gebhart/patrepeval huggingface dataset:
Insulin-degrading enzyme is exported via an unconventional protein secretion pathway (2009)

Insulin-degrading enzyme (IDE) is a ubiquitously expressed zinc-metalloprotease that degrades several pathophysiologically significant extracellular substrates, including insulin and the amyloid beta-protein (Abeta), and accumulating evidence suggests that IDE dysfunction may be operative in both type 2 diabetes mellitus and Alzheimer disease (AD). Although IDE is well known to be secreted by a variety of cell types, the underlying trafficking pathway(s) remain poorly understood. To address this topic, we investigated the effects of known inhibitors or stimulators of protein secretion on the secretion of IDE from murine hepatocytes and HeLa cells. IDE secretion was found to be unaffected by the classical secretion inhibitors brefeldin A (BFA), monensin, or nocodazole, treatments that readily inhibited the secretion of alpha1-antitrypsin (AAT) overexpressed in the same cells. Using a novel cell-based Abeta-degradation assay, we show further that IDE secretion was similarly unaffected by multiple stimulators of protein secretion, including glyburide and 3'-O-(4-benzoyl)benzoyl-ATP (Bz-ATP). The calcium ionophore, A23187, increased extracellular IDE activity, but only under conditions that also elicited cytotoxicity. Our results provide the first biochemical evidence that IDE export is not dependent upon the classical secretion pathway, thereby identifying IDE as a novel member of the select class of unconventionally secreted proteins. Further elucidation of the mechanisms underlying IDE secretion, which would be facilitated by the assays described herein, promises to uncover processes that might be defective in disease or manipulated for therapeutic benefit.
A Detailed Mathematical Analysis of a Class of Covert Channels Arising in Certain Anonymizing Networks (2003)

Abstract : There have long been threads of investigation into covert channels, and threads of investigation into anonymity, but these two closely related areas of information hiding have not been directly associated. This report represents an initial inquiry into the relationship between covert channel capacity and anonymity, and poses more questions than it answers. Even this preliminary work has proven difficult, but in this investigation lies the hope of a deeper understanding of the nature of both areas. Mixes have been used for anonymity, where the concern is shielding the identity of the sender or the receiver of a message, or both. Traffic analysis prevention (TAP) methods are used to conceal larger traffic patterns. Here, we are concerned with how much information a sender to a Mix can leak to an eavesdropping outsider, despite the concealment efforts of Mixes acting as firewalls.
Repeated tourniquet testing as a diagnostic tool in dengue infection. (2006)

Prospective evaluation of repeated standard tourniquet testing as a diagnostic indicator of dengue infection was done. Included were patients admitted to a children's hospital in Kuala Lumpur on a clinical suspicion of dengue infection based on the World Health Organization (WHO) criteria. A standard method of tourniquet was performed on 79 patients on a daily basis following admission. subjects and negative in the remaining 14 subjects. Fifty-eight subjects were serologically confirmed cases, 4 indeterminate and the remaining 17 subjects had negative serology. For diagnostic classification, 13 had dengue fever, 49 with dengue haemmorhagic fever (DHF) while 17 had non-dengue infection. The sensitivity and specificity of the tourniquet test was 82.8% and 23.5% respectively. The positive predictive value (PPV) was 78.7% while the negative predictive value (NPV) was 28.6%. In addition, the tourniquet test aided in the diagnosis of one-fifth of patients with DHF, who presented with a positive tourniquet test as the only bleeding manifestation. It seems that in a hospital setting, the tourniquet test adds little to the diagnosis of dengue infection/DHF. A positive tourniquet test, repeatedly performed, was found clinically useful as a preliminary screening test in dengue infection as recommended by WHO. However, it was not very specific and had a high false positive rate.
Design criteria for structurally stable, highly strained multiple quantum well devices (1994)

Strain compensation allows the synthesis of infinitely thick heterostructures with many highly strained quantum wells. Design criteria are given for optimized strain and thickness parameters in several device geometries. Strain compensation, using alternating layers of opposite strain, is quantitatively treated using an energy balance analysis. The upper bound to stability for strained multiple quantum wells with and without strain compensation is defined for geometries typically used in optoelectronic devices. Highly metastable structures (composed of many layers of high strain and/or thickness) require low epitaxy temperatures to avoid strain relaxation during growth of individual strained layers, prior to their stabilization in a strain compensated structure.
Robot Assembly: Another Source of Nonholonomic Control Problems (1991)

Assembly problems require that a robot with a few actuated degrees of freedom manipulate an environment with a greater number of unactuated degrees of freedom. Since the dynamical coupling between degrees of freedom in this setting is a function of their relative configuration, the motion of such systems is subject to constraints that preclude smooth feedback stabilization. This paper explores the extent to which assembly planning and control may be effected by recourse to some other methodical means of generating stabilizing feedback controllers. A partial solution is offered for a very simple assembly problem involving an intermittent dynamical environment.
<title>Analogously working micromirror arrays</title> (1999)

This paper deals with micromirror arrays for high frequency applications. The use of monocrystalline silicon as mechanical material results in a low hysteresis, good reproducibility and high reliability. General characteristics, advantages and limitations of large analogously working mirror arrays in comparison with single elements will be discussed with respect to the requirements of desired applications. Special aspects of the design of micromirror arrays, experimental results concerning the behavior of the electromechanical system and optical properties will be presented as well. It will be shown that cascaded elements allow beside higher quality factors or resonant band width concerning the dynamic behavior also higher quasistatic deflection angles at diminished electrode gaps and lower driving voltages.
DILUTED MAGNETIC SEMICONDUCTOR NANOWIRES (2008)

An idea for simultaneously manipulating spin and charge in a single semiconductor medium has resulted in the development of diluted magnetic semiconductors (DMSs), which exhibits surprisingly room temperature ferromagnetic signatures despite having controversial ferromagnetic origin. However, achievement of truly room temperature ferromagnetism by carrier mediation is still the subject of intense research to develop the practical spin-based devices. Nanowires with one-dimensional nanostructure, which offers thermodynamically stable features and typically single crystalline and defect free, have a number of advantages over thin films with respect to studying ferromagnetism in DMSs. This review focuses primarily on our works on GaN -based DMS nanowires, i.e., Mn -doped GaN , Mn -doped AlGaN and Cu -doped GaN nanowires. These DMS nanowires have room temperature ferromagnetism by the local magnetic moment of doping elements that are in a divalent state and in tetrahedral coordination, thus substituting Ga in the wurtzite-type network structure of host materials. Importantly, our evidences indicate that the magnetism is originated from the ferromagnetic interaction driven by the carrier. These outcomes suggest that nanowires are ideal building blocks to address the magnetism in DMS due to their thermodynamic stability, single crystallinity, free of defects and free standing nature from substrate. Nanowires themselves are ideal building blocks for nanodevices and, thus, it would also be helpful in developing DMS-based spin devices.
ChemInform Abstract: Chemical Constituents from the Colombian Medicinal Plant Niphogeton ternata. (2002)

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.
DJ-1 Up-regulates Glutathione Synthesis during Oxidative Stress and Inhibits A53T α-Synuclein Toxicity (2005)

DJ-1 is the third gene that has been linked to Parkinson disease. Mutations in the DJ-1 gene cause early onset PD with autosomal recessive inheritance. To clarify the mechanism of DJ-1 protection, we have overexpressed the gene in cultured dopaminergic cells that were then subjected to chemical stress. In the rat dopaminergic cell line, N27, and in primary dopamine neurons, overexpression of wild type DJ-1 protected cells from death induced by hydrogen peroxide and 6-hydroxydopamine. Overexpressing the L166P mutant DJ-1 had no protective effect. By contrast, knocking down endogenous DJ-1 with antisense DJ-1 rendered cells more susceptible to oxidative damage. We have found that DJ-1 improves survival by increasing cellular glutathione levels through an increase in the rate-limiting enzyme glutamate cysteine ligase. Blocking glutathione synthesis eliminated the beneficial effect of DJ-1. Protection could be restored by adding exogenous glutathione. Wild type DJ-1 reduced cellular reactive oxygen species and reduced the levels of protein oxidation caused by oxidative stress. By a separate mechanism, overexpressing wild type DJ-1 inhibited the protein aggregation and cytotoxicity usually caused by A53T human alpha-synuclein. Under these circumstances, DJ-1 increased the level of heat shock protein 70 but did not change the glutathione level. Our data indicate that DJ-1 protects dopaminergic neurons from oxidative stress through up-regulation of glutathione synthesis and from the toxic consequences of mutant humanalpha-synuclein through increased expression of heat shock protein 70. We conclude that DJ-1 has multiple specific mechanisms for protecting dopamine neurons from cell death.
One Water Molecule Stabilizes the Cationized Arginine Zwitterion (2007)

Singly hydrated clusters of lithiated arginine, sodiated arginine, and lithiated arginine methyl ester are investigated using infrared action spectroscopy and computational chemistry. Whereas unsolvated lithiated arginine is nonzwitterionic, these results provide compelling evidence that attachment of a single water molecule to this ion makes the zwitterionic form of arginine, in which the side chain is protonated, more stable. The experimental spectra of lithiated and sodiated arginine with one water molecule are very similar and contain spectral signatures for protonated side chains, whereas those of lithiated arginine and singly hydrated lithiated arginine methyl ester are different and contain spectral signatures for neutral side chains. Calculations at the B3LYP/6-31++G** level of theory indicate that solvating lithiated arginine with a single water molecule preferentially stabilizes the zwitterionic forms of this ion by 25-32 kJ/mol and two essentially isoenergetic zwitterionic structure are most stable. In these structures, the metal ion either coordinates with the N-terminal amino group and an oxygen atom of the carboxylate group (NO coordinated) or with both oxygen atoms of the carboxylate group (OO coordinated). In contrast, the OO-coordinated zwitterionic structure of sodiated arginine, both with and without a water molecule, is clearly lowest in energy for both ions. Hydration of the metal ion in these clusters weakens the interactions between the metal ion and the amino acid, whereas hydrogen-bond strengths are largely unaffected. Thus, hydration preferentially stabilizes the zwitterionic structures, all of which contain strong hydrogen bonds. Metal ion size strongly affects the relative propensity for these ions to form NO or OO coordinated structures and results in different zwitterionic structures for lithiated and sodiated arginine clusters containing one water molecule.
Estrogen Receptor Beta Gene Variant Is Associated with Vascular Dementia in Elderly Women (2009)

The ESR2 rs4986938 polymorphism is associated with susceptibility for VaD in elderly Jewish women. These results need to be confirmed in replicate studies in other populations.
New Synthetic Approach to Cyclopenta‐Fused Heterocycles Based upon a Mild Nazarov Reaction. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Hybrid C18-Bonded Silica Phases: Application in Acetaminophen Adsorption (2007)

Hybrid silicas bearing octadecylsilane ligands and Lewis acid centres were synthesized by grafting and sol-gel methods. In grafting, Cp 2 ZrCl 2 was employed, while ZrCl 4 was used in the sol-gel method. A very low grafted metal content (ca. 0.1 wt% Zr/SiO 2 ) was achieved, with the carbon percentage being dependent on the grafting time. However, a much higher Zr content (up to 20.5 wt% Zr/SiO 2 ) and carbon content (up to 49.3%) was obtained by the sol-gel method. The surface concentration of alkyl groups varied between 0.2 and 2.8 μmol/m 2 . The solids were characterized by infrared spectroscopy (IR), ultraviolet diffuse reflectance spectroscopy (DRS), atomic force microscopy (AFM), scanning electron microscopy (SEM) and nitrogen adsorption. The behaviour of the phases towards the adsorption of acetaminophen was evaluated. Two phases showed a higher retention capacity than that exhibited by the commercial octadecyl phase. Recovery results remained between 70% and 100%.
Structure-Function Analysis of the Human Ferroportin Iron Exporter (SLC40A1): Effect of Hemochromatosis Type 4 Disease Mutations and Identification of Critical Residues (2013)

Ferroportin (SLC40A1) is the only known iron exporter in mammals and is considered a key coordinator of the iron balance between intracellular and systemic iron homeostasis. However, the structural organization of ferroportin in the lipid bilayer remains controversial and very little is known about the mechanism underlying iron egress. In the present study, we have developed an approach based on comparative modeling, which has led to the construction of a model of the three-dimensional (3D) structure of ferroportin by homology to the crystal structure of a Major Facilitator Superfamily member (EmrD). This model predicts atomic details for the organization of ferroportin transmembrane helices and is in agreement with our current understanding of the ferroportin function and its interaction with hepcidin. Using in vitro experiments, we demonstrate that this model can be used to identify novel critical amino acids. In particular, we show that the tryptophan residue 42 (p.Trp42), which is localized within the extracellular end of the ferroportin pore, is likely involved in both the iron export function and in the mechanism of inhibition by hepcidin. Thus, our 3D model provides a new perspective for understanding the molecular basis of ferroportin functions and dysfunctions.
Transfer of E2F-1 to human glioma cells results in transcriptional up-regulation of Bcl-2. (2001)

Strong evidence exists to support the tenet that activation of E2F transcription factors, via alterations in the p16-cyclin D-Rb pathway, is a key event in the malignant progression of most human malignant gliomas. The oncogenic ability of E2F has been related to the E2F-mediated up-regulation of several proteins that positively regulate cell proliferation. However, E2F may indirectly enhance proliferation by activating antiapoptotic molecules. In this work, we sought to ascertain whether E2F-1-mediated events involve the up-regulation of the antiapoptotic molecule Bcl-2. Western blot analyses showed up-regulation of Bcl-2 but not of Bcl-x(L) by 24 h after the transfer of E2F-1. Northern blot studies showed that transfer of E2F-1 also up-regulated Bcl-2 RNA. In support of these findings and the concept that E2F-1 has a direct effect in the induction of Bcl-2, we found a putative E2F binding site within the Bcl-2 sequence. Subsequent gel-mobility shift and supershift experiments involving the CTCCGCGC site in the bcl-2 promoter showed that E2F-1 bound Bcl-2. Transactivation experiments consistently showed that ectopic E2F-1 activated responsive elements located in the -1448/-1441 region in the P1 promoter region of the bcl-2 gene. As expected, other members of the E2F family of transcription factors such as E2F-2 and E2F-4 also transactivated the bcl-2 promoter. Our results demonstrate that E2F-1 modulates the expression of the antiapoptotic molecule Bcl-2 and suggest that up-regulation of Bcl-2 may favor the oncogenic role of E2F-1 and other members of the E2F family of transcription factors.
Anyon statistics with continuous variables (2008)

We describe a continuous-variable scheme for simulating the Kitaev lattice model and for detecting statistics of Abelian anyons. The corresponding quantum optical implementation is solely based upon Gaussian resource states and Gaussian operations, hence allowing for a highly efficient creation, manipulation, and detection of anyons. This approach extends our understanding of the control and application of anyons and it leads to the possibility for experimental proof-of-principle demonstrations of anyonic statistics using continuous-variable systems.
[Treatment of 2-naphtholwastewater using air oxidation and ion exchange]. (2001)

The properties of 2-naphtholwastewater were studied in details in this paper, the wastewater was characterized by the strong acidity, high buffer capability and concentrated salt. Air oxidation and anion exchange were employed for the treatment of the wastewater. Under formal pH, room temperature and 1 BV/h rate, the result showed that the removal of COD reached to 97% and the recovery of sodium naphthalensulfonate to 98%. Besides, wastewater treated can be reused for washing the sodium naphthalensulfonate.
Individualizing Fueling And Hydration For An Olympic 50km Race-walker (2010)

The 2008 Olympics presented many challenges, which for endurance athletes mainly featured the extreme Beijing average August daily temperature (31[[Unsupported Character - and #8304;]]C) and humidity (75% hum), coupled with the chance for significant air pollution and possibilities for poor water and food quality. In conjunction, the 50km race-walk is one of the most metabolically challenging Olympic events, as energy expenditure is ∼3600 kcals during the ∼4hr race. PURPOSE: This thematic poster will highlight several key nutrition and hydration interventions that were tested and implemented with an Olympic 50km race-walker prior to and during the 2008 Beijing Olympic Games. METHODS: This veteran race-walker (43yrs, 180cm, 67kg) was making his 5th Olympic appearance over an 18 yr international career. Hydration and fuel testing was longitudinally conducted prior to and throughout the 10-day pre-Olympic training camp in Singapore, and implemented into the 50km race-walk final, and featured: daily weigh-ins, hydration tracking (via urine specific gravity) and sweat rate and fluid consumption in anticipated weather conditions. Race day nutrition was directly measured since athletes compete on a closed 2km loop with country aid stations. RESULTS: During the 10-day camp, the athlete's daily weight (67.5±1.6kg) and hydration status (1.012±0.006 g/ml) were relatively stable. During several key training sessions, in anticipated weather conditions, individual sweat rate was 1767±208 ml/hr and practiced carbohydrate (CHO) and fluid intake were 67±14 g CHO/hr and 947±276ml/hr, respectively. Race day presented hot and humid conditions (10AM, 29C, 55% hum), and the athlete's directly measured intake during the race was: 1200ml/hr of fluid, 74g/hr CHO, 1120 mg sodium/hr and 100mg caffeine/hr. CONCLUSIONS: The pre-Olympic camp allowed this athlete many of the comforts of his normal Western culture, a similar time-zone to Beijing, and the required 10 to 14 days needed to allow for optimal physiological heat and jet-lag acclimation. On race day this athlete had a drink profile and plan with which he had much experience and confidence in. This allowed for all his CHO, fluid, electrolyte and caffeine targets to be met with minimal GI side-effects and only a 2.6% body weight loss on race day.
Potential Alu Function: Regulation of the Activity of Double-Stranded RNA-Activated Kinase PKR (1998)

Cell stress, viral infection, and translational inhibition increase the abundance of human Alu RNA, suggesting that the level of these transcripts is sensitive to the translational state of the cell. To determine whether Alu RNA functions in translational homeostasis, we investigated its role in the regulation of double-stranded RNA-activated kinase PKR. We found that overexpression of Alu RNA by cotransient transfection increased the expression of a reporter construct, which is consistent with an inhibitory effect on PKR. Alu RNA formed stable, discrete complexes with PKR in vitro, bound PKR in vivo, and antagonized PKR activation both in vitro and in vivo. Alu RNAs produced by either overexpression or exposure of cells to heat shock bound PKR, whereas transiently overexpressed Alu RNA antagonized virus-induced activation of PKR in vivo. Cycloheximide treatment of cells decreased PKR activity, coincident with an increase in Alu RNA. These observations suggest that the increased levels of Alu RNAs caused by cellular exposure to different stresses regulate protein synthesis by antagonizing PKR activation. This provides a functional role for mammalian short interspersed elements, prototypical junk DNA.
ChemInform Abstract: A VIRTUALLY COMPLETELY ASYMMETRIC SYNTHESIS (1978)

Abstract Metallierung des Oxathians (Ia) und anschließende Reaktion mit Benzaldehyd ergeben stereo selektiv das äquatorial 2‐su.bstituierte Derivat (2R)‐(IIa) (Diastereomerengemisch), das zu dem Keton (2R)‐ (IIIa) oxidiert wird; Grignardierung des letzteren mit MeMgI führt zu dem Carbinol (IVa) mit S‐Konfiguration an dem exocyclischen C‐Atom.
Detection and characterization of a novel extracellular fungal enzyme that catalyzes the specific and hydrolytic cleavage of lignin guaiacylglycerol β‐aryl ether linkages (2003)

Cleavage of the arylglycerol beta-aryl ether linkage is the most important process in the biological degradation of lignin. The bacterial beta-etherase was described previously and shown to be tightly associated with the cellular membrane. In this study, we aimed to detect and isolate a new extracellular function that catalyses the beta-aryl ether linkage cleavage of high-molecular lignin in the soil fungi. We screened and isolated 2BW-1 cells by using a highly sensitive fluorescence assay system. The beta-aryl ether cleavage enzyme was produced by a newly isolated fungus, 2BW-1, and is secreted into the extracellular fraction. The beta-aryl ether cleavage enzyme converts the guaiacylglycerol beta-O-guaiacyl ether (GOG) to guaiacylglycerol and guaiacol. It requires the C alpha alcohol structure and p-hydroxyl group and specifically attacks the beta-aryl ether linkage of high-molecular mass lignins with addition of two water molecules at the C alpha and C beta positions.