gebhart/patrepeval huggingface dataset:
Glucocorticoid receptors in immunological subtypes of childhood acute lymphocytic leukemia cells: a Pediatric Oncology Group Study. (1985)

Glucocorticoid receptors were quantitated by a whole cell method in cells from 593 children with acute leukemia at the time of diagnosis. Leukemia cells were also immunologically typed and divided into early pre-B- (not reactive with antibodies to T-lymphocyte antigens, surface immunoglobulin-negative, cytoplasmic immunoglobulin-negative), pre-B- (not reactive with antibodies to T-lymphocyte antigens, surface immunoglobulin-negative, cytoplasmic immunoglobulin-positive), B- (not reactive with antibodies to T-lymphocyte antigens, surface immunoglobulin-positive), and T- (reactive with antibodies to T-lymphocyte antigens) subtypes. There was a median of 9.7 X 10(3) sites per cell in the 359 with early pre-B-acute lymphocytic leukemia, a median of 8.1 X 10(3) sites per cell from 103 patients with pre-B-cell leukemia, and a median of 4.0 X 10(3) sites per cell from 116 patients with T-cell leukemia. The distributions per cell were significantly different among these 3 groups (P less than 0.0001). The 15 patients with B-cell disease had a median of 3.2 X 10(3) sites per cell. At the time of analysis, remission induction data are available for most of these patients. Within the early pre-B- group 291 patients with a median receptor number of 9.9 X 10(3) achieved remission, while 13 with a median receptor number of 4.8 X 10(3) did not. These distributions were significantly different (P = 0.034). Within the pre-B- and T-cell groups the distributions of receptor numbers for responders and non-responders were not significantly different. We conclude that each immunological subtype has characteristic receptor distribution. High receptor number within the null group is associated with the ability of the patient to achieve remission; however, the range of values within each patient group is too broad to use this assay as a predictor of response for any individual patient.
Measuring and Predicting Dynamic Sag (2008)

Summary Weighting-material sag is a reoccurring problem with many oil-based drilling fluids. Attempts to correlate sag tendencies to various rheological properties commonly used to benchmark drilling fluids have had limited success in prevention and anticipation of sag problems in the field. This paper presents a new testing apparatus for dynamic and static settling-rate (sag) measurements, which has proved to provide a better understanding of the sag phenomena and a better means to characterize fluid performance. This apparatus greatly expands the precision of sag measurements over previous techniques and allows testing conditions similar to those experienced downhole. Good correlation has been found between settling-rate measurements and performance of drilling fluids in the field.
Immunization of Healthy Adults with Live Attenuated Varicella Vaccine (1988)

Live attenuated varicella vaccine was administered to healthy varicella-susceptible adults. Of 187 adults immunized with the Oka strain of vaccine, seroconversion to varicella-zoster virus (VZV) occurred in 82% after one dose and in 94% after two doses. Adverse effects were unusual. After immunization, one subject developed mild zoster caused by wild-type virus. Twelve adults developed a mild breakthrough case of chickenpox after exposure to VZV. Protection after household exposure was observed in nine (56%) of 16; however, the illness in all seven patients with breakthrough illness was modified, with an average of only 24 vesicles. Subjects seropositive at household exposure were unlikely to develop a breakthrough illness. Approximately 25% of vaccinees who seroconverted lost detectable antibodies to VZV after vaccination, but even those who became seronegative were partially protected. Varicella vaccine offered significant protection against severe chickenpox in healthy adults.
Vibrio cholerae non-O1 serogroup associated with cholera gravis genetically and physiologically resembles O1 E1 Tor cholera strains (1994)

Until recently, only Vibrio cholerae strains of the O1 serogroup have been associated with epidemic cholera. In December 1992, an outbreak of cholera gravis in Vellore, India, was attributed to a new serogroup of V. cholerae recently designated O139. Serogroup O139 cholera has since spread to 13 countries and has reached pandemic proportions. Serogroup O139 cholera evades immunity to O1 cholera and is not detected by the standard O1 antigen test. Understanding the origins of O139 cholera and determining the relatedness of O139 to O1 cholera are necessary to device strategies for detecting, reporting, and controlling this new pandemic. In order to determine the origins of this novel cholera serogroup, O139 was analyzed for virulence genes, for virulence proteins and their regulation, and for its genomic background. We found that O139 and O1 V. cholera strains of the E1 Tor biotype possess highly homologous virulence genes encoding cholera toxin and toxin-coregulated pili and that the regulation of virulence protein expression likewise was indistinguishable between O139 and O1. Pulsed-field gel electrophoresis (PFGE) revealed the restriction digest pattern of O139 strains to be closely related to that of O1 serogroup E1 Tor biotype cholera strains from the Indian subcontinent. However, PFGE showed minor differences among individual O139 cholera isolates, suggesting that O139 V. cholerae is evolving.
Role of cis-acting sequences of the ICPO promoter of herpes simplex virus type 1 in viral pathogenesis, latency and reactivation (1996)

A mutant herpes simplex virus type 1, termed delta Tfi, with a 350 bp deletion of the Sp1, NF-kappaB, TAATGARATs, C/EBP and F2 DNA-binding elements from -420 to -70 relative to the transcriptional start site of ICPO (Vmw 110), was generated and characterized. The efficiency of plating of delta Tfi was reduced on Vero cells and it expressed correctly initiated ICPO RNA in the presence of cycloheximide, although RNA levels were 2.5-fold lower than with wild-type (KOS) and marker-rescued (delta TfiR) viruses. This was consistent with a demonstrated reduction in ICPO protein expression for delta Tfi at early times post-infection and a 3-fold reduction in ICPO-dependent transactivation of the ICP6 promoter. KOS, delta Tfi and delta TfiR replication in murine corneas and trigeminal ganglia were comparable when measured on a complementing cell line, but delta Tfi titres appeared 15- to 50-fold lower when measured on Vero cells. delta Tfi was correspondingly less virulent than wild-type or marker-rescued viruses in both immunocompetent and SCID mice. delta Tfi, however, established and reactivated from latency with efficiencies comparable to wild-type and marker-rescued viruses. These results demonstrate that although this deletion of the ICPO promoter results in lower levels of ICPO in vitro and decreased virulence in vivo, the establishment of and reactivation from latency are unaffected. This indicates that elements which regulate ICPO expression and virulence during acute infection may be distinct from those involved in reactivation.
The Effectiveness and Safety of Brimonidine as Mono-, Combination, or Replacement Therapy for Patients with Primary Open-Angle Glaucoma or Ocular Hypertension: A Post Hoc Analysis of an Open-Label Community Trial (2000)

The purpose of this study was to determine the effectiveness and safety of brimonidine 0.2% (Alphagan, Allergan Inc., Irvine, CA) as mono-, combination, or replacement therapy for reducing intraocular pressure (IOP) in patients with primary open-angle glaucoma or ocular hypertension. The study method was an open-label, comparative clinical evaluation involving 2335 patients. During the 2-month trial, data were collected at baseline (visit 1), month 1 (visit 2), and month 2 (visit 3). Various parameters were evaluated, including glaucoma medications (visit 1), IOP (visit 1-visit 3), and adverse events. A subset cohort of 1254 patients was selected that met specific study criteria. Data from these 1254 patients were used to evaluate adverse events and the change in IOP from visit 1 to visit 3. Patient data were grouped according to specific drug regimen, and drug regimens were categorized into supergroups of mono-, combination, and replacement therapy. The results of the study revealed that the overall mean change in IOP for 1) monotherapy (n = 240) was -5.07 mm Hg (-20.2%), 2) combination therapy (n = 554) was -4.01 mm Hg (-16.9%), 3) replacement therapy (n = 460) was -2.33 mm Hg (-9.8%), and 4) overall (n = 1254) was -3.59 mm Hg (-14.9%) (p < 0.001 for all changes). Overall, 6.0% of the subjects reported adverse events, with no hypersensitivity or unexpected systemic or ocular adverse events. Eighty-five percent (85%) of clinicians rated brimonidine as "good" to "excellent". In conclusion, brimonidine is safe and effectively lowers IOP when used as mono-, combination, or replacement therapy as observed in a large community population.
Multiplex Immunoassay and Bead Based Multiplex (2012)

Optimal assay performance of multiplex immunoassay platforms depend on proprietary information about the antibody pair, the composition of diluents, and the software. The accuracy of quantification for multiplexed immunoassays depends, as with all ELISAs, on the quality of the calibration curves, assay imprecision (CV), recoveries, and assay linearity www.intechopen.com
{open_quotes}Unspecific{close_quotes} X-linked mental retardation: Clinical, genetic and molecular studies (1994)

Previous linkage studies have assigned a gene for non-syndromic X-linked mental retardation (XMR) to at least 8 different regions on the X-chromosome. The fragile X-syndrome (FRAXA) does not account for more than 40% of all cases; in most XMR families early diagnosis and prevention is not possible. As part of a systematic study into {open_quotes}unspecific{close_quotes} XMR involving more than 30 non-FRAXA families, linkage studies have enabled us to map the respective genes in 4 families to the Xp11.4-q12 interval with peak lod scores around the ALAS2 locus. In three other families, the gene defect could be assigned to the KAL-DMD, DXS424-FRAXAC2 and DSX52-Xqter intervals, respectively. In one of these families, small stature due to growth hormone deficiency was observed as a distinctive clinical feature. Molecular cloning of the breakpoint in a mentally retarded girl with a balanced t(Xq13;13q) translocation has enabled us to isolate an X-chromosomal gene which is disrupted in this patient and is highly expressed in brain. YAC cloning strategies are being employed to clone another XMR gene, which has been identified previously in the vicinity of the CHM locus and genes involved in mentally retarded patients with two different inversions, inv(X)(q21p11) and inv(X)(p21q24), respectively.
Systematic pathological component scores for skin-containing vascularized composite allografts (2016)

Clinical management of skin-containing vascularized composite allografts (VCA) requires accurate assessment of the graft status, typically based on skin biopsies. The Banff 2007 Working Classification proposed 4 grades of acute rejection, but did not score individual features or include vascular rejection. Here we report a systematic scoring system developed from MHC-mismatched porcine skin-containing VCA. Biopsies from 20 VCA, 9 autologous skin flaps and 9 normal skin were analyzed to optimize the methodology and set thresholds. The components quantified were: perivascular cells/dermal vessel (pc), perivascular dermal infiltrate area (pa), luminal leukocytes/capillary or venule (c), epidermal infiltrate (ei), epidermal apoptosis or necrosis (e), endarteritis (v), and chronic allograft vasculopathy (cav). To evaluate prognostic value, we scored a separate group of 28 serial biopsies from 8 recipients (4 that were ultimately accepted and 4 that rejected. Parameters on the initial biopsies predicting later graft rejection included pc (p < 0.02), pa (p < 0.03), ei (p < 0.0005), e (p < 0.003) and c (p < 0.005). Reproducibility between 2 pathologists blinded to clinical data was acceptable, with weighted kappa scores for pc (0.673), pa (0.399), ei (0.464), e (0.663), v (0.766), and c (0.642). This component scoring system can be adapted clinically, since human and porcine skin are highly similar. Vascular lesions in VCA are also highlighted in this system and could impact graft outcome. The component score approach complements Banff 2007 grades and will enable the establishment of clinically significant thresholds.
Evolving concepts of therapy for sepsis and septic shock and the use of hyperpermeable membranes (2000)

In sepsis and septic shock, excess and dysfunctional inflammation is destructive to vital tissues, resulting in the observed morbidity and mortality. The prevailing therapeutic hypothesis is that neutralization of some “pivotal” single inflammatory mediator can control this destructive inflammation. However, no single antimediator therapy has succeeded. An alternative hypothesis favors modulation of several inflammatory mediators. Implementation of this hypothesis by means of large pore, or hyperpermeable, membranes is discussed; the limited experience with these membranes is reviewed.
Association of C-Terminal Ubiquitin Hydrolase BRCA1-Associated Protein 1 with Cell Cycle Regulator Host Cell Factor 1 (2009)

Protein ubiquitination provides an efficient and reversible mechanism to regulate cell cycle progression and checkpoint control. Numerous regulatory proteins direct the addition of ubiquitin to lysine residues on target proteins, and these are countered by an army of deubiquitinating enzymes (DUBs). BRCA1-associated protein-1 (Bap1) is a ubiquitin carboxy-terminal hydrolase and is frequently mutated in lung and sporadic breast tumors. Bap1 can suppress growth of lung cancer cells in athymic nude mice and this requires its DUB activity. We show here that Bap1 interacts with host cell factor 1 (HCF-1), a transcriptional cofactor found in a number of important regulatory complexes. Bap1 binds to the HCF-1 beta-propeller using a variant of the HCF-binding motif found in herpes simplex virus VP16 and other HCF-interacting proteins. HCF-1 is K48 and K63 ubiquitinated, with a major site of linkage at lysines 1807 and 1808 in the HCF-1(C) subunit. Expression of a catalytically inactive version of Bap1 results in the selective accumulation of K48 ubiquitinated polypeptides. Depletion of Bap1 using small interfering RNA results in a modest accumulation of HCF-1(C), suggesting that Bap1 helps to control cell proliferation by regulating HCF-1 protein levels and by associating with genes involved in the G(1)-S transition.
Linkage and sib-pair analysis reveal a potential schizophrenia susceptibility gene on chromosome 13q32 (1996)

S: 1996 World Congress on Psychiatric Genetics: II. LINKAGE AND CANDIDATE LOCI FOR THE PSYCHOSES: EMPHASIS ON SCHIZOPHRENIA: PDF Only
Carbon monoxide reduces the expression and activity of matrix metalloproteinases 1 and 2 in alveolar epithelial cells. (2005)

Matrix metalloproteinases (MMPs), particularly MMP-1 and MMP-2, are involved in the pathophysiology of emphysema. MMPs contain zinc in the catalytic site and its expression is regulated transcriptionally via mitogen activated protein kinases (MAPKs). Carbon monoxide (CO), one of the end products of heme oxygenase activity, has anti-inflammatory properties, which are mediated, at least in part, by activation of p38 MAPK. Furthermore, CO has the unique ability to bind to metal centers in proteins and can affect their specific activity. Therefore, we hypothesized that CO could inhibit MMPs expression and/or activity. Here we show that a recently identified carbon monoxide-releasing molecule, [Ru(CO)3Cl2]2 (or CORM-2) inhibits MMP-1 and MMP-2 mRNA expression in the human lung epithelial cell line A549. The MMPs mRNA expression was unaffected by the p38 MAPK inhibitor SB203580, but in the case of MMP-1 was reversed by the antioxidant N-acetylcysteine. In addition, CORM-2 inhibited both MMP-1 and MMP-2 activities. Interestingly, no effect was observed with (Ru(DMSO)4Cl2), a negative control that does not contain CO groups. To the best of our knowledge this is the first evidence on the effect of CO on MMPs expression and activity. This effect could have important implications in the pathophysiology of emphysema and other diseases involving proteases/antiproteases imbalance.
A binary-BAC system for plant transformation with high-molecular-weight DNA (1997)

A binary-BAC (BIBAC) vector suitable for Agrobacterium-mediated plant transformation with high-molecular-weight DNA was constructed. A BIBAC vector is based on the bacterial artificial chromosome (BAC) library vector and is also a binary vector for Agrobacterium-mediated plant transformation. The BIBAC vector has the minimal origin region of the Escherichia coli F plasmid and the minimal origin of replication of the Agrobacterium rhizogenes Ri plasmid, and thus replicates as a single-copy plasmid in both E. coli and in A. tumefaciens. The T-DNA of the BIBAC vector can be transferred into the plant nuclear genome. As examples, a 30-kb yeast genomic DNA fragment and a 150-kb human genomic DNA fragment were inserted into the BIBAC vector; these constructs were maintained in both E. coli and A. tumefaciens. In order to increase the efficiency of transfer of unusually large BIBAC T-DNAs, helper plasmids that carry additional copies of A. tumefaciens virulence genes virG and virE were constructed. These helper plasmids are compatible with, and can be present in addition to, the BIBAC vector in the A. tumefaciens host. This report details the components of the BIBAC system, providing information essential to the general understanding and the application of this new technology.
Novel perspectives for evolving enzyme cocktails for lignocellulose hydrolysis in biorefineries (2013)

Abstract The unstable and uncertain availability of petroleum sources as well as rising cost of fuels have shifted global efforts to utilize renewable resources for the production of greener energy and a replacement which can also meet the high energy demand of the world. Bioenergy routes suggest that atmospheric carbon can be cycled through biofuels in carefully designed systems for sustainability. Significant potential exists for bioconversion of biomass, the most abundant and also the most renewable biomaterial on our planet. However, the requirements of enzyme complexes which act synergistically to unlock and saccharify polysaccharides from the lignocellulose complex to fermentable sugars incur major costs in the overall process and present a great challenge. Currently available cellulase preparations are subject to tight induction and regulation systems and also suffer inhibition from various end products. Therefore, more potent and efficient enzyme preparations need to be developed for the enzymatic saccharification process to be more economical. Approaches like enzyme engineering, reconstitution of enzyme mixtures and bioprospecting for superior enzymes are gaining importance. The current scenario, however, also warrants the need for research and development of integrated biomass production and conversion systems.
Brucellosis Vaccines: Assessment of Brucella melitensis Lipopolysaccharide Rough Mutants Defective in Core and O-Polysaccharide Synthesis and Export (2008)

The results demonstrate that no rough mutant is equal to Rev 1 in laboratory models and question the notion that rough vaccines are suitable for the control of brucellosis in endemic areas.
Herpes simplex virus alpha protein ICP27 possesses separable positive and negative regulatory activities (1989)

The HSV-1 alpha (immediate-early) protein ICP27 expressed in transfected cells can activate the expression of certain HSV-1 promoters as well as inhibit the transactivated expression of others. We constructed a set of plasmids encoding mutant ICP27 molecules truncated at their carboxyl termini and used transfection assays to determine the functional properties of the mutant proteins. A polypeptide containing the amino-terminal 263 amino acid residues of ICP27 retained partial ability to activate gene expression but was unable to inhibit transactivation. Mutant proteins possessing 406 or 504 amino acids of ICP27 were unable to activate gene expression but retained full ability to inhibit transactivation. These results define two separable regulatory activities of ICP27, one positive and one negative, which can modulate gene expression in transfected cells. Immunoblot and immunofluorescence experiments were used to study the immunological reactivities and intracellular localizations of the mutant proteins. All proteins possessing the amino-terminal 263 amino acids of ICP27 reacted with an ICP27-specific monoclonal antibody and were localized to the cell nucleus. The mutant proteins, however, exhibited a number of phenotypes with regard to intranuclear localization. A mutant possessing 504 residues of ICP27 was similar to the wild-type protein in apparently localizing to all regions of the nucleus. A mutant containing 406 residues of ICP27, on the other hand, was mostly excluded from the nucleolar regions, while a 263-residue mutant was localized predominantly in the nucleoli. Thus, some aspect of ICP27 structure or function can dramatically affect its intranuclear distribution.
TLR3 Is Essential for the Induction of Protective Immunity against Punta Toro Virus Infection by the Double-Stranded RNA (dsRNA), Poly(I:C12U), but not Poly(I:C): Differential Recognition of Synthetic dsRNA Molecules (2007)

In the wake of RNA virus infections, dsRNA intermediates are often generated. These viral pathogen-associated molecular patterns can be sensed by a growing number of host cell cytosolic proteins and TLR3, which contribute to the induction of antiviral defenses. Recent evidence indicates that melanoma differentiation-associated gene-5 is the prominent host component mediating IFN production after exposure to the dsRNA analog, poly(I:C). We have previously reported that Punta Toro virus (PTV) infection in mice is exquisitely sensitive to treatment with poly(I:C(12)U), a dsRNA analog that has a superior safety profile while maintaining the beneficial activity of the parental poly(I:C) in the induction of innate immune responses. The precise host factor(s) mediating protective immunity following its administration remain to be elucidated. To assess the role of TLR3 in this process, mice lacking the receptor were used to investigate the induction of protective immunity, type I IFNs, and IL-6 following treatment. Unlike wild-type mice, those lacking TLR3 were not protected against PTV infection following poly(I:C(12)U) therapy and failed to produce IFN-alpha, IFN-beta, and IL-6. In contrast, poly(I:C) treatment significantly protected TLR3(-/-) mice from lethal challenge despite some deficiencies in cytokine induction. There was no indication that the lack of protection was due to the fact that TLR3-deficient mice had a reduced capacity to fight infection because they were not found to be more susceptible to PTV. We conclude that TLR3 is essential to the induction of antiviral activity elicited by poly(I:C(12)U), which does not appear to be recognized by the cytosolic sensor of poly(I:C), melanoma differentiation-associated gene-5.