gebhart/patrepeval huggingface dataset:
Multiple nuclear proteins bind upstream sequences in the promotor region of a T-cell receptor beta-chain variable-region gene: evidence for tissue specificity. (1987)

DNA-nuclear protein binding interactions were examined in the promoter region of a representative T-cell receptor Ti beta-chain variable-region gene by means of electrophoretic mobility-shift and DNase I-protection analysis. Within 175 bases upstream of the transcription initiation site, four protected regions ("footprints") were identified on the coding strand, at nucleotides -46 to -68 (I), -72 to -92 (II), -113 to -134 (III), and -136 to -175 (IV). Nuclear proteins (0.6 M NaCl fraction from a heparin-Sepharose column chromatography of nuclear extracts) of a variety of cell types produced footprints I, III, and IV and a fifth footprint (beyond nucleotide -200). In contrast, footprint II was produced only by T-cell extracts, although nuclear extracts of a transformed B-lymphoblastoid line produced a partial footprint in this region. Furthermore, footprint analysis of the noncoding strand showed that a continuous region of protection corresponding to the entire region of footprints I and II was generated, along with a DNase I-hypersensitive site, by nuclear proteins derived from T cells but not other cell types. Footprint I has the sequence structure of many well-defined protein-DNA binding sites. Nucleotide sequences in the region of footprint II bore no homology to known sequences, whereas those in the areas of footprints III and IV were similar to motifs within immunoglobulin and other enhancers. These findings may have implications for the tissue specificity of human Ti beta-chain gene transcription.
Tissue Harmonic Imaging (2000)

Tissue harmonic scanning visually improves echocardiographic image quality. The aim of the present study was to objectively assess the improvement in harmonic image quality under controlled laboratory conditions. A tissue-mimicking phantom that contained 8-mm-diameter cystic lesions at depths ranging from 2 to 12 cm was used. Harmonic scans (1.7 MHz transmit, 3.4 MHz receive) of the phantom were obtained and lesion detectability was compared to that in scans acquired with 2 fundamental frequencies (2.0 and 3.3 MHz). A 2 cm-thick ethanol layer was also used to simulate the nonlinear effect of human fat. Cyst detectability was quantified by measurement of the contrast-to-speckle ratio (CSR). The results indicated no significant difference in the CSR between harmonic and fundamental images obtained without the ethanol layer. With images obtained with the ethanol layer, a relative increase of the CSR during harmonic imaging was observed with respect to fundamental imaging (p<0.05). In conclusion, a fat layer, here simulated by ethanol, plays a significant role in determining the resulting image quality. Without this layer, the contribution of the second harmonic mode was not significant. Thus, in a slim patient, the harmonic mode may not be as beneficial to image improvement as in an obese patient.
333 Development of a 4-Plex Quantitative PCR Assay for the Detection and Quantification of Species and Subspecies of Fusobacterium Necrophorum and Fusobacterium Varium in Bovine Rumen Fluid (2022)

Abstract The Fusobacterium genus contains Gram-negative, rod-shaped anaerobic bacteria. Fusobacterium necrophorum and its two subspecies, necrophorum and funduliforme, are normal ruminal inhabitants of cattle. Subsp. necrophorum is the primary causative agent of liver abscesses in feedlot cattle. Fusobacterium varium is also a normal rumen inhabitant, but its role in ruminal fermentation and involvement in liver abscesses is unknown. Currently, no PCR assays exist to quantify F. varium and both subspecies of F. necrophorum. Therefore, our objective was to develop, validate, and determine the applicability of a quantitative PCR assay for quantification of F. varium and the two subspecies of F. necrophorum. Assay targets were the species-specific hgdA gene, encoding for (R)-2-hydroxyglutarylCoA dehydratase subunit alpha, and the subspecies-specific promoter sequence of the leukotoxin gene, lktA. Assay specificity was validated with different species and strains of Fusobacterium, and other bacterial species. Assay sensitivity was determined using pure cultures. Applicability of the assay for quantification of F. necrophorum and F. varium was determined using ruminal fluid from slaughtered cattle. Species and subspecies-level specificity was confirmed. Pure culture quantification limits (CFU/ml) were 2.1x103 for the F. necrophorum species, 5.6x102 for subsp. necrophorum, 1.5x103 for subsp. funduliforme, and 1.8x103 for F. varium. Analysis of ruminal fluid collected from cattle with healthy livers (n=83) and abscessed livers (n=68) indicated that 97% of samples contained F. funduliforme, with mean concentrations of 7.8 x103, and 8.1x103, respectively. Additionally, subsp. necrophorum and F. varium were more prevalent in ruminal fluid from cattle with abscessed livers (41% and 59%) compared with samples from cattle with healthy livers (31% and 41%). In conclusion, subsp. funduliforme appears to be the normal inhabitant of the rumen, while subsp. necrophorum and F. varium are more prevalent in the rumen of cattle with abscessed livers than those with healthy livers.
Test-Driven Development of Relational Databases (2007)

In test-first development, developers formulate and implement a detailed design iteratively, one test at a time. Test-driven development (also called test-driven design) combines TFD with refactoring, wherein developers make small changes (refactorings) to improve code design without changing the code's semantics. When developers decide to use TDD to implement a new feature, they must first ask whether the current design is the easiest possible design to enable the feature's addition. Implementing test-driven database design involves database refactoring, regression testing, and continuous integration. TDDD is an integrated part of the overall development process, not a standalone activity that data professionals perform in parallel with application TDD. Although from a technical view point, TDDD is relatively straightforward, we must overcome several challenges to its whole sale adoption throughout the IT community
Transcriptional profiling enables molecular classification of adrenocortical tumours (2009)

Adrenocortical carcinomas are associated with a distinct molecular signature apparent in their gene expression profiles. Differentially expressed genes were identified associated with malignancy, survival as well as hormonal activity providing a resource of candidate genes for an exploration of possible drug targets and diagnostic and prognostic markers.
Plasmonic Nanostars as Efficient Broadband Scatterers for Random Lasing (2016)

Huge spectral coverage of random lasing throughout the visible up to the infrared range is achieved with star-shaped gold nanoparticles ("nanostars"). As intrinsically broadband scattering centers, the nanostars are suspended in solutions of various laser dyes, forming randomly arranged resonators which support coherent laser modes. The narrow emission line widths of 0.13 nm or below suggest that gold nanostars provide an efficient coherent feedback for random lasers over an extensive range of wavelengths, all together spanning almost a full optical octave from yellow to infrared.
Highly chemoselective cobalt-catalyzed biaryl coupling reactions (2012)

A practical cobalt-catalyzed hetero-biaryl coupling reaction between aryl chlorides and arylmagnesium halides with unprecedented selectivity has been developed. The protocol utilizes 1 mol% of cheap Co(acac)3 as pre-catalyst and effects clean reactions of deactivated chlorostyrenes with only 1.1 equiv. of the Grignard reagent under mild conditions (30 °C, 5–30 min). Highly chemoselective reactions were realized even in the presence of activated bromoarenes. The olefin substituent facilitates the activation of the C–Cl bond by coordination to the catalyst. Kinetic studies indicate the operation of an arylcobaltate(I) catalyst species. Catalyst formation during the induction period was studied in the presence of cobalt(III), (I), and (−I) pre-catalysts.
DILACERATION CAUSED BY PERIAPICAL LESIONS OF THE DECIDUOUS INCISOR : CASE REPORT (2001)

Dilaceration is a tooth abnormaly occuring in the histo-morphodifferention stage resulting from disturbance between the uncalcified and already calcified portion that affects both the crown and root. The involved tooth is usually the maxillary central incisor and it also shows high prevalence of impaction. The cause of dilaceration can be either from the trauma of the primary tooth, ectopic development of the tooth germ or from cysts. And it is also found in some cases of Otodental syndrome, Hurler syndrome, Cleidocranial dysostosis. The purpose of this study is to show that periapical lesions caused by dental caries can be another factor in causing dilaceration.
Experimental progress toward a 1 GW, 1 μs pulse length, high current relativistic klystron (2002)

A 1 /spl mu/s pulse-length, high-current relativistic klystron is being developed with a desired peak output power of 1 GW at 1.3 GHz. The tube consists of an input cavity, a single idler cavity, and an output cavity. Power levels as high as 475 MW have been experimentally observed. Current experimental results are presented. Physics and engineering issues affecting klystron performance are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improvement in Social Deficits in Autism Spectrum Disorders Using a Theatre‐Based, Peer‐Mediated Intervention (2013)

Social Emotional NeuroScience Endocrinology Theatre is a novel intervention program aimed at improving reciprocal social interaction in youth with autism spectrum disorder (ASD) using behavioral strategies and theatrical techniques in a peer-mediated model. Previous research using a 3-month model showed improvement in face perception, social interaction, and reductions in stress. The current study assessed a 2-week summer camp model. Typically developing peers were trained and paired with ASD youth (8-17 years). Social perception and interaction skills were measured before and after treatment using neuropsychological and parental measures. Behavioral coding by reliable, independent raters was conducted within the treatment context (theatre) and outside the setting (playground). Salivary cortisol levels to assess physiological arousal were measured across contexts (home, theatre, and playground). A pretest-posttest design for within-group comparisons was used, and prespecified pairwise comparisons were achieved using a nonparametric Wilcoxon signed-rank test. Significant differences were observed in face processing, social awareness, and social cognition (P < 0.05). Duration of interaction with familiar peers increased significantly over the course of treatment (P < 0.05), while engagement with novel peers outside the treatment setting remained stable. Cortisol levels rose on the first day of camp compared with home values yet declined by the end of treatment and further reduced during posttreatment play with peers. Results corroborate previous findings that the peer-mediated theatre program contributes to improvement in core social deficits in ASD using a short-term, summer camp treatment model. Future studies will explore treatment length and peer familiarity to optimize and generalize gains.
Hot Carrier Stress modeling: From degradation kinetics to trap distribution evolution (2015)

A complete TCAD model addressing Hot Carrier Degradation for Flash technology is presented. After having underlined the need for a power law with a low exponent for the aging kinetics and considered a high activation energy reflecting the single electron impact mode, a fine calibration is achieved. Finally, analysis on trap distribution and aging rates at different channel locations are provided
Biological safety of human skin-derived stem cells after long-term in vitro culture (2010)

The aim of this study was to investigate the biological safety of human skin-derived mesenchymal stem cells (HSMSCs) cultured in vitro by detecting changes in karyotype, major histocompatibility complex expression and tumorigenicity. Before the 21st passage of the in vitro culture, cell surface markers were analysed by flow cytometry; major histocompatibility complex expression was detected by RT-PCR and flow cytometry. The tumorigenicity of HSMSCs was tested using SCID mice and observing changes in the injection site and pathological sections. Flow cytometry demonstrated that HSMSCs express CD73, CD105 and vimentin, but haematopoietic markers CD34, CD45 and CD19 were not expressed. Human leukocyte antigen (HLA-I and HLA-DR) mRNA was detected by RT-PCR; the protein expression of HLA-I was 29.5-31.7%, but HLA-DR protein expression was not detected in HSMSCs. The result of karyotype analysis before the 21st passage was normal and tumour formation was not detected in the mice. Taken as a whole, our results suggest that HSMSCs cultured in vitro may be safely transplanted in vivo, due to moderate expression of HLA-I and low expression of HLA-DR, non-tumorigenicity and normal karyotype.
Lilienthal N et al., Immunokinase-based B-lymphotoxic delivery of activated DAPK1; Supplements from A Novel Recombinant Anti-CD22 Immunokinase Delivers Proapoptotic Activity of Death-Associated Protein Kinase (DAPK) and Mediates Cytotoxicity in Neoplastic B Cells (2023)

&lt;p&gt;Table S1: Expression of DAPK1 (a) and surface CD22 (b) in various cell lines; Table S2: Characteristics of CLL patients from whom samples were analyzed including for DAPK1/2 expression and responses to DK1KD-SGIII;Figure S1: Analysis of DAPK expression in B-cells and B-cell lymphomas; Figure S2: Short-term overexpression of DAPK mutants; Figure S3: Variants of the pMS expression vector; Figure S4: Principle of the kinase activity assay; Figure S5: DK1KD-SGIII binding differs between CD22 expressing cell lines; Figure S6: DK1KD-SGIII binds to primary CLL cells in a dose-dependent manner; Figure S7: DK1KD-SGIII, but not DK1KD and SGIII controls, induces profound and specific cell death in CD22(+) cells.&lt;/p&gt;
Detecting Malicious Exploit Kits using Tree-based Similarity Searches (2016)

Unfortunately, the computers we use for everyday activities can be infiltrated while simply browsing innocuous sites that, unbeknownst to the website owner, may be laden with malicious advertisements. So-called malvertising, redirects browsers to web-based exploit kits that are designed to find vulnerabilities in the browser and subsequently download malicious payloads. We propose a new approach for detecting such malfeasance by leveraging the inherent structural patterns in HTTP traffic to classify exploit kit instances. Our key insight is that an exploit kit leads the browser to download payloads using multiple requests from malicious servers. We capture these interactions in a "tree-like" form, and using a scalable index of malware samples, model the detection process as a subtree similarity search problem. The approach is evaluated on 3800 hours of real-world traffic including over 4 billion flows and reduces false positive rates by four orders of magnitude over current state-of-the-art techniques with comparable true positive rates. We show that our approach can operate in near real-time, and is able to handle peak traffic levels on a large enterprise network --- identifying 28 new exploit kit instances during our analysis period.
Improved quasi-orthogonal codes through constellation rotation (2003)

In this letter, we show that the performance of recently proposed quasi-orthogonal space-time codes can be improved by phase-shifting the constellations of the symbols constituting the code. The optimal rotation of the symbols increases the minimum distance of the corresponding space-time codewords, leading to substantially improved performance.
n Efficient Convolutional Coding/Decoding Stratew for Channels with Mernorv (1995)

Many digital communication channels are affected by errors that tend to occur in bursts. A great deal of work has been devoted to finding good burst-error-correcting codes and de- veloping burst-error-correcting schemes. However, burst-error- correcting codes are generally not effective for long bursts. Some burst-error-correcting schemes suffer long delay in decoding. Others are very sensitive to random errors in the guard space. Most of these schemes are not adaptive to channel conditions. In this paper, a new adaptive scheme is proposed to overcome these drawbacks. The scheme employs a combination of two complementary punctured convolutional (CPC) codes. One of the codes is used for burst detection and for channel state estimation, and both codes are used for error correction. The proposed scheme is analyzed over a two state Markov chain channel model. Unlike existing burst-error-correcting schemes, it is shown that the proposed scheme is adaptive to channel conditions and less sensitive to errors in the guard space. For the same delay, the proposed scheme offers better performance than the interleaving schemes. When the channel is heavily corrupted by bursts, the improvement is even more pronounced.
PREPARATION OF RED ORGANIC PIGMENT WITH SILICA GEL AS CORE (1981)

Abstract Red organic pigment with silica gel as core was prepared by deriving the surface silanols of silica gel to the structure similar to azo dyestuff, such as Sudan I. The surface silanols were esterified with phenylmethanol, and the introduced phenyl group was nitrated, reduced, diazotized and coupled with 2-naphthol as shown in Fig. 1. The prepared pigment showed approximately same color as Sudan I.
Engagement of the Medial Temporal Lobe in Verbal and Nonverbal Memory: Assessment with Functional MR Imaging in Healthy Subjects (2009)

The combination of these 3 undemanding memory tasks could be considered, following appropriate validation, as a tool to assess the functional status of the medial temporal lobe in clinical settings.
Artificial intelligence-assisted immunohistochemical (IHC) evaluation of tumor amphiregulin (AREG) and epiregulin (EREG) expression as a combined predictive biomarker for panitumumab (Pan) therapy benefit in RAS wild-type (wt) metastatic colorectal cancer (mCRC): Analysis within the phase III PICCOLO trial. (2021)

111 Background: High tumor mRNA levels of the EGFR ligands, AREG and EREG are associated with anti-EGFR agent response in patients (pts) with RAS-wt mCRC, regardless of tumor location. However, ligand RNA assays have not been adopted into routine clinical practice due to issues with analytical precision and practicality. Here we test whether AREG and EREG expression assessed by IHC can predict benefit from Pan. Methods: A retrospective biomarker study within the PICCOLO trial (NCT00389870; irinotecan [Ir] ± Pan in fluoropyrimidine-resistant RAS-wt mCRC). AREG and EREG positive tumor cells were assessed by IHC in all RAS-wt patients with available tumor tissue. Pathologists annotated tumor areas on digital images of glass slides. Artificial intelligence (AI) algorithms calculated the percentage of tumor cells staining positive for AREG and EREG within the tumor areas. More than 50% AREG and/or EREG tumor cell positivity was regarded as high ligand expression. The primary endpoint was progression-free survival (PFS) and secondary endpoints were RECIST response rate (RR) and overall survival (OS). Results: 274 RAS-wt pts had available tumor tissue. High ligand expression (n = 132) was associated with significant PFS benefit from IrPan compared with Ir (8.0 vs 3.2 months; HR 0.54 [0.37-0.79]; p = 0.001); whereas low ligand expression (n = 142) was not (3.4 vs 4.4 months; HR 1.05 [95% CI, 0.74-1.49]; p = 0.78). The ligand-treatment interaction was significant (p = 0.02) and independent of BRAF-mutation status and primary tumor location. Likewise RR was significantly improved in pts with high ligand expression (IrPan vs Ir: 48% vs 6%; risk ratio, 7.8 [2.90-20.69]; p &lt; 0.0001) but not those with low ligand expression (IrPan vs Ir: 25% vs 14%; risk ratio, 1.8 [95% CI, 0.89-3.65]; p = 0.10) (interaction p = 0.01). Lesser effect was seen on OS. Conclusions: IHC assessment of AREG and EREG identified pts who did or did not benefit from Pan, as has been previously demonstrated through mRNA quantification. IHC represents a more practicable technique as it can be provided at the point of care and is associated with shorter turn-around times. AREG and EREG IHC may be of use in routine practice to identify patients who would benefit from anti-EGFR therapy and those for whom alternative treatment strategies should be explored.
RF Tag Antenna Performance on Various Materials Using Radio Link Budgets (2006)

Passive radio frequency (RF) tags in the UHF and microwave bands have drawn considerable attention because of their great potential for use in many radio frequency identification (RFID) applications. However, more basic research is needed to increase the range and reliability of a passive RF tag's radio link, particularly when the RF tag is placed onto any lossy dielectric or metallic surface. This paper presents two new useful forms of the radio link budget that describe the power link of an RF tag system when the tag is attached to an object. These radio link budgets are dependent upon the gain penalty, a term which quantifies the reduction in RF tag antenna gain due to material attachment. A series of measurements, or radio assay, was used to measure the far-field gain pattern and gain penalty of several flexible 915 MHz antennas when attached to cardboard, pine plywood, acrylic, deionized water, ethylene glycol, ground beef, and an aluminum slab. It is shown that the gain penalty due to material attachment can result in more than 20 dB of excess loss in the backscatter communication link.
Building an effective ERP selection system for the technology industry (2008)

This paper models and analyzes the factors of enterprise resource planning (ERP) system selection on the fast changing technology industry. With growing pressures for collaborative information systems partnerships, ERP system selection has been an important activity for improving supply chains efficiency in technology industries. However, ERP system selection is tedious and time consuming, and the criteria used for ERP evaluation are numerous and influence one another. In this paper, we explore the potential of applying the decision making trial and evaluation laboratory (DEMATEL) approach. The DEMATEL not only can convert the relations between cause and effect of criteria into a visual structural model, but can also be used as a way to identify the key factors. A case study is used to illustrate the application of the proposed method.
Factorial design of reactive concrete powder containing electric arc slag furnace and recycled glass powder (2020)

El objetivo principal de esta investigación es desarrollar una mezcla optimizada de concreto de polvos reactivos (RPC) que contenga materiales cementícios suplementarios (SCM), como la escoria siderúrgica de arco eléctrico (EASF) y el polvo de vidrio reciclado (RGP) entre otros, utilizando el diseño factorial. Se calcularon diferentes regresiones polinómicas para predecir con precisión las variables respuesta (flujo estático y resistencia a compresión a distintas edades) en función de los factores considerados. A través de un algoritmo multiobjetivo, se determinó la mezcla que alcance la resistencia y flujo estático adecuados con un contenido mínimo de cemento. La verificación experimental de esta optimización matemática mostró que con 621 kg/m3 de cemento ASTM Tipo HE, y un contenido máximo de 100 kg/m3 de humo de sílice, se puede alcanzar una resistencia a compresión superior a los 150 MPa en un concreto, además, autocompactante.