gebhart/patrepeval huggingface dataset:
Outlier Kinase Expression by RNA Sequencing as Targets for Precision Therapy (2013)

Protein kinases represent the most effective class of therapeutic targets in cancer; therefore, determination of kinase aberrations is a major focus of cancer genomic studies. Here, we analyzed transcriptome sequencing data from a compendium of 482 cancer and benign samples from 25 different tissue types, and defined distinct "outlier kinases" in individual breast and pancreatic cancer samples, based on highest levels of absolute and differential expression. Frequent outlier kinases in breast cancer included therapeutic targets like ERBB2 and FGFR4, distinct from MET, AKT2, and PLK2 in pancreatic cancer. Outlier kinases imparted sample-specific dependencies in various cell lines, as tested by siRNA knockdown and/or pharmacologic inhibition. Outlier expression of polo-like kinases was observed in a subset of KRAS-dependent pancreatic cancer cell lines, and conferred increased sensitivity to the pan-PLK inhibitor BI-6727. Our results suggest that outlier kinases represent effective precision therapeutic targets that are readily identifiable through RNA sequencing of tumors.
Correction: Author Correction: Somatic chromosomal engineering identifies BCAN-NTRK1 as a potent glioma driver and therapeutic target (2018)

This corrects the article DOI: 10.1038/ncomms15987.
Increased production of collagen in Vivo by hepatocytes and nonparenchymal cells in rats with carbon tetrachloride-induced hepatic fibrosis (1988)

We have shown, using the proline:ornithine dual label method, that in normal rats, hepatocytes contribute in vivo about 80 to 90% of the newly synthesized hepatic collagen. In order to quantify the contribution of hepatocytes and nonparenchymal cells to collagen synthesis in vivo in hepatic fibrogenesis, rats with CCl4-induced liver fibrosis were given [5(3H)]proline and [14C]ornithine intraperitoneally. About 80% of the 14C in albumin and transferrin was present as arginine, following conversion of [14C]ornithine via the urea cycle. In contrast to hepatocyte proteins, in nonparenchymal cells and serum a negligible percentage of the radioactivity was present as [14C]arginine. These combined findings indicate that, in spite of the hepatocellular damage, the labeling of hepatocyte proteins was efficient and specific, validating the use of the proline:ornithine method in this experimental model of hepatic fibrosis. We calculated the [3H]proline/[14C]arginine ratio in hepatic collagen (after correcting for the relative frequencies of amino acids) as a percentage of the same ratio in either albumin or transferrin, the index hepatocyte proteins. In this experimental model, during active fibrogenesis, both hepatocytes and nonparenchymal cells increase their production of collagen 2-fold when compared to normal animals, and hepatocytes produce the majority of the newly synthesized hepatic collagen.
Pipelines and Size Constraints (2000)

Some types of documents need to meet size constraints, such as fitting into a limited number of pages. This can be a difficult constraint to enforce in a pipelined natural language generation (NLG) system, because size is mostly determined by content decisions, which usually are made at the beginning of the pipeline, but size cannot be accurately measured until the document has been completely processed by the NLG system. I present experimental data on the performance of single-solution pipeline, multiple-solution pipeline, and revision-based variants of the STOP system (which produces personalized smoking-cessation leaflets) in meeting a size constraint. This shows that a multiple-solution pipeline does much better than a single-solution pipeline, and that a revision-based system does best of all.
Repaired coarctation of the aorta, persistent arterial hypertension and the selfish brain (2019)

High Blood Pressure; Hypertension; Magnetic Resonance Imaging (MRI); Cardiovascular Surgery; Cerebrovascular Malformations.
Treatment of nonunions of the humeral shaft with nonvascularized fibular strut allograft: postoperative outcomes and review of a surgical technique (2020)

Fibular allograft is an effective and straightforward option for treating humeral midshaft and distal-shaft nonunions; however, treatment of proximal-third nonunions remains challenging.
Rethinking the Faster R-CNN Architecture for Temporal Action Localization (2018)

We propose TAL-Net, an improved approach to temporal action localization in video that is inspired by the Faster RCNN object detection framework. TAL-Net addresses three key shortcomings of existing approaches: (1) we improve receptive field alignment using a multi-scale architecture that can accommodate extreme variation in action durations; (2) we better exploit the temporal context of actions for both proposal generation and action classification by appropriately extending receptive fields; and (3) we explicitly consider multi-stream feature fusion and demonstrate that fusing motion late is important. We achieve state-of-the-art performance for both action proposal and localization on THUMOS'14 detection benchmark and competitive performance on ActivityNet challenge.
HindIIIpolymorphism in the DCC gene (1991)

Journal Article HindIII polymorphism in the DCC gene Get access P. Devilee, P. Devilee Search for other works by this author on: Oxford Academic PubMed Google Scholar M. van Vliet, M. van Vliet Search for other works by this author on: Oxford Academic PubMed Google Scholar K.R. Cho, K.R. Cho 1The Johns Hopkins Oncology Center, School of MedicineBaltimore, MD 21231, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar B. Vogelstein B. Vogelstein 1The Johns Hopkins Oncology Center, School of MedicineBaltimore, MD 21231, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 24, 25 December 1991, Page 6965, https://doi.org/10.1093/nar/19.24.6965 Published: 25 December 1991
Unclassified Renal Cell Carcinoma: Clinical Features and Prognostic Impact of a New Histological Subtype (2002)

We characterized the histopathological features and clinical behavior of unclassified renal cell carcinoma and compared the prognostic outcome in patients with unclassified and conventional (clear cell) renal cell carcinoma.A total of 31 patients with unclassified renal cell carcinoma are included in the kidney cancer database at our institution. Another 317 matched patients with clear cell carcinoma were used for comparing demographic, clinical, pathological and survival data.The incidence of unclassified renal cell carcinoma was 2.9%. At initial diagnosis 29 patients (94%) with unclassified and 264 (83%) with clear cell renal cell carcinoma had metastatic disease (p = 0.143). Compared with the clear cell variety unclassified disease was associated with larger tumors (p = 0.005), increased risk of adrenal gland involvement (25% of cases, p = 0.0001), direct invasion to adjacent organs (42%, p = 0.00001), bone (52%, p = 0.022), regional (52%, p = 0.0042) and nonregional lymph node (41%, p = 0.03) metastases. Nephrectomy was less likely to be attempted or completed in unclassified renal cell carcinoma cases (61%, p = 0.00007). Unclassified histology was a significant indicator for poor prognosis on multivariate analysis (p <0.0001). Median survival in patients with unclassified renal cell carcinoma was 4.3 months. Nephrectomy alone did not confer any survival advantage in these cases (p = 0.1086), while immunotherapy did (p = 0.008). The combination of nephrectomy and immunotherapy yielded improved survival over immunotherapy alone (p = 0.0356) but patients with unclassified renal cell carcinoma were significantly less likely than those with clear cell disease to be eligible for immunotherapy regimens (p = 0.05).Unclassified renal cell carcinoma is associated with distinct and highly aggressive biological behavior, and poor clinical outcome. Whenever feasible, immunotherapy with nephrectomy is warranted.
Nucleation-type magnetization reversal by spin-polarized current in perpendicularly magnetized FePt layers (2008)

The magnetic field dependence of current-induced magnetization reversal was investigated for current-perpendicular-to-plane giant magnetoresistance pillars with perpendicularly magnetized FePt layers. Current-induced magnetization reversal under the tilted external magnetic field showed that a reversed domain is nucleated by spin-transfer torque and then propagates to complete magnetization reversal, although the formation of a multiple-domain state is not observed by static measurement. This nucleation-type current-induced magnetization reversal is characteristic of a system having large magnetic anisotropy and a small number of pinning sites for the domain wall, and explains the large magnetic field dependence of the critical current density for magnetization reversal $({J}_{c})$. As the magnetic anisotropy of the FePt free layer is reduced, the magnetic field dependence of ${J}_{c}$ becomes close to the values theoretically calculated for the coherent rotation mode, implying that the mode of the current-induced magnetization reversal changes from the nucleation of a reversed domain to the rotation of magnetization.
Structure, Nanomechanical Properties, and Wettability of Organized Erucamide Layers on a Polypropylene Surface (2021)

Understanding the nanostructure and nanomechanical properties of surface layers of erucamide, in particular the molecular orientation of the outermost layer, is important to its widespread use as a slip additive in polymer materials. Extending our recent observations of nanomorphologies of erucamide layers on a <i>hydrophilic silica substrate</i>, here we evaluate its nanostructure on a <i>more hydrophobic polypropylene surface</i>. Atomic force microscopy (AFM) imaging revealed the molecular packing, thickness, and surface coverage of the erucamide layers, while peak force quantitative nanomechanical mapping (QNM) showed that erucamide reduced the adhesive response on polypropylene. Synchrotron X-ray reflectivity (XRR) was used to probe the out-of-plane structure of the surface layers. Static contact angle measurements further corroborated on the resulting wettability, also demonstrating the efficacy of erucamide physisorption in facilitating control over polypropylene surface wetting. The results show the formation of erucamide monolayers, bilayers and multilayers, depending on the concentration in the spin-cast solution. Correlation of AFM, XRR and wettability results consistently points to the molecular orientation in the outermost layer, i.e. with the erucamide tails pointing outward for the surface nanostructures with different morphologies (i.e., bilayers and multilayers). Rare occurrence of monolayers with exposed hydrophilic head groups were observed only at the lowest erucamide concentration. Compared with our previous observations on the hydrophilic surface, the erucamide surface coverage was much higher on the more hydrophobic propylene surface at similar erucamide concentrations in the spin-cast solution. Furthermore, the structure, molecular orientation and nanomechanical properties of the spin-cast erucamide multilayers atop polypropylene were also similar to those on industrially relevant polypropylene fibers coated with erucamide via <i>blooming</i>. These findings shed light on the nanostructural features of the erucamide surface layer underpinning its nanomechanical properties, relevant to many applications in which erucamide is commonly used as a slip additive.
Weighted random matching: a simple scheduling algorithm for achieving 100% throughput (2004)

Input-queuing is preferred to output-queuing in high-speed switches because it can be implemented with slower memories. Existing schedulers for input-queued switches that achieve 100% throughput without any speedup have extremely high time complexity and require significant hardware. It is known that a scheduler using maximal matches achieves 100% throughput with a speedup of 2. However, computing even maximal matches at line-speed is nontrivial. Most existing scheduling algorithms for input-queued switches require variable sized packets to be segmented into fixed size cells leading to significant overhead in both bandwidth and hardware. We present an extremely simple randomized algorithm, weighted random matching, for scheduling variable length packets in an input-queued switch. The amount of work that our scheduler does is less than a single iteration of parallel iterative matching (PIM). We show that our algorithm is guaranteed to achieve 100% throughput under any admissible traffic, with a speedup of 2.
Structure and function of the Orc1 BAH-nucleosome complex (2019)

The Origin Recognition Complex (ORC) is essential for replication, heterochromatin formation, telomere maintenance and genome stability in eukaryotes. Here we present the structure of the yeast Orc1 BAH domain bound to the nucleosome core particle. Our data reveal that Orc1, unlike its close homolog Sir3 involved in gene silencing, does not appear to discriminate between acetylated and non-acetylated lysine 16, modification states of the histone H4 tail that specify open and closed chromatin respectively. We elucidate the mechanism for this unique feature of Orc1 and hypothesize that its ability to interact with nucleosomes regardless of K16 modification state enables it to perform critical functions in both hetero- and euchromatin. We also show that direct interactions with nucleosomes are essential for Orc1 to maintain the integrity of rDNA borders during meiosis, a process distinct and independent from its known roles in silencing and replication.
Comparison of Activity Levels Derived from Two Accelerometers in Dogs with Osteoarthritis-Associated Pain: Implications for Clinical Trials (2019)

Introduction: Accelerometer data are frequently reported as total weekly activity counts (AC); however, methods of further utilizing the activity data to allow differentiation of activity intensities have been established. While this information offers significant clinical value for researchers, only a few investigators have utilized this methodology, likely due to the labor involved in deriving this data. Novel devices offer methods of collecting this data in efficient manners, however, have not been currently. The objectives of this study were to(a) validate a novel accelerometer (Heyrex), (b) compare automatically generated categories quantifying activity intensity to established manually derived cut-points (Actical), and (c) describe variability of AC in dogs with osteoarthritis-associated pain (Actical & Heyrex).
Prospects for Silicon Light‐Emitting Devices (2004)

This chapter contains sections titled: Erbium Doping Low-dimensional Structures Dislocation-engineered Emitters Raman Excitation Summary References
Open membership coalition formation of cognitive interference systems (2013)

We consider a cognitive radio setting in which a set of secondary transmitter-receiver pairs coexist with a primary user. In the channel sensing phase, each secondary system senses the primary user's channel to determine its occupancy. The existence of a fusion center enables joint processing of the sensing data. This would improve the joint sensing performance, however at the cost of a delay required for reporting the sensed data. In the channel access phase, noncooperative secondary transmission can lead to a degradation of secondary users' average achievable rates due to excessive mutual interference. We propose to coordinate the secondary system transmission by providing orthogonal multiple access rules for the secondary users which report their sensing data to the fusion center. Using models from game theory, a coalition formation algorithm is proposed to find a stable set of secondary users participating in sensing data fusion. It is shown by simulation that the proposed mechanism provides an incentive for the secondary users to participate in joint sensing at an extent depending on the signal-to-noise ratio and the reporting overhead.
Spotter: A model based active geolocation service (2011)

The localization of Internet hosts opens space for a wide scope of applications, from targeted, location aware content provision to localizing illegal content. In this paper we present a novel probabilistic approach, called Spotter, for estimating the geographic position of Internet devices with remarkable precision. While the existing methods use landmark specific calibration for building their internal models we show that the delay-distance data follow a generic distribution for each landmark. Hence, instead of describing the delay-distance space in a landmark specific manner our proposed method handles all the calibration points together and derives a common delay-distance model. This fundamental discovery indicates that, in contrast to prior techniques, Spotter is less prone to measurement errors and other anomalies such as indirect routing. To demonstrate the robustness and the accuracy of Spotter we test the performance on PlanetLab nodes as well as on a more realistic reference set collected by CAIDA explicitly for geolocation comparison purposes. To the best of our knowledge, we are the first to use this novel ground truth containing over 23000 network routers with their geographic locations.
Dynamics of epitaxial quantum dot laser on silicon subject to chip-scale back-reflection for isolator-free photonics integrated circuits (2021)

Silicon-based epitaxial quantum dot (QD) lasers with strong tolerance for back-reflections have paved the way for developing isolator-free photonics integrated circuits (PICs). This remarkable feature is attributed to the peculiar benefits of QDs, including a large material gain, a strong damping, and a small linewidth enhancement factor [1] . The laser performance can also be optimized by applying p-modulation doping in the active region [1] . In a previous study, the sensitivity of epitaxial QD lasers on silicon subject to short- and long-delay optical feedback were performed [2] . On the top of that, a further investigation of the feedback dynamics on the intra- and inter-chip scale is of significant importance for photonic integration applications.
Finished Genome Sequence of the Highly Multidrug-Resistant Human Urine Isolate Citrobacter freundii Strain SL151 (2016)

Citrobacter freundii is a Gram-negative opportunistic pathogen that is increasingly being recognized as a causative agent of hospital-acquired urinary tract infections and an important reservoir of antimicrobial resistance determinants. In this report, we describe the finished genome sequence of C. freundii strain SL151, a highly multidrug-resistant human urine isolate.
Sex modifies the risk of HIV-associated obstructive lung disease in Ugandans postpneumonia (2023)

HIV appears to increase the risk of OLD to a greater degree in women than in men in an urban Ugandan setting. The mechanistic explanation for this interaction by sex remains unclear and warrants further study.
Intracoronary Infusion of Bone Marrow-Derived Mononuclear Cells Abrogates Adverse Left Ventricular Remodelling Post-Acute Myocardial Infarction: Insights from the Reinfusion of Enriched Progenitor Cells and Infarct Remodelling in Acute Myocardial Infarction (REPAIR-AMI) Trial (2009)

Intracoronary administration of BMC eliminates the correlation between depressed LVEF after reperfusion therapy and LV expansion during follow-up and, thereby, abrogates early LV remodelling after AMI.
Influence ofN-acetylcysteine on chronic bronchitis or COPD exacerbations: a meta-analysis (2015)

In order to clarify the possible role of N-acetylcysteine (NAC) in the treatment of patients with chronic bronchitis and chronic obstructive pulmonary disease (COPD), we have carried out a meta-analysis testing the available evidence that NAC treatment may be effective in preventing exacerbations of chronic bronchitis or COPD and evaluating whether there is a substantial difference between the responses induced by low (≤ 600 mg per day) and high (> 600 mg per day) doses of NAC. The results of the present meta-analysis (13 studies, 4155 COPD patients, NAC n = 1933; placebo or controls n = 2222) showed that patients treated with NAC had significantly and consistently fewer exacerbations of chronic bronchitis or COPD (relative risk 0.75, 95% CI 0.66-0.84; p < 0.01), although this protective effect was more apparent in patients without evidence of airway obstruction. However, high doses of NAC were also effective in patients suffering from COPD diagnosed using spirometric criteria (relative risk 0.75, 95% CI 0.68-0.82; p = 0.04). NAC was well tolerated and the risk of adverse reactions was not dose-dependent (low doses relative risk 0.93, 95% CI 0.89-0.97; p = 0.40; high doses relative risk 1.11, 95% CI 0.89-1.39; p = 0.58). The strong signal that comes from this meta-analysis leads us to state that if a patient suffering from chronic bronchitis presents a documented airway obstruction, NAC should be administered at a dose of ≥ 1200 mg per day to prevent exacerbations, while if a patient suffers from chronic bronchitis, but is without airway obstruction, a regular treatment of 600 mg per day seems to be sufficient.
Characterization of the thyroid hormone response element in the skeletal alpha-actin gene: negative regulation of T3 receptor binding by the retinoid X receptor. (1993)

We have identified a T3 response element (TRE) in the human skeletal alpha-actin gene between nucleotide positions -273 and -249 (5' GGGCAACTGGGTCGGGTCAGGAGGG 3') that is accommodated by the core receptor binding motif, A/G GG T/A C A/G. This sequence conferred appropriate hormonal regulation in a thyroid hormone receptor (TR alpha) dependent manner to an enhancerless SV40 promoter. Electrophoretic mobility shift assay experiments showed that Escherichia coli expressed and affinity purified TR alpha bound to the skeletal alpha-actin TRE in a sequence specific manner. The alpha-actin TRE bound TR alpha dimers cooperatively. Mutagenesis of the alpha-actin TRE indicated that the core binding motifs and the gap sequences were the most important for efficient binding to TR alpha. The retinoid X receptor alpha (RXR alpha) interacted with the alpha-actin TRE in a sequence specific fashion and formed heterodimeric complexes with TR alpha on the alpha-actin TRE. However, increased levels of RXR alpha decreased the binding of TR alpha to the alpha-actin TRE, in contrast to promoting TR alpha binding to the alpha-myosin heavy chain TRE. Furthermore, the alpha-actin, palindromic, synthetic direct repeat, alpha-myosin heavy chain, and growth hormone TREs interacted with an identical nuclear factor in vitro in muscle cells. In conclusion, our data suggest that the human skeletal alpha-actin TRE is a target for direct cross-talk between two different hormonal signals (T3 and 9-cis-retinoic acid) at the receptor level.(ABSTRACT TRUNCATED AT 250 WORDS)
A Novel EXT1 Splice Site Mutation in a Kindred with Hereditary Multiple Exostosis and Osteoporosis (2005)

A novel heterozygous acceptor splice site mutation of EXT1 results in HME that is associated with a low peak bone mass, indicating a possible additional role for EXT1 in bone biology and in regulating BMD.