gebhart/patrepeval huggingface dataset:
Optimization of a Weak 3′ Splice Site Counteracts the Function of a Bovine Papillomavirus Type 1 Exonic Splicing Suppressor In Vitro and In Vivo (2000)

Alternative splicing is a critical component of the early to late switch in papillomavirus gene expression. In bovine papillomavirus type 1 (BPV-1), a switch in 3' splice site utilization from an early 3' splice site at nucleotide (nt) 3225 to a late-specific 3' splice site at nt 3605 is essential for expression of the major capsid (L1) mRNA. Three viral splicing elements have recently been identified between the two alternative 3' splice sites and have been shown to play an important role in this regulation. A bipartite element lies approximately 30 nt downstream of the nt 3225 3' splice site and consists of an exonic splicing enhancer (ESE), SE1, followed immediately by a pyrimidine-rich exonic splicing suppressor (ESS). A second ESE (SE2) is located approximately 125 nt downstream of the ESS. We have previously demonstrated that the ESS inhibits use of the suboptimal nt 3225 3' splice site in vitro through binding of cellular splicing factors. However, these in vitro studies did not address the role of the ESS in the regulation of alternative splicing. In the present study, we have analyzed the role of the ESS in the alternative splicing of a BPV-1 late pre-mRNA in vivo. Mutation or deletion of just the ESS did not significantly change the normal splicing pattern where the nt 3225 3' splice site is already used predominantly. However, a pre-mRNA containing mutations in SE2 is spliced predominantly using the nt 3605 3' splice site. In this context, mutation of the ESS restored preferential use of the nt 3225 3' splice site, indicating that the ESS also functions as a splicing suppressor in vivo. Moreover, optimization of the suboptimal nt 3225 3' splice site counteracted the in vivo function of the ESS and led to preferential selection of the nt 3225 3' splice site even in pre-mRNAs with SE2 mutations. In vitro splicing assays also showed that the ESS is unable to suppress splicing of a pre-mRNA with an optimized nt 3225 3' splice site. These data confirm that the function of the ESS requires a suboptimal upstream 3' splice site. A surprising finding of our study is the observation that SE1 can stimulate both the first and the second steps of splicing.
Iterative MIMO Signal Detection with Inter-Cell Interference Cancellation for Downlink Transmission in Coded OFDM Cellular Systems (2009)

MIMO/OFDM is receiving considerable attention for next generation mobile radio communication systems. These systems require improved throughput performance to users at cell-edges. In our previous study, we introduced an enhancement of MLD (Maximum Likelihood signal Detection) algorithm, in which desired and interference signals are jointly detected, to improve the cell-edge throughput in the downlink of single- cell-frequency-reuse MIMO/OFDM cellular systems. In order to achieve higher cell-edge throughput in coded OFDM cellular systems, this paper proposes an iterative signal detection with ICI cancellation based on an enhancement of MAP (Maximum A posteriori Probability) algorithm in which signal path search space includes not only desired signal space but also interference signal space. Its transmission characteristics are evaluated by computer simulation and it is confirmed that the proposed iterative signal detection can achieve higher ICI cancellation and improve BLER (BLock Error Rate) and throughput performance more than the conventional MLD-based signal detection.
Neonicotinoid exposure disrupts bumblebee nest behavior, social networks, and thermoregulation (2018)

Neonicotinoid pesticides can negatively affect bee colonies, but the behavioral mechanisms by which these compounds impair colony growth remain unclear. Here, we investigate imidacloprid's effects on bumblebee worker behavior within the nest, using an automated, robotic platform for continuous, multicolony monitoring of uniquely identified workers. We find that exposure to field-realistic levels of imidacloprid impairs nursing and alters social and spatial dynamics within nests, but that these effects vary substantially with time of day. In the field, imidacloprid impairs colony thermoregulation, including the construction of an insulating wax canopy. Our results show that neonicotinoids induce widespread disruption of within-nest worker behavior that may contribute to impaired growth, highlighting the potential of automated techniques for characterizing the multifaceted, dynamic impacts of stressors on behavior in bee colonies.
A Contribution to the settlement analysis of foundations on clay (1957)

Synopsis The settlement of a foundation on a saturated clay is composed chiefly of the “immediate” settlement due to deformations taking place at constant volume, and the “consolidation” settlement due to volume reduction consequent upon the dissipation of pore pressures. This latter component is therefore dependent on the pore pressures set up by the foundation load, and these pore pressures are themselves dependent on the type of clay. An approximate theory is described which takes account of the type of clay; and comparisons with observed settlements in a number of practical cases show the theory to be an improvement on existing methods of calculation. Le tassement d'une fondation sur une argile saturée se compose principalement du tassement “immediat” dû aux déformations ayant lieu suivant une ampleur constante, et le tassement “de consolidation” dû à la diminution d'ampleur parsuite de la dissipation de la pression interstitielle. Cette dernière composante dépend done des pressions interstitielles provoquées par la charge de fondation, et ces pressions interstitielles dépendent elles-mêmes du type d'argile. On décrit une théorie approximative qui tient compte du type d'argile; et des comparaisons avec les tassements observés dans un nombre de cas pratiques démontrent cette théorie comme étant une améliorationdes méthodes de calcul existantes.
Heterostructured ZnO/Au Nanoparticles-Based Resonant Raman Scattering for Protein Detection (2009)

A new method of protein detection was explored on the resonant Raman scattering signal of ZnO nanoparticles. A probe for the target protein was constructed by binding the ZnO/Au nanoparticles to secondary protein by eletrostatic interaction. The detection of proteins was achieved by an antibody-based sandwich assay. A first antibody, which could be specifically recognized by target protein, was attached to a solid silicon surface. The ZnO/Au protein probe could specifically recognize and bind to the complex of the target protein and first antibody. This method on the resonant Raman scattering signal of ZnO nanoparticles showed good selectivity and sensitivity for the target protein.
The contribution of the CEA marker to CA 15.3 in the follow-up of breast cancer. (2003)

The low sensitivity of studied tumor markers proved of limited use on a clinical scale.
Application of Isoelectric Focusing in Immobilized pH Gradients to the Study of Acetaldehyde‐Modified Hemoglobin (1986)

We applied the technique of isoelectric focusing (IEF) on immobilized pH gradients (LKB) to determine whether acetaldehyde-modified hemoglobins (Hb) prepared in vitro with unphysiological acetaldehyde concentrations have clinical relevance. This technique separates proteins with pl less than 0.01 and provides detail about hemoglobins not otherwise separable. We performed two kinds of studies. In one kind of study, we incubated red cells from control subjects with acetaldehyde. Products of these incubations were applied to IEF gels either directly or after reduction with sodium cyanoborohydride. Incubation of red cells with acetaldehyde in 1-150 mM concentration without cyanoborohydride reduction yielded hemoglobin bands of decreasing pl the appearance of which coincided with the disappearance of Hb A and Hb A1c. When the products of incubation were reduced with cyanoborohydride before IEF, an additional acidic Hb band appeared which we call the "anodal CNBH band." In a second kind of study, we compared IEF patterns of hemolysates from control subjects and alcoholism detoxification patients, without adding acetaldehyde. Again, samples were applied to IEF gels either directly or after reduction with cyanoborohydride. When samples were run on IEF without reduction, no differences were seen between patients and controls. When samples were reduced before IEF, an anodal CNBH band appeared having the same mobility as the band seen after in vitro incubations with acetaldehyde. These bands were often stronger in samples from patients, but not consistently so. Several experiments, including the use of glycolysis inhibitors, indicated that the anodal CNBH band is an adduct of fructose 1,6-diphosphate with hemoglobin. We suggest that in millimolar concentrations, acetaldehyde may function as an inhibitor of glycolysis at or below the aldolase step.
A lipophilic vasoactive intestinal peptide analog enhances the antiproliferative effect of chemotherapeutic agents on cancer cell lines (2001)

Chemotherapeutic treatment of advanced solid tumors, such as nonsmall cell lung carcinoma, colon carcinoma, or prostate carcinoma, achieves a response rate of between 10% and 30% with significant toxicity. Combination therapy with the lipophilic VIP analog SNH and the preferred chemotherapeutic agent may greatly enhance the response rate, and by permitting a dose reduction, should significantly reduce side effects.
Model dielectric function of hexagonal CdSe (1990)

We present a calculation of the complex dielectric function, ε(ω)=ε1(ω)+iε2(ω), at energies below and above the fundamental absorption edge of the hexagonal, wurtzite-type semiconductor CdSe. This model includes the E0, E1, and Eidg (indirect) gaps as the main dispersion mechanisms. The model is made to properly account for the excitonic effects at these critical points. Results are in satisfactory agreement with recent ellipsometric measurements over the entire range of photon energies (E=0–5.0 eV). Detailed discussions are presented on the results, with emphasis on the information about the electronic energy-band structures and their group-symmetrical selection rules of this material.
OBA開発入門 : OfficeとSharePoint Server 2007の連携によるビジネスアプリケーション構築 (2008)

第１章 ＯＢＡの概要 第２章 予算承認プロセスの管理と自動化 第３章 売上予測の管理 第４章 仮想ラーニングワークスペースのプロビジョニングとセキュリティ保護 第５章 Ｏｐｅｎ ＸＭＬ形式による作業範囲記述書の作成 第６章 営業支援システム（ＳＦＡ） 第７章 ビジネスインテリジェンス：製造現場における分析
Write Like a Patent Litigator: Avoid Common Mistakes Made by Non-Patent Lawyers, 17 J. Marshall Rev. Intell. Prop. L. 141 (2017) (2017)

Following, or not following, conventions as an attorney may lead to a question of credibility. Particularly with patent law, there are certain conventions and usage errors commonly made by practitioners who are not familiar with patent law. While these errors may be irrelevant in plain English, they are often important components in the specialized language of patent law. This article discusses the importance of these components by examining examples of particular usages that often give rise to error.
Combination technique of tumescent anesthesia during endovenous laser therapy of saphenous vein insufficiency☆ (2010)

Combination technique of administering tumescent anesthesia before ablation and continuously during the EVLT procedure may be an alternative way to reduce the patient's peroperative pain and discomfort.
Credit-based fair queueing (CBFQ) (1997)

A simple rate-based scheduling algorithm for packet-switched networks (e.g. Internet) is proposed. By using simple counters to keep track of the credits accumulated by each traffic stream, the algorithm decides which stream to serve next, based on the bandwidth share allocated to each traffic stream, and the sizes of the head of line (HOL) packets of the different streams. Our proposed CBFQ algorithm achieves the same fairness and delay bounds as the alternative approaches based on virtual time, while avoiding the implementation problems inherent in these methods.
Bag-of-Words Representation in Image Annotation: A Review (2012)

Content-based image retrieval (CBIR) systems require users to query images by their low-level visual content; this not only makes it hard for users to formulate queries, but also can lead to unsatisfied retrieval results. To this end, image annotation was proposed. The aim of image annotation is to automatically assign keywords to images, so image retrieval users are able to query images by keywords. Image annotation can be regarded as the image classification problem: that images are represented by some low-level features and some supervised learning techniques are used to learn the mapping between low-level features and high-level concepts (i.e., class labels). One of the most widely used feature representation methods is bag-of-words (BoW). This paper reviews related works based on the issues of improving and/or applying BoW for image annotation. Moreover, many recent works (from 2006 to 2012) are compared in terms of the methodology of BoW feature generation and experimental design. In addition, several different issues in using BoW are discussed, and some important issues for future research are discussed.
Solving Sparse Triangular Linear Systems in Modern GPUs: A Synchronization-Free Algorithm (2018)

Sparse triangular linear systems are ubiquitous in a wide range of science and engineering fields, and represent one of the most important building blocks of Sparse Numerical Lineal Algebra methods. For this reason, their parallel solution has been subject of exhaustive study, and efficient implementations of this kernel can be found for almost every hardware platform. However, the strong data dependencies that serialize a great deal of the execution and the load imbalance inherent to the triangular structure poses serious difficulties for its parallel performance, specially in the context of massively- parallel processors such as GPUs. To this day, the most widespread GPU implementation of this kernel is the one distributed in NVIDIA CUSPARSE library, which relies on a preprocessing stage to determine the parallel execution schedule. Although the solution phase is highly efficient, this strategy pays the cost of constant synchronizations with the CPU. In this work, we present a synchronization-free GPU al- gorithm to solve sparse triangular linear systems for the CSR format. The experimental evaluation shows performance improvements over CUSPARSE and a recently proposed synchronization-free method for the CSC matrix format.
Magnetostriction of Co-base amorphous alloys and high frequency permeability in their sputtered thin films (invited) (1984)

For new magnetic materials with high permeability at MHz frequencies as well as high magnetic induction, magnetic properties of Co-base amorphous alloys produced by a sputtering technique were investigated. Small magnetostrictions, important for this purpose, were found in the Co-Nb-Ti system and Co-(Fe, Mn)-Nb system. The dipole-type model explained the concentration dependence of magnetostriction. In order to increase permeability at high frequencies by reducing eddy current losses, these amorphous alloys were made into thin film form. It was found that dc coercivity for the single film (about 3 μm thick) of Co80 Nb20 with negative magnetostriction was larger than that for Co80Ti20 with positive magnetostriction, while the layered films of Co80Nb20 separated by a SiO2 insulator showed small coercivities. Permeabilities of about 4×103 at 1 MHz and 1×103 at 10 MHz were obtained in the Co80Nb20/SiO2 and Co80Ti20/SiO2 layered films.
Self-aligned double patterning compliant routing with in-design physical verification flow (2013)

Among double patterning techniques, Self-aligned double patterning (SADP) has the advantage of good mask overlay control, which has made SADP a popular double patterning method for sub-32nm technology nodes. However, SADP process places several limitations on design flexibility. This work exploits an alternative post routing approach that has the flexibility to resolve lithography violations without the overhead of repeated rule checking. In addition, it allows for successive refinement in the definition of lithographic violations as the process node matures, and implementation of fixes as localized ECO (Engineering Change Order) operations without needing to reroute the complete design.
Catalytic Antibodies: Contributions from Engineering and Expression in <i>Escherichia Coli</i> (2007)

Antibodies have been raised against the transition state of many reactions and shown to catalyse the relevant reaction. Their moderate catalytic efficiencies can be increased by protein engineering, if ways can be found to express the engineered antibody. We have developed a system by which fully functional Fv and Fab fragments can be expressed in Escherichia coli. The Fv fragment dissociates at low concentrations; we therefore devised methods to stabilize the fragment. We showed that the Fv fragment of the antibody McPC603, a phosphorylcholine-binding immunoglobulin A, binds the antigen with the same affinity as does the intact antibody isolated from mouse ascites. Phosphorylcholine is an analogue of the transition state for the hydrolysis of choline carboxylate ester. The Fv fragment of McPC603 catalysed this hydrolysis. Mutational analysis of the residues in the binding site of the antibody has shown which are essential for binding and for catalysis, and the importance of charged residues in certain positions. The E. coli expression system combined with protein engineering and screening methods will facilitate understanding of enzyme catalysis and the development of new catalytic antibodies.
The reactions of 2,2‐difluoro‐4‐methylnaphtho[l,2‐<i>e</i>] ‐1,3,2‐dioxaborin and Its [2,1‐<i>e</i>] Isomer with Carbonyl compounds and with Aniline (1969)

Abstract 2,2‐Difluoro‐4‐methylnaphtho[l,2‐ e ]‐l,3,2‐dioxaborin ( 1 ) and its [2,1‐ e ]isomer ( 2 ) react with equimolecular quantities of carbonyl compounds, giving colored ethylenic derivatives. With aniline, 1 and 2 give the corresponding oxazaborins 21 and 22 . The structures of 1 and 2 are discussed.
Coincidence detection of spatially correlated photon pairs with a novel type of monolithic time-resolving detector array (2017)

Spatially entangled photon states are used in experiments addressing fundamental properties of quantum mechanics as well as practical applications [1]. Thereby, the use of these states demands for time-saving detection mechanisms, capable of measuring coincidences between spatially separated photons with high spatial and temporal resolution. In this work, we demonstrate coincidence detection of spatially correlated photon pairs by means of the SPADnet-I sensor [2], a fully digital 8×16 pixel single photon detector array in CMOS technology developed for medical applications. It enables per-pixel time stamping with 265 ps resolution combined with a high frame rate of 500 kfps [3]. Commonly used optically or electrically amplified CCD based systems exhibit magnitudes lower frame rates and temporal resolution.
MgO/Ti bilaterally diffused LiNbO_3 optical switch (1990)

A MgO/Ti bilaterally diffused optical waveguide is proposed. It features controlling the waveguide spot size and strengthening the optical confinement. It is experimentally shown that the coupling loss with single-mode fiber is reduced to 0.6 dB/facet. The bending loss is also suppressed from 2.2 dB of the Ti diffused waveguide to 0.2 dB at a 30-mm bending radius. The performance of the switch using this method is demonstrated. Total insertion loss is 2.6 dB. Driving voltage is 5.6 V with no degradation of the EO effect.
Dirhodium-catalyzed C-H arene amination using hydroxylamines (2016)

Primary and N-alkyl arylamine motifs are key functional groups in pharmaceuticals, agrochemicals, and functional materials, as well as in bioactive natural products. However, there is a dearth of generally applicable methods for the direct replacement of aryl hydrogens with NH2/NH(alkyl) moieties. Here, we present a mild dirhodium-catalyzed C-H amination for conversion of structurally diverse monocyclic and fused aromatics to the corresponding primary and N-alkyl arylamines using NH2/NH(alkyl)-O-(sulfonyl)hydroxylamines as aminating agents; the relatively weak RSO2O-N bond functions as an internal oxidant. The methodology is operationally simple, scalable, and fast at or below ambient temperature, furnishing arylamines in moderate-to-good yields and with good regioselectivity. It can be readily extended to the synthesis of fused N-heterocycles.
Obesity, adipocytokines, and insulin resistance in breast cancer (2004)

The adipocytokines are biologically active polypeptides that are produced either exclusively or substantially by the adipocytes, and act by endocrine, paracrine, and autocrine mechanisms. Most have been associated with obesity, hyperinsulinaemia, type 2 diabetes, and chronic vascular disease; in addition, six adipocytokines--vascular endothelial growth factor, hepatocyte growth factor, leptin, tumour necrosis factor-alpha, heparin-binding epidermal growth factor-like growth factor, and interleukin-6--promote angiogenesis while one, adiponectin, is inhibitory. Obesity and insulin resistance have both been identified as risk factors for breast cancer and are associated with late-stage disease and poor prognosis. Angiogenesis is essential for breast cancer development and progression, and so it is plausible that obesity-related increases in adipocytokine production and a reduction in adiponectin may adversely affect breast cancer outcome by their angiogenesis-related activities. There is also experimental evidence that some adipocytokines can act directly on breast cancer cells to stimulate their proliferation and invasive capacity. Thus, adipocytokines may provide a biological mechanism by which obesity and insulin resistance are causally associated with breast cancer risk and poor prognosis. Both experimental and clinical studies are needed to develop this concept, and particularly in oestrogen-independent breast cancers where preventive and therapeutic options are limited.
An Oncolytic Virus Expressing a T-cell Engager Simultaneously Targets Cancer and Immunosuppressive Stromal Cells (2018)

: Effective immunotherapy of stromal-rich tumors requires simultaneous targeting of cancer cells and immunosuppressive elements of the microenvironment. Here, we modified the oncolytic group B adenovirus enadenotucirev to express a stroma-targeted bispecific T-cell engager (BiTE). This BiTE bound fibroblast activation protein on cancer-associated fibroblasts (CAF) and CD3ε on T cells, leading to potent T-cell activation and fibroblast death. Treatment of fresh clinical biopsies, including malignant ascites and solid prostate cancer tissue, with FAP-BiTE-encoding virus induced activation of tumor-infiltrating PD1<sup>+</sup> T cells to kill CAFs. In ascites, this led to depletion of CAF-associated immunosuppressive factors, upregulation of proinflammatory cytokines, and increased gene expression of markers of antigen presentation, T-cell function, and trafficking. M2-like ascites macrophages exhibited a proinflammatory repolarization, indicating spectrum-wide alteration of the tumor microenvironment. With this approach, we have actively killed both cancer cells and tumor fibroblasts, reversing CAF-mediated immunosuppression and yielding a potent single-agent therapeutic that is ready for clinical assessment. SIGNIFICANCE: An engineered oncolytic adenovirus that encodes a bispecific antibody combines direct virolysis with endogenous T-cell activation to attack stromal fibroblasts, providing a multimodal treatment strategy within a single therapeutic agent.