gebhart/patrepeval huggingface dataset:
Regulation of the ESC transcriptome by nuclear long noncoding RNAs (2015)

Long noncoding (lnc)RNAs have recently emerged as key regulators of gene expression. Here, we performed high-depth poly(A)(+) RNA sequencing across multiple clonal populations of mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs) to comprehensively identify differentially regulated lncRNAs. We establish a biologically robust profile of lncRNA expression in these two cell types and further confirm that the majority of these lncRNAs are enriched in the nucleus. Applying weighted gene coexpression network analysis, we define a group of lncRNAs that are tightly associated with the pluripotent state of ESCs. Among these, we show that acute depletion of Platr14 using antisense oligonucleotides impacts the differentiation- and development-associated gene expression program of ESCs. Furthermore, we demonstrate that Firre, a lncRNA highly enriched in the nucleoplasm and previously reported to mediate chromosomal contacts in ESCs, controls a network of genes related to RNA processing. Together, we provide a comprehensive, up-to-date, and high resolution compilation of lncRNA expression in ESCs and NPCs and show that nuclear lncRNAs are tightly integrated into the regulation of ESC gene expression.
Therapeutic Effects of Bruton’s Tyrosine Kinase Inhibitor HM71224 as Monotherapy and in Combination with Methotrexate on Collagen-Induced Arthritis in Rats (2020)

<title>Abstract</title> <bold>Background:</bold> The purpose of this study was to determine the potential effects of HM71224, a Bruton’s tyrosine kinase (BTK) inhibitor, as a monotherapy and in combination with methotrexate (MTX) in rats with collagen-induced arthritis (CIA) and to evaluate the effects of drug-drug interactions in combination therapy.<bold>Methods: </bold>The therapeutic effect of HM71224 and the combination effects with MTX were evaluated in CIA rats. Arthritis was induced through immunization by type II collagen in Lewis rats. The therapeutic effects were evaluated by arthritis score, paw volume, body weight changes, and histopathological examination. The effective dose levels (ED) were determined from arthritis score. Bone erosion, synovial inflammation, and cartilage degradation were assessed by staining with hematoxylin and eosin (H&amp;E) and safranin-O in ankle joints. The drug-drug interaction between HM71224 and MTX was investigated by the comparison of plasma levels and monitoring of liver enzymes, creatinine and blood cell counts in CIA rats. <bold>Results:</bold> HM71224 dose dependently ameliorated the clinical signs, paw volume and body weight loss on the development of arthritis in CIA rats, and ED<sub>50</sub> and ED<sub>90</sub> values were 1.0 and 2.5 mg/kg, respectively. The combination of HM71224 with MTX decreased the arthritis score, bone erosion, synovitis and cartilage degradation compared with HM71224 and MTX alone; however, no drug-drug interactions in the plasma and no abnormalities in the liver enzymes, creatinine or blood cell counts were observed. <bold>Conclusion:</bold> BTK inhibition by HM71224 prevented the development of arthritis and the combination therapy with MTX produced additive therapeutic effects with no drug-drug interactions in CIA rats. Therefore, we suggest that HM71224 may be useful as a monotherapy and in combination with MTX for the treatment of patients with rheumatoid arthritis.
Real‐world experience with leadless cardiac pacing (2019)

There are no significant differences in procedural complications among patients receiving LCP versus TVP. The Micra group had lower rates of device-related revision/extraction compared to the TVP group. Patients with leadless pacemaker were less likely to develop endocarditis or worsening TR.
Statistical Analysis of Second Order Differential Power Analysis (2009)

Second order Differential Power Analysis (2O-DPA) is a powerful side-channel attack that allows an attacker to bypass the widely used masking countermeasure. To thwart 2O-DPA, higher order masking may be employed but it implies a nonnegligible overhead. In this context, there is a need to know how efficient a 2O-DPA can be, in order to evaluate the resistance of an implementation that uses first order masking and, possibly, some hardware countermeasures. Different methods of mounting a practical 2O-DPA attack have been proposed in the literature. However, it is not yet clear which of these methods is the most efficient. In this paper, we give a formal description of the higher order DPA that are mounted against software implementations. We then introduce a framework in which the attack efficiencies may be compared. The attacks we focus on involve the combining of several leakage signals and the computation of correlation coefficients to discriminate the wrong key hypotheses. In the second part of this paper, we pay particular attention to 2O-DPA that involves the product combining or the absolute difference combining. We study them under the assumption that the device leaks the Hamming weight of the processed data together with an independent Gaussian noise. After showing a way to improve the product combining, we argue that in this model, the product combining is more efficient not only than absolute difference combining, but also than all the other combining techniques proposed in the literature.
Who have got answers? (2014)

On top of an enterprise social platform, we are building a smart social QA system that automatically routes questions to suitable employees who are willing, able, and ready to provide answers. Due to a lack of social QA history (training data) to start with, in this paper, we present an optimization-based approach that recommends both top-matched active (seed) and inactive (prospect) answerers for a given question. Our approach includes three parts. First, it uses a predictive model to find top-ranked seed answerers by their fitness, including their ability and willingness, to answer a question. Second, it uses distance metric learning to discover prospects most similar to the seeds identified in the first step. Third, it uses a constraint-based approach to balance the selection of both seeds and prospects identified in the first two steps. As a result, not only does our solution route questions to top-matched active users, but it also engages inactive users to grow the pool of answerers. Our real-world experiments that routed 114 questions to 684 people identified from 400,000+ employees included 641 prospects (93.7%) and achieved about 70% answering rate with 83% of answers received a lot/full confidence.
Selective activation of tumor growth-promoting Ca2+ channel MS4A12 in colon cancer by caudal type homeobox transcription factor CDX2 (2009)

Colon cancer-associated MS4A12 is a novel colon-specific component of store-operated Ca2+ (SOC) entry sensitizing cells for epidermal growth factor (EGF)-mediated effects on proliferation and chemotaxis. In the present study, we investigated regulation of the MS4A12 promoter to understand the mechanisms responsible for strict transcriptional restriction of this gene to the colonic epithelial cell lineage. DNA-binding assays and luciferase reporter assays showed that MS4A12 promoter activity is governed by a single CDX homeobox transcription factor binding element. RNA interference (RNAi)-mediated silencing of intestine-specific transcription factors CDX1 and CDX2 and chromatin immunoprecipitation (ChIP) in LoVo and SW48 colon cancer cells revealed that MS4A12 transcript and protein expression is essentially dependent on the presence of endogenous CDX2. In summary, our findings provide a rationale for colon-specific expression of MS4A12. Moreover, this is the first report establishing CDX2 as transactivator of tumor growth-promoting gene expression in colon cancer, adding to untangle the complex and conflicting biological functions of CDX2 in colon cancer and supporting MS4A12 as important factor for normal colonic development as well as for the biology and treatment of colon cancer.
Candidate biomarkers of PARP inhibitor sensitivity in ovarian cancer beyond the BRCA genes (2018)

Ovarian cancer patients with tumours harbouring loss-of-function mutations in HRR genes other than BRCA1/2 may constitute a small, molecularly identifiable and clinically relevant population who derive treatment benefit from olaparib similar to patients with BRCAm.
Characteristics and Ionization Coefficient Extraction of 1kV 4H-SiC Implanted Anode PiN Rectifiers with Near Ideal Performance Fabricated Using AlN Capped Annealing (2006)

4H-SiC PiN rectifiers with implanted anode and single-zone JTE were fabricated using AlN capped anneal. The surface damage during the high temperature activation anneal is significantly reduced by using AlN capped anneal. The forward drop of the PiN rectifiers at 100A/cm2 is 3.0V while the leakage current is less than 10-7A/cm2 up to 90% breakdown voltage at room temperature. With 6μm thick and 2×1016cm-3 doped drift layer, the PiN rectifiers can achieve near ideal breakdown voltage up to 1050V. Hole impact ionization rate was extracted and compared with previously reported results.
Enantioselective Allylation of Alkenyl Boronates Promotes a 1,2-Metalate Rearrangement with 1,3-Diastereocontrol (2021)

Alkenyl boronates add to Ir(π-allyl) intermediates with high enantioselectivity. A 1,2-metalate shift forms a second C-C bond and sets a 1,3-stereochemical relationship. The three-component coupling provides tertiary boronic esters that can undergo multiple additional functionalizations. An extension to trisubstituted olefins sets three contiguous stereocenters.
Bacillus anthracis SlaQ Promotes S-Layer Protein Assembly (2015)

S-layer proteins are endowed with the propensity for self-assembly into crystalline arrays. Factors promoting S-layer protein assembly have heretofore not been reported. We identified Bacillus anthracis SlaQ, a small cytoplasmic protein that facilitates S-layer protein assembly in vivo and in vitro.
CRISIS detector: The gas system (1983)

A low-pressure, high-flow, recirculating gas system has been designed and constructed for use on a large volume (250 ft3) ionization sampling drift chamber (CRISIS), which operates at an absolute pressure of less than 1 in. of water relative to atmospheric pressure. The system was also designed to control and monitor the detector gas mixture and to reduce the oxygen level in the detector below 4 ppm. In operation the system demonstrated very stable long and short term stability and also demonstrated the gas cost savings inherent in recirculating systems.
ChemInform Abstract: Preparation and Antibacterial Activity of Pyridopyridone Analogues: C‐ 1 Modifications. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Comparison of experimental results and calculated detector responses for PBFA II thermal source experiments (1992)

We performed experiments using proton beams to heat foam-filled cylinders on the Particle Beam Fusion Acceleration II. Preliminary analysis of these diagnostic results provides reasonable agreement between prediction and experiment. The diagnostic package allowed us to benchmark target response as well as diagnose driver performance. Soft x-ray images, both time and space resolved, and the results of broadband spectral measurements on bolometers and x-ray diodes provide qualitative agreement with LASNEX predictions of target features such as Au motion and soft x-ray emission profile. The analysis is consistent with a total beam deposition of 40–50 kJ and power depositions of approximately 180 TW/g. Estimates of target motion confirm the ability of the foam to retard wall motion.
The apelin receptor inhibits the angiotensin II type 1 receptor via allosteric trans‐inhibition (2012)

This article is commented on by Goupil et al., pp. 1101-1103 of this issue. To view this commentary visit http://dx.doi.org/10.1111/bph.12040.
Quantification of Campylobacter carriage in pigs using a real-time PCR assay (2007)

Campylobacter species are the major agent of bacterial gastroenteritis. C. jejuni and C. coli together are responsible for more than 95% of all cases of Campylobacter induced diarrheal d1sease 1n developped countries R1sk analysis shows consumption of foods of animal origin to be a maJor source of human 1nfect1on Pigs are known to be frequently infected with Campylobacter and to exh1bit h1gh counts of th1s pathogen in their faeces.
Two Years on Linaclotide: Tolerability and Treatment Satisfaction in IBS-C Patients With and Without Diarrhea: Presidential Poster (2014)

Introduction: Linaclotide has been shown to improve abdominal pain and stool frequency and was well tolerated in phase 3 clinical trials of IBS-C patients. Here we evaluate the most common LIN adverse event (AE), diarrhea, and assess tolerability and treatment satisfaction (Tx Sat) in IBS-C patients (pts) who rolled over (RO) from a phase 3 trial into a long-term study (LTS) of LIN. Methods: Patients meeting modified Rome II IBS-C criteria were randomized to oral 290 μg LIN or placebo (PBO) qd in a 6-month phase 3 trial. RO pts completed phase 3 and entered an open-label 18-month LTS. Treatment satisfaction (not at all, a little, moderately, quite, very satisfied) and AEs, including any reports of diarrhea, were recorded at all study visits; AE severity was assessed based on pt description. In the LTS, pts could suspend, reduce (145 μg), or withdraw from dosing due to AEs. Treatment satisfaction was assessed in pts with and without diarrhea. Results: Of 535 IBS-C RO pts in the 18-month LTS, 79% had ≥1 AE; 45 pts (8%) withdrew due to an AE. Diarrhea, the most common AE (171 pts; 32%; 0.29/pt-year), was mostly mild or moderate in severity and led to withdrawal in 18 pts (3%) (Table). There were no diarrhea-related SAEs. 131 patients (24%) decreased and/or suspended their LIN dose due to diarrhea; the majority of these patients completed the study (Table). Pts averaged at least moderate Tx Sat; >70% of pts were moderately to very satisfied with LIN treatment regardless of whether they had diarrhea (Figure 1).Figure 1Conclusion: During up to 2 years on LIN, IBS-C pts were moderately to quite satisfied with treatment on average, and LIN was well tolerated. Diarrhea AEs, reported in 32% of IBS-C pts in the 18-month LTS, were generally mild or moderate in severity, easily managed, and infrequently led to study withdrawal. IBS-C pts who reported diarrhea on LIN had similar Tx Sat relative to those who did not report diarrhea. (Studies sponsored by Forest Laboratories, Inc., and Ironwood Pharmaceuticals, Inc.)Table 1: Characterization of Diarrhea in IBS-C Pats on LIN Who Completed a Ph3 Trial and RO Into an LTSDisclosure - William Chey is a paid consultant for Astra Zeneca, Asubio, Astellas, Entera, Furiex, Ironwood, Forest, Merck, Prometheus, Salix, SK, Sunovian, Sucampo, and Takeda, and receives research grants from Coulter Foundation, Ironwood, Nestle, Perrigo, and Prometheus. Steve Shiff is an employee of Forest Research Institute, Inc. and own stock and/or stock options in Forest Laboratories, Inc. Harvey Schneider is a consultant to Forest Research Institute, Inc. Xinming Hao, Bernard Lavins, Jennifer Chickering, Mark Currie, and Jeffrey Johnston Taylor are employees of Ironwood Pharmaceuticals, Inc. and own stock and/or stock options in Ironwood Pharmaceuticals. This research was supported by an industry grant from Forest Research Institute and Ironwood Pharmaceuticals.
Molecular structure of rac-cis-1,4-2-butenylenebis(1-indenyl)zirconium dichloride (1999)

ansa-Metallocene catalysts have been designed by variation of the transition metals, the bridging groups, and the πligands in order to improve the α-olefin polymerization performance.1 The presence of bridging groups restricts the mobility of the ansa-metallocene onto the growing polymer chain in an enantiomorphic site controlled process.2 Slight structural variations of the bridging group are known to significantly affect the activity and the stereoregularity in αolefin polymerization reactions. In particular, the length of the bridging chain has an influence not only on the rigidity and the conformational geometry of π-ligands but also on the angle between the π-ligand centroids and the metal atom. Various bridging groups have been employed to investigate the influence of the corresponding ansa-metallocene catalysts on the polymerization behavior. The bridging unit is commonly oriented at the back side of the ansa-metallocene, i.e. disposed away from the σ-ligands at the pseudo-tetrahedrally coordinatied group 4 metal center. The catalytically active site is known to be the open front side of the ansametallocene catalyst where the σ-ligands are located. In previous work,3 we reported the synthesis of a four-carbon bridged zirconocene, rac-o-phenylenedimethylenebis(indenyl)zirconium dichloride (rac-1), and its polymerization results. A single crystal of rac-1 suitable for an X-ray diffraction study could not be obtained. We, therefore, prepared rac-cis1,4-2-butenylenebis(indenyl)zirconium dichloride (rac-2), which has a similar bridging moiety to that of compound rac-1, in order to understand structural details of rac-1. Herein we report structural characterization of rac-2.
Novel mesothelin antibody-drug conjugates: current evidence and future role in the treatment of ovarian cancer (2020)

<b>Introduction:</b> Ovarian cancer is the deadliest gynecologic malignancy in the United States, and effective therapies for recurrent, advanced, and progressive disease are limited. Mesothelin is known to be expressed in ovarian cancers, and antibody-drug conjugates targeting mesothelin are a promising novel therapeutic agent.<b>Areas Covered:</b> This article reviews the currently available literature of anti-mesothelin antibody-drug conjugates as a novel treatment for ovarian cancer. Preclinical in vitro and in vivo data as well as clinical results are reviewed for each available agent. Additionally, adverse effects are covered.<b>Expert Opinion:</b> Anti-mesothelin antibody-drug conjugates and their combination with chemotherapeutic agents have undergone phase II trials with encouraging results and demonstrated favorable adverse effect profiles. Phase III data will be necessary to establish its role in ovarian cancer, particularly in recurrent, advanced, or progressive disease.
Energy transport analysis in ultrashort pulse laser ablation through combined molecular dynamics and Monte Carlo simulation (2010)

Mechanisms of energy transport during ultrashort laser pulses (USLPs) ablation are investigated in this paper. Nonequilibrium electron-transport, material ionization, as well as density change effects, are studied using atomistic models---the molecular dynamics (MD) and Monte Carlo (MC) methods, in addition to the previously studied laser absorption, heat conduction, and stress wave propagation. The target material is treated as consisting of two subsystems: valence-electron system and lattice system. MD method is applied to analyze the motion of atoms while MC method is applied for simulating electron dynamics and multiscattering events between particles. Early-time laser-energy absorption and redistribution as well as later-time material ablation and expansion processes are analyzed. This model is validated in terms of ablation depth, lattice/electron temperature distribution as well as evolution, and plume front velocity, through comparisons with experimental or theoretical results in literature. It is generally believed that the hydrodynamic motion of the ablated material is negligible for USLP but this study shows it is true only for its effect on laser-energy deposition. This study shows that the consideration of hydrodynamic expansion and fast density change in both electron and lattice systems is important for obtaining a reliable energy transport mechanism in the locally heated zone.
Leader-Based Multi-Scale Attention Deep Architecture for Person Re-Identification (2019)

Person re-identification (re-id) aims to match people across non-overlapping camera views in a public space. This is a challenging problem because the people captured in surveillance videos often wear similar clothing. Consequently, the differences in their appearance are typically subtle and only detectable at particular locations and scales. In this paper, we propose a deep re-id network (MuDeep) that is composed of two novel types of layers - a multi-scale deep learning layer, and a leader-based attention learning layer. Specifically, the former learns deep discriminative feature representations at different scales, while the latter utilizes the information from multiple scales to lead and determine the optimal weightings for each scale. The importance of different spatial locations for extracting discriminative features is learned explicitly via our leader-based attention learning layer. Extensive experiments are carried out to demonstrate that the proposed MuDeep outperforms the state-of-the-art on a number of benchmarks and has a better generalization ability under a domain generalization setting.