gebhart/patrepeval huggingface dataset:
Zinc-finger Nuclease-induced Gene Repair With Oligodeoxynucleotides: Wanted and Unwanted Target Locus Modifications (2010)

Correcting a mutated gene directly at its endogenous locus represents an alternative to gene therapy protocols based on viral vectors with their risk of insertional mutagenesis. When solely a single-stranded oligodeoxynucleotide (ssODN) is used as a repair matrix, the efficiency of the targeted gene correction is low. However, as shown with the homing endonuclease I-SceI, ssODN-mediated gene correction can be enhanced by concomitantly inducing a DNA double-strand break (DSB) close to the mutation. Because I-SceI is hardly adjustable to cut at any desired position in the human genome, here, customizable zinc-finger nucleases (ZFNs) were used to stimulate ssODN-mediated repair of a mutated single-copy reporter locus stably integrated into human embryonic kidney-293 cells. The ZFNs induced faithful gene repair at a frequency of 0.16%. Six times more often, ZFN-induced DSBs were found to be modified by unfaithful addition of ssODN between the termini and about 60 times more often by nonhomologous end joining-related deletions and insertions. Additionally, ZFN off-target activity based on binding mismatch sites at the locus of interest was detected in in vitro cleavage assays and also in chromosomal DNA isolated from treated cells. Therefore, the specificity of ZFN-induced ssODN-mediated gene repair needs to be improved, especially regarding clinical applications.
Organizing WWW Images Based on the Analysis of Page Layout (2004)

Due to the rapid growth of the number of digital images on the Web, there is an increasing demand for effective and efficient method for organizing and retrieving the images available. This paper describes a method for clustering and embedding WWW images. By using a vision-based page segmentation algorithm, a web page is partitioned into blocks, and the textual and link information of an image can be accurately extracted from the block containing that image. By extracting the page-to-block, block-to-image, block-to-page relationships through link structure and page layout analysis, we construct an image graph. With the image graph model, we use techniques from spectral graph theory for image clustering and embedding. Some experimental results are given in the paper.
De novo design, synthesis and pharmacological evaluation of new azaindole derivatives as dual inhibitors of Abl and Src kinases (2012)

A new fragment based drug design approach implemented in our MedChem-Decision platform led to the discovery of a new series of 2,5 disubstituted 7-azaindole derivatives as potent dual Abl and Src kinase inhibitors. Extensive structure–activity relationships and structure-based drug design studies guided the exploration of the specificity pocket within the active conformation of the ATP site of the two kinases. This led to (1) the identification of a new binding mode of the 7-azaindole core to the two kinases and (2) the synthesis and pharmacological evaluation of compounds that exhibit low nanomolar inhibition on both Abl and Src kinases as well as moderate activity on the Abl 315I mutant.
Split ring resonator sensors for infrared detection of single molecular monolayers (2009)

We report a surface enhanced molecular detection technique with zeptomole sensitivity that relies on resonant coupling of plasmonic modes of split ring resonators and infrared vibrational modes of a self-assembled monolayer of octadecanthiol molecules. Large near-field enhancements at the gap of split ring resonators allow for this resonant coupling when the molecular absorption peaks overlap spectrally with the plasmonic resonance. Electromagnetic simulations support experimental findings.
<I>Thelohania solenopsae</I> (Microsporidia: Thelohaniidae) Infection in Reproductives of Red Imported Fire Ants (Hymenoptera: Formicidae) and Its Implication for Intercolony Transmission (2003)

The natural mechanism of intercolony transmission of Thelohania solenopsae, a pathogen of red imported fire ants, Solenopsis invicta, is unknown. However, T. solenopsae can be transmitted by introducing infected brood into an uninfected colony. We hypothesized that the transfer of brood among colonies during intercolony competition may be a mechanism for the horizontal transmission of T. solenopsae. Male and female reproductive caste alates, collected during the initiation of mating flights from infected colonies, had T. solenopsae infection rates of 93 and 75%, respectively. In addition, 47 field-collected, newly mated queens that were reared in the laboratory established T. solenopsae-infected colonies that contained egg, larvae, pupae, and adults. Because T. solenopsae is transovarially transmitted, this indicated that infected founding queens generated infected colonies. A life span of ≤52 wk was documented for 81% of the infected queens and 59% for uninfected queens. To determine whether imported fire ant colonies can become infected with T. solenopsae via colony raiding, seven pairs of S. invicta colonies consisting of large, uninfected and small, infected colonies were given access to each other in the laboratory. T. solenopsae infection was detected in four of seven of the large colonies. In the four large, infected colonies, brood levels declined an average of 64% after 22 wk in contrast to a 116% increase in the controls. Thus, there was evidence that incipient, T. solenopsae-infected colonies could provide a source of inocula for the horizontal transmission of T. solenopsae through the transfer of brood during colony raiding.
Rapidly in Situ-Forming Degradable Hydrogels from Dextran Thiols through Michael Addition (2007)

Thiol-functionalized dextrans (dex-SH) (M(n,dextran) = 14K or 31K) with degrees of substitution (DS) ranging from 12 to 25 were synthesized and investigated for in situ hydrogel formation via Michael type addition using poly(ethylene glycol) tetra-acrylate (PEG-4-Acr) or a dextran vinyl sulfone conjugate with DS 10 (dex-VS DS 10). Dex-SH was prepared by activation of the hydroxyl groups of dextran with 4-nitrophenyl chloroformate and subsequent reaction with cysteamine. Hydrogels were rapidly formed in situ under physiological conditions upon mixing aqueous solutions of dex-SH and either PEG-4-Acr or dex-VS DS 10 at polymer concentrations of 10 to 20 w/v%. Rheological studies showed that these hydrogels are highly elastic. By varying the DS, concentration, dextran molecular weight, and type of cross-linker, hydrogels with a broad range of storage moduli of 9 to 100 kPa could be obtained. Varying the ratio of thiol to vinyl sulfone groups from 0.9 to 1.1 did not alter the storage modulus of the hydrogels, whereas larger deviations from equimolarity (thiol to vinyl sulfone ratios of 0.75 and 1.5) considerably decreased the storage modulus. The plateau value of hydrogel storage modulus was reached much faster at pH 7.4 compared to pH 7, due to a higher concentration of the thiolate anion at higher pH. These hydrogels were degradable under physiological conditions. Degradation times were 3 to 7 weeks for dex-SH/dex-VS DS 10 hydrogels and 7 to over 21 weeks for dex-SH/PEG-4-Acr hydrogels, depending on the DS, concentration, and dextran molecular weight.
Genetic Diversity amongEscherichia coliIsolates Carryingf18Genes from Pigs with Porcine Postweaning Diarrhea and Edema Disease (1999)

Multilocus enzyme electrophoresis was applied to detect allelic variation and multilocus genotypes (electrophoretic types [ETs]) among 43 Escherichia coli isolates from weaned pigs suffering from edema disease or from diarrhea. ETs were analyzed in relation to O serogroups and virulence genes (sta, stb, lt, stx2, and f18) by DNA hybridization. Genomic diversity was the lowest in serogroup O138, while virulence genes (stx2 and f18) were the most uniform in serogroup O139. In general, the serogroups or toxin and F18 fimbria types were not related to selected ETs, suggesting that the toxin and f18 fimbria genes in E. coli isolates from pigs with postweaning diarrhea or edema disease occur in a variety of chromosomal backgrounds.
Anchorage of TiO2‐blasted, HA‐coated, and machined implants: An experimental study with rabbits (1995)

The purpose of this study was to evaluate the histometrical and biomechanical anchorage of TiO2-blasted implants and TiO2-blasted implants coated with hydroxyapatite. The control implants were machined. Twenty-six rabbits had a total of 156 implants placed in the proximal part of the tibia. Each rabbit had a machined, a TiO2-blasted, and a TiO2-blasted, HA-coated implant placed in each tibia. After a healing period of 3 and 12 weeks, respectively, the implants placed in the right tibia were used for removal torque test, and the implants placed in the left tibia were used for histomorphometrical measurements. Preoperatively, implants from the same batches were examined topographically with a TopScan 3D system. The TiO2-blasted implants demonstrated significantly higher removal torque values than the machined implants, and they also had a significantly more irregular surface. Furthermore, significantly higher bone-to-implant contact length fractions were measured adjacent to the TiO2-blasted implants in contrast to the machined implants. The advantages of a TiO2-blasted surface were more pronounced after 3 weeks than after 12 weeks. The results demonstrated that it was possible to influence the anchorage of implants by altering the surface structure morphology. The new method with TiO2 blasting on the titanium surface improves the anchorage of implants but is not yet practicable for HA coating.
Differences in Hyaluronic Acid-mediated Functions and Signaling in Arterial, Microvessel, and Vein-derived Human Endothelial Cells (2000)

Hyaluronic acid (HA), a nonsulfated glycosaminoglycan, regulates cell adhesion and migration. Small HA fragments (3-25 disaccharide units) induce neovascularization. We investigated the effect of HA and a HA fragment (10-15 disaccharide units, F1) on primary human endothelial cells (ECs). Human pulmonary ECs (HPAEC) and lung microvessel ECs (HMVEC-L) bound HA (K(d) approximately 1 and 2.3 nm, respectively) and expressed 17,780 and 16,690 HA binding sites, respectively. Both ECs showed HA-mediated cell adhesion; however, HMVEC-L was 1.5-fold better. Human umbilical vein ECs neither bound HA nor showed HA-mediated adhesion. All three ECs expressed CD44 ( approximately 110 kDa). The expression of receptor for HA-mediated motility (RHAMM) (approximately 80 kDa) was the highest in HMVEC-L, followed by HPAEC and human umbilical vein ECs. RHAMM, not CD44, bound HA in all three ECs. F1 was better than HA and stimulated a 2. 5- and 1.8-fold mitogenic response in HMVEC-L and HPAEC, respectively. Both HA and F1 induced tyrosine phosphorylation of p125(FAK), paxillin, and p42/44 ERK in HMVEC-L and HPAEC, which was blocked by an anti-RHAMM antibody. These results demonstrate that RHAMM is the functional HA receptor in primary human ECs. Heterogeneity exists among primary human ECs of different vascular origins, with respect to functional HA receptor expression and function.
Control of Doping by Impurity Chemical Potentials: Predictions forp-Type ZnO (2001)

Theoretical work has so far focused on the role of host-element chemical potentials in determining defect formation energies that control doping levels in semiconductors. Here, we report on our analysis of the role of the dopant-impurity chemical potential, which depends on the source gas. We present first-principles total-energy calculations that demonstrate a wide variation in the possible effective chemical potential of N. We account in detail for the recent puzzling observations of doping ZnO using N2 and N2O and predict that the use of dilute NO or NO2 gas would resolve the long-standing problem of achieving p-type ZnO.
Diabetes and Advanced Glycoxidation End Products (2006)

The incidence of diabetes, especially type 2 diabetes, is increasing at an alarming rate assuming epidemic proportions (1). Worldwide, 124 million people had diabetes by 1997, although an estimated 221 million people will have diabetes by the year 2010 (1).
Fast coding unit decision algorithm for HEVC (2013)

HEVC adopts a flexible Coding Unit (CU) quadtree structure. With more flexible CU size selection, the coding efficiency of HEVC increases significantly but its complexity is much higher than that of H.264/MPEG-4 AVC. To reduce computational complexity, we propose a fast algorithm, which consists of splitting decision and termination decision, in constructing the CU quadtree. This scheme is designed to be complementary to the current three fast tools included in HEVC TM5.0. In other words, when it is combined with the existing fast CU tools, it still provides additional time savings. The time reduction of our scheme is most noticeable on HD pictures. In comparison with the original HM5.0, our proposed method averagely saves about 43% encoding time and the BD rate increases by about 2.2% for the HD test sequences.
Formation of a Ternary Complex for Selenocysteine Biosynthesis in Bacteria (2015)

The synthesis of selenocysteine-containing proteins (selenoproteins) involves the interaction of selenocysteine synthase (SelA), tRNA (tRNA(Sec)), selenophosphate synthetase (SelD, SPS), a specific elongation factor (SelB), and a specific mRNA sequence known as selenocysteine insertion sequence (SECIS). Because selenium compounds are highly toxic in the cellular environment, the association of selenium with proteins throughout its metabolism is essential for cell survival. In this study, we demonstrate the interaction of SPS with the SelA-tRNA(Sec) complex, resulting in a 1.3-MDa ternary complex of 27.0 ± 0.5 nm in diameter and 4.02 ± 0.05 nm in height. To assemble the ternary complex, SPS undergoes a conformational change. We demonstrated that the glycine-rich N-terminal region of SPS is crucial for the SelA-tRNA(Sec)-SPS interaction and selenoprotein biosynthesis, as revealed by functional complementation experiments. Taken together, our results provide new insights into selenoprotein biosynthesis, demonstrating for the first time the formation of the functional ternary SelA-tRNA(Sec)-SPS complex. We propose that this complex is necessary for proper selenocysteine synthesis and may be involved in avoiding the cellular toxicity of selenium compounds.
Nanoimprinted superlattice metallic photonic crystal as ultraselective solar absorber (2015)

Here, a two-dimensional superlattice metallic photonic crystal (PhC) and its fabrication by nanoimprint lithography on tantalum substrates are presented. The superior tailoring capacity of the superlattice PhC geometry is used to achieve spectrally selective solar absorption optimized for high-temperature and high-efficiency solar-energy-conversion applications. The scalable fabrication route by nanoimprint lithography allows for a high-throughput and high-resolution replication of this complex pattern over large areas. Despite the high fill factor, the pattern of polygonal cavities is accurately replicated into a resist that hardens under ultraviolet radiation over an area of 10 mm<sup>2</sup>. In this way, cavities of 905 nm and 340 nm width are achieved with a period of 1 μm. After pattern transfer into tantalum via a deep reactive ion-etching process, the achieved cavities are 2.2 μm deep, separated by 85–95 nm wide ridges with vertical sidewalls. The room-temperature reflectance spectra of the fabricated samples show excellent agreement with simulated results, with a high spectral absorptance approaching blackbody absorption in the range from 300 to 1900 nm and a steep cutoff. The calculated solar absorptivity of this superlattice PhC is 96% and its thermal transfer efficiency is 82.8% at an operating temperature of 1500 K and an irradiance of 1000 kW/m<sup>2</sup>.
Analysis and Enhancement of Low-Light-Level Performance Photodiode-Type CMOS Active Pixel Imagers Operated with Sub-Threshold Reset (1999)

Noise in photodiode-type CMOS active pixel sensors (APS) is primarily due to the reset (kTC) noise at the sense node, since it is difficult to implement in-pixel correlated double sampling for a 2-D array. Signal integrated on the photodiode sense node (SENSE) is calculated by measuring difference between the voltage on the column bus (COL) - before and after the reset (RST) is pulsed. Lower than kTC noise can be achieved with photodiode-type pixels by employing softreset technique. Soft-reset refers to resetting with both drain and gate of the n-channel reset transistor kept at the same potential, causing the sense node to be reset using sub-threshold MOSFET current. However, lowering of noise is achieved only at the expense higher image lag and low-light-level non-linearity. In this paper, we present an analysis to explain the noise behavior, show evidence of degraded performance under low-light levels, and describe new pixels that eliminate non-linearity and lag without compromising noise.
Compression Characteristics of Selected Ground Agricultural Biomass (2009)

Agricultural biomass such as barley, canola, oat and wheat straw has the potential to be used as feedstock for bioenergy. However, the low bulk density straw must be processed and densified in order to facilitate handling, storage and transportation. It is important to understand the fundamental mechanism of the biomass compression process, which is required in the design of energy efficient compaction equipment to mitigate the cost of pre-processing and transportation of the product. Therefore, a comprehensive review of various compression models was performed and the compression behavior of selected ground agricultural biomass was studied. Five compression models were considered to determine the pressure-volume and pressure-density relationship to analyze the compression characteristics of biomass samples, namely:
Reduced Argininosuccinate Synthetase Is a Predictive Biomarker for the Development of Pulmonary Metastasis in Patients with Osteosarcoma (2010)

Pulmonary metastasis is the most significant prognostic determinant for osteosarcoma, but methods for its prediction and treatment have not been established. Using oligonucleotide microarrays, we compared the global gene expression of biopsy samples between seven osteosarcoma patients who developed pulmonary metastasis within 4 years after neoadjuvant chemotherapy and curative resection, and 12 patients who did not relapse. We identified argininosuccinate synthetase (ASS) as a gene differentially expressed with the highest statistical significance (Welch's t test, P = 2.2 x 10(-5)). Immunohistochemical analysis of an independent cohort of 62 osteosarcoma cases confirmed that reduced expression of ASS protein was significantly correlated with the development of pulmonary metastasis after surgery (log-rank test, P < 0.05). Cox regression analysis revealed that ASS was the sole significant predictive factor (P = 0.039; hazard ratio, 0.319; 95% confidence interval, 0.108-0.945). ASS is one of the enzymes required for the production of a nonessential amino acid, arginine. We showed that osteosarcoma cells lacking ASS expression were auxotrophic for arginine and underwent G(0)-G(1) arrest in arginine-free medium, suggesting that an arginine deprivation therapy could be effective in patients with osteosarcoma. Recently, phase I and II clinical trials in patients with melanoma and hepatocellular carcinoma have shown the safety and efficacy of plasma arginine depletion by stabilized arginine deiminase. Our data indicate that in patients with osteosarcoma, reduced expression of ASS is not only a novel predictive biomarker for the development of metastasis, but also a potential target for pharmacologic intervention.
Tissue factor expression in the metaplasia–adenoma–carcinoma sequence of gastric cancer in a European population (2012)

TF may be involved in tumour progression along the MACS of gastric cancer in the European population and is shown to start in precancerous lesions. However, clinical features may differ due to differences in biological features in the two populations, as reflected by differences in TF expression profile.
An Alternative Inhibitor Overcomes Resistance Caused by a Mutation of the Epidermal Growth Factor Receptor (2005)

Mutations of the epidermal growth factor receptor (EGFR) gene have been identified in non-small cell lung cancer specimens from patients responding to anilinoquinazoline EGFR inhibitors. However, clinical resistance to EGFR inhibitor therapy is commonly observed. Previously, we showed that such resistance can be caused by a second mutation of the EGFR gene, leading to a T790M amino acid change in the EGFR tyrosine kinase domain and also found that CL-387,785, a specific and irreversible anilinoquinazoline EGFR inhibitor, was able to overcome this resistance on the biochemical level. Here, we present the successful establishment of a stable Ba/F3 cell line model system for the study of oncogenic EGFR signaling and the functional consequences of the EGFR T790M resistance mutation. We show the ability of gefitinib to induce growth arrest and apoptosis in cells transfected with wild-type or L858R EGFR, whereas the T790M mutation leads to high-level functional resistance against gefitinib and erlotinib. In addition, CL-387,785 is able to overcome resistance caused by the T790M mutation on a functional level, correlating with effective inhibition of downstream signaling pathways. Similar data was also obtained with the use of the gefitinib-resistant H1975 lung cancer cell line. The systems established by us should prove useful for the large-scale screening of alternative EGFR inhibitor compounds against the T790M or other EGFR mutations. These data also support the notion that clinical investigations of compounds similar to CL-387,785 may be useful as a treatment strategy for patients with resistance to EGFR inhibitor therapy caused by the T790M mutation.
Serial, noninvasive, in vivo magnetic resonance microscopy detects the development of atherosclerosis in apolipoprotein E‐deficient mice and its progression by arterial wall remodeling (2003)

Serial MRM demonstrated the development and progression of atherosclerosis in mouse aorta. Importantly, progression of atherosclerosis could be identified within individual animals. By following the same aortic lesions over time, MRM demonstrated that progression of atherosclerosis in mice is associated with positive arterial remodeling.
A spread-spectrum clock generator with triangular modulation (2003)

A spread-spectrum clock generator (SSCG) with triangular modulation is presented. Only a divider and a programmable charge pump are added into a conventional clock generator to accomplish the spread-spectrum function. The proposed circuit has been fabricated in a 0.35-μm CMOS single-poly quadruple-metal process. The proposed SSCG can generate clocks of 66, 133, and 266 MHz with center spread ratios of 0.5%, 1%, 1.5%, 2%, and 2.5%. Experimental results confirm the theoretical analyses.
Production and utilization of palm fatty acid distillate (PFAD) (2010)

Abstract PFAD (palm fatty acid distillate) is a by‐product of physical refining of crude palm oil products and is composed of free fatty acids (81.7%), glycerides (14.4%), squalene (0.8%), vitamin E (0.5%), sterols (0.4%) and other substances (2.2%). PFAD is used in the animal feed and laundry soap industries as well as a raw material for the oleochemicals industry. Vitamin E, squalene and phytosterols are value‐added products which could be extracted from PFAD and are of potential value for the nutraceutical and cosmetic industries.