gebhart/patrepeval huggingface dataset:
Priming with Secreted Glycoprotein G of Respiratory Syncytial Virus (RSV) Augments Interleukin-5 Production and Tissue Eosinophilia after RSV Challenge (1998)

The respiratory syncytial virus (RSV) G glycoprotein promotes differentiation of type 2 CD4+ T lymphocytes and induces an eosinophilic response in lungs of RSV-infected mice. A unique feature of G is that a second initiation codon in the transmembrane region of the glycoprotein results in secretion of soluble protein from infected cells. Recombinant vaccinia viruses that express wild-type G (vvWT G), only secreted G (vvM48), or only membrane-anchored G (vvM48I) were used to define the influence of G priming on immunopathogenesis. Mice immunized with vvM48 had more severe illness following RSV challenge than did mice primed with vvWT G or vvM48I. Coadministration of purified G during priming with the construct expressing membrane-anchored G shifted immune responses following RSV challenge to a more Th2-like response. This was characterized by increased interleukin-5 in lung supernatants and an increase in G-specific immunoglobulin G1 antibodies. Eosinophils were present in the infiltrate of all mice primed with G-containing vectors but were greatest in mice primed with regimens including secreted G. These data suggest the form of G protein available for initial antigen processing and presentation is an important factor in promoting Th2-like immune responses, including the induction of lung eosinophilia. The ability of RSV to secrete G protein may therefore represent a viral strategy for immunomodulation and be a key determinant of disease pathogenesis.
Using C. elegans to discover therapeutic compounds for ageing-associated neurodegenerative diseases (2015)

Age-associated neurodegenerative disorders such as Alzheimer's disease are a major public health challenge, due to the demographic increase in the proportion of older individuals in society. However, the relatively few currently approved drugs for these conditions provide only symptomatic relief. A major goal of neurodegeneration research is therefore to identify potential new therapeutic compounds that can slow or even reverse disease progression, either by impacting directly on the neurodegenerative process or by activating endogenous physiological neuroprotective mechanisms that decline with ageing. This requires model systems that can recapitulate key features of human neurodegenerative diseases that are also amenable to compound screening approaches. Mammalian models are very powerful, but are prohibitively expensive for high-throughput drug screens. Given the highly conserved neurological pathways between mammals and invertebrates, Caenorhabditis elegans has emerged as a powerful tool for neuroprotective compound screening. Here we describe how C. elegans has been used to model various human ageing-associated neurodegenerative diseases and provide an extensive list of compounds that have therapeutic activity in these worm models and so may have translational potential.
THE NATURE OF THE CHEMICAL BOND. APPLICATION OF RESULTS OBTAINED FROM THE QUANTUM MECHANICS AND FROM A THEORY OF PARAMAGNETIC SUSCEPTIBILITY TO THE STRUCTURE OF MOLECULES (1931)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE NATURE OF THE CHEMICAL BOND. APPLICATION OF RESULTS OBTAINED FROM THE QUANTUM MECHANICS AND FROM A THEORY OF PARAMAGNETIC SUSCEPTIBILITY TO THE STRUCTURE OF MOLECULESLinus. PaulingCite this: J. Am. Chem. Soc. 1931, 53, 4, 1367–1400Publication Date (Print):April 1, 1931Publication History Published online1 May 2002Published inissue 1 April 1931https://pubs.acs.org/doi/10.1021/ja01355a027https://doi.org/10.1021/ja01355a027research-articleACS PublicationsRequest reuse permissionsArticle Views11206Altmetric-Citations1038LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Multidrug resistance in cancer therapy: role of the microenvironment. (2003)

Despite advances in the design of chemotherapeutic agents, and although many of these effective agents are now available for clinical use, most human cancers are resistant to therapy at presentation or become resistant after an initial response. The effectiveness of chemotherapy is compromised by several microenvironmental factors that affect the bioavailability and efficacy of chemotherapeutic agents. These factors vary from one tumor to another, and from one location to another, within the same tumor. A better comprehension of microenvironmental multidrug resistance mechanisms would lead to a clearer understanding of the reason for chemotherapeutic failure. This improved knowledge will permit a more rational utilization of chemotherapy.
Deformable templates using large deformation kinematics (1996)

A general automatic approach is presented for accommodating local shape variation when mapping a two-dimensional (2-D) or three-dimensional (3-D) template image into alignment with a topologically similar target image. Local shape variability is accommodated by applying a vector-field transformation to the underlying material coordinate system of the template while constraining the transformation to be smooth (globally positive definite Jacobian). Smoothness is guaranteed without specifically penalizing large-magnitude deformations of small subvolumes by constraining the transformation on the basis of a Stokesian limit of the fluid-dynamical Navier-Stokes equations. This differs fundamentally from quadratic penalty methods, such as those based on linearized elasticity or thin-plate splines, in that stress restraining the motion relaxes over time allowing large-magnitude deformations. Kinematic nonlinearities are inherently necessary to maintain continuity of structures during large-magnitude deformations, and are included in all results. After initial global registration, final mappings are obtained by numerically solving a set of nonlinear partial differential equations associated with the constrained optimization problem. Automatic regridding is performed by propagating templates as the nonlinear transformations evaluated on a finite lattice become singular. Application of the method to intersubject registration of neuroanatomical structures illustrates the ability to account for local anatomical variability.
Pathogenesis of Helicobacter pylori and perspectives of vaccine development against an emerging pathogen. (1994)

Infection of the stomach and the duodenum by Helicobacter pylori is the major cause of acute and chronic gastroduodenal pathologies in humans and increases the risk of gastric cancer. The recognition of the infectious nature of the illness is having a major impact in the management of the disease that is shifting from the treatment of symptoms by anti-H2 blockers to the eradication of the bacterial infection by antibiotic regimen. Experience with other bacterial diseases, suggests that antibiotic treatment will select resistant strains that in the long term will make the antibiotics infective. Vaccination that classically is the most effective way to prevent and control infectious diseases in large population, could be used to prevent infection and possibly also to treat the disease. Here we summarize the studies on the identification and characterization of the virulence factors that are important for the pathogenesis of the bacterium and that may be candidate components for a vaccine. Animal models of the infection are also described.
Update on lymphocyte specific kinase inhibitors: a patent survey (2010)

The search for a potent and orally active inhibitor of Lck has been an intense area of research for a number of years. Despite tremendous efforts, the identification of a highly selective and potent Lck inhibitor suitable for use as an immunosuppressive agent remains elusive.
Integrative analysis of the melanoma transcriptome (2010)

Global studies of transcript structure and abundance in cancer cells enable the systematic discovery of aberrations that contribute to carcinogenesis, including gene fusions, alternative splice isoforms, and somatic mutations. We developed a systematic approach to characterize the spectrum of cancer-associated mRNA alterations through integration of transcriptomic and structural genomic data, and we applied this approach to generate new insights into melanoma biology. Using paired-end massively parallel sequencing of cDNA (RNA-seq) together with analyses of high-resolution chromosomal copy number data, we identified 11 novel melanoma gene fusions produced by underlying genomic rearrangements, as well as 12 novel readthrough transcripts. We mapped these chimeric transcripts to base-pair resolution and traced them to their genomic origins using matched chromosomal copy number information. We also used these data to discover and validate base-pair mutations that accumulated in these melanomas, revealing a surprisingly high rate of somatic mutation and lending support to the notion that point mutations constitute the major driver of melanoma progression. Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types.
Processing of the hepatitis C virus precursor protein. (1995)

Proteins of hepatitis C virus (HCV) are produced from a polyprotein precursor by post-translational processing. Production of HCV proteins was analyzed with in vitro translation, as well as plasmid-based transient gene expression, in mammalian cell lines. A minimum of three different processing pathways yielded at least 10 viral proteins from the polyprotein precursor. One pathway depended on signal protease processing, and the other two pathways utilized viral proteinases. The signal peptidase cleaved the viral structural proteins, and two viral activities broke up the viral nonstructural proteins. With staggered cleavages, the signal peptidase produced two E2 products from the E2 region, gp70 type A and type B, differing in the C-terminal structure. Two viral proteinases partially overlapped in the N-terminal region of NS3; the functional amino acid residues required for those two activities differed. Most of the processed viral proteins bound together; some of the associated proteins were membrane bound.
High speed BiCMOS VLSI technology with buried twin well structure (1985)

Bipolar transistors of high cut off frequency ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f_{T}=9</tex> GHz) and small size have been fabricated on the same chip with a standard CMOS using the buried twin well structure. 1.3 µm LDD CMOS FETs were formed in the thin epitaxial layer(1-1.5µm) with the buried twin well, without degrading the device characteristics of the MOS FET. Ring oscillators of the BiCMOS gate have been fabricated. A 0.4ns gate delay time at 0.6pF and 3.5 times larger driveability than that of the same area CMOS gate were obtained.
Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. (1995)

The 5' nuclease PCR assay detects the accumulation of specific PCR product by hybridization and cleavage of a double-labeled fluorogenic probe during the amplification reaction. The probe is an oligonucleotide with both a reporter fluorescent dye and a quencher dye attached. An increase in reporter fluorescence intensity indicates that the probe has hybridized to the target PCR product and has been cleaved by the 5'-->3' nucleolytic activity of Taq DNA polymerase. In this study, probes with the quencher dye attached to an internal nucleotide were compared with probes with the quencher dye attached to the 3'-end nucleotide. In all cases, the reporter dye was attached to the 5' end. All intact probes showed quenching of the reporter fluorescence. In general, probes with the quencher dye attached to the 3'-end nucleotide exhibited a larger signal in the 5' nuclease PCR assay than the internally labeled probes. It is proposed that the larger signal is caused by increased likelihood of cleavage by Taq DNA polymerase when the probe is hybridized to a template strand during PCR. Probes with the quencher dye attached to the 3'-end nucleotide also exhibited an increase in reporter fluorescence intensity when hybridized to a complementary strand. Thus, oligonucleotides with reporter and quencher dyes attached at opposite ends can be used as homogeneous hybridization probes.
Combination bacteriolytic therapy for the treatment of experimental tumors (2001)

Current chemotherapeutic approaches for cancer are in part limited by the inability of drugs to destroy neoplastic cells within poorly vascularized compartments of tumors. We have here systematically assessed anaerobic bacteria for their capacity to grow expansively within avascular compartments of transplanted tumors. Among 26 different strains tested, one (Clostridium novyi) appeared particularly promising. We created a strain of C. novyi devoid of its lethal toxin (C. novyi-NT) and showed that intravenously injected C. novyi-NT spores germinated within the avascular regions of tumors in mice and destroyed surrounding viable tumor cells. When C. novyi-NT spores were administered together with conventional chemotherapeutic drugs, extensive hemorrhagic necrosis of tumors often developed within 24 h, resulting in significant and prolonged antitumor effects. This strategy, called combination bacteriolytic therapy (COBALT), has the potential to add a new dimension to the treatment of cancer.
Apoptosis Signal-Regulating Kinase 1 in Stress and Immune Response (2007)

Apoptosis signal-regulating kinase 1 (ASK1) is a mitogen-activated protein kinase (MAPK) kinase kinase of the c-Jun N-terminal kinase (JNK) and p38 MAPK pathways. ASK1 is preferentially activated by various cytotoxic stressors and plays pivotal roles in a wide variety of cellular response to them. Recent analyses of ASK1 orthologs in Caenorhabditis elegans and Drosophila melanogaster have revealed that ASK1 is an evolutionarily conserved signaling intermediate in stress responses and appears to constitute a primitive but efficient defense system against stimuli harmful to organisms. Consistent with this notion, ASK1 has been shown to be required for the innate immune response, which is essential for host defense against a wide range of pathogens. In this review, we focus on the molecular mechanisms by which ASK1 functions in stress and immune responses and discuss the possible involvement of ASK1 in human diseases.
Differentiation modifiers (1984)

This article summarizes evidence that indicates that a variety of relatively simple chemical compounds can induce murine erythroleukemia cells (MELCs) as well as a number of other transformed cell lines to differentiate with the loss of proliferative capacity and the expression of differentiated characteristics. These studies provide a potentially important new approach in the treatment of certain neoplastic diseases that may be an alternative to the use of cytotoxic agents, namely, agents that induce transformed cells to terminal cell division, expression of differentiated characteristics, and loss of oncogenic properties. A strong note of caution is needed concerning the potential therapeutic role of these agents that are able to induce transformed cells to terminal differentiation. In general, it appears that inducer-sensitive transformed cell lines are blocked at a particular stage in the development of these cells. The evidence suggests that these compounds trigger certain events that then are involved in the progression of differentiation of these cells with loss of proliferative capacity. It is not known how to predict which transformed cell lines are blocked in a stage of differentiation susceptible to the inducer-mediated effects of agents as described above. Nevertheless, it is reasonable to suggest that the pursuit of studies in this area may permit researchers to determine the potential efficacy of these inducers for in vivo controlled trials with certain select types of neoplasms.
Inflammation-induced reversible switch of the neuron-specific enolase promoter from Purkinje neurons to Bergmann glia (2016)

Neuron-specific enolase (NSE) is a glycolytic isoenzyme found in mature neurons and cells of neuronal origin. Injecting adeno-associated virus serotype 9 (AAV9) vectors carrying the NSE promoter into the cerebellar cortex is likely to cause the specific transduction of neuronal cells, such as Purkinje cells (PCs) and interneurons, but not Bergmann glia (BG). However, we found BG-predominant transduction without PC transduction along a traumatic needle tract for viral injection. The enhancement of neuroinflammation by the co-application of lipopolysaccharide (LPS) with AAV9 significantly expanded the BG-predominant area concurrently with the potentiated microglial activation. The BG-predominant transduction was gradually replaced by the PC-predominant transduction as the neuroinflammation dissipated. Experiments using glioma cell cultures revealed significant activation of the NSE promoter due to glucose deprivation, suggesting that intracellularly stored glycogen is metabolized through the glycolytic pathway for energy. Activation of the glycolytic enzyme promoter in BG concurrently with inactivation in PC may have pathophysiological significance for the production of lactate in activated BG and the utilization of lactate, which is provided by the BG-PC lactate shuttle, as a primary energy resource in injured PCs.
Automated Digital Microfluidic Platform for Magnetic-Particle-Based Immunoassays with Optimization by Design of Experiments (2013)

We introduce an automated digital microfluidic (DMF) platform capable of performing immunoassays from sample to analysis with minimal manual intervention. This platform features (a) a 90 Pogo pin interface for digital microfluidic control, (b) an integrated (and motorized) photomultiplier tube for chemiluminescent detection, and (c) a magnetic lens assembly which focuses magnetic fields into a narrow region on the surface of the DMF device, facilitating up to eight simultaneous digital microfluidic magnetic separations. The new platform was used to implement a three-level full factorial design of experiments (DOE) optimization for thyroid-stimulating hormone immunoassays, varying (1) the analyte concentration, (2) the sample incubation time, and (3) the sample volume, resulting in an optimized protocol that reduced the detection limit and sample incubation time by up to 5-fold and 2-fold, respectively, relative to those from previous work. To our knowledge, this is the first report of a DOE optimization for immunoassays in a microfluidic system of any format. We propose that this new platform paves the way for a benchtop tool that is useful for implementing immunoassays in near-patient settings, including community hospitals, physicians' offices, and small clinical laboratories.
CRISPR/Cpf1-mediated DNA-free plant genome editing (2017)

Cpf1, a type V CRISPR effector, recognizes a thymidine-rich protospacer-adjacent motif and induces cohesive double-stranded breaks at the target site guided by a single CRISPR RNA (crRNA). Here we show that Cpf1 can be used as a tool for DNA-free editing of plant genomes. We describe the delivery of recombinant Cpf1 proteins with in vitro transcribed or chemically synthesized target-specific crRNAs into protoplasts isolated from soybean and wild tobacco. Designed crRNAs are unique and do not have similar sequences (≤3 mismatches) in the entire soybean reference genome. Targeted deep sequencing analyses show that mutations are successfully induced in FAD2 paralogues in soybean and AOC in wild tobacco. Unlike SpCas9, Cpf1 mainly induces various nucleotide deletions at target sites. No significant mutations are detected at potential off-target sites in the soybean genome. These results demonstrate that Cpf1-crRNA complex is an effective DNA-free genome-editing tool for plant genome editing.
Use of Chromium Picolinate and Biotin in the Management of Type 2 Diabetes: An Economic Analysis (2005)

This paper addresses the potential economic benefits of chromium picolinate plus biotin (Diachrome) use in people with Type 2 diabetes (T2DM). The economic model was developed to estimate the impact on health care systems' costs by improved HbA1C levels with chromium picolinate plus biotin (Diachrome). Lifetimes cost savings were estimated by adjusting a benchmark from the literature, using a price index to adjust for inflation. The cost of diabetes is highly dependent on the HbA1C level with higher initial levels and higher annual increments increasing the cost. Improvement in glycemic control has proven to be cost-effective in delaying the onset and progression of T2DM, reducing the risk for diabetes-associated complications and lowering utilization and cost of care. Chromium picolinate plus biotin (Diachrome) showed greater improvement of glycemic control in poorly controlled T2DM patients (HbA(1C) > or = 10%) compared to their better controlled counterparts (HbA(1C) < 10%). This improvement was additive to that achieved by oral hypoglycemic medications and correlates to calculated levels of cost savings. Average 3-year cost savings for chromium picolinate plus biotin (Diachrome) use could range from 1,636 dollars for a poorly controlled patient with diabetes without heart diseases or hypertension, to 5,435 dollars for a poorly controlled patient with diabetes, heart disease, and hypertension. Average 3-year cost savings was estimated to be between 3.9 billion dollars and 52.9 billion dollars for the 16.3 million existing patients with diabetes. Chromium picolinate plus biotin (Diachrome) use among the 1.17 million newly diagnosed patients with T2DM each year could deliver lifetime cost savings of 42 billion dollars, or 36,000 dollars per T2DM patient. Affordable, safe, and convenient, chromium picolinate plus biotin (Diachrome) could prove to be a cost-effective complement to existing pharmacological therapies for controlling T2DM.