gebhart/patrepeval huggingface dataset:
Fast compressed sensing analysis for super-resolution imaging using L1-homotopy (2013)

In super-resolution imaging techniques based on single-molecule switching and localization, the time to acquire a super-resolution image is limited by the maximum density of fluorescent emitters that can be accurately localized per imaging frame. In order to increase the imaging rate, several methods have been recently developed to analyze images with higher emitter densities. One powerful approach uses methods based on compressed sensing to increase the analyzable emitter density per imaging frame by several-fold compared to other reported approaches. However, the computational cost of this approach, which uses interior point methods, is high, and analysis of a typical 40 µm x 40 µm field-of-view super-resolution movie requires thousands of hours on a high-end desktop personal computer. Here, we demonstrate an alternative compressed-sensing algorithm, L1-Homotopy (L1H), which can generate super-resolution image reconstructions that are essentially identical to those derived using interior point methods in one to two orders of magnitude less time depending on the emitter density. Moreover, for an experimental data set with varying emitter density, L1H analysis is ~300-fold faster than interior point methods. This drastic reduction in computational time should allow the compressed sensing approach to be routinely applied to super-resolution image analysis.
Evaluation of an ELISA for p16INK4a as a Screening Test for Cervical Cancer (2009)

An enhanced version of this prototypic p16(INK4a) ELISA showed promise in screening, particularly when combined with hc2.
Reorienting the Fab Domains of Trastuzumab Results in Potent HER2 Activators (2012)

The structure of the Fab region of antibodies is critical to their function. By introducing single cysteine substitutions into various positions of the heavy and light chains of the Fab region of trastuzumab, a potent antagonist of HER2, and using thiol chemistry to link the different Fabs together, we produced a variety of monospecific F(ab')(2)-like molecules with activities spanning from activation to inhibition of breast tumor cell growth. These isomers (or bis-Fabs) of trastuzumab, with varying relative spatial arrangements between the Fv-regions, were able to either promote or inhibit cell-signaling activities through the PI3K/AKT and MAPK pathways. A quantitative phosphorylation mapping of HER2 indicated that the agonistic isomers produced a distinct phosphorylation pattern associated with activation. This study suggests that antibody geometric isomers, found both in nature and during synthetic antibody development, can have profoundly different biological activities independent of their affinities for their target molecules.
TonB-Dependent Systems of UropathogenicEscherichia coli: Aerobactin and Heme Transport and TonB Are Required for Virulence in the Mouse (2001)

The uropathogenic Escherichia coli strain CFT073 has multiple iron acquisition systems, including heme and siderophore transporters. A tonB mutant derivative of CFT073 failed to use heme as an iron source or to utilize the siderophores enterobactin and aerobactin, indicating that transport of these compounds in CFT073 is TonB dependent. The TonB(-) derivative showed reduced virulence in a mouse model of urinary tract infection. Virulence was restored when the tonB gene was introduced on a plasmid. To determine the importance of the individual TonB-dependent iron transport systems during urinary tract infections, mutants defective in each of the CFT073 high-affinity iron transport systems were constructed and tested in the mouse model. Mouse virulence assays indicated that mutants defective in a single iron transport system were able to infect the kidney when inoculated as a pure culture but were unable to efficiently compete with the wild-type strain in mixed infections. These results indicate a role for TonB-dependent systems in the virulence of uropathogenic E. coli strains.
Efficacy and tissue distribution of DHP107, an oral paclitaxel formulation (2007)

Paclitaxel is indispensable in treating human cancers. Due to poor drug solubility and efflux systems in the gastrointestinal tract, peroral delivery of paclitaxel has been a significant challenge. We developed a mucoadhesive oral formulation (DHP107) that can directly and effectively deliver paclitaxel to intestinal endothelial cells without concomitant use of P-glycoprotein inhibitors. Here, we evaluated the tissue distribution of paclitaxel, the antitumor efficacy and the absorption mechanism of DHP107. DHP107, which contains 10 mg/mL of paclitaxel in a mixture of monoolein, tricarprylin, and Tween 80 was administered p.o. to female BALB/c mice at a 50 mg/kg dose. Diluted Taxol was administered via bolus tail-vein injection at 10 mg/kg as a control. Blood and tissue samples were harvested at various time points and analyzed by high-performance liquid chromatography. Tissue sections were observed using light microscopy after immunohistochemical and Oil Red O staining. By day 27, tumor volume after DHP107 and Taxol treatments was one-third of that in the untreated group. After p.o. administration, paclitaxel was widely distributed in various organs (T(max) = 2 h), especially liver, spleen, and lung. DHP107 was effectively absorbed through the intestinal lipid transport system. DHP107 changed spontaneously into <100-mum droplets and micelles in the intestine, which in turn adhered to mucoepithelial cells, were absorbed via lipid uptake mechanism, and formed lipid bodies in the epithelium. Paclitaxel in DHP107 was effectively absorbed through the gastrointestinal tract via lipid uptake mechanism and was distributed in various tissues. The detailed uptake mechanism is currently under investigation.
Total Synthesis of (−)-Callipeltoside A (2010)

A total synthesis of (-)-callipeltoside A (1) has been achieved. The core macrocycle was made via a dual macrolactonization/pyran hemiketal formation reaction, developed to circumvent issues related to the reversible nature of acylketene formation from β-keto lactone substrates. Initial approaches to the core of the natural product that revolved around ring-closing metathesis (RCM) and relay ring-closing metathesis (RRCM) reactions are also described.
Diterpenoids from the Roots of Euphorbia fischeriana (2006)

From the dried roots of Euphorbia fischeriana, seven new diterpenoids, 3alpha,17-dihydroxy-ent-pimara-8(14),15-diene (1), 7beta,11beta,12beta-trihydroxy-ent-abieta-8(14),13(15)-dien-16,12-olide (2), 17-acetoxyjolkinolide B (3), 13beta-hydroxy-ent-abiet-8(14)-en-7-one (4), 12-deoxyphorbaldehyde-13-acetate (5) 12-deoxyphorbaldehyde-13-hexadecacetate (6), and 12-deoxyphorbol-13-(9Z)-octadecanoate-20-acetate (7), and two known compounds, 12-deoxyphorbol-13-decanoate (8) and prostratin (9), were isolated. The structures of the new compounds were elucidated on the basis of spectroscopic analysis. The structure of compound 1 was confirmed by single-crystal X-ray crystallography. Compounds 3 and 8 exhibited potent cytotoxic activity to Ramos B cells with IC50 values of 0.023 and 0.0051 microg/mL, respectively.
Tumor Suppression by p53 Is Mediated in Part by the Antiangiogenic Activity of Endostatin and Tumstatin (2006)

Recent research shows that p53 suppresses tumor angiogenesis by transcriptionally activating the alpha(II) collagen prolyl-4-hydroxylase gene. This results in the extracellular release of the potent endogenous angiogenesis inhibitors endostatin and tumstatin from collagens 18 and 4, respectively. The involvement of these inhibitors elucidates a molecular mechanism. By simultaneously repressing a multitude of proangiogenic pathways and by inducing antiangiogenic pathways, a tumor suppressor protein can prevent an incipient tumor from switching to the angiogenic phenotype. Thus, p53 guards the genome from cancer by controlling the three fundamental processes that are critical for growth of a primary tumor and its metastases-tumor cell proliferation, apoptosis, and tumor angiogenesis.
Silkworm silk as an engineering material (1998)

While silk exhibits high values of tensile strength and stiffness, these properties are compromised by their poor reproducibility. We present the results of experiments aimed at characterizing the variability of tensile properties exhibited by cocoon silk from Bombyx mori silkworms. Scanning electron microscopy is used to measure an average diameter for individual test specimens; the interspecimen variability of diameter is quantified and found to be inadequately represented by standard deviation. When load-extension data are converted into stress-strain curves, a marked improvement in reproducibility is realized if each specimen cross-section is calculated from diameter measurements specific to that specimen. Nevertheless, a significant variability in fracture stress remains; a Weibull analysis reveals that silkworm silk has a failure predictability comparable with that of glass and nonengineering ceramics. Unloading/reloading tests demonstrate that stiffness is not significantly affected by cumulative deformation, and the stress–strain relationship is not sensitive to strain rate. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 70: 2439–2447, 1998
Vitamin E amides, a new class of vitamin E analogues with enhanced proapoptotic activity (2005)

Vitamin E (VE) analogues, epitomized by alpha-tocopheryl succinate (alpha-TOS), are proapoptotic agents with selective antineoplastic activity. The molecule of alpha-TOS comprises several structurally and functionally distinct moieties that can be modified in order to yield analogues with higher activity. In order to find analogues with higher apoptogenic efficacy, we prepared novel compounds where the ester bond was replaced by an amide bond. All of these analogues were significantly more proapoptotic than their ester counterparts, with alpha-tocopheryl maleyl amide being the most effective. Importantly, methylation of the free carboxylic group completely obliterated apoptogenic activity of the compounds. Similarly as shown for the ester analogues, the amides induced apoptosis by mitochondrial destabilization. Superiority of amides over the ester analogues may be due to their higher partitioning into the lipid phase, as suggested by the log p-values that were lower for the amides than the corresponding esters. In conclusion, we present evidence that modification of the ester bond of agents such as alpha-TOS can be used as a basis for generating novel analogues with higher efficacy of killing malignant cells, an activity that suggests anticancer effect of the agents.
Aza-Payne Rearrangement of Activated 2-Aziridinemethanols and 2,3-Epoxy Amines under Basic Conditions (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAza-Payne Rearrangement of Activated 2-Aziridinemethanols and 2,3-Epoxy Amines under Basic ConditionsToshiro Ibuka, Kazuo Nakai, Hiromu Habashita, Yuka Hotta, Akira Otaka, Hirokazu Tamamura, Nobutaka Fujii, Norio Mimura, Yoshihisa Miwa, , Yukiyasu Chounan, and Yoshinori YamamotoCite this: J. Org. Chem. 1995, 60, 7, 2044–2058Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/jo00112a028https://doi.org/10.1021/jo00112a028research-articleACS PublicationsRequest reuse permissionsArticle Views969Altmetric-Citations58LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Preservation of NADH Voltammetry for Enzyme-Modified Electrodes Based on Dehydrogenase (1999)

Minimizing overpotential and generating high faradaic currents are critical issues for fast-scan voltammetry of beta-nicotinamide adenine dinucleotide (NADH) for the sensitivity of enzyme-modified electrodes based on dehydrogenases. Although NADH voltammetry exhibits high overpotential and poor voltammetric peak shape at solid electrode surfaces, modification of the electrode surface can improve the electrochemical response at carbon fibers. However, these improvements are severely degraded upon the covalent attachment of enzyme. The creation of improved electron-transfer properties and the retention of these properties throughout the enzyme attachment process is the focus of this study. A novel polishing and electrochemical pretreatment method was developed which generated a decreased overpotential and a high faradaic current at carbon-fiber electrodes for NADH. Factors that lead to a degradation of voltammetric response during the enzyme fabrication were investigated, and both the aging and the covalent modification of the pretreated surface contributed to this degradation. Attachment processes that minimized the preparation time, in turn, maximized the retention of the facile electron-transfer properties. These attachment processes included varying the surface attachment reactions for the enzyme. Preparation time reduction techniques included modeling existing techniques and then improving kinetic and mass transport issues where possible. Alternate covalent attachment methods included a direct electrochemical amine reaction and an electrochemically reductive hydrazide reaction. The surface attachment and retention of electron-transfer properties of these probes were confirmed by fluorescence and electrochemical studies.
Tracking 3D Object using Flexible Models (2005)

This article proposes a flexible tracker which can estimate motion and deformations of 3D objects by considering their appearances as nonrigid surfaces. In this approach, a flexible model is built by matching features (key points) over training sequences and by learning the deformations of a spline based model. This statistical model captures the variations in the appearance of objects caused by 3D pose variations. Visual tracking is then possible, for each new frame, by matching local features of the model according to their local appearances as well as optimal optimization of the constraints provided by the flexible model. The approach is demonstrated on real-world images sequences.
High-power narrowband DUV laser source by frequency mixing in CLBO (2000)

We describe an all solid-state, high power, deep-UV (DUV) source based on sum-frequency mixing (SFM) of two single- frequency laser outputs. The system consists of a CW diode- pumped, Q-switched Nd:YLF laser operating at 1047 nm, a Ti:sapphire laser at 785-nm, and cascading SFM stages. Both laser sources are configured with an injection-seeded oscillator followed by amplifier to produce high power, single-frequency, TEM<SUB>00</SUB> outputs. The third harmonic of Nd:YLF MOPA is mixed with the output from Ti-sapphire MOPA to generate the first UV, which is used for the second mixing with the residual fundamental output to generate the DUV radiation. CLBO crystal is employed for each SFM process. The system produced UV pulses at 241.6 nm with 3.4 W, and also DUV at 196.3 nm with 1.5 W of average powers at a 5-kHz pulse- repetition rate. The linewidth of the DUV output was measured to be less than 0.05 pm.
Iron refractory iron deficiency anemia (2013)

Iron refractory iron deficiency anemia is a hereditary recessive anemia due to a defect in the TMPRSS6 gene encoding Matriptase-2. This protein is a transmembrane serine protease that plays an essential role in down-regulating hepcidin, the key regulator of iron homeostasis. Hallmarks of this disease are microcytic hypochromic anemia, low transferrin saturation and normal/high serum hepcidin values. The anemia appears in the post-natal period, although in some cases it is only diagnosed in adulthood. The disease is refractory to oral iron treatment but shows a slow response to intravenous iron injections and partial correction of the anemia. To date, 40 different Matriptase-2 mutations have been reported, affecting all the functional domains of the large ectodomain of the protein. In vitro experiments on transfected cells suggest that Matriptase-2 cleaves Hemojuvelin, a major regulator of hepcidin expression and that this function is altered in this genetic form of anemia. In contrast to the low/undetectable hepcidin levels observed in acquired iron deficiency, in patients with Matriptase-2 deficiency, serum hepcidin is inappropriately high for the low iron status and accounts for the absent/delayed response to oral iron treatment. A challenge for the clinicians and pediatricians is the recognition of the disorder among iron deficiency and other microcytic anemias commonly found in pediatric patients. The current treatment of iron refractory iron deficiency anemia is based on parenteral iron administration; in the future, manipulation of the hepcidin pathway with the aim of suppressing it might become an alternative therapeutic approach.
Long‐term oral branched chain amino acids in patients undergoing chemoembolization for hepatocellular carcinoma: a randomized trial (2004)

Nutritional supplementation with oral branched chain amino acids is beneficial in increasing the serum albumin level, reducing the morbidity and improving the quality of life in patients undergoing chemoembolization for inoperable hepatocellular carcinoma.
Functional analysis of the actin-binding protein, tropomyosin 1, in neuroblastoma (2003)

Tropomyosin 1 (TM1) is downregulated in a number of transformed cell types, and exogenous expression of TM1 can restore actin organisation and reverse cellular transformation. We find that TM1 is also downregulated in human neuroblastoma cell lines, correlating with increasing malignancy. However, exogenous TM1 does not restore actin cytoskeleton organisation in neuroblastoma cells.
Transport Layer Security (TLS) and Datagram Transport Layer Security (DTLS) Heartbeat Extension (2012)

This document describes the Heartbeat Extension for the Transport
Layer Security (TLS) and Datagram Transport Layer Security (DTLS)
protocol. The Heartbeat Extension provides a new protocol for
TLS/DTLS allowing the usage of keep-alive functionality without
performing a renegotiation and a basis for path maximum transmission
unit (PMTU) discovery for DTLS.
Effects of Carperitide on the Long-Term Prognosis of Patients With Acute Decompensated Chronic Heart Failure The PROTECT Multicenter Randomized Controlled Study (2008)

Acute-phase low-dose carperitide infusion improved the long-term prognosis of patients with ADHF.
Long-Term Depression and Depotentiation in the Sensorimotor Cortex of the Freely Moving Rat (2000)

Activity-dependent reductions in synaptic efficacy are central components of recent models of cortical learning and memory. Here, we have examined long-term synaptic depression (LTD) and the reversal of long-term potentiation (depotentiation) of field potentials evoked in sensorimotor cortex by stimulation of the white matter in the adult, freely moving rat. Prolonged, low-frequency stimulation (1 Hz for 15 min) was used to induce either depotentiation or LTD. LTD was expressed as a reduction in the amplitude of both monosynaptic and polysynaptic field potential components. Both LTD and depotentiation were reliably induced by stimulation of the ipsilateral white matter. Stimulation of the contralateral neocortex induced only a depotentiation effect, which decayed more rapidly than that induced by ipsilateral stimulation (hours vs days). Although ipsilateral LTD was effectively induced by a single session of low-frequency stimulation, multiple sessions of stimulation, either massed or spaced, induced LTD effects that were larger in magnitude and longer lasting. Previously, we showed that the induction of long-term potentiation in the neocortex of chronic preparations required multiple, spaced stimulation sessions to reach asymptotic levels. Here, we report that LTD also required multiple stimulation sessions to reach asymptotic levels, but massed and spaced patterns of low-frequency stimulation were equally effective.
Square Arrays of Vertical Cylinders of PS-b-PMMA on Chemically Nanopatterned Surfaces (2007)

Cylinder-forming polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) thin films were directed to assemble on chemically nanopatterned surfaces consisting of a square array of spots with varying diameters of lattice spacing and spot size. In all cases the patterned spots were preferentially wet by the PMMA block in a continuum of surface wet by the PS block. On this chemical pattern, cylindrical domains oriented perpendicular to the surfaces formed a square array of vertical cylinders, instead of a hexagonal array typically formed in the bulk morphology of cylinder-forming block copolymers. When the lattice spacing of chemical spot patterns was incommensurate with the natural dimension of diblock copolymer in a square array, surface reconstruction led to the formation of microdomain structures that do not appear naturally in the bulk state, such as a loop structure of PMMA cylinders connecting two neighboring PMMA cylindrical sections, and semicylinder domains located at the center of the square unit cell, which did not contact the bottom substrate. The chemically nanopatterned surface became ineffective at forming vertical cylinders with a square array when the cylindrical domains were a distance of 1.5 times the bulk cylinder diameter from the patterned surface. The novel morphologies and the variation of morphology with film thickness shed light on the reconstruction of the microphase-separated block copolymer morphology as it equilibrates in the presence of a chemically nanopatterned substrate.
Incidence and Prognostic Importance of Acute Renal Failure After Percutaneous Coronary Intervention (2002)

The overall incidence of ARF after PCI is low. Diabetic patients with baseline Cr values <2.0 mg/dL are at higher risk than nondiabetic patients, whereas all patients with a serum Cr >2.0 are at high risk for ARF. ARF was highly correlated with death during the index hospitalization and after dismissal.
Treating irritable bowel syndrome: overview, perspective and future therapies (2004)

This article summarizes the ongoing challenges in irritable bowel syndrome and the exciting opportunities for development of novel therapies for this common, enigmatic condition. The challenges include insufficient understanding of mechanisms, lack of specificity of symptoms, differentiation from other conditions, and lack of availability of noninvasive tests to identify dysfunctions. However, significant opportunities are reflected by the advances in clinical trial design and, particularly, clinically relevant end points for such trials, and the increasing understanding of basic neuroenteric science. The latter has delivered two new medications to the practice (alosetron and tegaserod), and other candidate therapies (other serotonergic, tachykininergic, opioid, cannabinoid modulators) are being carefully appraised as potential drugs for the future.
Therapeutic interventions for symptomatic treatment in Huntington's disease (2009)

No intervention proved to have a consistent symptomatic control in HD. Tetrabenazine is the anti-choreic drug with the best quality data available. Other symptomatic areas should be explored by well-designed randomised placebo-controlled studies.