gebhart/patrepeval huggingface dataset:
Isolation of Highly Purified and Viable Retinal Endothelial Cells (2020)

The neonatal mouse retinal vascularization model has been widely used in the vascular biology field to investigate mechanisms of angiogenesis and arterial-venous fate specification during blood vessel formation and maturation. Recent advances in next-generation sequencing can further elucidate mechanisms of blood vessel formation and remodeling in this, as well as other, vascular development models. However, an optimized method for isolating retinal endothelial cells that limits tissue digestion-induced cell damage is required for next-generation sequencing applications. In this study, we established a method for isolating neonatal retinal endothelial cells that optimizes cell viability and purity. The CD31+/CD45- endothelial cell population was fluorescence-activated cell sorting (FACS)-isolated from digested postnatal retinas, found to be highly enriched for endothelial cell gene expression, and exhibited no change in viability for 60 min post-FACS. Thus, this method for retinal endothelial cell isolation is compatible with next-generation sequencing applications. Combining this isolation method with next-generation sequencing will enable further delineation of mechanisms underlying vascular development and maturation.
CNS Inflammation and Obesity (2010)

Frontiers Events is a rapidly growing calendar management system dedicated to the scheduling of academic events. This includes announcements and invitations, participant listings and search functionality, abstract handling and publication, related events and post-event exchanges. Whether an organizer or participant, make your event a Frontiers Event!
Auxiliary-variable Exact Hamiltonian Monte Carlo Samplers for Binary\n Distributions (2013)

We present a new approach to sample from generic binary distributions, based\non an exact Hamiltonian Monte Carlo algorithm applied to a piecewise continuous\naugmentation of the binary distribution of interest. An extension of this idea\nto distributions over mixtures of binary and possibly-truncated Gaussian or\nexponential variables allows us to sample from posteriors of linear and probit\nregression models with spike-and-slab priors and truncated parameters. We\nillustrate the advantages of these algorithms in several examples in which they\noutperform the Metropolis or Gibbs samplers.\n
Index Modulation for STAR-RIS Assisted NOMA System (2022)

In this letter, we first incorporate the concept of index modulation (IM) into simultaneously transmitting and reflecting reconfigurable intelligent surface (STAR-RIS) aided non-orthogonal multiple access (NOMA) system to improve the spectral efficiency. Specifically, the proposed IM aided STAR-RIS-NOMA system enables extra information bits to be transmitted by allocating subsurfaces to different users in a pre-defined subsurface allocation pattern. Furthermore, an approximate closed form expression on bit error rate (BER) is derived. Simulation results demonstrate that the proposed IM aided STAR-RIS-NOMA system is able to acquire transmission rate improvement compared to the conventional STAR-RIS NOMA.
Weighted dynamic scheduling with many parallelism grains for offloading of numerical workloads to multiple varied accelerators (2015)

A wide variety of heterogeneous compute resources are available to modern computers, including multiple sockets containing multicore CPUs, one-or-more GPUs of varying power, and coprocessors such as the Intel Xeon Phi. The challenge faced by domain scientists is how to efficiently and productively use these varied resources. For example, in order to use GPUs effectively, the workload must have a greater degree of parallelism than a workload designed for a multicore-CPU. The domain scientist would have to design and schedule an application in multiple degrees of parallelism and task grain sizes in order to obtain efficient performance from the resources. We propose a productive programming model starting from serial code, which achieves parallelism and scalability by using a task-superscalar runtime environment to adapt the computation to the available resources. The adaptation is done at multiple points, including multi-level data partitioning, adaptive task grain sizes, and dynamic task scheduling. The effectiveness of this approach for utilizing multi-way heterogeneous hardware resources is demonstrated by implementing dense linear algebra applications.
Characterization and optimization of tin particle mitigation and EUV conversion efficiency in a laser produced plasma EUV light source (2011)

A laser produced plasma (LPP) extreme ultraviolet (EUV) light source of 13.5 nm has been developed for next generation lithography. Sn plasma is an efficient generator of 13.5 nm EUV light. On the other hand, deposition of Sn particles which strongly affects EUV collector mirror lifetime is a critical issue for long-term stable operation of the high-power EUV light source. In this paper we describe about the optimization of tin debris mitigation with a compact EUV generation system. We observe almost all of Sn fragments generated after a pre-pulse irradiation are vaporized by a main CO<sub>2</sub> pulse laser with a droplet of 20 &mu;m in diameter. An EUV conversion efficiency (CE) of 3.4% at a maximum is obtained for the 20 &mu;m droplet. These results indicate the debris mitigation can be achieved without degradation of the high EUV CE.
Tumor cell-selective regulation of NOXA by c-MYC in response to proteasome inhibition (2007)

The proteasome controls a plethora of survival factors in all mammalian cells analyzed to date. Therefore, it is puzzling that proteasome inhibitors such as bortezomib can display a preferential toxicity toward malignant cells. In fact, proteasome inhibitors have the salient feature of promoting a dramatic induction of the proapoptotic protein NOXA in a tumor cell-restricted manner. However, the molecular determinants that control this specific regulation of NOXA are unknown. Here, we show that the induction of NOXA by bortezomib is directly dependent on the oncogene c-MYC. This requirement for c-MYC was found in a variety of tumor cell types, in marked contrast with dispensable roles of p53, HIF-1alpha, and E2F-1 (classical proteasomal targets that can regulate NOXA mRNA under stress). Conserved MYC-binding sites identified at the NOXA promoter were validated by ChIP and reporter assays. Down-regulation of the endogenous levels of c-MYC abrogated the induction of NOXA in proteasome-defective tumor cells. Conversely, forced expression of c-MYC enabled normal cells to accumulate NOXA and subsequently activate cell death programs in response to proteasome blockage. c-MYC is itself a proteasomal target whose levels or function are invariably up-regulated during tumor progression. Our data provide an unexpected function of c-MYC in the control of the apoptotic machinery, and reveal a long sought-after oncogenic event conferring sensitivity to proteasome inhibition.
A Small-Molecule Inhibitor of PIM Kinases as a Potential Treatment for Urothelial Carcinomas (2014)

The proto-oncogene proviral integration site for moloney murine leukemia virus (PIM) kinases (PIM-1, PIM-2, and PIM-3) are serine/threonine kinases that are involved in a number of signaling pathways important to cancer cells. PIM kinases act in downstream effector functions as inhibitors of apoptosis and as positive regulators of G1-S phase progression through the cell cycle. PIM kinases are upregulated in multiple cancer indications, including lymphoma, leukemia, multiple myeloma, and prostate, gastric, and head and neck cancers. Overexpression of one or more PIM family members in patient tumors frequently correlates with poor prognosis. The aim of this investigation was to evaluate PIM expression in low- and high-grade urothelial carcinoma and to assess the role PIM function in disease progression and their potential to serve as molecular targets for therapy. One hundred thirty-seven cases of urothelial carcinoma were included in this study of surgical biopsy and resection specimens. High levels of expression of all three PIM family members were observed in both noninvasive and invasive urothelial carcinomas. The second-generation PIM inhibitor, TP-3654, displays submicromolar activity in pharmacodynamic biomarker modulation, cell proliferation studies, and colony formation assays using the UM-UC-3 bladder cancer cell line. TP-3654 displays favorable human ether-à-go-go-related gene and cytochrome P450 inhibition profiles compared with the first-generation PIM inhibitor, SGI-1776, and exhibits oral bioavailability. In vivo xenograft studies using a bladder cancer cell line show that PIM kinase inhibition can reduce tumor growth, suggesting that PIM kinase inhibitors may be active in human urothelial carcinomas.
Evidence of Yersinia pestis DNA from fleas in an endemic plague area of Zambia (2012)

We conclude that fleas may be responsible in the transmission of Y. pestis and that PCR may provide means of plague surveillance in the endemic areas of Zambia.
Data from Predicting Clinical Outcome through Molecular Profiling in Stage III Melanoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Patients with macroscopic stage III melanoma represent a heterogeneous cohort with average 5-year overall survival rates of &lt;30%. With current algorithms, it is not possible to predict which patients will achieve longer-term survival. We hypothesized that molecular profiling could be used to identify prognostic groups within patients with stage III melanoma while also providing a greater understanding of the biological programs underpinning these differences.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Lymph node sections from 29 patients with stage IIIB and IIIC melanoma, with divergent clinical outcome including 16 “poor-prognosis” and 13 “good-prognosis” patients as defined by time to tumor progression, were subjected to molecular profiling using oligonucleotide arrays as an initial training set. Twenty-one differentially expressed genes were validated using quantitative PCR and the 15 genes with strongest cross-platform correlation were used to develop two predictive scores, which were applied to two independent validation sets of 10 and 14 stage III tumor samples.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Supervised analysis using differentially expressed genes was able to differentiate the prognostic groups in the training set. The developed predictive scores correlated directly with clinical outcome. When the predictive scores were applied to the two independent validation sets, clinical outcome was accurately predicted in 90% and 85% of patients, respectively.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; We describe a gene expression profile that is capable of distinguishing clinical outcomes in a previously homogeneous group of stage III melanoma patients.&lt;/p&gt;&lt;/div&gt;
Supplementary Tables S1 - S8 from Discovery of Biomarkers Predictive of GSI Response in Triple-Negative Breast Cancer and Adenoid Cystic Carcinoma (2023)

&lt;p&gt;Table S1: Analysis of Notch gene rearrangements in triple negative breast cancer subtypes. Table S2: Genes whose expression correlates with Notch gene-rearrangement status in cancer cell lines. Table S3: Genes whose expression correlates with Notch gene-rearrangement in triple negative breast cancer. Table S4. Novel mutations identified in the NRR and PEST domains of NOTCH1 in solid tumors. Table S5: Notch NRR and PEST domain mutation frequency. Table S6: NOTCH1 mutational status, N1-ICD levels, MYC expression in Adenoid Cystic Carcinoma models. Table S7: Primary antibodies. Table S8: RT-PCR Primers.&lt;/p&gt;
Finding Sparse Representations in Multiple Response Models via Bayesian Learning (2005)

Given a large overcomplete dictionary of basis vectors, our goal is to efﬁciently represent L > 1 signal vectors using coefﬁcient expansions marked by a common sparsity proﬁle. This generalizes the standard sparse representation problem to the case where we have access to multiple responses that were putatively generated by the same small subset of features. Ideally, we would like to uncover the associated sparse generating weights, which can have physical signiﬁcance in many applications. The generic solution to this problem is combinatorial and therefore we seek approximate procedures. Sparse approximation algorithms tailored to the multiple response domain have typically fallen into two categories: Greedy algorithms such as Matching Pursuit or regularized least-squares methods such as Basis Pursuit and FOCUSS. While these approaches have been extensively analyzed by others, there has been comparably less progress with regard to the development new sparse approximation cost functions and algorithms. Herein, we derive an alternative cost function and associated learning rule based upon a sparse Bayesian learning formulation that improves upon existing methods in many cases.
Plasmon Resonance Enhanced Photocatalysis Under Visible Light with Au/Cu–TiO<SUB>2</SUB> Nanoparticles: Removal Cr (VI) from Water as a Case of Study (2013)

Gold modified copper doped titania (Au/Cu:TiO2) nanoparticles were synthesized by a modified sol gel method and characterized using XRD, optical and TEM based techniques. The as-prepared material contained anatase phase particles with quasi-spherical morphology, showing enhanced absorption in the visible region and low photoluminescence emission intensity. Photocatalytic reduction of Cr (VI) in aqueous suspension with the Au/Cu:TiO2catalyst under 532 nm laser radiation and a visible broad band lamp source yielded 96% and 45% removal, respectively, without any additives. The enhanced photocatalytic activity can be attributed to the improved plasmonic effect due to gold modification and the expanded visible absorption due to copper doping. Moreover a comparative study of the material properties and catalytic activity of TiO2, Cu-TiO2and Au/Cu-TiO2 was carried out. © 2013 by American Scientific Publishers.
A Solvent-Sensitive Aromatic Cotton Effect in Lysozyme1 (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Solvent-Sensitive Aromatic Cotton Effect in Lysozyme1Alexander N. Glazer and Norman S. SimmonsCite this: J. Am. Chem. Soc. 1965, 87, 10, 2287–2288Publication Date (Print):May 1, 1965Publication History Published online1 May 2002Published inissue 1 May 1965https://pubs.acs.org/doi/10.1021/ja01088a035https://doi.org/10.1021/ja01088a035research-articleACS PublicationsRequest reuse permissionsArticle Views50Altmetric-Citations23LEARN 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
An information theoretical model for quantum secret sharing schemes (2005)

Similarly to earlier models for quantum error correcting codes, we introduce a quantum information theoretical model for quantum secret sharing schemes. This model provides new insights into the theory of quantum secret sharing. By using our model, among other results, we give a shorter proof of Gottesman's theorem that the size of the shares in a quantum secret sharing scheme must be as large as the secret itself. Also, we introduced approximate quantum secret sharing schemes and showed robustness of quantum secret sharing schemes by extending Gottesman's theorem to the approximate case.
Construction and next-generation sequencing analysis of a large phage-displayed VNAR single-domain antibody library from six naïve nurse sharks (2018)

<b>Background:</b> Shark new antigen receptor variable domain (V<sub>NAR</sub>) antibodies can bind restricted epitopes that may be inaccessible to conventional antibodies. <b>Methods:</b> Here, we developed a library construction method based on polymerase chain reaction (PCR)-Extension Assembly and Self-Ligation (named "EASeL") to construct a large V<sub>NAR</sub> antibody library with a size of 1.2 × 10<sup>10</sup> from six naïve adult nurse sharks (<i>Ginglymostoma cirratum</i>). <b>Results:</b> The next-generation sequencing analysis of 1.19 million full-length V<sub>NAR</sub>s revealed that this library is highly diversified because it covers all four classical V<sub>NAR</sub> types (Types I-IV) including 11% of classical Type I and 57% of classical Type II. About 30% of the total V<sub>NAR</sub>s could not be categorized as any of the classical types. The high variability of complementarity determining region (CDR) 3 length and cysteine numbers are important for the diversity of V<sub>NAR</sub>s. To validate the use of the shark V<sub>NAR</sub> library for antibody discovery, we isolated a panel of V<sub>NAR</sub> phage binders to cancer therapy-related antigens, including glypican-3, human epidermal growth factor receptor 2 (HER2), and programmed cell death-1 (PD1). Additionally, we identified binders to viral antigens that included the Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS) spike proteins. The isolated shark single-domain antibodies including Type I and Type II V<sub>NAR</sub>s were produced in <i>Escherichia coli</i> and validated for their antigen binding. A Type II V<sub>NAR</sub> (PE38-B6) has a high affinity (K<sub>d</sub> = 10.1 nM) for its antigen. <b>Conclusions:</b> The naïve nurse shark V<sub>NAR</sub> library is a useful source for isolating single-domain antibodies to a wide range of antigens. The EASeL method may be applicable to the construction of other large diversity gene expression libraries.
High Surface Area of Polyhedral Chromia and Hexagonal Chromium Sulfide by the Thermolysis of Cyclohexylammonium Hexaisothiocyanatochromate(III) Sesquihydrate (2021)

Abstract A new organic‐inorganic hybrid salt of cyclohexylammonium hexaisothiocyanatochromate(III) sesquihydrate, (C 6 H 11 NH 3 ) 3 [Cr(NCS) 6 ] ⋅ 3/2H 2 O, was synthesized at room‐temperature by metathesis and ligand addition for the establishment of energy‐saving chemical synthesis approach. The formation of this new salt was confirmed by FT‐IR, UV‐Vis spectrophotometry, elemental microanalysis, and single‐crystal X‐ray diffraction. The TGA study showed low‐temperature thermal stability of this salt, where chromium oxide (Cr 2 O 3 ) formed under air and chromium sulfide (Cr 2 S 3 ) under argon, as PXRD confirmed their formation as nanocrystalline. The morphological studies by SEM and TEM revealed the formation of irregular polyhedron particles of Cr 2 O 3 and of hexagonal packed layers of Cr 2 S 3 . The textural study by nitrogen physisorption disclosed the mesoporous nature and high specific surface area of Cr 2 O 3 (∼132 m 2 g −1 ) and Cr 2 S 3 (∼241 m 2 g −1 ). Cyclohexylammonium could act as an organic self‐template for the formation of mesopores and the high temperature of thermolysis assisted the formation of such pores.
ChemInform Abstract: One‐ and Two‐Dimensional High‐Resolution Solid‐State NMR Studies of Zeolite Lattice Structures (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.
Fast and selective fluoride ion conduction in sub-1-nanometer metal-organic framework channels (2019)

Biological fluoride ion channels are sub-1-nanometer protein pores with ultrahigh F<sup>-</sup> conductivity and selectivity over other halogen ions. Developing synthetic F<sup>-</sup> channels with biological-level selectivity is highly desirable for ion separations such as water defluoridation, but it remains a great challenge. Here we report synthetic F<sup>-</sup> channels fabricated from zirconium-based metal-organic frameworks (MOFs), UiO-66-X (X = H, NH<sub>2</sub>, and N<sup>+</sup>(CH<sub>3</sub>)<sub>3</sub>). These MOFs are comprised of nanometer-sized cavities connected by sub-1-nanometer-sized windows and have specific F<sup>-</sup> binding sites along the channels, sharing some features of biological F<sup>-</sup> channels. UiO-66-X channels consistently show ultrahigh F<sup>-</sup> conductivity up to ~10 S m<sup>-1</sup>, and ultrahigh F<sup>-</sup>/Cl<sup>-</sup> selectivity, from ~13 to ~240. Molecular dynamics simulations reveal that the ultrahigh F<sup>-</sup> conductivity and selectivity can be ascribed mainly to the high F<sup>-</sup> concentration in the UiO-66 channels, arising from specific interactions between F<sup>-</sup> ions and F<sup>-</sup> binding sites in the MOF channels.
Front Matter: Volume 7531 (2010)

This PDF file contains the front matter associated with SPIE Proceedings volume 7531, including the Title Page, Copyright information, Table of Contents, Introduction, and the Conference Committee listing.
Absolute propagation rate coefficients in radical polymerization from gel permeation chromatography of polymers produced by intermittent initiation (1997)

Abstract The pulsed laser polymerization technique is now a well accepted method to determine propagation rate coefficients for radical polymerization from molar mass distributions resulting from intermittent initiation. A simplified apparatus for the periodic photoinitiation is used which is much less expensive than the laser equipment. The usefulness of the simplified equipment was proved by the determination of k p for styrene at technically relevant temperatures up to 130°C for the first time. Furthermore, careful inspection of the molar mass distribution (mmd) reveals that depending on the reaction conditions, inflection points ( L i ) can not only be found at integer multiples of k p • t o • [M] but also at 0.5 i • k p • t o • [M], i = 1, 2, 3, … . A rule to find the inflection points leading to correct values for k p is proposed. It is shown that the shape of the mmd inter alia depends on the amount of primary radical termination compared to the termination reaction between growing chains. With dominant primary termination, the maxima of the distribution will give the correct k p , whereas in the absence of primary termination the inflection points should be used. Experimental conditions like initiator concentration, light intensity etc. may influence the position of the L i at least to some extent, and so may give a small but principal error or uncertainty in k p . A new mathematical method for the time‐dependent simulation of the resulting mmd is presented which allows the calculations being performed on a PC within an acceptable time.
Geo-location for voice search language modeling (2015)

We investigate the benefit of augmenting with geo-location information the language model used in speech recognition for voice-search. We observe reductions in perplexity of up to 15% relative on test sets obtained from both typed query data, as well as transcribed voice search data; on a subset of the test data consisting of “local” queries — search results displaying a restaurant, some address, or similar — the reduction in perplexity is even higher, up to 30% relative. Automatic speech recognition experiments confirm the utility of geo-location information for improved language modeling. Significant reductions in word error rate are observed both on general voice search traffic, as well as “local” traffic, up to 2% and 8% relative, respectively.