gebhart/patrepeval huggingface dataset:
Crystal structure of human CDK4 in complex with a D-type cyclin (2009)

The cyclin D1-cyclin-dependent kinase 4 (CDK4) complex is a key regulator of the transition through the G(1) phase of the cell cycle. Among the cyclin/CDKs, CDK4 and cyclin D1 are the most frequently activated by somatic genetic alterations in multiple tumor types. Thus, aberrant regulation of the CDK4/cyclin D1 pathway plays an essential role in oncogenesis; hence, CDK4 is a genetically validated therapeutic target. Although X-ray crystallographic structures have been determined for various CDK/cyclin complexes, CDK4/cyclin D1 has remained highly refractory to structure determination. Here, we report the crystal structure of CDK4 in complex with cyclin D1 at a resolution of 2.3 A. Although CDK4 is bound to cyclin D1 and has a phosphorylated T-loop, CDK4 is in an inactive conformation and the conformation of the heterodimer diverges from the previously known CDK/cyclin binary complexes, which suggests a unique mechanism for the process of CDK4 regulation and activation.
Routine clozapine assay monitoring to improve the management of treatment-resistant schizophrenia (2021)

Routine clozapine assay monitoring has significant clinical utility. Our simple but targeted approach can be readily implemented to reduce the number of patients with high-risk clozapine assay levels, potentially reduce all-cause mortality and provide optimal treatment for those with treatment-resistant schizophrenia.
Unsupervised Keyphrase Extraction: Introducing New Kinds of Words to Keyphrases (2016)

Current studies often extract keyphrases by collecting adjacent important adjectives and nouns. However, the statistics on four public corpora shows that about 15% of keyphrases contain other kinds of words. Even so, incorporating such kinds of words to the noun phrase patterns is not a solution to improve the extraction performance. In this work, we propose a solution to improve the extraction performance by involving new kinds of words to keyphrases. We have experimented on four public corpora to demonstrate that our proposal improve the performance of keyphrase extraction and new kinds of words are introduced to keyphrases. In addition, our proposal is also superior to the current unsupervised keyphrase extraction approaches.
A Southern Italian Band Tradition Lives in Northeastern Ohio: Michael Lucente and the Lowellville Mount Carmel Band (2011)

Since their first description, liposomes have been put to a wide variety of uses. Encapsulation or incorporation of antigens into liposomes markedly enhances the immunogenicity of the antigen. The type of immune response elicited by the liposome is found to depend on their chemical and structural properties. Immunization with viral glycoproteins encapsulated in liposomes has resulted in enhancement of the humoral response seen as a rise in the serum antibody levels which is several fold higher than that elicited by free antigen alone. Furthermore, liposome encapsulation of peptide antigens which are poor immunogens by themselves not only increases the immunogenicity of the peptide but also play an important role in delivery. The adjuvant effect afforded by liposomes can be further enhanced by the concomitant encapsulation of adjuvants like lipid A or muramyl tripeptide-phosphatidylethanolamine. Formation of liposomes with special characteristics such as pH sensitivity has resulted in the use of liposomes to deliver soluble antigen to the cytosol where it can undergo class I pathway of processing and presentation. Therefore liposomes could provide valuable tools to further understand the pathways of antigen processing and the requirements for induction of cell mediated immunity.
Interstaple Dithiol Cross-Linking in Au<sub>25</sub>(SR)<sub>18</sub> Nanomolecules: A Combined Mass Spectrometric and Computational Study (2011)

A systematic study of cross-linking chemistry of the Au(25)(SR)(18) nanomolecule by dithiols of varying chain length, HS-(CH(2))(n)-SH where n = 2, 3, 4, 5, and 6, is presented here. Monothiolated Au(25) has six [RSAuSRAuSR] staple motifs on its surface, and MALDI mass spectrometry data of the ligand exchanged clusters show that propane (C3) and butane (C4) dithiols have ideal chain lengths for interstaple cross-linking and that up to six C3 or C4 dithiols can be facilely exchanged onto the cluster surface. Propanedithiol predominately exchanges with two monothiols at a time, making cross-linking bridges, while butanedithiol can exchange with either one or two monothiols at a time. The extent of cross-linking can be controlled by the Au(25)(SR)(18) to dithiol ratio, the reaction time of ligand exchange, or the addition of a hydrophobic tail to the dithiol. MALDI MS suggests that during ethane (C2) dithiol exchange, two ethanedithiols become connected by a disulfide bond; this result is supported by density functional theory (DFT) prediction of the optimal chain length for the intrastaple coupling. Both optical absorption spectroscopy and DFT computations show that the electronic structure of the Au(25) nanomolecule retains its main features after exchange of up to eight monothiol ligands.
The Effects of the Main Variables in the percussive Arc Welding of Electrical Interconnections (1965)

Before accepting percussive arc welding as a production process for making electrical interconnections, it was necessary to determine the effects of the main variables (materials, equipment, and operators) which are certain to be encountered in production. This report deals with a study made to develop the required information. The variables selected for study were materials (wire lots and connector pin lots), operators, and welding machines, each variable at two levels. Two different wire types were investigated. Statistically designed experiments were performed to determine the effects of these variables upon flexing strength, tensile strength, and electrical resistance. In general, significant effects were found for wire lots, operators, and welding machines (usually as interactions.) Although these effects are significant, the magnitude of the change does not appear to be excessive in terms of mean values. These results show that the process is controllable and that initial process standards can be calculated from the data presented.
Adaptive Imaging for Lesion Detection Using a Zoom-in PET System (2010)

Positron emission tomography (PET) has become a leading modality in molecular imaging. Demands for further improvements in spatial resolution and sensitivity remain high with growing number of applications. In this paper we present a novel PET system design that integrates a high-resolution depth-of-interaction (DOI) detector into an existing PET system to obtain higher-resolution and higher-sensitivity images in a target region around the face of the high-resolution detector. A unique feature of the proposed PET system is that the high-resolution detector can be adaptively positioned based on the detectability or quantitative accuracy of a feature of interest. This paper focuses on the signal-known-exactly, background-known-exactly (SKE-BKE) detection task. We perform theoretical analysis of lesion detectability using computer observers, and then develop methods that can efficiently calculate the optimal position of the high-resolution detector that maximizes the lesion detectability. We simulated incorporation of a high-resolution DOI detector into the microPET II scanner. Quantitative results verified that the new system has better performance than the microPET II scanner in terms of spatial resolution and lesion detectability, and that the optimal position for lesion detection can be reliably predicted by the proposed method.
Sphagnum Farming in Germany – a Review of Progress (2014)

In ombrotrophic, nutrient-poor peatlands, the cultivation of peatmoss ( Sphagnum spp.) is a promising paludiculture option. Since 2001 we have been studying peatmoss cultivation (‘Sphagnum farming’) in greenhouse and ﬁeld experiments, paying special attention to propagation, propagule storage, establishment, productivity and regeneration. Our studies show that Sphagnum farming in Germany may provide a sustainable high-quality alternative to fossil white peat as a raw material for horticultural growing media. Sphagnum farming is, furthermore, a climate-friendly and sustainable land use option for abandoned cut-over bogs and degraded bog grassland.
High Frequency Measurements and Noise in Electronic Circuits (1992)

Theoretical background. Practical background/probes. Probe ground lead effects, resonance, and induction. Probe compensation. Differential measurements. Non-contact measurements and magnetic loops. Current probes. Development lab EMC measurements. Measurements in a high inference environment. Digital scopes. Case histories.
Mitochondrial protein hyperacetylation in the failing heart (2016)

Myocardial fuel and energy metabolic derangements contribute to the pathogenesis of heart failure. Recent evidence implicates posttranslational mechanisms in the energy metabolic disturbances that contribute to the pathogenesis of heart failure. We hypothesized that accumulation of metabolite intermediates of fuel oxidation pathways drives posttranslational modifications of mitochondrial proteins during the development of heart failure. Myocardial acetylproteomics demonstrated extensive mitochondrial protein lysine hyperacetylation in the early stages of heart failure in well-defined mouse models and the in end-stage failing human heart. To determine the functional impact of increased mitochondrial protein acetylation, we focused on succinate dehydrogenase A (SDHA), a critical component of both the tricarboxylic acid (TCA) cycle and respiratory complex II. An acetyl-mimetic mutation targeting an SDHA lysine residue shown to be hyperacetylated in the failing human heart reduced catalytic function and reduced complex II-driven respiration. These results identify alterations in mitochondrial acetyl-CoA homeostasis as a potential driver of the development of energy metabolic derangements that contribute to heart failure.
Recent developments of cathepsin inhibitors and their selectivity (2002)

Cathepsins play an important role in the degradation of host connective tissues, the generation of bioactive proteins and antigen processing. They have been implicated in osteoporosis, muscular dystrophy, rheumatoid arthritis, bronchitis, emphysema, viral infection, cancer metastasis and neurodegenerative diseases, such as Alzheimer’s disease and Huntington’s disease. Recently, increased interest in cathepsin inhibitors has been generated with potential therapeutic targets, such as cathepsin K or cathepsin L for osteoporosis and cathepsin S for immune modulation. Of the 53 patents assessed in this review, granted between March 1998 and February 2001, there were 40 patents related to cysteine proteinase inhibitors, 7 related to aspartic proteinase inhibitors and 6 related to serine proteinase inhibitors. Of the 40 patents, 14 disclosed the novel compounds that were more selective against cathepsin K or cathepsin S than cathepsin B and cathepsin L. The compounds, showing experimental evidences, were evaluated and their biological activities in animal models determined. However, only 4 patents presented significant results in vivo. These patents may be a basis for promoting further evaluation and developing second generation cathepsin inhibitors.
Surface Treatment for Mitigation of Hydrogen Absorption and Penetration into AISI 4340 Steel (1993)

The effectiveness of underpotential deposition of Pb onto a membrane made of AISI 4340 steel on the reduction of the hydrogen evolution reaction on the membrane and the degree of hydrogen ingress into the membrane was determined. In the presence of a monolayer coverage of Pb on the membrane surface, the hydrogen evolution currents were reduced by a factor of two compared with the values obtained on bare steel, and the steady‐state hydrogen permeation flux through the steel membranes was reduced by 71%.
Ultrafast near-infrared sintering of a slot-die coated nano-silver conducting ink (2011)

Drying and sintering conductive inks for plastic electronics currently limits the rate of their roll-to-roll manufacture. Near infrared radiation is demonstrated to drastically reduce this process time, achieving conduction under 0.03 Ω per □ in 2 seconds compared to conventional hot-air oven (600 seconds) and infrared methods (84 seconds).
Oxidative metabolism of naphthalene by soil pseudomonads. The ring-fission mechanism (1964)

Research Article| May 01 1964 Oxidative metabolism of naphthalene by soil pseudomonads. The ring-fission mechanism JI Davies; JI Davies Search for other works by this author on: This Site PubMed Google Scholar WC Evans WC Evans Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1964) 91 (2): 251–261. https://doi.org/10.1042/bj0910251 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation JI Davies, WC Evans; Oxidative metabolism of naphthalene by soil pseudomonads. The ring-fission mechanism. Biochem J 1 May 1964; 91 (2): 251–261. doi: https://doi.org/10.1042/bj0910251 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1964 The Biochemical Society1964 Article PDF first page preview Close Modal You do not currently have access to this content.
Preconditioning rabbit cardiomyocytes: role of pH, vacuolar proton ATPase, and apoptosis. (1996)

Ischemic preconditioning signals through protein kinase C (PKC) to protect against myocardial infarction. This protection is characterized by diminished intracellular acidification. Acidification is also a feature of apoptosis, and several agents act to prevent apoptosis by preventing acidification through activation of ion channels and pumps to promote cytoplasmic alkalinization. We characterized metabolic inhibition, recovery, and preconditioning through a PKC-dependent pathway in cardiomyocytes isolated from adult rabbit hearts. Preconditioning reduced loss of viability assessed by morphology and reduced DNA nicking. Blockade of the vacuolar proton ATPase (VPATPase) prevented the effect of preconditioning to reduce metabolic inhibition-induced acidosis, loss of viability, and DNA nicking. The beneficial effect of Na+/H+ exchange inhibition, which is thought to be effective through reduced intracellular Na+ and Ca++, was also abrogated by VPATPase blockade, suggesting that acidification even in the absence of Na+/H+ exchange may lead to cell death. We conclude that a target of PKC in mediating preconditioning is activation of the VPATPase with resultant attenuation of intracellular acidification during metabolic inhibition. Inhibition of the "death protease," interleukin-1-beta converting enzyme or related enzymes, also protected against the injury that followed metabolic inhibition. This observation, coupled with the detection of DNA nicking in cells subjected to metabolic inhibition, suggests that apoptotic cell death may be preventable in this model of ischemia/reperfusion injury.
Investigations into the transcriptome of the toxigenic marine dinoflagellate Alexandrium minutum (2009)

Dinoflagellates of the A. minutum species complex are widely distributed bloom-forming, photosynthetic protists typically producing potent neurotoxins which cause paralytic shellfish poisoning (PSP). Human intoxications usually occur via the ingestion of filter-feeding bivalves, but intoxications after consumption of predatory crabs have also been reported. The same group of toxins is produced by certain freshwater cyanobacteria, in which the gene cluster coding for the PSP toxin-producing enzymes has recently been identified. However, the identification of corresponding genes in dinoflagellates is pending, which might be due to their unusual and little understood genomes.The aim of this thesis is to contribute to understanding gene expression and regulation in dinoflagellates by investigating the transcriptome-level gene expression in A. minutum. The gene expression experiments were based on an expressed sequence tag (EST) library, which was generated from pooled samples originating from different treatments to include the highest possible diversity of cDNA sequences. A set of microarray probes based on this library was used for different gene expression experiments, such as the comparison of toxic and non-toxic strains. Three stains were compared at two different times of the light phase, yielding a group of 192 genes differentially expressed between toxic and non-toxic strains at both timepoints. Another experiment was based on the induction of a fivefold increase in toxin levels by the presence of a copepod grazer. In combination with the data obtained from the strain comparison experiment, this resulted in the identification of two sequences potentially correlated to the ability to produce the toxins.Other treatments were designed to represent extreme values of ecologically significant parameters, such as different salinities or nutrient limitation. While the transcriptomic differences between cultures acclimatised to different salinities remained moderate and indicated a high prevalence of differences in post-transcriptional processes, the differences among growth phases and between nutrient-replete and nutrient-limited batch cultures were considerable. By using combinations of comparisons, several genes consistently up-regulated at the transition between exponential growth and stationary phase were identified, as well as 87 genes consistently associated with N- or P-limitation.In the course of this thesis, I identified several A. minutum genes apparently associated with intracellular toxins, as well as patterns of gene expression indicative of culture growth status and of nutrient limitation. These data substantially add to the emerging field of dinoflagellate transcriptomics. Additionally, they provide a starting point for the potential development of new monitoring tools testing the physiological status or toxin-producing potential of A. minutum populations.
Interactive Tree Comparison for Co-located Collaborative Information Visualization (2007)

In many domains increased collaboration has lead to more innovation by fostering the sharing of knowledge, skills, and ideas. Shared analysis of information visualizations does not only lead to increased information processing power, but team members can also share, negotiate, and discuss their views and interpretations on a dataset and contribute unique perspectives on a given problem. Designing technologies to support collaboration around information visualizations poses special challenges and relatively few systems have been designed. We focus on supporting small groups collaborating around information visualizations in a co-located setting, using a shared interactive tabletop display. We introduce an analysis of challenges and requirements for the design of co-located collaborative information visualization systems. We then present a new system that facilitates hierarchical data comparison tasks for this type of collaborative work. Our system supports multi-user input, shared and individual views on the hierarchical data visualization, flexible use of representations, and flexible workspace organization to facilitate group work around visualizations.
Investigations into electrically evoked stapedius reflex measures and subjective loudness percepts in the MED-EL COMBI 40+ cochlear implant (2005)

For several years there has been interest in using objective measures to set channel-specific upper programming limits when programming the speech processor of cochlear implant users. The present study aims to add to previous reports by examining correlations between electrically evoked stapedius reflex threshold (ESRT) and a range of psychophysical loudness estimates in a group of 22 adult users of the MED-EL COMBI 40+ system. Thirteen of the 15 subjects (87%) had recordable stapedius reflexes. Psychophysical measures of threshold, maximum comfort level (MCL) and maximum acceptable loudness (MAL) were recorded. Results showed that mean ESRT was closest to the MCL using 500 ms burst ('MCL500'), with MCL50 (MCL using 50 ms burst) and MAL500 some 2dB and MAL50 3dB higher. Correlations between ESRT and the behavioural loudness judgements were highest for MCL500 (R = 0.69, p < 0.001) and slightly less for MAL500. These results confirm the ease of measuring ESRT in a clinical setting and that a high level of confidence can be placed on the use of these measures for setting processor maps in the absence of behavioural data.
Peritoneal Sclerosis in Chronic Peritoneal Dialysis Patients: Analysis of Clinical Presentation, Risk Factors, and Peritoneal Transport Kinetics (1997)

The presenting symptoms of PS were bowel obstruction, ascites, and blood-stained effluent, often in combination with loss of net ultrafiltration. Peritoneal sclerosis is a complication of long-duration PD and could also become manifest after a successful renal transplant. Treatment should be conservative unless complications require surgical intervention. Patients with PS had lower net ultrafiltration and higher transport rates compared to controls who were matched for duration of PD. Although peritonitis incidence was similar, a relation of PS with severe peritonitis may be present in some patients. Glucose exposure is likely to be an important risk factor for PS.
Time-to-digital converter with 3-ps resolution and digital linearization algorithm (2010)

This paper presents a digital scrambling technique to improve the linearity of flash time-to-digital converters (TDCs) with sub-gate-delay time resolution. Thanks to this approach, a flash TDC using N time arbiters behaves as a quasi-stochastic TDC with an equivalent number of samples equal to N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , at the negligible area cost of doubling the number of minimum load capacitors. The concept is proved in a 65-nm CMOS technology 40MHz TDC, which achieves a 3ps resolution. The differential nonlinearity is reduced from 1LSB to less than 0.2LSB.
Parallel diurnal fluctuation of testosterone, androstenedione, dehydroepiandrosterone and 17OHprogesterone as assessed in serum and saliva: validation of a novel liquid chromatography-tandem mass spectrometry method for salivary steroid profiling (2017)

Our LC-MS/MS method allowed a sensitive evaluation of androgen salivary levels and represents an optimal technique to explore the relevance of a comprehensive androgen profile as measured in saliva for the study of androgen secretion modulation and activity in physiologic and pathologic states.