gebhart/patrepeval huggingface dataset:
The Rho kinase inhibitor fasudil inhibits tumor progression in human and rat tumor models (2006)

Abstract The ability of cancer cells to undergo invasion and migration is a prerequisite for tumor metastasis. Rho, a Ras-related small GTPase, and the Rho-associated coiled coil–containing protein kinases (Rho kinases, ROCK1 and ROCK2) are key regulators of focal adhesion, actomyosin contraction, and thus cell motility. Inhibitors of this pathway have been shown to inhibit tumor cell motility and metastasis. Here, we show that fasudil [1-(5-isoquinolinesulfonyl)-homopiperazine], an orally available inhibitor of Rho kinases, and its metabolite 1-(hydroxy-5-isoquinoline sulfonyl-homopiperazine) (fasudil-OH) modify tumor cell morphology and inhibit tumor cell migration and anchorage-independent growth. In addition, we show that fasudil inhibited tumor progression in three independent animal models. In the MM1 peritoneal dissemination model, tumor burden and ascites production were reduced by &amp;gt;50% (P &amp;lt; 0.05). In the HT1080 experimental lung metastasis model, fasudil decreased lung nodules by ∼40% (P &amp;lt; 0.05). In the orthotopic breast cancer model with MDA-MB-231, there were 3-fold more tumor-free mice in the fasudil-treated group versus saline control group (P &amp;lt; 0.01). Fasudil has been approved for the treatment of cerebral vasospasm and associated cerebral ischemic symptoms. In patients, fasudil is well tolerated without any serious adverse reactions. Therefore, the concept of Rho kinase inhibition as an antimetastatic therapy for cancer can now be clinically explored. [Mol Cancer Ther 2006;5(9):2158–64]
Cancer specific Mucin‐1 glycoforms are expressed on multiple myeloma (2006)

Present therapies cannot cure the large majority of patients with multiple myeloma (MM) and therefore new treatment strategies are imperative. This study analysed the different glycosylation profiles of Mucin-1 (MUC1) on MM and acute myeloid leukaemia (AML) cells using a series of anti-MUC1 antibodies. Seventy-three per cent of the MM patients had plasma cells that expressed the fully glycosylated forms of MUC1. In contrast to controls, normal bone marrow cells and AML cells, the differentiation-dependent and cancer-associated glycoforms of MUC1 were present on 59% and 36% MM tumour cells respectively. This indicated that aberrantly glycosylated MUC1 is a potential immunotherapeutic target in MM patients.
Proton Acid‐induced Rearrangements of α‐Alkynylestradiol Methyl Ethers (1993)

Abstract When subjected to proton catalysis, the α‐alkynylestradiol methyl ethers 1a and 1b furnish the Rupe or Meyer‐Schuster rearrangement products 2 , 4 , and 5a . In the presence of sulfuric acid, α‐ethynylestradiol 3‐methyl ether ( 1a ) is converted into the D‐homosteroid 3a . The use of deuterated acids gives rise to the formation of the corresponding deuterated steroids 2b , 2c , 3b , and 5b . Some mechanistic implications of these results are also discussed.
Detoxification of Cylindrospermopsin by Pyrite in Water (2019)

Cylindrospermopsin (CYN) is a cyanobacterial toxin released from eutrophic water. It persistently remains in the environment because its degradation under solar light is extremely low. In this study, pyrite, an abundant mineral, was investigated as a catalyst for decomposing and detoxifying CYN in water. A detailed examination of intermediates provided insights into the degradation pathway. Electron spin resonance spectra revealed that H2O2 and hydroxyl radicals (•OH) were generated at the pyrite surface while promoting the recycling of Fe(III) into Fe(II) during the degradation process. This degradation system could be uniquely efficient in the presence of relatively high levels of natural organic matter because the structure of the uracil ring is decomposed to detoxify CYN. This work confirms a new approach to selectively and effectively detoxifying CYN in water using an inexpensive, environmentally friendly, and bio-compatible mineral.
General Approach to First-Order Error Prediction in Rigid Point Registration (2010)

A general approach to the first-order analysis of error in rigid point registration is presented that accommodates fiducial localization error (FLE) that may be inhomogeneous (varying from point to point) and anisotropic (varying with direction) and also accommodates arbitrary weighting that may also be inhomogeneous and anisotropic. Covariances are derived for target registration error (TRE) and for weighted fiducial registration error (FRE) in terms of covariances of FLE, culminating in a simple implementation that encompasses all combinations of weightings and anisotropy. Furthermore, it is shown that for ideal weighting, in which the weighting matrix for each fiducial equals the inverse of the square root of the cross covariance of its two-space FLE, fluctuations of FRE and TRE are mutually independent. These results are validated by comparison with previously published expressions and by simulation. Furthermore, simulations for randomly generated fiducial positions and FLEs are presented that show that correlation is negligible (correlation coefficient < 0.1) in the exact case for both ideal and uniform weighting (i.e., no weighting), the latter of which is employed in commercial surgical guidance systems. From these results we conclude that for these weighting schemes, while valid expressions exist relating the covariance of FRE to the covariance of TRE, there are no measures of the goodness of fit of the fiducials for a given registration that give to first order any information about the fluctuation of TRE from its expected value and none that give useful information in the exact case. Therefore, as estimators of registration accuracy, such measures should be approached with extreme caution both by the purveyors of guidance systems and by the practitioners who use them.
Autophagy is a new protective mechanism against the cytotoxicity of platinum nanoparticles in human trophoblasts (2019)

Nanoparticles are widely used in commodities, and pregnant women are inevitably exposed to these particles. The placenta protects the growing fetus from foreign or toxic materials, and provides energy and oxygen. Here we report that autophagy, a cellular mechanism to maintain homeostasis, engulfs platinum nanoparticles (nPt) to reduce their cytotoxicity in trophoblasts. Autophagy was activated by nPt in extravillous trophoblast (EVT) cell lines, and EVT functions, such as invasion and vascular remodeling, and proliferation were inhibited by nPt. These inhibitory effects by nPt were augmented in autophagy-deficient cells. Regarding the dynamic state of nPt, analysis using ICP-MS demonstrated a higher accumulation of nPt in the autophagosome-rich than the cytoplasmic fraction in autophagy-normal cells. Meanwhile, there were more nPt in the nuclei of autophagy-deficient cells, resulting in greater DNA damage at a lower concentration of nPt. Thus, we found a new protective mechanism against the cytotoxicity of nPt in human trophoblasts.
Water adsorption effects of nitrate ion coordinated Al2O3 dielectric for high performance metal-oxide thin-film transistor (2013)

A solution-processed ionic amorphous Al2O3 dielectric with a low temperature annealing process at 350 °C shows good compatibility and high performance in metal oxide semiconductor thin film transitors (TFTs) such as Li–ZnO TFTs and In–ZnO TFTs. The Li–ZnO/Al2O3 and In–ZnO/Al2O3 TFTs, with solution-processability and low temperature annealing at a maximum of 350 °C, exhibited field-effect mobilities of 46.9 cm2 V−1 s−1 in crystalline Li–ZnO/Al2O3 TFTs and 44.2 cm2 V−1 s−1 in amorphous In–ZnO/Al2O3 TFTs with an on/off current ratio of more than 105. The proton mobile ion, such as hydrogen ion (H+) from chemisorbed water, in the ionic Al2O3 dielectric remarkably induces a high performance capacitance by the formation of an electrical double layer. The chemisorbed water was monitored by FT-IR and ellipsometric porosimetry measurements. Furthermore, the addition of H2O2 to the ionic Al2O3 dielectric precursor successfully suppressed the oxygen vacancies in the dielectric layer, which caused the electrical trap and pass, and confirmed the stable operation. These ionic amorphous Al2O3 dielectrics show good potential as switching TFTs devices in advanced displays, because they can satisfy the various demands of next-generation high-performance TFTs, such as low-cost, solution-processability, and a relatively low-temperature process.
Isolation and RNA sequencing of single nuclei from Drosophila tissues (2022)

Many insect cells are encapsulated within the exoskeleton and cannot be dissociated intact, making them inaccessible to single-cell transcriptomic profiling. We have used single-nucleus RNA sequencing to extract transcriptomic information from multiple <i>Drosophila</i> tissues. Here, we describe procedures for the (1) dissociation of single nuclei, (2) isolation of single nuclei using two popular cell sorters, and (3) preparation of libraries for Smart-seq2 and 10× Genomics. This protocol enables generation of high-quality transcriptomes from single nuclei and can be applied to other species. For complete details on the use and execution of this protocol, please refer to McLaughlin et al. (2021) and Li et al. (2022).
A Direct Synthesis based Sliding Mode Control of a Nonlinear Continuous Stirred Tank Reactor (2022)

This work proposes a sliding mode controller (SMCL) design approach based on direct synthesis method for non-linear continuous stirred tank reactor (NCSTR). The SMCL parameters are derived based on (i) NCSTR model obtained by performing the closed loop test on the nonlinear differential equations of the NCSTR, (ii) direct synthesis approach and (iii) grasshopper optimization scheme. The performance of the suggested approach is assessed by performing the simulation on the nonlinear differential equation of the NCSTR. The results indicate that the suggested approach delivers satisfactory performance under nominal and noisy conditions with minimal efforts by the controller.
Recurrent Meningitis in an Adult Due to Nontypable Haemophilus influenzae (1984)

Journal Article Recurrent Meningitis in an Adult Due to Nontypable Haemophilus influenzae Get access Bernard J. Hirschel, Bernard J. Hirschel Search for other works by this author on: Oxford Academic PubMed Google Scholar Raymond Auckenthaler, Raymond Auckenthaler Search for other works by this author on: Oxford Academic PubMed Google Scholar Stephen J. Barenkamp, Stephen J. Barenkamp Search for other works by this author on: Oxford Academic PubMed Google Scholar Dan M. Granoff Dan M. Granoff Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 149, Issue 4, April 1984, Page 656, https://doi.org/10.1093/infdis/149.4.656 Published: 01 April 1984
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing (2020)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Progressive Discrete Domains for Implicit Surface Reconstruction (2021)

Abstract Many global implicit surface reconstruction algorithms formulate the problem as a volumetric energy minimization, trading data fitting for geometric regularization. As a result, the output surfaces may be located arbitrarily far away from the input samples. This is amplified when considering i) strong regularization terms, ii) sparsely distributed samples or iii) missing data. This breaks the strong assumption commonly used by popular octree‐based and triangulation‐based approaches that the output surface should be located near the input samples. As these approaches refine during a pre‐process, their cells near the input samples, the implicit solver deals with a domain discretization not fully adapted to the final isosurface. We relax this assumption and propose a progressive coarse‐to‐fine approach that jointly refines the implicit function and its representation domain, through iterating solver, optimization and refinement steps applied to a 3D Delaunay triangulation. There are several advantages to this approach: the discretized domain is adapted near the isosurface and optimized to improve both the solver conditioning and the quality of the output surface mesh contoured via marching tetrahedra.
Monte Carlo simulations of liquid acetic acid and methyl acetate with the OPLS potential functions (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMonte Carlo simulations of liquid acetic acid and methyl acetate with the OPLS potential functionsJames M. Briggs, Toan B. Nguyen, and William L. JorgensenCite this: J. Phys. Chem. 1991, 95, 8, 3315–3322Publication Date (Print):April 1, 1991Publication History Published online1 May 2002Published inissue 1 April 1991https://pubs.acs.org/doi/10.1021/j100161a065https://doi.org/10.1021/j100161a065research-articleACS PublicationsRequest reuse permissionsArticle Views1464Altmetric-Citations141LEARN 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 options Get e-Alerts
Study on Driver's Car Following Abilities Based on an Active Haptic Support Function (2006)

&lt;div class="htmlview paragraph"&gt;A research prototype driver support system to augment perception to enhance situation awareness and control for car following applications is introduced and results from a field test evaluation are reported. The support system applies driving and braking force control and a gas-pedal push-back force whose magnitudes depend on the degree to which an undesirable region in a perceptual control space of time headway (THW) and time to collision (TTC) is penetrated (i.e. criticality based on perceptually meaningful cues [&lt;span class="xref"&gt;4&lt;/span&gt;]). Because the support system essentially extends the driver's: i) perception and criticality assessment (through dynamic force feedback on the gas pedal), ii) information processing (haptic information is provided earlier and more saliently than the visual information alone especially when visual attention is directed away from the driving task), and iii) control abilities (through automatic superposition of decelerations by the system), the system can be viewed an extension of the driver as a perceptual-motor controller. Therefore, changes in car following behavior with and without support system are quantified by identifying the coefficients of a simple practical car following model of the driver alone versus the driver plus support system.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The results clearly show that drivers who naturally follow closely, and thus operate frequently in the system's active support domain, effectively have a higher control bandwidth with the system which means that they are able to more rapidly and accurately respond to changes in the gap to the lead vehicle. These drivers exhibited an improvement of car following performance (i.e. less variability in gap at a longer target THW) as well as reported a reduction in workload. The support system effectively reduced the frequency with which drivers experienced close following and rapid gap closure situations.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The supported driver is essentially more vigilant to gap changes while following at a greater time-headway without an increase in workload.&lt;/div&gt;
The Radioimmunoassay of Human Urinary Kallikrein and Comparisons with Kallikrein Activity Measurements* (1980)

Human urinary kallikrein was purified to homogeneity, and an antiserum to it was raised in rabbits. A RIA was devised which uses this rabbit antiserum (Keq = 2.75 x 10(11) M-1) in a final dilution of 1:2,500,000 and the purified kallikrein labeled with 125I using a lactoperoxidase method. Assay sensitivity is 8 pg kallikrein. Thus far, the assay is specific for human and perhaps monkey urinary kallikrein. Correlations between this assay of immunoreactive kallikrein and the alpha-N-Tosyl-L-arginine-[3H]methylester (Tos-Arg-OMe) activity method or a kininogenase assay were highly significant (r = 0.94 and 0.96, respectively) and show that each assay measures human urinary kallikrein comparably. Low or high dietary sodium intakes, maneuvers known to change human urinary Tos-Arg-OMe esterase excretion, change immunoreactive kallikrein to an equivalent degree. Normal black children, already known to excrete significantly less Tos-Arg-OMe esterase than white children, excrete similarly reduced amounts of immunoreactive kallikrein. Kallikrein excretion in children with cystic fibrosis of the pancreas was not different from that in normal children. The data show that a specific and sensitive direct RIA for human urinary kallikrein has been developed and that both the Tos-Arg-OMe esterase and kininogenase assays measure human urinary kallikrein activity specifically, at least in the described circumstances.
Small signal dynamics of an electrically-pumped long-wavelength tunable VCSEL (2008)

The intrinsic dynamics of a micromachined tunable surface-emitting laser with buried tunnel junction are derived from amplitude modulation response and relative intensity noise. The dependence of resonance frequency on bias current and wavelength is reported.
Dual‐Function Cobalt–Nickel Nanoparticles Tailored for High‐Temperature Induction‐Heated Steam Methane Reforming (2018)

The tailored chemical synthesis of binary and ternary alloy nanoparticles with a uniform elemental composition is presented. Their dual use as magnetic susceptors for induction heating and catalytic agent for steam reforming of methane to produce hydrogen at temperatures near and above 800 °C is demonstrated. The heating and catalytic performance of two chemically synthesized samples of CoNi and Cu⊂CoNi are compared and held against a traditional Ni-based reforming catalyst. The structural, magnetic, and catalytic properties of the samples were characterized by X-ray diffraction, elemental analysis, magnetometry, and reactivity measurements. For induction-heated catalysts, the conversion rate of methane is limited by chemical reactivity, as opposed to the case of traditional externally heated reformers where heat transport limitations are the limiting factor. Catalyst production by the synthetic route allows controlled doping with miniscule concentrations of auxiliary metals.
Brain oxygen utilization is unchanged by hypoglycemia in normal humans: lactate, alanine, and leucine uptake are not sufficient to offset energy deficit (2005)

During hypoglycemia, substrates other than glucose have been suggested to serve as alternate neural fuels. We evaluated brain uptake of endogenously produced lactate, alanine, and leucine at euglycemia and during insulin-induced hypoglycemia in 17 normal subjects. Cross-brain arteriovenous differences for plasma glucose, lactate, alanine, leucine, and oxygen content were quantitated. Cerebral blood flow (CBF) was measured by Fick methodology using N(2)O as the dilution indicator gas. Substrate uptake was measured as the product of CBF and the arteriovenous concentration difference. As arterial glucose concentration fell, cerebral oxygen utilization and CBF remained unchanged. Brain glucose uptake (BGU) decreased from 36.3+/-2.6 to 26.6+/-2.1 micromol.100 g of brain(-1).min(-1) (P<0.001), equivalent to a drop in ATP of 291 micromol.100 g(-1).min(-1). Arterial lactate rose (P<0.001), whereas arterial alanine and leucine fell (P<0.009 and P<0.001, respectively). Brain lactate uptake (BLU) increased from a net release of -1.8+/- 0.6 to a net uptake of 2.5+/-1.2 micromol.100 g(-1).min(-1) (P<0.001), equivalent to an increase in ATP of 74 micromol.100 g(-1).min(-1). Brain leucine uptake decreased from 7.1+/-1.2 to 2.5 +/- 0.5 micromol.100 g(-1).min(-1) (P<0.001), and brain alanine uptake trended downward (P<0.08). We conclude that the ATP generated from the physiological increase in BLU during hypoglycemia accounts for no more than 25% of the brain glucose energy deficit.
Think Small: One Day It May Be Worth A Billion (1993)

The Perkin Medal Address given by Lubomyr T. Romankiw, The 1993 Perkin Medalist, on March 10, 1993.
Supplementary Movie Legends 1-12 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium (2023)

Supplementary Movie Legends 1-12 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
ChemInform Abstract: Steroids. Part 363. Brassinosteroids with Ester Function with Five Carbon Atoms at the 20 Position. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Science Translational Medicine Podcast: 28 March 2012 (2012)

A conversation with Bert Vogelstein about how far we have come in understanding cancer and what we still need to do to successfully conquer the disease.
CHAPTER 12. Key Intermediates in the Hydrogenation and Electrochemical Reduction of CO2 (2013)

Mimicking photosynthesis by (re)using carbon dioxide as a carbon feedstock for the production of hydrocarbons would enable a sustainable carbon cycle. Electrochemically, CO2 can be reduced on copper electrodes to hydrocarbons, mainly methane and ethylene, and the integration of this process in a photo-electrochemical device could be a promising way to close the carbon cycle. Understanding the mechanism of this reaction is one of the keys to open up new, sustainable routes to carbon based fuels. In this chapter we aim to obtain more insights in the key intermediates that determine the selectivity of CO2 reduction to various products, by comparing the electrochemical reduction of CO2 to the metal-catalyzed hydrogenation and reduction of CO2 both homogeneously in solution and heterogeneously in the gas phase. We distinguish four main pathways: (1) methane is formed via hydroxycarboxyl (COOH) and carbon monoxide (CO), (2) methanol is formed via formate (HCOO) and formaldehyde, (3) ethylene is formed via the coupling of CO, leading to surface enolates, and (4) CO2 is inserted into existing carbon chains, close to the way CO2 is fixed in nature.