gebhart/patrepeval huggingface dataset:
SPR Studies of the Nonspecific Adsorption Kinetics of Human IgG and BSA on Gold Surfaces Modified by Self-Assembled Monolayers (SAMs) (1997)

The nonspecific binding of human immunoglobulin G (hIgG) and bovine serum albumin (BSA) was studied on gold surfaces modified by self-assembled alkyl thiol monolayers (SAMs) with the following terminal groups: CH3, C6H4OH, COO-, NH2, OH, and oligoethylene oxide (OEO). The kinetics of hIgG and BSA adsorption and desorption were monitored in real time utilizing the surface plasmon resonance (SPR) technique with a flow cell. The surface concentration of hIgG molecules adsorbed on the SAMs decreased in the order: CH3 > C6H5OH > COO- > NH2 > OH > OEO SAM surfaces. Binding of BSA to the SAM surfaces decreased in the order: C6H5OH > CH3 > COO- > NH2 > OH > OEO. The results show that on the OEO SAM, the surface concentration of these proteins was less than 0.5 ng/cm2 (the detection limit of our SPR device) and approximately 10(3) times less than that on the hydrophobic CH3-terminated SAM surfaces. The kinetics of the binding curves for the adsorption of the proteins are described in terms of multiple states of adsorbed proteins that involve multipoint hydrophobic, electrostatic, and hydrogen bond interactions for the different surfaces and protein lateral interactions caused by the unfolding of adsorbed proteins.
Protective human hybridoma antibody to tetanus toxin. (1982)

Postimmunization human B lymphocytes and mouse myeloma cells were fused to produce interspecies hybridomas secreting human antibody of predefined specificity with an initial frequency comparable to intraspecies fusion. After 13 mo in culture, one clone continued to secrete high titers of human IgG antitetanus toxin antibody. This antibody binds to the B fragment of tetanus toxin and protects mice against tetanus. The demonstration of in vivo protection with a human monoclonal antibody is an important first step towards the ultimate goal of human administration of monoclonal antibodies for the prevention and therapy of human infections.
Eye development: a view from the retina pigmented epithelium (2004)

The retina pigment epithelium (RPE) is a highly specialised epithelium that serves as a multifunctional and indispensable component of the vertebrate eye. Although a great deal of attention has been paid to its transdifferentiation capabilities and its ancillary functions in neural retina development, little is known about the molecular mechanisms that specify the RPE itself. Recent advances in our understanding of the genetic network that controls the progressive specification of the eye anlage in vertebrates have provided some of the initial cues to the mechanisms responsible for RPE patterning. Here, we have outlined many recent findings that suggest that a limited number of transcription factors, including Otx2, Mitf and Pax6 and a few signalling cascades, are the elements required for the onset of RPE specification in vertebrates. Furthermore, using this information and the data available on the specification of the pigmented cells of primitive chordates, we have ventured some hypotheses on the origin of RPE cells during evolution.
Comparison of three weaning ages on cow-calf performance and steer carcass traits. (1999)

An experiment was conducted to compare three weaning ages on cow-calf performance and steer carcass traits. Crossbred steers (n = 168; 1/2 Simmental x 1/4 Angus x 1/4 Hereford) were randomly assigned to three treatments with eight pens per treatment: groups were 1) weaned at an average of 90 d of age (90 +/- 13 d) and placed in the feedlot, 2) weaned at an average of 152 d of age (152 +/- 13 d) and placed in the feedlot, and 3) weaned at an average of 215 d of age (215 +/- 13 d) and placed in the feedlot. The number of days steers were finished decreased by 55 and 38 d (linear, P = .0001) as weaning age increased when slaughtered at a constant fat end point (.81 cm). Weaning at an average of 90 and 152 d of age improved overall ADG by .15 and .07 kg/d, respectively, over weaning at an average of 215 d of age (linear, P = .005). Over the entire finishing period, intake increased (linear, P = .0006) and efficiency was poorer (linear, P = .004) as weaning age increased. Owing to differences in finishing days and intake, total concentrate consumed increased (linear, P = .03) as weaning age decreased. No differences (P > .21) were observed for carcass weight, longissimus muscle area, or yield grade. No differences (P > .19) were observed in marbling score or percentage of steers grading greater than or equal to Choice or Average Choice. Cow body condition score improved (linear, P = .0001) as weaning age decreased. Pregnancy rate improved 12 percentage units (linear, P = .15) for cows on the 90-d weaning treatment. In this study, early weaning improved gain and feed efficiency, but it increased total concentrate consumed.
Molecular-specific chromatographic detector using modified SERS substrates (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular-specific chromatographic detector using modified SERS substratesKeith T. Carron and Brian J. KennedyCite this: Anal. Chem. 1995, 67, 18, 3353–3356Publication Date (Print):September 15, 1995Publication History Published online1 May 2002Published inissue 15 September 1995https://pubs.acs.org/doi/10.1021/ac00114a036https://doi.org/10.1021/ac00114a036research-articleACS PublicationsRequest reuse permissionsArticle Views602Altmetric-Citations68LEARN 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
Analysis of embryonic motoneuron gene regulation: derepression of general activators function in concert with enhancer factors (2004)

The underlying transcriptional mechanisms that establish the proper spatial and temporal pattern of gene expression required for specifying neuronal fate are poorly defined. We have characterized how the Hb9 gene is expressed in developing motoneurons in order to understand how transcription is directed to specific cells within the developing CNS. We found that non-specific general-activator proteins such as E2F and Sp1 are capable of driving widespread low level transcription of Hb9 in many cell types throughout the neural tube; however, their activity is modulated by specific repressor and activator complexes. The general-activators of Hb9 are suppressed from triggering inappropriate transcription by repressor proteins Irx3 and Nkx2.2. High level motoneuron expression is achieved by assembling an enhancesome on a compact evolutionarily-conserved segment of Hb9 located from -7096 to -6896. The ensemble of LIM-HD and bHLH proteins that interact with this enhancer change as motoneuron development progresses, facilitating both the activation and maintenance of Hb9 expression in developing and mature motoneurons. These findings provide direct support for the derepression model of gene regulation and cell fate specification in the neural tube, as well as establishing a role for enhancers in targeting gene expression to a single neuronal subtype in the spinal cord.
Neuronal LR11/sorLA expression is reduced in mild cognitive impairment (2007)

Neuronal LR11 levels are reduced in prodomal AD. The correlation between LR11 expression and cognitive performance indicates that reduced LR11 levels reflect disease severity and may predict progression to AD in a subgroup of individuals with MCI.
Low-threshold nine-channel waveguide grating router-based continuous wave transmitter (1999)

This paper demonstrates a nine-channel waveguide grating router-based laser with low (18-22 mA) thresholds, which we believe to be a record for a monolithically integrated multiwavelength laser with a 1.1-cm long cavity and a single nondistributed amplifier. This result was achieved through a combination of techniques including reduced intracavity loss, improved router design and optimal active/passive transitions.
Identification of a GA-rich Sequence as a Protein-binding Site in the 3′-Untranslated Region of Chicken Elastin mRNA with a Potential Role in the Developmental Regulation of Elastin mRNA Stability (2000)

Synthesis of aortic elastin peaks in the perinatal period and then is strongly down-regulated with postnatal development and growth. Decreased stability of elastin mRNA contributes to this developmental decrease in chick aortic elastin production. We have previously shown that destabilization of elastin mRNA is correlated with decreased binding of cytosolic protein(s) to a large, GC-rich region of secondary structure in the 3'-untranslated region (3'-UTR) of elastin mRNA. In this study, using gel migration shift assays, deletion constructs, and antisense competition assays, we identify a major protein-binding site in the 3'-UTR of elastin as a GA-rich sequence (UGGGGGGAGGGAGGGAGGGA), which we have designated the G3A motif. This motif is present in the 3'-UTR of elastin from several species. Binding proteins are present in both nuclear and cytoplasmic extracts, and their abundance is associated with tissues producing elastin and correlated with circumstances in which elastin mRNA is stable. These results suggest that the conserved GA-rich sequence of the elastin 3'-UTR is an important element in the regulation of stability of the elastin mRNA.
Bootstrapping a multilingual part-of-speech tagger in one person-day (2002)

This paper presents a method for bootstrapping a fine-grained, broad-coverage part-of-speech (POS) tagger in a new language using only one person-day of data acquisition effort. It requires only three resources, which are currently readily available in 60-100 world languages: (1) an online or hard-copy pocket-sized bilingual dictionary, (2) a basic library reference grammar, and (3) access to an existing monolingual text corpus in the language. The algorithm begins by inducing initial lexical POS distributions from English translations in a bilingual dictionary without POS tags. It handles irregular, regular and semi-regular morphology through a robust generative model using weighted Levenshtein alignments. Unsupervised induction of grammatical gender is performed via global modeling of context-window feature agreement. Using a combination of these and other evidence sources, interactive training of context and lexical prior models are accomplished for fine-grained POS tag spaces. Experiments show high accuracy, fine-grained tag resolution with minimal new human effort.
Evaluation of novel multi-beam antenna configurations for TDMA (IS-136) systems (2003)

For the IS-136 digital PCS standard, downlink performance can be improved via the use of multi-beam arrays to statistically reduce interference at the mobile handsets. Adopting this downlink approach, it is then desirable to use the same antenna configuration for uplink reception for cost and space considerations. However, this presents a potential problem due to the limited diversity gain available from beamforming arrays, and a careful choice of the antenna configuration must be considered. In this paper, we examine this issue of maintaining acceptable uplink performance while implementing multi-beam arrays in the downlink for the IS-136 system. Specifically, different multi-beam array and diversity antenna configurations are compared using bit error-rate (BER) performance which allows an appropriate selection of the antenna configuration.
Activation of Soluble Guanylate Cyclase Reverses Experimental Pulmonary Hypertension and Vascular Remodeling (2006)

Activation of sGC reverses hemodynamic and structural changes associated with monocrotaline- and chronic hypoxia-induced experimental pulmonary hypertension. This effect is partially dependent on endogenous nitric oxide generated by NOS3.
Vaccinia virus 19-kilodalton protein: relationship to several mammalian proteins, including two growth factors. (1984)

We observed two unusual patterns of cysteine and glycine residues in transforming growth factor type 1 (TGF1); our computer search found only one other protein, the 19-kilodalton early protein of vaccinia virus, having both patterns. The sequences of epidermal growth factor (EGF) and of the light chains from several components of the blood coagulation system also have one of the patterns, but gaps are required to adjust conserved cysteine and glycine residues in the second pattern. We used several computer analyses to confirm these relationships; the 19-kilodalton protein appears to be related to TGF1 and EGF to the same degree that they are related to each other; all three are more distantly related to the coagulation factors. An evolutionary scheme is presented for these proteins. We suggest that the conservation of cysteine residues, which form the disulfide bonds present in the active EGF molecule, may extend to conservation of disulfide bonds in these other proteins. We also suggest that the structural similarities may be correlated with a protein-binding capability.
Novel sphingolipid derivatives promote keratinocyte differentiation (2008)

Sphingolipids are important components of the water permeability barrier of the skin. Moreover, ceramides were also shown to influence keratinocyte differentiation and regulate cellular signalling. A confluence-induced differentiation model of normal human keratinocytes was established to allow evaluation of pro- and anti-differentiation effects of exogenous compounds. The effects of phytosphingosine (PS), sphingosine (SO), sphinganine (SA) and their hexanoyl (-C6), stearoyl (-C18) and salicyl (-SLC) derivatives, C12-alkylamine-salicylate (C12-SLC), salicylate (SLC) along with vitamin D3 (VD3) and retinol as control substances were tested in this system. Cytotoxicity assays were carried out to optimize the incubation conditions of compounds and whole genome expression changes were monitored by DNA-microarray on days 0, 1 and 4. Geometric means of gene expression levels of a subset of known keratinocyte differentiation-related genes were calculated from the microarray data to compare effects of the sphingolipid derivatives. Compound treatment-induced transcriptional changes were analysed by the ExPlain software (BIOBASE GmbH). Five of the assayed substances (SA, SO-C6, PS-C6, SO-SLC, PS-SLC) were found to be potent promoters of keratinocyte differentiation compared with VD3, and C12-SLC revealed potential anti-differentiation properties. ExPlain analysis found a different regulatory profile in the computed transcriptional networks of the sphingoid bases versus their -C6 and especially -SLC derivatives suggesting that the change in their keratinocyte differentiation modifying potential is due to a unique effect of the covalent attachment of the salicylic acid. Taken together, these results demonstrate the gene regulatory potential of sphingolipid species that could be valuable for dermatological or cosmetic applications.
Differentiation Between Pancreaticobiliary and Upper Gastrointestinal Adenocarcinomas (2007)

Metastatic adenocarcinoma of unknown primary site, eg, to lymph nodes, liver, or lung, may originate from many organs. Microscopic differentiation of adenocarcinomas from the pancreaticobiliary and upper gastrointestinal tracts may be difficult because of shared histologic and immunohistologic features. A high prevalence of cytokeratin (CK)17 expression in pancreaticobiliary adenocarcinoma was reported, and preliminary data indicate infrequent or missing expression in gastric adenocarcinoma. The prevalence of CK17 expression in gastric cardiac and esophageal adenocarcinomas has not been studied. We studied CK17 expression in tissue microarrays of 67 distal gastric, 71 gastric cardiac, and 46 esophageal adenocarcinomas and compared it with expression in 55 pancreatic, 23 extrahepatic bile duct, and 49 colorectal adenocarcinomas. CK17 expression was as follows: pancreatic, 88%; bile duct, 59%; esophageal, 30%; distal gastric, 28%; gastric cardiac, 27%; and colorectal adenocarcinoma, 6%. These differences were statistically significant for all tumor types except in comparisons of esophageal, cardiac, and distal gastric adenocarcinoma. The prevalence of CK17 expression in pancreatic and extrahepatic bile duct adenocarcinomas is substantially higher than in upper gastrointestinal tract and colorectal adenocarcinomas. However, in individual cases of adenocarcinoma of unknown primary site, CK17 results alone are insufficient to differentiate the analyzed tumor entities.
Cancer immunogenicity, danger signals, and DAMPs: What, when, and how? (2013)

Cancer immunosurvelliance usually leads to formation of cancer cells that have been "immunoedited" to resist anti-tumor immunity. One of the consequences of immunoediting that is, reduced immunogenicity, is an important roadblock in revival of stable and long-lasting anti-tumor immune responses. Research done during the last decade has shown that emission by the dying cancer cells of immunomodulatory factors or damage-associated molecular patterns (DAMPs), which can act as danger signals, is a critical event in accentuating the immunogenicity of cancer cells, in response to a subset of anticancer treatments. Recent evidence has defined that an apoptotic cell death subroutine and its underlying biochemistry, which has been termed as "immunogenic cell death (ICD)" or "immunogenic apoptosis," is required for the efficient emission of DAMPs and inciting anti-tumor immunity. Here, we review the basic concepts of ICD, like cancer immunogenicity, danger signals, and DAMPs. Moreover, we discuss the emerging molecular links between endoplasmic reticulum (ER) stress, induction of a viral response-like gene expression, danger signals, and anti-tumor immunity. We envisage that along with ER stress-based trafficking of DAMPs (which is a "short-range communicator" of danger), the accompanying induction of a viral response-like gene expression and the secretion of anti-tumorigenic cytokines may become a crucial signature of ICD induction by anticancer therapy.
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes (2008)

Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a key role in the emerging field, synthetic biology. Five years after we constructed DEG, a database of essential genes, DEG 5.0 has significant advances over the 2004 version in both the number of essential genes and the number of organisms in which these genes are determined. The number of prokaryotic essential genes in DEG has increased about 10-fold, mainly owing to genome-wide gene essentiality screens performed in a wide range of bacteria. The number of eukaryotic essential genes has increased more than 5-fold, because DEG 1.0 only had yeast ones, but DEG 5.0 also has those in humans, mice, worms, fruit flies, zebrafish and the plant Arabidopsis thaliana. These updates not only represent significant advances of DEG, but also represent the rapid progress of the essential-gene field. DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org.
A phase 2a randomized, double-blind, placebo-controlled, sequential dose-escalation study to evaluate the efficacy and safety of ASP015K, a novel Janus kinase inhibitor, in patients with moderate-to-severe psoriasis (2015)

In patients with moderate-to-severe psoriasis, ASP015K demonstrated dose-dependent improvements in clinical and histological measures of severity over 6 weeks of treatment. At all doses, ASP015K was well tolerated, with no reported serious AEs.
Crystal Structure of Homo-DNA and Nature's Choice of Pentose over Hexose in the Genetic System (2006)

An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4' --> 6')-linked oligo(2',3'-dideoxy-beta-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4' --> 6') family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems.
A stable full-length yellow fever virus cDNA clone and the role of conserved RNA elements in flavivirus replication (2003)

Yellow fever virus (YF) is the prototype member of the Flavivirus genus. Here, we report the successful construction of a full-length infectious cDNA clone of the vaccine strain YF-17D. YF cDNA was cloned into a low-copy-number plasmid backbone and stably maintained in several E. coli strains. Transcribed RNAs had a specific infectivity of 10(5)-10(6) p.f.u. ( micro g RNA)(-1), and the resulting virus exhibited growth kinetics, plaque morphology and proteolytic processing similar to the parental virus in cell culture. This clone was used to analyse the importance of conserved flavivirus RNA sequences and the 3' stem-loop structure in virus replication. The conserved sequences 5'CS and CS1, as well as the 3' stem-loop structure, were found to be essential for virus replication in cell culture, whereas the conserved sequence CS2 and the region containing YF-specific repeated sequences were dispensable. This infectious clone will aid future studies on YF replication and pathogenesis, as well as facilitate the development of YF-17D-based recombinant vaccines.