gebhart/patrepeval huggingface dataset:
Cotton Plants Expressing a Hemipteran-Active Bacillus thuringiensis Crystal Protein Impact the Development and Survival of Lygus hesperus (Hemiptera: Miridae) Nymphs (2012)

The plant bugs Lygus hesperus Knight (Hemiptera: Miridae) and L. lineolaris (Palisot de Beauvois) have emerged as economic pests of cotton in the United States. These hemipteran species are refractory to the insect control traits found in genetically modified commercial varieties of cotton. In this article, we report the isolation and characterization of a 35 kDa crystal protein from Bacillus thuringiensis, designated TIC807, which causes reduced mass gain and mortality of L. hesperus and L. lineolaris nymphs when presented in an artificial diet feeding assay. Cotton plants expressing the TIC807 protein were observed to impact the survival and development of L. hesperus nymphs in a concentration-dependent manner. These results, demonstrating in planta activity of a Lygus insecticidal protein, represent an important milestone in the development of cotton varieties protected from Lygus feeding damage.
Phenomenon of End of Life in a Fluorescent Lamp under High-Frequency Operation (2003)

The mechanism that causes the end of lamp life (EOLL) phenomenon in a fluorescent lamp should be clarified to better understand the EOLL. The phenomenon, including the tungsten sputtering from an electrode, is investigated. We observed the electron emission from a lead in the vicinity of the stem glass resulting in the intermittent pulse discharge that heated up the stem glass. The comparison of the stem glass resistance and the glow discharge impedance at an interval of leads after disconnection of the filament indicates whether or not the stem glass will begin to soften. It was shown that the heating of a small glass portion around the lead by the intermittent pulse discharge or the concentration of discharge current into one of leads was a dominant factor that resulted in the final stage of EOLL.
Mono‐ and Multisite Solid Catalysts in Cascade Reactions for Chemical Process Intensification (2009)

Catscade reactions: Heterogeneous catalysis can enable sustainability by carrying out multistep reactions in one step. It is shown that single- and multisite solid catalysts can be designed to carry out cascade reactions for the synthesis of fine chemicals.
Second-Generation Total Synthesis of Prorocentin (2023)

After a recent total synthesis had resolved all issues surrounding the constitution and stereostructure of prorocentin, it was possible to devise a new approach aiming at an improved supply of this scarce marine natural product; this compound is a cometabolite of the prototypical phosphatase inhibitor okadaic acid but still awaits detailed biological profiling. The revised entry starts from 2-deoxy-d-glucose; keys to success were a telescoped hemiacetal reduction/acetal cleavage and an exquisitely selective gold/Brønsted acid-cocatalyzed spiroacetalization.
Micro-photoluminescence characterisation of structural disorder in resonant tunneling diodes for THz applications (2021)

We investigated the difference between a macro scale PL and μPL (excitation and detection area &le; 5μm<sup>2</sup>). Low-temperature micro-photoluminescence (μPL) is used to evaluate structural perfection of high current density InGaAs/AlAs/InP resonant tunnelling diodes (RTD) structure on different length scales. The thin and highly strained quantum wells (QWs) is subject to monolayer fluctuations in well and barrier thickness that can lead to random fluctuations in their band profile. μPL is performed reducing the laser spot size using a common photolithography mask to reach typical RTD mesa size (a few square microns). We observed that for spot size around 1μm<sup>2</sup> the PL line shape present strong differences on multiple points on the wafer. These variations in the PL is investigated by line-shape fitting and discussed in terms of variations in long-range disorder brought about by strain relaxation processes. We also highlight this μPL as a powerful and cost-effective non-destructive characterization method for RTD structures.
cFinder: definition and quantification of multiple haplotypes in a mixed sample (2015)

Our cFinder is implemented in an efficient algorithm that can be run on a low-performance desktop computer. Furthermore, it considers paired-end information (if available) and is generally open for any current next-generation sequencing technology and alignment strategy. To our knowledge, this is the first software that enables researchers without extensive bioinformatic support to designate multiple haplotypes and how they constitute to a sample.
Compact hyperspectral sensor development (2015)

Users of spectral information desire more compact, lower cost sensors. We examine design considerations for different types of compact hyperspectral sensors and propose a basis of metrics for the comparison of dissimilar spectrometers.
An Asymmetric Approach towards (–)‐Aphanorphine and Its Analogues (2009)

Abstract A short enantioselective approach towards the alkaloid(–)‐aphanorphine and its substituted analogues is described. The enantiomerically pure starting material for the synthesis was obtained by asymmetric hydrogenation in the presence of the Rh–( S )‐PipPhos complex. Microwave‐assisted Heckcyclization selectively provided the seven‐membered 3‐benzazepine ring. Further, the assembly of the tricyclic core of the alkaloid was accomplished by intramolecular radical cyclization. The X‐ray structure confirming the absolute configuration of the obtained products is described. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
Data from miRNA Biomarkers in Cyst Fluid Augment the Diagnosis and Management of Pancreatic Cysts (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The diagnosis of pancreatic cystic lesions has increased dramatically. Most are benign, whereas some, such as intraductal papillary mucinous neoplasms (IPMN), represent precursors of pancreatic adenocarcinoma. Therapeutic stratification of IPMNs is challenging without precise information on dysplasia grade and presence of invasion. We assessed the diagnostic benefit of using miRNAs as biomarkers in pancreatic cyst fluid, focusing on IPMNs because of their frequency and malignant potential.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; RNA was extracted from 55 microdissected formalin-fixed, paraffin-embedded (FFPE) IPMN specimens, and 65 cyst fluid specimens aspirated following surgical resection. Expression of 750 miRNAs was evaluated with TaqMan miRNA Arrays using 22 FFPE and 15 cyst fluid specimens. Differential expression of selected miRNA candidates was validated in 33 FFPE and 50 cyst fluid specimens using TaqMan miRNA Assays.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We identified 26 and 37 candidate miRNAs that distinguish low-grade from high-grade IPMNs using FFPE and cyst fluid specimens, respectively. A subset of 18 miRNAs, selected from FFPE and cyst fluid data, separated high-grade IPMNs from low-grade IPMNs, serous cystadenomas (SCA) and uncommon cysts, such as solid pseudopapillary neoplasms (SPN) and cystic pancreatic neuroendocrine tumors (PanNET). A logistic regression model using nine miRNAs allowed prediction of cyst pathology implying resection (high-grade IPMNs, PanNETs, and SPNs) versus conservative management (low-grade IPMNs, SCAs), with a sensitivity of 89%, a specificity of 100%, and area under the curve of 1.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; We found candidate miRNAs that helped identify patients with high-grade IPMN and exclude nonmucinous cysts. These classifiers will require validation in a prospective setting to ultimately confirm their clinical usefulness. &lt;i&gt;Clin Cancer Res; 18(17); 4713–24. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Proxy Mobile IPv6 Extensions to Support Flow Mobility (2016)

Proxy Mobile IPv6 (PMIPv6) allows a mobile node to connect to the same PMIPv6 domain through different interfaces.This document describes extensions to the PMIPv6 protocol that are required to support network-based flow mobility over multiple physical interfaces.This document updates RFC 5213.The extensions described in this document consist of the operations performed by the local mobility anchor and the mobile access gateway to manage the prefixes assigned to the different interfaces of the mobile node, as well as how the forwarding policies are handled by the network to ensure consistent flow mobility management.
An international data set for CMML validates prognostic scoring systems and demonstrates a need for novel prognostication strategies (2015)

Since its reclassification as a distinct disease entity, clinical research efforts have attempted to establish baseline characteristics and prognostic scoring systems for chronic myelomonocytic leukemia (CMML). Although existing data for baseline characteristics and CMML prognostication have been robustly developed and externally validated, these results have been limited by the small size of single-institution cohorts. We developed an international CMML data set that included 1832 cases across eight centers to establish the frequency of key clinical characteristics. Of note, we found that the majority of CMML patients were classified as World Health Organization CMML-1 and that a 7.5% bone marrow blast cut-point may discriminate prognosis with higher resolution in comparison with the existing 10%. We additionally interrogated existing CMML prognostic models and found that they are all valid and have comparable performance but are vulnerable to upstaging. Using random forest survival analysis for variable discovery, we demonstrated that the prognostic power of clinical variables alone is limited. Last, we confirmed the independent prognostic relevance of ASXL1 gene mutations and identified the novel adverse prognostic impact imparted by CBL mutations. Our data suggest that combinations of clinical and molecular information may be required to improve the accuracy of current CMML prognostication.
Differential Effects of IL-1α and IL-1β on Tumorigenicity Patterns and Invasiveness (2003)

In this study, we show that distinct compartmentalization patterns of the IL-1 molecules (IL-1alpha and IL-1beta), in the milieu of tumor cells that produce them, differentially affect the malignant process. Active forms of IL-1, namely precursor IL-1alpha (pIL-1alpha), mature IL-1beta (mIL-1beta), and mIL-1beta fused to a signal sequence (ssIL-1beta), were transfected into an established fibrosarcoma cell line, and tumorigenicity and antitumor immunity were assessed. Cell lines transfected with pIL-1alpha, which expresses IL-1alpha on the membrane, fail to develop local tumors and activate antitumor effector mechanisms, such as CTLs, NK cells, and high levels of IFN-gamma production. Cells transfected with secretable IL-1beta (mIL-1beta and ssIL-1beta) were more aggressive than wild-type and mock-transfected tumor cells; ssIL-1beta transfectants even exhibited metastatic tumors in the lungs of mice after i.v. inoculation (experimental metastasis). In IL-1beta tumors, increased vascularity patterns were observed. No detectable antitumor effector mechanisms were observed in spleens of mice injected with IL-1beta transfectants, mock-transfected or wild-type fibrosarcoma cells. Moreover, in spleens of mice injected with IL-1beta transfectants, suppression of polyclonal mitogenic responses (proliferation, IFN-gamma and IL-2 production) to Con A was observed, suggesting the development of general anergy. Histologically, infiltrating mononuclear cells penetrating the tumor were seen at pIL-1alpha tumor sites, whereas in mIL-1beta and ssIL-1beta tumor sites such infiltrating cells do not penetrate inside the tumor. This is, to our knowledge, the first report on differential, nonredundant, in vivo effects of IL-1alpha and IL-1beta in malignant processes; IL-1alpha reduces tumorigenicity by inducing antitumor immunity, whereas IL-1beta promotes invasiveness, including tumor angiogenesis, and also induces immune suppression in the host.
DNN-assisted Particle-based Bayesian Joint Synchronization and Localization (2021)

In this work, we propose a Deep neural network-assisted Particle Filter-based (DePF) approach to address the Mobile User (MU) joint synchronization and localization (sync\&amp;loc) problem in ultra dense networks. In particular, DePF deploys an asymmetric time-stamp exchange mechanism between the MUs and the Access Points (APs), which, traditionally, provides us with information about the MUs' clock offset and skew. However, information about the distance between an AP and an MU is also intrinsic to the propagation delay experienced by exchanged time-stamps. In addition, to estimate the angle of arrival of the received synchronization packet, DePF draws on the multiple signal classification algorithm that is fed by Channel Impulse Response (CIR) experienced by the sync packets. The CIR is also leveraged on to determine the link condition, i.e. Line-of-Sight (LoS) or Non-LoS. Finally, to perform joint sync\&amp;loc, DePF capitalizes on particle Gaussian mixtures that allow for a hybrid particle-based and parametric Bayesian Recursive Filtering (BRF) fusion of the aforementioned pieces of information and thus jointly estimate the position and clock parameters of the MUs. The simulation results verifies the superiority of the proposed algorithm over the state-of-the-art schemes, especially that of Extended Kalman filter- and linearized BRF-based joint sync\&amp;loc. In particular, only drawing on the synchronization time-stamp exchange and CIRs, for 90$\%$of the cases, the absolute position and clock offset estimation error remain below 1 meter and 2 nanoseconds, respectively.
Introduction to the Issue on Biophotonics (2023)

WELCOME to the IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS (JSTQE) Issue on Biophotonics. Biophotonics is a truly exciting multidisciplinary field as it combines state-of-the-art photonics technologies in quantum electronics, lasers, fiber optics, and electro-optics to the study of life sciences and medicine. Since the invention of the microscope, light has played a crucial role in the discovery of phenomena in all forms of life, from single-celled organisms to humans. The modern field of biophotonics represents a truly broad spectrum of research spanning from basic science studies in botany and zoology, to biomedicine and clinical technologies. Yet, all of these research themes have in common the use of photons on living cells and organisms, which leads to insights being shared and used to inspire new directions across the spectrum of applications. In the biomedical domain, biophotonics approaches often initiate at the “bench,” where promising technologies eventually lead to clinically relevant “bedside” diagnostics and therapeutics. Because of the low cost associated with biomedical technologies, and increasing use of integrated photonics in mobile technologies, this field is rapidly transforming our approach to health care by providing increasingly rapid, accurate, point-of-care, and cost-efficient diagnostics and surgical guidance techniques.
HER2/neu Antibody Conjugated Poly(amino acid)-Coated Iron Oxide Nanoparticles for Breast Cancer MR Imaging (2010)

Superparamagnetic iron oxide nanoparticles are widely used as nanoprobes for magnetic resonance imaging (MRI). Water-soluble iron oxide nanoparticles were synthesized by coating iron oxide nanoparticles with a hydrophilic, biocompatible, biodegradable poly(amino acid) derivative, poly(2-hydroxyethyl aspartamide) graft copolymer for negative contrast enhancement on T2 weighted MRI. HER2/neu antibodies were conjugated on the surface of poly(amino acid) coated iron oxide nanoparticles for the detection of breast cancer. The antibody-grafted iron oxide nanoparticles (PAION-Ab) were about 31.1 nm in diameter. The T2 relaxivity of PAION-Ab was 246 L·mmol(-1)·sec(-1) greater than that of the commercial product such as Feridex. PAION-Ab showed low cytotoxicity even at relatively high concentrations. Furthermore, Prussian blue staining and in vitro MRI study with SKBR-3, breast cancer cells overexpressing HER2/neu receptors indicated that PAION-Ab exhibited excellent cancer cell detection ability and enhanced signal intensities in the T2-weighted image.
Coordinate activation of c-Src by SH3- and SH2-binding sites on a novel p130Cas-related protein, Sin. (1996)

To understand how protein-protein interactions mediated by the Src-SH3 domain affect c-Src signaling, we screened for proteins that interact with the Src-SH3. We found a novel protein, Sin (Src interacting or signal integrating protein), that binds to Src-SH3 with high affinity, contains numerous tyrosine residues in configurations suggestive of SH2-binding sites, and is related to the v-Src substrate p130Cas. In cotransfection assays, a small fragment of Sin retaining the Src-SH3-binding site and one tyrosine-containing motif induced c-Src activation as measured by a transcriptional reporter. Phosphorylation of the peptide on tyrosine by c-Src, as a consequence of Src-SH3 binding, was necessary for its stable interaction with c-Src in vivo and for transcriptional activation. Phosphorylation of multiple tyrosine-containing motifs found on Sin correlated with c-Crk and cellular phosphoprotein binding to Sin as well as increased c-Src activity. These data suggest that (1) SH2 and SH3 ligand sites on Sin cooperatively activate the signaling potential of c-Src, (2) Sin acts as both an activator and a substrate for c-Src, and (3) phosphorylated Sin may serve as a signaling effector molecule for Src by binding to multiple cellular proteins.
Dynamics of gas bubbles in time-variant temperature fields (2010)

The effect of time-variant temperature on the dynamics of a single gas bubble in a liquid is investigated. With changes in temperature, several physical parameters controlling bubble behaviour change including surface tension, diffusivity, vapour pressure and gas solubility. A single-bubble model is formulated and a numerical simulation implemented to model the radius–time profile of a bubble, across a range of initial bubble sizes and rates of heating, taking into account the aforementioned parameter temperature dependences. The model is validated experimentally in a xanthan gum gel phantom, tracking the evolution of the bubbles using digital photography and an image analysis sizing algorithm. It is shown that the natural tendency for a bubble to dissolve can be reversed by an increase in temperature, but only above a certain radius-dependent threshold rate of heating.
MVA-Vectored Pentameric Complex (PC) and gB Vaccines Improve Pregnancy Outcome after Guinea Pig CMV Challenge, but Only gB Vaccine Reduces Vertical Transmission (2019)

(1) Background: A congenital cytomegalovirus (cCMV) vaccine is a major research priority, but the essential glycoprotein target(s) remain unclear. We compared CMV gB (gpgB), gH/gL (gp75/gL), and pentameric complex (gpPC, composed of gH/gL/GP129/GP131/GP133) vaccines in a guinea pig CMV (GPCMV) congenital infection model. (2) Methods: Modified vaccinia virus Ankara (MVA) vaccines expressing GPCMV glycoproteins were used to immunize GPCMV-seronegative, female Hartley guinea pigs (three-dose series, 3 × 10<sup>7</sup> pfu/dose). After pregnancy was established, the dams underwent an early third-trimester challenge with salivary gland (SG)-adapted GPCMV. (3) Results: All vaccines elicited GPCMV-specific binding and neutralizing antibodies. Preconception immunization resulted in 19.5-, 4.9-, and 698-fold reductions in maternal DNAemia in MVA-gp75/gL, MVA-gpPC and MVA-gpgB groups, respectively, at day 14, post-SG challenge. Vaccination improved pups' birth weight and reduced mortality and congenital CMV transmission. In controls, cCMV infection was observed in 100% of pups (mean viral load in all visceral organs, 2.4 × 10<sup>4</sup> genomes/mg), versus 50% in the gB group (visceral viral load, 9.4 × 10<sup>2</sup> genomes/mg; <i>p</i> < 0.05). No significant reductions in congenital transmission were noted in the MVA-gp75/gL and MVA-gpPC groups. (4) Conclusions: MVA-vectored gB, gH/gL, and PC vaccines were immunogenic, and protected against maternal DNAemia and pup mortality. These results support the inclusion of multiple glycoprotein complexes in a cCMV vaccine.
Formation of an intact liposome layer adsorbed on oxidized gold confirmed by three complementary techniques: QCM‐D, AFM and confocal fluorescence microscopy (2011)

Supported layers of vesicles of dimyristoyl and dipalmitoyl phosphatidylcholine (DMPC and DPPC) containing cholesterol (CHOL) are adequate models for eukaryotic plasma membranes. Among the possible substrates to support these layers, gold offers the possibility of being used as an electrode for application in sensors. However, the formation of intact liposome layers on gold is not completely understood and several authors use more or less complex strategies to bind the liposomes. In this work we investigate the adsorption of unilamellar vesicles of DMPC, DMPC/CHOL and DMPC/DPPC/CHOL on the surface of oxidized gold using a quartz crystal microbalance with dissipation, atomic force microscopy and laser scanning confocal fluorescence microscopy. The results of all techniques indicate that for lipid concentrations ≥ 0.7 mg⋅mL –1 a dense layer of intact liposomes irreversibly adsorbs on the gold surface. Copyright © 2011 John Wiley &amp; Sons, Ltd.
Fast and simple constant-time hashing to the BLS12-381 elliptic curve (2019)

Pairing-friendly elliptic curves in the Barreto-Lynn-Scott family are seeing a resurgence in popularity because of the recent result of Kim and Barbulescu that improves attacks against other pairing-friendly curve families. One particular Barreto-Lynn-Scott curve, called BLS12-381, is the locus of significant development and deployment effort, especially in blockchain applications. This effort has sparked interest in using the BLS12-381 curve for BLS signatures, which requires hashing to one of the groups of the bilinear pairing defined by BLS12-381.While there is a substantial body of literature on the problem of hashing to elliptic curves, much of this work does not apply to Barreto-Lynn-Scott curves. Moreover, the work that does apply has the unfortunate property that fast implementations are complex, while simple implementations are slow.In this work, we address these issues. First, we show a straightforward way of adapting the “simplified SWU” map of Brier et al. to BLS12-381. Second, we describe optimizations to this map that both simplify its implementation and improve its performance; these optimizations may be of interest in other contexts. Third, we implement and evaluate. We find that our work yields constant-time hash functions that are simple to implement, yet perform within 9% of the fastest, non–constant-time alternatives, which require much more complex implementations.
Modeling of effective rainfall rate based on attenuation measurements in converging terrestrial links (2006)

In this paper, the statistical characterization of the effective rainfall rate parameter is investigated based on the cumulative distribution of measured signal attenuation in converging links with different path lengths, spatial orientations and operation frequencies. Results indicate that the lognormal distribution provides the best fit for the effective rainfall rate. Also, an empirical expression for the effective rainfall rate as a function of path length and link orientation was obtained.