gebhart/patrepeval huggingface dataset:
Overexpression of a dominant-negative signal transducer and activator of transcription 3 variant in tumor cells leads to production of soluble factors that induce apoptosis and cell cycle arrest. (2001)

Gene therapy of B16 tumors with a dominant-negative signal transducer and activator of transcription (Stat3) variant, designated Stat3beta, results in inhibition of tumor growth and tumor regression. Although only 10-15% of the tumor cells are transfected in vivo, the Stat3beta-induced antitumor effect is associated with massive apoptosis of B16 tumor cells, indicative of a potent bystander effect. Here, we provide evidence that blocking Stat3 signaling in B16 cells results in release of soluble factors that are capable of inducing apoptosis and cell cycle arrest of nontransfected B16 cells. RNase protection assays using multi-template probes specific for key physiological regulators of apoptosis reveal that overexpression of Stat3beta in B16 tumor cells induces the expression of the apoptotic effector, tumor necrosis factor-related apoptosis-inducing ligand. These in vitro results suggest that the observed in vivo bystander effect leading to tumor cell growth inhibition is mediated, at least in part, by soluble factors produced as a result of overexpression of Stat3beta in tumor cells.
ViBERTgrid: A Jointly Trained Multi-Modal 2D Document Representation for Key Information Extraction from Documents (2021)

Recent grid-based document representations like BERTgrid allow the simultaneous encoding of the textual and layout information of a document in a 2D feature map so that state-of-the-art image segmentation and/or object detection models can be straightforwardly leveraged to extract key information from documents. However, such methods have not achieved comparable performance to state-of-the-art sequence- and graph-based methods such as LayoutLM and PICK yet. In this paper, we propose a new multi-modal backbone network by concatenating a BERTgrid to an intermediate layer of a CNN model, where the input of CNN is a document image and the BERTgrid is a grid of word embeddings, to generate a more powerful grid-based document representation, named ViBERTgrid. Unlike BERTgrid, the parameters of BERT and CNN in our multimodal backbone network are trained jointly. Our experimental results demonstrate that this joint training strategy improves significantly the representation ability of ViBERTgrid. Consequently, our ViBERTgrid-based key information extraction approach has achieved state-of-the-art performance on real-world datasets.
Exploring Ugi-Azide Four-Component Reaction Products for Broad-Spectrum Influenza Antivirals with a High Genetic Barrier to Drug Resistance (2018)

Influenza viruses are respiratory pathogens that are responsible for seasonal influenza and sporadic influenza pandemic. The therapeutic efficacy of current influenza vaccines and small molecule antiviral drugs is limited due to the emergence of multidrug-resistant influenza viruses. In response to the urgent need for the next generation of influenza antivirals, we utilized a fast-track drug discovery platform by exploring multi-component reaction products for antiviral drug candidates. Specifically, molecular docking was applied to screen a small molecule library derived from the Ugi-azide four-component reaction methodology for inhibitors that target the influenza polymerase PA<sub>C</sub>-PB1<sub>N</sub> interactions. One hit compound 5 was confirmed to inhibit PA<sub>C</sub>-PB1<sub>N</sub> interactions in an ELISA assay and had potent antiviral activity in an antiviral plaque assay. Subsequent structure-activity relationship studies led to the discovery of compound 12a, which had broad-spectrum antiviral activity and a higher in vitro genetic barrier to drug resistance than oseltamivir. Overall, the discovery of compound 12a as a broad-spectrum influenza antiviral with a high in vitro genetic barrier to drug resistance is significant, as it offers a second line of defense to combat the next influenza epidemics and pandemics if vaccines and oseltamivir fail to confine the disease outbreak.
94 NUCLEAR-CYTOPLASMIC INTERACTION AND DEVELOPMENT OF CLONED EMBRYOS (2008)

Although cloned canine offspring have been produced, the efficiency of nuclear transfer (NT) is still far from expectations. The most important factor interfering with the success of NT is the shortage of canine matured oocytes. In the present study, the nuclear-cytoplasmic interaction and in vitro development of porcine oocytes cloned with canine fetal fibroblasts (cFF) and canine mesenchymal stem cells (cMSC) were assessed by examining the developmental rate, embryonic morphology, total cell number, canine genome expression, and in vivo development following the transfer of iNT embryos into the oviducts of surrogate mother. Isolated cMSC from bone marrow were characterized by early transcription factors (Oct3/4, Sox2, and Nanog) and by differentiation into adipogenic, osteogenic, and neuronal cells under controlled in vitro conditions. Porcine cumulus–oocyte complexes (COC) were matured in vitro as described by Kim YS et al. (2005 Mol. Reprod. Dev. 70, 308–313). Porcine NT embryos were used for the control group. Canine MSC showed their characteristic property of attaching to plastic culture flasks and forming a monolayer of spindle-shaped cells. Adherent cells showed moderate expression of Oct3/4, Sox2, and Nanog protein by immunostaining. Following osteogenic cell induction, cMSC transformed into mineralized nodules by von Kossa staining. Oil red O staining revealed that MSC produced lipid droplets after incubation in adipogenic media. Neuronal-like cells with multipolar, round cell bodies organized into a network-like structure were confirmed by immunostaining of neuronal markers (NFM). The tissue-specific mRNA levels were confirmed after differentiation by RT-PCR (osteogenic cell, Osteocalcin; adipogenic cell, PPAR ?; neuronal cell, NFM). The control group blastocysts (porcine oocytes-pMSC) exhibited significantly (P &amp;lt; 0.05) greater development and total cell numbers of than blastocysts of interspecies groups (porcine oocytes-cFF and cMSC). The canine genome GAPDH was detected in cFF, cMSC, and interspecies NT embryos using PCR, whereas there was no detection in porcine oocytes and the negative control. Most of the embryos arrested at the 8- to 16-cell stage and only 5% of embryos developed to blastocyst stage. The interspecies-NT embryos (average 35 embryos/recipient dog) were surgically transferred into the oviducts of 3 recipient dogs. Two of them showed exterior signs of implantation; i.e. a slight thickening of the uterus and small pea-sized lumps. No pregnancies were detected in the recipients after ovariohysterectomy surgery. These results demonstrate the potential of cMSC isolated from bone marrow to differentiate into mesoderm (osteogenic and adipogenic cell) and ectoderm (neuronal cell)-like cells under specific induction conditions. Although interspecies NT embryos could not implant in the canine uterine wall, the results provided valuable information on canine MSC and interspecies NT. This work was supported by Grant No. 20070301034040 from Bio-Organ, Republic of Korea.
Supplementary Figure S4 from The Pharmacokinetic–Pharmacodynamic (PKPD) Relationships of AZD3229, a Novel and Selective Inhibitor of KIT, in a Range of Mouse Xenograft Models of GIST (2023)

&lt;p&gt;PKPD efficacy data of KIT probe compound (AZ12607208)&lt;/p&gt;
Low-Temperature Retinal Photoisomerization Dynamics in Bacteriorhodopsin (1998)

Retinal photoisomerization dynamics are studied at both room temperature and 20 K in wild-type bacteriorhodopsin using femtosecond pulses. We were able to resolve the decay at 20 K into two components with the dominant component having a similar lifetime to that observed at room temperature. This strongly suggests that the retinal lifetime at physiological temperature is barrierless. The minor, low-temperature long-lived component is discussed in terms of previous results obtained for fluorescence and transient absorption with lower time resolution, and the origin of this component is discussed in terms of low-temperature glass heterogeneity.
High-Performance Liquid Chromatography-Mass Spectrometry (1984)

Techniques for on-line coupling of high-performance liquid chromatography with mass spectrometry are reviewed with particular emphasis on those suitable for application to nonvolatile samples. The present status of various techniques is summarized and the strengths and weaknesses of the various approaches are assessed. The potential for future application of recently developed techniques for combined liquid chromatography and mass spectrometry is discussed.
Low CAIX expression and absence of VHL gene mutation are associated with tumor aggressiveness and poor survival of clear cell renal cell carcinoma (2008)

We attempted to describe, in a series of clear cell renal cell carcinoma (RCC), the relationship between CAIX expression, VHL gene mutations, tumor characteristics and outcome. Radical nephrectomy was performed in 100 patients. Genomic DNA was extracted from frozen tumor samples. Four amplimers covering the whole coding sequence of the VHL gene were synthesized by PCR and sequenced. The monoclonal antibody M75 was used to evaluate CAIX protein expression immunohistochemically. VHL mutations were identified in 58 patients (58%) and high CAIX expression (>85%) was observed in 78 (78%). Tumors with VHL mutation showed higher CAIX expression than those without (p = 0.02). Low CAIX expression and absence of VHL mutation were associated with a more advanced tumors e.g., higher T stages and presence of metastases. VHL mutation and high CAIX expression predicted longer progression-free survival (p = 0.037) and disease-specific survival (p = 0.001), respectively. In combination, they defined three prognostic groups (p = 0.002): (i) good prognosis, defined as VHL mutation and high CAIX (2-year survival: 86%), (ii) intermediate prognosis with either VHL mutation or high CAIX (69%), and (iii) poor prognosis with no VHL mutation and low CAIX (45%, median survival 18 months). CAIX expression, but not VHL mutational status, was an independent prognostic factor in multivariate analysis. Taken together, CAIX expression and VHL mutational status are able to stratify patients with clear cell RCC into distinct groups with regards to clinicopathological variables and prognosis, with low CAIX expression and absence of VHL mutation being associated with a poor clinicopathological phenotype and diminished survival.
A virtual frame rate control algorithm for efflcient MPEG-2 video encoding (2003)

This paper presents a virtual frame rate control algorithm and a bit allocation algorithm at frame level for efficient MPEG-2 video encoding. The proposed frame rate control scheme is composed of three steps. At the first step, the scan format of an input video sequence is converted into a progressive scan format before video encoding. At the second step, an average motion activity of the frames within a previous temporal window of a pre-defined size is examined, and a proper frame rate of a current temporal window is adaptively determined based on the computed average motion activity. At the final step, the frames located at particular positions in a current temporal window are virtually skipped according to the determined frame rate. We can skip the selected frames by deliberately fixing the coding types of all the macroblocks in those frames to 'skipped MB.' We also propose a modified version of MPEG-2 TM5 bit allocation algorithm suitable for virtual frame rate control. Experimental results show that the proposed algorithm noticeably improves the coding efficiency in comparison with conventional MPEG-2 video encoding.
Addendum: Test of lepton universality in beauty-quark decays (2023)

Addendum to: Nature Physics https://doi.org/10.1038/s41567-021-01478-8.
Application of Genetic Algorithm to Prediction of Artery Geometry (2007)

We used the genetic algorithm (GA) and two-dimensional blood flow analysis to examine the fluid dynamic and engineering factors in multi-objective optimization of blood tubes (vessels). We supposed two factors from fluid dynamics: the wall shear stress (WSS) and the pressure loss, and one materials saving factor: the artery length. As a result, we could get the optimum shapes for each factor. In the case of WSS and artery length, both smoothly curved artery shapes and shapes with bulges were obtained as lower WSS cases. The shapes with bulges were similar to those of aneurysms. In this case, it was found that the WSS increases after the bulge is removed. This means bulges in artery vessel areas with higher WSSs effectively reduce the WSS value. Only the case of WSS and artery length produced a shape like an aneurysm. These results indicate that WSS and artery length are significant factors in determining artery shape.
The Lms, Pnlms, And Exponentiated Gradient Algorithms (2004)

Publication in the conference proceedings of EUSIPCO, Viena, Austria, 2004
Association between stromal/TGF-β/EMT gene expression signature and response to pembrolizumab monotherapy in cisplatin-ineligible patients with locally advanced (unresectable) or metastatic urothelial carcinoma. (2019)

433 Background: PD-L1 immunohistochemistry and an 18-gene T cell–inflamed gene expression profile (GEP) are associated with response to anti–PD-1/PD-L1 therapy across tumor types, including urothelial carcinoma. A gene expression signature representing convergent biology related to stromal/EMT/TGF-β pathways was developed and prespecified for testing for association with pembrolizumab response in urothelial carcinoma patients treated on the KEYNOTE-052 trial (NCT02335424). Methods: KEYNOTE-052 was a single-arm phase 2 trial of pembrolizumab in cisplatin-ineligible patients with previously untreated, advanced urothelial carcinoma. Primary objective of this analysis was to assess the association between the Stromal/EMT/TGF-β signature and outcomes (best overall response [BOR], PFS, OS) as an independent biomarker and to understand its potential prognostic/predictive role beyond the T cell–inflamed GEP score or PD-L1 assessed using combined positive score (CPS). Cox regression models for PFS and OS and a logistic regression model for BOR evaluated associations between Stromal/EMT/TGF-β signature and outcomes adjusting for ECOG performance status (PS) and level of the GEP or CPS (1-sided P value). Results: RNA-Seq data from baseline tumor specimens were available for 187/370 patients on KEYNOTE-052. Lower Stromal/EMT/TGF-β score was associated with favorable BOR rate ( P &lt; 0.001), PFS ( P &lt; 0.001), and OS ( P = 0.002) after adjustment for ECOG PS and GEP (which remained significant at the 0.05 level in all cases). The patterns indicated a very consistent downward trend in the distribution of the Stromal/EMT/TGF-β score for responders versus nonresponders, regardless of GEP. In models that adjusted for both ECOG PS and PD-L1 CPS, the Stromal/EMT/TGF-β score remained significant (BOR rate, P = 0.002; PFS, P = 0.013; OS, P = 0.029). Conclusions: Higher Stromal/EMT/TGF-β signature was associated with resistance to pembrolizumab independently of GEP or PD-L1 in urothelial carcinoma patients on the KEYNOTE-052 trial. Clinical trial information: NCT02335424.
Upstream regulatory elements necessary for expression of the rat COL1A1 promoter in transgenic mice (1994)

The activity of fusion genes containing fragments of the COL1A1 promoter was measured in tissues from 6- to 8-day-old transgenic mice. ColCAT3.6 contains approximately 3.6 kb (-3521 to 115 bp) of the rat COL1A1 gene, the chloramphenicol acetyltransferase (CAT) reporter gene, and the SV40 splice and polyadenylation sequences. ColCAT2.3 and ColCAT1.7 are deletion constructs that contain 2296 and 1667 bp of COL1A1 upstream from the RNA start site, respectively. For each transgene, up to six lines of mice were characterized. Both ColCAT3.6 and ColCAT2.3 had similar activity in bone and tooth; ColCAT1.7 was inactive. In transgenic calvariae, levels of transgene mRNA paralleled levels of CAT activity. In tendon, the activity of ColCAT2.3 was 3- to 4-fold lower than that of ColCAT3.6, and the activity ColCAT1.7 was 16-fold lower than that of ColCAT2.3. There was little activity of the ColCAT constructs in liver and brain. These data show that DNA sequences between -2.3 and -1.7 kb are required for COL1A1 promoter expression in bone and tooth; sequences that control expression in tendon are distributed between -3.5 and -1.7 kb of the promoter, with sequences downstream of -1.7 kb still capable of directing expression to this tissue. The cis elements that govern basal expression of COL1A1 in transgenic calvariae appear to be different from those required for optimal expression of the COL1A1 promoter in stably transfected osteoblastic cells.
Stereoselective Inhibitors Based on Nonpolar Hydrocarbons for Polar Organic Crystals (2016)

Nonpolar aliphatic hydrocarbons are usually regarded as solely antisolvents in solution crystallization processes of polar organic crystals, because of their very weak interactions with the surfaces of polar crystals compared to polar solvent interactions. Here we show that such weak interfacial interactions induced by nonpolar aliphatic hydrocarbons can be additionally used for controlling the morphology of polar organic π-conjugated crystals. Various hydrocarbons, such as n-hexane, n-octane, and n-decane, act as stereoselective inhibitors for highly polar 2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene)malononitrile (OH1) crystals having large nonlinear optical and fluorescent activities. In the presence of hydrocarbons, a significant morphologic change of OH1 crystals is observed; OH1 crystals grown in conventional polar solvents exhibit a diamond-shaped plate morphology, while in the presence of nonpolar hydrocarbons, a belt-shaped morphology with an extremely large aspect ratio is obtained. The origin of the unusual stereoselective interfacial interactions on specific surfaces of OH1 crystals inducing the morphological change is investigated with molecular dynamics simulations. The theoretically predicted morphology is well-matched with the experimental morphology.
The Development of a Resource Recycling-oriented System in the Hachinohe Area (2009)

八戸地域の資源循環型システムにおいて大手素材産業5社によるエコタウン事業，およびそれと関係する事業や業種でのリサイクル事業の展開により，ゼロエミッションが顕著に進行している。とりわけ，八戸セメント(株)の役割が大きいが，大平洋金属(株)などの役目も大きな比重を占める。また，本業がゼロエミッションに密接な係りをもつ東北東京鉄鋼(株)や八戸鉄錬(株)の活動も特徴的である。これらの2事業所では本業が生産―販売―回収―再生利用のリサイクルを実現している。他方，農業においてもリサイクルが進展しており，長イモの残渣，鶏糞，豚糞が肥料として再生利用されている。そして，農業では，こうしたリサイクルに八戸広域農協 (現 八戸農協) や組合が大きな役割を担っている。ただし，八戸地域の資源循環型システムにおいても大量に発生するスラグや汚泥の処理の問題が存在し，その一つの方途として，東北東京鉄鋼(株)ではスラグの削減を，八戸製錬ではスラグの用途拡大に取り組んでいる。
Novel Pressure-Temperature BH Gauge for Hydraulic Fracturing Characterization… The key to Enhance Well Production in Complex Tight Reservoirs. Case Studies in Mexico (2015)

Abstract Propped hydraulic fractures are key to producing tight reservoirs, and knowledge of fracture geometry is fundamental for a proper field development plan. To this end, hydraulic fracture propagation characterization in tight gas reservoirs, pioneered by Amoco during the 1980s, is obtained by combining a dynamic closure test, fracture height determination, and pumping net pressure behavior. The result provides an estimated propped fracture geometry that can then be compared with pressure or rate transient analysis to validate the effective propped geometry. Although surface pressure is generally sufficient to establish bottomhole (BH) pressure decline behavior by correcting for a constant hydrostatic pressure, the inherent uncertainty of friction pressure of crosslinked gel in the tubular does not establish the correct pumping net pressure trend. BH sensor pressure recordings are operationally simple and inexpensive when a fracturing string is required and recovered after the operation (frac-pack operation, well with mechanical pump), but that is not the case with casing fracturing. To remediate this, a high-speed, high-accuracy, and miniaturized BH pressure and temperature sensor, based on microelectromechanical systems (MEMS), was developed under a project funded by the Mexican Secretary of Energy and combined with an economical and practical way to deploy a BH sensor hung from a slickline or wireline cable thereby enabling pressure recording during the entire operation including, the main proppant fracturing (patent pending). This paper presents the results and analysis of two case studies in Mexico where BH pressure and temperature were recorded with this novel sensor. Both jobs were conducted in vertical wells in tight sandstones. In the first field-test job, a post-fracture wellbore propped height determination using dipole sonic logs and radioactive tracer were used. In addition, the entire operation was monitored with microseismic monitoring. The results of these three measurements enabled validating the fracturing model for an increased confidence for field development. In the second field-test job, the BH gauges enabled visualization of the different events that occurred when proppant of different mesh sizes was used during the treatment, containing the fracture eliminating premature screenouts. Only direct measurement of the fracture behavior net pressure and its associated dimension allow the proper calibration of fracturing models required to correctly predict and optimize propped fracture and thus reduce the cost of hydrocarbons produced. This information is property of PEMEX; partial or total use is strictly prohibited without authorization.
Sub-nW Wake-Up Receivers With Gate-Biased Self-Mixers and Time-Encoded Signal Processing (2019)

A fully integrated wake-up receiver in 65-nm low-power (LP) CMOS technology is presented. The receiver's RF front end consists of a 40-stage MOS self-mixer using gate biasing to optimize the sensitivity; the baseband circuits use time-encoded analog signals to efficiently implement a matched filter with a DC offset cancellation loop at minimal power consumption. When operating at 434 MHz, the receiver has a -79.1-dBm sensitivity with a 110-ms latency while consuming 420 pW from 0.4 V. When operating at 1.016 GHz with the same latency, the sensitivity is -74 dBm and power consumption is 470 pW.
Improving AoI via Learning-based Distributed MAC in Wireless Networks (2022)

In this work, we consider a remote monitoring scenario in which multiple sensors share a wireless channel to deliver their status updates to a process monitor via an access point (AP). Moreover, we consider that the sensors randomly arrive and depart from the network as they become active and inactive. The goal of the sensors is to devise a medium access strategy to collectively minimize the long-term mean network Age of Information (AoI) of their respective processes at the remote monitor. For this purpose, we propose specific modifications to ALOHA-QT algorithm, a distributed medium access algorithm that employs a Policy Tree (PT) and Reinforcement Learning (RL) to achieve high throughput. We provide the upper bound on the mean network AoI for the proposed algorithm along with pointers for selecting its key parameter. The results reveal that the proposed algorithm reduces mean network AoI by more than 50 percent for state of the art stationary randomized policies while successfully adjusting to a changing number of active users in the network. The algorithm needs less memory and computation than ALOHA-QT while performing better in terms of AoI.