gebhart/patrepeval huggingface dataset:
Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles (2014)

Ribosomes are molecular machines that function in polyribosome complexes to translate genetic information, guide the synthesis of polypeptides, and modulate the folding of nascent proteins. Here, we report a surprising function for polyribosomes as a result of a systematic examination of the assembly of a large ribonucleoprotein complex, the vault particle. Structural and functional evidence points to a model of vault assembly whereby the polyribosome acts like a 3D nanoprinter to direct the ordered translation and assembly of the multi-subunit vault homopolymer, a process which we refer to as polyribosome templating. Structure-based mutagenesis and cell-free in vitro expression studies further demonstrated the critical importance of the polyribosome in vault assembly. Polyribosome templating prevents chaos by ensuring efficiency and order in the production of large homopolymeric protein structures in the crowded cellular environment and might explain the origin of many polyribosome-associated molecular assemblies inside the cell.
ADP inhibits function of the ABC transporter cystic fibrosis transmembrane conductance regulator via its adenylate kinase activity (2005)

ADP interacts with the nucleotide-binding domains (NBDs) of the cystic fibrosis transmembrane conductance regulator (CFTR) to inhibit its Cl- channel activity. Because CFTR NBD2 has reversible adenylate kinase activity (ATP + AMP<==> ADP + ADP) that gates the channel, we asked whether ADP might inhibit current through this enzymatic activity. In adenylate kinases, binding of the two ADP molecules is cooperative. Consistent with this hypothesis, CFTR current inhibition showed positive cooperativity for ADP. We also found that ADP inhibition of current was attenuated when we prevented adenylate kinase activity with P1,P5-di(adenosine-5') pentaphosphate. Additional studies suggested that adenylate kinase-dependent inhibition involved phosphotransfer between two nucleotide diphosphates. These data indicate that the adenylate kinase reaction at NBD2 contributed to the inhibitory effect of ADP. Finding that ADP inhibits function via an adenylate kinase activity also helps explain the earlier observation that mutations that disrupt adenylate kinase activity also disrupt ADP inhibition. Thus, the results reveal a previously unrecognized mechanism by which ADP inhibits an ABC transporter.
Automatic Dynamic Resource Management architecture in tactical network environments (2009)

Automatic dynamic resource management (AutoDRM) architecture is a framework to efficiently manage shared resources in the tactical network environments without human operator intervention. The autoDRM architecture was developed to resolve the resource contention issues and to improve the quality of service in the tactical network environments. The information herein describes key components of the autoDRM architecture. An experimental end-to-end network prototype test bed consisting of simulated satellite communications (SATCOM) and an OPNET system-in-the-loop (SITL) scenario was also developed to host the autoDRM system. Experimental results demonstrate improved network performance when AutoDRM is deployed.
Mean-Field Analysis of Coding Versus Replication in Large Data Storage Systems (2018)

We study cloud storage systems with a very large number of files stored in a very large number of servers. In such systems, files are either replicated or coded to ensure reliability, i.e., to guarantee file recovery from server failures. This redundancy in storage can further be exploited to improve system performance (mean file-access delay) through appropriate load-balancing (routing) schemes. However, it is unclear whether coding or replication is better from a system performance perspective since the corresponding queueing analysis of such systems is, in general, quite difficult except for the trivial case when the system load asymptotically tends to zero. Here, we study the more difficult case where the system load is not asymptotically zero. Using the fact that the system size is large, we obtain a mean-field limit for the steady-state distribution of the number of file access requests waiting at each server. We then use the mean-field limit to show that, for a given storage capacity per file, coding strictly outperforms replication at all traffic loads while improving reliability. Further, the factor by which the performance improves in the heavy traffic is at least as large as in the light-traffic case. Finally, we validate these results through extensive simulations.
The grading of soft tissue sarcomas results of a clinicohistopathologic correlation in a series of 163 cases (1984)

A multidisciplinary study of 163 patients treated at the NCI for soft tissue sarcomas allowed the correlation of a number of histologic features (histologic type, mitosis, necrosis, pleomorphism, cellularity, and matrix) of the primary lesion to time to recurrence and overall survival of the patients. The results of the stratified analyses show that necrosis is the single best histopathologic parameter to predict the time to recurrence (P = 0.025) and the overall survival of the patients (P = 0.002). Necrosis in the primary lesion is also of value in predicting survival after the first recurrence has taken place (P = 0.001). The value of necrosis in the primary lesions predicting the clinical course after recurrence appears to be independent of age, sex, location, and size of the tumor. The authors propose a grading system based on histologic typing and histologic parameters to identify a group of lesions with minimal metastatic potential (Grade 1), and on the use of necrosis to distinguish between aggressive lesions with good patient survival (Grade 2) and aggressive lesions with poor patient survival (Grade 3).
2521. The Potential Rise in the Incidence of Rotavirus G3P[8] in Kuwait (2018)

The group A rotavirus infections are associated with severe gastroenteritis in children. G1P[8] was the most prevalent genotype found in Kuwait in a study conducted between 2005 and 2006. The demographic change in Kuwait, and the recent decision to include the Rotateq vaccine in the Kuwait national immunization program, prompted us to investigate a potential change in the prevalence of rotavirus genotypes circulating in Kuwait, and to identify the VP4 and VP7 subgenomic lineages. Viral RNA was isolated from the stool samples of 101 children under 5 years of age, hospitalized for severe diarrhea. Rotavirus dsRNA was detected by RT-PCR in 24.7% of children with median age of 1 year. The genotype G3P[8] accounted for 47% of cases, followed by G1P[8] (26%), G9P[8] (10.5%), G4P[8] (10.5%), and G9P[4] (5%). Only VP7 nucleotide sequences of rotavirus G3 or G4 type clustered in the same lineage as RotaTeq, while most VP4 nucleotide sequences of rotavirus P[8] type clustered in a different lineage than Rotarix and RotaTeq vaccines. Our findings highlight the potential rise in the incidence of rotavirus G3P[8] in Kuwait, and invites future investigations to know whether the recent introduction of RotaTeq vaccine selects for certain genotypes and subgenomic lineages. All authors: No reported disclosures.
Effects of gemcitabine and gemcitabine in combination with carboplatin on five canine transitional cell carcinoma cell lines (2012)

Gemcitabine had antitumor effects on canine TCC cells in vitro, and the combination of gemcitabine and carboplatin had synergistic activity at biologically achievable concentrations.
Learning about perception of temporal fine structure by building audio codecs (2019)

The goal of audio coding is to efficiently describe an auditory experience while enabling a faithful reconstruction to the listener. The subjective quality compared to the original is measured by established psychoacoustic tests (BS.1116, 2015; BS.1534, 2015) and the description cost is measured in number of bits. As it is much cheaper to describe coarse scale signal properties than temporal fine structure (TFS), tools like noise fill, spectral extension, binaural cue coding, and machine learning have increased performance of audio codecs far beyond the first generation based on masking principles (e.g., mp3). In this evolution, implicit knowledge on hearing has been acquired by codec developers, but it has become increasingly difficult to construct tools to predict subjective quality. For example, it is yet unknown which aspects of the TFS that are essential for the listening impression to be preserved. To explore these issues, we study models of auditory representations with the mindset from audio coding. Given a method to solve the inverse problem of creating a signal with a specified representation, evaluating by listening can immediately reveal strengths and weaknesses of a candidate model.
Expression and function of vascular endothelial growth factor receptor–1 in human colon cancer cells (2004)

4334 Vascular endothelial growth factor (VEGF) has been shown to be associated with tumor angiogenesis and poor prognosis in human colon cancer. VEGF receptor-1 (VEGFR-1/Flt-1) is a high-affinity receptor for VEGF and is typically viewed as being endothelial cell specific. Here we report on the expression and function of VEGFR-1 on colon cancer cell lines. VEGFR-1 was expressed in 7/7 colon cancer cell lines as determined by Western blot analysis. Treatment of the human colon cancer cell line SW480 with VEGF-A (ligand for both VEGFR-1 and VEGFR-2) or VEGF-B (a ligand specific for VEGFR-1) led to activation of Erk 1/2. A blocking antibody to VEGFR-1 (18F1) completely inhibited the ability of VEGF-A and -B to activate Erk 1/2 in SW480 cells. VEGF-A and B did not increase colon cancer cell proliferation as determined by the MTT assay. However, VEGF-A and VEGF-B led to a significant induction of cancer cell motility and invasion through Matrigel. VEGF-A and -B stimulation of colon tumor cells also led to larger and more numerous colonies in soft agar. These data demonstrate that VEGFR-1 is functional on colon cancer cells and may contribute to colon cancer progression.
A multiparametric magnetic resonance imaging-based virtual reality surgical navigation tool for robotic-assisted radical prostatectomy (2019)

We deployed a preliminary VR-assisted surgical navigation tool for robotic-assisted radical prostatectomies.
Estudio de las propiedades termo-mecánicas y de inflamabilidad de mezclas poliméricas de PP con residuos sólidos pirolíticos de desechos vehiculares (2019)

The final disposal of vehicles out of use gives rise to an environmental issue, so that, in Europe there are companies dedicated to the disassembly and recovery of those components that can be reused, among these components are plastic waste. In the present research, it is proposed to treat those plastics through a pyrolytic process with the purpose of transforming them into solid residue, in order to be used as part of the additives in a flame retardant system in a polypropylene matrix. Vehicle wastes were segregated by relative density method (ASTM D 792-08), characterized and were subsequently incorporated into a process of thermal pyrolysis. Using the resultant pyrolytic solid residue (PSR), a polymer mixture was prepared which had the polypropylene as matrix. Its thermal, mechanical and flammability properties were evaluated through the Thermogravimetric analysis, Modulus of elasticity, Tensile strength, Percentage of deformation and the Limiting oxygen index. Vehicle waste (DPV) are formed by 82.97% of high density residue, which allowed to obtain 32.08% of High density pyrolytic solid residue (HDSR), while using low density waste, 6.69% of Low density pyrolytic solid waste (LDSR) was obtained. Regarding its thermo-mechanical and flammability properties, it was noted that adding the PSR obtained from low density and high density wastes influenced the properties of the polypropylene matrix. As for their mechanical properties, if we compare the matrix formed by polypropylene and retarding additives with and without PSR; the maximum strength in the polypropylene matrix with LDSR showed a slight decrease, while the matrix with HDSR showed a slight increase. In addition, in the LDSR and HDSR samples, the percentage of deformation of the material decreased by 52.02% and 49.17%, respectively. While the modulus of elasticity was increased by 30.12% for the sample with LDSR and 30.73% with HDSR. Likewise, the addition of PSR did not increase its flame retardant activity since the Limiting oxygen index value remained the same as when flame retardant additives were added, in 30%; while with HDSR it decreased to 29%. This indicates that the composition of the above-mentioned solid residues favors to the polypropylene composites considering that the addition of the PSR brought with it the decrease of the concentration of other additives used and of the polypropylene. This due to the chemical composition of the pyrolytic solid residues that act as a source of carbon and flame retardant minerals reinforcing their fireproof properties.
Expression of endocrine gland-derived vascular endothelial growth factor in ovarian carcinoma. (2003)

The first tissue-specific angiogenic molecule, endocrine gland-derived vascular endothelial growth factor (EG-VEGF), was identified recently in human ovary, raising hopes of developing tumor type-specific angiogenesis inhibitors. In the present study, we analyzed the expression of EG-VEGF mRNA in normal human tissues and ovarian neoplasms by quantitative real-time reverse transcription-PCR. EG-VEGF mRNA was expressed in all ovarian neoplasms examined. No significant difference was identified among benign, low malignant potential neoplasms or stage I ovarian cancer, all of which exhibited 2-fold lower mRNA levels compared with normal premenopausal ovaries. EG-VEGF mRNA levels further decreased in late stage compared with early stage carcinomas (P < 0.05) and were consistently lower in laser capture microdissected tumor islets compared with surrounding stroma. EG-VEGF was undetectable by reverse transcription-PCR in 17 established epithelial ovarian cancer cell lines or in cultured human ovarian surface epithelial cells, whereas it was detected in peripheral blood as well as tumor-infiltrating T lymphocytes. Finally, in contrast to VEGF, EG-VEGF mRNA levels did not correlate with clinical outcome in advanced ovarian carcinoma. These results suggest that EG-VEGF is most likely derived from nonepithelial components of ovarian carcinomas and may play a marginal role in promoting angiogenesis in advanced ovarian carcinoma. We postulate that EG-VEGF-targeted antiangiogenic therapy may prove useful in early stage but not in advanced stage ovarian carcinoma.
Gauge invariant spectral Cauchy characteristic extraction (2015)

We present gauge invariant spectral Cauchy characteristic extraction. We compare gravitational waveforms extracted from a head-on black hole merger simulated in two different gauges by two different codes. We show rapid convergence, demonstrating both gauge invariance of the extraction algorithm and consistency between the legacy Pitt null code and the much faster Spectral Einstein Code (SpEC).
Tutorial 1B: Transistors: Past, present and future (2016)

Summary form only given, as follows. The complete presentation was not made available for publication as part of the conference proceedings. In this tutorial evolution of transistors from planar technology will be discussed. Scaling limitations of conventional transistors that led to development of Finfet (or 3D) transistors will be presented in detail. Circuit Design challenges associated with 3D transistors will be analysed in this tutorial. Lastly, a brief overview of future transistor architectures beyond Finfet's will be provided.
CETP genetic variant rs1800777 (allele A) is associated with abnormally low HDL-C levels and increased risk of AKI during sepsis (2018)

High-density cholesterol (HDL-C) levels are influenced by genetic variation in several genes. Low levels of HDL-C have been associated with increased risk of acute kidney injury (AKI). We investigated whether genetic polymorphisms in ten genes known to regulate HDL-C levels are associated with both HDL-C levels and AKI development during sepsis. Two cohorts were retrospectively analyzed: Derivation Cohort (202 patients with sepsis enrolled at the Emergency Department from 2011 to 2014 in Vancouver, Canada); Validation Cohort (604 septic shock patients enrolled into the Vasopressin in Septic Shock Trial (VASST)). Associations between HDL-related genetic polymorphisms and both HDL-C levels, and risk for clinically significant sepsis-associated AKI (AKI KDIGO stages 2 and 3) were evaluated. In the Derivation Cohort, one genetic variant in the Cholesteryl Ester Transfer Protein (CETP) gene, rs1800777 (allele A), was strongly associated with lower HDL-C levels (17.4 mg/dL vs. 32.9 mg/dL, P = 0.002), greater CETP mass (3.43 µg/mL vs. 1.32 µg/mL, P = 0.034), and increased risk of clinically significant sepsis-associated AKI (OR: 8.28, p = 0.013). Moreover, the same allele was a predictor of sepsis-associated AKI in the Validation Cohort (OR: 2.38, p = 0.020). Our findings suggest that CETP modulates HDL-C levels in sepsis. CETP genotype may identify patients at high-risk of sepsis-associated AKI.
Blind RF Self-Interference Cancellation for In-Band Distribution Link in ATSC 3.0 (2022)

Wireless in-band backhaul technology was recently proposed for the next-generation TV broadcasting system with Single Frequency Networks as a spectrum and cost-efficient alternative to conventional fibre-optic or dedicated microwave links. Self-interference cancellation (SIC) is the key technology enabling wireless in-band backhaul to operate in the more spectrum efficient full-duplex mode. For the broadcasting headend transceiver, although the separation between the co-located transmit and receive antennas and digital/baseband SIC can achieve significant self-interference reduction and cancellation, it is desirable to have an analog/Radio Frequency (RF) SIC before the digital/baseband SIC, to relax the hardware dynamic range requirement and reduce the effect of nonlinear distortions due to the hardware imperfection as well as adjacent channel interferences. In this paper, a frequency-domain blind RF SIC (RF-SIC) framework with a novel filter weight optimization algorithm is proposed, which does not require a training process and can achieve fast convergence with the capability of tracking the self-interference channel variation with affordable computation complexity. The proposed techniques can work with different broadcasting and communications systems such as ATSC 3.0, DVB-T/T2, WiFi and 4G/5G.
NOSER: An algorithm for solving the inverse conductivity problem (1990)

The inverse conductivity problem is the mathematical problem that must be solved in order for electrical impedance tomography systems to be able to make images. Here we show how this inverse conductivity problem is related to a number of other inverse problems. We then explain the workings of an algorithm that we have used to make images from electrical impedance data measured on the boundary of a circle in two dimensions. This algorithm is based on the method of least squares. It takes one step of a Newton's method, using a constant conductivity as an initial guess. Most of the calculations can therefore be done analytically. The resulting code is named NOSER, for Newton's One-Step Error Reconstructor. It provides a reconstruction with 496 degrees of freedom. The code does not reproduce the conductivity accurately (unless it differs very little from a constant), but it yields useful images. This is illustrated by images reconstructed from numerical and experimental data, including data from a human chest.
The use of radiation for stage I seminoma: Analysis of the National Cancer Database. (2015)

385 Background: Primary radiotherapy has historically been the preferred treatment for stage I seminoma. However, there is emerging consensus that observation or primary chemotherapy may be preferred in order to reduce overtreatment and risk of secondary malignancy. Hypothesizing that the use of radiotherapy has decreased in the modern era, our objective was to assess temporal practice patterns in stage I seminoma using a large national cancer registry. Methods: The National Cancer Database (NCDB) was queried for all patients diagnosed with stage I seminoma from 1998 to 2011. Temporal trends for receipt of systemic chemotherapy, radiation, and observation (defined as no treatment) were assessed. Following adjustment for patient, demographic, and clinicopathologic characteristics, generalized estimating equations were used to assess for associations between covariates and receipt of primary radiotherapy. Results: Of the 34,251 patients identified with stage I seminoma in the NCDB, 20,627 were treated with radiation (60.2%), 2,278 were treated with chemotherapy (6.7%), and 11,346 were managed with observation (33.1%). Radiation use significantly declined from 73.5% in 1998 to 29.6% in 2011 (p&lt;0.0001), while utilization of chemotherapy (1.9% to 16.5%, p&lt;0.0001) and observation (24.6% to 53.9%, p&lt;0.0001) increased. Following adjustment, age categories 30−39 years (OR 1.06 [CI 1.01−1.13]) and 40−49 years (OR 1.10 [CI 1.03−1.17]), and stage T2 (OR 1.25 [CI 1.17−1.32]) and T3 (OR 1.21 [CI 1.04−1.41]) were associated with increased utilization of radiotherapy. Uninsured patients (OR 0.78 [CI 0.71−0.86]) and those with Medicaid (OR 0.82 [CI 0.73−0.92]) or Medicare (OR 0.62 [CI 0.55−0.69]) were less likely to undergo primary radiotherapy, while those with non-Medicare/Medicaid government insurance were more likely to receive radiation (OR 1.40 [CI 1.13-1.75]). Conclusions: In the largest known cohort of patients with Stage I seminoma reported to date, these data demonstrate that utilization of radiation therapy for stage I seminoma is on the decline. Coinciding with shifts in evidence−based guidelines, observation is now the most commonly employed management strategy for patients with Stage I seminoma.
Parallel Computing for Graphics. (1990)

The cost in computing cycles for state-of-the-art imagery continues to rise exponentially. Fortunately, so does the cost-effectiveness of state-of-the-art computer processors. However, that leaves us continually several orders of magnitude short on processing power if we wish to make state-of-the-art images in real-time or even interactive time. An obvious answer to this dilemma lies in parallel processing. As massively parallel supercomputers become reality and promise a future including massively parallel everyday computers, it is no longer a silly exercise to consider how to use thousands or even millions of processors in computer graphics.