gebhart/patrepeval huggingface dataset:
Cooperation of LIM domain‐binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia (2021)

Genomic defects with large effect size can help elucidate unknown pathologic architecture of mental disorders. We previously reported on a patient with schizophrenia and a balanced translocation between chromosomes 4 and 13 and found that the breakpoint within chromosome 4 is located near the LDB2 gene. We show here that Ldb2 knockout (KO) mice displayed multiple deficits relevant to mental disorders. In particular, Ldb2 KO mice exhibited deficits in the fear-conditioning paradigm. Analysis of the amygdala suggested that dysregulation of synaptic activities controlled by the immediate early gene Arc is involved in the phenotypes. We show that LDB2 forms protein complexes with known transcription factors. Consistently, ChIP-seq analyses indicated that LDB2 binds to > 10,000 genomic sites in human neurospheres. We found that many of those sites, including the promoter region of ARC, are occupied by EGR transcription factors. Our previous study showed an association of the EGR family genes with schizophrenia. Collectively, the findings suggest that dysregulation in the gene expression controlled by the LDB2-EGR axis underlies a pathogenesis of subset of mental disorders.
Antenna Loss and Receiving Efficiency for Mutually Coupled Arrays (2017)

For phased arrays used in satellite communications and radio astronomy, high sensitivity is required, and minimizing antenna losses is critical. Losses for single antennas can be minimized using high conductivity materials. It is less well understood that loss for array antennas is also influenced by mutual coupling between array elements and the beamformer weights applied to the signal from each element. In this paper, we study the antenna loss and receiving efficiency for phased array antennas and focal plane phased array feeds. To better elucidate the physics of array antenna loss related to mutual coupling and beamformer weights, losses for a coupled array can be lumped into an array effective resistance similar to the loss resistance of an equivalent single antenna. Numerical results show that although the antenna loss for a single isolated array element is low, the array antenna loss can be significantly increased by mutual coupling, particularly for beams with a large scan angle.
Research data supporting: The Entangled Triplet Pair State in Acene and Heteroacene Materials (2017)

The data comprise the underpinning data of the main text figures and supplementary figures of a paper accepted for publication in Nature Communications. The paper investigates the role of an entangled triplet pair state in the singlet fission process occurring in organic semiconductors.
Significance of different response evaluation criteria in predicting progression‐free survival of lung cancer with certain imaging characteristics (2016)

RECIST1.1 provides the best assessment of tumor response and prediction of PFS in patients with basic tumor cavitation. mRECIST provides better PFS prognostic information in patients with post-therapeutic cavitation. Short axis criteria provides better PFS prognostic information in patients with changes in the short axis of tumor diameter. Changes in tumor density were not a useful prognostic sign.
RICE: Refining Instance Masks in Cluttered Environments with Graph Neural Networks (2021)

Segmenting unseen object instances in cluttered environments is an important capability that robots need when functioning in unstructured environments. While previous methods have exhibited promising results, they still tend to provide incorrect results in highly cluttered scenes. We postulate that a network architecture that encodes relations between objects at a high-level can be beneficial. Thus, in this work, we propose a novel framework that refines the output of such methods by utilizing a graph-based representation of instance masks. We train deep networks capable of sampling smart perturbations to the segmentations, and a graph neural network, which can encode relations between objects, to evaluate the perturbed segmentations. Our proposed method is orthogonal to previous works and achieves state-of-the-art performance when combined with them. We demonstrate an application that uses uncertainty estimates generated by our method to guide a manipulator, leading to efficient understanding of cluttered scenes. Code, models, and video can be found at https://github.com/chrisdxie/rice .
Wafer scale Ge-on-Si metalens for the mid-infrared (2023)

We report the first demonstration of metalens devices fabricated on an 8-inch Ge-on-Si wafer for the mid-infrared regime. Experimental observations of beam focusing show good match with the design.
Graphics processing unit accelerated one‐dimensional blood flow computation in the human arterial tree (2013)

One-dimensional blood flow models have been used extensively for computing pressure and flow waveforms in the human arterial circulation. We propose an improved numerical implementation based on a graphics processing unit (GPU) for the acceleration of the execution time of one-dimensional model. A novel parallel hybrid CPU-GPU algorithm with compact copy operations (PHCGCC) and a parallel GPU only (PGO) algorithm are developed, which are compared against previously introduced PHCG versions, a single-threaded CPU only algorithm and a multi-threaded CPU only algorithm. Different second-order numerical schemes (Lax-Wendroff and Taylor series) are evaluated for the numerical solution of one-dimensional model, and the computational setups include physiologically motivated non-periodic (Windkessel) and periodic boundary conditions (BC) (structured tree) and elastic and viscoelastic wall laws. Both the PHCGCC and the PGO implementations improved the execution time significantly. The speed-up values over the single-threaded CPU only implementation range from 5.26 to 8.10 × , whereas the speed-up values over the multi-threaded CPU only implementation range from 1.84 to 4.02 × . The PHCGCC algorithm performs best for an elastic wall law with non-periodic BC and for viscoelastic wall laws, whereas the PGO algorithm performs best for an elastic wall law with periodic BC.
Improvements in Reservoir Fracture Network Characterization Using High Resolution Logging While Drilling Resistivity Images In Extended Reach Wells Under High Stick Slip Conditions (2014)

Middle East carbonates frequently are heterogeneous in nature, encompassing variable pore types, strong diagenetic overprints, variable wettability and fracture networks amongst other effects. Resistivity borehole images have long been an integral constituent to understanding their complexity and unlocking volumes. High resolution LWD resistivity images were first introduced in the 1990’s, however as downhole environments became progressively more challenging, resistivity images suffered from the dynamic acquisition environment resulting in severely degraded images. The Al Shaheen field has been developed with Extended Reach Drilling (ERD) wells, and wells of 30,000 feet are commonplace. Early LWD resistivity image data suffered from excessive stick and slip, with approximately half of the wellbore suffering from poor quality image data, degrading with depth. The outer portion of the wellbore is prohibitive to impossible to access via conventional drill pipe conveyed tools, resulting in an absolute requirement for high quality LWD resistivity images. The new methodology redefines the acquisition and processing methodology, resulting in images unaffected by stick slip with a 100% success rate in the most challenging of ERD environments. This paper illustrates the improvements in logging while drilling images (LWD) and subsequent fracture network characterization as a result of implementing a new image acquisition strategy and processing algorithm. The paper explores the close collaboration necessary to drive the innovation to dramatically enhance existing technology, and demonstrates the results with comparisons of the LWD images using the old and new methodologies.
Oxygen supply for oxycoal CO2 capture (2011)

The oxygen requirements for oxycoal combustion in a coal-fired power station are unusual in several respects. The amount of oxygen required is large, for instance a 500 MWe power plant will require around 10,000 tonnes per day of oxygen. The oxygen purity is low and the pressure required is essentially atmospheric pressure. There is no demand for any significant quantity of co-products, such as argon or nitrogen. The parasitic nature of the power means that high efficiency is important but the large scale means that capital cost should also be minimised. These factors open up new possibilities to optimise the process cycle and machinery configuration to minimise the power consumption of the air separation unit without compromising the requirement for low cost. This paper presents the results of a study to develop Air Products’ air separation unit (ASU) offerings for oxycoal CO2 capture projects. A scalable “reference plant” concept is described to match particular sizes of power generation equipment, taking into account factors such as safety, reliability, operating flexibility, efficiency, and of course low capital cost. We describe the selection of a process cycle to exploit the low purity requirements as well as the options for compression machinery and drivers as the scale of the plant increases and the sizes of referenced equipment limit the possibilities. We also explore integration with other elements of the oxycoal system, such as preheating condensate or heating and expanding pressurised nitrogen. Finally, the advantages and disadvantages of different execution strategies for air separation unit projects are discussed, as well as alternative commercial models for the supply of oxygen.
Ultrafast acousto-optic imaging with ultrasonic plane waves (2016)

Due to multiple light scattering inside biological tissues, deep non-invasive optical medical imaging is very challenging. Acousto-optic imaging is a technique coupling ultrasound and light that allows recovering optical contrast at depths of few centimeters with a millimeter resolution. Recent advances in acousto-optic imaging are using short focused ultrasound pulses often averaged over several hundred or thousand pulses. As the pulsing rate of commercial probes is limited to about few ultrasound cycles every 100 μs, acquiring an acousto-optic image usually takes several tens of seconds due to the high number of acoustic pulses excitation. We propose here a new acousto-optic imaging technique based on the use of ultrasound plane waves instead of focused ones that allows increasing drastically the imaging rate.
Efficacy and safety of adalimumab when added to inadequate therapy for the treatment of psoriasis: results of PRIDE, an open‐label, multicentre, phase IIIb study (2011)

Adalimumab was safe, well-tolerated and effective for treatment of active plaque psoriasis in patients who had not adequately responded to prior therapy.
Taxonomy of breast cancer based on normal cell phenotype predicts outcome (2020)

Accurate classification is essential for understanding the pathophysiology of a disease and can inform therapeutic choices. For hematopoietic malignancies, a classification scheme based on the phenotypic similarity between tumor cells and normal cells has been successfully used to define tumor subtypes; however, use of normal cell types as a reference by which to classify solid tumors has not been widely emulated, in part due to more limited understanding of epithelial cell differentiation compared with hematopoiesis. To provide a better definition of the subtypes of epithelial cells comprising the breast epithelium, we performed a systematic analysis of a large set of breast epithelial markers in more than 15,000 normal breast cells, which identified 11 differentiation states for normal luminal cells. We then applied information from this analysis to classify human breast tumors based on normal cell types into 4 major subtypes, HR0–HR3, which were differentiated by vitamin D, androgen, and estrogen hormone receptor (HR) expression. Examination of 3,157 human breast tumors revealed that these HR subtypes were distinct from the current classification scheme, which is based on estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Patient outcomes were best when tumors expressed all 3 hormone receptors (subtype HR3) and worst when they expressed none of the receptors (subtype HR0). Together, these data provide an ontological classification scheme associated with patient survival differences and provides actionable insights for treating breast tumors.
Methyltrioxorhenium as Catalyst for Olefin Metathesis (1991)

No cocatalysts are needed as additives when methyltrioxorhenium (MTO) supported on acidic carriers is employed to catalyze the metathesis of functionalized olefins. A typical system is MTO/Al 2 O 3 −SiO 2 , which is active, for instance, in the metathesis of ally1 halides, allylsilanes, unsaturated carboxylates, and nitriles. MTO in combination with R n AlCl 3‐ n is a homogeneous catalyst in ring‐opening polymerizations (RCH 3 , C 2 H 5 ; n = 1,2).
Recombinant acyl-CoA:cholesterol acyltransferase-1 (ACAT-1) purified to essential homogeneity utilizes cholesterol in mixed micelles or in vesicles in a highly cooperative manner. (1999)

Page 35136, left-hand column:The last three lines should read: “...the specific activity of HisACAT-1 in the final preparation ranges from 2,000 to 4,000 nmol/min/mg, representing approximately 7,000-fold purification in specific activity from the crude cell extracts.”
Photoluminescence properties of selectively grown InN microcrystals (2012)

Abstract We investigated the photoluminescence (PL) properties of regularly arranged N‐polar InN microcrystals with m ‐plane sidewall facets. We observed narrow PL emission at 0.678 eV with a linewidth of ∼14 meV at 4 K and a clear band‐filling effect with increasing excitation power. We also observed a normal red shift of the PL peak energy as large as 51 meV (∼150 nm) with increasing temperature from 4 to 300 K, similar to that observed for non‐degenerated semiconductors. The integrated PL intensity ratio I 300K / I 4K was measured to be 6.1%. These results indicate that InN microcrystals have a low residual carrier density and excellent optical properties without being adversely affected by surface electron accumulation, despite their relatively high surface area. (© 2012 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Enhancement of electron-capture detection of chlorocarbons by iodination (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnhancement of electron-capture detection of chlorocarbons by iodinationAndrew J. Watson, Gwendolyn L. Ball, and Donald H. StedmanCite this: Anal. Chem. 1981, 53, 1, 132–134Publication Date (Print):January 1, 1981Publication History Published online1 May 2002Published inissue 1 January 1981https://doi.org/10.1021/ac00224a037Request reuse permissionsArticle Views36Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (360 KB) Get e-Alertsclose Get e-Alerts
Biological Pathways and In Vivo Anti-Tumor Activity Induced by Atiprimod in Multiple Myeloma (MM). (2006)

Abstract Atiprimod (N-N-diethl-8, 8-dipropyl-2-azaspiro [4.5] decane-2-propanamine) is a novel orally bio-available agent with anti-inflammatory properties. Although its in vitro anti-MM activity have been previously reported, here we have investigated molecular changes induced by Atiprimod as well as its in vivo activity in murine models of MM. Atiprimod inhibits in vitro growth and survival of IL-6 dependent as well as independent MM cell-lines in a time- and dose-dependent manner. Evaluation of changes in gene expression profile following treatment with Atiprimod identified down-regulation of genes involved in adhesion, cell-signalling, cell-cycle and BMP pathways and up-regulation of genes implicated in apoptosis and bone metabolism. The signalling pathway analysis identified the integrin, TGF-beta and FGF signaling as well as Wnt/b-catenin, IGF1 and cell cycle regulation networks as being most modulated by Atiprimod treatment. Next, we evaluated its in vivo activity in three different murine models of MM. A xenograft model bearing subcutaneous MM cells confirmed in vivo the anti-MM activity of Atiprimod and established its dose-response activity; a model based on engraftment of human fetal bone chip implanted in SCID mice (SCID-hu) with INA-6 cells, confirmed its ability to overcome the protective effects of the bone marrow milieu on MM cell growth, survival and drug resistance; and a SCID-hu model engrafted with primary patient MM cells confirmed its activity in the context of primary human disease recapitulating the clinical condition. Finally, we observed reduced number of osteoclasts, following Atiprimod treatment, compared to control bone samples confirming its beneficial effects on bone remodelling. Taken together, these data demonstrate the in vitro and in vivo anti-tumor activity of Atiprimod and delineate potential molecular targets triggered by this agent, providing a preclinical rational for its clinical evaluation in MM.
The skin microbiome of caspase‐14‐deficient mice shows mild dysbiosis (2014)

Caspase-14, an important proteinase involved in filaggrin catabolism, is mainly active in terminally differentiating keratinocytes, where it is required for the generation of skin natural moisturizing factors (NMFs). Consequently, caspase-14 deficient epidermis is characterized by reduced levels of NMFs such as urocanic acid and 2-pyrrolidone-5-carboxylic acid. Patients suffering from filaggrin deficiency are prone to develop atopic dermatitis, which is accompanied with increased microbial burden. Among several reasons, this effect could be due to a decrease in filaggrin breakdown products. In this study, we found that caspase-14(-/-) mice show enhanced antibacterial response compared to wild-type mice when challenged with bacteria. Therefore, we compared the microbial communities between wild-type and caspase-14(-/-) mice by sequencing of bacterial 16S ribosomal RNA genes. We observed that caspase-14 ablation leads to an increase in bacterial richness and diversity during steady-state conditions. Although both wild-type and caspase-14(-/-) skin were dominated by the Firmicutes phylum, the Staphylococcaceae family was reduced in caspase-14(-/-) mice. Altogether, our data demonstrated that caspase-14 deficiency causes the imbalance of the skin-resident bacterial communities.
Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis (2022)

Patients with non-small cell lung cancer (NSCLC) who have distant metastases have a poor prognosis. To determine which genomic factors of the primary tumor are associated with metastasis, we analyzed data from 759 patients originally diagnosed with stage I-III NSCLC as part of the AACR Project GENIE Biopharma Collaborative consortium. We found that TP53 mutations were significantly associated with the development of new distant metastases. TP53 mutations were also more prevalent in patients with a history of smoking, suggesting that these patients may be at increased risk for distant metastasis. Our results suggest that additional investigation of the optimal management of patients with early-stage NSCLC harboring TP53 mutations at diagnosis is warranted in light of their higher likelihood of developing new distant metastases.
Measurement of rotational property for a baseball in flight with acceleration sensors (2019)

We attempt to measure the rotational characteristics of a ball in flight by using a baseball-like ball with a built-in acceleration sensor unit which consists of one three-axis sensor for low G and three sensors for High G. Two approaches for obtaining the rotational speed and its axis of the ball from outputs of the sensors are formulated; one is based on rotational component in the acceleration outputs and the other is based on translational one. We employ in the present approaches the assumption that the time variation of rotation axis can be neglected because it is sufficiently slow. In flight experiments, we obtain nine time series data of acceleration for straight and curve ball trajectories, respectively. By using these experimental data, we estimate the rotational speed and rotation axis with the present two algorithms. As the results, it is shown that the rotation axis keeps almost constant during the flight in each algorithm’s result and this means the validity of our assumption on rotation axis. The difference in the rotation axis obtained by the two algorithms ranges from 3.5 to 10.6 degrees in the straight ball data while it does from 3.9 to 18.8 degrees in the data of curve ball. Also, the averaged rotational speed in the nine trials is 12.56 rps in the straight data, and the difference between the algorithms indicates 0.10 rps (after pitching) and 0.17 rps (before catching). In the curve ball data, the averaged value and the difference between the algorithms are 19.22 rps, 0.10 rps (after pitching) and 0.14 rps (before catching), respectively. The present result shows the decrease of the rotational speed along flight trajectories, and it is probably the effect of aerodynamic torque.
Colocalization of the p185HER2 oncoprotein and integrin α6β4 in Calu‐3 lung carcinoma cells (1994)

Anti-p185HER2 monoclonal antibodies often show intense reactivity with the basement membrane of tumor cells that overexpress the HER2/neu gene product (p185HER2). To evaluate a possible interaction between p185HER2 and adhesion molecules or their receptors, the polarity of p185HER2 was tested in lung carcinoma cell line Calu-3, which overexpresses this protein, in cultures grown as confluent monolayers or as aggregates. MAb immunostaining patterns indicated that p185HER2 is concentrated on the baso-lateral membrane of cells and that it colocalizes with the integrin alpha 6 beta 4 at the cell-cell junctions where laminin is also found. The same membrane region showed intense reactivity with antiphosphotyrosine antibodies. Furthermore, integrin clustering induced by the specific antibody was accompanied by the clustering of p185HER2, as indicated by immunoelectron microscopy, and by a subsequent increase in p185HER2 tyrosine phosphorylation. Treatment with exogenous laminin also resulted in increased basal levels of p185HER2 phosphorylation. These data suggest a physical interaction between the integrin and the oncoprotein that might be functionally relevant in directly controlling the tyrosine phosphorylation of the catalytic domain of p185HER2.