gebhart/patrepeval huggingface dataset:
Basic mechanisms of development of airway structural changes in asthma: Fig. 1— (2007)

Airway remodelling is a complex process that involves all of the component tissues of the airway from the epithelium to the adventitia. Each of the changes has the potential to alter airway physiology so as to promote airway narrowing, hyperresponsiveness and inflammation. Structural changes, such as epithelial metaplasia, airway fibrosis and airway smooth muscle hyperplasia, have been successfully modelled in animals. These models are being extensively characterised and are providing valuable insights into mechanisms that are likely to be quite relevant to human asthma. Remodelling is induced by factors synthesised and secreted both by inflammatory cells and by structural cells, the latter frequently under the influence of the former. While information concerning the genesis of inflammation is abundant, the precise factors responsible for cellular hyperplasia, hypertrophy and altered matrix deposition are far from resolved. Elucidation of these factors will no doubt lead to novel therapies designed to prevent or reverse these changes.
Membrane Anchoring of a Human IgG Fc Receptor (CD16) Determined by a Single Amino Acid (1989)

CD16 is a low-affinity immunoglobulin G (IgG) Fc receptor that is expressed on natural killer (NK) cells, granulocytes, activated macrophages, and some T lymphocytes. Two similar genes, CD16-I and CD16-II, encode membrane glycoproteins that are anchored by phosphatidylinositol (PI)-glycan and transmembrane polypeptides, respectively. The primary structural requirements for PI-linkage were examined by constructing a series of hybrid cDNA molecules. Although both cDNA's have an identical COOH-terminal hydrophobic segment, CD16-I has Ser203 whereas CD16-II has Phe203. Conversion of Phe to Ser in CD16-II permits expression of a PI-glycan-anchored glycoprotein, whereas conversion of Ser to Phe in CD16-I prevents PI-glycan linkage.
Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration (2018)

Transcriptome deconvolution in cancer and other heterogeneous tissues remains challenging. Available methods lack the ability to estimate both component-specific proportions and expression profiles for individual samples. We present DeMixT, a new tool to deconvolve high-dimensional data from mixtures of more than two components. DeMixT implements an iterated conditional mode algorithm and a novel gene-set-based component merging approach to improve accuracy. In a series of experimental validation studies and application to TCGA data, DeMixT showed high accuracy. Improved deconvolution is an important step toward linking tumor transcriptomic data with clinical outcomes. An R package, scripts, and data are available: https://github.com/wwylab/DeMixTallmaterials.
Synthesis of Nucleobase‐Functionalized Morpholino‐Modified Nucleoside Monomers Through Palladium‐Catalyzed Cross‐Coupling Reactions (2013)

Abstract Morpholino‐modified nucleoside analogues have widespread applications in developmental biology. To achieve nucleobase‐functionalized forms of morpholino nucleosides, syntheses of 5‐substituted cytidine, 8‐substituted adenosine, and 8‐substituted guanosine morpholino nucleoside monomers are described for the first time. The syntheses are based on the use of 5‐iodocytidine, 8‐bromoadenosine, and 8‐bromoguanosine morpholino nucleosides as the key starting materials. These iodo or bromo derivatives have also been synthesized for the first time. Palladium‐mediated cross‐coupling reactions (Sonogashira, Suzuki, and Heck) were then employed with the halo derivatives to accomplish the substitutions. Different reaction conditions for C, A, and G were standardized to achieve the conversions. The strategy was devised in such a way that the useful N ‐trityl protecting groups remain at the end. The catalyst combinations used for Sonogashira, Suzuki, and Heck reactions were Pd(PPh 3 ) 2 Cl 2 · CuI, Pd(dppf)Cl 2 · CH 2 Cl 2 , and Pd(OAc) 2 , respectively. Heck coupling between 5‐iodocytidine monomer and methyl acrylate worked well, whereas with acrylonitrile the exocyclic amine of cytidine was found to form the aza‐Michael adduct. In this context, treatment of iodocytidine with methyl acrylate under two different sets of conditions was found to produce either the Michael addition product or the Heck coupling product. Four of the functionalized morpholino monomers have been further confirmed by single‐crystal X‐ray structural analysis. All of these functionalized monomers were obtained in good to excellent overall yields.
On fast surface reconstruction methods for large and noisy point clouds (2009)

In this paper we present a method for fast surface reconstruction from large noisy datasets. Given an unorganized 3D point cloud, our algorithm recreates the underlying surface's geometrical properties using data resampling and a robust triangulation algorithm in near realtime. For resulting smooth surfaces, the data is resampled with variable densities according to previously estimated surface curvatures. Incremental scans are easily incorporated into an existing surface mesh, by determining the respective overlapping area and reconstructing only the updated part of the surface mesh. The proposed framework is flexible enough to be integrated with additional point label information, where groups of points sharing the same label are clustered together and can be reconstructed separately, thus allowing fast updates via triangular mesh decoupling. To validate our approach, we present results obtained from laser scans acquired in both indoor and outdoor environments.
Variability in the structural polypeptides of herpes simplex virus 1 strains: potential application in molecular epidemiology (1976)

This paper reports on the variability of structural polypeptides of 53 strains of herpes simplex virus 1 isolated from Italy, Uganda, South Africa, and various locations in the United States. Most strains were passaged a limited number of times at low multiplicity outside the human host; a few strains were characterized by numberous passages at variable multiplicities in cell culture and experimental animals. The acrylamide gel electrophoresis of polypeptides from purified virions revealed seven variable polypeptides. Virion polypeptides (VP) 7, 11, 13, 14, 15.2 and 23 were present in at least two isotypic forms characterized by fast and slow electrophoretic mobilities. VP8 could not be detected in three strains. In addition, VP13, 15.2, and 23 in some strains were either absent or comigrated with other polypeptides. A variety of tests showed that the variability in electrophoretic mobility of polypeptides was reproducible and could not be attributed to artifacts of purification, solubilization, or electrophoresis. Attempts to classify the strains on the basis of electrophoretic mobility of five or all seven variable polypeptides yielded 14 and 19 groups, respectively. The bulk of the strains (41 to 53) fell into six groups. Not all possible permutations of variable polypeptides were observed. Comparison of early and late passages of laboratory strains showed that in the few instances tested the variability could not be attributed to the propagation of the virus outside the human host. Clustering of strains on the basis of country of origin was not observed. Some clustering of isolates on the basis of site of isolation was observed, and the data do suggest that further analyses of isolates for evidence of a correlation between the site of localization on the human body and the structural polypeptides might be useful. Electrophoretic characterization of structural polypeptides has the potential of becoming a powerful tool for epidemiological studies of herpes simplex virus infections.
Polymorphism of the Signaling Molecule c-di-GMP (2006)

Using UV, CD, and NMR, we demonstrate that the important bacterial signaling molecule involved in biofilm formation, cyclic diguanosine monophosphate (c-di-GMP), exists as a mixture of five different but related structures in an equilibrium that is sensitive both to its concentration and to the metal present. At the lower concentrations used for UV and CD work (0.05-0.5 mM), Li(+), Na(+), Cs(+), and Mg(2+) favor a bimolecular self-intercalated structure, while K(+), Rb(+), and NH(4)(+) favor formation of one or more guanine quartet complexes as well. At the higher NMR concentrations ( approximately 30 mM), the bimolecular structures associate and rearrange to a mixture of all-syn and all-anti tetramolecular and octamolecular quartet complexes. With K(+) the octamolecular complexes predominate, while with Li(+) the tetramolecular and octamolecular quartet complexes are present in approximately equal amounts, along with the bimolecular structure. We also find that both guanine amino groups in c-di-GMP are essential for formation of the quartets, because substitution of inosine for one guanosine allows formation of only the bimolecular structure. Further, two molecules of c-di-GMP tethered together are constrained in such a way that limits their ability to form these quartet complexes. The polymorphism we describe may provide different options for this signaling molecule when performing its functions in a bacterial cell, with K(+) and its own local concentration controlling the equilibrium.
Synthesis and in Vitro T-Cell Immunogenicity of Conjugates with Dual Specificity:  Attachment of Epitope Peptides of 16 and 38 kDa Proteins fromMycobacterium tuberculosisto Branched Polypeptide (1998)

T-cell epitope containing peptides covalently attached to macromolecular carriers can be considered as synthetic immunogens for the development of skin-test diagnostics and of vaccines. As a carrier, an amphoteric branched chain polypeptide, poly[Lys-(Glui-DL-Alam)] (EAK) with poly(L-lysine) backbone has been used. This polypeptide with free alpha-amino and gamma-carboxyl groups at the end of the side chains was conjugated with peptides representing two immunodominant regions of the 16 and 38 kDa proteins of Mycobacterium tuberculosis, respectively. Peptide C91SEFAYGSFVRTVSLPVGADE110 was elongated by Cys at the N-terminal and attached to the carrier containing protected SH groups to form disulfide bridges. Peptide 65FNLWGPAFHERYPNVTITA83 was conjugated to the 3-(2-pyridyldithio)propionic acid N-hydroxysuccinimide ester (SPDP) modified and acetylated EAK by introducing amide bond between the free alpha-amino group of peptide and the free gamma-COOH group of Glu at the terminal position of the branches. This strategy lead to chemically well-defined synthetic immunogens that contain two different epitopes in multiple copies covalently linked to a synthetic branched polypeptide carrier. In vitro T-cell immunogenicity of a prototype conjugate was studied using T-cell hybridomas, lymph node cells from 38 kDa protein immunized mice, and human peripheral blood mononuclear cell (PBMC) cultures from sensitized individuals. These data document that the specific T-cell stimulatory effect of each mycobacterial epitope was maintained in this conjugate. Taken together, these findings suggest that it is feasible to use a biodegradable polymeric polypeptide for producing macromolecular bioconjugates for the stimulation of T-cell responses.
Reduction of phosphoinositide-phospholipase C beta1 methylation predicts the responsiveness to azacitidine in high-risk MDS (2009)

Lipid signaling pathways are involved in cell growth, differentiation, and apoptosis, and could have a role in the progression of myelodysplastic syndromes (MDS) into acute myeloid leukemia (AML). Indeed, recent studies showed that phosphoinositide-phospholipase (PI-PL)Cbeta1 mono-allelic deletion correlates with a higher risk of AML evolution. Also, a single patient treated with azacitidine, a DNA methyltransferase inhibitor currently used in MDS, displayed a direct correlation between PI-PLCbeta1 gene expression and drug responsiveness. Consequently, we hypothesized that PI-PLCbeta1 could be a target for demethylating therapy. First, we analyzed the structure of PI-PLCbeta1 gene promoter, then quantified the degree of PI-PLCbeta1 promoter methylation and gene expression in MDS patients at baseline and during azacitidine administration. Indeed, PI-PLCbeta1 mRNA increased in responder patients, along with a reduction of PI-PLCbeta1 promoter methylation. Also, the molecular response correlated to and anticipated the clinical outcome, thus suggesting that PI-PLCbeta1 gene reactivation could predict azacitidine responsiveness. Our results demonstrate not only that PI-PLCbeta1 promoter is hypermethylated in high-risk MDS patients, but also that the amount of PI-PLCbeta1 mRNA could predict the clinical response to azacitidine, therefore indicating a promising new therapeutic approach.
Photochemical inactivation of viruses and bacteria in platelet concentrates by use of a novel psoralen and long‐wavelength ultraviolet light (1997)

Photochemical treatment of platelet concentrates offers the potential for reducing transfusion-related viral and bacterial diseases.
Zur Stratigraphie und Paläogeographie des Helvetikums im Raum von Neubeuern am Inn (1989)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Technological disadvantage of the digital age (2004)

Debates continue about the relative benefits, costs and risks of the diffusion of computer-based technologies throughout society and schooling. One area that has received considerable attention is gender equity. Early work on gender and computers focused on differences between male and female access and use (e.g. Huff, Fleming &amp; Cooper, 1992; Kirkman, 1993; Morritt, 1997; Nelson &amp; Cooper, 1997; Sofia, 1993), with concerns focused on the potential for girls to be disadvantaged. In some respects, it is arguable that problems of gender equity in schools with respect to computers have been overcome. For example, in a small study I conducted in two New Zealand senior primary classrooms in 2003, I found that both boys and girls were motivated to use computers and appeared to have equal opportunities to access computers in the classroom. The students in my study expressed a belief in the importance of using computers, and this belief can also be discerned from educational policy and media coverage. In this paper I argue that, although gender by itself no longer appears to be a source of disadvantage in terms of access to and use of computers in schools, many questions about technology, schooling and power relations still remain unanswered. I present two alternative viewpoints on the new digital age. First, I explore Melanie Stewart Millar’s (1998) analysis of digital discourse as one which reproduces the power of white, middle-class, educated, well-paid males, and excludes anything else it considers ‘Other’. Second, I review arguments that the digital age has provided sites for the transcendence of traditional hierarchies and inequalities (e.g. Spender, 1995). I conclude that, despite the discrepancies between these two viewpoints, both concur that technological disadvantage will exacerbate any existing inequality that might result from intersections of identity categories, such as, gender, ethnicity, age, and socio-economic status.
Synthesis, characterization and photovoltaic applications of a low band gap polymer based on s-tetrazine and dithienosilole (2010)

A new copolymer of dithienosilole (DTS) and dithienyl-s-tetrazine (TTz), PDTSTTz, has been designed and synthesized. This solution processable polymer shows a low band gap, strong absorption and good thermal stability. Solar cells from the blend of this polymer with PC(71)BM showed power conversion efficiency (PCE) up to 4.2%.
From historical perspectives to modern therapy: a review of current and future biological treatments for Crohn’s disease (2015)

Crohn's disease (CD) is a debilitating, systemic inflammatory disorder with both gastrointestinal and extraintestinal manifestations. Its existence predates modern medicine, but its precise etiology remains incompletely understood. Most authorities suggest a multifactorial pathogenesis owing to a mixture of genetic disorders, immunologic dysregulation, microbiota disequilibrium and environmental influences. Of these factors, the overactive immunologic response seen in CD appears to be the most promising target of medical therapy. Biological agents comprise a relatively new class of drugs that can induce and maintain remission in moderate to severe CD, as well as in ulcerative colitis. This review will provide an overview of CD, its history, clinical features, pathophysiology, and treatment options focusing on current and future biological agents with an emphasis on drug development, dosage and administration.
Chicken Embryonic Stem Cells and Transgenic Strategies (1999)

The production of transgenic birds is an important goal for both fundamental and applied biology. Different methods have been employed to generate transgenic chickens, including microinjection, use of retroviruses and transfection of primordial germ or embryonic germ cells. In this review we will briefly describe these techniques and our efforts to obtain genetically modified avian embryonic stem (ES) cells using liposomes. This latter technique should allow us to modify chicken ES cells with a high efficiency, permitting the rapid generation of transgenic bird lines.
Studies of intestinal stem cells using normal, chimeric, and transgenic mice 1 (1992)

The mouse intestinal epithelium represents a continuous developmental system. Its four principal differentiated cell types--enterocytes, goblet, enteroendocrine, and Paneth cells--are derived from a common multipotent stem cell located near the base of monoclonal crypts. Members of these four lineages undergo rapid and perpetual renewal along an anatomically well-defined pathway. The gut epithelium provides a unique mammalian model for studying the biological features of stem cells (e.g., their ability to undergo asymmetric division, their enormous proliferative potential, their capacity for functional anchorage in a niche), examining how stem cell hierarchies are established and maintained in renewing cell populations, analyzing the relationships between passage through the cell cycle and lineage allocation (commitment), and defining the mechanisms that give stem cells a "positional address" along the cephalocaudal axis, allowing them to generate regional differences in the differentiation programs of their derived lineages (axial pattern formation).
Performance of a nonisotopic DNA probe for detection of Chlamydia trachomatis in urogenital specimens (1991)

The Gen-Probe PACE 2 assay (GP), a nonisotopic DNA probe, was evaluated by using cell culture as the method of reference. Specimens were collected from 260 men and 482 women visiting the outpatient department for sexually transmitted diseases at the University Hospital in Rotterdam, The Netherlands. The prevalences of Chlamydia culture-positive men and women were 13.2 and 8.6%, respectively. Sensitivity values for the male and female patients were 70.6 and 92.7%, respectively. Specificity values for these groups were 98.2 and 97.7%, respectively. Sensitivity was significantly lower when the number of inclusions in cell culture was low. Samples which showed a discordance between cell culture and GP results were retested by the polymerase chain reaction. If the results of the polymerase chain reaction were considered as the points of reference, the sensitivity and specificity of both GP and cell culture could be calculated. The performance of GP for females was comparable to that of cell culture. In males, the sensitivity of GP was considerably lower than that of cell culture (77.2 versus 91.4%), while specificity was somewhat higher (99.6 versus 99.1%). Compared with cell culture, the GP is a relatively simple and rapid test that is suitable for diagnosing Chlamydia infections in urogenital specimens.
The Forgotten Teachers in K-12 Online Learning (2014)

Like many K-12 online learning programs, the Illinois Virtual High School (IVHS) began by utilizing vendor content to populate its online courses. In its fourth year, the IVHS began a concerted effort to design more of its own online course content internals. The aim of this study was to examine the nature of the support needed and application of tools used by IVHS course developers. The data consisted of a two-part, web-based survey and telephone interviews that were analyzed using descriptive statistics and inductive analysis. The results showed these developers had a strong desire to use interactive elements in their course as well as working in cooperative teams. Further, developers were opposed to using a forced template, but indicated a need for general structural guidance and additional professional development. Finally, developers recommended that subject matter teacher-developers and multimedia specialists be split into two separate roles, and these individuals work together as a part of a design team. Further research should be conducted on the intended use of technology tools requested.
Cutting Tissue With Ultrashort Pulsed Laser Light (2004)

Ultrashort pulsed laser light can be used to cut biological tissue in a highly localized and controlled manner. Among the practical applications that are beginning to emerge: an all-optical technique for automated, three-dimensional histology of brain tissue and an optical-based technique to incorporate plasmid DNA into living cells.
Convergence Rates of Efficient Global Optimization Algorithms (2011)

In the efficient global optimization problem, we minimize an unknown function f, using as few observations f(x) as possible. It can be considered a continuum-armed-bandit problem, with noiseless data, and simple regret. Expected-improvement algorithms are perhaps the most popular methods for solving the problem; in this paper, we provide theoretical results on their asymptotic behaviour. Implementing these algorithms requires a choice of Gaussian-process prior, which determines an associated space of functions, its reproducing-kernel Hilbert space (RKHS). When the prior is fixed, expected improvement is known to converge on the minimum of any function in its RKHS. We provide convergence rates for this procedure, optimal for functions of low smoothness, and describe a modified algorithm attaining optimal rates for smoother functions. In practice, however, priors are typically estimated sequentially from the data. For standard estimators, we show this procedure may never find the minimum of f. We then propose alternative estimators, chosen to minimize the constants in the rate of convergence, and show these estimators retain the convergence rates of a fixed prior.
Colonic lavage solutions: plain versus flavored. (1993)

Many patients dislike the taste of the oral gastrointestinal lavage solutions utilized prior to colonoscopy. Specifically, patients dislike the salty taste and the quantity of the polyethylene glycol-electrolyte solution that they are required to ingest. In an attempt to reduce the salty taste and potentially improve patient compliance and tolerance of the preparation, flavoring was added to the lavage solution. Fifty-six patients received standard or flavored polyethylene glycol-electrolyte lavage solution in random order prior to colonoscopy. In group I, lemon-flavored Colyte was compared with standard Colyte: 93% (25/27) of subjects preferred the flavored solution. In group II, standard Colyte was compared with lemon/lime-flavored Colyte, and 80% (8/10) of subjects preferred standard Colyte. In group III, lemon-flavored Colyte, standard Colyte, and NuLYTELY were compared. Ninety percent (17/19) of the subjects preferred lemon-flavored Colyte, 10% of the subjects preferred standard Colyte, and none of the subjects preferred NuLYTELY. Overall, patients preferred lemon-flavored solution over other solutions.