gebhart/patrepeval huggingface dataset:
Scanning mutagenesis of interleukin-8 identifies a cluster of residues required for receptor binding. (1991)

In order to identify residues required for the binding of interleukin-8 (IL-8) to its receptor, mutants were constructed in which clusters of charged amino acids were systematically replaced with alanine along the entire IL-8 sequence. The mutants were tested for their ability to induce a receptor-mediated rise in cytosolic free Ca2+, a property of wild-type IL-8 which can readily be detected by flow cytometry using neutrophils loaded with the calcium probe Indo-1. Eleven of the 12 mutants caused neutrophil calcium mobilization at 5 nM; the exception being a triple alanine mutant at positions K3, E4, and R6, which was inactive at all concentrations tested (150 nM maximum). A second set of mutants was generated in which residues 1-15 were individually mutated to alanine. Mutants E4A, L5A, or R6A were all inactive in the Ca2+ assay at 5 nM and competed poorly with 125I-IL-8 for neutrophil receptor binding; I10A, E4A, L5A, and R6A had approximately 30-, 100-, 100-, and 1000-fold reduced affinity, as compared with control IL-8, respectively. The nuclear magnetic resonance structure of IL-8 indicates that, in solution, the side chains of E4, L5, R6, and I10 point away from the core of the protein and do not participate in any intramolecular hydrogen bonds or salt bridges (Clore, G. M., and Gronenborn, A. M. (1991) J. Mol. Biol. 217, 611-620).
Prevention of type 1 diabetes mellitus using a novel vaccine (2010)

Type 1 diabetes mellitus (T1DM) affects 1 in 300 people and the incidence of the disease is rising worldwide. T1DM is caused by chronic autoimmune destruction of the insulin-producing β-cells. The exact etiology and primary auto-antigen are not yet known. The autoimmune, chronic, and progressive nature of the disease raises the possibility of intervention, preferably by slowing down or stopping the destruction of the β-cells as early as the prediabetic stage. Since the 1980s, several attempts have been made to maintain β-cell function using immunosuppressive agents, immune modulation such as plasmapheresis, cytokine therapy, or antibody treatment. These agents were not diabetes specific; the occasionally observed beneficial effect did not compensate for the often very severe side effects. According to the latest assumption, the administration of diabetes-specific auto-antigens can elicit tolerance, which can prevent the destruction of the β-cells, hopefully without serious side effects. The authors summarize current understanding of the immunology of T1DM, review the trials on prevention, and discuss their vaccination study.
Wave optics theory and 3-D deconvolution for the light field microscope (2013)

Light field microscopy is a new technique for high-speed volumetric imaging of weakly scattering or fluorescent specimens. It employs an array of microlenses to trade off spatial resolution against angular resolution, thereby allowing a 4-D light field to be captured using a single photographic exposure without the need for scanning. The recorded light field can then be used to computationally reconstruct a full volume. In this paper, we present an optical model for light field microscopy based on wave optics, instead of previously reported ray optics models. We also present a 3-D deconvolution method for light field microscopy that is able to reconstruct volumes at higher spatial resolution, and with better optical sectioning, than previously reported. To accomplish this, we take advantage of the dense spatio-angular sampling provided by a microlens array at axial positions away from the native object plane. This dense sampling permits us to decode aliasing present in the light field to reconstruct high-frequency information. We formulate our method as an inverse problem for reconstructing the 3-D volume, which we solve using a GPU-accelerated iterative algorithm. Theoretical limits on the depth-dependent lateral resolution of the reconstructed volumes are derived. We show that these limits are in good agreement with experimental results on a standard USAF 1951 resolution target. Finally, we present 3-D reconstructions of pollen grains that demonstrate the improvements in fidelity made possible by our method.
Continuous tone representation of three-dimensional objects taking account of shadows and interreflection (1985)

The effect of shadows and interreflection created by room obstructions is an important factor in the continuous tone representation of interiors. For indirect illumination, in most cases a uniform ambient light has been considered, even though the interreflection gives very complex effects with the shaded images.The proposed method for indirect lighting with shadows results in the following advanced points:1) The indirect illuminance caused by the surfaces of objects such as ceilings, floors, walls, desks, bookcases etc. gives added realism to images.2) The proposed method is suitable for every type of light source such as point sources, linear sources, and area sources.
ELISA Guidebook, The (2000)

John R. Crowther provides today's premier practical guide to the understanding and application of ELISA. Updating and greatly expanding his widely appreciated earlier publication, ELISA Theory and Pra
Modification of adriamycin cardiotoxicity by Damvar. (1979)

In experiments performed in mice, Adriamycin (15 mg/kg i. p.) produced serious damage of the heart muscle. Damvar (2 x 200 mg/kg orally) a new cytostatic drug combined with Adriamycin decreased conspicuously its cardiotoxicity.
[The role of tissue steroids in benign hyperplasia and prostate cancer]. (1987)

This paper presents a large body of data relating to benign prostatic hyperplasia, which have been derived from fundamental endocrinological research. For the urologist, the data open up interesting aspects of the pathomorphology of prostatic hyperplasia. The most interesting findings can be summed up as follows: 1. Testosterone is the circulating androgenic prohormone that mediates the intracellular message leading to androgen secretion, though by way of its metabolite dihydrotestosterone, which is really the active substance. 2. This metabolic conversion is catalyzed by 5 alpha-reductase, which is predominantly a stromal enzyme. 3. The estrogen metabolism in the stromal cells of the prostate may be associated with the abnormal growth of the prostate. 4. In the presence of benign prostatic hyperplasia dihydrotestosterone and 17 beta-estradiol accumulate in the nuclei of the stromal cells. 5. Adrenal androgens are also metabolized in the human prostate, yielding some substances with androgenic and some with estrogenic potency. 6. Changes in sex hormone binding globulins (SHBG) are found with age whether benign prostatic hyperplasia is present or not. It is therefore questionable whether it has any influence on the development of prostatic hyperplasia. 7. Although in some cases it is not yet possible to determine whether the findings presented in this paper have any causal significance, the data can be used as a rational basis for hormonal treatment of prostatic disease.
Nickel-catalyzed conjugate addition of zirconium alkenyls to .alpha.,.beta.-unsaturated ketones (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNickel-catalyzed conjugate addition of zirconium alkenyls to .alpha.,.beta.-unsaturated ketonesMelanie J. Loots and Jeffrey SchwartzCite this: J. Am. Chem. Soc. 1977, 99, 24, 8045–8046Publication Date (Print):November 1, 1977Publication History Published online1 May 2002Published inissue 1 November 1977https://pubs.acs.org/doi/10.1021/ja00466a044https://doi.org/10.1021/ja00466a044research-articleACS PublicationsRequest reuse permissionsArticle Views450Altmetric-Citations77LEARN 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
A Liquid-Handling Robot for Automated Attachment of Biomolecules to Microbeads (2015)

Diagnostics, drug delivery, and other biomedical industries rely on cross-linking ligands to microbead surfaces. Microbead functionalization requires multiple steps of liquid exchange, incubation, and mixing, which are laborious and time intensive. Although automated systems exist, they are expensive and cumbersome, limiting their routine use in biomedical laboratories. We present a small, bench-top robotic system that automates microparticle functionalization and streamlines sample preparation. The robot uses a programmable microcontroller to regulate liquid exchange, incubation, and mixing functions. Filters with a pore diameter smaller than the minimum bead diameter are used to prevent bead loss during liquid exchange. The robot uses three liquid reagents and processes up to 10(7) microbeads per batch. The effectiveness of microbead functionalization was compared with a manual covalent coupling process and evaluated via flow cytometry and fluorescent imaging. The mean percentages of successfully functionalized beads were 91% and 92% for the robot and manual methods, respectively, with less than 5% bead loss. Although the two methods share similar qualities, the automated approach required approximately 10 min of active labor, compared with 3 h for the manual approach. These results suggest that a low-cost, automated microbead functionalization system can streamline sample preparation with minimal operator intervention.
CD28 is required for germinal center formation (1996)

Previous studies have demonstrated that the T cell costimulatory molecule, CD28, is important in the development of humoral immunity. CD28-deficient mice exhibit defects in isotype switching and are more susceptible to pathogens that depend on an effective Ab response. To determine the basis of these defects, we have examined B cell responses of CD28-deficient mice at the microenvironmental level. Early in a normal T-dependent immune response, small numbers of B cells undergo activation in the T cell-rich zone of secondary lymphoid tissues and then migrate to B cell areas. These migrant B cells found developing germinal centers by proliferative expansion, during which individual cells acquire mutations in their rearranged Ig genes. B cell mutants retaining higher affinities for Ag undergo positive selection in germinal centers, resulting in the establishment of the memory B cell compartment. In the present study, we demonstrate that although potentially Ag-reactive cells within the lymphoid follicle accumulate following antigenic challenge, these cells fail to undergo proliferative expansion to form germinal centers and do not acquire somatic mutations in CD28-deficient animals. Thus, the CD28 activation pathway is required for Ab responses to T-dependent Ags. cell compartment. In the present study, we demonstrate that although potentially Ag-reactive cells within the lymphoid follicle accumulate following antigenic challenge, these cells fail to undergo proliferative expansion to form germinal centers and do not acquire somatic mutations in CD28-deficient animals. Thus, the CD28 activation pathway is required for Ab responses to T-dependent Ags.
Gender differences in glucoregulatory responses to intense exercise (2000)

We compared glucoregulatory responses to intense exercise (14 min at 88% maximum O(2) uptake) between genders (16 men, 12 women). Analysis of covariance of maximum O(2) uptake showed no gender effect, with 82% of variance due to fat-free mass (FFM). Glycemia rose comparably during exercise but was higher in women during recovery (P = 0.02). Glucose production [rate of appearance (R(a)); in mg/min] increased markedly in both; stepwise multiple regression and analysis of covariance of R(a) (peak and incremental area under the curve) showed no effect of gender, body weight, or FFM. Glucose uptake [rate of disappearance (R(d))] increased less than R(a) and slower in women. R(d) area under the curve related to FFM (P = 0.01) but not gender or body weight. Norepinephrine and epinephrine responses (13-18x baseline) were the same and correlated significantly with R(a). Exercise insulin and glucagon changes were slight, but postexercise hyperinsulinemia was greater in women (P = 0.018), along with higher R(d). Therefore, intense exercise glucoregulation is qualitatively similar between genders, with a "feed-forward" regulation of R(a) (consistent with catecholamine mediation). However, women have a lesser R(d) response, related to FFM. This combination leads to greater recovery-period hyperglycemia and hyperinsulinemia.
A mouse IgM allotypic determinant (Igh-6.5) recognized by a monoclonal rat antibody. (1981)

Two monoclonal rat anti-mouse IgM antibodies, Bet 1 and Bet 2, are described in this paper. Bet 1 defines a new allotypic determinant, Igh-6.5, expressed on IgM molecules in serum and on B lymphocytes, whereas Bet 2 recognizes a determinant on IgM molecules of all mouse strains tested. Both reagents bind to the IgM myeloma protein MOPC104E, but not to IgG myeloma proteins, including FLOPC21, MOPC21, and UPC10. Using serum from various mouse strains to inhibit the binding of Bet 1 to MOPC104E, 3 distinct inhibition patterns were found. BALB/c, DBA/2, and CBA sera inhibited strongly, C56BL/6 (B6), SJL, AKR, and NZB sera inhibited weakly, and A and AL sera showed no inhibition of binding of BET 1 to MOPC104E. All sera tested were equivalent in their inhibition of the binding of Bet 2 to MOPC104E. When spleen cells from different mouse strains were reacted with fluorescein-conjugated Bet 1 (F-Bet 1) and subjected to flow microfluorometry analysis, 3 types of staining patterns, corresponding to those obtained with the serum inhibition assay, were also found. The determinant recognized by Bet 1 is controlled by a gene linked to the Igh-C gene complex. C.AL20 behaved like AL, and C.B20 and BAB/14 behaved like B6, both in the serum inhibition assay and in flow microfluorometry analysis of spleen cells stained with F-Bet 1. In addition, the capacity of serum from individual (BALB/c X B6) X B6 backcross progeny to inhibit the binding of Bet 1 to MOPC104E was linked to the expression of the Ig-1a marker.
Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization (2014)

As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.
Achievable Throughput of MIMO Downlink Beamforming with Limited Channel Information (2007)

We consider a MIMO fading broadcast channel and study the achievable throughput of zero-forcing downlink beamforming when the channel state information (CSI) available to the transmitter and/or receivers is imperfect. Each receiver (mobile) acquires imperfect CSI via downlink training pilots, and the transmitter acquires CSI through explicit feedback from each mobile. We analyze both analog and digital (i.e., quantized) channel feedback techniques. Our analysis quantifies the throughput degradation due to limited training, limited feedback resources (measured in feedback channel symbols rather than bits), and errors on the feedback channel. Using these results we are able to quantify scenarios in which digital feedback outperforms analog and also provide guidelines for the optimal allocation of resources to training and channel feedback.
The Importance of Perceived Consumption Delay in Internet Shopping (2007)

This study examines the effect of delivery-time–related information (stock availability and shipping/handling cycle) on perceived consumption delay, perceived time risk, attitude toward the Web site, and online purchase intention. In addition, the authors examine the interrelationships among dependent variables using a causal model analysis. Participants (213 female undergraduates) evaluated a mock Web site under four treatment conditions. The findings indicate statistically significant main effects for time-related information on all four dependent variables and support the causal relationships among dependent variables. Based on the results, Internet apparel retailers may benefit from establishing a prompt restocking system to reduce the waiting time for apparel products and in turn, perceptions of consumption delay.
ChemInform Abstract: Microbial Transformation of Lanosterol Derivatives with Mycobacterium sp. (NRRL B‐3805). (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Sport and Nation Building: Gymnastics and Sport in the Ottoman State and the Committee of Union and Progress, 1908-18 (2003)

(2003). Sport and Nation Building: Gymnastics and Sport in the Ottoman State and the Committee of Union and Progress, 1908-18. The International Journal of the History of Sport: Vol. 20, No. 1, pp. 152-156.
Antisense oligonucleotide-mediated exon skipping as a strategy to reduce proteolytic cleavage of ataxin-3 (2016)

Spinocerebellar ataxia type-3 (SCA3) is a neurodegenerative disorder caused by a polyglutamine repeat expansion in the ataxin-3 protein. Cleavage of mutant ataxin-3 by proteolytic enzymes yields ataxin-3 fragments containing the polyglutamine stretch. These shorter ataxin-3 fragments are thought to be involved in SCA3 pathogenesis due to their increased cellular toxicity and their involvement in formation of the characteristic neuronal aggregates. As a strategy to prevent formation of toxic cleavage fragments, we investigated an antisense oligonucleotide-mediated modification of the ataxin-3 pre-mRNA through exon skipping of exon 8 and 9, resulting in the removal of a central 88 amino acid region of the ataxin-3 protein. This removed protein region contains several predicted cleavage sites and two ubiquitin-interacting motifs. In contrast to unmodified mutant ataxin-3, the internally truncated ataxin-3 protein did not give rise to potentially toxic cleavage fragments when incubated with caspases. In vitro experiments did not show cellular toxicity of the modified ataxin-3 protein. However, the modified protein was incapable of binding poly-ubiquitin chains, which may interfere with its normal deubiquitinating function. Low exon skipping efficiencies combined with reduction in important ataxin-3 protein functions suggest that skipping of exon 8 and 9 is not a viable therapeutic option for SCA3.
Alteration of fibrin network by activated protein C (1994)

The antithrombotic plasma enzyme, activated protein C (APC), may play a role in thrombolysis. In vitro, acceleration of clot lysis by APC depends on its ability to inhibit the activation of prothrombin. The effect of APC on the assembly and dispersion of fibrin network was studied using turbidimetry, plasmin digestion of fibrin, and electron microscopy of plasma clots. The addition of APC before clotting but not after clotting accelerated clot lysis. The rate of increase in the turbidity of clotting plasma was reduced by APC. The turbidity of plasma clots containing APC was directly related to the clot lysis time. Fibrin from plasma clots that were formed in the presence of APC yielded less fibrin degradation products than fibrin from clots without added APC. Furthermore, APC reduced the diameter and relative number of fibrin fibers in plasma clots during gel assembly. We propose that APC may enhance the efficacy of thrombolysis by reducing the relative mass of fibrin within maturing thrombi.
T cell recognition of nonpolymorphic determinants on H-2 class I molecules. (1988)

Recognition of polymorphic determinants on class I or class II MHC Ag is required for T lymphocyte responses. Using cell-size artificial membranes (pseudocytes) bearing H-2 class I Ag it is demonstrated that T cells can, in addition, recognize nonpolymorphic determinants on class I proteins. Pseudocytes bearing class I alloantigen stimulate in vitro generation of secondary allogeneic CTL responses. At a suboptimal alloantigen surface density, incorporation of class I molecules identical to those of the responder cells (self-H-2) or from third-party cells resulted in dramatically enhanced responses, whereas incorporation of class II proteins had no effect. The receptor that mediates recognition of conserved class I determinants has not been identified, but results of antibody blocking studies are consistent with the Lyt-2/3 complex of CTL having this role. Thus, class I proteins on Ag-bearing cells can have two distinct roles in T cell activation, one involving recognition of polymorphic determinants by the Ag-specific receptor and the other involving recognition of conserved determinants.
Antagonistic TNF Receptor One-Specific Antibody (ATROSAB): Receptor Binding and In Vitro Bioactivity (2013)

The data corroborate ATROSAB's unique function as a TNFR1-selective antagonist efficiently blocking both TNF and LTα action. In agreement with recent studies of TNFR1 complex formation and activation, we suggest a model of the underlying mechanism of TNFR1 inhibition by ATROSAB.
Synthesis of 4H‐furo[3,2‐b]indole derivatives. III. Preparation of 4H‐furo[3,2‐b]indole‐2‐carboxylic acid derivatives (1979)

Abstract Methyl or ethyl 4 H ‐furo[3,2‐ b ]indole‐2‐carboxylates (Va,b) were prepared from deoxygenation of methyl or ethyl 5‐(2‐nitrophenyl)‐2‐furoates (IIIa,b) and thermolysis of methyl or ethyl 5‐(2‐azidophenyl)‐2‐furoates (VIIIa,b). 4 H ‐Furo[3,2‐ b ]indole‐2‐carboxylic acid amides (XIa‐h) were obtained by the reaction of 4 H ‐furo[3,2‐ b ]indole‐2‐carboxyl chloride (X) with the appropriate amines.