gebhart/patrepeval huggingface dataset:
Bayesian localization microscopy based on intensity distribution of fluorophores (2015)

Super-resolution microscopy techniques have overcome the limit of optical diffraction. Recently, the Bayesian analysis of Bleaching and Blinking data (3B) method has emerged as an important tool to obtain super-resolution fluorescence images. 3B uses the change in information caused by adding or removing fluorophores in the cell to fit the data. When adding a new fluorophore, 3B selects a random initial position, optimizes this position and then determines its reliability. However, the fluorophores are not evenly distributed in the entire image region, and the fluorescence intensity at a given position positively correlates with the probability of observing a fluorophore at this position. In this paper, we present a Bayesian analysis of Bleaching and Blinking microscopy method based on fluorescence intensity distribution (FID3B). We utilize the intensity distribution to select more reliable positions as the initial positions of fluorophores. This approach can improve the reconstruction results and significantly reduce the computational time. We validate the performance of our method using both simulated data and experimental data from cellular structures. The results confirm the effectiveness of our method.
Clinical and Biological Correlates of Neurotoxicity Associated with CAR T-cell Therapy in Patients with B-cell Acute Lymphoblastic Leukemia (2018)

CD19-specific chimeric antigen receptor (CAR) T-cell therapy is highly effective against relapsed or refractory acute lymphoblastic leukemia (ALL), but is hindered by neurotoxicity. In 53 adult patients with ALL, we found a significant association of severe neurotoxicity with high pretreatment disease burden, higher peak CAR T-cell expansion, and early and higher elevations of proinflammatory cytokines in blood. Patients with severe neurotoxicity had evidence of blood-cerebrospinal fluid (CSF) barrier disruption correlating with neurotoxicity grade without association with CSF white blood cell count or CAR T-cell quantity in CSF. Proinflammatory cytokines were enriched in CSF during severe neurotoxicity with disproportionately high levels of IL6, IL8, MCP1, and IP10, suggesting central nervous system-specific production. Seizures, seizure-like activity, myoclonus, and neuroimaging characteristics suggested excitatory neurotoxicity, and we found elevated levels of endogenous excitatory agonists in CSF during neurotoxicity.<b>Significance:</b> We detail the neurologic symptoms and blood, CSF, and neuroimaging correlates of neurotoxicity associated with CD19 CAR T cells and identify neurotoxicity risk factors. Our findings implicate cellular components other than T cells and suggest novel links between systemic inflammation and characteristic neurotoxicity symptoms. <i>Cancer Discov; 8(8); 958-71. ©2018 AACR.</i><i>This article is highlighted in the In This Issue feature, p. 899</i>.
Purification and properties of xylanase fromAureobasidium (1989)

The yeast-like fungus Aureobasidium is a promising source of xylanase (EC 3.2.1.8) with an exceptionally high specific activity. For enzyme production in volumes of several liters, xylose was the preferred carbon source and inducer. Xylanase in clarified cultures was concentrated by reversible adsorption to cation-exchange matrix to 5% of the initial volume, and recovered at nearly 2 million IU/1. Selective conditions permitted 97% recovery of xylanase with a 1.8-fold enrichment in specific activity, to 70% of purity. The predominant xylanase species (20 kDa) was subsequently purified to > 99% of homogeneity by gel filtration chromatography. Purified enzyme exhibited an isoelectric point of 8.5, and specific activity of 2100 IU/mg under optimal conditions, determined to be pH 4.5 and 45~ The activity of purified enzyme was specific for polymeric xylan.
Characterization of Serum Cytokine Profile in Predominantly Colonic Inflammatory Bowel Disease to Delineate Ulcerative and Crohn's Colitides (2015)

The current knowledge available about circulating cytokines in IBD is often contradictory. The development of an evidence-based tool using cytokines for diagnostic accuracy is still preliminary.
Transformation of <i>Arabidopsis thaliana</i> with the <i>codA</i> gene for choline oxidase; accumulation of glycinebetaine and enhanced tolerance to salt and cold stress (1997)

Glycinebetaine is one of the compatible solutes that accumulate in the chloroplasts of contain halotolerant plants when these plants are exposed to salt or cold stress. The codA gene for choline oxidase, the enzyme that converts choline into glycinebetaine, has previously been cloned from a soil bacterium, Arthrobacter globiformis. Transformation of Arabidopsis thaliana with the cloned codA gene under the control of the 35S promoter of cauliflower mosaic virus enabled the plant to accumulate glycinebetaine and enhanced its tolerance to salt and cold stress. At 300 mM NaCl, considerable proportions of seeds of transformed plants germinated well, whereas seeds of wild-type plants failed to germinate. At 100 mM NaCl, transformed plants grew well whereas wild-type plants did not do so. The transformed plants tolerated 200 mM NaCl, which was lethal to wild-type plants. After plants had been incubated with 400 mM NaCl for two days, the photosystem II activity of wild-type plants had almost completely disappeared, whereas that of transformed plants remained at more than 50% of the original level. When exposed to a low temperature in the light, leaves of wild-type plants exhibited symptoms of chlorosis, whereas those of transformed plants did not. These observations demonstrate that the genetic modification of Arabidopsis thaliana that allowed it to accumulate glycinebetaine enhanced its ability to tolerate salt and cold stress.
Near-Infrared Reflectance Analysis (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNear-Infrared Reflectance AnalysisDavid L. WetzelCite this: Anal. Chem. 1983, 55, 12, 1165A–1176APublication Date (Print):October 1, 1983Publication History Published online29 May 2012Published inissue 1 October 1983https://pubs.acs.org/doi/10.1021/ac00262a718https://doi.org/10.1021/ac00262a718research-articleACS PublicationsRequest reuse permissionsArticle Views496Altmetric-Citations173LEARN 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
Tin and germanium monochalcogenide IV–VI semiconductor nanocrystals for use in solar cells (2011)

The incorporation of colloidal semiconductor nanocrystals into the photoabsorbant material of photovoltaic devices may reduce the production costs of solar cells since nanocrystals can be readily synthesized on a large scale and are solution processable. While the lead chalcogenide IV-VI nanocrystals have been widely studied in a variety of photovoltaic devices, concerns over the toxicity of lead have motivated the exploration of less toxic materials. This has led to the exploration of tin and germanium monochalcogenide IV-VI semiconductors, both of which are made up of earth abundant elements and possess properties similar to the lead chalcogenides. This feature article highlights recent efforts made towards achieving synthetic control over nanocrystal size and morphology of the non-lead containing IV-VI monochalcogenides (i.e., SnS, SnSe, SnTe, GeS and GeSe) and their application toward photovoltaic devices.
Improved sensitivity in flow cytometric intracellular ionized calcium measurement using fluo‐3/Fura Red fluorescence ratios (1994)

Measurement of changes in intracellular ionized calcium concentrations ([Ca2+]i) has proved to be of wide use in the study of cellular responses to activating stimuli. The fluorescent dye Indo-1 has successfully been used in flow cytometry for this purpose, and when used as a ratiometric indicator it provides optimum sensitivity and accuracy. Unfortunately, this dye requires ultraviolet (UV) excitation which is often not available. We show here that similar results can be obtained using a ratio of green to red fluorescence from the simultaneous loading of the dyes Fura Red and fluo-3. Both Fura Red and fluo-3 are excited using the commonly available blue 488 nm laser line. With appropriate concentrations of the two dyes, the magnitude of response with the fluo-3/Fura Red ratio is greater than that achieved with indo-1, while the intercellular variation in measurement is similar to that seen with indo-1. Analyses can be simultaneously combined with immunofluorescent detection of PE-labeled antibodies to enable [Ca2+]i measurement within cell subsets.
The G185R Mutation Disrupts Function of the Iron Transporter Nramp2 (1998)

Microcytic anemia (mk) mice and Belgrade (b) rats have severe iron deficiency anemia due to defects in intestinal iron transport and erythroid iron utilization. Both animal mutants carry the same missense mutation in Nramp2, the first mammalian iron transporter to be identified. This mutation, in which glycine 185 is changed to arginine (G185R), occurs within predicted transmembrane domain 4 of the protein. We have performed site-directed mutagenesis of murine Nramp2, focusing on amino acids of transmembrane domain 4 that are highly conserved among Nramp-like proteins. We have expressed each mutant form in transfected cells and examined iron transport function, subcellular localization, and protein amounts. All tested forms of Nramp2 localize to the plasma membrane and to transferrin-containing endosomes. Most transmembrane domain 4 mutations affect the amount of protein detected and consequently show diminished iron transport. The G185R mutation, however, causes near total loss of Nramp2 function that cannot be fully explained by a decreased amount of protein, indicating that G185R disrupts iron transport through an alteration in the function of Nramp2, rather than degradation of the protein. © 1998 by The American Society of Hematology.
An operating system for the home (2012)

Network devices for the home such as remotely controllable locks, lights, thermostats, cameras, and motion sensors are now readily available and inexpensive. In theory, this enables scenarios like remotely monitoring cameras from a smartphone or customizing climate control based on occupancy patterns. However, in practice today, such smarthome scenarios are limited to expert hobbyists and the rich because of the high overhead of managing and extending current technology.

We present HomeOS, a platform that bridges this gap by presenting users and developers with a PC-like abstraction for technology in the home. It presents network devices as peripherals with abstract interfaces, enables cross-device tasks via applications written against these interfaces, and gives users a management interface designed for the home environment. HomeOS already has tens of applications and supports a wide range of devices. It has been running in 12 real homes for 4-8 months, and 42 students have built new applications and added support for additional devices independent of our efforts.
Enzymatic Nitrate Assay by a Kinetic Method Employing Escherichia coli Nitrate Reductase (1985)

An enzymatic assay system for nitrate employing the membrane-bound nitrate reductase (EC 1.7.99.4) of E. coli is described. Contrary to previous enzymatic assay systems, the present method is a kinetic one, i.e. the substrate, nitrate, is assayed by measuring the reaction rate of the nitrate reductase-catalyzed reaction. Based on the observation that the nitrate reductase-catalyzed reaction obeys pseudo-first order kinetics, a test system is described allowing the assay of nitrate at a concentration as low as 1 ppm. The relatively high Michaelis-Menten constant for nitrate (0.3 mM) of the E. coli nitrate reductase favours nitrate assay by the kinetic method.
A theoretical analysis of feedback flow control (1990)

Congestion is a longstanding problem in datagram networks. One congestion avoidance technique is feedback flow control, in which sources adjust their transmission rate in response to congestion signals sent (implicitly or explicitly) by network gateways. The goal is to design flow control algorithms which provide time-scale invariant, fair, stable, and robust performance. In this paper we introduce a simple model of feedback flow control, in which sources make synchronous rate adjustments based on the congestion signals and other local information, and apply it to a network of Poisson sources and exponential servers. We investigate two different styles of feedback, aggregate and individual, and two different gateway service disciplines, FIFO and Fair Share. The purpose of this paper is to identify, in the context of our simple model, which flow control design choices allow us to achieve our performance goals.
Detection of MDM2-CDK4 Amplification by Fluorescence In Situ Hybridization in 200 Paraffin-embedded Tumor Samples: Utility in Diagnosing Adipocytic Lesions and Comparison With Immunohistochemistry and Real-time PCR (2007)

Atypical lipomatous tumor/well-differentiated liposarcomas and dedifferentiated liposarcomas are characterized by the amplification of MDM2 and CDK4 genes. To evaluate the accuracy of fluorescence in situ hybridization (FISH) analysis in the differential diagnosis of adipose tissue tumors, we investigated MDM2-CDK4 status by FISH, real-time polymerase chain reaction (PCR) [quantitative PCR (Q-PCR)] and immunohistochemistry (IHC) in a series of 200 adipose tumors. First, we evaluated MDM2-CDK4 amplification and expression in a series of 94 well-defined adipose tissue tumors. Results showed that FISH was interpretable in 45 of 50 cases (90%), and was more specific and sensitive than Q-PCR and IHC. We then used the same techniques as complementary diagnostic tools in a series of 106 adipose and soft tissue tumors of unclear diagnosis to distinguish between (i) lipomas and atypical lipomatous tumor/well-differentiated liposarcomas, (ii) malignant undifferentiated tumors and dedifferentiated liposarcomas, and (iii) a variety of benign tumors and liposarcomas. Our results indicate that although helpful, IHC alone is often insufficient to solve diagnostic problems. FISH and Q-PCR methods gave concordant results and were equally informative in most cases. However, the proportion of noninterpretable cases was slightly higher with FISH than with Q-PCR. When tumor cells represented a minor component of the tumor tissue, such as with inflammatory tumors, FISH was more powerful than Q-PCR by allowing visualization of individual cells. In conclusion, we recommend that the evaluation of MDM2-CDK4 amplification using FISH or Q-PCR be used to supplement IHC analysis when diagnosis of adipose tissue tumors is not possible based on clinical and histologic information alone.
Mutation rates in mammalian genomes (2002)

Knowledge of the rate of point mutation is of fundamental importance, because mutations are a vital source of genetic novelty and a significant cause of human diseases. Currently, mutation rate is thought to vary many fold among genes within a genome and among lineages in mammals. We have conducted a computational analysis of 5,669 genes (17,208 sequences) from species representing major groups of placental mammals to characterize the extent of mutation rate differences among genes in a genome and among diverse mammalian lineages. We find that mutation rate is approximately constant per year and largely similar among genes. Similarity of mutation rates among lineages with vastly different generation lengths and physiological attributes points to a much greater contribution of replication-independent mutational processes to the overall mutation rate. Our results suggest that the average mammalian genome mutation rate is 2.2 x 10(-9) per base pair per year, which provides further opportunities for estimating species and population divergence times by using molecular clocks.
A color matching experiment using two displays: design considerations and pilot test results (2010)

International audience
Utilization of polymerase chain reaction technology in the detection of solid tumors (1998)

PCR can detect tumor marker-expressing cells that are otherwise undetectable by other means in patients with localized or metastatic cancer. Reports from various study groups have lacked uniformity in their protocols, and this has prevented adequate comparison. The clinical utility of this assay as a tool for the prognosis and management of cancer patients remains and area of active investigation. PCR is a powerful tool in the study of the biology of cancer metastasis and will likely serve as a useful adjunct to clinical decision-making in the future.
Application of Brønsted-Type LFER in the Study of the Phospholipase C Mechanism (2003)

Phosphatidylinositol-specific phospholipase C cleaves the phosphodiester bond of phosphatidylinositol to form inositol 1,2-cyclic phosphate and diacylglycerol. This enzyme also accepts a variety of alkyl and aryl inositol phosphates as substrates, making it a suitable model enzyme for studying mechanism of phosphoryl transfer by probing the linear free-energy relationship (LFER). In this work, we conducted a study of Brønsted-type relationship (log k = beta(lg) pK(a) + C) to compare mechanisms of enzymatic and nonenzymatic reactions, confirm the earlier proposed mechanism, and assess further the role of hydrophobicity in the leaving group as a general acid-enabling factor. The observation of the high negative Brønsted coefficients for both nonenzymatic (beta(lg) = -0.65 to -0.73) and enzymatic cleavage of aryl and nonhydrophobic alkyl inositol phosphates (beta(lg) = -0.58) indicates that these reactions involve only weak general acid catalysis. In contrast, the enzymatic cleavage of hydrophobic alkyl inositol phosphates showed low negative Brønsted coefficient (beta(lg) = -0.12), indicating a small amount of the negative charge on the leaving group and efficient general acid catalysis. Overall, our results firmly support the previously postulated mechanism where hydrophobic interactions between the enzyme and remote parts of the leaving group induce an unprecedented negative-charge stabilization on the leaving group in the transition state.
Mechanical properties of medical grade expanded polytetrafluoroethylene: The effects of internodal distance, density, and displacement rate (1999)

Expanded polytetrafluoroethylene (e-PTFE) is used successfully in a multitude of biomedical and clinical applications. The success of this biomaterial is due to its microporous structure that allows biointegration for fixation, as well as overall mechanical integrity. The mechanical properties and degree of tissue ingrowth depend on the microstructure of the expanded polymer foam, yet little is known about the correlation of the internodal distance and other microstructural features with the monotonic tensile properties. Complete structure–property correlation can be used to provide invaluable knowledge for the design of biomedical devices. The purpose of this study was to investigate the monotonic tensile properties of e-PTFE over a range of medically relevant microstructural features and manufacturing parameters. The microstructural and manufacturing parameters considered were internodal distance, linear density, volumetric density, and reduction ratio. Additionally, the effect of displacement rate on mechanical properties was studied. We found that the ultimate stress and strain increased linearly with linear density (R2 = 0.88 and 0.67, respectively). Surprisingly, elastic modulus did not correlate with any parameter measured and only weak correlations were found between all properties and internodal distance. The yield and ultimate stresses increased with increasing displacement rate (R2 = 0.88 and 0.57, respectively). The findings from this study indicate that linear density is a better predictor of mechanical properties than internodal distance and may be the preferred parameter to control when specifying a material for implantation in load bearing situations. © 1999 John Wiley & Sons, Inc. J Biomed Mater Res (Appl Biomater) 48: 187–192, 1999
A CMOS image sensor with dark-current cancellation and dynamic sensitivity operations (2003)

An ultralow dark-signal and high-sensitivity pixel has been developed for an embedded active-pixel CMOS image sensor by using a standard 0.35-/spl mu/m CMOS logic process. To achieve in-pixel dark-current cancellation, we developed a combined photogate/photodiode photon-sensing device with a novel operation scheme. The experimental results demonstrate that the severe dark signal degradation of a CMOS active pixel sensor is reduced more than an order of magnitude. Through varying the bias conditions on the photogate, dynamic sensitivity can be obtained to increase maximum allowable illumination level. Combining the above two operation schemes, the dynamic range of this new cell can be extended by more than 20/spl times/.
Design and Synthesis of Potent, Selective, and Orally Bioavailable Tetrasubstituted Imidazole Inhibitors of p38 Mitogen-Activated Protein Kinase (1999)

Novel potent and selective diarylimidazole inhibitors of p38 MAP (mitogen-activated protein) kinase are described which have activity in both cell-based assays of tumor necrosis factor-alpha (TNF-alpha) release and an animal model of rheumatoid arthritis. The SAR leading to the development of selectivity against c-Raf and JNK2alpha1 kinases is presented, with key features being substitution of the 4-aryl ring with m-trifluoromethyl and substitution of the 5-heteroaryl ring with a 2-amino substituent. Cell-based activity was significantly enhanced by incorporation of a 4-piperidinyl moiety at the 2-position of the imidazole which also enhanced aqueous solubility. In general, oral bioavailability of this class of compounds was found to be poor unless the imidazole was methylated on nitrogen. This work led to identification of 48, a potent (p38 MAP kinase inhibition IC50 0.24 nM) and selective p38 MAP kinase inhibitor which inhibits lipopolysaccharide-stimulated release of TNF-alpha from human blood with an IC50 2.2 nM, shows good oral bioavailability in rat and rhesus monkey, and demonstrates significant improvement in measures of disease progression in a rat adjuvant-induced arthritis model.