gebhart/patrepeval huggingface dataset:
Deoxyribonucleic Acid Homologies Among Species of the GenusNeisseria (1967)

Eleven aerobic species of Neisseria, a Mima sp., and a Herellea sp. were tested for deoxyribonucleic acid (DNA) homology in direct hybridization experiments. DNA labeled with either (14)C or (32)P was prepared from five species of Neisseria. Unlabeled DNA from the various microorganisms was immobilized on membrane filters, which, after pretreatment, were incubated with labeled DNA (4,000 counts per min per filter) for 14 hr at 67 C. The measure of relatedness was expressed as the relative percentage of direct binding compared to that obtained with homologous DNA. All serological types of N. meningitidis, including the newly proposed types, were homologous to the standard strain of N. meningitidis with one possible exception, type Z. The genus Neisseria is heterogeneous in nature, forming at least three distinct groups: first, N. meningitidis and N. gonorrhoeae; second, N. perflava, N. subflava, N. sicca, N. flavescens, and N. flava; third, N. catarrhalis and N. caviae. Mima and Herellea species show no significant homology with the Neisseria.
Antiviral activity of telaprevir (VX-950) and peginterferon alfa-2a in patients with hepatitis C (2007)

This study confirmed the substantial antiviral effects of telaprevir and showed an increased antiviral effect of telaprevir combined with peginterferon alfa-2a.
An EOQ model for a deteriorating item with non-linear demand under inflation and a trade credit policy (2005)

This paper develops an infinite time-horizon deterministic economic order quantity (EOQ) inventory model with deterioration based on discounted cash flows (DCF) approach where demand rate is assumed to be non-linear over time. The effects of inflation and time-value of money are also taken into account under a trade-credit policy of type "?/T1 net T". The results are illustrated with a numerical example. Sensitivity analysis of the optimal solution with respect to the parameters of the system is carried out.
Dynamic Protein−Water Relationships during β-Sheet Formation (2008)

We investigated the polymer−water interaction in a model fibrous protein. Bombyx mori silk fibroin film, a typical model of biodegradable material, was cast from aqueous solution and analyzed in this study. Differential scanning calorimetry (DSC), its temperature-modulated variant (TMDSC), and the time-resolved technique of Fourier transform infrared spectroscopy (FTIR) were used for the first time to monitor the detailed structural changes of silk fibroin during heating and during isothermal crystallization above the glass transition temperature, Tg ∼ 451 K (178 °C). Results show that intermolecular bound water molecules, acting as a plasticizer, will strongly affect the secondary structure of silk fibroin. DSC study shows that silk fibroin initially displays a water-induced glass transition around 80 °C during heating, resulting from a temporary bound water-silk structure. Quantitative thermal analysis of the heat capacity changes of this system during heating revealed that no β-sheet crystals were formed below Tg. FTIR scans also confirmed that no β-sheets were formed during heating and removal of bound water below Tg. During water removal, the amide II region shifts to lower frequency, and the 1515 cm−1 band increases slightly, indicating change of the microenvironment in the silk fibroin chains. During isothermal crystallization above Tg, the amide I region of silk fibroin spectra showed a phase transition from the secondary structures of noncrystalline random coils and α-helices to the β-pleated-sheet crystals, while the amide II region and the 1515 cm−1 band remain stable during β-sheet formation. Analogy is made between the crystallization of synthetic polymers according to the four-state scheme of Strobl and the crystallization process of silk fibroin, which we suggest proceeds through an intermediate precursor stage associated with water removal. This study provides a deeper understanding of the formation of β-pleated sheets during the crystallization process in silk fibroin, with implications for the crystallization of naturally occurring silk fibers from animals such as the silkworm and spider.
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes (2010)

Genome-wide association studies (GWAS) can identify common alleles that contribute to complex disease susceptibility. Despite the large number of SNPs assessed in each study, the effects of most common SNPs must be evaluated indirectly using either genotyped markers or haplotypes thereof as proxies. We have previously implemented a computationally efficient Markov Chain framework for genotype imputation and haplotyping in the freely available MaCH software package. The approach describes sampled chromosomes as mosaics of each other and uses available genotype and shotgun sequence data to estimate unobserved genotypes and haplotypes, together with useful measures of the quality of these estimates. Our approach is already widely used to facilitate comparison of results across studies as well as meta-analyses of GWAS. Here, we use simulations and experimental genotypes to evaluate its accuracy and utility, considering choices of genotyping panels, reference panel configurations, and designs where genotyping is replaced with shotgun sequencing. Importantly, we show that genotype imputation not only facilitates cross study analyses but also increases power of genetic association studies. We show that genotype imputation of common variants using HapMap haplotypes as a reference is very accurate using either genome-wide SNP data or smaller amounts of data typical in fine-mapping studies. Furthermore, we show the approach is applicable in a variety of populations. Finally, we illustrate how association analyses of unobserved variants will benefit from ongoing advances such as larger HapMap reference panels and whole genome shotgun sequencing technologies.
Neuronal nicotinic receptors : pharmacology and therapeutic opportunities (1999)

MOLECULAR BIOLOGY AND BIOCHEMISTRY. Purification and Cloning of Nicotinic Acetylcholine Receptors (J. Lindstrom). Transcriptional Regulation of Neuronal Nicotinic Receptor Subunit Genes (D. Fornasari, et al.). Molecular Composition and Biophysical Characteristics of Nicotinic Receptors (J. Ramirez--Latorre, et al.). Desensitization and the Regulation of Neuronal Nicotinic Receptors (M. Marks). Cell Lines as Models for Studies of Nicotinic Acetylcholine Receptors (R. Lukas). Stable Expression of Human Neuronal Nicotinic Receptors (B. Buisson, et al.). PHYSIOLOGICAL ROLES OF NICOTINIC RECEPTORS. Functional Anatomy of Nicotinic Acetylcholine Receptors in Mammalian Brain (P. Clarke). Nicotinic Receptor Modulation of Neurotransmitter Release (S. Kaiser & S. Wonnacott). Functional Diversity of Nicotinic Acetylcholine Receptors in the Mammalian Central Nervous System: Physiological Relevance (E. Pereira, et al.). Diverse Functions of Neuronal Nicotinic Receptors Determined by Subcellular Location (D. Berg, et al.). Immunosuppressive and Anti--inflammatory Properties of Nicotine (M. Sopori). PHARMACOKINETICS OF NICOTINE--LIKE ALKALOIDS. Pharmacokinetics and Metabolism of Nicotine and Related Alkaloids (N. Benowitz & P. Jacob). Nicotine and Related Compounds as PET and SPECT Ligands (V. Villemagne, et al). MEDICINAL CHEMISTRY. Natural Products as a Source of Nicotinic Acetylcholine Receptor Modulators and Leads for Drug Discovery (M. Holladay, et al.). Nicotinic Cholinergic Receptor Pharmacophores (R. Glennon & M. Dukat). CURRENT AND POTENTIAL THERAPEUTIC APPLICATIONS. Neuronal Nicotinic Receptor Channel Dysfunction in a Human Epilepsy Syndrome (D. Bertrand & S. Berkovic). The Role of Nicotine and Nicotinic Receptors in Psychopathology (S. Leonard, et al.). Nicotine and Non--Nicotine Formulations for Smoking Cessation (S. Leischow & G. Cook). Preclinical Evidence on the Neuroprotective Effects of Nicotinic Ligands (D. Donnelly--Roberts & J. Brioni). Transdermal Nicotine Treatment of Attention Deficit Hyperactivity Disorder (E. Levin, et al.). Neuronal Nicotinic Receptors: New Targets in the Treatment of Pain (C. Flores & K. Hargreaves). Subtype--Selective nAChR Agonists for the Treatment of Neurological Disorders: SIB--1508Y and SIB--1553A (F. Menzaghi, et al.). Nicotinic Acetylcholine Receptor--Targeted Compounds: A Summary of the Development Pipeline and Therapeutic Potential (M. Decker & S. Arneric). Index.
Analysis of HLA-D micropolymorphism by a simple procedure: RNA oligonucleotide hybridization. (1987)

Recent progress in the molecular genetics of HLA class II antigens has revealed the existence of multiple loci and of a large degree of polymorphism, with more individual alleles than was expected. An accurate detection and analysis of this extensive polymorphism is essential for optimal HLA typing for transplantation and for a reevaluation of HLA-disease association. Because of the limitations of the current typing methods, including restriction fragment length polymorphisms, we have proposed a DNA typing procedure based on hybridization with loci- and allele-specific oligonucleotides. Here we present a much simpler way of analyzing class II micropolymorphism down to the level of single nucleotide differences. RNA oligonucleotide typing (ROT) relies on RNA dot blots and requires 10-20 ml of blood. It is shown that with appropriate oligonucleotide probes, ROT can reliably and unambiguously identify any polymorphism at any of the HLA loci, including new alleles, not identified with previous methods. This illustrates the importance of oligonucleotide typing to optimize HLA matching, in particular for transplantation involving unrelated donors.
Role of Phosphatidylserine Receptors in Enveloped Virus Infection (2014)

Envelope phosphatidylserine has previously been shown to be important for replication of various envelope viruses, but details of this mechanism(s) were unclear. We were the first to report that a bifunctional serum protein, Gas6, bridges envelope phosphatidylserine to a cell surface receptor, Axl. Recent studies demonstrated that many envelope viruses, including vaccinia, dengue, West Nile, and Ebola viruses, utilize Axl/Gas6 to facilitate their entry, suggesting that the phosphatidylserine-mediated viral entry mechanism can be shared by various enveloped viruses. In addition to Axl/Gas6, various molecules are known to recognize phosphatidylserine; however, the effects of these molecules on virus binding and entry have not been comprehensively evaluated and compared. In this study, we examined most human phosphatidylserine-recognizing molecules for their abilities to facilitate viral infection. The results provide insights into the role(s) of envelope phosphatidylserine in viral infection, which can be applicable to the development of novel antiviral reagents that block phosphatidylserine-mediated viral entry.
Prompt Eschar Excision (1986)

Mortality at the Adult Burn Center of the Massachusetts General Hospital (MGH) has declined from 24% in 1974 to an average of 7% for 1979-1984. From 1974 to 1976, prompt eschar excision and immediate wound closure therapy was initiated and standardized. After 1976, this therapy was the standard treatment. Detailed statistical analysis is necessary to determine the influence of this treatment on the improved survival. Therefore, logistical regression analysis was used to examine the influence of variables such as burn size, age, and treatment on mortality for 1103 patients during 1974-1984. Survival rates during the treatment development phase (1974-1977) were compared to the survival rates of the last 5 years of standardized excisional treatment (1979-1984). Survival rates for the standardized excisional treatment were also compared to the results of previously published studies from this hospital that were probit analyses of burn mortality for 1939-1955 and 1955-1970. This latter comparison provided 45 years' experience with burn mortality at a single institution. Results of the statistical analysis of the survival data from 1974 to 1984 indicate that mortality strongly depends on burn size, age, and treatment (p less than 0.001 for each independent variable). In addition, length of stay (LOS) for the total group decreased significantly from 32 to 22 days. The improved survival for 1974-1984 occurred independently of changes in the annual distributions of burn size, age, or sex. Comparison of survival rates shows improved survival during standardized excisional treatment when compared to the treatment development phase. The most extensive increases in survival during 1974-1984 were seen in the treatment of elderly patients and patients with massive burn injuries. Survival for the period 1974-1984 was markedly improved as compared to the 1939-1970 published experiences.
Oral Sequelae of Head and Neck Radiotherapy (2003)

In addition to anti-tumor effects, ionizing radiation causes damage in normal tissues located in the radiation portals. Oral complications of radiotherapy in the head and neck region are the result of the deleterious effects of radiation on, e.g., salivary glands, oral mucosa, bone, dentition, masticatory musculature, and temporomandibular joints. The clinical consequences of radiotherapy include mucositis, hyposalivation, taste loss, osteoradionecrosis, radiation caries, and trismus. Mucositis and taste loss are reversible consequences that usually subside early post-irradiation, while hyposalivation is normally irreversible. Furthermore, the risk of developing radiation caries and osteoradionecrosis is a life-long threat. All these consequences form a heavy burden for the patients and have a tremendous impact on their quality of life during and after radiotherapy. In this review, the radiation-induced changes in healthy oral tissues and the resulting clinical consequences are discussed.
Current and Emerging Directions in the Treatment of Eating Disorders (2012)

Eating disorders are a significant source of psychiatric morbidity in young women and demonstrate high comorbidity with mood, anxiety, and substance use disorders. Thus, clinicians may encounter eating disorders in the context of treating other conditions. This review summarizes the efficacy of current and emerging treatments for anorexia nervosa (AN), bulimia nervosa (BN), and binge eating disorder (BED). Treatment trials were identified using electronic and manual searches and by reviewing abstracts from conference proceedings. Family based therapy has demonstrated superiority for adolescents with AN but no treatment has established superiority for adults. For BN, both 60 mg fluoxetine and cognitive behavioral therapy (CBT) have well-established efficacy. For BED, selective serotonin reuptake inhibitors, CBT, and interpersonal psychotherapy have demonstrated efficacy. Emerging directions for AN include investigation of the antipsychotic olanzapine and several novel psychosocial treatments. Future directions for BN and BED include increasing CBT disseminability, targeting affect regulation, and individualized stepped-care approaches.
De-escalation therapy in ventilator-associated pneumonia (2006)

De-escalation is a promising strategy for optimizing the responsible use of antibiotics while allowing the delivery of prompt and appropriate empiric therapy of ventilator-associated pneumonia.
Mouse strain variability in the expression of the hematopoietic stem cell antigen Ly-6A/E by bone marrow cells (1993)

The cell surface molecule Ly-6A/E provides a convenient marker for primitive stem cells in the hematopoietic tissues of both fetal and adult mice. However, previous studies have shown that Ly-6A/E expression by lymphocytes is variable depending on the haplotype of the Ly-6 locus. Therefore, strain-specific variation in Ly-6A/E expression by bone marrow (BM) cells was investigated. The results show that Ly-6a mice have, on average, 50% of the number of BM cells expressing Ly-6A/E relative to that for Ly-6b mice. Furthermore, among the 5% of BM cells that do not express antigens characteristic of mature T, B, myeloid, or erythroid lineages, which include the primitive hematopoietic stem cell compartment, Ly-6a mice have, on average, more than fivefold fewer Ly- 6A/E+ cells relative to that for Ly-6b mice. Isolation of Ly-6A/E- and Ly-6A/E+ cells from mice of both haplotypes showed that, whereas 99% of the marrow repopulating activity (MRA) of C57BL/Ka (Ly-6b) mice could be recovered in the Ly-6A/E+ fraction, only about 25% of the MRA of BALB/c (Ly-6a) was recoverable in the same population. On a per-cell basis, the Ly-6A/E+ cells that were isolated from BALB/c mice were essentially equivalent in MRA to those isolated from C57BL/Ka mice. Thus, whereas a large percentage of the hematopoietic stem cells of Ly- 6a mice do not express the Ly-6A/E molecule, the antigen may be used to isolate a subset of stem cells from these mice. These results show that hematopoietic stem cell phenotype can vary between mouse strains and imply that caution should be exercised in the identification of human stem cell antigens such as CD34, because a similar variability may occur between individual humans. To further explore the influence of Ly- 6 haplotype on Ly-6A/E expression by specific cell subsets, lymph-node lymphocytes from a panel of mouse strains were analyzed by multiparameter flow cytometry for correlated expression of Ly-6A/E, CD4, and CD8. All Ly-6a strains examined had less than 20% Ly-6A/E+ cells, and those cells were predominantly CD8+ T lymphocytes. In contrast, the Ly-6b strains had greater than 30% Ly-6A/E+ cells, and those cells included CD4+, CD8+, and B lymphocytes.
CK8/18 expression, the basal phenotype, and family history in identifying BRCA1‐associated breast cancer in the Ontario site of the Breast Cancer Family Registry (2010)

CK8/18 expression was independently associated with BRCA1-associated breast cancers. Reduced CK8/18 expression in conjunction with the basal-like phenotype and family history may have improved the ability to identify which tumors were likely to be associated with a BRCA1 germline mutation and thereby help streamline genetic testing.
Peroxidase-catalyzed generation of catechin oligomers that inhibit glucosyltransferase from Streptococcus sobrinus (1996)

Oolong tea extract (OTE) and the purified polymeric polyphenols from OTE have been found to inhibit glucosyltransferase (GTase) of mutans streptococci. In view of the partial fermentation characteristic of oolong tea, we describe here an in vitro model reaction system to produce partially fermented products of d-(+)-catechin or green tea extract (GTE) using horseradish peroxidase. A dimeric catechin molecule was identified as dehydro-dicatechin A by instrumental analyses. The molecular size of some oligomeric catechins was estimated by the elution profile with HPLC. These catechin oligomers markedly inhibited GTase from Streptococcus sobrinus 6715. As the degree of polymerization of catechin or GTE increased, GTase was inhibited more effectively. These results suggest that polymeric polyphenols found in OTE are synthesized by partial fermentation due to oxidases/peroxidases present in tea leaves.
DEVELOPING A COST EFFECTIVE ENVIRONMENTAL SOLUTION FOR PRODUCED WATER AND CREATING A ''NEW'' WATER RESOURCE (1997)

This report summarizes the status of this project for the quarter January 1, 1997 to March 31, 1997. Phase II has been started and Task 7, Develop Pilot Scale Test Work Plan has been completed. The operational portion of this phase, Task 8 has been initiated with several pieces of pilot equipment already on-site. The start up of the full process train will not occur until the next quarter. The project is slightly behind schedule. A no cost extension was requested and was granted. The anticipated completion date is December 31, 1997. The project is on budget.
Diffraction and focusing of spectral energy in multiphoton processes (1992)

We demonstrate an analogy between a two-photon process driven by a chirped pulse and Fresnel diffraction from a slit: in both situations interference between different ``paths'' leading to the same ``final state'' determines the resulting ``diffraction pattern.'' On the basis of this analogy, a spectral Fresnel zone plate was designed for ``focusing of spectral energy'': at the two-photon level the spectral energy can be concentrated in an effective bandwidth that is much smaller than the bandwidth of the original excitation pulse. To show this effect, two experiments were performed with femtosecond laser pulses with a well-controlled power spectrum and chirp: frequency doubling in a nonlinear crystal and two-photon excitation of Rydberg states in rubidium.
Inhibition of HER2/neu (erbB-2) and mitogen-activated protein kinases enhances tamoxifen action against HER2-overexpressing, tamoxifen-resistant breast cancer cells. (2000)

HER2/neu (erbB-2) overexpression has been causally associated with tamoxifen resistance in human breast cancer cells. Forced expression of HER2 in MCF-7 breast cancer cells resulted in mitogen-activated protein kinase (MAPK) hyperactivity and tamoxifen resistance. Inhibition of HER2 and MAPKs with AG1478 and U0126, respectively, as well as dominant-negative MEK-1/2 constructs restored the inhibitory effect of tamoxifen on estrogen receptor (ER)-mediated transcription and cell proliferation. Both AG1478 and U0126 also restored the tamoxifen-mediated association of ER with nuclear receptor corepressor (N-CoR) in the antiestrogen-resistant MCF-7 cells. Treatment with a combination of tamoxifen and a HER2 kinase inhibitor reduced tumor MAPK activity and markedly prevented growth of HER2-overexpressing MCF-7 xenografts in athymic mice. Thus, blockade of HER2 and MAPK signaling may enhance tamoxifen action and abrogate antiestrogen resistance in human breast cancer.
Synthesis of a Library of 3-Oxopiperazinium and Perhydro-3-oxo-1,4-diazepinium Derivatives and Identification of Bioactive Compounds (2003)

The design and synthesis of a library of novel families of 3-oxopiperazinium and perhydro-3-oxo-1,4-diazepinium derivatives is reported. The library was composed of 44 3-oxopiperazinium derivatives (11 of these compounds had a spiranic skeleton) and 22 perhydro-3-oxo-1,4-diazepinium compounds. The synthetic procedure involved a 6-step sequence carried out in solution, along with the use of solid-phase linked scavengers and microwave activation for the rapid removal of the excess of amine reagents. A final cyclization step performed under mild conditions led to the charged heterocyclic moiety. Screening of this library in two biological assays identified active compounds that inhibit the activity of the vanilloid receptor TRPV1 and modulators of the multidrug resistance phenomenon. Thus, this synthetic sequence represents a facile and convenient entry to unprecedented libraries of this sort of tetraalkylammonium derivatives that may be of use for identification of novel scaffolds of diverse biological activity.