gebhart/patrepeval huggingface dataset:
Strukturelle Analyse von Phenothiazin‐Derivaten als allosterische Inhibitoren der MALT1‐Paracaspase (2013)

Die Kristallstruktur von humanem MALT1 (mucosa-associated lymphoid tissue lymphoma translocation protein 1), bestehend aus der Paracaspase und der C-terminalen Ig3-Domäne, in Komplex mit dem tricyclischen Phenothiazin-Derivat Thioridazin (violett im Bild) zeigt den Inhibitor an einer weit vom aktiven Zentrum entfernten Bindungsstelle. Dies erklärt warum Phenothiazin-Derivate als nichtkompetitive, reversible Inhibitoren wirken. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. 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.
Electrostatic interaction chromatography : aspects of the salt dependent interactions of proteins (1999)

This thesis studies the ionic strength dependence of protein retention in ion-exchange chromatography (IEC). It discusses some aspects of the use and applicability of retention models in describing the interaction between a protein and the highly charged stationary phase. The two models that are used in the four papers of this thesis are based on the Poisson-Boltzmann equation that describes the distance dependent interaction energy due to the double layer outside a charged surface. The used models have different degrees of simplification in the assumptions regarding the physical properties of the system. Two of the papers use a linear model based on the assumption of two planar surfaces and a linearised potential (the slab model). The non-linear model used in the two remaining papers studies the interaction between a spherical protein of defined size and a planar stationary phase (the sphere model). The latter model does not require a linearised electrostatic potential. In the models, it is assumed that the proteins have an evenly distributed surface charge. Thus, the net charge of the protein can be obtained from an evaluation of the retention data. Experiments performed with proteins in IEC often require gradient elution. Consequently, the two models have been extended to gradient elution conditions. The results are discussed in terms of how well the models describe the ionic strength dependence of the interaction. Further, an evaluation of the parameters obtained by fitting the model to the experimental data is made. Conclusively, this thesis demonstrates the impact of the protein charge distribution on protein retention in IEC through evaluating a set of very similar, well-defined proteins. It shows that the slab model can be applied in gradient elution mode which enables accurate retention prediction in gradient elution mode basedon gradient experiments. By using this procedure determination of isocratic parameters from gradient experiment is also possible. The determination of the isocratic parameters is difficult and requires a model with closer fit to the experimental data, the sphere model. Thereby, it was possible to accurately predict the retention time for human albumin at isocratic elution form gradient data. By using the sphere model, it was shown that the elution behaviour for late eluting proteins are the same in both elution modes whereas it differs for early eluting proteins.
Future advances in uncooled IR sensor technology (2000)

This paper presents an insight into advances in uncooled IR sensor technology. The paper does not speculate on long term futuristic concepts, but addresses what it should be possible to achieve during the next decade. Furthermore, the subject matter is mainly concerned with resistance microbolometer and associated sensor technology. Commercial sensitivity precludes detailed description of new initiatives in this field; however it is possible to outline key avenues of development. If the full potential of uncooled IR technology is to be realized, novel production methods will need to be introduced, particularly for the high volume consumer market. This will involve new detector concepts, focal plane array fabrication technology, readout and signal processing techniques, optical design, and packaging methods. This paper will discuss many of these issues highlighting detector design, performance and fabrication.
Collaborative Memory Pool in Cluster System (2007)

With the developments of network technologies, many mechanisms have been introduced to improve system performance in cluster systems by exploiting remote idle memory. However, none of them can satisfy the requirements from different applications. Most methods can only improve the performance of a particular type of applications but not for others. One important reason is they failed to provide unified interfaces. In this paper, we propose collaborative memory pool (CMP) to solve this problems. CMP brings scalability and high performance. It has five features: (1) Providing malloc-like interfaces, block device interfaces and kernel API for different applications, which benefit both user-level and kernel-level applications; (2) Retaining traditional VM mechanism, programmers and uses have the freedom to select CMP or not; (3) Improving kernel applications performance by eliminating remote swapping; (4) Avoiding loan while in debt problem with dynamic workload; (5) Providing optional memory servers to further improve performance. In our testbed with CMP-based swap devices, Qsort gets 83.28% improvement comparing with the case using disk-based swap devices.
DNA methylation at a CCGG sequence in the large intron of the rabbit β-globin gene: tissue-specific variations (1978)

We have analysed DNA modification in a HapII site (CCGG) present in the major intron of the discontinuous rabbit beta-globin gene. In most somatic tissues, including erythroid and non-erythroid tissues, about 50% of the DNA is resistant to cleavage at this site by HapII, though 100% cleavage is found with the isoschizomer MspI. Since the former enzyme is unable to cleave CCGG sites if the internal C residue is 5-methyl C (and since methylation is the only form of CpG modification documented in animal DNA), while the latter enzyme cleaves DNA irrespective of methylation at this residue, we infer that 50% of the CCGG sites in the beta-globin gene intron are methylated in these tissues. The same site appears to be 100% methylated (judged by the same criterium) in sperm DNA and about 80% methylated in brain DNA. DNA from the rabbit SIRC cell line is entirely unmethylated at this site.
Influence of Pt Catalyst Nanoparticle Size on the Electrochemical Performance of PEM Fuel Cells (2011)

Proton exchange membrane fuel cells (PEMFCs) are alternative high efficiency energy conversion devices considered for automotive and stationary applications. However, the durability of the fuel cell materials used in PEMFCs falls short of the 5,000 operating hour requirement. One of the major reasons for the degradation of PEMFCs is thought to be the loss of electrochemical activity during operation. In this work, we present a systematic study on the impact of Pt nanocatalyst size of PEMFC cathodes on stability and electrochemical performance decay.
Value of serum IgG4 in the diagnosis of IgG4-related disease and in differentiation from rheumatic diseases and other diseases (2012)

IgG4-related disease (IgG4-RD) is a novel disease entity that includes Mikulicz’s disease, autoimmune pancreatitis (AIP), and many other conditions. It is characterized by elevated serum IgG4 levels and abundant IgG4-bearing plasmacyte infiltration of involved organs. We postulated that high levels of serum IgG4 would comprise a useful diagnostic tool, but little information is available about IgG4 in conditions other than IgG4-RD, including rheumatic diseases. Several reports have described cutoff values for serum IgG4 when diagnosing IgG4-RD, but these studies mostly used 135 mg/dL in AIP to differentiate from pancreatic cancer instead of rheumatic and other common diseases. There is no evidence for a cutoff serum IgG4 level of 135 mg/dL for rheumatic diseases and common diseases that are often complicated with rheumatic diseases. The aim of this work was to re-evaluate the usual cutoff serum IgG4 value in AIP (135 mg/dL) that is used to diagnose whole IgG4-RD in the setting of a rheumatic clinic by measuring serum IgG4 levels in IgG4-RD and various disorders. We therefore constructed ROC curves of serum IgG4 levels in 418 patients who attended Sapporo Medical University Hospital due to IgG4-RD and various rheumatic and common disorders. The optimal cut-off value of serum IgG4 for a diagnosis of IgG4-RD was 144 mg/dL, and the sensitivity and specificity were 95.10 and 90.76%, respectively. Levels of serum IgG4 were elevated in IgG4-RD, Churg–Strauss syndrome, multicentric Castleman’s disease, eosinophilic disorders, and in some patients with rheumatoid arthritis, systemic sclerosis, chronic hepatitis, and liver cirrhosis. The usual cut-off value of 135 mg/dL in AIP is useful for diagnosing whole IgG4-RD, but high levels of serum IgG4 are sometimes observed in not only IgG4-RD but also other rheumatic and common diseases.
Towards high-throughput metabolomics using ultrahigh-field Fourier transform ion cyclotron resonance mass spectrometry (2020)

With unmatched mass resolution, mass accuracy, and exceptional detection sensitivity, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS) has the potential to be a powerful new technique for high-throughput metabolomic analysis. In this study, we examine the properties of an ultrahigh-field 12-Tesla (12T) FTICR-MS for the identification and absolute quantitation of human plasma metabolites, and for the untargeted metabolic fingerprinting of inbred-strain mouse serum by direct infusion (DI). Using internal mass calibration (mass error ≤1 ppm), we determined the rational elemental compositions (incorporating unlimited C, H, N and O, and a maximum of two S, three P, two Na, and one K per formula) of approximately 250 out of 570 metabolite features detected in a 3-min infusion analysis of aqueous extract of human plasma, and were able to identify more than 100 metabolites. Using isotopically-labeled internal standards, we were able to obtain excellent calibration curves for the absolute quantitation of choline with sub-pmol sensitivity, using 500 times less sample than previous LC/MS analyses. Under optimized serum dilution conditions, chemical compounds spiked into mouse serum as metabolite mimics showed a linear response over a 600-fold concentration range. DI/FTICR-MS analysis of serum from 26 mice from 2 inbred strains, with and without acute trichloroethylene (TCE) treatment, gave a relative standard deviation (RSD) of 4.5%. Finally, we extended this method to the metabolomic fingerprinting of serum samples from 49 mice from 5 inbred strains involved in an acute alcohol toxicity study, using both positive and negative electrospray ionization (ESI). Using these samples, we demonstrated the utility of this method for high-throughput metabolomics, with more than 400 metabolites profiled in only 24 h. Our experiments demonstrate that DI/FTICR-MS is well-suited for high-throughput metabolomic analysis.
Single Particle Heating and Drying (2014)

This chapter is devoted to the development of a computational fluid dynamics (CFD) based model and a so-called subgrid model for the modeling of the convective heating and drying of a single nonporous and porous coal particle moving in a hot air atmosphere. The CFD-based model utilizes a continuum approach, where the mass, species, momentum, and energy conservation equations are solved numerically for the gas and solid phase using a fixed Eulerian grid. Based on the results of the numerical simulations, subgrid models are developed and validated against analytical, numerical, and experimental data. Finally, we illustrate the model performance by studying the influence of drying conditions such as the ambient temperature (413–1000 K) and particle velocity on the drying process using the CFD and the subgrid model.
Cumulative Impacts of Water Abstraction on a Recreational Salmon Fishery on the Rangitata River, New Zealand (2021)

This study investigates factors contributing to the unexpected loss of a recreational Chinook salmon fishery in a reach of the Rangitata River in Canterbury, New Zealand. The Rangitata is one of only 14 rivers nationwide in which flows are protected by water conservation orders to provide for instream values in the face of competition from extractive uses. However, the river has experienced significant water abstraction or takes for irrigation and hydroelectricity generation, even recently. In this study, local fishers determined flow requirements and conditions for successful fishing based on historical catch data and gauged flows. Relationships between preferred and historical flows were examined using scenario analyses to identify the cumulative impacts of water takes on the conditions required for fishing. An irrigation take of 19.6 m3/s beginning in 2013 was found to have severely reduced the duration of flows in a 30 m3/s flow range that previously supported fishing success. A recently proposed further take of 10 m3/s will completely remove any remaining flows from this preferred flow range. These results show that cumulative takes of water from river systems may have profound and unintended consequences when the flow regimes that support recreational uses are not well understood and retained or protected. Impact assessments that address both cumulative takes and flow-specific values are needed to reliably detect and manage adverse effects. In this case, additional controls are required to maintain the values specifically recognized by the water conservation order.
Short term memory in the calcium messenger system. Evidence for a sustained activation of protein kinase C in adrenal glomerulosa cells (1986)

If adrenal glomerulosa cells are treated with angiotensin II for a period of 20-30 min, their subsequent response to either a rechallenge with the same concentration of angiotensin II or treatment with BAY K 8644, a calcium channel agonist, differs from the responses of control cells. Perifusion of control cells with 10 nM-angiotensin II leads to an increase in aldosterone secretory rate from 44 +/- 7 to 166 +/- 9 pg/min per 10(6) cells, but perifusion of cells pretreated for a 20 min period with angiotensin II leads to an increase in secretory rate from 51 +/- 9 to 209 +/- 18 pg/min per 10(6) cells. Likewise, treatment of control cells with 10 nM-BAY K 8644 leads to no significant increase in aldosterone secretory rate, but treatment of previously exposed cells to angiotensin II leads to an increase in rate from 51 +/- 9 to 130 +/- 11 pg/min per 10(6) cells. This memory effect is time-dependent in two ways: cells must be exposed to angiotensin II for 20 min or more before it is apparent; the longer the time between removal of angiotensin II and the rechallenge, the less effect these agents have on aldosterone secretory rate. When cells are exposed to angiotensin II for 20 min and then treated with [Sar1,Ala8]angiotensin II, a competitive antagonist of angiotensin II action, the aldosterone secretory rate falls to basal with a half time of 5-7 min. If BAY K 8644 is added simultaneously with [Sar1,Ala8]angiotensin II, the secretory rate falls with a halftime of 35-60 min. BAY K 8644 increases Ca2+ influx rate to the same extent in the presence or absence of [Sar1,Ala8]angiotensin II, and does not alter the effect of either angiotensin II or [Sar1,Ala8]angiotensin II on the production of inositol tris-, bis-, or mono-phosphate. In cells treated with 10 nM-angiotensin II for either 20, 30 or 45 min, the extent of phosphorylation of four cellular proteins is increased. If cells treated for 20 min with angiotensin II are then treated with [Sar1,Ala8]angiotensin II, and examined 15 min later (35 min), there is no longer an increase in the extent of phosphorylation of any of the four proteins. If such cells are then treated with 10 nM-BAY K 8644 and re-examined 5 min later (40 min), all four patients show an increase in the extent of phosphorylation.(ABSTRACT TRUNCATED AT 400 WORDS)
22nm half-pitch patterning by CVD spacer self alignment double patterning (SADP) (2008)

Self-aligned double patterning (SADP) is a patterning technique that uses CVD spacers formed adjacent to a core (template) pattern that is defined by conventional lithography. After stripping the core (template) material, the spacers serve as a hardmask with double the line density of the original lithographically defined template. This integration scheme is an alternative to conventional double patterning for extending the half-pitch resolution beyond the current lithography tool's half-pitch limit. Using a positive tone (spacer as mask) approach, we show capability to create 22nm line and space arrays, on 300mm wafers, with full wafer critical dimension uniformity (CDU) < 2nm (3 sigma) and line edge roughness (LER) < 2nm. These 22nm line and space results stem from template lithography using 1.2NA 193nm water immersion lithography. In this paper, we also demonstrate lot to lot manufacturability, the patterning of two substrate types (STI and silicon oxide trench), as well as demonstrate the formation of gridded design rule (GDR) building blocks for circuit design.
Transcriptional regulation of wound suberin deposition in potato cultivars with differential wound healing capacity (2021)

Wounding during mechanical harvesting and post-harvest handling results in tuber desiccation and provides an entry point for pathogens resulting in substantial post​-harvest crop losses. Poor wound healing is a major culprit of these losses. Wound tissue in potato (Solanum tuberosum) tubers, and all higher plants, is composed of a large proportion of suberin that is deposited in a specialized tissue called the wound periderm. However, the genetic regulatory pathway controlling wound-induced suberization remains unknown. Here, we implicate two potato transcription factors, StMYB102 (PGSC0003DMG400011250) and StMYB74 (PGSC0003DMG400022399), as regulators of wound suberin biosynthesis and deposition. Using targeted metabolomics and transcript profiling from the wound healing tissues of two commercial potato cultivars, as well as heterologous expression, we provide evidence for the molecular-genetic basis of the differential wound suberization capacities of different potato cultivars. Our results suggest that (i) the export of suberin from the cytosol to the apoplast and ligno-suberin deposition may be limiting factors for wound suberization, (ii) StMYB74 and StMYB102 are important regulators of the wound suberization process in tubers, and (iii) polymorphisms in StMYB102 may influence cultivar-specific wound suberization capacity. These results represent an important step in understanding the regulated biosynthesis and deposition of wound suberin and provide a practical foundation for targeted breeding approaches aimed at improving potato tuber storage life.
Whole-Body Contrast-Enhanced Magnetic Resonance Angiography (2007)

During the past decade, technical improvements and numerous advances in scanner hardware and software have significantly improved image quality, speed, and reliability of 3-dimensional (3-D) contrast-enhanced magnetic resonance angiography (CE-MRA). The accuracy of CE-MRA is now comparable with that of computed tomography angiography or even conventional catheter angiography. Peripheral vascular disease (PVD) accounts for 50,000 to 60,000 cases of percutaneous transluminal angioplasty and for about 100,000 cases of amputation annually in the United States. Proper treatment of the arterial disease requires a comprehensive assessment of the underlying vascular morphology because it is crucial to localize and gauge the severity of arterial lesions for further therapeutic decision making.Contrast-enhanced magnetic resonance angiography has been widely implemented in noninvasive evaluation of PVD with high diagnostic accuracy. The lack of ionizing radiation and the use of contrast agent with relatively small potential nephrotoxicity in population of PVD with high prevalence of renal impairment are the appealing features for broad acceptance of CE-MRA in initial diagnosis and repeated follow-up studies of patients with PVD. The minimum anatomical coverage for evaluation of PVD comprises the aortic bifurcation to the ankles; however, because of the systemic nature of atherosclerosis hypertension, renal or cerebrovascular disease frequently coexist. Thus, many clinicians regard evaluation of the whole-body arterial vasculature as desirable.
An Interactive and Multimodal Virtual Mind Map for Future Workplace (2019)

Traditional types of mind maps involve means of visually organizing information. They can be created either using physical tools like paper or post-it notes or through the computer-mediated process. Although their utility is established, mind maps and associated methods usually have several shortcomings with regards to effective and intuitive interaction as well as effective collaboration. Latest developments in virtual reality demonstrate new capabilities of visual and interactive augmentation, and in this paper, we propose a multimodal virtual reality mind map that has the potential to transform the ways in which people interact, communicate, and share information. The shared virtual space allows users to be located virtually in the same meeting room and participate in an immersive experience. Users of the system can create, modify, and group notes in categories and intuitively interact with them. They can create or modify inputs using voice recognition, interact using virtual reality controllers, and then make posts on the virtual mind map. When a brainstorming session is finished, users are able to vote about the content and export it for later usage. A user evaluation with 32 participants assessed the effectiveness of the virtual mind map and its functionality. Results indicate that this technology has the potential to be adopted in practice in the future, but a comparative study needs to be performed to have a more general conclusion.
Cellular localization of activated N‐WASP using a conformation‐sensitive antibody (2004)

The main regulators of Arp2/3 activity appear to be N-WASP and the other members of the Scar/WAVE family of proteins. We show here that after EGF stimulation, N-WASP is recruited to the nucleation zone of the dynamic leading edge compartment of carcinoma cells, with maximal recruitment of N-WASP within 1 min after EGF stimulation. The timing of N-WASP recruitment mirrors the timing of barbed-end formation at the leading edge. To determine the cellular activation of N-WASP after EGF stimulation, we made a conformation-sensitive antibody (CSA) against the CRIB domain of N-WASP that is predicted to recognize N-WASP in its open, active conformation, but not in its closed, inactive conformation. The ability of CSA to detect only active N-WASP was demonstrated by in vitro experiments using immunoprecipitation of active N-WASP from EGF-stimulated cells and Cdc42 activation of N-WASP activity. In cell staining experiments, N-WASP is maximally accessible to CSA 40 sec after EGF stimulation and this activated N-WASP is in the nucleation zone. These results indicate that active N-WASP is present at the leading edge of lamellipods, an unexpected finding given its reported involvement in filopod formation. This work establishes the feasibility of using antibodies directed against specific conformations or epitopes with changing accessibilities as a window on the status and localization of activity.