gebhart/patrepeval huggingface dataset:
Cloning and characterization of hcKrox, a transcriptional regulator of extracellular matrix gene expression (1997)

cKrox is a novel zinc finger-containing transcription factor that binds to the alpha1(I) and alpha2(I) collagen gene promoters. The gene coding for cKrox is a new member of a family of early growth response genes, that play important roles in development. In the mouse, cKrox is expressed, beginning at 9.5 days of gestation and at 10.5 days in regions destined to become skin. In adult animals, expression is predominantly in skin, one of the two major organs where type I collagen is expressed. We have isolated cDNA clones for human cKrox. Theoretical translation of the nucleic acid sequence reveals 90% conservation of amino acids between the mouse and human proteins; however, the human gene product contains a 117-amino-acid N-terminal extension. The amino acid sequences of the zinc-finger DNA binding domains of mouse and human cKrox are identical. RT-PCR analysis of human fibroblasts indicates constitutive low-level expression of cKrox which can be transiently elevated by treatment with retinoic acid. Transient transfection assays indicate that hcKrox represses transcription of the alpha1(I) procollagen promoter, and electrophoretic mobility shift assays demonstrate that hcKrox binds to both the human and murine promoter DNA. Deletion derivatives of hcKrox demonstrate transcription-activating potential that is promoter-dependent. NIH3T3 cells permanently expressing hcKrox demonstrate a threefold and 10-fold decrease in alpha1(I) procollagen and fibronectin mRNA levels, respectively, compared to control cells. Consistent with this finding, a fibronectin promoter reporter construct is repressed more than 80% by hcKrox. These data suggest that hcKrox represses collagen transcription directly, and it may function as a repressor of fibronectin and possibly other matrix genes.
Building and registering parameterized 3D models of vessel trees for visualization during intervention (2004)

In this paper, we address the problem of multimodal registration of coronary vessels by developing a 3D parametrical model of vessel trees from computer tomography data and registering it to angiography images during intervention. Thus, the interventionist takes profit from 3D data otherwise only available before the intervention. This facilitates orientation in ambiguous radiographs, interactive visualization of all vessel structures to estimate their mutual position and navigation within the vessel system and ultimately reduces the radiation the patient and the physicians are exposed to. The model is build by exploring the branching vessel tree starting from a single position and successively expanding through the vessels guided by a local deformable surface. The result is a tree of cylindrical segments each adapted to the vessel walls that is registered to angiography images in a fast and robust way. Validation on 8 patients confirms the robustness of our method.
Supplementary Figures from Overcoming Resistance to DNA-Targeted Agents by Epigenetic Activation of Schlafen 11 (<i>SLFN11)</i> Expression with Class I Histone Deacetylase Inhibitors (2023)

&lt;p&gt;Supplementary Fig. S1. Romidepsin derepresses SLFN11 expression in cancer cell lines from the NCI-60. Supplementary Fig. S2. Forcing SLFN11 expression sensitizes human colon cancer HCT116 cells to camptothecin. Supplementary Fig. S3. Induction of SLFN11 independently of FLI1, rapid reversal of the romidepsin effect and short half-life of SLN11 transcripts. Supplementary Fig. 4. Derepression of SLFN11 by entinostat sensitizes H82 and HH cells to camptothecin and exhibit additive effect in H446 cells.&lt;/p&gt;
A Stereo Thermographic System for Intra-operative Surgery (2005)

A stereo far-infrared (FIR) system based on the trigonometric parallax is presented in this paper for locating the distal arterial tree from the coronary artery bypass graft. The system can obtain the wide angle-of-view range information in the near distance by changing the optical path of one fixed uncooled FIR camera. Meanwhile, the speed of pixel movement on the FIR imaging plane is discussed for avoiding the problem on the imaging blur because the images are taken in sequence from a scanning mirror for the real-time monitor of the operation. Besides, the view range is also considered under the different system parameter conditions. After the structure parameters are simulated for evaluating the performance, the optimum system can be designed. This thermal imaging technique is inexpensive, noninvasive and feasible for intra-operative surgery.
Optical visualization and electrical characterization of fast-rising pulsed dielectric barrier discharge for airflow control applications (2012)

Flow control consists of manipulating flows in an effective and robust manner to improve the global performances of transport systems or industrial processes. Plasma technologies, and particularly surface dielectric barrier discharge (DBD), can be a good candidate for such purpose. The present experimental study focuses on optical and electrical characterization of plasma sheet formed by applying a pulse of voltage with rising and falling periods of 50 ns for a typical surface DBD geometry. Positive and negative polarities are compared in terms of current behavior, deposited energy, fast-imaging of the plasma propagation, and resulting modifications of the surrounding medium by using shadowgraphy acquisitions. Positive and negative pulses of voltage produce streamers and corona type plasma, respectively. Both of them result in the production of a localized pressure wave propagating in the air with a speed maintained at 343 m/s (measurements at room temperature of 20 °C). This suggests that the produced pressure wave can be considered as a propagating sound wave. The intensity of the pressure wave is directly connected to the dissipated energy at the dielectric wall with a linear increase with the applied voltage amplitude and a strong dependence toward the rising time. At constant voltage amplitude, the pressure wave is reinforced by using a positive pulse. The present investigation also reveals that rising and decaying periods of a single pulse of voltage result in two distinct pressure waves. As a result, superposition or successive pressure wave can be produced by adjusting the width of the pulse.
<title>Deep trench process performance enhancements in an MERIE reactor</title> (1993)

The development of a 16 Mb DRAM capable, deep trench etch in an applied materials P5000E, 200 mm, reactor is discussed in this paper. In order to meet the stringent device requirements extensive system modification, better process control tool development, and process optimization were necessary. The system modification activities have included: (1) a monopolar electrostatic chuck in place of the normal mechanical clamp to reduce trench profile tilt at the wafer edge, (2) an increase in cathode size, and (3) magnetic field modification. Both (2) and (3) improved the trench etch rate uniformity. For better process control, a blue laser diffraction etch rate monitor system has been demonstrated for 0.8 micrometers X 4 to approximately 7 micrometers 16 Mb trenches using two chemistries, HBr/SiF<SUB>4</SUB>/He-O<SUB>2</SUB> and HBr/NF<SUB>3</SUB>/He-O<SUB>2</SUB>. By means of process optimization, both HBr/SiF<SUB>4</SUB>/He-O<SUB>2</SUB> and HBr/NF<SUB>3</SUB>/He-O<SUB>2</SUB> chemistries are able to meet the requirements for 16 Mb trench.
Energy and latency control in low duty cycle MAC protocols (2005)

Recently, several MAC protocols, such as S-MAC and T-MAC, have exploited scheduled sleep/wakeup cycles to conserve energy in sensor networks. Until now, most protocols have assumed all nodes in the network were configured to follow the same schedule, or have assumed border nodes would follow multiple schedules, but those cases have not been evaluated. The paper develops two new algorithms to control and exploit the presence of multiple schedules to reduce energy consumption and latency. The first one is the global schedule algorithm (GSA). Through experiments, we demonstrate that, because of radio propagation vagaries, large sensor networks have very ragged, overlapping borders where many nodes listen to two or more schedules. GSA is a fully distributed algorithm that allows a large network to converge on a single global schedule to conserve energy. Secondly, we demonstrate that strict schedules incur a latency penalty in a multi-hop network when packets must wait for the next schedule for transmission. To reduce latency in multi-hop paths, we develop the fast path algorithm (FPA). FPA provides fast data forwarding paths by adding additional wake-up periods on the nodes along paths from sources to sinks. We evaluate both algorithms through experiments on Berkeley motes and demonstrate that the protocols accomplish their goals of reducing energy consumption and latency in large sensor networks.
Twenty-four hour intra-arterial infusion of 5-fluorouracil, cisplatin, and leucovorin is more effective than 6-hour infusion for advanced hepatocellular carcinoma (2007)

瞄准：评估 intra 动脉的 5 氟尿嘧啶(5-FU ) 的时间依赖为先进肝细胞癌(aHCC ) 的治疗。方法：有 aHCC 和肝肝硬化的 37 个成年日本病人与联合 intra 动脉的 5-FU， cisplatin (CDDP ) ，和甲酰四氢叶酸(LV ) 被对待。每个病人的日本综合阶段分数(JIS 分数) 是 3 或更多的。病人被划分成二个组，在组 S 的 15 个病人与 6-h 注入化疗在以后被对待(在 12 mg/h 的 LV ，在 10 mg/h 的 CDDP ，并且在 250 mg/m ( 2 )的 5-FU 每 4 h )并且在组 L 的 22 个病人与 24-h 注入化疗(在 12 mg/h ，在 10 mg/h 的 CDDP ，和在每 22 h 的 250 mg/ m ( 2 )的 5-FU 的 LV )被对待。连续注入化疗经由合适的肝的动脉被执行为用一座植入的药水库的 4 wk 的每 5 d。结果：有在化疗的 4 wk 以后的部分回答的病人的百分比在组 S 是 6.7% 并且 31.8% 在组 L。组 L 的幸存比组 S 的显著地好，与是的中部的生存时间在组 L 的 496 d 和在组 S 的 226 d (P < 0.05 ) 。结论：连续 24-h intra 动脉的注入为 aHCC 是更有效的并且能显著地作为与 6-h 相比延长生存时间注入。
Performance of R-Tree with Slim-Down and Reinsertion Algorithm (2010)

With the development of information technology, the amount of the multimedia data become more and more. The growth of these data brings the need for more effective methods in retrieval. The multimedia retrieval systems always index these data on the basis of feature vectors. In order to handle these vectors efficiently, the index structures such as the R-tree family are used to manage them. Slim-down algorithm is used in Slim-tree, and it can improve the number of disk accesses for range queries in average 10%-20% for vector datasets. Especially for datasets with bigger bloat-factors, the average improvement rise to 25%-35%. In this paper, we use Slim-down algorithm in R-tree index structure to test whether it's efficient in rectangle node management, and compare it with Reinsertion algorithm. The experiment results show that the Slim-down algorithm is not suitable for reducing the intersection of rectangle regions as it do to the Slim-tree nodes. It can not improve the performance of R-tree distinctly.
Design for sustainable development—Household drinking water filter for arsenic and pathogen treatment in Nepal (2007)

In the last 20 years, the widespread adoption of shallow tubewells in Nepal Terai region enabled substantial improvement in access to water, but recent national water quality testing showed that 3% of these sources contain arsenic above the Nepali interim guideline of 50 microg/L, and up to 60% contain unsafe microbial contamination. To combat this crisis, MIT, ENPHO and CAWST together researched, developed and implemented a household water treatment technology by applying an iterative, learning development framework. A pilot study comparing 3 technologies against technical, social, and economic criteria showed that the Kanchan Arsenic Filter (KAF) is the most promising technology for Nepal. A two-year technical and social evaluation of over 1000 KAFs deployed in rural villages of Nepal determined that the KAF typically removes 85-90% arsenic, 90-95% iron, 80-95% turbidity, and 85-99% total coliforms. Then 83% of the households continued to use the filter after 1 year, mainly motivated by the clean appearance, improved taste, and reduced odour of the filtered water, as compared to the original water source. Although over 5,000 filters have been implemented in Nepal by January 2007, further research rooted in sustainable development is necessary to understand the technology diffusion and scale-up process, in order to expand access to safe water in the country and beyond.
The Role of Late INa and Antiarrhythmic Drugs in EAD Formation and Termination in Purkinje Fibers (2006)

Multiple components of cardiac Na current play a role in determining electrical excitation in the heart. Recently, the role of nonequilibrium components in controlling cardiac action potential plateau duration, and their importance in regulating the occurrence of afterdepolarizations and arrhythmias have garnered more attention. In particular, late Na current (late I(Na)) has been shown to be important in LQT2 and LQT3 arrhythmias. Class III agents like dofetilide, clofilium, and sotalol, which can all cause a drug-induced form of LQT2, significantly lengthen action potential duration at 50% and 90% repolarization in isolated rabbit Purkinje fibers, and can initiate the formation of early afterdepolarizations, and extra beats. These actions can lead to the development of a serious ventricular tachycardia, torsades de pointes, in animal models and patients. However, pretreatment with agents that block late I(Na), like lidocaine, mexiletine, and RSD1235, a novel mixed ion channel blocker for the rapid pharmacologic conversion of atrial fibrillation, significantly attenuates the prolonging effects of Class III agents or those induced by ATX-II, a specific toxin that delays Na channel inactivation and amplifies late I(Na) greatly, mimicking LQT3. The Na channel block caused by lidocaine and RSD1235 can be through the open or inactivated states of the channel, but both equivalently inhibit a late component of Na current (I(Na)), recorded at 22 degrees C using whole-cell patch clamp of Nav 1.5 expressed in HEK cells. These protective actions of lidocaine, mexiletine, and RSD1235 may result, at least in part, from their ability to inhibit late I(Na) during action potential repolarization, and inhibition of the inward currents contributing to EAD and arrhythmia formation.
Effect of post-etch treatment on chlorine concentration of AlSi and Ti-capped AlSi films (1990)

Ti-capped Al–Si films are more susceptible to post-etch corrosion than uncapped Al–Si films. The extent of corrosion of Ti-capped films is related to post-etch treatment. Various post-etch treatments to reduce chlorine concentration are evaluated by x-ray fluorescence analysis. Results of single- and multiple-step treatment, such as baking, partial resist stripping in oxygen plasma in the exit chamber, water rinse, and resist partial stripping followed by wet stripping are presented. A method to estimate the surface concentration of chlorine in atoms/cm2 is described; the chlorine concentration in most cases is less than 5×1015 atoms/cm2.
Low temperature reactive bonding (1995)

Disclosed is a joining technique that requires no external heat source and generates very little heat. It involves the reaction of thin multilayered films deposited on faying (closely fit or joining) surfaces to create a stable compound that functions as an intermediate or braze material in order to create a high strength bond. While high temperatures are reached in the reaction of the multilayer film, very little heat is generated because the films are very thin. It is essentially a room temperature joining process. It can be used for joining silicon wafers and integrated circuits.
Validating network protocols using a flexible verifier (2002)

As a means of developing high reliability communication systems, the combined use of formal description techniques (such as SDL and LOTOS) and verification techniques is desirable. The paper gives a flexible, user-friendly verifier Vega which is based on a model-theoretic methodology that supports verification of temporal properties (e.g., cause-and-effect relationships) expressed in temporal logic for protocol specifications described in LOTOS. Vega is provided with an effective interface function, as well as the function of simple model checking, to give some degree of flexibility for the expression of temporal properties to be verified. Specifically, it allows the user to define useful expressions by combining built-in temporal logic formulas and enter them for use at any time.
Genetically Programmable Thermoresponsive Plasmonic Gold/Silk-Elastin Protein Core/Shell Nanoparticles (2014)

The design and development of future molecular photonic/electronic systems pose the challenge of integrating functional molecular building blocks in a controlled, tunable, and reproducible manner. The modular nature and fidelity of the biosynthesis method provides a unique chemistry approach to one-pot synthesis of environmental factor-responsive chimeric proteins capable of energy conversion between the desired forms. In this work, facile tuning of dynamic thermal response in plasmonic nanoparticles was facilitated by genetic engineering of the structure, size, and self-assembly of the shell silk-elastin-like protein polymers (SELPs). Recombinant DNA techniques were implemented to synthesize a new family of SELPs, S4E8Gs, with amino acid repeats of [(GVGVP)4(GGGVP)(GVGVP)3(GAGAGS)4] and tunable molecular weight. The temperature-reversible conformational switching between the hydrophilic random coils and the hydrophobic β-turns in the elastin blocks were programmed to between 50 and 60 °C by site-specific glycine mutation, as confirmed by variable-temperature proton NMR and circular dichroism (CD) spectroscopy, to trigger the nanoparticle aggregation. The dynamic self-aggregation/disaggregation of the Au-SELPs nanoparticles was regulated in size and pattern by the β-sheet-forming, thermally stable silk blocks, as revealed by transmission electron microscopy (TEM) and dynamic light scattering (DLS). The thermally reversible, shell dimension dependent, interparticle plasmon coupling was investigated by both variable-temperature UV-vis spectroscopy and finite-difference time-domain (FDTD)-based simulations. Good agreement between the calculated and measured spectra sheds light on design and synthesis of responsive plasmonic nanostructures by independently tuning the refractive index and size of the SELPs through genetic engineering.
Massive Vacancy Concentration Yields Strong Room-Temperature Ferromagnetism in Two-Dimensional ZnO (2019)

Two-dimensional (2D) ZnO nanosheets with highly concentrated Zn vacancies (V<sub>Zn</sub>) of up to approximately 33% were synthesized by ionic layer epitaxy at the water-toluene interface. This high cation vacancy concentration is unprecedented for ZnO and may provide unique opportunities to realize exotic properties not attainable in the conventional bulk form. After annealing, the nanosheets showed characteristic magnetic hysteresis with saturation magnetization of 57.2 emu/g at 5 K and 50.9 emu/g at room temperature. This value is 1 order of magnitude higher than other ZnO nanostructures and comparable to the conventional ferrimagnetic Fe<sub>3</sub>O<sub>4</sub>. Density functional theory calculations, with the support of experimental results, suggest that a high concentration of V<sub>Zn</sub> (approximately one-third of the Zn sites) can form spontaneously during synthesis when stabilized by H ions, and the formation of V<sub>Zn</sub> could be further facilitated by the presence of grain boundaries. It is essential to remove the H for the nanosheets to show ferromagnetism. The mechanisms identified for the origin of the high magnetism in ZnO nanosheets presents an intriguing example of a kinetically stabilized, non-equilibrium, highly defective 2D nanomaterial with a significantly enhanced physical property.
KDM6B epigenetically regulates odontogenic differentiation of dental mesenchymal stem cells (2013)

Mesenchymal stem cells (MSCs) have been identified and isolated from dental tissues, including stem cells from apical papilla, which demonstrated the ability to differentiate into dentin-forming odontoblasts. The histone demethylase KDM6B (also known as JMJD3) was shown to play a key role in promoting osteogenic commitment by removing epigenetic marks H3K27me3 from the promoters of osteogenic genes. Whether KDM6B is involved in odontogenic differentiation of dental MSCs, however, is not known. Here, we explored the role of KDM6B in dental MSC fate determination into the odontogenic lineage. Using shRNA-expressing lentivirus, we performed KDM6B knockdown in dental MSCs and observed that KDM6B depletion leads to a significant reduction in alkaline phosphate (ALP) activity and in formation of mineralized nodules assessed by Alizarin Red staining. Additionally, mRNA expression of odontogenic marker gene SP7 (osterix, OSX), as well as extracellular matrix genes BGLAP (osteoclacin, OCN) and SPP1 (osteopontin, OPN), was suppressed by KDM6B depletion. When KDM6B was overexpressed in KDM6B-knockdown MSCs, odontogenic differentiation was restored, further confirming the facilitating role of KDM6B in odontogenic commitment. Mechanistically, KDM6B was recruited to bone morphogenic protein 2 (BMP2) promoters and the subsequent removal of silencing H3K27me3 marks led to the activation of this odontogenic master transcription gene. Taken together, our results demonstrated the critical role of a histone demethylase in the epigenetic regulation of odontogenic differentiation of dental MSCs. KDM6B may present as a potential therapeutic target in the regeneration of tooth structures and the repair of craniofacial defects.
Drone-Based Parcel Delivery Using the Rooftops of City Buildings: Model and Solution (2020)

In general, the demand for delivery cannot be fulfilled efficiently due to the excessive traffic in dense urban areas. Therefore, many innovative concepts for intelligent transportation of freight have recently been developed. One of these concepts relies on drone-based parcel delivery using rooftops of city buildings. To apply drone logistics system in cities, the operation design should be adequately prepared. In this regard, a mixed integer programming model for drone operation planning and a heuristic based on block stacking are newly proposed to provide solutions. Additionally, numerical experiments with three different problem sizes are conducted to check the feasibility of the proposed model and to assess the performance of the proposed heuristic. The experimental results show that the proposed model seems to be viable and that the developed heuristic provides very good operation plans in terms of the optimality gap and the computation time.
Flavor Evaluation of Light and Dark Meat from Broilers Fed Capsaicin (1995)

Thirty-two broilers were reared from 1 to 42 d of age on a diet containing 0 or 20 ppm of capsaicin and then conventionally processed. When the cooked meat was served to untrained consumer panelists in a triangle difference test, there was no difference in flavor between control and capsaicin-fed birds for either the Pectoralis muscle (light meat) or the Biceps femoris muscle (dark meat). These data suggest that incorporation of capsaicin into the diets of broilers at 20 ppm does not result in a change in the flavor of the meat.
Demonstration of three-dimensional microstructure self-assembly (1995)

Self-assembly of three-dimensional microstructures using the surface tension force of molten solder to produce out-of-plane rotation is demonstrated. The generic nature of the technique is illustrated by reconfiguring structures formed in both Ni metal and single crystal Si. The structures do not have a hinge to constrain the rotation. This considerably simplifies fabrication and eliminates problems associated with the compatibility of a suitable hinge material. Details of the fabrication processes are given and results are presented for rotated structures.