gebhart/patrepeval huggingface dataset:
Decrease in RNase HII and Accumulation of lncRNAs/DNA Hybrids: A Causal Implication in Psoriasis? (2022)

Functional long non-coding RNAs (lncRNAs) have been in the limelight in aging research because short telomeres are associated with higher levels of TERRA (Telomeric Repeat containing RNA). The genomic instability, which leads to short telomeres, is a mechanism observed in cell aging and in a class of cancer cells. Psoriasis, a skin disease, is a disorder of epidermal keratinocytes, with altered telomerase activity. Research on the fraction of nascent RNAs in hybrid with DNA offers avenues for new strategies. Skin and blood samples from patients were fractionated to obtain the RNA associated with DNA as a R-loop structure. The higher amount of TERRA levels attached with each chromosome end was found with psoriasis patients in blood and skin. In addition to telomeric TERRA, we evidenced accumulation of others non-coding RNA, such as non-telomeric TERRA and centromeric transcripts. Increased levels of non-coding RNAs attached to DNA correlates with a decreased in Ribonuclease HII (<i>RNase-HII</i>) transcript which means that overall unresolved DNA-RNA hybrids can ultimately weaken DNA and cause skin lesions. Since the genome is actively transcribed, cellular <i>RNase-HII</i> is essential for removing RNA from the DNA-RNA hybrid in controls of genome stability and epigenome shaping and can be used as a causal prognostic marker in patients with psoriasis.
Does conservation account for splicing patterns? (2016)

These findings suggest that one mechanism for the evolutionary transition from constitutive to alternative splicing is the emergence of cis-acting splicing inhibitors. The association of our ISREs with differences in splicing suggests the existence of novel RNA-binding proteins and/or novel splicing roles for known RNA-binding proteins.
Energetic disorder limits energy transfer in semiconductor nanocrystal–DNA–dye conjugates (2009)

We demonstrate the influence of spectral linewidths of individual donor-acceptor couples on energy transfer efficiency in semiconductor nanocrystal–DNA–organic dye conjugates. Temperature-dependent single molecule and ensemble spectroscopy data are analyzed using the Förster theory within the macroscopic and microscopic approaches. The results obtained evidence on the importance of the spectral overlap between emission of a single donor and absorption of a single acceptor in its close vicinity, which determines the microscopic resonance and transfer efficiency between individual neighbors. This realization poses important implications on the applicability of ensemble spectral overlap for the analysis of distance dependencies of nanoscopic objects.
Convex combination framework for a priori SNR estimation in speech enhancement (2017)

The paper proposes a convex combination fusion function based on a sigmoid function for the estimation of the a priori SNR in a speech enhancement framework with critical frequency band processing. The proposed method does not only eliminate the one frame delay generated by the well-known decision directed approach but also increases the adaptation speed during abrupt changes in the SNR estimation. As a result, the advantage of low musical noise has been maintained while more weak speech components have been preserved. Experimental results using instrumental and subjective measures also indicate improvement in speech quality compared to the reference methods.
Effect of VEGF on the Regenerative Capacity of Muscle Stem Cells in Dystrophic Skeletal Muscle (2009)

We have isolated a population of muscle-derived stem cells (MDSCs) that, when compared with myoblasts, display an improved regeneration capacity, exhibit better cell survival, and improve myogenesis and angiogenesis. In addition, we and others have observed that the origin of the MDSCs may reside within the blood vessel walls (endothelial cells and pericytes). Here, we investigated the role of vascular endothelial growth factor (VEGF)-mediated angiogenesis in MDSC transplantation-based skeletal muscle regeneration in mdx mice (an animal model of muscular dystrophy). We studied MDSC and MDSC transduced to overexpress VEGF; no differences were observed in vitro in terms of phenotype or myogenic differentiation. However, after in vivo transplantation, we observe an increase in angiogenesis and endogenous muscle regeneration as well as a reduction in muscle fibrosis in muscles transplanted with VEGF-expressing cells when compared to control cells. In contrast, we observe a significant decrease in vascularization and an increase in fibrosis in the muscles transplanted with MDSCs expressing soluble forms-like tyrosine kinase 1 (sFlt1) (VEGF-specific antagonist) when compared to control MDSCs. Our results indicate that VEGF-expressing cells do not increase the number of dystrophin-positive fibers in the injected mdx muscle, when compared to the control MDSCs. Together the results suggest that the transplantation of VEGF-expressing MDSCs improved skeletal muscle repair through modulation of angiogenesis, regeneration and fibrosis in the injected mdx skeletal muscle.
Metastatic prostate cancer diagnosed by fine‐needle aspiration: Contemporary cytopathologic and biomarker assessment with clinical correlates (2022)

Aggressive cytomorphologic variants were commonly identified in patients with prior ADT. Identification of nonconventional cytomorphology and increased proliferation can provide important prognostic information. Recognition of these changes is important for an accurate diagnosis, and the identification of high-grade variants can affect therapeutic decision-making. Clinically actionable biomarkers such as PDL1 and ARv7 can be assessed by IHC.
An empirical study of the statistics of phase drift of off-the-shelf oscillators for distributed MIMO applications (2014)

We report on the results of an empirical study of the phase drift of commercial RF oscillators, and the performance limitations implied by these drifts for distributed multi-input multi-output (DMIMO) wireless systems. The stochastic clock drifts of the oscillators at the nodes of the virtual array and the resulting synchronization errors limit the performance of DMIMO systems. Furthermore the synchronization requirements for DMIMO applications are subtly different from other synchronization problems. We examine two commercially available oscillators and present a series of measurements and calculations to characterize their short-term stability. Specifically we quantify the decrease in phase drift for a temperature controlled oscillator (TCXO) as compared to an uncompensated (VCXO) crystal oscillator. We also present the results of tracking the clock drifts of both oscillators using a simple algorithm based on an Extended Kalman Filtering framework. One key observation coming out of our study is that while the temperature compensated oscillators are an order of magnitude better than the uncompensated ones as measured by their frequency stability, the corresponding performance improvement for DMIMO applications is quite modest. This suggests the need for new figures of merit and novel oscillator designs specifically optimized for DMIMO applications.
Ectopic and Visceral Fat Deposition in Lean and Obese Patients With Type 2 Diabetes (2016)

Irrespective of body mass index, diabetes is related to significant abnormalities in cardiac structure, energetics, and cardiac and hepatic steatosis. Obese patients with T2D show a greater propensity for ectopic and visceral fat deposition.
Bistatic Radar Cross Section of a Perfectly Conducting Rhombus-Shaped Flat Plate (1990)

Abstract : The bistatic radar cross section of a perfectly conducting flat plate that has a rhombus shape (equilateral parallelogram) is investigated. The Ohio State University electromagnetic surface patch code (ESP version 4) is used to compute the theoretical bistatic radar cross section of a 35- x 27-in rhombus plate at 1.3 GHz over the bistatic angles 15 deg to 142 deg. The ESP-4 computer code is a method of moments FORTRAN-77 program which can analyze general configurations of plates and wires. This code has been installed and modified at Lincoln Laboratory on a SUN 3 computer network. Details of the code modifications are described. Comparisons of the method of moments simulations and measurements of the rhombus plate are made. It is shown that the ESP-4 computer code provides a high degree of accuracy in the calculation of copolarized and cross-polarized bistatic radar cross section patterns. Keywords: Electromagnetic surfaces; Method of moments; Computer programs; Radar cross sections.
Immunostaining to identify molecular subtypes of diffuse large B-cell lymphoma in a population-based epidemiologic study in the pre-rituximab era. (2011)

Gene expression profiling studies have distinguished diffuse large B-cell lymphomas (DLBCLs) by cell of origin, with distinct pathogenetic mechanisms and prognosis. We attempted to identify DLBCL molecular subtypes in an epidemiologic study of 214 DLBCL patients diagnosed during 1998-2000 with archival tissues to investigate etiology. Immunohistochemical staining for CD10, BCL6, LMO2, MUM1/IRF4, and BCL2 and fluorescence in situ hybridization for t(14;18) were conducted, with ≥93% blinded duplicate agreement. CD10, LMO2, and BCL2 expression was similar to previous reports (32%, 44%, and 44% of DLBCLs, respectively), but BCL6 and MUM1/IRF4 expression was lower than expected (29% and 5%, respectively). We classified 112/214 (52%) cases as germinal center B-cell-like DLBCL (GCB-DLBCL; Hans et al., Blood 2004; CD10+ or CD10-/BCL6+/MUM1-), with no difference in prognosis compared with non-GCB-DLBCL (Cox regression, P=0.48). Comparing other GCB correlates, LMO2 expression and t(14;18) were more common but not exclusive to GCB-DLBCL as defined in our study, whereas BCL2 expression did not differ between DLBCL molecular subtypes. We could not confidently identify patients with GCB-DLBCL using these immunohistochemistry-based markers on archival tissues.
In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species (1999)

We have investigated mRNA 3'-end-processing signals in each of six eukaryotic species (yeast, rice, arabidopsis, fruitfly, mouse, and human) through the analysis of more than 20,000 3'-expressed sequence tags. The use and conservation of the canonical AAUAAA element vary widely among the six species and are especially weak in plants and yeast. Even in the animal species, the AAUAAA signal does not appear to be as universal as indicated by previous studies. The abundance of single-base variants of AAUAAA correlates with their measured processing efficiencies. As found previously, the plant polyadenylation signals are more similar to those of yeast than to those of animals, with both common content and arrangement of the signal elements. In all species examined, the complete polyadenylation signal appears to consist of an aggregate of multiple elements. In light of these and previous results, we present a broadened concept of 3'-end-processing signals in which no single exact sequence element is universally required for processing. Rather, the total efficiency is a function of all elements and, importantly, an inefficient word in one element can be compensated for by strong words in other elements. These complex patterns indicate that effective tools to identify 3'-end-processing signals will require more than consensus sequence identification.
Two-dimensional thermal-hydraulics analyses of the Pellet Bed Reactor for Nuclear Thermal Propulsion (1993)

Thermal-hydraulics design and analyses of the Pellet Bed Reactor for nuclear thermal propulsion are performed using the nuclear propulsion thermal-hydraulic analysis model to determine the 2D steady-state temperature, pressure, and flow fields in the core and optimize the orificing in the hot-frit to avoid hot spots in the core at full power operation. Results show that by properly adjusting the axial porosity profile in the hot frit, hot spots in the core can be essentially eliminated during full power operation. This important accomplishment is achieved at the expense of slightly larger pressure losses in the core because of flow restriction at the hot frit. However, the overall pressure losses is only about 11 percent of the propellant inlet pressure.
Multi-core Fiber Technology for SDM: Coupling Mechanisms and Design (2021)

This tutorial will describe coupling mechanism and design issues in multi-core fibers for SDM. The effect of random perturbations on the inter-core crosstalk in uncoupled MCFs and modal dispersion in coupled MCFs will be discussed.
Lattice Coding and Decoding for Multiple-Antenna Ergodic Fading Channels (2017)

For ergodic fading, a lattice coding and decoding strategy is proposed and its performance is analyzed for the single-input single-output (SISO) and multiple-input multiple-output (MIMO) point-to-point channel as well as the multiple-access channel (MAC), with channel state information available only at the receiver (CSIR). At the decoder a novel strategy is proposed consisting of a time-varying equalization matrix followed by decision regions that depend only on channel statistics, not individual realizations. Our encoder has a similar structure to that of Erez and Zamir. For the SISO channel, the gap to capacity is bounded by a constant under a wide range of fading distributions. For the MIMO channel under Rayleigh fading, the rate achieved is within a gap to capacity that does not depend on the signal-to-noise ratio (SNR), and diminishes with the number of receive antennas. The analysis is extended to the K-user MAC where similar results hold. Achieving a small gap to capacity while limiting the use of CSIR to the equalizer highlights the scope for efficient decoder implementations, since decision regions are fixed, i.e., independent of channel realizations.
Abstract 15708: In Both Hypertrophic And Dilated Cardiomyopathy, Non-contrast T1 Mapping Provides Myocardial Tissue Characterization Beyond That Achieved By Late Gadolinium Enhancement. (2011)

Introduction: Non contrast T1 mapping provides a novel quantitative method for myocardial tissue characterization. Although T1 mapping has been investigated in ischaemic heart disease, its role in ...
Information-theoretic User Interaction: Significant Inputs for Program Synthesis (2020)

Programming-by-example technologies are being deployed in industrial products for real-time synthesis of various kinds of data transformations. These technologies rely on the user to provide few representative examples of the transformation task. Motivated by the need to find the most pertinent question to ask the user, in this paper, we introduce the {\em significant questions problem}, and show that it is hard in general. We then develop an information-theoretic greedy approach for solving the problem. We justify the greedy algorithm using the conditional entropy result, which informally says that the question that achieves the maximum information gain is the one that we know least about. In the context of interactive program synthesis, we use the above result to develop an {\em{active program learner}} that generates the significant inputs to pose as queries to the user in each iteration. The procedure requires extending a {\em{passive program learner}} to a {\em{sampling program learner}} that is able to sample candidate programs from the set of all consistent programs to enable estimation of information gain. It also uses clustering of inputs based on features in the inputs and the corresponding outputs to sample a small set of candidate significant inputs. Our active learner is able to tradeoff false negatives for false positives and converge in a small number of iterations on a real-world dataset of %around 800 string transformation tasks.
A New Bioartificial Pancreas Utilizing Amphiphilic Membranes for the Immunoisolation of Porcine Islets (2009)

We have developed a replaceable bioartificial pancreas to treat diabetes utilizing a unique cocontinous amphiphilic conetwork membrane created for macroencapsulation and immunoisolation of porcine islet cells (PICs). The membrane is assembled from hydrophilic poly(N,N-dimethyl acrylamide) and hydrophobic/oxyphilic polydimethylsiloxane chains cross-linked with hydrophobic/oxyphilic polymethylhydrosiloxane chains. Our hypothesis is that this membrane allows the survival of xenotransplanted PICs in the absence of prevascularization or immunosuppression because of its extraordinarily high-oxygen permeability and small hydrophilic channel dimensions (3-4 nm). The key components are a 5-10 microm thick semipermeable amphiphilic conetwork membrane reinforced with an electrospun nanomat of polydimethylsiloxane-containing polyurethane, and a laser-perforated nitinol scaffold to provide geometric stability. Devices were loaded with PICs and tested for their ability to maintain islet viability without prevascularization, prevent rejection, and reverse hyperglycemia in three pancreatectomized dogs without immunosuppression. Tissue tolerance was good and there was no systemic toxicity. The bioartificial pancreas protected PICs from toxic environments in vitro and in vivo. Islets remained viable for up to 3 weeks without signs of rejection. Neovascularization was observed. Hyperglycemia was not reversed, most likely because of insufficient islet mass. Further studies to determine long-term islet viability and correction of hyperglycemia are warranted.
Epitaxial lateral overgrowth of InN by rf-plasma-assisted molecular-beam epitaxy (2011)

The orientation-dependent lateral growth of InN was studied and the epitaxial lateral overgrowth (ELO) of InN by rf-plasma-assisted molecular-beam epitaxy was demonstrated for the first time using stripe molybdenum (Mo)-mask-patterned sapphire (0001) substrates. Transmission electron microscopy observation revealed a high dislocation density of ∼5x10-9 cm-2 in the window region. By contrast, very few threading dislocations were observed in the wing region. In particular, there were no threading dislocations in the superficial layer of up to 3 μm width. An InN ELO sample exhibited narrow near-IR emission with a peak photon energy of 0.677 eV and a linewidth of 16.7 meV at 4 K.
Validation of moulding consistency with a self-regulating melt pressure valve (2004)

Net shape manufacturing of plastic products through injection moulding, extrusion and other polymer forming processes has been limited by a lack of observability and controllability of the state of the polymer melt. For this reason, a self-regulating melt pressure valve has been developed that utilizes a valve pin to adjust the juncture loss to balance a provided control force with the force exerted by the melt pressure on an exposed surface of the valve pin. Since the valve pin position is adjusted in accordance with natural laws, an open-loop control system design is feasible without the need for any instrumentation or process feedback for closed-loop control. The process capability of a hot-runner injection moulding process with two self-regulating melt pressure valves is validated with respect to part weight consistency. A resolution four fractional factorial design characterized the main effects for conventional hot-runner injection moulding and injection moulding with the self-regulating valve operated in both open and closed-loop control schemes. It was observed that the self-regulating valve operating in an open-loop control mode reduced the sensitivity of the part weight to changes in the moulding process by 73% compared with conventional injection moulding; short-term part-to-part variation was also reduced by 60%. While it might be expected that closed-loop control would provide even greater results, the relatively slow response of the pneumatic control valve actually tended to induce process variation compared with the open-loop control of the self-regulating valve.
Data from Potentiation of antileukemic therapies by Smac mimetic, LBW242: effects on mutant FLT3-expressing cells (2023)

&lt;div&gt;Abstract&lt;p&gt;Members of the inhibitor of apoptosis protein (IAP) family play a role in mediating apoptosis. Studies suggest that these proteins may be a viable target in leukemia because they have been found to be variably expressed in acute leukemias and are associated with chemosensitivity, chemoresistance, disease progression, remission, and patient survival. Another promising therapeutic target, FLT3, is mutated in about one third of acute myelogenous leukemia (AML) patients; promising results have recently been achieved in clinical trials investigating the effects of the protein tyrosine kinase inhibitor PKC412 on AML patients harboring mutations in the FLT3 protein. Of growing concern, however, is the development of drug resistance resulting from the emergence of point mutations in targeted tyrosine kinases used for treatment of acute leukemia patients. One approach to overriding resistance is to combine structurally unrelated inhibitors and/or inhibitors of different signaling pathways. The proapoptotic IAP inhibitor, LBW242, was shown in proliferation studies done &lt;i&gt;in vitro&lt;/i&gt; to enhance the killing of PKC412-sensitive and PKC412-resistant cell lines expressing mutant FLT3 when combined with either PKC412 or standard cytotoxic agents (doxorubicin and Ara-c). In addition, in an &lt;i&gt;in vivo&lt;/i&gt; imaging assay using bioluminescence as a measure of tumor burden, a total of 12 male NCr-nude mice were treated for 10 days with p.o. administration of vehicle, LBW242 (50 mg/kg/day), PKC412 (40 mg/kg/day), or a combination of LBW242 and PKC412; the lowest tumor burden was observed in the drug combination group. Finally, the combination of LBW242 and PKC412 was sufficient to override stromal-mediated viability signaling conferring resistance to PKC412. [Mol Cancer Ther 2007;6(7):1951–61]&lt;/p&gt;&lt;/div&gt;
The Drosophila snr1 and brm proteins are related to yeast SWI/SNF proteins and are components of a large protein complex. (1995)

During most of Drosophila development the regulation of homeotic gene transcription is controlled by two groups of regulatory genes, the trithorax group of activators and the Polycomb group of repressors. brahma (brm), a member of the trithorax group, encodes a protein related to the yeast SWI2/SNF2 protein, a subunit of a protein complex that assists sequence-specific activator proteins by alleviating the repressive effects of chromatin. To learn more about the molecular mechanisms underlying the regulation of homeotic gene transcription, we have investigated whether a similar complex exists in flies. We identified the Drosophila snr1 gene, a potential homologue of the yeast SNF5 gene that encodes a subunit of the yeast SWI/SNF complex. The snr1 gene is essential and genetically interacts with brm and trithorax (trx), suggesting cooperation in regulating homeotic gene transcription. The spatial and temporal patterns of expression of snr1 are similar to those of brm. The snr1 and brm proteins are present in a large (> 2 x 10(6) Da) complex, and they co-immunoprecipitate from Drosophila extracts. These findings provide direct evidence for conservation of the SWI/SNF complex in higher eucaryotes and suggest that the Drosophila brm/snr1 complex plays an important role in maintaining homeotic gene transcription during development by counteracting the repressive effects of chromatin.