gebhart/patrepeval huggingface dataset:
Identification of Novel Human WW Domain-containing Proteins by Cloning of Ligand Targets (1997)

A recently described protein module consisting of 35-40 semiconserved residues, termed the WW domain, has been identified in a number of diverse proteins including dystrophin and Yes-associated protein (YAP). Two putative ligands of YAP, termed WBP-1 and WBP-2, have been found previously to contain several short peptide regions consisting of PPPPY residues (PY motif) that mediate binding to the WW domain of YAP. Although the function(s) of the WW domain remain to be elucidated, these observations strongly support a role for the WW domain in protein-protein interactions. Here we report the isolation of three novel human cDNAs encoding a total of nine WW domains, using a newly developed approach termed COLT (cloning of ligand targets), in which the rapid cloning of modular protein domains is accomplished by screening cDNA expression libraries with specific peptide ligands. Two of the new genes identified appear to be members of a family of proteins, including Rsp5 and Nedd-4, which have ubiquitin-protein ligase activity. In addition, we demonstrate that peptides corresponding to PY and PY-like motifs present in several known signaling or regulatory proteins, including RasGAP, AP-2, p53BP-2 (p53-binding protein-2), interleukin-6 receptor-alpha, chloride channel CLCN5, and epithelial sodium channel ENaC, can selectively bind to certain of these novel WW domains.
Age and Sex Dependent Regulation of the Factor IX Gene in Mice (1996)

Plasma factor IX and liver factor IX mRNA levels in two normal mouse strains (B6D2F1 and BALB/CJNIA) were determined in relation to aging and sex of the animals. With male B6D2F1 mice, mean plasma factor IX activity levels for the 14 and 21 approximately 22 month-old animals were found to be 124% and 226%, respectively, of the 5 month-old group. Similarly, liver factor IX mRNA levels for the same age animal groups were 145% and 227%, respectively, of the reference group. Mean plasma factor IX levels for the same age female animals were 132% and 175%, respectively, and were accompanied by similarly elevated liver factor IX mRNA levels, 119 and 175%, respectively, of the 5 month-old female group. Factor IX activity and mRNA levels for the 5, 14 and 21 approximately 22 month-old female animal groups were lower than those of the corresponding male age groups by 25, 20 and 37%, and 20, 36 and 38%, respectively. With BALB/CJNIA mice, similar correlation was observed between the advancing age and substantial elevations in the factor IX mRNA level as well as on the unequal factor IX mRNA levels in females and males. These results indicate that the plasma factor IX level in both male and female mice is greatly elevated with aging, in general agreement with a similar phenomenon observed for human populations, and that this increase is due to a similar elevation in the factor IX mRNA level in the liver. In mice, both factor IX activity and mRNA levels are significantly higher in males than in females, which has not been described for humans.
Rizatriptan vs Sumatriptan in the Acute Treatment of Migraine (1996)

The antimigraine effect of 10- and 20-mg rizatriptan was superior to placebo, and comparable with that of 100-mg sumatriptan succinate; the efficacy of 40-mg rizatriptan was superior to that of both placebo and 100-mg sumatriptan succinate, although it was associated with a high frequency of adverse events.
Differential effects of interleukins 10 and 4 on the production of interleukin‐6 by blood and synovium monocytes in rheumatoid arthritis (1995)

The ability of IL-10 and IL-4 to suppress IL-6 production was dependent on 1) differences in the state of differentiation of blood and synovial tissue monocytes, and 2) local production of cytokine inside the synovium.
Pixelated phase computer holograms for the accurate encoding of scalar complex fields (2007)

We discuss a class of phase computer-generated holograms for the encoding of arbitrary scalar complex fields. We describe two holograms of this class that allow high quality reconstruction of the encoded field, even if they are implemented with a low-resolution pixelated phase modulator. In addition, we show that one of these holograms can be appropriately implemented with a phase modulator limited by a reduced phase depth.
Is the modulation of retinoid and retinoid‐associated signaling a future therapeutic strategy in neurological trauma and neurodegeneration? (2007)

The complex molecular pathways that mediate the effects of vitamin A and its derivatives, are increasingly recognized as a component of the repair capacity that could be activated to induce protection and regeneration in the mature nervous tissue. Retinoid and retinoid-associated signaling plays an essential role in normal neurodevelopment and appears to remain active in the adult CNS. In this paper, we review evidence which supports the hypothesis of an activation of retinoid-associated signaling molecular pathways in the mature nervous tissue and its significance in the context of neurodegenerative, trauma-induced and psychiatric disorders, at spinal and supra-spinal levels. Finally, we summarize the potential therapeutic avenues based on the modulation of retinoid targets undergoing reactivation under conditions of acute injury and chronic degeneration in the central nervous system, and discuss some of the unresolved issues linked to this treatment strategy.
Effects of proline mutations in the major house dust mite allergen Der f 2 on IgE‐binding and histamine‐releasing activity (2000)

Der f 2 is the major group 2 allergen from house dust mite Dermatophagoides farinae and is composed of 129 amino-acid residues. Wild-type and six proline mutants of Der f 2 (P26A, P34A, P66A, P79A, P95A, and P99A) expressed in Escherichia coli were refolded and purified. Formations of intramolecular disulfide bonds in the purified proteins were confirmed correct. The apparent molecular masses analyzed by gel-filtration were 14-15 kDa. The IgE-binding capacity in the sera of seven mite-allergic patients, inhibitory activity for IgE-binding to immobilized wild-type Der f 2, and activity to stimulate peripheral blood basophils to release histamine in two volunteers were analyzed. P95A and P99A, which slightly differed from the wild-type Der f 2 in their CD spectrum, showed reduced IgE-binding, reduced inhibitory activity, and less histamine-releasing activity than the wild-type. P34A also showed reduced allergenicity. Considering that Pro95, Pro99 and Pro34 are closely located in loops at one end of the tertiary structure of Der f 2, we concluded that these loop regions included an IgE-binding site common to all tested patients. P66A showed reduced IgE-binding in two sera out of seven. P26A and P79A showed no reduced allergenicity. However, in immunoblot analysis after SDS/PAGE under reduced conditions, P79A showed no or markedly reduced IgE-binding while the other mutants showed IgE-binding corresponding to that in the assay using correctly refolded proteins. This suggests that Pro79 is involved in refolding of Der f 2. The findings in this study are important for the understanding of the antigenic structure of mite group 2 allergens and for manipulation of the allergens for specific immunotherapy.
Methods for the quantitative estimation of N-acetylneuraminic acid and their application to hydrolysates of sialomucoids (1961)

The sialic acids They are readily obtained from these com- plexes by mild acid hydrolysis and more specifically by hydrolysis with neuraminidase, an enzyme found in many bacterial filtrates and the myxo group of viruses
Tumor Therapy by Immune Recruitment with Bispecific Antibodies (1995)

Many strategies for experimental immunotherapy of cancers aim at inducing and expanding tumor-specific cytotoxic T-lymphocytes. One of the most promising approaches uses bispecific monoclonal antibodies (Bi-MAbs) which are able to accumulate and activate human effector cells at the tumor site. Human resting peripheral NK- or T cells targeted by appropriate Bi-MAbs to tumor cells expressing a tumor-associated antigen display multiple signs of activation including proliferation, cytokine secretion, upregulation of cytotoxic peptides and enzymes and induce an efficient tumor cell lysis in vivo. Moreover, tumor-bearing SCID which were treated by effector cell-triggering Bi-MAbs and human peripheral blood lymphocytes had complete regressions of established tumors and most or all animals were cured by human NK-cell or T-cell cytotoxicity, respectively. Local tumor site-specific activation of T-cells was demonstrated, and enhanced granzyme and perforin expression together with the results of inhibition experiments suggest both mechanisms as the major contributors to the cytolytic machinery of Bi-MAb-mediated T-cell cytotoxicity in vivo. The encouraging results of this approach, which is able to cure animals with even advanced disseminated tumors, together with the local site-specific effector cell activation, which suggests minimal side effects, warrant the clinical evaluation of this Bi-MAb approach. As lymphocytes from tumor patients can be adequately activated by the respective Bi-MAbs, the clinical application of Bi-MAbs promises to become a safe, efficient and simple approach which should be readily applicable to the treatment of human malignancies that cannot be cured by standard regimens.
In the Midst of Multiplicity: How to Stay in the Saddle (2012)

The author asks the question, how is the human psyche impacted by the current rapid cultural change, globalization, etc., that is presently occurring in our world. She describes the relationship between the horse and the rider as an amplification of the relationship between the psyche and the ego in coping with change. How does one build a good relationship? In times of confusion and rapid change, the horse will likely panic and throw the rider if there is a poor relationship between them. She describes some of the clients in therapeutic riding centers, particularly the more vulnerable teenage clients, as being “unhorsed”—disconnected from their positive instincts—and how this form of therapy is particularly helpful because it reconnects them with their “inner horse.” She describes how she learned to develop a bonded relationship with her own horse and how that kind of relationship can operate within a context of the cutting horse competition.
Road signs recognition using a dynamic pixel aggregation technique in the HSV color space (2002)

We present a system for the whole road sign detection and recognition task. Road sign regions are detected and extracted from real-world scenes on the basis of their color and shape features. Color segmentation is performed introducing a dynamic threshold in the pixel aggregation process on the HSV color space. The dynamic threshold allows the reduction of hue instability in real scenes depending on external brightness variation. Experimental results, using real road images in different environment conditions, are also reported.
Evaluation of Flip-Flop Jet Nozzles for Use as Practical Excitation Devices (1994)

This paper describes the flowfield characteristics of the flip-flop jet nozzle and the potential for using this nozzle as a practical excitation device. It appears from the existing body of published information that there is a lack of data on the parameters affecting the operation of such nozzles and on the mechanism of operation of these nozzles. An attempt is made in the present work to study the important parameters affecting the operation and performance of a flip-flop jet nozzle. Measurements were carried out to systematically assess the effect of varying the nozzle pressure ratio (NPR) as well as the length and volume of the feedback tube on the frequency of oscillation of this device. Flow visualization was used to obtain a better understanding of the jet flowfield and of the processes occurring within the feedback tube. The frequency of oscillation of the flip-flop jet depended significantly on the feedback tube length and volume as well as on the nozzle pressure ratio. In contrast, the coherent velocity perturbation levels did not depend on the above-mentioned parameters. The data presented in this paper would be useful for modeling such flip-flop excitation devices that are potentially useful for controlling practical shear flows.
Not every polymorphism close to the AUG codon can be explained by invoking context effects on initiation of translation (2003)

The −1C>T change in the annexin V gene, which reduces the risk of myocardial infarction,[1][1] cannot be explained as simply as your editorial note suggests.[2][2]

The demonstration by Gonzalez-Conejero et al[1][1] that −1T increases the efficiency of translation might be correct (the fourth
Epoxidation of Oleic Acid, Methyl Oleate and Oleyl Alcohol with Perbenzoic Acid (1944)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEpoxidation of Oleic Acid, Methyl Oleate and Oleyl Alcohol with Perbenzoic AcidDaniel Swern, Thomas W. Findley, and John T. ScanlanCite this: J. Am. Chem. Soc. 1944, 66, 11, 1925–1927Publication Date (Print):November 1, 1944Publication History Published online1 May 2002Published inissue 1 November 1944https://pubs.acs.org/doi/10.1021/ja01239a038https://doi.org/10.1021/ja01239a038research-articleACS PublicationsRequest reuse permissionsArticle Views803Altmetric-Citations54LEARN 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
Location-aware event-based middleware: A paradigm for collaborative mobile applications? (2003)

Abstract—Existing research on event-based middleware for mobile computing has mainly focused on supporting nomadic applications using wireless data communication based on the infrastructure network model. Relatively little work has been done to accommodate collaborative applications that often use ad hoc networks. This paper describes a novel kind of event-based middleware, called STEAM, that has been designed for use in ad hoc networks. STEAM differs from other event-based middleware in that its architecture does not rely on the presence of any separate infrastructure and event notification filters may be used to define geographical areas within which event notifications are valid, thereby bounding the propagation of these notifications. Such proximity-based filtering represents a natural way to filter events of interest in collaborative mobile applications. I.
Antibiotics induce redox-related physiological alterations as part of their lethality (2014)

Deeper understanding of antibiotic-induced physiological responses is critical to identifying means for enhancing our current antibiotic arsenal. Bactericidal antibiotics with diverse targets have been hypothesized to kill bacteria, in part by inducing production of damaging reactive species. This notion has been supported by many groups but has been challenged recently. Here we robustly test the hypothesis using biochemical, enzymatic, and biophysical assays along with genetic and phenotypic experiments. We first used a novel intracellular H2O2 sensor, together with a chemically diverse panel of fluorescent dyes sensitive to an array of reactive species to demonstrate that antibiotics broadly induce redox stress. Subsequent gene-expression analyses reveal that complex antibiotic-induced oxidative stress responses are distinct from canonical responses generated by supraphysiological levels of H2O2. We next developed a method to quantify cellular respiration dynamically and found that bactericidal antibiotics elevate oxygen consumption, indicating significant alterations to bacterial redox physiology. We further show that overexpression of catalase or DNA mismatch repair enzyme, MutS, and antioxidant pretreatment limit antibiotic lethality, indicating that reactive oxygen species causatively contribute to antibiotic killing. Critically, the killing efficacy of antibiotics was diminished under strict anaerobic conditions but could be enhanced by exposure to molecular oxygen or by the addition of alternative electron acceptors, indicating that environmental factors play a role in killing cells physiologically primed for death. This work provides direct evidence that, downstream of their target-specific interactions, bactericidal antibiotics induce complex redox alterations that contribute to cellular damage and death, thus supporting an evolving, expanded model of antibiotic lethality.
Inhibition of Fatty Acid Synthase Induces Endoplasmic Reticulum Stress in Tumor Cells (2007)

Fatty acid synthase (FAS), the cellular enzyme that synthesizes palmitate, is expressed at high levels in tumor cells and is vital for their survival. Through the synthesis of palmitate, FAS primarily drives the synthesis of phospholipids in tumor cells. In this study, we tested the hypothesis that the FAS inhibitors induce endoplasmic reticulum (ER) stress in tumor cells. Treatment of tumor cells with FAS inhibitors induces robust PERK-dependent phosphorylation of the translation initiation factor eIF2alpha and concomitant inhibition of protein synthesis. PERK-deficient transformed mouse embryonic fibroblasts and HT-29 colon carcinoma cells that express a dominant negative PERK (DeltaC-PERK) are hypersensitive to FAS inhibitor-induced cell death. Pharmacologic inhibition of FAS also induces the processing of X-box binding protein-1, indicating that the IRE1 arm of the ER stress response is activated when FAS is inhibited. Induction of ER stress is further confirmed by the increased expression of the ER stress-regulated genes CHOP, ATF4, and GRP78. FAS inhibitor-induced ER stress is activated prior to the detection of caspase 3 and PARP cleavage, primary indicators of cell death, whereas orlistat-induced cell death is rescued by coincubation with the global translation inhibitor cycloheximide. Lastly, FAS inhibitors cooperate with the ER stress inducer thapsigargin to enhance tumor cell killing. These results provide the first evidence that FAS inhibitors induce ER stress and establish an important mechanistic link between FAS activity and ER function.
Soybean Oil (2005)

Abstract This chapter includes information on the composition of soybeans, soybean oil, and other soybean lipids, especially as affected by environment, variety, and genetic modification. Other topics discussed are the physical properties of soybean oil, grading of soybeans, oil extraction, and the effect of various extraction techniques on oil quality and the various soy protein ingredients. Basic refining and processing of soybean oil includes degumming, neutralization, bleaching, hydrogenation, and deodorization, but alternative refining methods are also discussed along with soybean refinery coproducts (lecithin, deodorizer distillate, and soapstock). The major uses of soybean oil are itemized and trading rules for crude and refined soybean oil are provided. The major food products produced from soybean oil are cooking and salad oils, frying fats, mayonnaise, margarine, shortening, confectionary and imitation dairy products, and “low‐calorie fat substitutes.” The oxidative quality of soybean oil is reviewed, including flavor reversion, factors affecting oil oxidation, measures of control and measures of finished oil quality, storage and handling, and special processing for off‐quality soybean oil. The chapter concludes with a discussion of the health aspects of soybean oil, including the health effects of cholesterol, unsaturated oils, trans ‐isomers, and total fat intake.
An Undetectable Computer Virus (2000)

One of the few solid theoretical results in the study of computer viruses is Cohen&amp;apos;s 1987 demonstration that there is no algorithm that can perfectly detect all possible viruses [1]. This brief paper adds to the bad news, by pointing out that there are computer viruses which no algorithm can detect, even under a somewhat more liberal definition of detection. We also comment on the senses of &amp;quot;detect&amp;quot; used in these results, and note that the immediate impact of these results on computer virus detection in the real world is small.
FXYD3 (Mat-8), a New Regulator of Na,K-ATPase (2005)

Four of the seven members of the FXYD protein family have been identified as specific regulators of Na,K-ATPase. In this study, we show that FXYD3, also known as Mat-8, is able to associate with and to modify the transport properties of Na,K-ATPase. In addition to this shared function, FXYD3 displays some uncommon characteristics. First, in contrast to other FXYD proteins, which were shown to be type I membrane proteins, FXYD3 may have a second transmembrane-like domain because of the presence of a noncleavable signal peptide. Second, FXYD3 can associate with Na,K- as well as H,K-ATPases when expressed in Xenopus oocytes. However, in situ (stomach), FXYD3 is associated only with Na,K-ATPase because its expression is restricted to mucous cells in which H,K-ATPase is absent. Coexpressed in Xenopus oocytes, FXYD3 modulates the glycosylation processing of the beta subunit of X,K-ATPase dependent on the presence of the signal peptide. Finally, FXYD3 decreases both the apparent affinity for Na+ and K+ of Na,K-ATPase.
Application of Ruppert’s reagent in preparing novel perfluorinated porphyrins, chlorins and bacteriochlorins (1999)

G. Li, Y. Chen, J. R. Missert, A. Rungta, T. J. Dougherty, Z. D. Grossman and R. K. Pandey, J. Chem. Soc., Perkin Trans. 1, 1999, 1785 DOI: 10.1039/A904252K
Formation of Gold−Silver Nanowires in Thin Surfactant Solution Films (2005)

Thin, long gold/silver nanowires were grown on substrates in thin surfactant solution films. This growth process occurred exclusively in thinning aqueous films as the water evaporated, and elongated surfactant template structures were formed. The nanowire growth depended on the presence of a relatively high concentration of silver ions (typical Ag:Au mole ratio of 1:1). Tuning the pH value to about 5 in the growth solution was crucial for the nanowire growth. Further development of this process may lead to a simple wet chemical technique for the fabrication of relatively uniform arrays of metal nanowires on surfaces.