gebhart/patrepeval huggingface dataset:
TM-align: a protein structure alignment algorithm based on the TM-score (2005)

We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is approximately 4 times faster than CE and 20 times faster than DALI and SAL. On average, the resulting structure alignments have higher accuracy and coverage than those provided by these most often-used methods. TM-align is applied to an all-against-all structure comparison of 10 515 representative protein chains from the Protein Data Bank (PDB) with a sequence identity cutoff <95%: 1996 distinct folds are found when a TM-score threshold of 0.5 is used. We also use TM-align to match the models predicted by TASSER for solved non-homologous proteins in PDB. For both folded and misfolded models, TM-align can almost always find close structural analogs, with an average root mean square deviation, RMSD, of 3 A and 87% alignment coverage. Nevertheless, there exists a significant correlation between the correctness of the predicted structure and the structural similarity of the model to the other proteins in the PDB. This correlation could be used to assist in model selection in blind protein structure predictions. The TM-align program is freely downloadable at http://bioinformatics.buffalo.edu/TM-align.
Thermal conductivity 21 (1990)

Fifty-one papers (and three keynote addresses) on contemporary theoretical issues and experimental techniques pertaining to the underlying factors that control heat-conduction behavior of materials. The latest findings on insulation, fluids, and low-dimensional solids and composites are reviewed as
Advances in Immunological Treatment of Allergy (2003)

Allergic diseases such as asthma, atopic dermatitis, rhinitis and urticaria are immunological disorders, affecting more than 30% of the population in industrialized countries. Advances in the understanding of the molecular and immunological mechanisms of allergic inflammation have identified several new targets that might contribute to new therapies for allergic diseases in the future. Complexity of natural allergen extracts can be recreated using recombinant allergens and hypoallergenic derivates of these are being engineered to increase treatment efficacy and safety. In addition, the use of modern T cell and antigen-presenting cell modulating adjuvants conjugated to recombinant allergens are promising for the future of allergen-specific immunotherapy. T cells are important players in initiating and maintaining the allergic inflammation through release of cytokines, like IL-4, IL-5 and / or IL-13. The blockage of events that are not allergen-specific, such as T cell costimulation and downstream events dependent on IgE, cytokines and chemokines represent important strategies for the treatment of allergy. Nevertheless, all these approaches face the inherent difficulty of attempting to counteract an already established pathological immune response. In addition to the treatment of established allergy, it is essential to consider prophylactic approaches against allergy before initial sensitization has taken place. This article reviews the recent developments in allergen-specific immunotherapy as well as novel agents targeting the immune system in the treatment of allergic diseases. Keywords: immunotherapy, vaccine development, allergy, tolerance, prophylactic approaches, ige, t cells, apoptosis, chemotaxis, histamine
Applications of high efficiency lithium acetate transformation of intact yeast cells using single‐stranded nucleic acids as carrier (1991)

The highly efficient yeast lithium acetate transformation protocol of Schiestl and Gietz (1989) was tested for its applicability to some of the most important needs of current yeast molecular biology. The method allows efficient cloning of genes by direct transformation of gene libraries into yeast. When a random gene pool ligation reaction was transformed into yeast, the LEU2, HIS3, URA3, TRP1 and ARG4 genes were found among the primary transformants at a frequency of approximately 0.1%. The RAD4 gene, which is toxic to Escherichia coli, was also identified among the primary transformants of a ligation library at a frequency of 0.18%. Non-selective transformation using this transformation protocol was shown to increase the frequency of gene disruption three-fold. Co-transformation showed that 30-40% of the transformation-competent cells take up more than one DNA molecule which can be used to enrich for integration and deletion events 30- to 60-fold. Co-transformation was used in the construction of simultaneous double gene disruptions as well as disrupting both copies of one gene in a diploid which occurred at 2-5% the frequency of the single event.
Diffractive Bifocal Intraocular Lens (1989)

A bifocal intraocular lens is described which has been surgically implanted in a number of patients in the United States and Europe with promising results. The posterior surface of this lens includes a blazed phase zone plate which directs most of the light to two diffractive orders. The combination of this diffractive structure and the conventional refractive surfaces of the lens provides simultaneous bifocal vision for the patient.
Identification of oral bacteria associated with crevicular epithelial cells from chronic periodontitis lesions (2006)

Bacterial invasion of host epithelial cells plays an important role in the pathogenesis of periodontal diseases; however, the interactions between subgingival species and the gingival crevice cells are not fully understood. This study determined the prevalence of a group of oral bacterial species on or in epithelial cells derived from periodontal pockets and the gingival crevice of subjects with periodontitis. Samples of epithelial cells were obtained from 120 sites with periodontal pockets > or =4 mm and 92 periodontally healthy sites from 49 patients (mean age 46.3+/-1.4 years; 43% males) with chronic periodontitis. Bacteria in or on epithelial cells were separated from unattached bacteria by Percoll density-gradient centrifugation. The presence and levels of 33 oral species were determined in epithelial cell samples by whole genomic DNA probes and the checkerboard method. The most frequently detected species were Porphyromonas gingivalis (42%), Treponema denticola (38%), Prevotella intermedia (37%), Streptococcus intermedius (36%), Campylobacter rectus (35%), Streptococcus sanguinis (35%) and Streptococcus oralis (34%). Species of Actinomyces were found in low prevalence and levels. The data indicated that there were more micro-organisms on or in epithelial cells obtained from periodontal pockets than from healthy sulci; however, no significant differences regarding the percentage and level of any specific species were found between these sites. Veillonella parvula, S. oralis, Streptococcus gordonii and Streptococcus mitis tended to be more prevalent in sites without disease. These findings demonstrated that a wide range of oral species may be detected on or in crevicular epithelial cells from sites with periodontitis and from periodontally healthy sulci.
Altered catalytic activity of and DNA cleavage by DNA topoisomerase II from human leukemic cells selected for resistance to VM-26 (1988)

The simultaneous development of resistance to the cytotoxic effects of several classes of natural product anticancer drugs, after exposure to only one of these agents, is referred to as multiple drug resistance (MDR). At least two distinct mechanisms for MDR have been postulated: that associated with P-glycoprotein and that thought to be due to an alteration in DNA topoisomerase II activity (at-MDR). We describe studies with two sublines of human leukemic CCRF-CEM cells approximately 50-fold resistant (CEM/VM-1) and approximately 140-fold resistant (CEM/VM-1-5) to VM-26, a drug known to interfere with DNA topoisomerase II activity. Each of these lines is cross-resistant to other drugs known to affect topoisomerase II but not cross-resistant to vinblastine, an inhibitor of mitotic spindle formation. We found little difference in the amount of immunoreactive DNA topoisomerase II in 1.0 M NaCl nuclear extracts of the two resistant and parental cell lines. However, topoisomerase II in nuclear extracts of the resistant sublines is altered in both catalytic activity (unknotting) of and DNA cleavage by this enzyme. Also, the rate at which catenation occurs is 20-30-fold slower with the CEM/VM-1-5 preparations. The effect of VM-26 on both strand passing and DNA cleavage is inversely related to the degree of primary resistance of each cell line. Our data support the hypothesis that at-MDR is due to an alteration in topoisomerase II or in a factor modulating its activity.
Botanical insecticides for controlling agricultural pests: Piperamides and the Colorado potato beetle Leptinotarsa decemlineata say (Coleoptera: Chrysomelidae) (2003)

Abstract The efficacy of extracts from two Piperaceae species, Piper nigrum L. and P. tuberculatum Jacq. were evaluated using larvae and adults of the Colorado Potato Beetle Leptinotarsa decemlineata (Say). Young larvae and neonates were the most susceptible; a 24‐h LD 50 of 0.064% extract of P. tuberculatum was determined for 4‐day‐old larvae, while 0.05% extract of P. nigrum reduced larval survival up to 70% within one week after treatment of potato Solanum tuberosum L. (Solanaceae) plants. When an insecticide resistant strain of L. decemlineata larvae was tested with the P. tuberculatum extract, there was less than a 2‐fold tolerance ratio compared to the 22‐fold tolerance ratio to cypermethrin, a pyrethroid. Older larvae, pre‐pupal stage and adults, were less sensitive to the P. nigrum extracts; the 24‐h LD 50 was 0.5% (95% C.I. = 0.36, 0.65). However, the same concentration was equally effective under field conditions. In the greenhouse, P. nigrum at 0.5% was as effective at reducing adult L. decemlineata feeding as combinations with 2 separate botanical mixtures, garlic and lemon grass oil. Under field conditions, the residual activity of the P. nigrum extracts was less than 3 h. When adult L. decemlineata were placed on treated plants exposed to full sunlight for 0, 1.5, and 3 h, leaf damage progressively increased as the main active compound, piperine, was found to degrade by 80% after 3 h. An in vitro polysubstrate monoxygenase (PSMO) enzyme assay, using the substrate methoxyresorufin O‐demethylation (MROD), determined that the principal P. nigrum active compound, piperine, is responsible for inhibition of that specific enzyme. The results suggest that Piper extracts could be used effectively as contact botanical insect control agents to protect potato plants from developing L. decemlineata larvae at concentrations less than 0.1%. There is also potential for Piper extracts to control insecticide resistant populations in conjunction with other integrated pest management (IPM) strategies used in conventional and organic agriculture. Arch. Insect Biochem. Physiol. 54:212–225, 2003. © 2003 Wiley‐Liss, Inc.
Modified Ingelman-Sundberg Bladder Denervation Procedure for Intractable Urge Incontinence (1996)

In patients with urge incontinence and medically refractory detrusor instability, with few simple choices for treatment, the modified Ingelman-Sundberg procedure is an excellent surgical option that yields good results with minimal morbidity.
Monoclonal antibodies for brain tumour treatment (2004)

Conventional treatment of brain tumours includes surgical, radiotherapeutic and chemotherapeutic modalities. Nonetheless, the outcome of patients with brain tumours, in particular glioblastoma, remains poor. Immunotherapy with armed or unarmed monoclonal antibodies targeting tumour-specific antigens has emerged in the last two decades as a novel potential adjuvant treatment for all types of neoplasia. Many challenges to its implementation as a safe and viable therapy for brain tumours still need to be addressed; nevertheless, results from ongoing Phase I/II clinical trials are encouraging, as disease stabilisation and patient survival prolongation have been observed. Advances in preclinical and clinical research indicate that treatment of brain tumours with monoclonal antibodies can be increasingly adjusted to the characteristics of the targeted tumour and its environment. This aspect relies on the careful selection of the target antigen and corresponding specific monoclonal antibody, and antibody format (size, class, affinity), conjugation to the appropriate toxin or radioactive isotope (half-life, range), and proper compartmental administration.
Characterization of mutations in the genedoublecortin in patients with double cortex syndrome (1999)

Mutations in the X-linked gene doublecortin, which encodes a protein with no dear structural homologues, are found in pedigrees in which affected females show "double cortex" syndrome (DC; also known as subcortical band heterotopia or laminar heterotopia) and affected males show X-linked lissencephaly. Mutations in doublecortin also cause sporadic DC in females. To determine the incidence of doublecortin mutations in DC, we investigated a cohort of eight pedigrees and 47 sporadic patients with DC for mutations in the doublecortin open reading frame as assessed by single-stranded conformational polymorphism analysis. Mutations were identified in each of the eight DC pedigrees (100%), and in 18 of the 47 sporadic DC patients (38%). Identified mutations were of two types, protein truncation mutations and single amino acid substitution mutations. However, pedigrees with DC displayed almost exclusively single amino acid substitution mutations, suggesting that patients with these mutations may have less of a reproductive disadvantage versus those patients with protein truncation mutations. Single amino acid substitution mutations were tightly clustered in two regions of the open reading frame, suggesting that these two regions are critical for the function of the Doublecortin protein.
Color Control in π-Conjugated Organic Polymers for Use in Electrochromic Devices (2010)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTColor Control in π-Conjugated Organic Polymers for Use in Electrochromic DevicesPierre M. Beaujuge* and John R. Reynolds*View Author Information The George and Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science and Engineering, Department of Chemistry, University of Florida, Gainesville, Florida 32611Cite this: Chem. Rev. 2010, 110, 1, 268–320Publication Date (Web):January 13, 2010Publication History Received8 April 2009Published online13 January 2010Published inissue 13 January 2010https://pubs.acs.org/doi/10.1021/cr900129ahttps://doi.org/10.1021/cr900129areview-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views24926Altmetric-Citations1600LEARN 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 SUBJECTS:Color,Oxidation,Plastics,Polymers,Redox reactions Get e-Alerts
Generation of anti-p53 cytotoxic T lymphocytes from human peripheral blood using autologous dendritic cells. (1999)

CTLs recognizing the HLA-A2.1-restricted, wild-type sequence p53 epitopes p53(149-157) and p53(264-272) were generated from CD8-enriched populations of nonadherent peripheral blood lymphocytes (PBLs) obtained from healthy donors. The PBLs were restimulated in vitro with peptide-pulsed granulocyte macrophage colony-stimulating factor- and interleukin (IL)-4-induced autologous dendritic cells in the presence of IL-6 and IL-12 and subsequently cultivated with IL-1alpha, IL-2, IL-4, IL-6, and IL-7. Bulk anti-p53(264-272) CTL populations were generated from PBLs obtained from two of five donors. Both CTL populations were cytotoxic against peptide-pulsed HLA-A2+ target cells, but not against untreated target cells. A CD8+ anti-p53 CTL clone designated p264#2 was isolated from one of the bulk populations. It was found to have an intermediate affinity of approximately 10(-9) M for the epitope and to mediate cytotoxicity against several human tumor cell lines, including the squamous cell carcinoma of the head and neck cell line SCC-9, which is known to present the wild-type sequence p53(264-272) epitope. In addition, CTLs reactive against p53(149-157)-pulsed targets as well as a HLA-A2+ tumor cell line were cloned from a bulk population of antitumor CTLs obtained from one of the five normal PBLs restimulated with this epitope. The results indicate that CTLs recognizing wild-type sequence epitopes can be generated from precursors present in PBLs obtained from some normal individuals using autologous dendritic cells as antigen-presenting cells and suggest that vaccine strategies targeting these epitopes can lead to antitumor CTL generation, thereby emphasizing the therapeutic potential of p53-based cancer vaccines.
SOLID SUBSTRATE PHOSPHORESCENT IMMUNOASSAY BASED ON BIOCONJUGATED NANOPARTICLES (2001)

Room-temperature phosphorescent (RTP) immunoassay based on dye embedded polyglutaraldehyde nanoparticles was described. Phosphorescent nanoparticles had been covalently linked to antibody to probe specifically antigen. The immunoassay was conducted by the typical procedure of sandwich type assay with polyamide membrane (PAM) sheet as solid substrate. In comparison with single organic dye molecule, the nanoparticle probe was bright, and more stable against photobleaching. Moreover, the solid substrate at room temperature offered high signal and low background, which led to gain rather perfect sensitivity. The concentration of immunoglobulin (IgG) in reaction with nanoparticles was optimized and the dependence of the phosphorescence intensity on the concentration of antigen was studied.
Non-thermal inactivation of Lactobacillus plantarum as influenced by pressure and temperature of pressurized carbon dioxide (1999)

Abstract Non-thermal inactivation of Lactobacillus plantarum cells as influenced by pressure and temperature of pressurized carbon dioxide was investigated to evaluate its potential use for preservation of foods and biological substances. Microbial inactivation by the pressurized CO2 was dependent principally on the transfer rate of CO2 into cells and effectiveness could be improved by increasing pressure and temperature. Microbial reduction of more than 6 logs occurred within 30 min under CO2 pressure of 2000 psi at 30 °C. The results showed that the pressurized CO2 treatment could be used as a potential non-thermal preservation technology for foods.
Innovative Color Interpolation Using Fuzzy Logic and Linear Regression (2005)

To reduce the cost of digital cameras, the color filter array (CFA) is usually coated upon a single-chip image sensor. Each pixel of the image sensor can sense only one of the R, G and B colors under CFA. The two missing colors of a pixel are estimated using the CFA interpolation algorithm. The interpolation algorithm may generate color distortion and degrade the quality of interpolated images. In this paper, we propose a new algorithm &#x201C;fuzzy logic and linear regression method (FLLRM)&#x201D; to solve this problem.We use fuzzy logic method based on the effect between pixels to avoid color distortion around the edges. The linear regression method is used to process the interaction effect among R, G and B channels. The proposed method can successfully eliminate false color, color moire, aliasing and color shifts in the full color camera output. Finally, we implement our method on the digital camera platform that is designed by Industrial Technology Research Institute (ITRI). The processed image shows a very good quality, which also demonstrates our approach is a better CFA interpolation algorithm than the previous processed methods.
Toward Attogram Mass Measurements in Solution with Suspended Nanochannel Resonators (2010)

Using suspended nanochannel resonators (SNRs), we demonstrate measurements of mass in solution with a resolution of 27 ag in a 1 kHz bandwidth, which represents a 100-fold improvement over existing suspended microchannel resonators and, to our knowledge, is the most precise mass measurement in liquid today. The SNR consists of a cantilever that is 50 microm long, 10 microm wide, and 1.3 microm thick, with an embedded nanochannel that is 2 microm wide and 700 nm tall. The SNR has a resonance frequency near 630 kHz and exhibits a quality factor of approximately 8000 when dry and when filled with water. In addition, we introduce a new method that uses centrifugal force caused by vibration of the cantilever to trap particles at the free end. This approach eliminates the intrinsic position dependent error of the SNR and also improves the mass resolution by increasing the averaging time for each particle.
Oxytocin Levels Inversely Correlate With Skin Age Score and Solar Damage (2020)

This study links previously published evidence of oxytocin&rsquo;s protective role against inflammatory cytokine release in the skin with clinical evidence of OT levels correlating with SAS scores. Furthermore, it shows OT is likely inducing a protective function in the epidermis in the case of sun exposure and possibly with intrinsic aging. J Drugs Dermatol. 2020;19(12): doi:10.36849/JDD.2020.5063.
The regulation of inflammation by galectin‐3 (2009)

Galectin-3 is a beta-galactoside-binding animal lectin of approximately 30 kDa and is evolutionarily highly conserved. Galectin-3 is promiscuous, its localization within the tissue micro-environment may be extracellular, cytoplasmic, or nuclear, and it has a concentration-dependent ability to be monomeric or form oligomers. These properties impart great flexibility on galectin-3 as a specific regulator of many biological systems including inflammation. For example, in acute tissue damage galectin-3 is a key component in the host defense against microbes such as Streptococcus pneumoniae. However, if tissue injury becomes repetitive galectin-3 also appears to be intimately involved in the transition to chronic inflammation, facilitating the walling off of tissue injury with fibrogenesis and organ scarring. Therefore galectin-3 can be viewed as a regulatory molecule acting at various stages along the continuum from acute inflammation to chronic inflammation and tissue fibrogenesis. In this review, we examine the role of galectin-3 in inflammation, and discuss the manipulation of galectin-3 expression as a potentially novel therapeutic strategy in the treatment of a broad range of inflammatory diseases.
DNA SEQUENCING: Massively Parallel Genomics (1997)

Using the URL at the end of this item, readers can immediately offer feedback and suggestions on this topic.

An enormous amount of genetic sequence data has been obtained with gel-based DNA sequencing methods [[HN1][1]]. To understand the function of the genes and their health implications, genetic