gebhart/patrepeval huggingface dataset:
00Ar134-1, a spring wheat line of intergeneric origin (2016)

00Ar134-1 is an intergeneric spring wheat line derived from Elymus repens (quack grass). The line was developed as a potentially new source of resistance to Fusarium head blight (FHB) in wheat. 00Ar134-1 is resistant to Fusarium head blight as well as leaf rust, stem rust, and common bunt. Although lower yielding and taller than commercial cultivars, this line is of similar maturity and kernel weight. 00Ar134-1 can potentially be used as a resistant parent for improving Fusarium head blight resistance in common wheat.
QUANTITATIVE MEASUREMENTS WITH DIGITAL FLUOROSCOPY (1982)

Department of Radiological Sciences, and School of Engineering, University of California. Irvine. CA 92717.
Tissue-specific and Hormonal Regulation of Calbindin-D9K Fusion Genes in Transgenic Mice (1996)

The rat Calbindin-D9K (CaBP9K) gene is mainly expressed in intestine, uterus, and lung and is regulated in a complex tissue-specific manner. To analyze the role of potential regulatory elements, previously defined by DNaseI hypersensivity, we made transgenic mice containing truncated rat CaBP9K fusion gene with simian virus 40 large T antigen and the chloramphenicol acetyltransferase as reporter genes. The transgenes contained CaBP9K promoter fragments with 5' end points at -4400, -1011, and -117 base pairs (bp), whereas the 3' end points was at +365 bp. Northern blot analysis of T antigen expression and chloramphenicol acetyltransferase enzyme-linked immunosorbent assay indicated that a positive element, probably the distal intestine-specific DNaseI HS, necessary to target the expression of the transgene in the intestine, is present between -4400 and -1011 bp. The cephalo-caudal gradient of expression of the transgene along the small intestine was similar to those of the endogenous gene, but an ectopic expression of the transgene was observed in the colon. The -1011 transgene was expressed in epithelial alveolar cells of the lung, in renal proximal tubule cells, and in uterine myometrium, as judged from immunocytochemical, histological, and Northern blot analyses. The shortest, -117 construct was only expressed in uterine myometrium, and it was under a strict estrogen dependence like the endogenous gene. Finally, responsiveness to vitamin D in the duodenum was observed with the largest, -4400 construct. Thus, different tissues utilize distinct cis-acting elements to direct and regulate the expression of the rat CaBP9K gene.
Percutaneous tumor ablation with radiofrequency (2002)

Consensus indications in oncology are ill-defined, despite widespread proliferation of the technology. A brief review is presented of the current status of image-guided tumor ablation therapy. More rigorous scientific review, long-term follow-up, and randomized prospective trials are needed to help define the role of RFA in oncology.
TEMPERATURE EFFECTS ON LEUKOCYTE REACTIVITY (1999)

Society of Critical Care Medicine; 28th Educational and Scientific Symposium; San Francisco, California, USA; January 23-27, 1999: Poster Presentations: Poster Hall
Dosimetry computation from tissue distribution data entered in an electronic mouse model with convolution of the beta ray deposition profile (1994)

When mice data are used as model of therapeutic administration of radiopharmaceuticals, there may be an important distortion, due to the fact that the range of the particular emission is relatively large. To estimate this effect and eventually account for it, we propose an alternative to the classical MIRD approach. A three-dimensional MRI image from a mouse was used to define organ size and location by image segmentation. The segmented image is used as an anatomically correct set of three dimensional regions of interest. Data obtained from tissue distribution studies over time in sacrificed mice are entered in the organ regions as cumulative beta doses (microcurie hour/g x rad.g/microcurie hour). The resulting cumulative dose image is then convoluted in three dimensions by the point spread function which describes the spatial distribution of the appropriate beta ray (s) energy deposition in tissue equivalent medium. In the resulting image cross irradiation between organs is accounted for by the redistribution of the original cumulative doses. The results indicate that for beta rays with high average energy, small organ doses are significantly lower than expected and that cross-irradiation is significant.
Supplementary Figure S6 from Small-Molecule ONC201/TIC10 Targets Chemotherapy-Resistant Colorectal Cancer Stem–like Cells in an Akt/Foxo3a/TRAIL–Dependent Manner (2023)

&lt;p&gt;Effect of DR5 and Foxo3 siRNA knockdown on ONC201/TIC10-mediated anti-CSC effect.&lt;/p&gt;
A scalable method for the production of high-titer and high-quality adeno-associated type 9 vectors using the HSV platform (2016)

Recombinant adeno-associated vectors based on serotype 9 (rAAV9) have demonstrated highly effective gene transfer in multiple animal models of muscular dystrophies and other neurological indications. Current limitations in vector production and purification have hampered widespread implementation of clinical candidate vectors, particularly when systemic administration is considered. In this study, we describe a complete herpes simplex virus (HSV)-based production and purification process capable of generating greater than 1 × 10(14) rAAV9 vector genomes per 10-layer CellSTACK of HEK 293 producer cells, or greater than 1 × 10(5) vector genome per cell, in a final, fully purified product. This represents a 5- to 10-fold increase over transfection-based methods. In addition, rAAV vectors produced by this method demonstrated improved biological characteristics when compared to transfection-based production, including increased infectivity as shown by higher transducing unit-to-vector genome ratios and decreased total capsid protein amounts, shown by lower empty-to-full ratios. Together, this data establishes a significant improvement in both rAAV9 yields and vector quality. Further, the method can be readily adapted to large-scale good laboratory practice (GLP) and good manufacturing practice (GMP) production of rAAV9 vectors to enable preclinical and clinical studies and provide a platform to build on toward late-phases and commercial production.
Performance engineering of multicore software : developing a science of fast code for the post-Moore era (2016)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2016.
Supplementary Figures 1 and 2 from Improving CART-Cell Therapy of Solid Tumors with Oncolytic Virus–Driven Production of a Bispecific T-cell Engager (2023)

&lt;p&gt;S1. Therapeutic index of EGFR-targeting CART cells and the OAd-BiTE. S2. The Combination of FR-CART cells and OAd-BiTE mediates tumor regression in mice bearing pancreatic xenograft tumors.&lt;/p&gt;
Localization and Segmentation of A 2D High Capacity Color Barcode (2008)

A 2D color barcode can hold much more information than a binary barcode. Barcodes are often intended for consumer use where using a cellphone, a consumer can take an image of a barcode on a product, and retrieve relevant information about the product. The barcode must be read using computer vision techniques. While a color barcode can hold more information, it makes this vision task in consumer scenarios unusually challenging. We present our approach to the localization and segmentation of a 2D color barcode in such challenging scenarios, along with its evaluation on a diverse collection of images of Microsoft's recently launched High Capacity Color Barcode (HCCB). We exploit the unique trait of barcode reading: the barcode decoder can give the vision algorithm feedback, and develop a progressive strategy to achieve both - high accuracy in diverse scenarios as well as computational efficiency.
Over-the-Air Evaluation of the Antenna Performance of Popular Mobile Phones (2019)

Mobile terminals have become an integral part of people's everyday life. The ability of the handset to transmit and to receive power determines how good communication link it can establish. This paper presents results from a comprehensive study on the radio performance, in terms of total radiated power (TRP) and total isotropic sensitivity (TIS), of 16 mobile terminals, common in the Nordic countries, in different use scenarios - free space, talk mode using right and left hand phantom next to head phantom, and data mode with right hand phantom. The phones are tested following the standardized non-invasive procedure for 2G, 3G and 4G communication standards. It is found that there is a large spread in the performance among the tested phones even in free space (up to 9 dB for TRP and up to 5 dB for TIS) and the case is more severe when the user is located next to the handset. The results indicate that the vicinity of the user to the mobile terminal can lead to degradation up to 22 dB in the transmit performance and up to 8 dB in the receive performance.
Protein Nanoparticles Formed by Self-assembly of Human Serum Albumin with a Fatty Acid Arm (2019)

We report the preparation of spherical protein nanoparticles comprising self-assembled human serum albumin (HSA) with an N-(11-carboxyundecyl)succinimido (CU) arm in aqueous medium at pH 5.0. Molecular dynamics simulation implied that the alternate CU chain bindings and multiple hydrogen bonds contribute the interprotein interaction. Cross-linking of the protein components by glutaraldehyde stabilized the particle under physiological pH. This paper describes the preparation of spherical nanoparticles comprising self-assembled human serum albumin with an N-(11-carboxyundecyl)succinimido (CU) arm in aqueous medium at pH 5. Molecular dynamics simulation implied that the alternate CU chain bindings and hydrogen bonds contribute the interprotein interaction. Cross-linking of the protein components stabilized the particle under physiological pH.
Profiling Signal Pathway Activation during Lymphangiogenesis (2007)

A number of studies have shown that VEGF‐C is a potent mitogen for the lymphatic endothelium and a key lymphangiogenic factor. However, the biochemical signaling pathways activated via VEGFR‐3 upon stimulation by VEGF‐C in the lymphatic endothelium (LEC) are not well defined. We have employed an in vitro cell culture model of lymphangiogenesis to profile protein phosphorylation coupled with reverse‐phase protein microarrays and phosphor‐specific antibodies. The goal is to examine the activation status of key molecular steps in LEC survival, proliferation signaling leading to differentiation. With VEGF‐C stimulation, the levels of activated ERK showed correlations between proliferating status versus tube forming. In addition, p38 showed variations in LEC stimulated with VEGF‐C and marked changes were noted between the various stages of lymphangiogenesis for phospho‐p38 and total p38, of the MAPKK pathway. Activated AKT, an indicator of the state of PI3kinase/AKT pro‐survival pathway exhibited intense activation within the different stages of lymphangiogenesis. These results support a different mechanism for lymphangiogenesis versus blood endothelial angiogenesis, and is in keeping with our previous results showing that the lymph proteome is distinct from the plasma proteome. By employing this high throughput technology for the analysis of signal pathway profiling in LEC during lymphangiogenesis it will be possible to gain further insight into the molecular modification of proteins in the lymphatic endothelium during various physiological and pathological conditions.
Effects of a mindfulness‐based weight loss intervention in adults with obesity: A randomized clinical trial (2016)

Mindfulness enhancements to a diet-exercise program did not show substantial weight loss benefit but may promote long-term improvement in some aspects of metabolic health in obesity that requires further study.
Lithium Niobate Band Pass Response Microwave Modulator With Phase Reversal Electrodes (1988)

External modulation is advantageous in digital large signal 1 as well as in small signal modulation applications. The effects of the dynamics of direct modulation (chirping, patterning) are avoided (of specific significance in digital applications which require large extinction ratios) and the basic bandwidth limiting factors of the direct modulation process (gain coefficient, photon density and lifetime) are replaced by modulator parameters such as "walk off" (difference in optical and microwave velocities) and microwave attenuation in traveling wave type modulators. A further factor of importance in microwave applications is that the high speed modulator and the laser can be optimized separately for high speed and high output power, respectively, such that increased modulated optical power can be achieved with unchanged microwave power. In LiNbO 3 baseband traveling wave modulators, the difference in propagation velocities of the optical signal and the microwave signal sets a limit to the bandwidth. However, microwave applications do not require baseband response and generally only require small signal modulation. A number of techniques have been devised to circumvent the walk off problem; closer matching of the propagation velocities 2 , and different velocity mismatch compensation schemes 3, 4, 5, 6. Baseband, bandpass or periodic frequency responses are obtained, with improved figures of merit. We report here a bandpass response modulator based on a two section phase reversal electrode scheme, and compare its performance as a small signal microwave modulator to a conventional baseband modulator.
Discovery and Characterization of a Novel Allosteric Small-Molecule Inhibitor of NADP+-Dependent Malic Enzyme 1 (2022)

NADP<sup>+</sup>-dependent malic enzyme 1 (ME1) decarboxylates malate to form pyruvate and NADPH in the cytoplasm, where it mediates diverse biological functions related to the generation of lipids and other cellular building blocks. As such, ME1 has been implicated in the progression of cancers and has received attention as a promising drug target. Here we report the identification of a novel small-molecule inhibitor of ME1, designated AS1134900. AS1134900 is highly selective for ME1 compared with ME2 and uncompetitively inhibits ME1 activity in the presence of its substrates NADP<sup>+</sup> and malate. In addition, X-ray crystal structure analysis of the enzyme-inhibitor complex revealed that AS1134900 binds outside the ME1 active site in a novel allosteric site. Structural comparison of the ME1 quaternary complex with AS1134900, NADPH, and Mn<sup>2+</sup>, alongside known crystal structures of malic enzymes, indicated the determined crystal ME1-inhibitor complex is in the open form conformation. These results provide insights and a starting point for further discovery of drugs that inhibit ME1 activity in cancer cells.
Solder-based chip-to-tube and chip-to-chip packaging for microfluidic devices (2007)

Constructing a microsystem compatible with a large variety of chemistries requires a system design that will be robust in the presence of different compounds and at a wide range of conditions. Although microreactors themselves can accommodate a great span of conditions, few packaging schemes are compatible with cryogenic temperatures, high pressures, and aggressive organic solvents. Solder-based connections are designed and implemented on silicon-based microreactors and are demonstrated to withstand elevated pressures (up to 200 atm), a wide range of temperatures (-78 to 160 degrees C) and a variety of solvent systems. Through the deposition of metal bonding pads directly onto silicon and glass surfaces, solder-based chip-to-tube connections can be reliably formed using handheld soldering tools. Packaging techniques are also described for fluidic chip-to-chip bonds, facilitating direct connection of microfluidic modules. This method greatly expands the utility of microfluidic reactors while enabling easy and reproducible fluidic packaging.
Surface Effect for Gas Loading Micrograin Palladium for Low Energy Nuclear Reactions LENR (2012)

Cold fusion and heavy element generation in palladium and similar crystals by low energy nuclear reactions LENR are manifested by crystal shock experiments with million times increased neutron emission, and furthermore by the Maruhn-Greiner small local maximum of the generated element distribution within a large scale minimum similar to the distribution for uranium fission. The role of deuterium reactions in two picometer distance are based on Coulomb screening and on results of cluster generation with very high density deuterons.
Gravity-Balancing Leg Orthosis and Its Performance Evaluation (2006)

In this paper, we propose a device to assist persons with hemiparesis to walk by reducing or eliminating the effects of gravity. The design of the device includes the following features: 1) it is passive, i.e., it does not include motors or actuators, but is only composed of links and springs; 2) it is safe and has a simple patient-machine interface to accommodate variability in geometry and inertia of the subjects. A number of methods have been proposed in the literature to gravity-balance a machine. Here, we use a hybrid method to achieve gravity balancing of a human leg over its range of motion. In the hybrid method, a mechanism is used to first locate the center of mass of the human limb and the orthosis. Springs are then added so that the system is gravity-balanced in every configuration. For a quantitative evaluation of the performance of the device, electromyographic (EMG) data of the key muscles, involved in the motion of the leg, were collected and analyzed. Further experiments involving leg-raising and walking tasks were performed, where data from encoders and force-torque sensors were used to compute joint torques. These experiments were performed on five healthy subjects and a stroke patient. The results showed that the EMG activity from the rectus femoris and hamstring muscles with the device was reduced by 75%, during static hip and knee flexion, respectively. For leg-raising tasks, the average torque for static positioning was reduced by 66.8% at the hip joint and 47.3% at the knee joint; however, if we include the transient portion of the leg-raising task, the average torque at the hip was reduced by 61.3%, and at the knee was increased by 2.7% at the knee joints. In the walking experiment, there was a positive impact on the range of movement at the hip and knee joints, especially for the stroke patient: the range of movement increased by 45% at the hip joint and by 85% at the knee joint. We believe that this orthosis can be potentially used to design rehabilitation protocols for patients with stroke
Data from CRM1 Inhibition Promotes Cytotoxicity in Ewing Sarcoma Cells by Repressing EWS-FLI1–Dependent IGF-1 Signaling (2023)

&lt;div&gt;Abstract&lt;p&gt;Ewing sarcoma (EWS) is an aggressive bone malignancy that mainly affects children and young adults. The mechanisms by which EWS (EWSR1) fusion genes drive the disease are not fully understood. CRM1 (XPO1) traffics proteins from the nucleus, including tumor suppressors and growth factors, and is overexpressed in many cancers. A small-molecule inhibitor of CRM1, KPT-330, has shown therapeutic promise, but has yet to be investigated in the context of EWS. In this study, we demonstrate that CRM1 is also highly expressed in EWS. shRNA-mediated or pharmacologic inhibition of CRM1 in EWS cells dramatically decreased cell growth while inducing apoptosis, cell-cycle arrest, and protein expression alterations to several cancer-related factors. Interestingly, silencing of CRM1 markedly reduced EWS–FLI1 fusion protein expression at the posttranscriptional level and upregulated the expression of the well-established EWS-FLI1 target gene, insulin-like growth factor binding protein 3 (IGFBP3), which inhibits IGF-1. Accordingly, KPT-330 treatment attenuated IGF-1–induced activation of the IGF-1R/AKT pathway. Furthermore, knockdown of IGFBP3 increased cell growth and rescued the inhibitory effects on IGF-1 signaling triggered by CRM1 inhibition. Finally, treatment of EWS cells with a combination of KPT-330 and the IGF-1R inhibitor, linsitinib, synergistically decreased cell proliferation both &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;. Taken together, these findings provide a strong rationale for investigating the efficacy of combinatorial inhibition of CRM1 and IGF-1R for the treatment of EWS. &lt;i&gt;Cancer Res; 76(9); 2687–97. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Identification of Active Gold Nanoclusters on Iron Oxide Supports for CO Oxidation (2008)

Gold nanocrystals absorbed on metal oxides have exceptional properties in oxidation catalysis, including the oxidation of carbon monoxide at ambient temperatures, but the identification of the active catalytic gold species among the many present on real catalysts is challenging. We have used aberration-corrected scanning transmission electron microscopy to analyze several iron oxide-supported catalyst samples, ranging from those with little or no activity to others with high activities. High catalytic activity for carbon monoxide oxidation is correlated with the presence of bilayer clusters that are approximately 0.5 nanometer in diameter and contain only approximately 10 gold atoms. The activity of these bilayer clusters is consistent with that demonstrated previously with the use of model catalyst systems.
The Impact of the Hippo Pathway and Cell Metabolism on Pathological Complete Response in Locally Advanced Her2+ Breast Cancer: The TRISKELE Multicenter Prospective Study (2022)

The Hippo pathway and its two key effectors, Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ), are consistently altered in breast cancer. Pivotal regulators of cell metabolism such as the AMP-activated protein kinase (AMPK), Stearoyl-CoA-desaturase 1 (SCD1), and HMG-CoA reductase (HMGCR) are relevant modulators of TAZ/YAP activity. In this prospective study, we measured the tumor expression of TAZ, YAP, AMPK, SCD1, and HMGCR by immunohistochemistry in 65 Her2+ breast cancer patients who underwent trastuzumab-based neoadjuvant treatment. The aim of the study was to assess the impact of the immunohistochemical expression of the Hippo pathway transducers and cell metabolism regulators on pathological complete response. Low expression of cytoplasmic TAZ, both alone and in the context of a composite signature identified by machine learning including also low nuclear levels of YAP and HMGCR and high cytoplasmic levels of SCD1, was a predictor of residual disease in the univariate logistic regression. This finding was not confirmed in the multivariate model including estrogen receptor > 70% and body mass index > 20. However, our findings were concordant with overall survival data from the TCGA cohort. Our results, possibly affected by the relatively small sample size of this study population, deserve further investigation in adequately sized, ad hoc prospective studies.
Cache conscious data layout organization for conflict miss reduction in embedded multimedia applications (2004)

Cache misses form a major bottleneck for real-time multimedia applications due to the off-chip accesses to the main memory. This results in both a major access bandwidth overhead (and related power consumption) as well as performance penalties. We propose a new technique for organizing data in the main memory for data dominated multimedia applications so as to reduce the majority of the conflict cache misses. The focus of this paper is on the formal and heuristic algorithm we use to steer the data layout decisions and the experimental results obtained using a prototype tool. Experiments on real-life demonstrators illustrate that we are able to reduce up to 82 percent of the conflict misses for applications which are already aggressively transformed at source-level. At the same time, we also reduce the off-chip data accesses by up to 78 percent. In addition, we are able to reduce up to 20 percent more conflict misses compared to existing techniques.