gebhart/patrepeval huggingface dataset:
Location-independent information object security (2002)

Users are mobile and use multiple platforms with differing applications over time. These users have no security service applications which are independent of location or computing environment. The IOS project has developed syntax and applications which provide these services. The IOS Tools allow one or more users to apply security services to documents. The project has also investigated third-party security services and has developed an Electronic Signature Timestamp Server (ESTS) which provides the services of document registration (timestamping), validation, and non-repudiation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Discovery of Nanomolar Ligands for 7-Transmembrane G-Protein-Coupled Receptors from a Diverse N-(Substituted)glycine Peptoid Library (1994)

Screening a diverse, combinatorial library of ca. 5000 synthetic dimer and trimer N-(substituted)glycine "peptides" yielded novel, high-affinity ligands for 7-transmembrane G-protein-coupled receptors. The peptoid library was efficiently assembled using readily available chemical building blocks. The choice of side chains was biased to resemble known ligands to 7-transmembrane G-protein-coupled receptors. All peptides were screened in solution-phase, competitive radioligand-binding assays. Peptoid trimer CHIR 2279 binds to the alpha 1-adrenergic receptor with a Ki of 5 nM, and trimer CHIR 4531 binds to the mu-opiate receptor with a Ki of 6 nM. This represents the first example of the discovery of high-affinity receptor ligands from a combinatorial library of non-natural chemical entities.
Progesterone supplementation for preventing preterm birth: a systematic review and meta-analysis (2005)

Aim. The aim of this study is to assess the role of progesterone in preterm birth prevention. Methods. A MEDLINE search (from 1966 to the present; date of last search January 2005) was performed – using the key words progesterone, pregnancy, preterm birth, preterm labor, and randomized, controlled trial – in order to identify randomized, controlled trials in which progesterone (either intramuscular or vaginal administration) was compared with placebo or no treatment. Data were extracted and a meta-analysis was performed. Results. Seven randomized, controlled trials were identified. Women who received progesterone were statistically significantly less likely to give birth before 37 weeks (seven studies, 1020 women, RR = 0.58, 95% CI = 0.48–0.70), to have an infant with birth weight of ≤2.5 kg (six studies, 872 infants, RR = 0.62, 95% CI = 0.49–0.78), or to have an infant diagnosed with intraventricular hemorrhage (one study, 458 infants, RR = 0.25, 95% CI = 0.08–0.82). Conclusions. For progesterone supplementation to be advocated for women at the risk of preterm birth, the prolongation of gestation demonstrated in this meta-analysis must translate into improved infant outcomes, including a reduction in mortality. There is currently insufficient information to allow recommendations regarding the optimal dose, route, and timing of administration of progesterone supplementation.
Phylogenetic Analysis of the Genus Chlamydia Based on 16S rRNA Gene Sequences (1997)

The phylogenetic relationships among Chlamydia spp. were investigated by comparing 16S rRNA gene sequences. In this analysis we used 14 strains of Chlamydia psittaci, including seven feline isolates, two avian isolates, two human isolates, one bovine isolates, one ovine isolate, and one koala isolate; and nine strains of Chlamydia trachomatis, including six human isolates, two swine isolates, and one mouse isolate. A phylogenetic analysis of the 16S rRNA gene sequences of these organisms and seven previously published sequences revealed eight genetic groups which formed two clusters. The first cluster was composed of C. pecorum, Chlamydia pneumoniae, and C. psittaci and included three genetic groups (one group containing avian, human, and ovine strains, one group containing feline strains, and one group containing guinea pig strains). The second cluster was composed of C. trachomatis and also included three genetic groups (one group containing human strains, one group containing swine isolates, and one group containing rodent strains). The strains in each genetic group exhibited similar genetic distances. The results of the phylogenetic analysis agreed with the results of previous genomic DNA, ompA gene allele, and biotyping studies. Therefore, the genetic groups based on genetic distances may be considered a criterion for species identification.
Heterogeneity of multiple sclerosis lesions: Implications for the pathogenesis of demyelination (2000)

Multiple sclerosis (MS) is a disease with profound heterogeneity in clinical course, neuroradiological appearance of the lesions, involvement of susceptibility gene loci, and response to therapy. These features are supported by experimental evidence, which demonstrates that fundamentally different processes, such as autoimmunity or virus infection, may induce MS-like inflammatory demyelinating plaques and suggest that MS may be a disease with heterogeneous pathogenetic mechanisms. From a large pathology sample of MS, collected in three international centers, we selected 51 biopsies and 32 autopsies that contained actively demyelinating lesions defined by stringent criteria. The pathology of the lesions was analyzed using a broad spectrum of immunological and neurobiological markers. Four fundamentally different patterns of demyelination were found, defined on the basis of myelin protein loss, the geography and extension of plaques, the patterns of oligodendrocyte destruction, and the immunopathological evidence of complement activation. Two patterns (I and II) showed close similarities to T-cell-mediated or T-cell plus antibody-mediated autoimmune encephalomyelitis, respectively. The other patterns (III and IV) were highly suggestive of a primary oligodendrocyte dystrophy, reminiscent of virus- or toxin-induced demyelination rather than autoimmunity. At a given time point of the disease--as reflected in autopsy cases--the patterns of demyelination were heterogeneous between patients, but were homogenous within multiple active lesions from the same patient. This pathogenetic heterogeneity of plaques from different MS patients may have fundamental implications for the diagnosis and therapy of this disease.
Iron state in association with retinoid metabolism in non‐alcoholic fatty liver disease (2010)

The results of the present study suggest that the reasons responsible for iron accumulation in NASH in the present study may partly be due to enhanced expression of TfRs, especially TfR2, and hyperdynamic state of retinoid metabolism is closely related to iron metabolism in the disease.
Automatic image captioning (2005)

We examine the problem of automatic image captioning. Given a training set of captioned images, we want to discover correlations between image features and keywords, so that we can automatically find good keywords for a new image. We experiment thoroughly with multiple design alternatives on large datasets of various content styles, and our proposed methods achieve up to a 45% relative improvement on captioning accuracy over the state of the art.
Fine Definition of the Epitope on the gp41 Glycoprotein of Human Immunodeficiency Virus Type 1 for the Neutralizing Monoclonal Antibody 2F5 (2001)

Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS), in combination with proteolytic protection assays, has been used to identify the functional epitope on human immunodeficiency virus envelope glycoprotein gp41 for the broadly neutralizing anti-gp41 human monoclonal antibody 2F5. In this protection assay-based procedure, a soluble gp140 protein with a stabilizing intermolecular disulfide bond between the gp120 and gp41 subunits (SOS gp140) was affinity bound to immobilized 2F5 under physiological conditions. A combination of proteolytic enzymatic cleavages was then performed to remove unprotected residues. Residues of SOS gp140 protected by their binding to 2F5 were then identified based on their molecular weights as determined by direct MALDI-MS of the immobilized antibody beads. The epitope, NEQELLELDKWASLWN, determined by this MALDI-MS protection assay approach consists of 16 amino acid residues near the C terminus of gp41. It is significantly longer than the ELDKWA core epitope previously determined for 2F5 by peptide enzyme-linked immunosorbent assay. This new knowledge of the structure of the 2F5 epitope may facilitate the design of vaccine antigens intended to induce antibodies with the breadth and potency of action of the 2F5 monoclonal antibody.
Digital Image Enhancement and Noise Filtering by Use of Local Statistics (1980)

Computational techniques involving contrast enhancement and noise filtering on two-dimensional image arrays are developed based on their local mean and variance. These algorithms are nonrecursive and do not require the use of any kind of transform. They share the same characteristics in that each pixel is processed independently. Consequently, this approach has an obvious advantage when used in real-time digital image processing applications and where a parallel processor can be used. For both the additive and multiplicative cases, the a priori mean and variance of each pixel is derived from its local mean and variance. Then, the minimum mean-square error estimator in its simplest form is applied to obtain the noise filtering algorithms. For multiplicative noise a statistical optimal linear approximation is made. Experimental results show that such an assumption yields a very effective filtering algorithm. Examples on images containing 256 × 256 pixels are given. Results show that in most cases the techniques developed in this paper are readily adaptable to real-time image processing.
Upgrading Bio-oil through Emulsification with Biodiesel: Thermal Stability (2010)

Storage properties and thermal stability of fuels are important background information when dealing with a new potential fuel. Following the first paper on the preparation and characterization of the fuel mixture produced through emulsification of bio-oil and biodiesel, the second part of this investigation reports on the storage and thermal stability of the bio-oil/biodiesel mixture. The physicochemical properties of the samples stored at different temperatures (60 and 80 °C) for up to 180 h are measured. Fuel properties, such as viscosity, water content, acid number, and average molecular weight of the bio-oil/biodiesel mixture, are measured before and after aging. In contrast to the aging properties of bio-oil alone, very little changes in water content and viscosity are shown for the mixtures aged at 80 °C for 180 h. Overall, a slight decrease in acid numbers is observed for the aged mixtures. Chemical changes are characterized using gel permeation chromatography (GPC), showing a slight increase in the molecular weight over time, possibly because of some polymerization and condensation reactions during storage. Further confirmation of the changes is shown through a Fourier transform infrared spectrometer (FTIR), thermal decomposition analysis using a thermogravimetric analyzer (TGA), and proton assignment using proton nuclear magnetic residence (1H NMR) spectroscopy. Finally, the study indicates that the bio-oil/biodiesel mixture is stable within the conditions tested as a fuel.
Therapeutic potential of RhoA/Rho kinase inhibitors in pulmonary hypertension (2008)

A burgeoning body of evidence suggests that RhoA/Rho kinase (ROCK) signalling plays an important role in the pathogenesis of various experimental models of pulmonary hypertension (PH), including chronic hypoxia-, monocrotaline-, bleomycin-, shunt- and vascular endothelial growth factor receptor inhibition plus chronic hypoxia-induced PH. ROCK has been incriminated in pathophysiologic events ranging from mediation of sustained abnormal vasoconstriction to promotion of vascular inflammation and remodelling. In addition, the 3-hydroxy-3-methylglutaryl CoA reductase inhibitors, statins, which inhibit activation of RhoA by preventing post-translational isoprenylation of the protein and its translocation to the plasma membrane ameliorate PH in several different rat models, and may also be effective in PH patients. Also, phosphorylation of RhoA and prevention of its translocation to the plasma membrane are involved in the protective effect of the type 5-PDE inhibitor, sildenafil, against hypoxia- and bleomycin-induced PH. Collectively, these and other observations indicate that independent of the cause of PH, activation of the RhoA/ROCK pathway serves as a point of convergence of various signalling cascades in the pathogenesis of the disease. We propose that ROCK inhibitors and other drugs that inhibit this pathway might be useful in the treatment of various forms of PH.
Characterization of a panel of novel anti-p21Waf1/Cip1 monoclonal antibodies and immunochemical analysis of p21Waf1/Cip1 expression in normal human tissues. (1996)

As a universal inhibitor of cyclin-dependent kinases and one of the target genes of the tumor suppresser p53, p21Waf1/Cip1 can act as a tumor suppresser through its ability to control cell cycle progression. To study the function of p21Waf1/Cip1 protein and to investigate its tissue distribution, a panel of anti-p21Waf1/Cip1 monoclonal antibodies was generated. These anti-p21Waf1/Cip1 monoclonal antibodies were initially raised against a GST-p21Waf1/Cip1 fusion protein produced in bacteria. Detailed characterization of the antibodies showed that they can specifically detect p21Waf1/Cip1 by immunoblotting, immunoprecipitation, and immunostaining. The specific induction of p21Waf1/Cip1 expression in response to gamma-radiation in cells containing p53 was also detected by these antibodies. The ability to detect p21Waf1/Cip1 expression in conventionally fixed tissue sections allowed us to investigate the distribution of p21Waf1/Cip1 in 23 different types of normal human tissues, and p21Waf1/Cip1 expression was found in most tissues. A close inverse relationship between p21Waf1/Cip1 expression and proliferation was seen in some tissues, including gastrointestinal tract. However, such association is not universal. In tissues such as lung, kidney, thyroid, pancreatic ducts and acini, and liver, despite the fact that most of the cells are quiescent, expression of p21Waf1/Cip1 was detected only in occasional epithelial cells. All these suggest that the expression of p21Waf1/Cip1 varies among different human tissues. Finally, epitope mapping of the anti-p21Waf1/Cip1 antibodies using a peptide library covering the entire p21Waf1/Cip1 protein sequence indicates that two of the antibodies recognize a region of p21Waf1/Cip1 close to that bound by proliferating cell nuclear antigen. These two monoclonal antibodies will therefore be additionally useful in further understanding the functions of p21Waf1/Cip1 both in vitro and in vivo.
A Mouse Model for the Molecular Characterization of Brca1-Associated Ovarian Carcinoma (2006)

Little is known about the mechanisms that underlie Brca1-associated ovarian tumorigenesis, mainly due to the lack of an appropriate experimental model. We developed genetically defined primary mouse ovarian surface epithelial (OSE) cell lines in which the loss of functional Brca1 and p53 recapitulates the events that are thought to occur in early ovarian cancer development in patients with Brca1 mutations. This system allows for the introduction of additional oncogenes that are thought to cooperate with the loss of Brca1 and p53 to induce tumorigenesis. We showed that Myc is sufficient to induce transformation of ovarian cells that are deficient for both Brca1 and p53 but not sufficient for the transformation of cells that are deficient for either Brca1 or p53. The transformed Brca1-deficient OSE cells display an increased number of centrosomes, acquire complex chromosome aberrations, and lack Rad51 nuclear foci in the presence of DNA-damaging agents, such as mitomycin C and cisplatin. Immunocompetent mice injected with transformed OSE cells develop tumors that resemble human metastatic serous ovarian carcinoma, the most common type of ovarian cancer in women. Consistent with the reported platinum chemosensitivity in patients with Brca1-associated ovarian cancer, the Brca1-deficient OSE cells have increased sensitivity to the DNA-damaging agent cisplatin, whereas sensitivity to the microtubule poison paclitaxel is similar between Brca1 wild-type and Brca1-deficient cells. The Brca1 wild-type and Brca1-deficient mouse ovarian tumors and cell lines provide a new experimental system for the evaluation of therapies that target the Brca1 pathway.
At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1 (2010)

Lactobacilli have long been regarded as important constituents of the healthy human vagina. Lactobacillus iners is the most frequently detected bacterial species in the vagina, but little is known about its characteristics. We report a description of the whole-genome sequence of L. iners AB-1 along with comparative analysis of published genomes of closely related strains of lactobacilli. The genome is the smallest Lactobacillus reported to date, with a 1.3-Mbp single chromosome. The genome seems to have undergone one or more rapid evolution events that resulted in large-scale gene loss and horizontal acquisition of a number of genes for survival in the vagina. L. iners may exhibit specialized adaptation mechanisms to the vaginal environment, such as an iron–sulfur cluster assembly system, and several unique σ factors to regulate gene transcription in this fluctuating environment. A potentially highly expressed homolog of a cholesterol-binding lysin may also contribute to host cell adhesion or act as a defense mechanism against other microbes. Notably, there is a lack of apparent adhesion proteins, but several cell-anchor proteins were identified and may be important for interaction with the host mucosal tissues. L. iners is widely present in healthy females as well as those suffering from bacterial vaginosis or who have undergone antimicrobial therapy, suggesting that it is an important indigenous species of the vagina.
Noncontact speckle contrast diffuse correlation tomography of blood flow distributions in tissues with arbitrary geometries (2018)

A noncontact electron multiplying charge-coupled-device (EMCCD)-based speckle contrast diffuse correlation tomography (scDCT) technology has been recently developed in our laboratory, allowing for noninvasive three-dimensional measurement of tissue blood flow distributions. One major remaining constraint in the scDCT is the assumption of a semi-infinite tissue volume with a flat surface, which affects the image reconstruction accuracy for tissues with irregular geometries. An advanced photometric stereo technique (PST) was integrated into the scDCT system to obtain the surface geometry in real time for image reconstruction. Computer simulations demonstrated that a priori knowledge of tissue surface geometry is crucial for precisely reconstructing the anomaly with blood flow contrast. Importantly, the innovative integration design with one single-EMCCD camera for both PST and scDCT data collection obviates the need for offline alignment of sources and detectors on the tissue boundary. The in vivo imaging capability of the updated scDCT is demonstrated by imaging dynamic changes in forearm blood flow distribution during a cuff-occlusion procedure. The feasibility and safety in clinical use are evidenced by intraoperative imaging of mastectomy skin flaps and comparison with fluorescence angiography.
Inhibition of human lung cancer cell growth by angiotensin-(1-7) (2004)

Angiotensin-(1-7) [Ang-(1-7)] is an endogenous peptide hormone of the renin-angiotensin system with vasodilator and anti-proliferative properties. Human adenocarcinoma SK-LU-1 and A549 cells as well as non-small lung cancer SK-MES-1 cells were treated with serum in the presence and absence of Ang-(1-7), to determine whether Ang-(1-7) inhibits the growth of lung cancer cells. Ang-(1-7) caused a significant reduction in serum-stimulated growth in all three lung cancer cell lines. Treatment with Ang-(1-7) resulted in both a dose- and time-dependent reduction in serum-stimulated DNA synthesis in all three cell lines, with IC(50)'s in the sub-nanomolar range. The Ang-(1-7) receptor antagonist [D-Ala(7)]-Ang-(1-7) blocked the attenuation of the serum-stimulated DNA synthesis of SK-LU-1 cells by Ang-(1-7), while neither AT(1) nor AT(2) angiotensin receptor subtype antagonists prevented the response to the heptapeptide. MAS mRNA and protein, a receptor for Ang-(1-7), was detected in the three lung cancer cell lines, suggesting that the anti-proliferative effect of Ang-(1-7) in the cancer cells may be mediated by the non-AT(1), non-AT(2), AT((1-7)) receptor MAS. Other angiotensin peptides [Ang I, Ang II, Ang-(2-8), Ang-(3-8) and Ang-(3-7)] did not attenuate mitogen-stimulated DNA synthesis of SK-LU-1 cells, demonstrating that Ang-(1-7) selectively inhibits SK-LU-1 cancer cell growth. Pre-treatment of SK-LU-1 cells with 10 nM Ang-(1-7) reduced serum-stimulated phosphorylation of extracellular signal-regulated kinase (ERK)1 and ERK2, indicating that the anti-proliferative effects may occur, at least in part, through inhibition of the ERK signal transduction pathway. The results of this study suggest that Ang-(1-7) inhibits lung cancer cell growth through the activation of an angiotensin peptide receptor and may represent a novel chemotherapeutic and chemopreventive treatment for lung cancer.
Isolation and characterization of the complement-inhibiting protein CD59 antigen from platelet membranes (1992)

Several groups have recently described the isolation of a 20 kDa membrane-attack-complex (MAC)-inhibiting protein, termed 'CD59 antigen', from human erythrocyte membranes. Antibodies raised against erythrocyte CD59 antigen detect antigen on the surface of many other cell types, and in some of these cells the antigen has been shown to have a molecular mass similar to that of the erythrocyte protein and to confer resistance to lysis by the MAC. A platelet-membrane form of CD59 antigen has been described and reported to be much larger than the erythrocyte protein. Here I report the isolation of CD59 antigen from platelet membranes and its molecular and functional characterization. The platelet protein is not significantly larger than the erythrocyte form and possesses similar MAC-inhibiting activity. Platelet CD59 antigen is anchored to the membrane via a glycosyl-phosphatidylinositol link, and consequently it is suggested that deficiency of this protein might be responsible for the increased thrombotic tendency observed in paroxysmal nocturnal haemoglobinuria.
Deep sclerectomy with collagen implant: medium term results (1999)

Deep sclerectomy with collagen implant appears to provide reasonable control of IOP at medium term follow up, with few immediate postoperative complications.