gebhart/patrepeval huggingface dataset:
Phylogenetic study on Shiraia bambusicola by rDNA sequence analyses (2004)

Abstract In this study, 18S rDNA and ITS‐5.8S rDNA regions of four Shiraia bambusicola isolates collected from different species of bamboos were amplified by PCR with universal primer pairs NS1/NS8 and ITS5/ITS4, respectively, and sequenced. Phylogenetic analyses were conducted on three selected datasets of rDNA sequences. Maximum parsimony, distance and maximum likelihood criteria were used to infer trees. Morphological characteristics were also observed. The positioning of Shiraia in the order Pleosporales was well supported by bootstrap, which agreed with the placement by Amano (1980) according to their morphology. We did not find significant inter‐hostal differences among these four isolates from different species of bamboos. From the results of analyses and comparison of their rDNA sequences, we conclude that Shiraia should be classified into Pleosporales as Amano (1980) proposed and suggest that it might be positioned in the family Phaeosphaeriaceae . (© 2004 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Cellular requirements for tumor-specific immunity elicited by heat shock proteins: tumor rejection antigen gp96 primes CD8+ T cells in vivo. (1994)

Purified preparations of 96-kDa heat shock proteins (gp96) have been previously shown to elicit tumor-specific immunity to the tumor from which gp96 is obtained but not to antigenically distinct chemically induced tumors. The cellular requirements of gp96-elicited immunity have been examined. It is observed that depletion of CD8+, but not CD4+, T cells in the priming phase abrogates the immunity elicited by gp96. The CD8+ T cells elicited by immunization with gp96 are active at least up to 5 weeks after immunization. Depletion of macrophages by treatment of mice with carrageenan during the priming phase also results in loss of gp96-elicited immunity. In the effector phase, all three compartments, CD4+ and CD8+ T cells and macrophages, are required. Immunity elicited by whole irradiated tumor cells shows a different profile of cellular requirements. In contrast to immunization with gp96, depletion of CD4+, but not CD8+, T cells during priming with whole tumor cells abrogates tumor immunity. Further, ablation of macrophage function during priming or effector phases has no effect on tumor immunity elicited by whole cells. Our results suggest the existence of a macrophage-dependent and a macrophage-independent pathway of tumor immunity. Our observations also show that in spite of exogenous administration, vaccination with gp96 preparations elicits a CD8+ T-cell response in vivo, and it is therefore a useful method of vaccination against cancer and infectious diseases.
Single-Chip Multiple-Frequency ALN MEMS Filters Based on Contour-Mode Piezoelectric Resonators (2007)

This paper reports experimental results on a new class of single-chip multiple-frequency (up to 236 MHz) filters that are based on low motional resistance contour-mode aluminum nitride piezoelectric micromechanical resonators. Rectangular plates and rings are made out of an aluminum nitride layer sandwiched between a bottom platinum electrode and a top aluminum electrode. For the first time, these devices have been electrically cascaded to yield high performance, low insertion loss (as low as 4 dB at 93MHz), and large rejection (27 dB at 236 MHz) micromechanical bandpass filters. This novel technology could revolutionize wireless communication systems by allowing cofabrication of multiple frequency filters on the same chip, potentially reducing form factors and manufacturing costs. In addition, these filters require terminations (1 kOmega termination is used at 236 MHz) that can be realized with on-chip inductors and capacitors, enabling their direct interface with standard 50-Omega systems
Immunity to Murine Chlamydial Genital Infection (2002)

Chlamydia trachomatis sexually transmitted infections cause considerable morbidity and socioeconomic burden worldwide, despite significant advances in our understanding of the biology (29, 31, 57), pathogenesis (11, 83, 117), genomics (94), and epidemiology (91) of this parasite. Chlamydial urogenital tract infections are readily cured with antibiotics, but control measures based on antimicrobial chemotherapy alone are hampered by the frequency of asymptomatic infections and delayed diagnosis (9). Definitive control of C. trachomatis sexually transmitted diseases (STDs) is possible through the development of a safe and efficacious vaccine (24). Progress toward the development of an effective vaccine has been disappointingly modest, as it has been for vaccines to other sexually transmitted pathogens that infect the genital tract mucosae. The strict tropism for mucosal epithelial cells, the complex biology and antigenic structure, and the predilection to cause persistent infection have presented formidable challenges to chlamydial vaccine development. A heightened understanding of protective immunity to C. trachomatis urogenital infection has emerged in the past decade from studies using a mouse model of chlamydial genital tract infection. The insights are of considerable interest because they offer promise for the development of an efficacious chlamydial vaccine. This review focuses on that progress and summarizes the current understanding of protective immune mechanisms that function against murine chlamydial urogenital infection. We also discuss specific requirements for a vaccine to protect against chlamydial STDs and the challenges presently confronting us in achieving that goal.
Single amino acid substitutions affecting the specificity of the fungal ribotoxin mitogillin (2000)

Mitogillin and related fungal ribotoxins are small basic ribonucleolytic proteins that inhibit protein synthesis by specifically hydrolyzing a single phosphodiester bond in the universally conserved alpha-sarcin/ricin loop (SRL) of large subunit ribosomal RNAs. It was previously shown that mitogillin is a natural derivative of a T1/U2-like ribonuclease with inserted domains that are involved in target selection and specificity. Site-directed mutagenesis was used to substitute single amino acids in the previously identified functional domains Ala1-Tyr24 (B1-L1-B2 domain) and Lys106-Lys113 (L4 region). Examination of the activities of the mutants in the digestion of polyinosinic acid (a ribonuclease substrate) and specific cleavage of the SRL shows that Asn7Ala and Lys111Gln substitutions lead to altered ribonuclease activity and diminished substrate specificity consistent with the proposed functions of these domains.
Abnormal bone growth and selective translational regulation in basic fibroblast growth factor (FGF-2) transgenic mice. (1995)

Basic fibroblast growth factor (FGF-2) is a pleiotropic growth factor detected in many different cells and tissues. Normally synthesized at low levels, FGF-2 is elevated in various pathologies, most notably in cancer and injury repair. To investigate the effects of elevated FGF-2, the human full-length cDNA was expressed in transgenic mice under control of a phosphoglycerate kinase promoter. Overexpression of FGF-2 caused a variety of skeletal malformations including shortening and flattening of long bones and moderate macrocephaly. Comparison by Western blot of FGF-2 transgenic mice to nontransgenic littermates showed expression of human FGF-2 protein in all major organs and tissues examined including brain, heart, lung, liver, kidney, spleen, and skeletal muscle; however, different molar ratios of FGF-2 protein isoforms were observed between different organs and tissues. Some tissues preferentially synthesize larger isoforms of FGF-2 while other tissues produce predominantly smaller 18-kDa FGF-2. Translation of the high molecular weight isoforms initiates from unconventional CUG codons and translation of the 18-kDa isoform initiates from an AUG codon in the FGF-2 mRNA. Thus the Western blot data from the FGF-2 transgenic mice suggest that tissue-specific expression of FGF-2 isoforms is regulated translationally.
True Electrocautery in the Treatment of Syringomas and other Benign Cutaneous Lesions (1997)

Background: A number of methods to treat benign cutaneous lesions are available, including surgical excision, electrosurgery, chemical cauterizing agents, cryotherapy, and carbon dioxide laser vaporization. Electrocautery has been used for more than a century and is in danger of becoming a forgotten treatment modality. Objective: The aim of this review is to describe the procedure of electrocautery and bring attention to this treatment method. Methods: The principles of electrocautery and our experience in selected cases are reviewed. Results: Excellent results were achieved using electrocautery to treat syringomas, linear epidermal nevus, and dermatosis papulosa nigra. Conclusion: Electrocautery is a useful technique for treating selected benign cutaneous lesions and should not be discarded in the rush to embrace new technologies.
Motion Induced Radiation from a Vibrating Cavity (1996)

We study the radiation emitted by a cavity moving in vacuum. We give a quantitative estimate of the photon production inside the cavity as well as of the photon flux radiated from the cavity. A resonance enhancement occurs not only when the cavity length is modulated but also for a global oscillation of the cavity. For a high finesse cavity the emitted radiation surpasses radiation from a single mirror by orders of magnitude.
New Drugs for Asthma, Allergy and COPD (2001)

This book provides a state-of-the-art account by academic respiratory physicians and senior pharmaceutical industry personnel on the development of new drugs for asthma, allergy and COPD. It contains 80 chapters of highly condensed information, presented in an attractive, reader-friendly format with much use of tables, figures and diagrams. In addi
3D subband coder for very low bit rates (2002)

A video coder based on 3D subband coding system (SBC) targetted for very low bit rate applications is developed and simulated. It employs QMF subband analysis to decompose an input sequence into 4 temporal bands. A low-complexity block-based motion detection scheme is then applied to all bands followed by motion classification and reduced motion search on the baseband which is H.261-like coded and the high temporal bands are vector-quantised (VQ) with a bank of codebooks (switched codebook VQ). Simulations are performed at 9.6 kbit/sand 14.4 kbit/s at 5 frame/s for QCIF format and results showed that it achieved better performance than the ITU-T short-term reference model SlM3 coder at similar bit rates. Subjective evaluation favours the 3D SBC coder because it does not suffer from 'blocking' artifacts.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Oral Immunization with Attenuated Salmonella Expressing Human Sperm Antigen Induces Antibodies in Serum and the Reproductive Tract1 (1995)

Induction of immune responses in the reproductive tract will be crucial for a functional gamete antigen-based antifertility vaccine. Here we describe the construction and development of an avirulent Salmonella as an oral vaccine delivery vector to elicit sperm-specific immune responses in reproductive tract secretions. A cDNA sequence encoding the human sperm antigen SP10 was cloned on an asd+vector and expressed to a high level in an avirulent delta cya, delta crp, and delta asd vaccine strain of Salmonella typhimurium. Oral immunization of female BALB/c mice with this recombinant Salmonella elicited high-titer anti-SP10 IgG antibodies in serum and IgA antibodies in vaginal secretions. Anti-SP10 antibody titers could be increased by secondary and tertiary oral administrations of the recombinant Salmonella. Induction of sperm-specific antibodies in the reproductive tract following oral administration of a recombinant Salmonella could lead to the development of a simple, safe, efficient, and easy-to-use antifertility vaccine.
Cytotoxic sensitivity to tumor necrosis factor‐α in PC3 and LNCaP prostatic cancer cells is regulated by extracellular levels of SGP‐2 (clusterin) (1999)

BACKGROUND SGP-2 is a ubiquitous secreted glycoprotein that prevents cellular apoptosis. This study was carried out to determine the extracellular action of SGP-2 in a model of tumor necrosis factor-α (TNF)-induced cytotoxicity using two human prostatic cancer lines, LNCaP and PC3. These two lines were selected because LNCaP cells are highly sensitive to the cytotoxic effect of TNF, while PC3 cells are resistant to TNF at 24 hr. METHODS Cells were cultured in the presence or absence of TNF (10 ng/ml). LNCaP cells were treated with varying concentrations of exogenous SGP-2, while PC3 cells were treated with antisera to SGP-2 with and without exogenous SGP-2. Following a 24-hr treatment, cultures were assessed by counting of cell number and by the trypan blue exclusion assay. RESULTS Western blot analysis of conditioned media revealed that PC3 secreted more SGP-2 than did LNCaP. The sensitivity to TNF in LNCaP cells was reduced by the addition of exogenous SGP-2. PC3 cells became sensitive to TNF when SGP-2 antibody was added to the culture. The effect of SGP-2 antibody on PC3 cells was reversed by the addition of exogenous SGP-2 to the culture. CONCLUSIONS These results suggest that SGP-2 can act as an extracellular mediator of anti-TNF-induced cytotoxicity. Prostate 39:87–93, 1999. © 1999 Wiley-Liss, Inc.
Are Patients Fed Appropriately According to Their Caloric Requirements? (1998)

Because energy expenditure is difficult to predict on the basis of conventional equations, patients in long-term acute care facilities routinely are overfed and underfed, with only 25% receiving calories within 10% of required needs. Measuring a patient's energy requirement at least once by IC is important, because the degree of metabolism predicts how easily a patient will be underfed or overfed. The amount of infused calories should be compared with caloric requirements measured by IC, because the accuracy or degree of underfeeding or overfeeding has an impact on ventilatory status and the likelihood for developing azotemia. Although physician practice or bias may reduce the optimal clinical effect, the use of IC to determine caloric requirements may result in significant cost savings.
Peptide Synthesis (1974)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Chromosomes 4 and 8 implicated in a genome wide SNP linkage scan of 762 prostate cancer families collected by the ICPCG (2011)

These results will be useful in prioritizing future susceptibility gene discovery efforts in this common cancer.
A Novel Pulsatile, Laminar Flow Bioreactor for the Development of Tissue-Engineered Vascular Structures (2002)

Exposure of vascular cell-seeded, tubular, biodegradable polymers to pulsatile flow conditions has been proposed as a method to develop tissue-engineered blood vessels by "maturing" structural integrity, and increasing collagen content, suture retention, burst pressure, and tissue formation. These in vitro tissue-engineered arteries demonstrate contractile responses to pharmacologic agents and express markers of vascular differentiation. Current methods to induce pulsatile flow in a bioreactor system are limited by the creation of nonphysiologic pressure waveforms and noncompliant reservoirs to house the tissue-engineered vascular constructs. We have developed a novel method for the in vitro development of tubular vascular structures by using a mechanical ventilator to induce pulsatile, laminar flow into a fluid column, resulting in pressurized waveforms similar to mammalian physiology. The vascular constructs are housed in semicompliant tubing to facilitate an additional variable of circumferential stretch as a potential signaling mechanism. This approach more closely approximates mammalian physiology and we hypothesize that it will facilitate mechanical signaling necessary for the development of tissue-engineered vessels for clinical applications.
Anhydrosis in the diabetic foot: a comparison of two urea creams (2003)

A study was carried out to compare the efficacy of two urea creams of different percentages in controlling anhydrosis in the diabetic foot. A total of 30 outpatients with evidence of bilateral anhydrosis participated in a double-blind incidental study. The study comprised a 6 week treatment regimen, with the application of 10% urea cream to the right foot and 25% urea cream to the left foot of participants. Analysis of results showed that both urea creams resulted in a statistically significant increase in skin hydration. However, the 25% urea cream produced a significantly greater increase in skin hydration than the 10% cream.
Evidence for a Role for Notch Signaling in the Cytokine-Dependent Survival of Activated T Cells (2006)

Peripheral T cell homeostasis results from a balance between factors promoting survival and those that trigger deletion of Ag-reactive cells. The cytokine IL-2 promotes T cell survival whereas reactive oxygen species (ROS) sensitize T cells to apoptosis. Two pathways of activated T cell apoptosis-one triggered by Fas ligand and the other by cytokine deprivation-depend on ROS, with the latter also regulated by members of the Bcl-2 family. Notch family proteins regulate several cell-fate decisions in metazoans. Ectopic expression of the Notch1 intracellular domain (NICD) in T cells inhibits Fas-induced apoptosis. The underlying mechanism is not known and the role, if any, of Notch in regulating apoptosis triggered by cytokine deprivation or neglect has not been examined. In this study, we use a Notch1/Fc chimera; a blocking Ab to Notch1 and chemical inhibitors of gamma-secretase to investigate the role of Notch signaling in activated T cells of murine origin. We show that perturbing Notch signaling in activated CD4+/CD8+ T cells maintained in IL-2 results in the accumulation of ROS, reduced Akt/protein kinase B activity, and expression of the antiapoptotic protein Bcl-xL, culminating in apoptosis. A broad-spectrum redox scavenger inhibits apoptosis but T cells expressing mutant Fas ligand are sensitive to apoptosis. Activated T cells isolated on the basis of Notch expression (Notch+) are enriched for Bcl-xL expression and demonstrate reduced susceptibility to apoptosis triggered by neglect or oxidative stress. Furthermore, enforced expression of NICD protects activated T cells from apoptosis triggered by cytokine deprivation. Taken together, these data implicate Notch1 signaling in the cytokine-dependent survival of activated T cells.
Identification and Expression Analysis of a Gene Encoding a Bacterial-Type Phosphoenolpyruvate Carboxylase from Arabidopsis and Rice (2003)

Phosphoenolpyruvate carboxylase (PEPC) is distributed in plants and bacteria but is not found in fungi and animal cells. Important motifs for enzyme activity and structure are conserved in plant and bacterial PEPCs, with the exception of a phosphorylation domain present at the N terminus of all plant PEPCs reported so far, which is absent in the bacterial enzymes. Here, we describe a gene from Arabidopsis, stated as Atppc4, encoding a PEPC, which shows more similarity to Escherichia coli than to plant PEPCs. Interestingly, this enzyme lacks the phosphorylation domain, hence indicating that it is a bacterial-type PEPC. Three additional PEPC genes are present in Arabidopsis, stated as Atppc1, Atppc2, and Atppc3, encoding typical plant-type enzymes. As most plant PEPC genes, Atppc1, Atppc2, and Atppc3 are formed by 10 exons interrupted by nine introns. In contrast, Atppc4 gene has an unusual structure formed by 20 exons. A bacterial-type PEPC gene was also identified in rice (Oryza sativa), stated as Osppc-b, therefore showing the presence of this type of PEPC in monocots. The phylogenetic analysis suggests that both plant-type and bacterial-type PEPCs diverged early during the evolution of plants from a common ancestor, probably the PEPC from gamma-proteobacteria. The diversity of plant-type PEPCs in C3, C4, and Crassulacean acid metabolism plants is indicative of the evolutionary success of the regulation by phosphorylation of this enzyme. Although at a low level, the bacterial-type PEPC genes are expressed in Arabidopsis and rice.
HIGH STRAIN RATE DUCTILITY IN UNIAXIAL TENSION : A REVIEW (1985)

The specific problems involved by high strain rate tension tests are first examined, as well as the various parameters describing ductility. Some experimental data relative to a high purity copper then illustrate the typical increase of dynamic ductility with strain rate. Finally, the main factors which are expected to determine ductility are reviewed. It is concluded that the dominant factor is the increase of stability with strain rate, which in turn may result from the occurrence of a linear flow rule and/or from inertia effects.
Transplantation ofex vivoexpanded endothelial progenitor cells for therapeutic neovascularization (2000)

Animal studies and preliminary results in humans suggest that lower extremity and myocardial ischemia can be attenuated by treatment with angiogenic cytokines. The resident population of endothelial cells that is competent to respond to an available level of angiogenic growth factors, however, may potentially limit the extent to which cytokine supplementation enhances tissue neovascularization. Accordingly, we transplanted human endothelial progenitor cells (hEPCs) to athymic nude mice with hindlimb ischemia. Blood flow recovery and capillary density in the ischemic hindlimb were markedly improved, and the rate of limb loss was significantly reduced. Ex vivo expanded hEPCs may thus have utility as a "supply-side" strategy for therapeutic neovascularization.
Treatment of Relapsed Chronic Lymphocytic Leukemia by 72-Hour Continuous Infusion or 1-Hour Bolus Infusion of Flavopiridol: Results from Cancer and Leukemia Group B Study 19805 (2005)

Flavopiridol has modest, schedule-dependent clinical activity in relapsed CLL and warrants future investigation utilizing alternative schedules of administration.
Controllability/observability analysis of digital circuits (1979)

The testability of a digital circuit is directly related to the difficulty of controlling and observing the logical values of internal nodes from circuit inputs and outputs, respectively. This paper presents a method for analyzing digital circuits in terms of six functions which characterize combinational and sequential controllability and observability.
Orphanin FQ: A Neuropeptide That Activates an Opioidlike G Protein-Coupled Receptor (1995)

A heptadecapeptide was identified and purified from porcine brain tissue as a ligand for an orphan heterotrimeric GTP-binding protein (G protein)-coupled receptor (LC132) that is similar in sequence to opioid receptors. This peptide, orphanin FQ, has a primary structure reminiscent of that of opioid peptides. Nanomolar concentrations of orphanin FQ inhibited forskolin-stimulated adenylyl cyclase activity in cells transfected with LC132. This inhibitory activity was not affected by the addition of opioid ligands, nor did the peptide activate opioid receptors. Orphanin FQ bound to its receptor in a saturable manner and with high affinity. When injected intracerebroventricularly into mice, orphanin FQ caused a decrease in locomotor activity but did not induce analgesia in the hot-plate test. However, the peptide produced hyperalgesia in the tail-flick assay. Thus, orphanin FQ may act as a transmitter in the brain by modulating nociceptive and locomotor behavior.