gebhart/patrepeval huggingface dataset:
A Bayesian missing value estimation method for gene expression profile data (2003)

The software is available at http://hawaii.aist-nara.ac.jp/~shige-o/tools/.
Visualization of microvasculature by dual-beam phase-resolved Doppler optical coherence tomography (2011)

We present a dual-beam Doppler optical coherence tomography system for visualizing the microvasculature within the retina. The sample arm beams from two identical spectral domain optical coherence tomography (SD-OCT) systems are combined such that there is a small horizontal offset between them at the retina. Thereby we record two tomograms which are slightly separated in time. Phase-resolved Doppler analysis is performed between these two data sets. This system allows blood capillary imaging with high flow sensitivity and variable velocity range. To demonstrate the performance of our system we present images of the microvascular network around the fovea and around the optic nerve head of the human eye.
Nitrogen Fixation in Cereals (2018)

Cereals such as maize, rice, wheat and sorghum are the most important crops for human nutrition. Like other plants, cereals associate with diverse bacteria (including nitrogen-fixing bacteria called diazotrophs) and fungi. As large amounts of chemical fertilizers are used in cereals, it has always been desirable to promote biological nitrogen fixation in such crops. The quest for nitrogen fixation in cereals started long ago with the isolation of nitrogen-fixing bacteria from different plants. The sources of diazotrophs in cereals may be seeds, soils, and even irrigation water and diazotrophs have been found on roots or as endophytes. Recently, culture-independent molecular approaches have revealed that some rhizobia are found in cereal plants and that bacterial nitrogenase genes are expressed in plants. Since the levels of nitrogen-fixation attained with nitrogen-fixing bacteria in cereals are not high enough to support the plant's needs and never as good as those obtained with chemical fertilizers or with rhizobium in symbiosis with legumes, it has been the aim of different studies to increase nitrogen-fixation in cereals. In many cases, these efforts have not been successful. However, new diazotroph mutants with enhanced capabilities to excrete ammonium are being successfully used to promote plant growth as commensal bacteria. In addition, there are ambitious projects supported by different funding agencies that are trying to genetically modify maize and other cereals to enhance diazotroph colonization or to fix nitrogen or to form nodules with nitrogen-fixing symbiotic rhizobia.
Effect of the Gas6 c.834+7G>A Polymorphism and the Interaction of Known Risk Factors on AMD Pathogenesis in Hungarian Patients (2012)

Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly in the developed world. Numerous genetic factors contribute to the development of the multifactorial disease. We performed a case-control study to assess the risk conferred by known and candidate genetic polymorphisms on the development of AMD. We searched for genetic interactions and for differences in dry and wet AMD etiology. We enrolled 213 patients with exudative, 67 patients with dry AMD and 106 age and ethnically matched controls. Altogether 12 polymorphisms in Apolipoprotein E, complement factor H, complement factor I, complement component 3, blood coagulation factor XIII, HTRA1, LOC387715, Gas6 and MerTK genes were tested. No association was found between either the exudative or the dry form and the polymorphisms in the Apolipoprotein E, complement factor I, FXIII and MerTK genes. Gas6 c.834+7G>A polymorphism was found to be significantly protective irrespective of other genotypes, reducing the odds of wet type AMD by a half (OR = 0.50, 95%CI: 0.26-0.97, p = 0.04). Multiple regression models revealed an interesting genetic interaction in the dry AMD subgroup. In the absence of C3 risk allele, mutant genotypes of both CFH and HTRA1 behaved as strongly significant risk factors (OR = 7.96, 95%CI: 2.39 = 26.50, p = 0.0007, and OR = 36.02, 95%CI: 3.30-393.02, p = 0.0033, respectively), but reduced to neutrality otherwise. The risk allele of C3 was observed to carry a significant risk in the simultaneous absence of homozygous CFH and HTRA1 polymorphisms only, in which case it was associated with a near-five-fold relative increase in the odds of dry type AMD (OR = 4.93, 95%CI: 1.98-12.25, p = 0.0006). Our results suggest a protective role of Gas6 c.834+7G>A polymorphism in exudative AMD development. In addition, novel genetic interactions were revealed between CFH, HTRA1 and C3 polymorphisms that might contribute to the pathogenesis of dry AMD.
Noncoding RNAs database (ncRNAdb) (2006)

The noncoding RNA database (ncRNAdb) was created as a source of information on RNA molecules, which do not possess protein-coding capacity. It is now widely accepted that, in addition to constitutively expressed, housekeeping or infrastructural RNAs, there is a wide variety of RNAs participating in mechanisms involved in regulation of gene expression at all levels of transmission of genetic information from DNA to proteins. Noncoding RNAs' activities include chromatin structure remodeling, transcriptional and translational regulation of gene expression, modulation of protein function and regulation of subcellular distribution of RNAs as well as proteins. Noncoding transcripts have been identified in organisms belonging to all domains of life. Currently, the ncRNAdb contains >30,000 ncRNA sequences from Eukaryotes, Eubacteria and Archaea, but does not include housekeeping transcripts or microRNAs and snoRNAs for which more specialized databases are available. The contents of the database can be accessed via the WWW at http://biobases.ibch.poznan.pl/ncRNA/.
Parathyroid Hormone-Receptor Interactions Identified Directly by Photocross-linking and Molecular Modeling Studies (1998)

Direct mapping of the interface between parathyroid hormone (PTH) and its receptor (hPTH1-Rc) was carried out by photoaffinity scanning studies. Photoreactive analogs of PTH singularly substituted with a p-benzoylphenylalanine (Bpa) at each of the first six N-terminal positions have been prepared. Among these, the analog [Bpa1,Nle8,18,Arg13,26,27,L-2-Nal23,Tyr34]bPTH-(1-34)N H2 (Bpa1-PTH-(1-34)) displayed in vitro activity with potency similar to that of PTH-(1-34). The radioiodinated analog 125I-Bpa1-PTH-(1-34) cross-linked specifically to the hPTH1-Rc stably expressed in human embryonic kidney cells. A series of chemical and enzymatic digestions of the hPTH1-Rc-125I-Bpa1-PTH-(1-34) conjugate suggested that a methionine residue (either Met414 or Met425) within the contact domain hPTH1-Rc-(409-437), which includes the transmembrane helix 6 and part of the third extracellular loop, as the putative contact point. Site-directed mutagenesis (M414L or M425L) identified Met425 as the putative contact point. Molecular modeling of the hPTH1-Rc together with the NMR-derived high resolution structure of hPTH-(1-34), guided by the cross-linking data, strongly supports Met425, at the extracellular end of transmembrane helix 6, as the residue interacting with the N-terminal residue of the hPTH-(1-34). The photocross-linking and molecular modeling studies provide insight into the topologic arrangement of the receptor-ligand complex.
Automatic fault detection and diagnosis for photovoltaic systems using combined artificial neural network and analytical based methods (2015)

Long term exposure of photovoltaic (PV) systems under relatively harsh and changing environmental conditions can result in fault conditions developing during the operational lifetime. The present solution is for system operators to manually perform condition monitoring of the PV system. However, it is time-consuming, inaccurate and dangerous. Thus, automatic fault detection and diagnosis is a critical task to ensure the reliability and safety in PV systems. The current state-of-the-art techniques either cannot provide enough detailed fault information with high accuracy or have too much complexity. This work presents an automatic fault detection and diagnosis method for string based PV systems. It combines an artificial neural network (ANN) with the conventional analytical method to conduct the fault detection and diagnosis tasks. A two-layered ANN is applied to predict the expected power which is then compared with the measured power from the real PV system. Based on the difference between the ANN estimated power and the measured power, the open circuit voltage and short circuit current of the PV string determined using analytical equations are used to identify any of the six defined fault types. The proposed method has a fast detection, compact structure and good accuracy. Simulation results show the effective fault detection and diagnosis capability of the proposed method.
IgE Antibody Responses against Japanese Cedar Pollen in the Mouse (1986)

IgE antibody responses against Japanese cedar pollen in the mouse were investigated to develop a mouse model of human allergy for combinations of factors including pollen administration routes, elicitation antigens and inbred mouse strains. Daily short term inhalation of native pollen or intratracheal administration of pollen suspended in saline induced IgE antibody responses in DBA/2, BDF1 and Balb/c mice, but failed to induce any detectable responses in C57BL/6 and C57BL/10 mice. Intraperitoneal injection of pollen suspension also induced IgE antibody responses in DBA/2, BDF1 and Balb/c mice but not in C57BL/6 mice. IgE antibody responses against pollen described above were detected by passive cutaneous anaphylaxis (PCA) reactions using crude extract of pollen as an elicitation antigen. On the other hand, IgE antibodies specific for antigen Sugi basic protein (AgSBP), which is a major allergen of pollen in humans (Yasueda, H., Yui, Shimizu, T., and Shida, T., 1983. Isolation and partial characterization of the major allergen from Japanese cedar (Cryptomeria japonica) pollen. J. Allergy Clin. Immunol. 71: 77-86), were also detected by PCA reactions using AgSBP in the sera from mice which received secondary or the tertiary stimulation by pollen. These results suggest that IgE antibody responses against Japanese cedar pollen in the mouse can be induced by airway sensitization and that the responses are genetically controlled by H-2-linked immune response genes. The results also suggest that not only IgE antibody responses specific for components other than AgSBP but also responses specific for AgSBP can be induced in the mouse by repeating appropriate sensitization by pollen.
Acetaminophen (paracetamol) hepatotoxicity with regular intake of alcohol: Analysis of instances of therapeutic misadventure (1995)

Hepatic injury in alcoholics due to intake of acetaminophen (APAP or acetylparaaminophenol) with therapeutic intent has been reported, but the extent of the phenomenon is not clear, pertinent details of the association remain insufficiently clarified, and the importance of the phenomenon is not widely appreciated. The present report describes 67 patients who developed hepatic injury after ingestion of APAP with therapeutic intent. All were regular users of alcohol. Sixty-four percent of the patients were considered to be "alcoholic" or reported intakes greater than 80 g/d, 35% took 60 g/d or less, and the remainder were vague in their reporting. Doses of APAP were in the "nontoxic" range ( < 6 g/d) in 60% of the group, within the recommended range ( < 4 g/d) in 40%, and at 4.1 to 6 g/d in 20%. Characteristic feature was the towering level reached by aspartate transaminase (AST) with figures ranging from 3,000 to 48,000 IU in more than 90% of cases. Almost 20% of the patients died. The data on these patients were similar to 94 cases of injury from APAP taken with therapeutic intent reported in the literature. This study provides further evidence of hepatic injury in regular uses of alcohol, especially chronic alcoholics, who take APAP with therapeutic intent. Susceptibility is presumably caused by induction of cytochrome P-4502EI by ethanol and by depletion of glutathione (GSH) because of the effects of alcohol, the malnutrition often associated with alcoholism, and the depletion associated with chronic use of APAP and impaired glucuronidation caused by fasting perhaps as well. The syndrome of liver injury is distinctive, marked by uniquely elevated levels of AST, and poses a significant threat.(ABSTRACT TRUNCATED AT 250 WORDS)
Electrochemical oxidation of reduced nicotinamide adenine dinucleotide (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrochemical oxidation of reduced nicotinamide adenine dinucleotideW. J. Blaedel and Roger A. JenkinsCite this: Anal. Chem. 1975, 47, 8, 1337–1343Publication Date (Print):July 1, 1975Publication History Published online1 May 2002Published inissue 1 July 1975https://pubs.acs.org/doi/10.1021/ac60358a034https://doi.org/10.1021/ac60358a034research-articleACS PublicationsRequest reuse permissionsArticle Views813Altmetric-Citations254LEARN 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
Solid Phase Synthesis and Evaluation of Tyr-Tic-Phe-Phe(p-NHCOCH2Br) ([Phe(p-bromoacetamide)4]TIPP), a Potent Affinity Label for δ Opioid Receptors (2002)

Derivatives of the delta opioid receptor selective peptide Tyr-Tic-Phe-Phe-OH (TIPP) containing a p-bromoacetamide moiety on the phenyl ring of Phe(3) or Phe(4) were prepared by solid phase synthesis. [Phe(p-NHCOCH(2)Br)(4)]TIPP exhibited high affinity for cloned delta receptors (IC(50) = 5.4 nM), and incubation with only 2.5 nM resulted in 85% wash resistant inhibition of radioligand binding to delta receptors. Therefore, this peptide is a potent affinity label for further study of delta opioid receptors.
Mutations in cystathionine β‐synthase or methylenetetrahydrofolate reductase gene increase N ‐homocysteinylated protein levels in humans (2008)

Severely elevated plasma homocysteine (Hcy) levels observed in genetic disorders of Hcy metabolism are associated with pathologies in multiple organs and lead to premature death due to vascular complications. In addition to elevating plasma Hcy, mutations in cystathionine beta-synthase (CBS) or methylenetetrahydrofolate reductase (MTHFR) gene lead to markedly elevated levels of circulating Hcy-thiolactone. The thiooester chemistry of Hcy-thiolactone underlies its ability to form isopeptide bonds with protein lysine residues (N-Hcy-protein), which may impair or alter the protein's function. However, it was not known whether genetic deficiencies in Hcy metabolism affect N-Hcy-protein levels in humans. Here we show that plasma N-Hcy-protein levels are significantly elevated in CBS- and MTHFR-deficient patients. We also show that CBS-deficient patients have significantly elevated plasma levels of prothrombotic N-Hcy-fibrinogen. These results provide a possible explanation for increased atherothrombosis observed in CBS-deficient patients.
Developments of mucus penetrating nanoparticles (2015)

Mucus can effectively protect the exposed mucosal surfaces due to its adhesive and viscoelastic properties. Most foreign particulates are efficiently trapped in mucus layers via steric obstruction and adhesion. Trapped particles are typically removed from the mucosal tissue within seconds to a few hours depending on their location sites. This article focuses on describing the tenacious mucus barrier properties, the strategies to investigate the interaction of nanoparticles with the mucus as well as the novel developments of mucus penetrating nanoparticles.
Scalable culture and cryopreservation of human embryonic stem cells on microcarriers (2009)

As a result of their pluripotency and potential for unlimited self-renewal, human embryonic stem cells (hESCs) hold tremendous promise in regenerative medicine. An essential prerequisite for the widespread application of hESCs is the establishment of effective and efficient protocols for large-scale cell culture, storage, and distribution. At laboratory scales hESCs are cultured adherent to tissue culture plates; these culture techniques are labor-intensive and do not scale to high cell numbers. In an effort to facilitate larger scale hESC cultivation, we investigated the feasibility of culturing hESCs adherent to microcarriers. We modified the surface of Cytodex 3 microcarriers with either Matrigel or mouse embryonic fibroblasts (MEFs). hESC colonies were effectively expanded in a pluripotent, undifferentiated state on both Matrigel-coated microcarriers and microcarriers seeded with a MEF monolayer. While the hESC expansion rate on MEF-microcarriers was less than that on MEF-plates, the doubling time of hESCs on Matrigel-microcarriers was indistinguishable from that of hESCs expanded on Matrigel-coated tissue culture plates. Standard hESC cryopreservation methodologies are plagued by poor viability and high differentiation rates upon thawing. Here, we demonstrate that cryopreservation of hESCs adherent to microcarriers in cryovials provides a higher recovery of undifferentiated cells than cryopreservation of cells in suspension. Together, these results suggest that microcarrier-based stabilization and culture may facilitate hESC expansion and storage for research and therapeutic applications.
A carbon nanotube field emission cathode with high current density and long-term stability (2009)

Carbon nanotube (CNT) field emitters are now being evaluated for a wide range of vacuum electronic applications. However, problems including short lifetime at high current density, instability under high voltage, poor emission uniformity, and pixel-to-pixel inconsistency are still major obstacles for device applications. We developed an electrophoretic process to fabricate composite CNT films with controlled nanotube orientation and surface density, and enhanced adhesion. The cathodes have significantly enhanced macroscopic field emission current density and long-term stability under high operating voltages. The application of this CNT electron source for high-resolution x-ray imaging is demonstrated.
Combined adjuvants of poly(I:C) plus LAG‐3‐Ig improve antitumor effects of tumor‐specific T cells, preventing their exhaustion (2016)

Therapeutic cancer vaccines are designed to treat cancer by boosting the endogenous immune system to fight against the cancer. In the development of clinically effective cancer vaccines, one of the most practical objectives is to identify adjuvants that are capable of optimizing the vaccine effects. In this study, we explored the potential of polyinosinic-polycytidylic acid (poly(I:C)) and LAG-3-Ig (soluble recombinant protein of lymphocyte activation gene-3 [LAG-3] extracellular domain fused with human IgG Fc region) as adjuvants for P1A tumor antigen peptide vaccine in a pre-established P815 mouse tumor model with a transfer of tumor-specific T cells. Whereas the use of poly(I:C) or LAG-3-Ig as a signal adjuvant induced a slight enhancement of P1A vaccine effects compared to incomplete Freund's adjuvant, combined treatment with poly(I:C) plus LAG-3-Ig remarkably potentiated antitumor effects, leading to complete rejection of pre-established tumor and long-term survival of mice. The potent adjuvant effects of poly(I:C) plus LAG-3-Ig were associated with an enhanced infiltration of T cells in the tumor tissues, and an increased proliferation and Th1-type cytokine production of tumor-reactive T cells. Importantly, the combined adjuvant of poly(I:C) plus LAG-3-Ig downregulated expressions of PD-1, LAG-3, and TIGIT on P1A-specific T cells, indicating prevention of T cell exhaustion. Taken together, the results of the current study show that the combined adjuvants of poly(I:C) plus LAG-3-Ig with tumor peptide vaccine induce profound antitumor effects by activating tumor-specific T cells.
The localization of populations of lymphocytes defined by monoclonal antibodies in rat lymphoid tissues. (1981)

The localisation of subpopulations of T lymphocytes as defined by the monoclonal antibodies W3/25 and MRC OX 8 was determined by an indirect immunoperoxidase technique on cryostat sections of rat lymphoid tissues. Both subpopulations were present throughout T-dependent areas with only scattered T cells, largely W3/25 positive, in the B areas. The W3/25 antigen was also found on macrophages in the medulla of lymph nodes and in the peritoneal cavity and liver.
Vasoprotective effects of resveratrol and SIRT1: attenuation of cigarette smoke-induced oxidative stress and proinflammatory phenotypic alterations (2008)

The dietary polyphenolic compound resveratrol, by activating the protein deacetylase enzyme silent information regulator 2/sirtuin 1 (SIRT1), prolongs life span in evolutionarily distant organisms and may mimic the cytoprotective effects of dietary restriction. The present study was designed to elucidate the effects of resveratrol on cigarette smoke-induced vascular oxidative stress and inflammation, which is a clinically highly relevant model of accelerated vascular aging. Cigarette smoke exposure of rats impaired the acetylcholine-induced relaxation of carotid arteries, which could be prevented by resveratrol treatment. Smoking and in vitro treatment with cigarette smoke extract (CSE) increased reactive oxygen species production in rat arteries and cultured coronary arterial endothelial cells (CAECs), respectively, which was attenuated by resveratrol treatment. The smoking-induced upregulation of inflammatory markers (ICAM-1, inducible nitric oxide synthase, IL-6, and TNF-alpha) in rat arteries was also abrogated by resveratrol treatment. Resveratrol also inhibited CSE-induced NF-kappaB activation and inflammatory gene expression in CAECs. In CAECs, the aforementioned protective effects of resveratrol were abolished by knockdown of SIRT1, whereas the overexpression of SIRT1 mimicked the effects of resveratrol. Resveratrol treatment of rats protected aortic endothelial cells against cigarette smoking-induced apoptotic cell death. Resveratrol also exerted antiapoptotic effects in CSE-treated CAECs, which could be abrogated by knockdown of SIRT1. Resveratrol treatment also attenuated CSE-induced DNA damage in CAECs (comet assay). Thus resveratrol and SIRT1 exert antioxidant, anti-inflammatory, and antiapoptotic effects, which protect the endothelial cells against the adverse effects of cigarette smoking-induced oxidative stress. The vasoprotective effects of resveratrol will likely contribute to its antiaging action in mammals and may be especially beneficial in pathophysiological conditions associated with accelerated vascular aging.