gebhart/patrepeval huggingface dataset:
Interdiffused quantum-well infrared photodetectors for color sensitive arrays (1999)

Proton implantation and rapid thermal annealing were used to tune the infrared spectral response of quantum-well infrared photodetectors (QWIP) by up to 1.4 μm. Multiple proton implants at energies between 200 and 420 keV were used to create homogeneous quantum-well intermixing throughout the device’s multiple-quantum-well structure. Photoluminescence and spectral response measurements were used to study the effect of proton implantation on QWIPs for a series of doses up to 3.5×1015 protons cm−2. By using a mask during implantation, a method of constructing a color sensitive array is proposed.
Neuropeptide F: a novel parasitic flatworm regulatory peptide from Moniezia expansa (Cestoda: Cyclophyllidea) (1991)

SUMMARY Using a C-terminally directed pancreatic polypeptide (PP) antiserum and immunocytochemical methods, PP-immuno-reactivity (IR) was localized throughout the central (CNS) and peripheral nervous systems (PNS) of the cestode, Moniezia expansa . In the CNS, immunostaining was evident in the paired cerebral ganglia (primitive brain), connecting commissure, and the paired longitudinal nerve cords that are cross-linked by numerous regular transverse connectives. The PNS was seen to consist of a fine anastomosing nerve-net of immunoreactive fibres, many of which were closely associated with reproductive structures. Radioimmunoassay of this peptide IR in acid-alcohol extracts of the worm measured 192·8 ng/g of PP–IR. HPLC analyses of the M. expansa PP–IR identified a single molecular form which was purified to homogeneity. Plasma desorption mass spectrometry (PDMS) of purified parasite peptide resolved a single peptide with a molecular mass of 4599±10 Da. Automated gas-phase Edman degradation identified a 39-amino acid peptide with a C-terminal phenyl-alaninamide. Examination of its primary structure shows that it displays significant sequence homology with the vertebrate neuropeptide Y superfamily, suggesting that this platyhelminth-derived peptide is the phylogenetic precursor. Neuropeptide F ( M. expansa ) is the first regulatory peptide to be fully sequenced from the phylum Platyhelminthes and may represent a member of an important new class of invertebrate neuropeptide.
Protease-activated “prodrugs” for cancer chemotherapy (1980)

Many types of malignant cells and human tumors display increased concentrations of the protease plasminogen activator that converts plasminogen to the highly active protease, plasmin. Because plasmin rapidly cleaves various low molecular weight compounds coupled to appropriate peptide specifiers, we hypothesized that coupling of such peptide specifiers to anticancer drugs might create "prodrugs" which would be locally activated by tumor-associated plasmin and consequently would be less toxic to normal cells. To provide an initial test of this concept we have synthesized peptidyl prodrugs of the structure D-Val-Leu-Lys-X in which the peptidyl portion has been designed to allow the prodrug to serve as an excellent plasmin substrate and X is an anticancer drug-either the glutamine analog (alphaS,5S) alpha-amino-3-chloro-4,5-dihydro-5-isoxazole-acetic acid (AT-125) or the alkylating agent N,N-bis(2-chloroethyl)-p-phenylenediamine (phenylenediamine mustard). Treatment of these prodrugs with plasmin generated the free peptide and the free drug, demonstrating that these prodrugs are plasmin substrates. The prodrugs and free drugs were tested in an in vitro system against either normal chicken embryo fibroblasts, which display a low level of plasminogen activator, or their virally transformed counterparts, which produce high levels of plasminogen activator. In each case the peptidyl prodrugs displayed at least a 5-fold increase in selectivity for the transformed cells compared to the free drug. The greater selectivity of action of the peptidyl prodrugs against transformed cell cultures suggests that these or similar prodrugs that are substrates for tumor-associated proteases may show increased therapeutic effectiveness in the treatment of tumors that produce sufficiently increased amounts of plasminogen activator.
Bile acids: Chemistry, physiology, and pathophysiology (2009)

The family of bile acids includes a group of molecular species of acidic steroids with very peculiar physical-chemical and biological characteristics. They are synthesized by the liver from cholesterol through several complementary pathways that are controlled by mechanisms involving fine-tuning by the levels of certain bile acid species. Although their best-known role is their participation in the digestion and absorption of fat, they also play an important role in several other physiological processes. Thus, genetic abnormalities accounting for alterations in their synthesis, biotransformation and/or transport may result in severe alterations, even leading to lethal situations for which the sole therapeutic option may be liver transplantation. Moreover, the increased levels of bile acids reached during cholestatic liver diseases are known to induce oxidative stress and apoptosis, resulting in damage to the liver parenchyma and, eventually, extrahepatic tissues. When this occurs during pregnancy, the outcome of gestation may be challenged. In contrast, the physical-chemical and biological properties of these compounds have been used as the bases for the development of drugs and as pharmaceutical tools for the delivery of active agents.
Longitudinal Effects of Aging on Serum Total and Free Testosterone Levels in Healthy Men (2001)

Many studies have shown cross-sectional (and two small studies, longitudinal) declines in total and/or free testosterone (T) levels, with age, in men. The extent to which decline in T is the result of the aging process per se, as opposed to chronic illness, medication use, and other age-related factors, remains controversial. The frequency with which aging leads to T levels consistent with hypogonadism has also not been defined. These issues bear on the potential use of T replacement in aging men, because aging and hypogonadism have, in common, reduced bone and lean body mass and muscle strength and increased total and abdominal fat. We measured T and sex hormone-binding globulin (SHBG), by RIA, in stored samples from 890 men in the Baltimore Longitudinal Study on Aging. Using a mixed-effects model, we found independent effects of age and date of sampling to reduce T levels. After compensating for date effects, which investigation suggested was artifactual, we observed significant, independent, age-invariant, longitudinal effects of age on both T and free T index (free T index = T/SHBG), with an average change of -0.124 nmol/L.yr and -0.0049 nmol T/nmol SHBG.yr. T, but not free T index, also decreased with increasing body mass index. Use of beta-blocking drugs was associated with higher T and higher free T index levels. Using total T criteria, incidence of hypogonadal T levels increased to about 20% of men over 60, 30% over 70 and 50% over 80 yr of age, and even greater percentages when free T index criteria were employed. Our observations of health factor independent, age-related longitudinal decreases in T and free T, resulting in a high frequency of hypogonadal values, suggest that further investigation of T replacement in aged men, perhaps targeted to those with the lowest serum T concentrations, are justified.
Synctree for Single Point Installation, Upgrades, and OS Patches (1998)

The combination of large networks, frequent operating system security patches, and software updates can create a daunting task for a systems administration team. This paper presents a system created to address these challenges with system security and ‘‘uptime’ ’ as the primary concerns. By using a file-form ‘‘database,’ ’ the Synctree system holds a full network’s configuration in an understandable, secure, location. This paper also compares this system with previously published works.
PmpG 303-311 , a Protective Vaccine Epitope That Elicits Persistent Cellular Immune Responses in Chlamydia muridarum-Immune Mice (2012)

Urogenital Chlamydia serovars replicating in reproductive epithelium pose a unique challenge to host immunity and vaccine development. Previous studies have shown that CD4 T cells are necessary and sufficient to clear primary Chlamydia muridarum genital tract infections in the mouse model, making a protective CD4 T cell response a logical endpoint for vaccine development. Our previous proteomics studies identified 13 candidate Chlamydia proteins for subunit vaccines. Of those, PmpG-1 is the most promising vaccine candidate. To further that work, we derived a PmpG(303-311)-specific multifunctional Th1 T cell clone, designated PmpG1.1, from an immune C57BL/6 mouse and used it to investigate the presentation of the PmpG(303-311) epitope by infected epithelial cells. Epithelial presentation of the PmpG(303-311) epitope required bacterial replication, occurred 15 to 18 h postinfection, and was unaffected by gamma interferon (IFN-γ) pretreatment. Unlike epitopes recognized by other Chlamydia-specific CD4 T cell clones, the PmpG(303-311) epitope persisted on splenic antigen-presenting cells (APC) of mice that cleared primary genital tract infections. PmpG1.1 was activated by unmanipulated irradiated splenocytes from immune mice without addition of exogenous Chlamydia antigen, and remarkably, activation of PmpG1.1 by unmanipulated immune splenocytes was stronger 6 months postinfection than it was 3 weeks postinfection. Enhanced presentation of PmpG(303-311) epitope on splenic APC 6 months postinfection reflects some type of "consolidation" of a protective immune response. Understanding the antigen-presenting cell populations responsible for presenting PmpG(303-311) early (3 weeks) and late (6 months) postinfection will likely provide important insights into stable protective immunity against Chlamydia infections of the genital tract.
Pituitary irradiation with high-energy proton beams: a preliminary report. (1958)

Summary There has been described a multiple-plane, rotational technic for irradiation of the human pituitary gland with the 340-Mev proton beam from the 184-inch synchrocyclotron. Peak doses of 14,000–30,000 rad at the center of the pituitary have been administered to 26 patients with metastatic breast cancer, and decreased pituitary function and gross and microscopic damage of the pituitary gland have been demonstrated. The most common laboratory findings were depression of I131 uptake by the thyroid and decrease of 24-hour urinary gonadotropins. There was clinical evidence of improvement in a few of the patients treated. Four patients with acute lymphatic leukemia, embryonal dysgerminoma of the testis, chronic lymphatic leukemia and diabetes mellitus, and malignant exophthalmos have also been irradiated, but they are not reported in detail at this time.
Gene Synthesis for Protein Production (2007)

Abstract Synthetic gene production is an enabling technology for improved protein production since it can be used to produce totally novel gene sequences that are optimized for codon usage and other sequence features anticipated to facilitate improved protein expression in defined expression systems. Computer aided gene design algorithms of increasing sophistication, allow researchers to exploit the degeneracy of the genetic code to engineer expression optimized synthetic gene sequences and the overlapping oligonucleotides needed to manufacture the desired synthetic gene by polymerase chain reaction (PCR) methods. Low cost synthetic gene production is ushering in a new era of synthetic biology for improved protein production.
Stereochemistry Control in the Lewis Acid Mediated Lactonization Reaction of γ,δ-Epoxy-β-silyloxy Esters (2001)

ZnCl2-triggered lactonization reactions of γ,δ-epoxy-β-silyloxy esters with remote alkoxy groups (CH2)nOR (n = 2, 3), producing five- and/or six-membered ring lactones, have been investigated. Under such conditions, the regiochemistry of the reaction is governed by the cis or trans nature of the starting epoxy ester and also by its C(3) stereochemistry. An X-ray crystallographic structure of a γ-lactone (compound 24′) and a 13C NMR correlation for the C(4) carbon chemical shifts of all γ-lactones were obtained and used to determine the regioselectivity of the epoxide ring-opening. A mechanistic hypothesis, involving an oxocarbenium ion as a common intermediate, is presented in interpretation of the results.
Clustering of mutations affecting alginic acid biosynthesis in mucoid Pseudomonas aeruginosa (1985)

A 10-kilobase DNA fragment previously shown to contain the phosphomannose isomerase gene (pmi) of Pseudomonas aeruginosa was used to construct a pBR325-based hybrid that can be propagated in P. aeruginosa only by the formation of a chromosomal-plasmid cointegrate. This plasmid, designated pAD4008, was inserted into the P. aeruginosa chromosome by recombination at a site of homology between the cloned P. aeruginosa DNA and the chromosome. Mobilization of pAD4008 into P. aeruginosa PAO and 8830 and selection for the stable acquisition of tetracycline resistance resulted in specific and predictable changes in the pattern of endonuclease restriction sites in the phosphomannose isomerase gene region of the chromosomes. Chromosomal DNA from the tetracycline-resistant transformants was used to clone the drug resistance determinant with Bg/II or XbaI, thereby allowing the "walking" of the P. aeruginosa chromosome in the vicinity of the pmi gene. Analysis of overlapping tetracycline-resistant clones indicated the presence of sequences homologous to the DNA insert of plasmid pAD2, a recombinant clone of P. aeruginosa origin previously shown to complement several alginate-negative mutants. Restriction mapping, subcloning, and complementation analysis of a 30-kilobase DNA region demonstrated the tight clustering of several genetic loci involved in alginate biosynthesis. Furthermore, the tetracycline resistance determinant in PAO strain transformed by pAD4008 was mapped on the chromosome by plasmid FP2-mediated conjugation and was found to be located near 45 min.
A colour atlas of the anatomy of small laboratory animals (1992)

A colour atlas of the anatomy of small laboratory animals , A colour atlas of the anatomy of small laboratory animals , کتابخانه دانشگاه علوم پزشکی و خدمات بهداشتی درمانی کرمان
Metalloproteinase inhibitors improve the recovery and hemostatic function of in vitro–aged or –injured mouse platelets (2003)

Platelet transfusions are a crucial component of support for patients with severe thrombocytopenia. Storage of platelet concentrates, however, is associated with a reduction in platelet posttransfusion recovery and hemostatic function. In this study, we established a model of mitochondrial injury that resembles platelet storage lesion. Mitochondrial injury, provoked by incubation of platelets with carbonyl cyanide m-chlorophenylhydrazone (CCCP), led to reduced posttransfusion recovery in mice, an effect that directly correlated with the duration of treatment. Damaged platelets were characterized by shape change, disruption of membrane asymmetry, surface expression of P-selectin, and profound proteolysis of GPIbalpha. Using our model, we identified a key role for endogenous metalloproteinase(s) in platelet clearance, as their inhibition markedly improved posttransfusion recovery of both the mitochondria-injured and in vitro-aged mouse platelets. Metalloproteinase inhibition also prevented proteolysis of GPIbalpha on damaged platelets, thereby improving the hemostatic function of these cells in vivo. We propose that inhibition of metalloproteinase activity during storage could significantly improve the effectiveness of platelet transfusions. Surface expression of GPIbalpha might be a powerful marker to determine the quality of platelet concentrates, because it reflects metalloproteinase activity in vitro.
Structural and biological properties of peptide nucleic acid (PNA) (1998)

Abstract
The diagnostic dilemma of undifferentiated inflammatory synovitis of the knee joint/joints: a comprehensive approach (2007)

Abstract Objective: The objective of this pilot study was to describe clinical features, laboratory investigations and enhanced MRI features in patients presenting with undifferentiated inflammatory synovitis of the knee. Patient and methods: Fifteen patients with undifferentiated inflammatory synovitis of the knee joint were recruited for this study. All patients underwent full history‐taking, detailed rheumatological examination, synovial fluid analysis including polarized microscopy, rheumatoid factor (RF), anti‐nuclear antibody (ANA), anti‐cyclic citrullinated peptide (CCP), C‐reactive protein, and erythrocyte sedimentation rate. MRI/gadolinium‐enhanced MRI was done for all patients with unilateral presentation and for the most symptomatic knee in cases of bilateral knee involvement. Results: Enhanced MRI showed the following findings: synovial enhancement and effusion 15/15, pannus formation 13/15, bone marrow edema 3/15, bone erosions 2/15, cartilaginous erosions 1/15, synovial cysts 2/15, Baker's cyst 2/15, periarticular soft tissue edema 3/15, and lipoma arborescencs 2/15. Conclusions: Undifferentiated synovitis of the knee is not necessarily a benign condition. It represents a diagnostic dilemma in rheumatological practice that deserves early identification and early treatment in order to prevent inevitable and irreversible articular damage if left untreated. The ability of MRI to detect early changes like bone marrow edema and bony and cartilaginous erosions (usually not obvious on plain X‐rays) makes this a highly sensitive tool for evaluation of patients presenting with undifferentiated synovitis affecting the knee joint. When combined with gadolinium, it allows accurate assessment of the degree of synovial thickening (pannus) and picks up local intra‐articular lesions especially in patients with unilateral disease.
Authoritative sources in a hyperlinked environment (1999)

The network structure of a hyperlinked environment can be a rich source of information about the content of the environment, provided we have effective means for understanding it. We develop a set of algorithmic tools for extracting information from the link structures of such environments, and report on experiments that demonstrate their effectiveness in a variety of context on the World Wide Web. The central issue we address within our framework is the distillation of broad search topics, through the discovery of “authorative” information sources on such topics. We propose and test an algorithmic formulation of the notion of authority, based on the relationship between a set of relevant authoritative pages and the set of “hub pages” that join them together in the link structure. Our formulation has connections to the eigenvectors of certain matrices associated with the link graph; these connections in turn motivate additional heuristrics for link-based analysis.
Role of Trabecular Microarchitecture in Whole-Vertebral Body Biomechanical Behavior (2009)

The role of trabecular microarchitecture in whole-vertebral biomechanical behavior remains unclear, and its influence may be obscured by such factors as overall bone mass, bone geometry, and the presence of the cortical shell. To address this issue, 22 human T(9) vertebral bodies (11 female; 11 male; age range: 53-97 yr, 81.5 +/- 9.6 yr) were scanned with microCT and analyzed for measures of trabecular microarchitecture, BMC, cross-sectional area, and cortical thickness. Sixteen of the vertebrae were biomechanically tested to measure compressive strength. To estimate vertebral compressive stiffness with and without the cortical shell for all 22 vertebrae, two high-resolution finite element models per specimen-one intact model and one with the shell removed-were created from the microCT scans and virtually compressed. Results indicated that BMC and the structural model index (SMI) were the individual parameters most highly associated with strength (R(2) = 0.57 each). Adding microarchitecture variables to BMC in a stepwise multiple regression model improved this association (R(2) = 0.85). However, the microarchitecture variables in that regression model (degree of anisotropy, bone volume fraction) differed from those when BMC was not included in the model (SMI, mean trabecular thickness), and the association was slightly weaker for the latter (R(2) = 0.76). The finite element results indicated that the physical presence of the cortical shell did not alter the relationships between microarchitecture and vertebral stiffness. We conclude that trabecular microarchitecture is associated with whole-vertebral biomechanical behavior and that the role of microarchitecture is mediated by BMC but not by the cortical shell.
Efficient 3D Frequency-domain Full Waveform Inversion (FWI) with Phase Encoding (2009)

3D high resolution imaging methods such as full waveform inversion still suffer from their expensive computational cost, for instance because of the huge amount of data characterized by numerous shots and receivers. Performing shot assemblages or super-sh
SAR and X-ray. A New Approach Combining Fragment-Based Screening and Rational Drug Design:  Application to the Discovery of Nanomolar Inhibitors of Src SH2 (2002)

(pp60)Src is a protein involved in signal transduction and is mainly expressed in neurones, platelets, and osteoclasts. Its precise biological role was recently discovered with the KO experiments by Soriano that gave rise to no other apparent phenotype than osteopetrosis, a disease resulting in excedent bone formation. The SH2 domain of the Src family specifically recognizes a sequence of tetrapeptide featuring a phosphotyrosine and a lipophilic aminoacid at the +1 and +3 positions. Recently we engaged in the search for SH2 ligands via modular peptidomimicry of this tetrapetide. This gave rise to several families of nanomolar inhibitors; the best one incorporated a caprolactam scaffold, a biphenyl moiety, and a phosphotyrosine. However, these inhibitors still incorporated the phosphate group that confers good binding affinity to the protein. Phosphates have undesirable features for drug candidates, namely, high rate of hydrolysis of the phosphate group by phosphatases and high charge content precluding cell penetration. Therefore, while searching for optimal non-peptide ligands for Src SH2, we looked for phosphate replacements. For this, we have designed an SAR by fragment crystallography approach. The start of this work resulted from two experimental observations. First, the fact that phenyl phosphate itself displayed detectable binding affinity for Src SH2 permitted us to perform a screening of small aromatic compounds as phenyl phosphate surrogates. Second, the obtention of large Src SH2 crystals displaying a channel large enough for soaking purposes allowed structure determination of over 40 of these small aromatic compounds bound in the phosphotyrosine binding pocket. This search and the way it gave rise to low nanomolar range Src SH2 inhibitors devoid of phosphate groups will be the subject of the present paper.
Extreme damping in compliant composites with a negative-stiffness phase (2001)

Compliant composite unit cells were made with negative stiffness constituents. Flexible silicone rubber tubes were incorporated in a post-buckled condition to achieve negative stiffness. Large peaks in the mechanical damping tan delta were observed in these systems. Maximum damping was orders of magnitude in excess of the material damping of the silicone rubber.