gebhart/patrepeval huggingface dataset:
High‐resolution mapping of amplifications and deletions in pediatric osteosarcoma by use of CGH analysis of cDNA microarrays (2003)

Conventional cytogenetic and comparative genomic hybridization (CGH) studies have shown that osteosarcomas (OSs) are characterized by complex structural and numerical chromosomal alterations and gene amplification. In this study, we used high-resolution CGH to investigate recurrent patterns of genomic imbalance by use of DNA derived from nine OS tumors hybridized to a 19,200-clone cDNA microarray. In six OSs, there was copy number gain or amplification of 6p, with a minimal region of gain centering on segment 6p12.1. In seven OSs, the pattern of amplification affecting chromosome arm 8q showed high-level gains of 8q12-21.3 and 8q22-q23, with amplification of the MYC oncogene at 8q24.2. Seven OSs showed copy number gain or amplification of 17p between the loci bounded by GAS7 and PMI (17p11.2-17p12), and three of these tumors also showed small losses at 17p13, including the region containing TP53. An in silico analysis of the distribution of segmental duplications (duplicons) in this region identified a large number of tracts consisting of paralogous sequences mapping to the 17p region, encompassing the region of deletions and amplifications in OS. Interestingly, within this same region there were clusters of duplicons and several genes that are expressed during bone morphogenesis and in OS. In summary, microarray CGH analysis of the chromosomal imbalances of OS confirm the overall pattern observed by use of metaphase CGH and provides a more precise refinement of the boundaries of genomic gains and losses that characterize this tumor.
Human T-cell lymphotropic virus oncoprotein Tax represses TGF-β1 signaling in human T cells via c-Jun activation: a potential mechanism of HTLV-I leukemogenesis (2002)

Human T-cell leukemia virus I is the etiologic agent of adult T-cell leukemia (ATL), an aggressive T-cell malignancy. The viral oncoprotein Tax, through the activation of nuclear factorkappaB (NF-kappaB), CCAAT-enhancer binding protein (CREB), and activated protein-1 (AP-1) pathways, is a transcriptional regulator of critical genes for T-cell homeostasis. In ATL cells, activated AP-1 complexes induce the production of transforming growth factor beta1 (TGF-beta1). TGF-beta1 is an inhibitor of T-cell proliferation and cytotoxicity. Here we show that, in contrast to normal peripheral T cells, ATL cells are resistant to TGF-beta1-induced growth inhibition. The retroviral transduction of the Tax protein in peripheral T cells resulted in the loss of TGF-beta1 sensitivity. Transient transfection of Tax in HepG2 cells specifically inhibited Smad/TGF-beta1 signaling in a dose-dependent manner. In the presence of Tax transfection, increasing amounts of Smad3 restored TGF-beta1 signaling. Tax mutants unable to activate NF-kappaB or CREB pathways were also able to repress Smad3 transcriptional activity. Next we have demonstrated that Tax inhibits TGF-beta1 signaling by reducing the Smad3 DNA binding activity. However, Tax did not decrease the expression and the nuclear translocation of Smad3 nor did it interact physically with Smad3. Rather, Tax induced c-Jun N-terminal kinase (JNK) activity and c-Jun phosphorylation, leading to the formation of Smad3/c-Jun complexes. Whereas c-Jun alone abrogates Smad3 DNA binding, cotransfection of Tax and of a dominant-negative form of JNK or a c-Jun antisense-restored Smad3 DNA binding activity and TGF-beta1 responsiveness. In ATL and in normal T cells transduced by Tax, c-Jun was constitutively phosphorylated. Thus, we describe a new function of Tax, as a repressor of TGF-beta1 signaling through JNK/c-Jun constitutive activation, which may play a critical role in ATL leukemogenesis.
Highly Pathogenic Avian Influenza Virus Infection in Feral Raccoons, Japan (2011)

Although raccoons (Procyon lotor) are susceptible to influenza viruses, highly pathogenic avian influenza virus (H5N1) infection in these animals has not been reported. We performed a serosurvey of apparently healthy feral raccoons in Japan and found specific antibodies to subtype H5N1 viruses. Feral raccoons may pose a risk to farms and public health.
Formation of wormlike micelles and vesicles in thermoset resins (2002)

We report the formation of wormlike micelles and vesicles in a system of self-assembled reactive block copolymer-high temperature novolac epoxy nanocomposites. The mixtures of reactive poly(methyl acrylate-co-glycidyl methacrylate)-b-polyisoprene (MG5.5kI6k) block copolymer with a commercial high temperature novolac epoxy resin (Epon 164) were cured with 4,4’-methylene aniline (MDA). Incorporating epoxy-reactive functionality in one block enables the MG5.5kI6k copolymer to template the epoxy resin. The cured materials were characterized by transmission electron microscopy and small-angle X-ray scattering. Macroscopic phase separation was absent with MG5.5kI6k content up to 30 wtstructures with nanoscopic features. Vesicles were formed in the reactive block copolymer-high temperature epoxy nanocomposites containing 2.5-10 wtblock copolymer. Wormlike micelles were observed in the nanocomposites containing 20 and 30 wtcopolymer.
Fractal Sampling Grids For Holographic Interconnections (1989)

The optical implementation of weighted interconnections is investigated and basic relationships are derived between the number of neurons, the number of connections and the size of the optical system that is used to perform the connections. Specific methods for selecting the positions of the neurons to achieve the maximum density of independent connections are presented.
Influence of motor operating parameters on discharge bearing current activity (2010)

While the cause-and-effect chains of inverter-induced bearing currents have been well understood today, not much is known about the damage mechanism inside the bearings. Research has suggested that the bearing degradation is approximately proportional to the frequency of occurrence of the bearing currents. For bearing currents that occur statistically distributed-such as discharge bearing currents-this parameter has not been thoroughly researched yet. In this paper, we present an analysis of the influence of different motor operating parameters on the frequency of occurrence (“discharge activity”) of discharge bearing currents, using a non-intrusive detection method. When analyzed individually, the motor speed, motor shaft temperature, inverter switching frequency, and inverter dc-link voltage influence the discharge activity. However, the overall running time of the motor, the state-steady-state versus instantaneous-and the “operating history” on the time-scale of several days have the strongest effect on the frequency of the discharge bearing current occurrence.
25  Gbps low-voltage waveguide Si–Ge avalanche photodiode (2016)

Silicon-germanium (Si–Ge)-based avalanche photodiodes (APDs) have shown a significant improvement in receiver sensitivity compared to their III–V counterparts due to the superior impact ionization property of silicon. However, conventional Si–Ge APDs typically operate at high voltages and low speed, limiting the application of this technology to data communication. In this paper, we present a waveguide Si–Ge avalanche photodiode using a thin silicon multiplication region with a breakdown voltage of −10  V, a speed of 25 GHz, and a gain-bandwidth product (GBP) of 276 GHz. At 1550 nm, sensitivities of −25  dBm and −16  dBm are achieved at 12.5 Gbps and 25 Gbps, respectively. This design will enable implementation of Si–Ge APDs for optical interconnects in data centers and high-performance computers, allowing significant reductions in aggregate system laser power (and therefore cost).
Analysis of deep brain stimulation electrode characteristics for neural recording (2014)

This study determined recording conditions and electrode designs that influence ECAP and LFP recording fidelity.
Trapping constant, thermal conductivity, and the microstructure of suspensions of oriented spheroids (1991)

The n-point probability function Sn(rn) is fundamental to the study of the macroscopic properties of two-phase random heterogeneous media. This quantity gives the probability of finding n points with positions rn ≡{r1,...,rn} all in one of the phases, say phase 1. For media composed of distributions of oriented, possibly overlapping, spheriods of one material with aspect ratio ε in a ‘‘matrix’’ of another material, it is shown that there is a scaling relation that maps results for the Sn for sphere systems (ε=1) into equivalent results for spheriod systems with arbitrary aspect ratio ε. Using this scaling relation it is then demonstrated that certain transport and microstructural properties of spheriodal systems generally depend upon purely shape-dependent functions and lower-order spatial moments of S2 (minus its long-range value) of the equivalent spherical system. Specifically, the following three distinct calculations are carried out for both hard, oriented spheroids and overlapping (i.e., spatially uncorrelated), oriented spheroids: (1) bounds on the diffusion-controlled trapping constant; (2) bounds on the effective conductivity tensor; and (3) fluctuations in the local volume fraction as measured by the ‘‘coarseness.’’ These computations enable us to investigate the effects of statistical anisotropy (i.e., particle asymmetry) and particle exclusion volume on the aforementioned quantities.
Systems and methods for expanding flow in a waste heat recovery system (2023)

A waste heat recovery system includes a first heat exchanger, a second heat exchanger, and an expander. The first heat exchanger receives working fluid from a first portion of a first loop and provides the working fluid to a second portion of the first loop. The second heat exchanger receives the working fluid from a first portion of a second loop and provides the working fluid to a second portion of the second loop. The expander provides the working fluid to a first portion of a common line. The expander includes a stator. The stator includes a first inlet and a second inlet. The common line provides the working fluid to both the first loop and the second loop upstream of the first portion of the first loop and upstream of the first portion of the second loop.
A New Method to Lightweight Magnesium Using Syntactic Composite Core (2020)

Light weighting of magnesium-based materials is crucial for its extensive use in transportation applications. Hybrid processing of these materials in a shell-core pattern can substantially improve the specific properties of magnesium. In the present study, the Mg/Mg-20GMB (glass microballoon) hybrid composite was prepared using a disintegrated melt deposition technique. Microstructural characterization and mechanical properties of the developed as-cast Mg/Mg-20GMB hybrid composite were investigated. Results revealed that a unified metallurgical interface was formed between the Mg-20GMB core material and the pure Mg shell. Energy dispersive X-ray spectroscopy (EDX) results confirmed the existence of Mg2Si as the secondary phase in the Mg-20GMB core material. The hybrid Mg/Mg-20GMB composite exhibited much superior compressive yield strength (↑71.6%), lower ultimate compressive strength (↓23.25%), and enhanced ductility (↑186.48%) when compared to as-cast pure magnesium.
Anionic Lipid Nanoparticles Preferentially Deliver mRNA to the Hepatic Reticuloendothelial System (2022)

Lipid nanoparticles (LNPs) are the leading nonviral technologies for the delivery of exogenous RNA to target cells in vivo. As systemic delivery platforms, these technologies are exemplified by Onpattro, an approved LNP-based RNA interference therapy, administered intravenously and targeted to parenchymal liver cells. The discovery of systemically administered LNP technologies capable of preferential RNA delivery beyond hepatocytes has, however, proven more challenging. Here, preceded by comprehensive mechanistic understanding of in vivo nanoparticle biodistribution and bodily clearance, an LNP-based messenger RNA (mRNA) delivery platform is rationally designed to preferentially target the hepatic reticuloendothelial system (RES). Evaluated in embryonic zebrafish, validated in mice, and directly compared to LNP-mRNA systems based on the lipid composition of Onpattro, RES-targeted LNPs significantly enhance mRNA expression both globally within the liver and specifically within hepatic RES cell types. Hepatic RES targeting requires just a single lipid change within the formulation of Onpattro to switch LNP surface charge from neutral to anionic. This technology not only provides new opportunities to treat liver-specific and systemic diseases in which RES cell types play a key role but, more importantly, exemplifies that rational design of advanced RNA therapies must be preceded by a robust understanding of the dominant nano-biointeractions involved.
Approaches to crystallization from ionic liquids: complex solvents–complex results, or, a strategy for controlled formation of new supramolecular architectures? (2006)

There are now more than 1200 papers a year describing research results using the 'neoteric' solvents, known as ionic liquids (ILs). If ILs are such highly studied solvents, why has there been so comparatively little research in their use in crystallization? Here we explore this question and discuss possible strategies for utilization of the mundane and the unique aspects of ILs for novel crystallization strategies including crystallization of high and low melting solids using thermal shifts; "solvothermal" techniques; slow diffusion; electrocrystallization; and use of a co-solvent. The results presented here and those appearing in the literature indicate both the complex nature of these solvents and their promise in delivering unique solvation, metal ion coordination numbers, coordination polymer motifs, and metal-anion interactions, to name but a few. These complex, but fascinating, results and the promise of much more intimate control over crystallization processes will drive a growing interest in using ILs as crystallization solvents.
The influence of the angle of incidence in megasonic cleaning (2010)

Abstract. The megasonic cleaning efficiency is evaluated as a function of the angle of incidence of acoustic waves on a Si wafer. Acoustic Schlichting streaming alone is not able to remove nanoparticles smaller than 400 nm. It is shown that oscillating or collapsing behavior of bubbles are responsible for removing nanoparticles smaller than 400 nm during a cleaning process with ultrasound. Optimal particle removal efficiency is obtained around the angle of acoustic transmission of the silicon wafer.
HIV Diversity Considerations in the Application of the Intact Proviral DNA Assay (IPDA) (2020)

Opening Paragraph (serves as abstract for submission) and Body The Intact Proviral DNA Assay (IPDA) was developed to address the critical need for a precise and scalable method for intact HIV reservoir quantification 1 . This duplexed droplet digital PCR (ddPCR) assay simultaneously targets the HIV Packaging Signal (Ψ) and the Rev Responsive Element (RRE) within Envelope ( env ) to distinguish genomically intact proviruses against a large background of defective ones 2 . The IPDA requires less time, resources, and biological material than the gold standard for replication-competent HIV reservoir measurement, the Quantitative Viral Outgrowth Assay (QVOA) 3 , and is being adopted in research and clinical studies 4–7 . In our cohort of HIV-1 subtype B-infected individuals from North America however, the IPDA yielded a 28% failure rate due to HIV polymorphism. We further demonstrate that within-host HIV diversity can lead the IPDA to underestimate intact HIV reservoir size, which could negatively impact clinical trial results interpretation. While the IPDA represents an important methodological advance, HIV diversity should be addressed before its widespread adoption.
Effects of Donor Fibroblasts Expressing OCT4 on Bovine Embryos Generated by Somatic Cell Nuclear Transfer (2013)

The production of healthy, live, cloned animals by somatic cell nuclear transfer (SCNT) has been hampered by low efficiencies. Significant epigenetic changes must take place to ensure proper chromatin remodeling in SCNT. We hypothesized that exogenous expression of OCT4 in donor fibroblasts prior to its fusion with enucleated oocytes would facilitate SCNT reprogramming. We infected bovine adult fibroblasts with retroviral vectors containing yellow fluorescent protein (YFP) only, or the OCT4 gene fused to YFP (YO). We found that development to the blastocyst stage was not different between NT-YFP and NT-YO groups. NT-YFP embryos had the fewest trophoblast cells, measured by numbers of CDX2-positive cells. Fibroblasts expressing OCT4 had reduced levels of histone 3 lysine 9 or 27 trimethylation (H3K9me3 and H3K27me3, respectively). NT-YO blastocysts displayed higher H3K9me3 levels than IVF and NT-YFP embryos; however, they did not have different H3K27me3 levels. Levels of XIST mRNA expression in NT-YO and NT-YF were higher when compared to in vitro-fertilized blastocysts. We observed no differences in the expression of SOX2, NANOG, and CDX2. Although overexpression of OCT4 in donor cells increased H3K9me3 and did not reduce XIST gene expression, we show that a single transcription factor can affect the number of trophectoderm cells in bovine SCNT embryos.
Silane grafting and moisture crosslinking of polypropylene (2010)

Abstract Different approaches for free‐radical initiated grafting of functional monomers to polypropylene (PP) have been investigated with a view to enabling crosslinking of the polymer upon subsequent exposure to moisture, resulting in gel contents as high as 50–60 wt%. The first approach involved grafting a co‐agent such as triallyl trimellitate (TATM) to the polymer using peroxide initiator to add carbon–carbon double bond functionality to the polymer, followed by peroxide‐initiated grafting of mercaptopropyltrimethoxysilane (MPTMS) to the PP‐TATM adduct. The second approach was the more traditional peroxide‐mediated grafting of vinyltrimethoxysilane (VTMS) to polypropylene, and was most effective at increasing melt state dynamic storage modulus. In the third approach, peroxide‐mediated grafting of VTMS was followed by peroxide‐initiated grafting of MPTMS. This process took advantage of the unsaturation created via chain scission in the first step to provide graft sites for the MPTMS in the second step. POLYM. ENG. SCI., 2011. © 2010 Society of Plastics Engineers
Amsterdam Oxford Joint Rescue Forces: Team description paper: Virtual Robot competition: Rescue Simulation League: RoboCup 2008 (2008)

With the progress made in active exploration, the robots of the Joint Rescue Forces are capable of making deliberative decisions about the frontiers to be explored. The robots select the frontiers having maximum information gain, taking into account potential communication limitations. The robots incorporate the positions of their team mates into their decisions, to optimize the gain for the team as a whole. Active exploration is based on a shared occupancy map, which is generated online. The images of the omnidirectional camera can be used to automatically detect victims and to add additional information to the map.
Phosphodiesterase type 5 (PDE5) inhibition and cognitive enhancement (2005)

Drug development for the treatment of dementia and age-related cognitive decline has been slow to produce clinically viable alternatives to the two existing FDA approved drug treatments, AChE inhibitors and the noncompetitive NMDA receptor antagonist, memantine. Recent human and preclinical animal studies suggest that phosphodiesterase type 5 (PDE5) inhibitors, already in clinical use for the treatment of erectile dysfunction in men, may have central cognitive enhancing effects. Recent behavioral pharmacological studies with rodents demonstrate that PDE5 inhibitors improve memory consolidation in young animals using passive avoidance and object recognition tasks. In addition, we have shown that pretraining administration of the PDE5 inhibitor sildenafil citrate can attenuate a spatial learning impairment in the 14-unit T-maze. Research findings with aged animals show that pretraining administration of sildenafil can improve the long-term retention of spatial memory 1 week following maze acquisition. We propose that the available research findings provide preclinical support for a possible alternative use of PDE5 inhibitors as cognitive enhancing agents that improve different kinds of learning and memory and protect brain systems against neurodegeneration.
Neural Mesh Flow: 3D Manifold Mesh Generation via Diffeomorphic Flows (2020)

Meshes are important representations of physical 3D entities in the virtual world. Applications like rendering, simulations and 3D printing require meshes to be manifold so that they can interact with the world like the real objects they represent. Prior methods generate meshes with great geometric accuracy but poor manifoldness. In this work, we propose Neural Mesh Flow (NMF) to generate two-manifold meshes for genus-0 shapes. Specifically, NMF is a shape auto-encoder consisting of several Neural Ordinary Differential Equation (NODE)[1] blocks that learn accurate mesh geometry by progressively deforming a spherical mesh. Training NMF is simpler compared to state-of-the-art methods since it does not require any explicit mesh-based regularization. Our experiments demonstrate that NMF facilitates several applications such as single-view mesh reconstruction, global shape parameterization, texture mapping, shape deformation and correspondence. Importantly, we demonstrate that manifold meshes generated using NMF are better-suited for physically-based rendering and simulation. Code and data are released.
High-temperature sensors for NO and NO2 based on stabilized zirconiaand spinel-type oxide electrodes (1997)

Zirconia-based electrochemical devices attached with an oxide sensing electrode have been examined for gas sensing properties towards NO and NO 2 at high temperature. Among the twelve kinds of spinel-type oxides tested, CdCr 2 O 4 was the most sensitive electrode material to both NO and NO 2 in air at 500–600 °C, also being endowed with quick response and recovery characteristics. Values of E EMF of the CdCr 2 O 4 -attached device decreased or increased linearly with an increase in the logarithm of NO or NO 2 concentration, respectively. The same device gave small or insignificant cross-sensitivities to H 2 , CO, CH 4 , CO 2 and H 2 O. Sensing mechanisms involving mixed potential were confirmed from the measurements of polarization curves.
Modelling Human Clarification Strategies (2013)

We model human responses to speech recognition errors from a corpus of human clarification strategies. We employ learning techniques to study 1) the decision to either stop and ask a clarification question or to continue the dialogue without clarification, and 2) the decision to ask a targeted clarification question or a more generic question. Targeted clarification questions focus specifically on the part of an utterance that is misrecognized, in contrast with generic requests to ‘please repeat’ or ‘please rephrase’. Our goal is to generate targeted clarification strategies for handling errors in spoken dialogue systems, when appropriate. Our experiments show that linguistic features, in particular the inferred part-ofspeech of a misrecognized word are predictive of human clarification decisions. A combination of linguistic features predicts a user’s decision to continue or stop a dialogue with accuracy of 72.8 % over a majority baseline accuracy of 59.1%. The same set of features predict the decision to ask a targeted question with accuracy of 74.6 % compared with the majority baseline of 71.8%. 1 1