gebhart/patrepeval huggingface dataset:
Enhanced Transformation by a Simian Virus 40 Recombinant Virus Containing a Harvey Murine Sarcoma Virus Long Terminal Repeat (1983)

We have constructed a recombinant simian virus 40 (SV40) DNA containing a copy of the Harvey murine sarcoma virus long terminal repeat (LTR). This recombinant viral DNA was converted into an infectious SV40 virus particle and subsequently infected into NIH 3T3 cells (either uninfected or previously infected with Moloney leukemia virus). We found that this hybrid virus, SVLTR1, transforms cells with 10 to 20 times the efficiency of SV40 wild type. Southern blot analysis of these transformed cell genomic DNAs revealed that simple integration of the viral DNA within the retrovirus LTR cannot account for the enhanced transformation of the recombinant virus. A restriction fragment derived from the SVLTR-1 virus which contains an intact LTR was readily identified in a majority of the transformed cell DNAs. These results suggest that the LTR fragment which contains the attachment sites and flanking sequences for the proviral DNA duplex may be insufficient by itself to facilitate correct retrovirus integration and that some other functional element of the LTR is responsible for the increased transformation potential of this virus. We have found that a complete copy of the Harvey murine sarcoma virus LTR linked to well-defined structural genes lacking their own promoters (SV40 early region, thymidine kinase, and G418 resistance) can be effectively used to promote marker gene expression. To determine which element of the LTR served to enhance the biological activity of the recombinant virus described above, we deleted DNA sequences essential for promoter activity within the LTR. SV40 virus stocks reconstructed with this mutated copy of the Harvey murine sarcoma virus LTR still transform mouse cells at an enhanced frequency. We speculate that when the LTR is placed more than 1.5 kilobases from the SV40 early promoter, the cis-acting enhancer element within the LTR can increase the ability of the SV40 promoter to effectively operate when integrated in a murine chromosome. These data are discussed in terms of the apparent cell specificity of viral enhancer elements.
Protection against malaria by vaccination with sporozoite surface protein 2 plus CS protein (1991)

The circumsporozoite (CS) protein has been the target for development of malaria sporozoite vaccines for a decade. However, immunization with subunit vaccines based on the CS protein has never given the complete protection found after immunization with irradiated sporozoites. BALB/c mice immunized with irradiated Plasmodium yoelii sporozoites produced antibodies and cytotoxic T cells against a 140-kilodalton protein, sporozoite surface protein 2 (SSP2). Mice immunized with P815 cells that had been transfected with either SSP2 or CS genes were partially protected, and those immunized with a mixture of SSP2 and CS transfectants were completely protected against malaria. These studies emphasize the importance of vaccine delivery systems in achieving protection and define a multi-antigen sporozoite vaccine.
Code based efficient maximum-likelihood decoding of short polar codes (2012)

Polar codes are known as the first provable code construction to achieve Shannon capacity for arbitrary symmetric binary-input channels. Although, there exist efficient sub-optimal decoders with reduced complexity for polar codes, the complexity of the optimum ML decoder increases exponentially. Hence the optimum decoder is infeasible for the practical implementation of polar coding. In this paper, our motivation is about developing efficient ML decoder with reduced complexity. In this purpose, polar code based sphere decoding algorithm is proposed with the optimal performance. Additionally, proposed technique exploits two properties of polar coding to reduce decoding complexity. By this way, the reduced complexity of optimal decoding is only cubic, not exponential.
Gene Expression Profiling of Breast Cancer in Relation to Estrogen Receptor Status and Estrogen-Metabolizing Enzymes: Clinical Implications (2005)

Interactions between luminal epithelial cells and their surrounding microenvironment govern the normal development and function of the mammary gland. Estradiol plays a key role in abnormal intracellular signaling, which contributes to the development and progression of breast tumors. The present article summarizes the results from a microarray whole genome gene expression analysis as well as a quantitative analysis of the mRNA expression of members of the estradiol metabolic and signaling pathways in the tumors of postmenopausal breast cancer patients. The analysis of the variation in whole genome gene expression resulted in a tumor classification comprising several distinct groups with distinct expression of the estrogen receptor (ER). The parallel study on the expression of only nine mRNA transcripts of members of the estradiol pathways resulted in two main clusters, representing ER- and ER tumors. The mRNA expression of the estradiol-metabolizing enzymes did not follow the expression of the ER in all cases, leading to the recognition of several further subclasses of tumors. When the tumor classes obtained by whole genome gene expression analysis were compared with those obtained by independent quantitation of the estradiol-metabolizing enzymes, a statistically significant association between both classification groups was observed. These findings point to a possible association between development of a tumor with a particular expression profile and its capacity to synthesize estradiol as measured by the expression of the transcripts for the necessary key enzymes. Further, whole genome expression patterns were studied in 12 patients treated with anastrozole. Using significance analysis of microarrays, we identified 298 genes significantly differently expressed between partial response and progressive disease groups.
GMI-1271, a novel E-selectin antagonist, in combination with chemotherapy in relapsed/refractory AML. (2017)

2520 Background: GMI-1271 is a novel antagonist of E-selectin (E-sel) that down-regulates cell survival pathways and enhances chemotherapy response. We assessed GMI-1271 plus salvage chemotherapy with mitoxantrone, etoposide, and cytarabine (MEC) for the treatment of patients (pts) with relapsed/refractory (R/R) AML. Methods: A phase (Ph) 1trial in pts with R/R AML escalated GMI-1271 across pharmacologically active doses from 5-20 mg/kg combined with MEC. Safety, tolerability and anti-leukemia activity were assessed. GMI-1271 was given 24 hrs prior, then every 12 hrs during and for 48 hrs post induction/consolidation. Eligible pts had an ECOG score 0-2, received ≤2 prior inductions, WBC &lt; 20K ( &lt; 40K after 2 dose levels), no active CNS disease, and adequate renal/hepatic function. E-sel expression was assessed. After confirming safety and tolerability, a Ph 2 study of GMI-1271 at 10 mg/kg plus MEC was initiated. Results: To date, 47 pts have enrolled (Ph 1 = 19; Ph 2 = 28 of planned 47). The recommended Ph 2 dose is 10 mg/kg based on drug exposure, time over IC50 for E-sel binding, lack of DLT, and clinical outcomes. Ph1/Ph2 combined median age was 55yrs (range 26-84) with 70% male pts. Prior AML history included 26% primary refractory, 36% CR1 &lt; 6 mos; 17% prior SCT; 55% unfavorable cytogenetics (by SWOG). Common Gr 3/4 AEs were febrile neutropenia (36%), sepsis (26%), bacteremia (13%), hypoxia (13%). 30 and 60 d mortality were 0 and 7%, respectively. ORR (CR/CRi/MLFS/PR) was 21/42 evaluable (50%). Remission rate (CR/CRi) was 45%. Observed/expected remission (CR/CRi) ratio was &gt; 2.75 (Estey, Blood 1996). With a median follow-up of 11 mos, the Ph 1 median Leukemia Free Survival was not reached and Overall Survival was 7.6 mos. The median E-sel ligand binding at baseline was 35% of blasts (range, 1-75%) and was higher in those achieving remission. Conclusions: The addition of GMI-1271, a novel E-sel antagonist, to MEC chemotherapy is well tolerated with a high ORR, low induction mortality, and promising initial survival outcomes in pts with R/R AML. Furthermore, the baseline expression of E-sel ligand is predictive of response. Clinical trial information: NCT02306291.
ORAL TOLERANCE FOR THE TREATMENT OF AUTOIMMUNE DISEASES (1997)

Orally administered autoantigens suppress autoimmunity in animal models, including experimental allergic encephalomyelitis, collagen and adjuvant-induced arthritis, uveitis, and diabetes in the non-obese diabetic mouse. Low doses of oral antigen induce antigen-specific regulatory T-cells in the gut, which act by releasing inhibitory cytokines such as transforming growth factor-beta, interleukin-4, and interleukin-10 at the target organ. Thus, one can suppress inflammation at a target organ by orally administering an antigen derived from the site of inflammation, even if it is not the target of the autoimmune response. Initial human trials of orally administered antigen have shown positive findings in patients with multiple sclerosis and rheumatoid arthritis. A double-blind, placebo-controlled, phase III multi-center trial of oral myelin in 515 relapsing-remitting multiple sclerosis patients is in progress, as are phase II clinical trials investigating the oral administration of type II collagen in rheumatoid arthritis, S-antigen in uveitis, and insulin in type I diabetes.
Relationship of oxygen radical‐induced lipid peroxidative damage to disease onset and progression in a transgenic model of familial ALS (1998)

Transgenic mice that overexpress a mutated human CuZn superoxide dismutase (SOD1) gene (gly93→ala) found in some patients with familial ALS (FALS) have been shown to develop motor neuron disease, as evidenced by motor neuron loss in the lumbar and cervical spinal regions and a progressive loss of voluntary motor activity. The mutant Cu,Zn SOD exhibits essentially normal dismutase activity, but in addition, generates toxic oxygen radicals as a result of an enhancement of a normally minor peroxidase reaction. In view of the likelihood that the manifestation of motor neuron disease in the FALS transgenic mice involves an oxidative injury mechanism, the present study sought to examine the extent of lipid peroxidative damage in the spinal cords of the TgN(SOD1-G93A)G1H mice over their life span compared to nontransgenic littermates or transgenic mice that overexpress the wild-type human Cu,Zn SOD (TgN(SOD1)N29). Lipid peroxidation was investigated in terms of changes in vitamin E and malondialdehyde (MDA) levels measured by HPLC methods and by MDA-protein adduct immunoreactivity. Four ages were investigated: 30 days (pre-motor neuron pathology and clinical disease); 60 days (after initiation of pathology, but predisease); 100 days (approximately 50% loss of motor neurons and function); and 120 days (near complete hindlimb paralysis). Compared to nontransgenic mice, the TgN(SOD1-G93A)G1H mice showed blunted accumulation of spinal cord vitamin E and higher levels of MDA (P < 0.05 at 30 and 60 days) over the 30–120 day time span. In the TgN(SOD1)N29 mice, levels of MDA at age 120 days were significantly lower than in either the TgN(SOD1-G93A)G1H or nontransgenic mice. MDA-protein adduct immunoreactivity was also significantly increased in the lumbar spinal cord at age 30, 100, and 120 days, and in the cervical cord at 100 and 120 days. The results clearly demonstrate an increase in spinal cord lipid peroxidation in the FALS transgenic model, which precedes the onset of ultrastructural or clinical motor neuron disease. However, the greatest intensity of actual motor neuronal lipid peroxidative injury is associated with the active phase of disease progression. These findings further support a role of oxygen radical-mediated motor neuronal injury in the pathogenesis of FALS and the potential benefits of antioxidant therapy. J. Neurosci. Res. 53:66–77, 1998. © 1998 Wiley-Liss, Inc.
ANIMAL MODELS OF CHRONIC BRONCHITIS AND THEIR RELEVANCE TO STUDIES OF PARTICLE-INDUCED DISEASE (2000)

Chronic bronchitis is a significant cause of morbidity and mortality. Chronic irritation of the conducting airways by inhaled substances, most importantly cigarette smoke, air pollution, and occupational exposures, is thought to be a key factor in the pathogenesis of chronic bronchitis. Microbial infections have been implicated in acute exacerbations of bronchitis and in its progression. Several animal models of chronic bronchitis have been developed. This review examines similarities and dissimilarities among commonly used animal models of bronchitis and the human disease. The most commonly used animal models of chronic bronchitis are those employing SO2, tobacco smoke, lipopolysaccharide (endotoxin), proteases, and secretagogues. Bronchiolitis induced by nickel and nitric acid have also been reported. Rats, hamsters, and dogs are the species most frequently used; sheep and monkeys have been used less frequently. These models vary in the extent or location of mucous-cell hyperplasia and metaplasia, airway inflammation, chronicity, ease of induction, and reproducibility. Frequently, the deficiencies in these models are attributable to anatomic differences between human and animal airways, differences in the severity or chronicity of inflammation or fibrosis, or lack of complete characterization of the responses and their time course in the animal model. These animal models may be useful for investigating how, and under what exposure conditions, ambient pollutants might exacerbate airway inflammation, mucus hypersecretion, and airflow limitation.
Handbook of Tourette's Syndrome and Related Tic and Behavioral Disorders (2004)

Part 1 Phenomemology of the tic disorder: motor and vocal tics, Stanley Fahn premonitory sensory experiences, Anthony E. Lang the natural history of Gilles de la Tourette syndrome, Ruth Dowling Bruun and Cathy L. Budman. Part 2 Associated behavioural disorders: obsessive-compulsive disorder and self-injurious behaviour, Mary May Robertson and Jessica W. Yakeley attention deficit hyperactivity disorder, Kenneth E. Towbin and Mark A. Riddle comorbid behavioural disorders, David E. Comings and Brenda G. Comings. Part 3 Diagnosis and assessment: primary tic disorders, Gerald Erenberg tics in other neurological disorders, Joseph Jankovic drug-induced tics, Juan R. Sanchez-Ramos and William J. Weiner rating tic severity, Roger Kurlan and Michael P. McDermott neuropsychological testing, Peter G. Como. Part 4 Neurobiology: basal ganlia-limbic system interactions, Suzanne N. Haber and Eileen Lynd-Balta pathobiology, Harvey S. Singer neuroimaging, Lewis R. Baxter Jr and Barry H. Guze. Part 5 Genetics and epidemiology: the inheritance pattern, David L. Pauls progress in gene localization, P. Heutink et al epidemiology, Caroline M. Tanner. Part 6 Clinical care: neuroleptic drugs, Arthur K. Shapiro and Elaine Shapiro clonidine, Christopher G. Goetz pharmacotherapy beyond the catecholaminergic systems, Peter A. LeWitt the treatment of obsessive-compulsive disorder in Tourette's syndrome, Robert A. King et al treatment of attention deficit hyperactivity disorder, Gerald S. Golden education and psychosocial interventions - executive dysfunction and its consequences, Martha Bridge Denckla and Mark Jay Reader. Part 7 Special topics: the child and adolescent with Tourette's syndrome - clinical perspectives in phenomenology and treatment, Donald J. Cohen and James F. Leckman future therapies, Amos D. Korczyn recent advances in research into Tourette's syndrome, Paul Ruben Silva and Arnold J. Friedhoff Tourette's syndrome - a human condition, Oliver Sacks the Tourette Syndrome Association Inc., Sue Levi-Pearl.
Isolation of nonobligate bacterial predators of bacteria from soil (1986)

A procedure is described for the isolation from soil of various Gram-positive and Gram-negative, nonobligate, bacterial predators of bacteria.
Millimeter wave evanescent mode power combiner-Gunn oscillator in suspended stripline configuration (2002)

In the search for low cost high power semiconductor diode oscillator devices, a new millimeter wave evanescent mode power combiner with Gunn diode oscillator at 35 GHz employing combination of suspended stripline and evanescent mode resonator is developed. With a 35 GHz diode rated at 100 mW, stable power output of more than 180 mW is achieved over a tuning range of about 3.5 GHz. The oscillator is simple in fabrication, cost effective and is amenable for integration with other planar circuits.
Identification of the Principal Binding Site for RGD-Containing Ligands in the αVβ3 Integrin:  A Photoaffinity Cross-Linking Study (2002)

By superimposing data obtained by photo-cross-linking RGD-containing ligands to the human alpha(V)beta(3) integrin onto the crystal structure of the ectopic domain of this receptor (Xiong et al. (2001) Science 294, 339-345), we have identified the binding site for the RGD triad within this integrin. We synthesized three novel analogues of the 49-amino acid disintegrin, echistatin: [Bpa(21),Leu(28)]-, [Bpa(23),Leu(28)]-, and [Bpa(28)]echistatin. Each contains a photoreactive p-benzoyl-phenylalanyl (Bpa) residue in close proximity to the RGD motif which spans positions 24-26; together, the photoreactive positions flank the RGD motif. The analogues bind with high affinity to the purified recombinant alpha(V)beta(3) integrin, but very poorly to the closely related human alpha(IIb)beta(3) platelet integrin. While echistatin analogues containing Bpa in either position 23 or 28 cross-link specifically and almost exclusively to the beta(3) subunit of alpha(V)beta(3), [Bpa(21),Leu(28)]echistatin cross-links to both the alpha(V) and the beta(3) subunits, with cross-linking to the former favored. [Bpa(23),Leu(28)]echistatin cross-links 10-30 times more effectively than the other two analogues. We identified beta(3)[109-118] as the domain that encompasses the contact site for [Bpa(28)]echistatin. This domain is included in beta(3)[99-118] (Bitan et al. (2000) Biochemistry 39, 11014-11023), a previously identified contact domain for a cyclic RGD-containing heptapeptide with a benzophenone moiety in a position that is similar to the placement of the benzophenone in [Bpa(28)]echistatin relative to the RGD triad. Recently, we identified beta(3)[209-220] as the contact site for an echistatin analogue with a photoreactive group in position 45, near the C-terminus of echistatin (Scheibler et al. (2001) Biochemistry 40, 15117-14126). Taken together, these results support the hypothesis that the very high binding affinity of echistatin to alpha(V)beta(3) results from two distinct epitopes in the ligand, a site including the RGD triad and an auxiliary epitope at the C-terminus of echistatin. Combining our results from photoaffinity cross-linking studies with data now available from the recently published crystal structure of the ectopic domain of alpha(V)beta(3), we characterize the binding site for the RGD motif in this receptor.
CYLOSERINE AS AN ANTIDEPRESSANT AGENT (1959)

Cycloserine appears to be a psychopharmacological agent in that 1. It reverses depressions to normal or hyperactive mood and at the same time causes subtle changes in behavior; 2. It may aggravate mental disorders; and 3. It seems to potentiate Marsilid. Cycloserine may become a valuable tool in psychopharmacological research and may also find therapeutic use in depressions, provided the initial dose does not exceed 500 mg. a day and potentially psychotic patients receive more than average supervision.
NO donors prevent integrin-induced leukocyte adhesion but not P-selectin-dependent rolling in postischemic venules (1994)

The objective of this study was to examine the effect of nitric oxide (NO) donors on polymorphonuclear leukocyte (PMN) interactions in the microvasculature of postischemic tissue and to compare the antiadhesive properties of NO donors with the responses observed after immunoneutralization of three key adhesion glycoproteins (CD11/CD18, intercellular adhesion molecule-1, and P-selectin). Rolling and firm adhesion (adherence) of leukocytes and shear rate were monitored in cat mesenteric venules subjected to 60 min of ischemia (blood flow reduced to 20% of control), followed by 60 min of reperfusion. Immediately before reperfusion, the mesentery was superfused with a NO donor (3-morpholinosydonimine-N-ethyl-carbamide or spermine-NO) or a monoclonal antibody (MAb) against an adhesion glycoprotein that was administered intravenously. In untreated animals, a profound influx in rolling PMNs was observed during reperfusion that was subsequently followed by increased firm adhesion. The anti-P-selectin antibody completely abolished the rise in the flux of rolling PMNs, whereas the anti-CD18 antibody prevented firm adhesion. Both NO donors attenuated ischemia/reperfusion-induced leukocyte adhesion to a level comparable with that observed after administration of a MAb against CD11/CD18 without affecting PMN rolling. The antiadhesive effect of the NO donors could not be attributed solely to an improvement of venular wall shear rate. In vitro data did not reveal a direct effect of NO donors on the expression of CD18 or neutrophil adhesion to endothelial cells. These observations suggest that NO donors may provide protection from tissue injury by preventing PMN adhesion.(ABSTRACT TRUNCATED AT 250 WORDS)
The measurement of vitamins D2 and D3 and seven major metabolites in a single sample of human plasma using gas chromatography/Mass Spectrometry (1988)

Selected ion monitoring of vitamin D metabolites has previously been described but there has been only one detailed description of the measurement by gas chromatography/mass spectrometry (GC/MS) of a number of metabolites in a single plasma sample. We describe here a GC/MS method, using stable isotope labelled internal standards, which allows the estimation of vitamins D2 and D3, and their 25-hydroxy, 24,25-dihydroxy and 25,26-dihydroxy metabolites in a single 2 ml sample of plasma, although more is needed for the measurement of 1,25-dihydroxyvitamin D3. Plasma was extracted on Bond Elut C18 cartridges and initial fractionation carried out on Sep-Pak SIL. Straight-phase high-performance liquid chromatography was required for separation of polyhydroxylated metabolites prior to GC/MS using an LKB 2091 mass spectrometer with conventional packed columns. n-Butylboronate esters were formed across vicinal hydroxyls, followed by formation of trimethylsilyl ethers using trimethylsilylimidazole. The [M - 90 - 15]+ ion for each compound was monitored. Deuterated internal standards were not available for all metabolites and it was necessary to use (2H6)D3 and (2H6)25OHD3 as standards for the measurement of D2 and D3, and 25OHD3 and 25OHD2, respectively, and (2H6)24,25(OH)2D3 as a standard for 24,25(OH)2D3 and 25,26(OH)2D2. Although the [M - 90 - 15]+ ion of 24,25(OH)2D and 25,26(OH)2D has the same mass: charge ratio, derivatives of these compounds are completely separated in the GC system used. The intra-assay precision for all these assays is usually less than 5%.