gebhart/patrepeval huggingface dataset:
Differential Effects of Alcohols on Conformational Switchovers in α-Helical and β-Sheet Protein Models (2006)

Organic solvents may induce non-native structures of proteins that mimic folding intermediates and/or conformations that occur in proximity to biological membranes. Here we systematically investigate the effects of simple (i.e., MeOH and EtOH) and fluorinated (i.e., trifluoroethanol, TFE) alcohols on the secondary structure and thermodynamic stability of two complementary model proteins using a combination of circular dichroism, fluorescence, and Fourier transform infrared (FTIR) detection methods. The selected proteins are alpha-helical Borrelia burgdorferi VlsE and beta-sheet human mitochondrial co-chaperonin protein 10 (cpn10). We find that switches between VlsE's native and non-native superhelical and beta-sheet structures readily occur (pH 7, 20 degrees C). The pathway depends on the alcohol: addition of MeOH induces a transition to a superhelical structure that is followed by conversion to beta-structure, whereas EtOH only unfolds the protein. TFE unfolds VlsE at low percentages but promotes the formation of a superhelical state upon further additions. For cpn10, both MeOH and TFE additions govern initial unfolding; however, further additions of MeOH result in the formation of a non-native beta-structure, whereas subsequent additions of TFE induce a superhelical structure. EtOH additions promptly unfold and precipitate cpn10. Both VlsE's and cpn10's non-native structures exhibit high stability toward chemical and thermal perturbations. This study demonstrates that in response to different alcohols, polypeptides can readily adopt both alpha- and beta-enriched conformations. The biological significance of these findings is discussed.
Cytokine-enhanced expression of glycoprotein Ib alpha in human endothelium. (1990)

Platelet glycoprotein Ib is a major platelet membrane protein composed of two disulfide-linked chains, termed the alpha and beta chains. The larger alpha chain (GpIb alpha), a platelet receptor for von Willebrand factor, plays a major role in mediating platelet adhesion to the subendothelium. Our laboratories have previously reported synthesis of a protein in human endothelial cells that is immunoprecipitated with polyclonal and monoclonal antibodies to platelet GpIb alpha. Lopez et al. (Lopez, J. A., Chung, D. W., Fujikawa, K., Hagan, F. S., Papayannopoulou, T., and Roth, G. J. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 5615-5619) have reported the cloning of GpIb alpha from a human erythroleukemia (HEL) cell cDNA library. Using this clone as probe, we have isolated two partial GpIb alpha clones from a human umbilical vein endothelial cell lambda gt11 cDNA library. These clones were localized within HEL-derived GpIb alpha cDNA by sequence and restriction enzyme analysis. Additionally, they detected the same message species in HEL and tonsilar RNA that was detected with the HEL GpIb alpha cDNA. Low level GpIb alpha mRNA expression was detected in cultured human umbilical vein endothelial cells, which was increased by treatment of the cells with tumor necrosis factor-alpha. This effect was enhanced by pretreatment with interferon-gamma. Additionally, localization of GpIb alpha in endothelium of fresh tonsilar tissue was demonstrated by immunohistochemistry and in situ hybridization. GpIb alpha may play a role in mediating platelet or other effector cell adhesion to activated endothelium.
Magnetic Resonance Imaging in Coronary Artery Disease (1995)

The cardiovascular applications of nuclear magnetic resonance (MR) techniques in coronary artery disease have increased considerably in recent years. Technical advantages of MR imaging in comparison with other techniques are the excellent spatial resolution, the characterization of myocardial tissue, and the potential for three-dimensional imaging. This allows the accurate assessment of left ventricular mass and volume, the differentiation of infarcted tissue from normal myocardial tissue, and the determination of systolic wall thickening and regional wall motion abnormalities. Myocardial perfusion, metabolism, and inducible myocardial ischemia with the use of pharmacological stress also can be assessed by MR techniques. Future technical improvements in real-time imaging and development of noninvasive visualization of the coronary arteries and coronary artery bypasses will constitute a tremendous progress in clinical cardiology. Early detection and flow assessment of stenosed coronary arteries by MR angiography with the use of flow velocity measurements may outweigh the cost inherent to the MR imaging procedure. A particular strength of the MR technique is the potential to encompass cardiac anatomy, perfusion, function, metabolism, and coronary angiography in a single test. The replacement of multiple diagnostic tests with one MR test may have major effects on cardiovascular healthcare economics.
Rare presentation of a common disease of tropics. (2008)

A 19 years male presented with fever, oliguria and purpuric lesions involving both hands. The patient was diagnosed as a case of purpura fulminans with disseminated intravascular coagulation due to complicated falciparum malaria. The case is presented to sensitize the physicians to keep malaria as a differential in cases of fever with purpura fulminans.
Robust cable remote control for set-top boxes (2003)

In developing countries, analogue TV sets can significantly outnumber telephones or PCs. Advances in the multimedia industry, particularly the advent of digital TV can turn the subscriber into an active viewer. Interactivity is one of the key works at the present time. However, full digital domestic TV receivers are rather expensive and therefore, meanwhile a solution is to use a gateway, commonly called a set-top-box (STB), connected to the conventional analogue TV set. Commercially available STBs are locally controlled by infrared (IR) devices. This is the main reason to keep the TV set close to the STB. This paper investigates a solution for an electrical remote control for STBs. Thus, the analogue TV set can be placed far way from the STB. The novelty of this paper consists in a FSK receiver without PLL, leading to a phase error free system as well as to a low cost implementation.
Human erythrocyte protein 4.1 is a phosphatidylserine binding protein. (1988)

The aminophospholipids phosphatidylethanolamine (PE) and phosphatidylserine (PS) are the major phospholipids contained in the cytoplasmic leaflet of the human erythrocyte (RBC) plasma membrane and are largely confined to that leaflet over the entire RBC lifespan. In particular, PS, which comprises approximately 13% of total RBC membrane phospholipids, is normally restricted entirely to the cytoplasmic leaflet. However, molecular mechanisms that regulate this asymmetric distribution of phospholipids are largely unknown. We examined elliptocytic RBCs that completely lacked protein 4.1 (HE [4.1 degrees]), but contained normal amounts of all other peripheral membrane proteins, and found approximately 10% of total membrane PS was accessible in the exoplasmic leaflet of these membranes. Inside out vesicles (IOVs) derived from HE [4.1 degrees] RBCs bound fewer PS liposomes than did IOVs derived from normal RBCs. Normal IOVs that were depleted of proteins 2.1 (ankyrin), 4.1, and 4.2 bound fewer PS liposomes similar to HE [4.1 degrees] IOVs, and repletion with protein 4.1 restored PS liposome binding to control levels. Addition of purified protein 4.1 to PS liposomes resulted in saturable binding with the extent of binding being proportional to the liposome PS content. Our data suggests that human RBC protein 4.1 is a PS binding protein and may be involved in the molecular mechanisms that stabilize PS in the cytoplasmic leaflet of the human RBC plasma membrane.
Carbothermal synthesis of TiB2 powders of micron size (2016)

The characteristic details of the carbothermal synthesis of TiB2 powders from the stoichiometric mixture TiO2–H3BO3–C at temperatures lower 1700 K are investigated using thermal analysis (ТG—thermogravimetry and DSC—differential scanning calorimetry), as well as X-ray diffraction and scanning electron microscopy. In the temperature interval 300 K → 1673 K → 1273 K and at a heating rate of 10 K/min, the reaction in the powder mixture begins at approximately 1300 K and ends at 1470 K during cooling. After 3 h of isothermal synthesis at 1473 K, the TiB2 yield is more than 90%. The resulting products are hexagonal plate-like crystals 5–10 μm across with thickness of 3 to 4 μm. Kinetic analysis showed that in the temperature range of 1330 to 1673 K the TiB2 synthesis reaction is of the first-order, and the calculated activation energy of the process is 315 ± 24 kJ/mol.
Regret Minimizing Audits: A Learning-Theoretic Basis for Privacy Protection (2011)

Audit mechanisms are essential for privacy protection in permissive access control regimes, such as in hospitals where denying legitimate access requests can adversely affect patient care. Recognizing this need, we develop the first principled learning-theoretic foundation for audits. Our first contribution is a game-theoretic model that captures the interaction between the defender (e.g., hospital auditors) and the adversary (e.g., hospital employees). The model takes pragmatic considerations into account, in particular, the periodic nature of audits, a budget that constrains the number of actions that the defender can inspect, and a loss function that captures the economic impact of detected and missed violations on the organization. We assume that the adversary is worst-case as is standard in other areas of computer security. We also formulate a desirable property of the audit mechanism in this model based on the concept of regret in learning theory. Our second contribution is an efficient audit mechanism that provably minimizes regret for the defender. This mechanism learns from experience to guide the defender's auditing efforts. The regret bound is significantly better than prior results in the learning literature. The stronger bound is important from a practical standpoint because it implies that the recommendations from the mechanism will converge faster to the best fixed auditing strategy for the defender.
It is Time to Individualize the Dialysate Sodium Prescription (2015)

Sodium mass balance in hemodialysis patients is primarily dependent on dietary salt intake and sodium removal during dialysis. One of the most important goals of dialysis therapy is to fully remove the mass of sodium that has accumulated in the interdialytic period. It is currently the practice in dialysis centers all over the world to use a standardized dialysate sodium concentration (Na(+) D) for all patients. The aim of the present article was to summarize the current evidence for an individualized Na(+) D prescription. Three main points are discussed: (i) Na(+) D prescription, which must necessarily take into account the sodium setpoint and the sodium gradient; (ii) clinical experience with an individualized Na(+) D prescription, and (iii) guidelines for individualizing the Na(+) D prescription. To summarize, recent data suggest that tailoring Na(+) D to an individual's sodium setpoint has the potential for short- and long-term benefits for patients. Prospective interventional studies are warranted to further understand its effects, stratified for patients with low or high serum sodium levels.
Development of a Cy3‐Labeled Glucose Bioprobe and Its Application in Bioimaging and Screening for Anticancer Agents (2007)

Tracing glucose uptake: Fluorescent glucose analogues were synthesized, and the importance of stereochemistry for cellular uptake efficiency was demonstrated. The chiral bioprobe 1 showed superior properties as a glucose-uptake tracer. The cellular uptake of 1 was demonstrated under various concentrations of D-glucose. A screening system was developed for the discovery of anticancer agents by the measurement of glucose uptake in cancer cells with 1. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z604364_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Somatic embryogenesis and plant regeneration from suspension cultures of <i>Picea glauca</i> (White spruce) (1988)

Hakman, I. and von Arnold, S. 1988. Somatic embryogenesis and plant regeneration from suspension cultures of Picea glauca (White spruce). ‐ Physiol. Plant. 72: 579–587. Plantlets were regenerated from long‐term embryogenic cultures of Picea glauca (Moench) Voss. (White spruce). Embryogenic calli, initiated from immature zygotic embryos and maintained by monthly subculture for 16 months, were used to establish suspension cultures. Small somatic embryos were continuously produced in liquid culture medium containing auxin and cytokinin and the cultures showed a sustained regeneration capacity for >6 months. Somatic embryos propagated in the suspension cultures developed further into embryos bearing cotyledons, about 1 month after transfer to solidified medium containing abscisic acid. Electron microscopic examination revealed that storage nutrients, lipids, proteins and carbohydrates, accumulated in the somatic embryos during this treatment with abscisic acid (ABA). Upon subculture to medium lacking plant growth regulators such embryos could develop into small green plantlets.
Mapping of antigenic determinants of human apolipoprotein B using monoclonal antibodies against low density lipoproteins. (1982)

The reactivity of a series of monoclonal antibodies directed against human low density lipoproteins (LDL) has been tested with hepatic and intestinal apolipoprotein B (apo-B) termed B-100 and B-48, respectively (Kane, J. P., Hardman, D. A., and Paulus, H. E. (1980) Proc. Natl. Acad. Sci. U. S. A. 77, 2465-2469). Whereas those antibodies that have been previously shown to recognize determinants close to the LDL receptor recognition site reacted only with B-100, two antibodies specific for other regions of apo-B reacted with both B-100 and B-48. Therefore, it is probable that sequence homologies exist between the two proteins and it must be considered that all or parts of the B-48 sequence may be contained within that of B-100. The specificity of the reaction of these antibodies with proteins designated B-74 and B-26 supports the concept that they represent complementary fragments of B-100. The present results have been incorporated in a theoretical map of the antigenic determinants recognized by these antibodies on the LDL apo-B.
Regulation of cadherin expression in nervous system development (2013)

This review addresses our current understanding of the regulatory mechanisms for classical cadherin expression during development of the vertebrate nervous system. The complexity of the spatial and temporal expression patterns is linked to morphogenic and functional roles in the developing nervous system. While the regulatory networks controlling cadherin expression are not well understood, it is likely that the multiple signaling pathways active in the development of particular domains also regulate the specific cadherins expressed at that time and location. With the growing understanding of the broader roles of cadherins in cell-cell adhesion and non-adhesion processes, it is important to understand both the upstream regulation of cadherin expression and the downstream effects of specific cadherins within their cellular context.
Resveratrol potently reduces prostaglandin E2production and free radical formation in lipopolysaccharide-activated primary rat microglia (2007)

These findings suggest that the naturally occurring polyphenol resveratrol is able to reduce microglial activation, an effect that might help to explain its neuroprotective effects in several in vivo models of brain injury.
Tyrosine kinase gene fusions in cancer: translating mechanisms into targeted therapies (2011)

Tyrosine kinase fusion genes represent an important class of oncogenes associated with leukaemia and solid tumours. They are produced by translocations and other chromosomal rearrangements of a subset of tyrosine kinase genes, including ABL, PDGFRA, PDGFRB, FGFR1, SYK, RET, JAK2 and ALK. Based on recent findings, this review discusses the common mechanisms of activation of these fusion genes. Enforced oligomerization and inactivation of inhibitory domains are the two key processes that switch on the kinase domain. Activated tyrosine kinase fusions then signal via an array of transduction cascades, which are largely shared. In addition, the fusion partner provides a scaffold for the recruitment of proteins that contribute to signalling, protein stability, cellular localization and oligomerization. The expression level of the fusion protein is another critical parameter. Its transcription is controlled by the partner gene promoter, while translation may be regulated by miRNA. Several mechanisms also prevent the degradation of the oncoprotein by proteasomes and lysosomes, leading to its accumulation in cells. The selective inhibition of the tyrosine kinase activity by adenosine-5'-triphosphate competitors, such as imatinib, is a major therapeutic success. Imatinib induces remission in leukaemia patients that are positive for BCR-ABL or PDGFR fusions. Recently, crizotinib produced promising results in a subtype of lung cancers with ALK fusion. However, resistance was reported in both cases, partially due to mutations. To tackle this problem, additional levels of therapeutic interventions are suggested by the complex mechanisms of fusion tyrosine kinase activation. New approaches include allosteric inhibition and interfering with oligomerization or chaperones.
Prophylaxis of early ventricular fibrillation by inhibition of acylcarnitine accumulation. (1989)

Hypoxia in isolated myocytes results in accumulation of long-chain acylcarnitines (LCA) in sarcolemma. Inhibition of carnitine acyltransferase I (CAT-I) with sodium 2-[5-(4-chlorophenyl)-pentyl]-oxirane-2-carboxylate (POCA) prevents both the accumulation of LCA in the sarcolemma and the initial electrophysiologic derangements associated with hypoxia. Another amphiphilic metabolite, lysophosphatidylcholine (LPC), accumulates in the ischemic heart in vivo, in part because of inhibition of its catabolism by accumulating LCA. It induces electrophysiologic alterations in vitro analogous to early changes induced by ischemia in vivo. The present study was performed to determine whether POCA could prevent accumulation of both LCA and LPC induced by ischemia in vivo and if so, whether attenuation of early arrhythmogenesis would result. LAD coronary artery occlusions were induced for 5 min in chloralose-anesthetized cats. Coronary occlusion in untreated control animals elicited prompt, threefold increases of LCA (73 +/- 8 to 286 +/- 60 pmol/mg protein) and twofold increase of LPC (3.3 +/- 0.4 to 7.5 +/- 0.9 nmol/mg protein) selectively in the ischemic zone, associated with ventricular tachycardia (VT) or ventricular fibrillation (VF) occurring within the 5-min interval before acquisition of myocardial samples in 64% of the animals. POCA prevented the increase of both LCA and LPC. It also prevented the early occurrence of VT or VF (within 5 min of occlusion) in all animals studied. The antiarrhythmic effect of POCA was not attributable to favorable hemodynamic changes or to changes in myocardial perfusion measured with radiolabeled microspheres. Thus, inhibition of CAT-I effectively reduced the incidence of lethal arrhythmias induced early after the onset of ischemia. Accordingly, pharmacologic inhibition of this enzyme provides a promising approach for prophylaxis of sudden cardiac death, that typically occurs very soon after the onset of acute ischemia, in man.
Emerging high-speed xDSL access services: architectures, issues, insights, and implications (1999)

High-speed asymmetric and symmetric digital subscriber line loop access systems, designed by numerous computer networking and telecommunications equipment companies, are currently the focus of technical trials, market trials, and commercial services deployment around the world. This is to provide millions of residential and business customers worldwide with high-speed always-on connectivity to the Internet, corporate intranets, and various online services. It is estimated that over 460 million copper loops worldwide could potentially be equipped end-to-end with xDSL access systems. Large-scale deployment of broadband access systems offering always-on connectivity to the global Internet and corporate intranets is seen as a key enabler of the bold vision articulated worldwide to utilize open Internet protocols and emerging technologies such as Java to create a unified software-defined (IP) global networking infrastructure. Such a networking platform would serve as a de facto medium for generation and delivery of integrated multimedia content, and revolutionize the way people around the world learn, do business, and interact with each other.
A genetically encoded fluorescent tRNA is active in live-cell protein synthesis (2016)

Transfer RNAs (tRNAs) perform essential tasks for all living cells. They are major components of the ribosomal machinery for protein synthesis and they also serve in non-ribosomal pathways for regulation and signaling metabolism. We describe the development of a genetically encoded fluorescent tRNA fusion with the potential for imaging in live Escherichia coli cells. This tRNA fusion carries a Spinach aptamer that becomes fluorescent upon binding of a cell-permeable and non-toxic fluorophore. We show that, despite having a structural framework significantly larger than any natural tRNA species, this fusion is a viable probe for monitoring tRNA stability in a cellular quality control mechanism that degrades structurally damaged tRNA. Importantly, this fusion is active in E. coli live-cell protein synthesis allowing peptidyl transfer at a rate sufficient to support cell growth, indicating that it is accommodated by translating ribosomes. Imaging analysis shows that this fusion and ribosomes are both excluded from the nucleoid, indicating that the fusion and ribosomes are in the cytosol together possibly engaged in protein synthesis. This fusion methodology has the potential for developing new tools for live-cell imaging of tRNA with the unique advantage of both stoichiometric labeling and broader application to all cells amenable to genetic engineering.
Federated Identity Architecture of the European eID System (2018)

Federated identity management is a method that facilitates management of identity processes and policies among the collaborating entities without a centralized control. Nowadays, there are many federated identity solutions, however, most of them covers different aspects of the identification problem, solving in some cases specific problems. Thus, none of these initiatives has consolidated as a unique solution and surely it will remain like that in a near future. To assist users choosing a possible solution, we analyze different federated identify approaches, showing main features, and making a comparative study among them. The former problem is even worst when multiple organizations or countries already have legacy eID systems, as it is the case of Europe. In this paper, we also present the European eID solution, a purely federated identity system that aims to serve almost 500 million people and that could be extended in midterm also to eID companies. The system is now being deployed at the EU level and we present the basic architecture and evaluate its performance and scalability, showing that the solution is feasible from the point of view of performance while keeping security constrains in mind. The results show a good performance of the solution in local, organizational, and remote environments.