gebhart/patrepeval huggingface dataset:
Tailoring Enzyme‐Like Activities of Gold Nanoclusters by Polymeric Tertiary Amines for Protecting Neurons Against Oxidative Stress (2016)

The cytotoxicity of nanozymes has drawn much attention recently because their peroxidase-like activity can decompose hydrogen peroxide (H2 O2 ) to produce highly toxic hydroxyl radicals (•OH) under acidic conditions. Although catalytic activities of nanozymes are highly associated with their surface properties, little is known about the mechanism underlying the surface coating-mediated enzyme-like activities. Herein, it is reported for the first time that amine-terminated PAMAM dendrimer-entrapped gold nanoclusters (AuNCs-NH2 ) unexpectedly lose their peroxidase-like activity while still retaining their catalase-like activity in physiological conditions. Surprisingly, the methylated form of AuNCs-NH2 (i.e., MAuNCs-N(+) R3 , where R = H or CH3 ) results in a dramatic recovery of the intrinsic peroxidase-like activity while blocking most primary and tertiary amines (1°- and 3°-amines) of dendrimers to form quaternary ammonium ions (4°-amines). However, the hidden peroxidase-like activity is also found in hydroxyl-terminated dendrimer-encapsulated AuNCs (AuNCs-OH, inside backbone with 3°-amines), indicating that 3°-amines are dominant in mediating the peroxidase-like activity. The possible mechanism is further confirmed that the enrichment of polymeric 3°-amines on the surface of dendrimer-encapsulated AuNCs provides sufficient suppression of the critical mediator •OH for the peroxidase-like activity. Finally, it is demonstrated that AuNCs-NH2 with diminished cytotoxicity have great potential for use in primary neuronal protection against oxidative damage.
Guest Editorial: Databases and Bioinformatics Tools (2013)

Bioinformatics is a field at the crossroads of Chemistry and Biology encompassing databases and computational tools for the analysis of biological processes. With the enormous increase in speed of both genome sequencing and determination of 3D structures of biological macromolecules, this area has become incredibly important as a discipline that is able to discover key information and ideas from this astonishing large amount of data. This special issue of the Israel Journal of Chemistry is focused on this field, with ten papers discussing widely different aspects. The papers range from analysis of plant breeding (Ophir), mass-spectrometry (Linial), analysis of effect of single-base effects on nucleosomes (Trifonov) and on their mutations as to their effect on protein function (Unger), protein-protein interactions (Wolfson), tools for prediction of metal bindings in proteins (Edelman), predicting function from either structure (Kosloff) or via evolutionary tools (Ben-Tal), new ways to visualize 3D structures of biomacromolecules (Hanson & Prilusky) to an overview of synergistic data tools for examining biological activity (Lancet). These articles are from scientists in Israel where bioinformatics is a key area of research, but has also involved a great deal of interaction between Israeli scientists and those from around the world as can be seen in several of the papers where the authors are from Europe, USA, Japan and China. Bioinformatics is a field that has no borders. The tools described here are being used both by students and scientists throughout the world and students and scientists from theses different countries are also actively contributing data and methods. As the generation of new data continues to explode it is likely that databases and bioinformatics tools will play an ever-increasing role in our attempt to understand the chemical basis of the molecules of life. 1 1
High Efficiency Satellite Multiple Access Scheme for Machine-to-Machine Communications (2012)

The work presented here describes the key design drivers and performance of a high efficiency satellite mobile messaging system well adapted to the machine-to-machine communication services targeting, in particular, the vehicular market. It is shown that the proposed return link multiple access solution is providing a random access channel (RACH) aggregated spectral efficiency around 2 bit/s/Hz in the presence of power unbalance with reliable packet delivery over typical land mobile satellite (LMS) channels.
Attenuated defense response and low basal blood pressure in orexin knockout mice (2003)

The perifornical area of the hypothalamus has been known as the center for the defense response, or "fight or flight" response, which is characterized by a concomitant rise in arterial blood pressure (AP), heart rate (HR), and respiratory frequency (Rf). We examined whether orexin, a recently identified hypothalamic neuropeptide, contributes to the defense response and basal cardiovascular regulation using orexin knockout mice. Microinjection of a GABA-A receptor antagonist, bicuculline methiodide (0.1-1 mM in 20 nl), to the perifornical area in urethane-anesthetized wild-type mice elicited dose-dependent increases in AP, HR, and Rf. Although similar changes were observed in orexin knockout mice, intensities were smaller and duration was shorter than those in wild-type mice. Moreover, in an awake and freely moving condition, telemeter-indwelling orexin knockout mice showed diminished cardiovascular and behavioral responses to emotional stress in the resident-intruder test. We also found that basal AP in orexin knockout mice was significantly lower in both anesthetized (117 +/- 8 mmHg in wild type and 92 +/- 3 in knockout) and conscious (125 +/- 6 mmHg in wild type and 109 +/- 2 in knockout) conditions. alpha-Adrenergic blockade with prazosin or ganglion blockade with hexamethonium canceled the difference in basal AP. HR and cardiac contractile parameters by echocardiography did not differ between the two strains of mice. These results indicate lower sympathetic vasoconstrictor tone in knockout mice. The present study suggests that orexin-containing neurons in the perifornical area play a role as one of the efferent pathways of defense response and also operate as a regulator of AP at basal condition by activating sympathetic outflow.
Ubiquitin-binding proteins: similar, but different (2005)

Covalent modification of proteins with ubiquitin is a common regulatory mechanism in eukaryotic cells. Typically, ubiquitinated proteins are targeted for degradation by the 26 S proteasome. However, more recently the ubiquitin signal has also been connected with many other cell processes, including endocytosis, vesicle fusion, DNA repair and transcriptional silencing. Hence ubiquitination may be comparable with phosphorylation in its importance as an intracellular switch, controlling various signal-transduction pathways. Similar to the regulation of the extent of phosphorylation by kinases and phosphatases, specific sets of ubiquitinating/deubiquitinating enzymes control the degree of ubiquitination. A large number of ubiquitin-binding proteins act at different steps in the downstream pathways, followed by the ubiquitinated protein. Different families of ubiquitin-binding proteins have been described. UBA (ubiquitin-associated) domain-containing proteins is the largest family and includes members involved in different cell processes. The smaller groups of UIM (ubiquitin-interacting motif), GAT [GGA (Golgi-associated gamma-adaptin homologous) and Tom1 (target of Myb 1)], CUE (coupling of ubiquitin conjugation to endoplasmic reticulum degradation), UEV [ubiquitin E2 (ubiquitin-conjugating enzyme) variant] and NZF (nuclear protein localization gene 4 zinc finger) domain-containing proteins appear to have more specialized functions. Here we discuss functional and structural properties of ubiquitin-binding proteins.
Data from Inhibition of Melanoma Cell–Intrinsic Tim-3 Stimulates MAPK-Dependent Tumorigenesis (2023)

&lt;div&gt;Abstract&lt;p&gt;T-cell immunoglobulin mucin family member 3 (Tim-3) is an immune checkpoint receptor that dampens effector functions and causes terminal exhaustion of cytotoxic T cells. Tim-3 inhibitors are under investigation in immuno-oncology (IO) trials, because blockade of T-cell-Tim-3 enhances antitumor immunity. Here, we identify an additional role for Tim-3 as a growth-suppressive receptor intrinsic to melanoma cells. Inhibition of melanoma cell-Tim-3 promoted tumor growth in both immunocompetent and immunocompromised mice, while melanoma-specific Tim-3 overexpression attenuated tumorigenesis. Ab-mediated Tim-3 blockade inhibited growth of immunogenic murine melanomas in T-cell–competent hosts, consistent with established antitumor effects of T-cell-Tim-3 inhibition. In contrast, Tim-3 Ab administration stimulated tumorigenesis of both highly and lesser immunogenic murine and human melanomas in T-cell–deficient mice, confirming growth-promoting effects of melanoma-Tim-3 antagonism. Melanoma-Tim-3 activation suppressed, while its blockade enhanced, phosphorylation of pro-proliferative downstream MAPK signaling mediators. Finally, pharmacologic MAPK inhibition reversed unwanted Tim-3 Ab-mediated tumorigenesis in T-cell–deficient mice and enhanced desired antitumor activity of Tim-3 interference in T-cell–competent hosts. These results identify melanoma-Tim-3 blockade as a mechanism that antagonizes T-cell-Tim-3–directed IO therapeutic efficacy. They further reveal MAPK targeting as a combination strategy for circumventing adverse consequences of unintended melanoma-Tim-3 inhibition.&lt;/p&gt;Significance:&lt;p&gt;Tim-3 is a growth-suppressive receptor intrinsic to melanoma cells, the blockade of which promotes MAPK-dependent tumorigenesis and thus counteracts antitumor activity of T-cell–directed Tim-3 inhibition.&lt;/p&gt;&lt;/div&gt;
Determination of oxygen and water vapour in modified atmosphere packages for meat sausages with and without an oxygen absorber (1997)

A gas chromatographic method has been developed that measures both the residual oxygen concentration and the level of relative humidity during the same run in modified atmosphere packages (N2/CO2) with and without an oxygen absorber. A processed meat product with a high content of water served as the foodstuff in those packages. The chromatographic system consists mainly of a loop-injector connected to capillary columns coupled in series and a thermocouple detector. The introduction of an oxygen absorber seems to be attractive, since the concentrations obtained for the residual amount of oxygen in the packages with an oxygen absorber varied between 0.0043 and 0.029%. For packages without an absorber, the oxygen concentrations were much higher and fluctuated between 0.26 and 0.56%. The whole measuring period lasted for 27 days. The relative humidity, also a factor that can cause food deterioration, was 100%. © 1997 John Wiley & Sons, Ltd.
Unusual Nitrile–Nitrile and Nitrile–Alkyne Coupling of FcCN and FcCCCN (2014)

The reactions of the Group 4 metallocene alkyne complexes, [Cp*2M(η2-Me3SiC2SiMe3)] (1 a: M=Ti, 1 b: M=Zr, Cp*=η5-pentamethylcyclopentadienyl), with the ferrocenyl nitriles, Fc-CN and Fc-C≡C-C≡N (Fc=Fe(η5-C5H5)(η5-C5H4)), is described. In case of Fc-C≡N an unusual nitrile–nitrile C-C homocoupling was observed and 1-metalla-2,5-diaza-cyclopenta-2,4-dienes (3 a, b) were obtained. As the first step of the reaction with 1 b, the nitrile was coordinated to give [Cp*2Zr(η2-Me3SiC2SiMe3)(N≡C-Fc)] (2 b). The reactions with the 3-ferrocenyl-2-propyne-nitrile FcC≡C-C≡N lead to an alkyne–nitrile C-C coupling of two substrates and the formation of 1-metalla-2-aza-cyclopenta-2,4-dienes (4 a, b). For M=Zr, the compound is stabilized by dimerization as evidenced by single-crystal X-ray structure analysis. The electrochemical behavior of 3 a, b and 4 a, b was investigated, showing decomposition after oxidation, leading to different redox-active products.
Expression of angiogenic factors and hypoxia inducible factors HIF 1, HIF 2 and CA IX in non‐Hodgkin's lymphoma (2002)

Our results suggest that non-Hodgkin's lymphomas may be less angiogenic and hypoxically driven than most solid tumours, which has implications for possible future therapies.
Digitale Vollfeldmammographie (2000)

Due to the extremely high image quality requirements in mammography, there has for a long time been no adequate digital alternative to conventional film-screen mammography. The longest experience so far exists with digital mammography on the basis of storage phosphor (CR) systems. However, at normal dose this technique has a relatively poor signal-to-noise ratio and has not found general acceptance. Recently three novel systems for digital mammography by the companies Fischer (slot-scan detector), Trex (CCD-array), and GE (amorphous silicon detector) have been introduced and are currently under clinical investigation. The main advantage of digital mammography is the linear relationship between dose and detector signal with the possibility of a tailored optimization of image contrast. Other advantages include digital image storage, telemammography, and computer-assisted diagnosis.
Modulation of α-Adrenergic Receptors and their Intracellular Coupling in the Ischemic Heart (1991)

The alpha 1-adrenergic receptor exists as at least two distinct subtypes, alpha 1a and alpha 1b. Based on hydrophobic exclusion studies and limited proteolysis of the cloned receptor, it appears to possess characteristics analogous to other membrane-bound receptors including seven membrane spanning domains, three extracellular, and three intracellular loops, with extensive glycosylation near the extracellular amino terminus. Although the receptor is coupled to phospholipase C in cardiac myocytes, with activation resulting in the production of inositol trisphosphate (IP3) and diacylglycerol, recent findings suggest that the receptor may also be linked to phospholipase A2, phospholipase D, and cyclic nucleotide phosphodiesterase. The alpha 1-adrenergic receptor has been shown to increase in response to myocardial ischemia in a number of different species and to mediate not only positive inotropic effects, but also to contribute substantially to arrhythmogenesis. The increase in alpha 1-adrenergic receptors can also occur in isolated adult ventricular myocytes in response to hypoxia, a mechanism which appears to be secondary to the sarcolemmal accumulation of long-chain acylcarnitines. This increase in alpha 1-adrenergic receptors in hypoxic myocytes is also linked to an enhanced increase in IP3 in response to receptor stimulation. These and other findings obtained in vivo during ischemia suggest that alpha 1-adrenergic mechanisms can become prominent in myocardium under pathophysiologic conditions in which a depressed contractile state exists and may therefore serve as a secondary inotropic system. However, the arrhythmogenic effects of stimulation of the alpha 1-adrenergic receptor in the ischemic heart in man may contribute substantially to arrhythmogenesis and, thereby, to the incidence of sudden cardiac death.
Noninvasive and Invasive Pulmonary Function in Mouse Models of Obstructive and Restrictive Respiratory Diseases (2009)

Pulmonary function analysis is an important tool in the evaluation of mouse respiratory disease models, but much controversy still exists on the validity of some tests. Most commonly used pulmonary function variables of humans are not routinely applied in mice, and the question of which pulmonary function is optimal for the monitoring of a particular disease model remains largely unanswered. Our study aimed to delineate the potential and restrictions of existing pulmonary function techniques in different respiratory disease models, and to determine some common variables between humans and mice. A noninvasive (unrestrained plethysmography) and two invasive pulmonary function devices (forced maneuvers system from Buxco Research Systems [Wilmington, NC] and forced oscillation technique from SCIREQ [Montreal, PQ, Canada]) were evaluated in well-established models of asthma (protein and chemical induced): a model of elastase-induced pulmonary emphysema, and a model of bleomycin-induced pulmonary fibrosis. In contrast to noninvasive tests, both invasive techniques were efficacious for the quantification of parenchymal disease via changes in functional residual capacity, total lung capacity, vital capacity, and compliance of the respiratory system. Airflow obstruction and airflow limitation at baseline were only present in emphysema, but could be significantly induced after methacholine challenge in mice with asthma, which correlated best with an increase of respiratory resistance. Invasive pulmonary functions allow distinction between respiratory diseases in mice by clinically relevant variables, and should become standard in the functional evaluation of pathological disease models.
Synthesis of a Glyoxalase I Inhibitor from Streptomyces griseosporeus NIIDAet OGASAWARA (1985)

Abstract The pseudolactones 6 and 12 were prepared in a straightforward way from methyl α‐ D ‐glucopyranoside and methyl α‐ D ‐mannopyranoside, respectively. The pseudolactone 6 reacted with tert ‐butyl lithioacetate to give the protected, trihydroxylated cyclohexenone carboxylate 7 (51 %). The sterically hindered, L‐ ribo ‐configurated pseudolactone 12 reacted with diethyl ethylphosphonate and dimethyl methylphosphonate to give the protected trihydroxycyclohexenones 17 (49 %) and 18 (62 %), respectively. The hydroxymethylated cyclohexenone 21 was obtained from 18 by treatment with Me 2 AlSPh and then formaldehyde, oxidation of the product 19 , and elimination. Deprotection of 21 gave 2 , identical with KD16‐Ul. Esterification of 2 gave 1 , identical with the title compound. Alternatively, 1 was obtained in higher yields by esterification of 21 , followed by deprotection of the hydroxy groups. This synthesis gave 1 and 2 from methyl α‐ D ‐mannopyranoside in an overall yield of 18 and 20 %, respectively, confirming their absolute configuration.
Bilinear Channel Estimation for MIMO OFDM: Lower Bounds and Training Sequence Optimization (2021)

Time-varying narrowband Multiple-Input Multiple- Output Orthogonal Frequency Division Multiplexing (MIMO OFDM) channel estimation is considered. The effect of finite bandwidth and practical pulse shapes renders the sparse MIMO-OFDM channel, non-sparse - this effect is denoted leakage. It is shown that the leaked MIMO OFDM channel is effectively separable in the delay and Doppler domains. A convex optimization approach, based on the atomic norm, is posed to estimate the channel parameters. With respect to the mean-squared error, the proposed scheme offers a 4 dB improvement over methods that ignore leakage and a 1.3 dB gain over a method that does consider leakage. The Cramér Rao bound (CRB) for the leaked channel parameters is derived and also exhibits decoupling in delay and Doppler. Training sequences that optimize the CRBs for delay and Doppler parameters are determined via solving key fixed-point equations. The optimized random sequences offer a performance gain on the order of 5-2.5 dB over purely random sequences. The proposed channel estimation algorithm nearly achieves the CRB, suggesting near optimality. Finally, the proposed estimation strategy, when employed on experimental data (SPACE'08), provides an average performance gain of 3 dB with respect to the probability of error in comparison to a traditional sparse channel estimation scheme.
Fullscale implementation of external nitrification biological nutrient removal in the Daspoort Water Care Works (2004)

In the external nitrification (EN) biological nutrient removal (BNR) activated sludge (AS) system, the nitrification process is removed from the main BNRAS system to a fixed media system external to the AS system (Hu et al., 2003). The ENBNRAS system provides considerable advantages over the conventional BNRAS system, e.g. reduced bioreactor volumes, secondary settling tank surface area and oxygen demand. Further, the ENBNRAS system provides opportunity for substantial system intensification. The performance and characterization of the ENBNRAS system has been successfully demonstrated at lab-scale (Hu et al., 2000, Sötemann et al., 2002), but has not yet been tested in full-scale implementation. In collaboration between the City of Tshwane Metropolitan Municipality (CTMM) and the University of Cape Town, ENBNR activated sludge is being implemented at fullscale at the Daspoort Waste Water Treatment Works (DWWTW) in Central Pretoria, South Africa. This paper describes the preliminary design of this full-scale plant and initial implementation.
Multi-Fluid Geothermal Energy Production and Storage in Stratigraphic Reservoirs (2013)

Abstract not provided
The Sandwich seal systems: A large-scale shaft sealing experiment at the Mont Terri rock laboratory – Installation and materials (2023)

Shaft seals are part of the engineered barrier system (EBS) that belongs to the multi-barrier system for deep underground repositories of high-level radioactive waste. The German regulator demands that with respect to the reliability of containment, the interplay of barriers has to be optimized in diverse redundancy and shaft seals should also be constructed of diverse redundant components. The design of shaft seals for generic site models of Germany contains hydraulic sealing elements that should be realized as Sandwich sealing systems. In contrast to conventional hydraulic seals of monolithic bentonite the Sandwich sealing system consists of sealing segments (DS) of bentonite and hydraulically conductive equipotential segments (ES) (N&amp;#252;esch et al., 2002). Formation water that is penetrating the hydraulic seal via preferential flow paths is contained in the ES and evenly distributed over the cross section of the seal. Thus, a more homogeneous hydration and swelling of the DS is obtained.In July 2019 a large-scale experiment was launched at the Mont Terri rock laboratory (MTRL) to demonstrate the feasibility of installation, to investigate the saturation process and to assess the sealing effectiveness. The in-situ experiment consists of two experimental shafts of 1.18 m diameter and 10&amp;#160;&amp;#8209;&amp;#160;12.6 m depth in the sandy facies of the Opalinus Clay. The DS in both shafts are constructed of German Ca-bentonites from Bavaria (Calcigel) and Westerwald region (Secursol), respectively. Both Sandwich sealing systems are hydrated with Pearson water type A3 and are intensely monitored, together with the surrounding rock. The in-situ experiment is accompanied by extensive laboratory work and numerical modelling. The laboratory work comprises mineralogical analyses, Oedometer tests, MiniSandwich experiments and semi-technical scale experiments. The variety of experiments on different scales and with different model geometries allow us to recognize and understand different scale-dependent and nonlinear effects on the system behaviour.The presentation will focus on the differences of the two German bentonites with respect to HMC properties and the installation of the Sandwich sealing systems in both shafts at MTRL. The bentonite from Westerwald is characterized by a high smectite content and had to be blended with non-swellable material to adapt expected maximum swelling pressure to the specific site conditions of the in-situ experiment. Both bentonites were then installed as binary mixtures of bentonite pillows and bentonite granular material with similar EMDD, water content and dry density.AcknowledgmentThe Sandwich pre-project and the Sandwich in-situ experiment were/are funded by the German Federal Ministry for Economic Affairs and Energy under contracts 02E11587 and 02E11799.