gebhart/patrepeval huggingface dataset:
Expanding the Scope of Replicable Unnatural DNA: Stepwise Optimization of a Predominantly Hydrophobic Base Pair (2013)

As part of an ongoing effort to expand the genetic alphabet for in vitro and eventually in vivo applications, we have synthesized a wide variety of predominantly hydrophobic unnatural base pairs exemplified by d5SICS-dMMO2 and d5SICS-dNaM. When incorporated into DNA, the latter is replicated and transcribed with greater efficiency and fidelity than the former; however, previous optimization efforts identified the para and methoxy-distal meta positions of dMMO2 as particularly promising for further optimization. Here, we report the stepwise optimization of dMMO2 via the synthesis and evaluation of 18 novel para-derivatized analogs of dMMO2, followed by further derivatization and evaluation of the most promising analogs with meta substituents. Subject to size constraints, we find that para substituents can optimize replication via both steric and electronic effects and that meta methoxy groups are unfavorable, while fluoro substituents can be beneficial or deleterious depending on the para substituent. In addition, we find that improvements in the efficiency of unnatural triphosphate insertion translate most directly into higher fidelity replication. Importantly, we identify multiple, unique base pair derivatives that when incorporated into DNA are well replicated. The most promising, d5SICS-dFEMO, is replicated under some conditions with greater efficiency and fidelity than d5SICS-dNaM. These results clearly demonstrate the generality of hydrophobic forces for the control of base pairing within DNA, provide a wealth of new SAR data, and importantly identify multiple new candidates for eventual in vivo evaluation.
Synthetic β-(1→6)-Linked N-Acetylated and Nonacetylated Oligoglucosamines Used To Produce Conjugate Vaccines for Bacterial Pathogens (2009)

Vaccines for pathogens usually target strain-specific surface antigens or toxins, and rarely is there broad antigenic specificity extending across multiple species. Protective antibodies for bacteria are usually specific for surface or capsular antigens. beta-(1-->6)-Poly-N-acetyl-d-glucosamine (PNAG) is a surface polysaccharide produced by many pathogens, including Staphylococcus aureus, Escherichia coli, Yersinia pestis, Bordetella pertussis, Acinetobacter baumannii, and others. Protective antibodies to PNAG are elicited when a deacetylated glycoform (deacetylated PNAG [dPNAG]; <30% acetate) is used in conjugate vaccines, whereas highly acetylated PNAG does not induce such antibodies. Chemical derivation of dPNAG from native PNAG is imprecise, so we synthesized both beta-(1-->6)-d-glucosamine (GlcNH(2)) and beta-(1-->6)-d-N-acetylglucosamine (GlcNAc) oligosaccharides with linkers on the reducing termini that could be activated to produce sulfhydryl groups for conjugation to bromoacetyl groups introduced onto carrier proteins. Synthetic 5-mer GlcNH(2) (5GlcNH(2)) or 9GlcNH(2) conjugated to tetanus toxoid (TT) elicited mouse antibodies that mediated opsonic killing of multiple S. aureus strains, while the antibodies that were produced in response to 5GlcNAc- or 9GlcNAc-TT did not mediate opsonic killing. Rabbit antibodies to 9GlcNH(2)-TT bound to PNAG and dPNAG antigens, mediated killing of S. aureus and E. coli, and protected against S. aureus skin abscesses and lethal E. coli peritonitis. Chemical synthesis of a series of oligoglucosamine ligands with defined differences in N acetylation allowed us to identify a conjugate vaccine formulation that generated protective immune responses to two of the most challenging bacterial pathogens. This vaccine could potentially be used to engender protective immunity to the broad range of pathogens that produce surface PNAG.
Expression of MAGE Gene Family in Lung Cancers. (1996)

MAGE gene family encodes tumor-specific antigens recognized on HLA-A1 by cytotoxic T lymphocytes. We have investigated the mRNA expression of MAGE gene family in lung cancers using MAGE gene specific primers, reverse transcription-polymerase chain reaction (RT-PCR) and restriction enzyme analysis. MAGE-1, -3, -4, -41 or -6 gene was respectively expressed in 6, 5, 6, 7, and 4 of 53 lung cancer tissues (8 to 13%) or in 0, 6, 6, 7 or 8 of 14 lung cancer cell lines (0 to 53%). These results suggest that a substantial proportion of lung cancers express MAGE genes.
Polymerase Chain Reaction Detection and Clinical Significance of Varicella‐Zoster Virus in Cerebrospinal Fluid from Human Immunodeficiency Virus‐Infected Patients (1997)

Varicella-zoster virus (VZV) causes ocular and other central nervous system (CNS) disease in human immunodeficiency virus (HIV)-infected persons. To study the prevalence of CNS disease due to VZV, cerebrospinal fluid (CSF) specimens from 84 consecutive HIV-infected patients with new neurologic symptoms were tested for VZV DNA by a polymerase chain reaction (PCR) assay. Six patients were PCR-positive for VZV in CSF; 3 additional patients were subsequently identified who were not part of the serial population sample. Among these 9 patients, all had clinical presentations consistent with ocular and other CNS disease due to VZV; 4 were without zoster on presentation. Sustained improvement in association with antiviral therapy was observed in 3. Therefore, VZV DNA was detected in the CSF of 7% of HIV-infected patients presenting with neurologic symptoms; the diagnosis of VZV-related CNS disease was facilitated by this assay; improvement in association with antiviral therapy was observed in some patients.
Hemoglobin-fortified biscuits: bioavailability and its effect on iron nutriture in school children. (1990)

School-age children in Chile received 30 g of wheat-flour biscuits daily through a National School Lunch Program. To improve iron nutrition, these biscuits were fortified with 6% of a bovine hemoglobin concentrate. Hemoglobin iron bioavailability, measured with a double isotope technique, showed that heme-iron absorption in fortified biscuits was high (19.7%). In a pilot field trial, a cohort of 215 school-children received fortified biscuits (30 g) daily during two school periods, and their iron nutrition status was compared with that of children who received non-fortified biscuits (n = 212). Acceptability of both types of biscuits was excellent. Initially, both groups had comparably good iron nutrition. The fortified children presented higher mean ferritin values at the end of the first and second school periods. Good iron stores (serum ferritin greater than or equal to 20 micrograms/lt) were present in 92% and 79% of the fortified and control subjects, respectively (P less than 0.004). The high-iron bioavailability, the good organoleptic characteristics and the biological effect on iron nutriture make this product an appealing alternative to combat iron deficiency.
Experimental investigation of hotspot removal using superlattice cooler (2010)

Thermal management of high performance microprocessors is becoming increasingly challenging due to the presence of hotspots. Temperature at the hotspot can be substantially greater than rest of the microprocessor, potentially compromising performance and reliability. In this paper, we have presented a hybrid cooling scheme which combines microfluidic and solidstate cooling techniques. Localized hotspot with heat flux close to 250 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> has been successfully removed using this hybrid scheme. The effect of ambient temperature, hotspot size, and superlattice cooler electrode location is also studied.
A 30% efficient (>250 Watt) module using multijunction solar cells and their one-year on-sun field performance (2007)

Concentrator systems are emerging as a low-cost, high-volume option for solar-generated electricity due to the very high utilization of the solar cell, leading to a much lower $/Watt cost of a photovoltaic system. Parallel to this is the onset of alternative solar cell technologies, such as the very high efficiency multi-junction solar cells developed at NREL and Spectrolab over the last two decades. The relatively high cost of these types of solar cells has relegated their use to non-terrestrial applications. However, recent advancements in both multi-junction concentrator cell efficiency and their stability under high flux densities has made their large-scale terrestrial deployment significantly more viable. Amonix has designed, developed and fabricated modules using the high efficiency multi-junction cells from Spectrolab. One of these modules has been deployed at the University of Nevada, Las Vegas. The module has been in continuous operation beginning May 2006. The efficiency has been measured periodically and has shown a range from 26.1% to 28.5%. The latest measurement, made on February 20<sup>th</sup> showed an efficiency of 28.0 % at 956 DNI and an ambient temperature of 13 &deg;C. This excellent stability of the multi-junction module's performance promises to pave the way for future installations of this advanced technology. One short-term example of this is a new Amonix-designed module capable of 30% efficiency and 300 Watts per module. This module's performance, along with more testing of the long-term performance of the initial design will be presented at the time of the conference.
Chemical and Enzymatic Synthesis of DNA Fragments Containing 5-(β-D-Glucopyranosyloxymethyl)-2′-deoxycytidine − a Modified Nucleoside in T4 Phage DNA (2001)

DNA fragments 23 and 25, containing 5-hydroxymethyl-2′-deoxycytidine (5-HMdC) and 5-(β-D-glucopyranosyloxymethyl)-2′-deoxycytidine (5-GlcMdC) units, respectively, were assembled by means of a solid support-assisted synthesis using phosphoramidite building blocks 4 and 5, respectively. In addition, 20-mer 23 was converted into fragment 26 by a glycosylation with uridine diphosphoglucose (UDPG), catalyzed by T4 β-glucosyltransferase (BGT).
Selective Inhibition of FLICE-like Inhibitory Protein (FLIP) Expression With Small Interfering RNA Oligonucleotides (siRNAs) Is Sufficient to Sensitize Tumor Cells for TRAIL-Induced Apoptosis (2002)

Inhibition of FLIP expression was sufficient to sensitize tumor cells for TRAIL-induced apoptosis. The combination of TRAIL and FLIP-targeting siRNA could therefore be a useful strategy to attack cancer cells, which are resistant to TRAIL alone.
ATP-Dependent Human Erythrocyte Glutathione-Conjugate Transporter. II. Functional Reconstitution of Transport Activity (1998)

Purified dinitrophenyl S-glutathione (DNP-SG) ATPase was reconstituted into artificial liposomes prepared from soybean asolectin. Electron micrography confirmed the formation of unilamellar vesicles with an average radius of 0.25 micron. Intravesicular volume estimated by incorporation of radiolabled inulin into the vesicles was found to be 19.7 +/- 1.3 microL/mL reconstitution solution. Accumulation of the glutathione-conjugate of CDNB, DNP-SG, and of doxorubicin (DOX) in the proteoliposomes was increased in the presence of ATP as compared to equimolar ADP or adenosine 5'-[beta,gamma-methylene]triphosphate tetralithium. ATP-dependent transmembrane movement of DOX and DNP-SG into DNP-SG ATPase-reconstituted vesicles was saturable with respect to time, sensitive to the osmolarity of the assay medium, and temperature dependent. The energy of activation was found to be 12 and 15 kcal/mol for DNP-SG and DOX, respectively. Optimal temperature for transport was 37 degrees C. Saturable transport was demonstrated for DNP-SG (Vmax of 433 +/- 20 nmol/min/mg of protein, KmATP = 2.4 +/- 0. 3 mM and KmDNP-SG = 36 +/- 5 microM) as well as DOX (Vmax = 194 +/- 19 nmol/min/mg of protein, KmATP = 2.5 +/- 0.6 mM and KmDOX = 2.4 +/- 0.7 microM). The kinetic data for both DNP-SG and DOX transport were consistent with a random bi-bi sequential reaction mechanism. DOX was found to be a competitive inhibitor of DNP-SG transport with Kis of 1.2 +/- 0.2 microM and DNP-SG was found to be a competitive inhibitor of DOX transport with Kis of 13.3 +/- 2.6 microM.
A survey of clearing techniques for 3D imaging of tissues with special reference to connective tissue (2016)

For 3-dimensional (3D) imaging of a tissue, 3 methodological steps are essential and their successful application depends on specific characteristics of the type of tissue. The steps are 1° clearing of the opaque tissue to render it transparent for microscopy, 2° fluorescence labeling of the tissues and 3° 3D imaging. In the past decades, new methodologies were introduced for the clearing steps with their specific advantages and disadvantages. Most clearing techniques have been applied to the central nervous system and other organs that contain relatively low amounts of connective tissue including extracellular matrix. However, tissues that contain large amounts of extracellular matrix such as dermis in skin or gingiva are difficult to clear. The present survey lists methodologies that are available for clearing of tissues for 3D imaging. We report here that the BABB method using a mixture of benzyl alcohol and benzyl benzoate and iDISCO using dibenzylether (DBE) are the most successful methods for clearing connective tissue-rich gingiva and dermis of skin for 3D histochemistry and imaging of fluorescence using light-sheet microscopy.
Elevated Circulating Levels of C-C Chemokines in Patients With Congestive Heart Failure (1998)

This first demonstration of increased circulating levels of C-C chemokines in CHF with particularly high levels in patients with severe disease may represent previously unrecognized pathogenic factors in CHF.
Particle beam induced reactions between peptides and liquid matrices (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTParticle beam induced reactions between peptides and liquid matricesChhabil. Dass and Dominic M. DesiderioCite this: Anal. Chem. 1988, 60, 24, 2723–2729Publication Date (Print):December 15, 1988Publication History Published online1 May 2002Published inissue 15 December 1988https://pubs.acs.org/doi/10.1021/ac00175a017https://doi.org/10.1021/ac00175a017research-articleACS PublicationsRequest reuse permissionsArticle Views24Altmetric-Citations19LEARN 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
Immune System Stimulation by Probiotics (1995)

The immune system consists of organs and several cell types. Antigen interaction with these cells induces a cellular immune response mediated by activated cells and a humoral immune response mediated by antibodies. The cellular interactions are enhanced by adhesion molecules, and the activated cells release different cytokines. These complex cellular interactions induce a systemic immune response. If the antigen penetrates by the oral route, a secretory immune response is obtained, which is mediated by secretory IgA. The determination of the number of T or B cells, the quantitative or qualitative measure of the cytokines, antibody levels, or the study of cellular function such as phagocytic activity is used to evaluate the state of the immune system. The effects of lactic acid bacteria on the systemic immune response and on the secretory immune system are described. Potential health benefits of lactic acid bacteria include protection against enteric infections, use as an oral adjuvant, the immunopotentiator in malnutrition, and the prevention of chemically induced tumors. The results showed that Lactobacillus casei could prevent enteric infections and stimulate secretory IgA in malnourished animals, but could produce bacteria translocation. Yogurt could inhibit the growth of intestinal carcinoma through increased activity of IgA, T cells, and macrophages.
Uterine Sensitization-Associated Gene-1: A Novel Gene Induced Within the Rat Endometrium at the Time of Uterine Receptivity/Sensitization for the Decidual Cell Reaction1 (2002)

For successful implantation, the embryo must develop to the blastocyst stage and the endometrium must attain a state that is receptive to the implanting blastocyst. In rodents, the timing, duration, and hormonal regulation of this receptive state has been well defined. However, the molecular cascade of events involved in the onset of the receptive phase remains unclear. In the present study, we sought to identify genes involved in the onset of the receptivity using the technique of suppressive subtraction hybridization. Herein we report the isolation, cloning, and characterization of a novel gene, uterine sensitization-associated gene-1 (UASG-1), that is preferentially expressed within the maximally sensitized/receptive rat endometrium. USAG-1 mRNA encodes a putative protein of 206 amino acids that contains a possible N-terminal secretion signal and a C-terminal cystine knotlike motif. Northern blot analysis revealed that induction of USAG-1 mRNA was restricted to the Day 5 pregnant or pseudopregnant uterus. In situ hybridization experiments demonstrated that this induction was restricted to the uterine glandular epithelial cells. Given the remarkably tight restriction of its expression, USAG-1 may be involved in the onset of endometrial receptivity for implantation/sensitization for the decidual cell reaction.
The XT-1 Vision Architecture (1996)

A mobile robot navigating in an unstructured environment faces many difficult problems for which vision may potentially offer useful solutions. The XT-1 (eXpectation based Template matching) architecture was developed in an attempt to address many of these problems with similar constructions. The current system handles such diverse problems as landmark and place recognition, the generation of orienting and anticipatory saccades, smooth pursuit, as well as visual servoing during locomotion.
Specific Antibodies to the External Vestibule of Voltage-gated Potassium Channels Block Current (1998)

Using delayed-rectifier potassium channels as examples, we have designed two specific blockers by generating specific antipeptide antibodies to epitopes in the external vestibules of two channel proteins, Kv1.2 and Kv3.1. These antibodies reduced whole-cell Kv1.2 or Kv3.1 currents in transfected cells and the effect was blocked by the corresponding peptide antigen, but not by control peptides. A control antibody had little effect on Kv1.2 currents and the Kv1.2 blocker antibody had limited effect on other related potassium currents. Furthermore, the Kv1.2 blocking antibody inhibited dendrotoxin binding to Kv1.2 channel proteins in transfected cells. Moreover, using the Kv1.2 blocker antibody, we determined the presence and relative contribution of endogenous Kv1.2 to the overall endogenous K+ currents in NG108 neuronal cells. This guided design of specific channel blockers will facilitate future physiological studies on ion channel functions.
Monoclonal antibody PAL-E specific for endothelium. (1985)

A monoclonal antibody, PAL-E, is described that is specific for endothelial cells. The monoclonal antibody, an IgG2a, markedly stains endothelium of capillaries, medium-sized and small veins, and venules in frozen sections of human and some animal tissues tested. It reacts not at all or only weakly with endothelium of large, medium-sized, and small arteries, arterioles, and large veins and does not stain the endothelial lining of lymphatic vessels and sinus histiocytes. The cellular staining pattern and tissue staining were different from those obtained with antifactor VIII R:AG antiserum and Ulex europaeus I lectin. Blocking experiments indicated that these three reagents recognize different endothelial binding sites. Therefore, PAL-E is a new staining reagent for endothelium in frozen sections. Based on immunoelectronmicroscopic observations, the antigenic determinant recognized by PAL-E is associated with endothelial vesicles.
Functionalizing Liposomes with anti-CD44 Aptamer for Selective Targeting of Cancer Cells (2014)

CD44 receptor protein is found to be overexpressed by many tumors and is identified as one of the most common cancer stem cell surface markers including tumors affecting colon, breast, pancreas, and head and neck, making this an attractive receptor for therapeutic targeting. In this study, 2'-F-pyrimidine-containing RNA aptamer (Apt1), previously selected against CD44, was successfully conjugated to the surface of PEGylated liposomes using the thiol-maleimide click reaction. The conjugation of Apt1 to the surface of liposomes was confirmed by the change in size and zeta potential and by migration on agarose gel electrophoresis. The binding affinity of Apt1 was improved after conjugation compared to free-Apt1. The cellular uptake for Apt1-Lip was tested by flow cytometry and confocal imaging using the two CD44(+) cell lines, human lung cancer cells (A549) and human breast cancer cells (MDA-MB-231), and the CD44(-) cell line, mouse embryonic fibroblast cells (NIH/3T3). The results showed higher sensitivity and selectivity for Apt1-Lip compared to the blank liposomes (Mal-Lip). In conclusion, we demonstrate a successful conjugation of anti-CD44 aptamer to the surface of liposome and binding preference of Apt1-Lip to CD44-expressing cancer cells and conclude to a promising potency of Apt1-Lip as a specific drug delivery system.
Signal transduction during apoptosis implications for cancer therapy (1998)

Programmed cell death is a fundamental aspect of organismal development and stasis through its role in the maintenance of the balance between cell growth and cell death. If the balance is tipped, e.g. by unregulated cell growth, the result can be cancer. If tipped the other direction, e.g. by dysregulated cell death, and the result can again be cancer. The concept of dysregulated cell death, which until recently was not considered by oncologists, has forced a shift in the paradigm of cancer development. Along with this shift in thinking comes the likelihood that radiation and chemotherapy, both major modalities of cancer therapy, can benefit from strategies that modulate programmed cell death. One form of programmed cell death that is distinguished by its morphological features is called apoptosis. This form of programmed cell death is an energy dependent biochemically regulated process that is contingent upon a set of factors: the initial stimulatory event or in some cases a cellular insult, the organism, the cell type, the cellular environment, and other factors. This biochemical process is the result of the expression of a number of genes. In this review, the roles of several genes and gene families considered to be critical to the signal transduction cascade of apoptosis are described. Growth factors and cytokines are also discussed in the context of their interaction with these genes. We also discuss how these genes and their protein products are being used as prognostic indicators for cancer and cancer therapy and/or how they are the focus of strategies that either cause apoptosis or alter a cancer cell's propensity to initiate apoptosis when insulted by chemotherapy agents or radiation in the course of cancer therapy.