gebhart/patrepeval huggingface dataset:
Attenuation of and Protection Induced by a Leucine Auxotroph ofMycobacterium tuberculosis (2000)

Attenuated mutants of Mycobacterium tuberculosis represent potential vaccine candidates for the prevention of tuberculosis. It is known that auxotrophs of a variety of bacteria are attenuated in vivo and yet provide protection against challenge with wild-type organisms. A leucine auxotroph of M. tuberculosis was created by allelic exchange, replacing wild-type leuD (Rv2987c), encoding isopropyl malate isomerase, with a mutant copy of the gene in which 359 bp had been deleted, creating a strain requiring exogenous leucine supplementation for growth in vitro. The frequency of reversion to prototrophy was <10(-11). In contrast to wild-type M. tuberculosis, the DeltaleuD mutant was unable to replicate in macrophages in vitro. Its attenuation in vivo and safety as a vaccine were established by the fact that it caused no deaths in immunodeficient SCID mice. Complementation of the mutant with wild-type leuD abolished the requirement for leucine supplementation and restored the ability of the strain to grow both in macrophages and in SCID mice, thus confirming that the attenuated phenotype was due to the DeltaleuD mutation. As a test of the vaccine potential of the leucine auxotroph, immunocompetent BALB/c mice, susceptible to fatal infection with wild-type M. tuberculosis, were immunized with the DeltaleuD mutant and subsequently challenged with virulent M. tuberculosis by both the intravenous and aerosol routes. A comparison group of mice was immunized with conventional Mycobacterium bovis BCG vaccine. Whereas all unvaccinated mice succumbed to intravenous infection within 15 weeks, mice immunized with either BCG or the DeltaleuD mutant of M. tuberculosis exhibited enhanced and statistically equivalent survival curves. However, the leuD auxotroph was less effective than live BCG in reducing organ burdens and tissue pathology of mice challenged by either route. We conclude that attenuation and protection against M. tuberculosis challenge can be achieved with a leucine auxotroph and suggest that to induce optimal protection, attenuated strains of M. tuberculosis should persist long enough and be sufficiently metabolically active to synthesize relevant antigens for an extended period of time.
Enzyme immunoassay for detection of immunoglobulin G (IgG), IgM, and IgA antibodies against type 6B pneumococcal capsular polysaccharide and cell wall C polysaccharide in chinchilla serum (1992)

Conjugation of the capsular polysaccharides of Streptococcus pneumoniae to protein carriers has introduced a new generation of pneumococcal vaccines which may be efficacious in preventing pneumococcal otitis media during infancy. The chinchilla model has been used extensively for studying the pathogenesis of pneumococcal otitis media and for testing the efficacy of early pneumococcal capsular polysaccharide (PCP) vaccines, but immunologic studies in the chinchilla have been limited by the lack of antibodies against specific immunoglobulin isotypes. By using affinity-purified rabbit immunoglobulin G (IgG) anti-chinchilla IgG, IgM, and IgA, we developed a sensitive enzyme immunoassay that is highly specific for IgG, IgM, and IgA antibodies against type 6B PCP (anti-6B) and against C polysaccharide in chinchilla serum. Antibody titers increased in serum from five chinchillas immunized with a type 6B outer membrane protein complex vaccine. Increases of anti-6B IgG and IgM antibody titers were more striking than increases of anti-6B IgA or anti-C polysaccharide IgG, IgM, or IgA titers were.
Cytotoxic and viral neutralizing antibodies crossreact with streptococcal M protein, enteroviruses, and human cardiac myosin. (1992)

The development of autoimmunity in certain instances is related to infectious agents. In this report, cytotoxic monoclonal antibodies (mAbs) that recognize epitopes on both enteroviruses and the bacterium Streptococcus pyogenes are described. Murine anti-streptococcal mAbs that were crossreactive with streptococcal M protein, human cardiac myosin, and other alpha-helical coiled-coil molecules were found to neutralize coxsackieviruses B3 and B4 or poliovirus type 1. The viral-neutralizing anti-streptococcal mAbs were also cytotoxic for heart and fibroblast cell lines and reacted with viral capsid proteins on a Western immunoblot. Alignment of amino acid sequences shared between streptococcal M protein, coxsackie-virus B3 capsid protein VP1, and myosin revealed 40% identity in a 14- to 15-amino acid overlap. Synthetic peptides containing these sequences blocked mAb reactivity with streptococcal M protein. The data show that antibodies against alpha-helical structures of bacterial and viral antigens can lead to cytotoxic reactions and may be one mechanism to explain the origin of autoimmune heart disease.
All-trans-Retinoic Acid Improves Differentiation of Myeloid Cells and Immune Response in Cancer Patients (2006)

Abnormal dendritic cell differentiation and accumulation of immature myeloid suppressor cells (ImC) is one of the major mechanisms of tumor escape. We tested the possibility of pharmacologic regulation of myeloid cell differentiation using all-trans-retinoic acid (ATRA). Eighteen patients with metastatic renal cell carcinoma were treated with ATRA followed by s.c. interleukin 2 (IL-2). Eight healthy individuals comprised a control group. As expected, the cancer patients had substantially elevated levels of ImC. We observed that ATRA dramatically reduced the number of ImC. This effect was observed only in patients with high plasma concentration of ATRA (>150 ng/mL), but not in patients with lower ATRA concentrations (<135 ng/mL). Effects of ATRA on the proportions of different dendritic cell populations were minor. However, ATRA significantly improved myeloid/lymphoid dendritic cell ratio and the ability of patients' mononuclear cells to stimulate allogeneic T cells. This effect was associated with significant improvement of tetanus-toxoid-specific T-cell response. During the IL-2 treatment, the ATRA effect was completely eliminated. To assess the role of IL-2, specimens from 15 patients with metastatic renal cell carcinoma who had been treated with i.v. IL-2 alone were analyzed. In this group also, IL-2 significantly reduced the number and function of dendritic cells as well as T-cell function. These data indicate that ATRA at effective concentrations eliminated ImC, improved myeloid/lymphoid dendritic cell ratio, dendritic cell function, and antigen-specific T-cell response. ATRA treatment did not result in significant toxicity and it could be tested in therapeutic combination with cancer vaccines.
Behavioral aspects of Lesch–Nyhan disease and its variants (2005)

Self-injury is a defining feature of lesch-nyhan disease (LND) but does not occur in the less severely affected Lesch-Nyhan variants (LNV). The aim of this study was to quantify behavioral and emotional abnormalities in LND and LNV. Thirty-nine informants rated 22 patients with LND (21 males, 1 female), 11 males with LNV, and 11 healthy controls (HC; 10 males, 1 female) using two well-validated rating scales. The age of patients with LND ranged from 12 years 7 months to 38 years 3 months (mean 22 y 11 mo; sd 7 y 8 mo), whereas the age range of those with LNV was 12 years 9 months to 65 years (mean 30 y 7 mo; sd 15 y 2 mo), and the healthy controls were aged 12 years 4 months to 31 years 3 months (mean 17 y 10 mo; sd 5 y 7 mo). Behavioral ratings were based on the Child Behavior Checklist and the American Association On Mental Retardation's Adaptive Behavior Scale--Residential And Community, 2nd edition. Statistical analyses revealed that patients with LND showed severe self-injury together with problematic aggression, anxious-depressed symptoms, distractibility, motor stereotypes, and disturbing interpersonal behaviors. Patients with LNV were rated as being intermediate between the HC and LND groups on all behavior scales. Although the LNV group did not differ from hcs on most scales, their reported attention problems were as severe as those found in LND. We conclude that self-injurious and aggressive behaviors are nearly universal and that other behavioral abnormalities are common in LND. Although patients with LNV typically do not self-injure or display severe aggression, attention problems are common and a few patients demonstrate other behavioral anomalies.
Folliculin-interacting proteins Fnip1 and Fnip2 play critical roles in kidney tumor suppression in cooperation with Flcn (2015)

Folliculin (FLCN)-interacting proteins 1 and 2 (FNIP1, FNIP2) are homologous binding partners of FLCN, a tumor suppressor for kidney cancer. Recent studies have revealed potential functions for Flcn in kidney; however, kidney-specific functions for Fnip1 and Fnip2 are unknown. Here we demonstrate that Fnip1 and Fnip2 play critical roles in kidney tumor suppression in cooperation with Flcn. We observed no detectable phenotype in Fnip2 knockout mice, whereas Fnip1 deficiency produced phenotypes similar to those seen in Flcn-deficient mice in multiple organs, but not in kidneys. We found that absolute Fnip2 mRNA copy number was low relative to Fnip1 in organs that showed phenotypes under Fnip1 deficiency but was comparable to Fnip1 mRNA copy number in mouse kidney. Strikingly, kidney-targeted Fnip1/Fnip2 double inactivation produced enlarged polycystic kidneys, as was previously reported in Flcn-deficient kidneys. Kidney-specific Flcn inactivation did not further augment kidney size or cystic histology of Fnip1/Fnip2 double-deficient kidneys, suggesting pathways dysregulated in Flcn-deficient kidneys and Fnip1/Fnip2 double-deficient kidneys are convergent. Heterozygous Fnip1/homozygous Fnip2 double-knockout mice developed kidney cancer at 24 mo of age, analogous to the heterozygous Flcn knockout mouse model, further supporting the concept that Fnip1 and Fnip2 are essential for the tumor-suppressive function of Flcn and that kidney tumorigenesis in human Birt-Hogg-Dubé syndrome may be triggered by loss of interactions among Flcn, Fnip1, and Fnip2. Our findings uncover important roles for Fnip1 and Fnip2 in kidney tumor suppression and may provide molecular targets for the development of novel therapeutics for kidney cancer.
Incidence of Traumatic Brain Injury in the United States, 2003 (2006)

Traumatic brain injury (TBI) is an important public health problem in the United States. In 2003, there were an estimated 1,565,000 TBIs in the United States: 1,224,000 emergency department visits, 290,000 hospitalizations, and 51,000 deaths. Findings were similar to those from previous years in which rates of TBI were highest for young children (aged 0-4) and men, and the leading causes of TBI were falls and motor vehicle traffic.
CD34 Splice Variant: An Attractive Marker for Selection of Gene-Modified Cells (2000)

This study presents a promising selection system for gene-modified cells other than human hematopoietic progenitor and endothelial cells based on transgenic expression of human CD34. Three retrovirally transduced variants of CD34 were compared, differing in the length of their cytoplasmic domains. These were the full-length transmembrane protein (flCD34), a truncated form (tCD34) that is found as a naturally occurring splice variant and has a partial deletion of the cytoplasmic domain for signal transduction, and an engineered variant which is completely deprived of its cytoplasmic tail (dCD34). All three variants allowed selection of gene-modified cells using commercially available immunoaffinity technology. However, examination by flow cytometry as well as by Southern, Northern, and Western blot revealed that dCD34, as opposed to tCD34, is not stably anchored in the membrane and thus is expressed at low levels on the surface of transduced cells. Therefore, tCD34 was chosen as the more promising candidate for a clinically applicable cell surface marker. We show that gene-modified human primary T lymphocytes expressing tCD34 can be enriched to high purity (>95%) using clinically approved immunoaffinity columns. In addition, we demonstrate the utility of tCD34 for surface marking of murine hematopoietic cells in vivo, including primary T lymphocytes detected 9 weeks after bone marrow transplantation.
C–H Functionalization Reactivity of a Nickel–Imide (2012)

We report bifunctional reactivity of the β-diketiminato Ni(III)-imide [Me(3)NN]Ni═NAd (1), which undergoes H-atom abstraction (HAA) reactions with benzylic substrates R-H (indane, ethylbenzene, toluene). Nickel-imide 1 competes with the nickel-amide HAA product [Me(3)NN]Ni-NHAd (2) for the resulting hydrocarbyl radical R(•) to give the nickel-amide [Me(3)NN]Ni-N(CHMePh)Ad (3) (R-H = ethylbenzene) or aminoalkyl tautomer [Me(3)NN]Ni(η(2)-CH(Ph)NHAd) (4) (R-H = toluene). A significant amount of functionalized amine R-NHAd is observed in the reaction of 1 with indane along with the dinickel imide {[Me(3)NN]Ni}(2)(μ-NAd) (5). Kinetic and DFT analyses point to rate-limiting HAA from R-H by 1 to give R(•), which may add to either imide 1 or amide 2, each featuring significant N-based radical character. Thus, these studies illustrate a fundamental competition possible in C-H amination systems that proceed via a HAA/radical rebound mechanism.
Malignant transformation of human fibroblast strain MSU‐1.1 by v‐fes requires an additional genetic change (1995)

Abstract To determine whether the v‐fes oncogenc can malignantly transform human fibroblasts that have acquired an infinite life span and are partially growth‐factor‐independent, we trans‐fected cell strain MSU‐1.1 with a plasmid containing the v‐fes oncogene and a bacterial histidinol dehydrogenase gene. Of the 60 independent histidinol‐resistant clones isolated and assayed for v‐fes expression using a fes‐specific monoclonal antibody, 6 were found to express the v‐fes protein at a detectable level. When progeny cells from these 6 clones were further characterized, 3 of the 6 clonal populations exhibited a significant increase in the ability to form medium‐sized colonies in agarose, but none were tumorigenic in athymic mice. However, when the 6 populations were propagated for many generations, the same 3 populations acquired the ability to form very large colonies in agarose (± 100 μm in diameter) at a frequency of 2% to 17%, and formed malignant tumors in athymic mice. This suggests that an additional genetic change required for malignant transformation had been spontaneously acquired in 3 of the v‐fes ‐transformed cell strains. To determine whether the change or changes were the equivalent of an activated sis or ras proto‐oncogene, we transfected the v‐fes oncogene into derivative strains of MSU‐1.1 that express a transfected v‐sis, c‐H‐ras or c‐N‐ras oncogene, but that do not form tumors, and assayed the v‐fes‐expressing transfectants for tumorlgenicity. The results showed that when complemented either by a ras oncogene expressed at a somewhat enhanced level or by the v‐sis oncogene, v‐fes can supply the additional change required for malignant transformation.
Correlating Cerebral Hypometabolism With Future Memory Decline in Subsequent Converters to Amnestic Pre–Mild Cognitive Impairment (2008)

Individuals with amnestic pre-MCI showed significantly greater correlations between cerebral hypometabolism and subsequent long-term memory decline than nondecliners in Alzheimer disease-affected brain regions.
1H NMR of albumin in human blood plasma: drug binding and redox reactions at Cys34 (1995)

1H NMR methods are described which allow direct studies of the Cys34 binding site of albumin in intact human blood plasma in vitro. Antiarthritic gold drugs and the alcohol-aversive drug disulfiram induce a structural transition detectable via H epsilon 1 and H delta 2 resonances of His3 of albumin, and reactions of cystine, glutathione and captopril in plasma have also been investigated. Contrary to most assumptions, little of the albumin in normal plasma appears to be blocked at Cys34 as a cystine disulfide.
Extracellular Tau Levels Are Influenced by Variability in Tau That Is Associated with Tauopathies (2012)

Tauopathies are a class of neurodegenerative diseases marked by intracellular aggregates of hyperphosphorylated Tau. These diseases may occur by sporadic mechanisms in which genetic variants represent risk factors for disease, as is the case in Alzheimer disease (AD). In AD, cerebrospinal fluid (CSF) levels of soluble Tau/pTau-181 are higher in cases compared with controls. A subset of frontotemporal dementia (FTD) cases occur by a familial mechanism in which MAPT, the gene that encodes Tau, mutations are dominantly inherited. In symptomatic FTD patients expressing a MAPT mutation, CSF Tau levels are slightly elevated but are significantly lower than in AD patients. We sought to model CSF Tau changes by measuring extracellular Tau in cultured cells. Full-length, monomeric extracellular total Tau and pTau-181 were detectable in human neuroblastoma cells expressing endogenous Tau, in human non-neuronal cells overexpressing wild-type Tau, and in mouse cortical neurons. Tau isoforms influence the rate of Tau release, whereby the N terminus (exons 2/3) and microtubule binding repeat length contribute to Tau release from the cell. Compared with cells overexpressing wild-type Tau, cells overexpressing FTD-associated MAPT mutations produce significantly less extracellular total Tau without altering intracellular total Tau levels. This study demonstrates that cells actively release Tau in the absence of disease or toxicity, and Tau release is modified by changes in the Tau protein that are associated with tauopathies.
TERT Promoter Mutations Occur Early in Urothelial Neoplasia and Are Biomarkers of Early Disease and Disease Recurrence in Urine (2013)

Activating mutations occur in the promoter of the telomerase reverse transcriptase (TERT) gene in 66% of muscle-invasive urothelial carcinomas. To explore their role in bladder cancer development and to assess their utility as urine markers for early detection, we sequenced the TERT promoter in 76 well-characterized papillary and flat noninvasive urothelial carcinomas, including 28 pTa low-grade transitional cell carcinomas (TCC), 31 pTa high-grade TCCs, and 17 pTis carcinoma in situ lesions. We also evaluated the sequence of the TERT promoter in a separate series of 14 early bladder neoplasms and matched follow-up urine samples to determine whether urine TERT status was an indicator of disease recurrence. A high rate of TERT promoter mutation was observed in both papillary and flat lesions, as well as in low- and high-grade noninvasive urothelial neoplasms (mean: 74%). In addition, among patients whose tumors harbored TERT promoter mutations, the same mutations were present in follow-up urines in seven of eight patients that recurred but in none of the six patients that did not recur (P < 0.001). TERT promoter mutations occur in both papillary and flat lesions, are the most frequent genetic alterations identified to date in noninvasive precursor lesions of the bladder, are detectable in urine, and seem to be strongly associated with bladder cancer recurrence. These provocative results suggest that TERT promoter mutations may offer a useful urinary biomarker for both early detection and monitoring of bladder neoplasia.
Assessment of the effectiveness of descending aortomyoplasty for nonischemic cardiac failure by means of the subendocardial viability index. (2001)

Descending Aortomyoplasty as a technique to support circulation in cases of acute heart failure, improves the parameters of ventricular function, aiding the functional recovery of the left ventricle and improving significantly cardiac output as well as diastolic and systolic cardiac pressure. In addition to this, improves the Subendocardial Viability Index in cases of acute heart failure, which indirectly reflects an improvement of the Transmural and Subendocardial Perfusion of the failing heart.
Design and characterization of molecular tools for a Synthetic Biology approach towards developing cyanobacterial biotechnology (2010)

Cyanobacteria are suitable for sustainable, solar-powered biotechnological applications. Synthetic biology connects biology with computational design and an engineering perspective, but requires efficient tools and information about the function of biological parts and systems. To enable the development of cyanobacterial Synthetic Biology, several molecular tools were developed and characterized: (i) a broad-host-range BioBrick shuttle vector, pPMQAK1, was constructed and confirmed to replicate in Escherichia coli and three different cyanobacterial strains. (ii) The fluorescent proteins Cerulean, GFPmut3B and EYFP have been demonstrated to work as reporter proteins in cyanobacteria, in spite of the strong background of photosynthetic pigments. (iii) Several promoters, like P(rnpB) and variants of P(rbcL), and a version of the promoter P(trc) with two operators for enhanced repression, were developed and characterized in Synechocystis sp. strain PCC6803. (iv) It was shown that a system for targeted protein degradation, which is needed to enable dynamic expression studies, is working in Synechocystis sp. strain PCC6803. The pPMQAK1 shuttle vector allows the use of the growing numbers of BioBrick parts in many prokaryotes, and the other tools herein implemented facilitate the development of new parts and systems in cyanobacteria.
Endoscopic screening for esophageal cancer in 788 patients with head and neck cancers. (1996)

Esophageal cancer has a poor prognosis because it is difficult to detect in its early stages and, even if an operation is possible, the postoperative quality of life is much impaired. An early diagnosis can lead to a good prognosis and enables treatment by endoscopic mucosal resection (EEMR), contributing to a postoperative good quality of life. As head and neck cancers are known to have a high risk of concomitant esophageal cancer, endoscopic screening with iodine staining was performed on 788 patients with head and neck cancers. Among them, 93 cases of esophageal cancers (11.8%) and 23 cases of gastric cancers (2.9%) were detected. Seventy-two cases (77.4%) of the 93 esophageal cancers were superficial cancers limited to the submucosal layer. Twenty cases, treated by EEMR, had a good postoperative course without local recurrence. We suggest that endoscopic screening for esophageal cancer should be performed on all patients with head and neck cancers, because it allows early detection and a good prognosis, and the treatment can be completed by endoscopic maneuver.
3-Hydroxy-3-methylglutaryl-coenzyme A reductase from Arabidopsis thaliana is structurally distinct from the yeast and animal enzymes. (1989)

We have isolated the Arabidopsis thaliana gene (HMG1) encoding 3-hydroxy-3-methylglutaryl-CoA reductase [HMG-CoA reductase; (S)-mevalonate:NAD+ oxido-reductase (CoA-acylating), EC 1.1.1.88], the catalyst of the first committed step in isoprenoid biosynthesis. cDNA copies of the plant gene were identified by hybridization with a short, highly conserved segment of yeast HMG-CoA reductase as probe. DNA sequence analysis reveals that the COOH-terminal domain of the Arabidopsis HMG-CoA reductase (containing the catalytic site of the enzyme) is highly conserved with respect to the yeast, mammalian, and Drosophila enzymes, whereas the membrane-bound amino terminus of the Arabidopsis protein is truncated and lacks the complex membrane-spanning architecture of the yeast and animal reductases. Expression of the Arabidopsis gene from the yeast GAL1 promoter in a yeast mutant lacking HMG-CoA reductase activity suppresses the growth defect of the yeast mutant. Taken together, the sequence similarity to other cloned HMG-CoA reductase genes and the suppression of the yeast hmg- mutant provide strong evidence that the novel Arabidopsis gene we have cloned encodes a functional HMG-CoA reductase enzyme.