gebhart/patrepeval huggingface dataset:
Data from Targeting Bladder Tumor Cells <i>In vivo</i> and in the Urine with a Peptide Identified by Phage Display (2023)

&lt;div&gt;Abstract&lt;p&gt;Bladder cancer is one of the most common tumors of the genitourinary tract. Here, we use phage display to identify a peptide that targets bladder tumor cells. A phage library containing random peptides was screened for binding to cells from human bladder tumor xenografts. Phage clones were further selected for binding to a bladder tumor cell line in culture. Six clones displaying the consensus sequence CXNXDXR&lt;sup&gt;X&lt;/sup&gt;/&lt;sub&gt;R&lt;/sub&gt;C showed selective binding to cells from primary human bladder cancer tissue. Of these, the CSNRDARRC sequence was selected for further study as a synthetic peptide. Fluorescein-conjugated CSNRDARRC peptide selectively bound to frozen sections of human bladder tumor tissue, whereas only negligible binding to normal bladder tissue was observed. When the fluorescent peptide was introduced into the bladder lumen, in a carcinogen-induced rat tumor model, it selectively bound to tumor epithelium. Moreover, when the peptide was intravenously injected into the tail vein, it homed to the bladder tumor but was not detectable in normal bladder and control organs. Next, we examined whether the peptide can detect tumor cells in urine. The fluorescent peptide bound to cultured bladder tumor cells but not to other types of tumor cell lines. Moreover, it bound to urinary cells of patients with bladder cancer, while showing little binding to urinary cells of patients with inflammation or healthy individuals. The CSNRDARRC peptide may be useful as a targeting moiety for selective delivery of therapeutics and as a diagnostic probe for the detection of bladder cancer. (Mol Cancer Res 2007;5(1):11–19)&lt;/p&gt;&lt;/div&gt;
Pharmacology of predatory and defensive venom peptides in cone snails (2017)

Cone snails are predatory gastropods whose neurotoxic venom peptides (conotoxins) have been extensively studied for pharmacological probes, venom evolution mechanisms and potential therapeutics. Conotoxins have a wide range of structural and functional classes that continue to undergo accelerated evolution that underlies the rapid expansion of the genus over their short evolutionary history. A number of pharmacological classes, driven by separately evolved defensive and predatory venoms, have been hypothesised to facilitate shifts in prey that exemplify the adaptability of cone snails. Here we provide an overview of these pharmacological families and discuss their ecological roles and evolutionary impact.
Active Surveillance for Avian Influenza Virus, Egypt, 2010–2012 (2014)

Continuous circulation of influenza A(H5N1) virus among poultry in Egypt has created an epicenter in which the viruses evolve into newer subclades and continue to cause disease in humans. To detect influenza viruses in Egypt, since 2009 we have actively surveyed various regions and poultry production sectors. From August 2010 through January 2013, >11,000 swab samples were collected; 10% were positive by matrix gene reverse transcription PCR. During this period, subtype H9N2 viruses emerged, cocirculated with subtype H5N1 viruses, and frequently co-infected the same avian host. Genetic and antigenic analyses of viruses revealed that influenza A(H5N1) clade 2.2.1 viruses are dominant and that all subtype H9N2 viruses are G1-like. Cocirculation of different subtypes poses concern for potential reassortment. Avian influenza continues to threaten public and animal health in Egypt, and continuous surveillance for avian influenza virus is needed.
Effect of channeling of halo ion implantation on threshold voltage shift of metal oxide semiconductor field-effect transistor (1996)

In this letter, we report threshold voltage shift of metal oxide semiconductor field effect transistor (MOSFET) after the halo ion implantation process. Although halo implantation can significantly reduce the short channel effect, it causes a threshold voltage shift of a long channel device due to dopant channeling through polycrystalline silicon grain boundary. Although the chemical vapor deposited (CVD) cap oxide on polycrystalline silicon gate was used as a blocking layer of dopant, threshold voltages shift clearly indicate dopant channeling through polycrystalline silicon. To avoid a channeling problem, a thicker cap oxide layer or lower halo implantation energy is necessary.
Rigorous estimation of post-translational proteasomal splicing in the immunopeptidome (2021)

ABSTRACT Recently, de novo peptide sequencing has made it possible to gain new insights into the human immunopeptidome without relying on peptide databases, while identifying peptides of unknown origin. Many recent studies have attributed post-translational proteasomal splicing as the origin of those peptides. Here, we describe a peptide source assignment workflow to rigorously assign the source of de novo sequenced peptides and find that the estimated extent of post-translational splicing in the immunopeptidome is much lower than previously reported. Our approach demonstrates that many peptides that were thought to be post-translationally spliced are likely linear peptides, and many peptides that were thought to be trans-spliced could be cis-spliced. We believe our approach furthers the understanding of post-translationally spliced peptides and thus improves the characterization of immunopeptidome which plays a critical role in the immune response to antigens in cancer, autoimmune disease, and infections.
Data from Reversible Dysfunction of Wild-Type p53 following Homeodomain-Interacting Protein Kinase-2 Knockdown (2023)

&lt;div&gt;Abstract&lt;p&gt;About half of cancers sustain mutations in the &lt;i&gt;TP53&lt;/i&gt; gene, whereas the other half maintain a wild-type p53 (wtp53) but may compromise the p53 response because of other alterations. Homeodomain-interacting protein kinase-2 (HIPK2) is a positive regulator of p53 oncosuppressor function. Here, we show, by microarray analysis, that wtp53 lost the target gene activation following stable knockdown of HIPK2 (HIPK2i) in colon cancer cell line. Our data show that the stable knockdown of HIPK2 led to wtp53 misfolding, as detected by p53 immunoprecipitation with conformation-specific antibodies, and that p53 protein misfolding impaired p53 DNA binding and transcription of target genes. We present evidence that zinc supplementation to HIPK2i cells increased p53 reactivity to conformation-sensitive PAb1620 (wild-type conformation) antibody and restored p53 sequence-specific DNA binding &lt;i&gt;in vivo&lt;/i&gt; and transcription of target genes in response to Adriamycin treatment. Finally, combination of zinc and Adriamycin suppressed tumor growth &lt;i&gt;in vivo&lt;/i&gt; and activated misfolded p53 that induced its target genes in nude mice tumor xenografts derived from HIPK2i cells. Bioinformatics analysis of microarray data from colon cancer patients showed significant association of poor survival with low HIPK2 expression only in tumors expressing wtp53. These results show a critical role of HIPK2 in maintaining the transactivation activity of wtp53 and further suggest that low expression of HIPK2 may impair the p53 function in tumors harboring wtp53. [Cancer Res 2008;68(10):3707–13]&lt;/p&gt;&lt;/div&gt;
Photoinduced electron transfer in a carbon nanohorn–C60 conjugate (2014)

A nanohybrid combining two allotropic forms of carbon, namely carbon nanohorns (CNH) and C60, has been obtained from a C60 derivative bearing a benzocrown ether subunit (crown–C60) and a CNH functionalized with NH3+ groups (CNH-sp-NH3+F−) through ammonium–crown ether interactions. The resulting CNH–C60 nanohybrid has been characterized by Raman and XPS spectroscopies, thermogravimetric analysis (TGA) and high-resolution transmission electron microscopy (HR-TEM). The photophysical properties of the CNH–C60 conjugate have been investigated in benzonitrile. Femtosecond laser flash photolysis measurements revealed the occurrence of an efficient electron transfer from the singlet excited state of the C60 moiety to the CNH with a rate constant of 6.5 × 1010 s−1 to produce a radical ion pair, which decayed by charge recombination with a lifetime of 1.0 ns to afford the triplet excited state of CNH-sp-NH3+F− and crown–C60. The two carbon nanoforms play therefore complementary roles in the CNH–C60 conjugate, the CNH acting as an electron donor and C60 as an electron acceptor.
Reconstitution and Characterization of a New Desosaminyl Transferase, EryCIII, from the Erythromycin Biosynthetic Pathway (2004)

EryCIII converts alpha-mycarosyl erythronolide B into erythromycin D using TDP-d-desosamine as the glycosyl donor. We report the heterologous expression, purification, in vitro reconstitution, and preliminary characterization of EryCIII. Coexpression of EryCIII with the GroEL/ES chaperone complex was found to enhance greatly the expression of soluble EryCIII protein. The enzyme was found to be highly active with a kcat greater than 100 min-1. EryCIII was quite selective for the natural nucleotide sugar donor and macrolide acceptor substrates, unlike several other antibiotic glycosyl transferases with broad specificity such as desVII, oleG2, and UrdGT2. Within detectable limits, neither 6-deoxyerythronolide B nor 10-deoxymethynolide were found to be glycosylated by EryCIII. Furthermore, TDP-d-mycaminose, which only differs from TDP-d-desosamine at the C4 position, could not be transferred to alphaMEB. These studies lay the groundwork for detailed structural and mechanistic analysis of an important member of the desosaminyl transferase family of enzymes.
Use of the Pseudo-Rigid Body Model to Simplify the Description of Complliant Micro-Mechanisms (1996)

It is shown that for some structures the computationally simple pseudo-rigid body model can accurately predict the motion of these structures with error of less than the measurement accuracy of 0.5m for deflections as large as 30m. This paper also discusses the use of the pseudo-rigid body model to provide a hierarchical approach to CMEMS desi gn that sharply reduces the computation time required to predict the motion of complex CMEMS structures.
ChemInform Abstract: Highly Diastereo‐ and Enantioselective Catalytic Domino Thia‐Michael/Aldol Reactions: Synthesis of Benzothiopyrans with Three Contiguous Stereocenters. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
<title>Flat-panel fluorescent lamp backlights with controlled illumination angle: backlighting optics at the thermodynamic limit</title> (1993)

Interest in improving backlight performance is increasing rapidly, driven by the large world-wide investment in high-perfonnance LCD display screens. At the simplest level, afl backlights consist of one or more light sources (usually tubular fluorescent lamps) and an optical system. The optical system collects the fluorescent light and causes it to pass through the LCD display screen towards the viewer. NiOptics' proprietary optical designs have been used to increase flat-panel backlight luminance by a factor of 2 to 2.5 over comparable conventional systems. This dramatic improvement results from matching illumination to preferred viewing angles. The maximum theoretical improvement is quantified by deriving the fundamental thermodynamic limits which restrict two key backlight sub-systems, the light source and the distribution panel. These sub-system analyses are then combined to show thesurprisingly complex set oftrade-offs intrinsic to all backlight designs, completely independent ofthe specific device architecture. Specifically, we show that backlight luminance has an upper bound given by Po ILot&lt; x— D1D2Sin90t cxlcclL hsinOi 1—cx In this expression L0t is the output luminance, øout is the vertical output half-angle, P is the lamp luminous output, Di and D2 are the linear dimensions of the backlight emission surface, h is the backlight thickness, dL is the lamp I.D., and a is the lamp's effective self-absorptivity coefficient. Two limiting special cases of this expression are developed to illustrate the design trade-offs. The comparisondemonstrates that superior performance requires that angular reduction be achieved within the distribution panel. Finally, we compare these two theoretical limits to NiOptics' experimental results. The results show that NiOptics proprietary backlights perform at 66% of the theoretical limit, with shortfall due primarily to material absorption and reflection losses.
Convexity in Non-convex Optimizations of Streaming Applications (2012)

Streaming data applications are frequently pipelined and deployed on application-specific systems to meet performance requirements and resource constraints. Typically, there are several design parameters in the algorithms and architectures used that impact the application performance as well as resource utilization. Efficient exploration of this design space is the goal of this research. When using architecturally diverse systems to accelerate streaming applications, the design search space is often complex. The search complexity can be reduced by recognizing and exploiting convex variables to perform convex decomposition, preserving optimality even in the context of a non-convex optimization problem. This paper presents a formal treatment of convex variables and convex decomposition, including a proof that the technique preserves optimality. It also quantifies the reduction in the search space that is realized, at minimum equal to the number of distinct values of the convex variable and potentially much higher.
On the Natural Frequencies of High-Speed Spindles with Angular Contact Bearings (1991)

Experimental evidence has shown that the natural frequencies of a high-speed spindle decrease with increasing rotational speeds. While this phenomenon is important to the design and operation of high-speed machine tools, it has not been thoroughly analysed. This paper presents a spindle model that can be used to analyse the changes in bearing stiffness and the natural frequencies of the system. It is shown that the system dynamics can vary substantially due to bearing centrifugal force and shaft gyroscopic effects. The findings can be utilized in optimizing the design and control of high-speed spindle systems.
Deep conservation of cis-element variants regulating plant hormonal responses (2019)

Phytohormones regulate many aspects of plant life by activating transcription factors (TFs) that bind sequence-specific response elements (REs) in regulatory regions of target genes. Despite their short length, REs are degenerate, with a core of just 3 to 4 bp. This degeneracy is paradoxical, as it reduces specificity and REs are extremely common in the genome. To study whether RE degeneracy might serve a biological function, we developed an algorithm for the detection of regulatory sequence conservation and applied it to phytohormone REs in 45 angiosperms. Surprisingly, we found that specific RE variants are highly conserved in core hormone response genes. Experimental evidence showed that specific variants act to regulate the magnitude and spatial profile of hormonal response in Arabidopsis (<i>Arabidopsis thaliana</i>) and tomato (<i>Solanum lycopersicum</i>). Our results suggest that hormone-regulated TFs bind a spectrum of REs, each coding for a distinct transcriptional response profile. Our approach has implications for precise genome editing and for rational promoter design.
On the typology of negative concord (2016)

This paper has three main points. First, contrary to what is often stated, negative concord is not all that frequent and certainly not the most frequent strategy to express single clausal negation in a clause with an indefinite noun phrase or adverbial in the scope of the negation. Second, the subtype of negative concord called ‘strict negative concord’ is much more frequent than the subtype of ‘non-strict negative concord’. These two claims are based on a worldwide sample of 179 languages. Third, it is argued that non-strict negative concord shows too much variation for it to be seen as the one choice of a two-way split between strict and non-strict negative concord. Given the relative rarity of non-strict negative concord, this claim is not based on the worldwide sample, but on a survey of the research literature.
Measurements of terrestrial digital TV signals at two cities in South America (2010)

This work describes campaigns of measurements of propagation channel characteristics for Terrestrial Digital TV, carried on the metropolitan region of Rio de Janeiro, Brazil and Caracas, Venezuela. Measurements of propagation loss obtained from these experiment are compared with predictions using the ITU-R Recommendation P.1546–3 method. Measured multipath time delay profiles for LOS and NLOS reception are also presented.
Partitioning of unsaturated hydrophilic monomer in microemulsion media monitored by pyrene fluorescence method (2003)

Abstract The extent of intra‐ and interchain associations of (un)charged water‐soluble monomers in the homogeneous and micellar solutions was studied with steady‐state fluorescence spectroscopy. Fluorescence spectroscopic experiments were performed on uncharged (acryl amide) and charged hydrophilic monomers [zwitterionic 3‐dimethyl(methacryloyloxyethyl)ammonium propane sulfonate (DMAPS), etc.] with pyrene as a probe. In both the homogeneous and micellar solutions, linear Stern–Volmer plots were obtained that implied that the quenching process can be considered as totally dynamic. The Stern–Volmer constant ( K SV ) for DMAPS decreased with an increasing dielectric constant of solvent and the concentration of simple electrolyte. An abrupt decrease in K SV was observed in the presence of a small amount of anionic emulsifier [below the critical micelle concentration (cmc)]. The dependence of K SV on pH for DMAPS was described by a curve with a maximum at about pH = 7. This was interpreted in terms of segregation of DMAPS and the variation of a optimal microenvironment for the probe and quencher with pH. The quenching rate in the micellar solutions strongly increased above the cmc but was lower than that in the homogeneous solutions. In the micellar solutions (above the cmc), the microenvironment for an interaction between the probe and quencher was suggested to be the whole microdroplet. The dependence of K SV on pH for DMAPS is described by a curve with a maximum at about pH = 9.3. The synergistic effect arises from the segregation of charged quencher molecules within the microdroplets. The complex (or strong interaction) between quencher and additive(s) is supposed to increase the dynamic nature of microdroplets that provides an optimal microenvironment for probe and quencher. A good coemulsifier, however, removes quencher from the interface and creates a barrier for entering monomer (quencher) into the core of micelles; therefore, quenching is depressed. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 571–581, 2003
A Small Fission Power System for NASA Planetary Science Missions (2011)

Mitral valve stenosis (MS) associated with rheumatic disease no longer represents a major heart problem during the perinatal period in Japan. Here we present a case of acute heart failure due to MS after emergency cesarean section (CS). The patient was transferred due to the development of fetal distress at 36 weeks gestation and underwent an emergency CS under general anesthesia. She developed acute heart failure immediately postoperatively and was diagnosed with MS associated with pulmonary artery hypertension for the first time. She underwent percutaneous transvenous mitral commissurotomy and was discharged from our hospital in good condition.
An analytical three-dimensional field model of a perpendicular recording head (1988)

A simple analytical three-dimensional head-field model has been developed for a single-pole perpendicular recording head with a soft magnetic interlayer below the recording medium. A large-scale (5000:1) model of a perpendicular recording head has also been constructed. The normalized head fields obtained by the analytical model show good agreement with the experimental results from the large-scale model. Using the analytical model, it was confirmed that the side fringe of a perpendicular head diminishes rapidly compared with that of a longitudinal head, providing a higher potential for narrow-track recording.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Figure 4 from STC1 Expression By Cancer-Associated Fibroblasts Drives Metastasis of Colorectal Cancer (2023)

&lt;p&gt;PDF file - 8870K, Histopathological analysis of primary tumors.&lt;/p&gt;
Workshop summary for the 5th international workshop on multimedia for cooking and eating activities (CEA'13) (2013)

This summary introduces the aim of the CEA'13 workshop and the list of papers presented in the workshop.
Abstract 2371: Heterogeneity of resistance mechanisms in lung adenocarcinoma patients with acquired resistance to EGFR inhibitors (2014)

Abstract Drug resistance is a major obstacle in overcoming cancer. Understanding the origin, extent and heterogeneity of resistance mechanisms within a patient is crucial to guide treatment and developing drugs/combinations to circumvent resistance. To this end, we studied autopsy samples collected from four EGFR-mutant lung adenocarcinoma patients who developed resistance to EGFR inhibitors. We used whole-exome sequencing to characterize genomic profiles of multiple metastasis tumors within each patient. To address the challenge of non-uniform variant detection power at sequenced genetic loci across multiple samples, we developed a computational framework that tackles variant detection from pooled tumor followed by a genotyping module. After the identification of somatic alterations, we determined the extent of heterogeneity of resistance mechanisms between multiple tumor samples. Our results revealed that multiple metastasis samples in a single patient can potentially use one common resistance mechanism. For example, one patient harbored a resistant EGFR T790M mutation in all 11 metastasis samples with a correlated allele frequency to the original L858R mutation. However, in some other cases, we found heterogeneous resistance mechanisms coexisting in multiple metastasis samples with various allele frequencies. For instance, one patient harbored both the resistance EGFR T790M mutation and an activating PIK3CA E542K mutation that appear with a range of allelic frequencies in multiple metastatic samples. Furthermore, branched evolutionary patterns of tumors were constructed using a phylogenetic approach, which inform resistance in the context of tumor evolution. Our findings are consistent with the model that cells harboring a variety of resistance mechanisms coexist in each metastasis tumor, and those subclones with higher selective advantage outgrow the others. Citation Format: Xinmeng Jasmine Mu, Eli Van Allen, Nikhil Wagle, Curtis Chong, Mohit Butaney, Deborah Farlow, Gad Getz, Pasi A. Jänne, Levi A. Garraway. Heterogeneity of resistance mechanisms in lung adenocarcinoma patients with acquired resistance to EGFR inhibitors. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2371. doi:10.1158/1538-7445.AM2014-2371