gebhart/patrepeval huggingface dataset:
Two‐Photon Fluorescent Probes for Acidic Vesicles in Live Cells and Tissue (2008)

Move with the groove: Two-photon fluorescent pH probes and a two-photon lysotracker (AL1) can visualize acidic vesicles in live cells and living tissue for a long period of time without mistargeting and photobleaching problems. Using AL1, vesicles can be tracked in real time (see picture).
Coverage based test-case generation using model checkers (2002)

Presents a method for automatically generating test cases according to structural coverage criteria. We show how a model checker can be used to automatically generate complete test sequences that provide a pre-defined coverage of any software development artifact that can be represented as a finite state model. Our goal is to help reduce the high cost of developing test cases for safety-critical software applications that require a certain level of coverage for certification, e.g. safety-critical avionics systems that need to demonstrate MC/DC (modified condition and decision) coverage of the code. We define a formal framework which is suitable for modeling software artifacts like requirements models, software specifications or implementations. We then show how various structural coverage criteria can be formalized and used to make a model checker provide test sequences to achieve this coverage. To illustrate our approach, we demonstrate how a model checker can be used to generate test sequences for MC/DC coverage of a small case example.
Carbon-13 enriched S-methyl probe at the active site of an enzyme: [S-[13C]methylmethionine-192]-.alpha.-chymotrypsin (MSMC) (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbon-13 enriched S-methyl probe at the active site of an enzyme: [S-[13C]methylmethionine-192]-.alpha.-chymotrypsin (MSMC)H. Neal Bramson, Nancy Thomas, William F. DeGrado, Patricia A. Henderson, Mark W. Russo, and Richard L. ThomasCite this: J. Am. Chem. Soc. 1980, 102, 23, 7151–7152Publication Date (Print):November 5, 1980Publication History Published online1 May 2002Published inissue 5 November 1980https://pubs.acs.org/doi/10.1021/ja00543a065https://doi.org/10.1021/ja00543a065research-articleACS PublicationsRequest reuse permissionsArticle Views40Altmetric-Citations6LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Role ofBurkholderia pseudomallei–Specific IgG2 in Adults with Acute Melioidosis, Thailand (2021)

Melioidosis is a life-threatening infectious disease caused by the gram-negative bacillus Burkholderia pseudomallei. An effective vaccine is needed, but data on protective immune responses in human melioidosis are lacking. We used ELISA and an antibody-dependent cellular phagocytosis assay to identify the major features of protective antibodies in patients with acute melioidosis in Thailand. We found that high levels of B. pseudomallei-specific IgG2 are associated with protection against death in a multivariable logistic regression analysis adjusting for age, diabetes, renal disease, and neutrophil count. Serum from melioidosis survivors enhanced bacteria uptake into human monocytes expressing FcγRIIa-H/R131, an intermediate-affinity IgG2-receptor, compared with serum from nonsurvivors. We did not find this enhancement when using monocytes carrying the low IgG2-affinity FcγRIIa-R131 allele. The findings indicate the importance of IgG2 in protection against death in human melioidosis, a crucial finding for antibody-based therapeutics and vaccine development.
Un cas de lymphome malin primitif non hodgkinien du muscle squelettique traité par chimiothérapie seule A case of malignant primary non-Hodgkin's lymphoma in skeletal muscle treated by exclusive chemotherapy (2009)

A case of malignant primary non-Hodgkin’s lymphoma in skeletal muscle treated by exclusive chemotherapy Jean-Michel Laffosse a,∗, Anne Gomez-Brouchet b, Francois Molinier a, Philippe Chiron a, Henri Roche c, Jean Puget a a Service de chirurgie orthopedique et traumatologique, CHU Rangueil, 1, avenue Jean-Poulhes TSA 50032, 31059 Toulouse cedex 9, France b Service d’anatomo-cyto-pathologie, CHU Rangueil, 31000 Toulouse, France c Institut Claudius-Regaud, Toulouse, France Accepte le 1er fevrier 2008 Disponible sur Internet le 18 decembre 2008
Human and Climatic Influences on Fire Occurrence in California’s North Coast Range, USA (2009)

Outside of the immediate coastal environments, little is known of fire history in the North Coast Range of California. Fire scar specimens were collected from ponderosa pine (Pinus ponderosa C. Lawson), sugar pine (Pinus lambertiana Douglas), incense cedar (Calocedrus decurrens [Torr] Florin), and Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) for seven plots in mixed-conifer forests from the Mendocino National Forest, California, USA. Five plots were on high ridges immediately adjacent to the Sacramento Valley (DRY plots). The other two plots were on mesic north facing slopes interior in the range (MESIC plots), and were separated from the Sacramento Valley by at least one to several ridge systems. These two plots were selected because they supported populations of rare lady’s slipper orchids (Cypripedium fasciculatum [Kellogg ex S. Watson] and C. montanum [Douglas ex Lindl.]). We found that DRY plots had unusually short fire return intervals (FRI) compared to other areas in northwestern California. The median FRI for these plots ranged from 4.5 yr to 6 yr in comparison with a tenth percentile of 11 yr, grand median of 24 yr, and ninetieth percentile of 66 yr for FRIs from other mixed conifer plots (n = 109) in the region. In northwestern California, most fire scars have been found primarily at ring boundary (68%) and secondarily in latewood (23%) with few in earlywood (9%). In contrast, in the DRY plots 35% (88) of the fire scars were in earlywood with only 15% (39) at the ring boundary. Fire occurrence was associated with drought conditions in the year of fire, and with wet conditions three years before the fire year. Before ∼1850, fires that scarred at least two trees on a site were quite frequent for the DRY plots while being less frequent and more variable on the MESIC plots. However, the MESIC orchid habitats burned with frequency and seasonality similar to mixed conifer forests in the Klamath Mountains of northern California. Fires were less frequent after ∼1850, with fires ceasing on most plots shortly after 1900. We suggest that these unusually low FRIs and high incidence of fire scars in earlywood were due to the adjacency of the DRY plots to the hot, relatively dry Sacramento Valley grasslands that were likely influenced by the burning practices of Native Americans.
Inflammation and Subclinical Infection in Chronic Kidney Disease: A Molecular Approach (2006)

Inflammation and infection seem to be important causes of morbidity and mortality in chronic kidney disease (CKD) patients; subclinical infections have been proposed as an important cause of inflammatory syndrome, but to date this hypothesis remains speculative. We developed a method for the molecular detection of the presence of bacterial DNA in a population of CKD patients in order to correlate the molecular data with the degree and level of inflammation and to evaluate its usefulness in the diagnosis of subclinical infection. The study was divided into two phases: (1) a population of 81 CKD patients was screened for the prevalence and level of inflammation and the presence of possible infection, and (2) a subgroup of 38 patients, without evident clinical causes of inflammation, underwent complete molecular evaluation for subclinical infection using bacterial DNA primers for sequencing. Additionally, complete analysis was carried out in the blood and dialysate compartments of the hemodialyzers used. The general population showed a certain degree of subclinical inflammation and no difference was found between patients with and without evident causes of inflammation. Hemoculture-negative patients were positive for the presence of bacterial DNA when molecular methods were used. We found a correlation trend between the presence of bacterial DNA and the increase in hs-CRP, IL-6 and oxidative stress (advanced oxidation protein product) levels and a reduction in the mean fluorescence intensity for HLA-DR. Hemodialyzer membranes seem to have properties that stick to bacteria/bacterial DNA and work as concentrators. In fact, patients with negative bacterial DNA in the circulating blood displayed positivity in the blood compartment of the dialyzer. The dialysate was negative for bacterial DNA but the dialysate compartment of the hemodialyzers used was positive in a high percentage. Moreover our data suggest that bacterial DNA can traverse hemodialysis membranes. Molecular methods have been found to be far more sensitive than standard methods in detecting subclinical infection. The presence of bacterial DNA seems to influence the variation in some parameters of inflammation and immunity. Apart from the limitations and pitfalls, the molecular method could be useful to screen for subclinical infection and diagnose subclinical sepsis when the hemoculture is negative. However, the identification of the microorganism implicated must be done with species-specific primers.
T-ray Tomographic Imaging (2002)

We present three T-ray (terahertz wave) tomographic imaging modalities: T-ray computed tomography, T-ray diffraction tomography, and tomographic imaging with a Fresnel binary lens. Each of these techniques uses pulses of broadband terahertz radiation to obtain 3-dimensional images of targets with wide potential application. We present images demonstrating the performance of each technique and discuss their relative advantages.
Laser frequency offset synthesizer (1985)

A method for servolocking the beat frequency between two lasers is described in which the lasers in effect replace the voltage-controlled oscillator in an indirect frequency synthesizer. The system is simple, relatively free from systematic frequency errors, and has good stability as characterized by Allan variance measurements.
Impact of Local Adjuncts to Scaling and Root Planing in Periodontal Disease Therapy: A Systematic Review (2005)

Whether such improvements, even if statistically significant, are clinically meaningful remains a question. A substantial agenda of future research to address this and other issues (e.g., costs, patient-oriented outcomes) is suggested.
Analytical and numerical simulation of multipactor within a helical resonant filter (2017)

Multipactor analysis of a helical resonant filter has been performed using CST Particle Studio and analytically using a 1-D particle tracking code, based on the Runge-Kutta-Nystrom method. A comparison of results is presented.
Protection against peroxynitrite (1999)

Peroxynitrite formed in vivo from superoxide and nitric oxide can mediate oxidation, nitration, or nitrosation reactions, leading to impaired function, toxicity, and alterations in signaling pathways. Protection against peroxynitrite is important for defense of normal tissue, especially during inflammation. Biological protection against peroxynitrite is organized in three categories: prevention, interception, and repair. Prevention is the control of the formation of peroxynitrite precursors, nitric oxide and superoxide. Interception is by direct reaction with peroxynitrite, leading to non-toxic products. In this regard, organoselenium compounds, metalloporphyrin derivatives, and peroxidases (e.g. glutathione peroxidase and myeloperoxidase) exhibit high second-order rate constants with peroxynitrite. Ebselen, like glutathione peroxidase, protects in a catalytic fashion utilizing glutathione as reductant in the peroxynitrite reductase reaction. Protection by metalloporphyrins can be maintained through glutathione or ascorbate. Repair processes remove damaged products and restitute intact biomolecules.
PointCloudExplore 2: Visual exploration of 3D gene expression (2008)

To better understand how developmental regulatory networks are defined inthe genome sequence, the Berkeley Drosophila Transcription Network Project (BDNTP)has developed a suite of methods to describe 3D gene expression data, i.e.,the output of the network at cellular resolution for multiple time points. To allow researchersto explore these novel data sets we have developed PointCloudXplore (PCX).In PCX we have linked physical and information visualization views via the concept ofbrushing (cell selection). For each view dedicated operations for performing selectionof cells are available. In PCX, all cell selections are stored in a central managementsystem. Cells selected in one view can in this way be highlighted in any view allowingfurther cell subset properties to be determined. Complex cell queries can be definedby combining different cell selections using logical operations such as AND, OR, andNOT. Here we are going to provide an overview of PointCloudXplore 2 (PCX2), thelatest publicly available version of PCX. PCX2 has shown to be an effective tool forvisual exploration of 3D gene expression data. We discuss (i) all views available inPCX2, (ii) different strategies to perform cell selection, (iii) the basic architecture ofPCX2., and (iv) illustrate the usefulness of PCX2 using selected examples.
Principal metabolic maps of major metabolites illustrated using VANTED from Metabolome Analyses Uncovered a Novel Inhibitory Effect of Acyclic Retinoid on Aberrant Lipogenesis in a Mouse Diethylnitrosamine-Induced Hepatic Tumorigenesis Model (2023)

&lt;p&gt;The relative quantities of the detected metabolites involved in glycolysis/glyconeogenesis (A), the urea cycle (B), pyrimidine metabolism (C), amino acid metabolism (D), and nicotinate and nicotinamide metabolism (E) are represented as bar graphs (from left to right: DEN group, DEN-0.03ACR group, DEN-0.06 group, and 0.06ACR group). N.D., not detected.&lt;/p&gt;
Combination of whole exome sequencing and animal modeling identifies TMPRSS9 as a candidate gene for autism spectrum disorder (2020)

Abstract Autism spectrum disorders are associated with some degree of developmental regression in up to 30% of all cases. Rarely, however, is the regression so extreme that a developmentally advanced young child would lose almost all ability to communicate and interact with her surroundings. We applied trio whole exome sequencing to a young woman who experienced extreme developmental regression starting at 2.5 years of age and identified compound heterozygous nonsense mutations in TMPRSS9, which encodes for polyserase-1, a transmembrane serine protease of poorly understood physiological function. Using semiquantitative polymerase chain reaction, we showed that Tmprss9 is expressed in various mouse tissues, including the brain. To study the consequences of TMPRSS9 loss of function on the mammalian brain, we generated a knockout mouse model. Through a battery of behavioral assays, we found that Tmprss9−/− mice showed decreased social interest and social recognition. We observed a borderline recognition memory deficit by novel object recognition in aged Tmprss9−/− female mice, but not in aged Tmprss9−/− male mice or younger adult Tmprss9−/− mice in both sexes. This study provides evidence to suggest that loss of function variants in TMPRSS9 are related to an autism spectrum disorder. However, the identification of more individuals with similar phenotypes and TMPRSS9 loss of function variants is required to establish a robust gene–disease relationship.
The Use of Murata Ceramic Bluetooth Antenna for Wrist Device Based on Flexible Printed Circuit Boards (2008)

In this paper, the Murata ceramic Bluetooth antenna, which has been successfully used on rigid printed circuit boards, is now applied to flexible printed circuit boards. Based on this Bluetooth antenna, a novel wrist device that can be wirelessly connected to mobile phones is developed. In particular, to reduce the height of the wrist device, the ground-clearance type Murata Bluetooth antenna is adopted. It is demonstrated that the wrist device works very well in real environments.
Actin polymerization downstream of integrins: signaling pathways and mechanotransduction (2020)

A cell constantly adapts to its environment. Cell decisions to survive, to proliferate or to migrate are dictated not only by soluble growth factors, but also through the direct interaction of the cell with the surrounding extracellular matrix (ECM). Integrins and their connections to the actin cytoskeleton are crucial for monitoring cell attachment and the physical properties of the substratum. Cell adhesion dynamics are modulated in complex ways by the polymerization of branched and linear actin arrays, which in turn reinforce ECM-cytoskeleton connection. This review describes the major actin regulators, Ena/VASP proteins, formins and Arp2/3 complexes, in the context of signaling pathways downstream of integrins. We focus on the specific signaling pathways that transduce the rigidity of the substrate and which control durotaxis, i.e. directed migration of cells towards increased ECM rigidity. By doing so, we highlight several recent findings on mechanotransduction and put them into a broad integrative perspective that is the result of decades of intense research on the actin cytoskeleton and its regulation.
A Review of the Role of Cytogenetics in the Diagnosis of Orbital Rhabdomyosarcoma (2019)

Rhabdomyosarcoma (RMS) is the most common sarcoma of childhood and adolescence. Approximately 10% arise in the orbit, where the embryonal type is most common variant. The alveolar variant is less frequent and has a worse prognosis. Cytogenetic studies have revealed that most alveolar rhabdomyosarcomas have translocations involving the PAX and the FOX01 genes, giving rise to fusion genes that contribute to lack of differentiation and proliferation of the tumor cells. However, approximately 20% of alveolar rhabdomyosarcomas lack translocations and have been found to behave more similarly to embryonal cases. Histopathology remains the basis of diagnosis, but cytogenetic features and molecular signatures are becoming part of the routine analysis of RMS, since they determine not only prognosis, but also management and treatment regimens. A comprehensive review of the recent published literature in relation to orbital rhabdomyosarcomas and their cytogenetic features as well as clinical and therapeutic implications will be discussed.
Isolation and Physiological Activities of Piericidin A, A Natural Insecticide Produced byStreptomyces (1963)

In the course of screening research on new insecticides among metabolites of microorganisms, two active components were isolated from mycellia of Streptomyces sp. 16–22. The names, Piericidin A and B, were proposed to these active metabolites. Isolation procedure, physical and chemical properties and physiological activities of Piericidin A were presented. From the results of taxonomic study on Streptomyces sp. 16–22, it was found that this is a new species, to which the name, Streptomyces mobaraensis Nagatsu et Suzuki, was proposed.
An Actualized Survey of Micellar Nematic Lyophases (1988)

Abstract A table is given for nematic solutions from amphiphilic compounds providing literature data up to 1986. The table includes the solutions reported in the summary of Forrest from 1981. The phases are classified according to their type Nc +, Nc −, ND + and ND − and grouped according to their composition.
Probability Density Functions for Multilook (1994)

We derive closed-form expressions for the proba- bility density functions (PDF's) for copolar and cross-polar ra- tios and for the copolar phase difference for multilook polari- metric SAR data, in terms of elements of the covariance matrix for the backscattering process. We begin with the case in which scattering-matrix data are jointly Gaussian-distributed. The resulting copolar-phase PDF is formally identical to the phase PDF arising in the study of SAR interferometry, so our results also apply in that setting. By direct simulation, we verify the closed-form PDF's. We show that estimation of signatures from averaged covariance matrices results in smaller biases and variances than averaging single-look signature estimates. We then generalize our derivation to certain cases in which back- scattered intensities and amplitudes are K-distributed. We find in a range of circumstances that the PDF% of polarimetric sig- natures are unchanged from those derived in the Gaussian case. We verify this by direct simulation, and also examine a case that fails to satisfy an important assumption in our derivation. The forms of the signature distributions continue to describe data well in the latter case, but parameters in distributions fit- ted to (simulated) data differ from those used to generate the data. Finally, we examine samples of K-distributed polarimet- ric SAR data from Arctic sea ice and find that our theoretical distributions describe the data well with a plausible choice of parameters. This allows us to estimate the precision of polari- metric-signature estimates as a function of the number of SAR looks and other system parameters.
Glucocorticoid augmentation of prolonged exposure therapy: rationale and case report (2010)

While no general conclusion can be derived from comparison of two patients, the findings are consistent with the rationale for augmentation. These case reports support the potential for an appropriately designed and powered clinical trial to examine the efficacy of glucocorticoids in augmenting the effects of psychotherapy for PTSD.
Study on next-generation DC electric railway systems incorporating superconducting power cables (2012)

We have studied how to introduce superconducting power cables effectively and economically to a DC electric railway. Numerical analysis models were constructed, and the energy saving by the superconducting power cable was investigated with the influences of the number of substations, the train operation interval, the energy storage, etc. also taken into account. The results show that the superconducting power cables can improve regenerative energy and system energy saving, and reduce the substation capacity.