, and recoverability. The primary motivation for this multi-tier organization is cost, as storage tier costs vary considerably. In this paper, we describe a file system called TierFS that stores files at multiple storage tiers while providing high recoverability at all tiers. To achieve this goal, TierFS uses several novel techniques that leverage coupling between multiple tiers to reduce data loss, take consistent snapshots across tiers, provide continuous data protection, and improve recovery time. We evaluate TierFS with analytical models, showing that TierFS can provide better recoverability than a conventional design of similar cost.
Cleavage of Holliday Junctions by the Escherichia coli RuvABC Complex (2000)

The Escherichia coli RuvABC proteins process recombination intermediates during genetic recombination and recombinational repair. Although early biochemical studies indicated distinct RuvAB-mediated branch migration and RuvC-mediated Holliday junction resolution reactions, more recent studies have shown that the three proteins act together as a "resolvasome" complex. In this work we have used recombination intermediates made by RecA to determine whether the RuvAB proteins affect the sequence specificity of the RuvC resolvase. We find that RuvAB proteins do not alter significantly the site specificity of RuvC-dependent cleavage, although under certain conditions, they do affect the efficiency of cleavage at particular sites. The presence of RecA also influences cleavage at some sites. We also show that the RuvAB proteins act upon transient strand exchange intermediates made using substrates that have the opposite polarity of those preferred by RecA. Together, our results allow us to develop further a model for the recombinational repair of DNA lesions that lead to the formation of post-replication gaps during DNA replication. The novel features of this model are as follows: (i) the RuvABC resolvasome recognizes joints made by RecA; (ii) resolution by RuvABC occurs at specific sites containing the RuvC consensus cleavage sequence 5'-(A/T)TT downward arrow(G/C)-3'; and (iii) Holliday junction resolution often occurs close to the initiating gap without significant heteroduplex DNA formation.
Selective fluorination of alkyl C–H bonds via photocatalysis (2014)

We report the generation of cationic N-radicals from Selectfluor® via energy transfer with anthraquinone as a photocatalyst for the fluorination of unactivated C-H bonds.
A Glimpse of Matrix Metalloproteinases in Diabetic Nephropathy (2014)

Matrix metalloproteinases (MMPs) are proteolytic enzymes belonging to the family of zinc-dependent endopeptidases that are capable of degrading almost all the proteinaceous components of the extracellular matrix (ECM). It is known that MMPs play a role in a number of renal diseases, such as, various forms of glomerulonephritis and tubular diseases, including some of the inherited kidney diseases. In this regard, ECM accumulation is considered to be a hallmark morphologic finding of diabetic nephropathy, which not only is related to the excessive synthesis of matrix proteins, but also to their decreased degradation by the MMPs. In recent years, increasing evidence suggest that there is a good correlation between the activity or expression of MMPs and progression of renal disease in patients with diabetic nephropathy and in various experimental animal models. In such a diabetic milieu, the expression of MMPs is modulated by high glucose, advanced glycation end products (AGEs), TGF-β, reactive oxygen species (ROS), transcription factors and some of the microRNAs. In this review, we focused on the structure and functions of MMPs, and their role in the pathogenesis of diabetic nephropathy.
Activation of AKT-mTOR Signaling Directs Tenogenesis of Mesenchymal Stem Cells (2018)

Tendon repair is a clinical challenge because of the limited understanding on tenogenesis. The synthesis of type I collagen (Collagen I) and other extracellular matrix are essential for tendon differentiation and homeostasis. Current studies on tenogenesis focused mostly on the tenogenic transcriptional factors while the signaling controlling tenogenesis on translational level remains largely unknown. Here, we showed that mechanistic target of rapamycin (mTOR) signaling was activated by protenogenic growth factor, transforming growth factors beta1, and insulin-like growth factor-I. The expression of mTOR was upregulated during tenogenesis of mesenchymal stem cells (MSCs). Moreover, mTOR was downregulated in human tendinopathy tissues and was inactivated upon statin treatment. Both inhibition and depletion of AKT or mTOR significantly reduced type I collagen production and impaired tenogenesis of MSCs. Tendon specific-ablation of mTOR resulted in tendon defect and reduction of Collagen I. However, there is no evident downregulation of tendon associated collagens at the transcription level. Our study demonstrated that AKT-mTOR axis is a key mediator of tendon differentiation and provided a novel therapeutic target for tendinopathy and tendon injuries. Stem Cells 2018;36:527-539.
Theranostic Performance of Acoustic Nanodroplet Vaporization-Generated Bubbles in Tumor Intertissue (2017)

Solid tumors with poorly perfused regions reveal some of the treatment limitations that restrict drug delivery and therapeutic efficacy. Acoustic droplet vaporization (ADV) has been applied to directly disrupt vessels and release nanodroplets, ADV-generated bubbles (ADV-Bs), and drugs into tumor tissue. In this study, we investigated the <i>in vivo</i> behavior of ADV-Bs stimulated by US, and evaluated the possibility of moving intertissue ADV-Bs into the poorly perfused regions of solid tumors. Intravital imaging revealed intertissue ADV-B formation, movement, and cavitation triggered by US, where the distance of intertissue ADV-B movement was 33-99 µm per pulse. When ADV-Bs were applied to tumor cells, the cell membrane was damaged, increasing cellular permeability or inducing cell death. The poorly perfused regions within solid tumors show enhancement due to ADV-B accumulation after application of US-triggered ADV-B. The intratumoral nanodroplet or ADV-B distribution around the poorly perfused regions with tumor necrosis or hypoxia were demonstrated by histological assessment. ADV-B formation, movement and cavitation could induce cell membrane damage by mechanical force providing a mechanism to overcome treatment limitations in poorly perfused regions of tumors.
The Unified Dyskinesia Rating Scale: Presentation and clinimetric profile (2008)

We developed and tested a rating scale aimed to capture the essential features of dyskinesia in Parkinson's disease (PD). Although several scales assess selected attributes of PD-dyskinesias, no comprehensive rating tool exists. Available rating scales were evaluated by the investigators and patient focus groups. Modifications were finalized into the Unified Dyskinesia Rating Scale (UDysRS). The UDysRS has four parts: I: Historical Disability (patient perceptions) of On-Dyskinesia impact (maximum 44 points); II: Historical Disability (patient perceptions) of Off-Dystonia impact (maximum 16 points); III: Objective Impairment (dyskinesia severity, anatomical distribution over seven body regions, and type (choreic or dystonic) based on four activities observed or video-recorded (28 points); IV: Objective Disability based on Part III activities (maximum 16 points). For clinimetric testing, 70 PD patients with all severities of dyskinesia were interviewed and videotaped. Twenty movement disorder experts rated the videotapes with the UDysRS. Internal consistency was examined with Cronbach's alpha. Inter- and intra-rater reliability was evaluated with generalized weighted and nonweighted Kappa coefficients, and intraclass correlation coefficients. Both subjective (Sections I and II) and objective (Sections III and IV) demonstrated high internal consistency (alpha: 0.915, 0.971). Interrater reliability for the objective sections was acceptable for all items and likewise for intrarater reliability except for right leg. Reliable factor structures were found for both subjective (six factors) and objective sections (five factors). The UDysRS is a clinimetrically sound rating scale for dyskinesia in PD, demonstrating acceptable levels of internal consistency and inter- and intra-rater reliability. Testing scale responsivity to treatment interventions is planned.
Disruption of TRI101 , the Gene Encoding Trichothecene 3- O -Acetyltransferase, from Fusarium sporotrichioides (1999)

We screened a Fusarium sporotrichioides NRRL 3299 cDNA expression library in a toxin-sensitive Saccharomyces cerevisiae strain lacking a functional PDR5 gene. Fourteen yeast transformants were identified as resistant to the trichothecene 4,15-diacetoxyscirpenol, and each carried a cDNA encoding the trichothecene 3-O-acetyltransferase that is the F. sporotrichioides homolog of the Fusarium graminearum TRI101 gene. Mutants of F. sporotrichioides NRRL 3299 produced by disruption of TRI101 were altered in their abilities to synthesize T-2 toxin and accumulated isotrichodermol and small amounts of 3, 15-didecalonectrin and 3-decalonectrin, trichothecenes that are not observed in cultures of the parent strain. Our results indicate that TRI101 converts isotrichodermol to isotrichodermin and is required for the biosynthesis of T-2 toxin.
Characterization of the epitope of anti-lipoarabinomannan antibodies as the terminal hexaarabinofuranosyl motif of mycobacterial arabinans (2002)

mAb CS-35 is representative of a large group of antibodies with similar binding specificities that were generated against the Mycobacterium leprae lipopolysaccharide, lipoarabinomannan (LAM), and which cross-reacted extensively with LAMs from Mycobacterium tuberculosis and other mycobacteria. That this antibody also cross-reacts with the arabinogalactan (AG) of the mycobacterial cell wall, suggesting that it recognizes a common arabinofuranosyl (Araf)-containing sequence in AG and LAM, is demonstrated. The antibody reacted more avidly with 'AraLAM' (LAM with naked Araf termini) compared to 'ManLAM' (in which many Araf termini are capped with mannose residues) and mycolylarabinogalactan-peptidoglycan complex (in which the terminal Araf units are substituted with mycolic acids). Neither did the antibody bind to AG from emb knock-out mutants deficient in the branched hexa-Araf termini of AG. These results indicate that the terminal Araf residues of mycobacterial arabinan are essential for binding. Competitive ELISA using synthetic oligosaccharides showed that the branched hexa-Araf methyl glycoside [beta-D-Araf-(1-->2)-alpha-D-Araf-(1-)(2)-(3 and 5)-alpha-D-Araf-(1-->5)-alpha-D-Araf-OCH(3)] was the best competitor among those tested. The related linear methyl glycoside, beta-D-Araf-(1-->2)-alpha-D-Araf-(1-->5)-alpha-D-Araf-(1-->5)-alpha-D-Araf-OCH(3), representing one linear segment of the branched hexa-Araf, was less effective and the other linear tetrasaccharide, beta-D-Araf-(1-->2)-alpha-D-Araf-(1-->3)-alpha-D-Araf-(1-->5)-alpha-D-Araf-OCH(3), was ineffective. The combined results suggest that the minimal epitope recognized by antibody CS-35 encompasses the beta-D-Araf-(1-->2)-alpha-D-Araf-(1-->5)-alpha-D-Araf-(1-->5)-alpha-D-Araf within the branched hexa-Araf motif of mycobacterial arabinans, whether present in LAM or AG.
Direct evidence for mRNA binding and post-transcriptional regulation by Escherichia coli aconitases (1999)

Escherichia coli contains a stationary-phase aconitase (AcnA) that is induced by iron and oxidative stress, and a major but less stable aconitase (AcnB) synthesized during exponential growth. These enzymes were shown to resemble the bifunctional iron-regulatory proteins (IRP1)/cytoplasmic aconitases of vertebrates in having alternative mRNA-binding and catalytic activities. Affinity chromatography and gel retardation analysis showed that the AcnA and AcnB apo-proteins each interact with the 3' untranslated regions (3'UTRs) of acnA and acnB mRNA at physiologically significant protein concentrations. AcnA and AcnB synthesis was enhanced in vitro by the apoaconitases and this enhancement was abolished by 3'UTR deletion from the DNA templates, presumably by loss of acn-mRNA stabilization by bound apoaconitase. In vivo studies showed that although total aconitase activity is lowered during oxidative stress, synthesis of the AcnA and AcnB proteins and the stabilities of acnA and acnB mRNAs both increase, suggesting that inactive aconitase mediates a post-transcriptional positive autoregulatory switch. Evidence for an iron-sulphur-cluster-dependent switch was inferred from the more than threefold higher mRNA-binding affinities of the apo-aconitases relative to the holo-enzymes. Thus by modulating translation via site-specific interactions between apo-enzyme and relevant transcripts, the aconitases provide a new and rapidly reacting component of the bacterial oxidative stress response.
A high‐affinity human monoclonal antibody specific to the alternatively spliced EDA domain of fibronectin efficiently targets tumor neo‐vasculature in vivo (2008)

The alternatively spliced extra-domain B of fibronectin is one of the best characterized markers of tumor angiogenesis. Similarly, the extra-domain A (EDA), which can also be inserted in the fibronectin transcript by a mechanism of alternative splicing, has been shown to preferentially accumulate around new blood vessels in certain tumors, but this antigen has not been investigated so far as a target for antibody-based biomolecular intervention. We here describe the generation of 3 human monoclonal antibodies (named F8, B7 and D5), which recognize the same epitope of EDA, but which differ in terms of their dissociation constant to the human antigen (K(D) = 3.1, 16 and 17 nM, measured for monomeric preparations of the F8, B7 and D5 antibodies, respectively, in recombinant scFv format). When the 3 antibody fragments were cloned and expressed with a 5 amino acid linker, the 3 resulting homodimeric antibody preparations displayed comparable tumor: organ ratios in quantitative biodistribution studies, performed in immunocompetent 129SvEv mice, bearing subcutaneous syngeneic F9 murine tumors. The percent injected dose per gram (%ID/g) values in tumors 24 hr after intravenous injection were 9.3, 10.2 and 13 for F8, B7 and D5, respectively. The F8 antibody may serve as useful building block for the development of antibody-based targeted anti-cancer therapeutics. Preclinical and clinical investigations are facilitated by the fact that F8 recognizes the human and mouse antigen with comparable affinity, and by the observation that EDA over-expression is detectable not only in solid tumors, but also in hematological malignancies.
Giant Viruses Infecting Algae (1999)

Paramecium bursaria chlorella virus (PBCV-1) is the prototype of a family of large, icosahedral, plaque-forming, double-stranded-DNA-containing viruses that replicate in certain unicellular, eukaryotic chlorella-like green algae. DNA sequence analysis of its 330, 742-bp genome leads to the prediction that this phycodnavirus has 376 protein-encoding genes and 10 transfer RNA genes. The predicted gene products of approximately 40% of these genes resemble proteins of known function. The chlorella viruses have other features that distinguish them from most viruses, in addition to their large genome size. These features include the following: (a) The viruses encode multiple DNA methyltransferases and DNA site-specific endonucleases; (b) PBCV-1 encodes at least part, if not the entire machinery to glycosylate its proteins; (c) PBCV-1 has at least two types of introns--a self-splicing intron in a transcription factor-like gene and a splicesomal processed type of intron in its DNA polymerase gene. Unlike the chlorella viruses, large double-stranded-DNA-containing viruses that infect marine, filamentous brown algae have a circular genome and a lysogenic phase in their life cycle.
Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies (2008)

Database-searching programs generally identify only a fraction of the spectra acquired in a standard LC/MS/MS study of digested proteins. Subtle variations in database-searching algorithms for assigning peptides to MS/MS spectra have been known to provide different identification results. To leverage this variation, a probabilistic framework is developed for combining the results of multiple search engines. The scores for each search engine are first independently converted into peptide probabilities. These probabilities can then be readily combined across search engines using Bayesian rules and the expectation maximization learning algorithm. A significant gain in the number of peptides identified with high confidence with each additional search engine is demonstrated using several data sets of increasing complexity, from a control protein mixture to a human plasma sample, searched using SEQUEST, Mascot, and X! Tandem database-searching programs. The increased rate of peptide assignments also translates into a substantially larger number of protein identifications in LC/MS/MS studies compared to a typical analysis using a single database-search tool.