gebhart/patrepeval huggingface dataset:
Why typos in DNA may help to fuel atherogenesis and inflammation prior to heart attacks, ischemic heart disease, and sudden-death ischemic heart disease: roles of unrecognized ionized hypomagnesemia and epigenetics (2020)

When any cell divides, its six billion letters of DNA are copied with each new copy going to each daughter cell. During this duplication process, it is now known that so-called "typos" inevitably occur, and a cell's DNA-proofreading mechanism (s) "usually catch and correct" these typos. But, sometimes this "catch-up and correct mechanism" fails, and if this occurs in certain critical regions of the genome, this can shuttle a cell into a new form of growth and differentiation. Using this hypothesis, a team led by Tomasetti, Liu and Vogelstein, in 2017, with mathematical analyses, suggested "typos in DNA "were found in 32 different cancer types. They attributed these "typos" either to a heredity environment or "random DNA copying errors. Tomasetti et al calculated that 66% of cancer mutations occur from DNA copying errors. Most of the others occurred via environmental factors according to their calculations.
Motion planning in dynamic environments with bounded time temporal logic specifications (2015)

In this paper, we consider the problem of robotic motion planning that satisfies some bounded time high level specifications. Although temporal logic can efficiently express high level specifications such as coverage, obstacle avoidance, temporal ordering of tasks etc., it fails to address problems with explicit timing constraints. The inherent limitations of Linear Temporal Logic (LTL) to address problems with explicit timing constraints have been overcome by translating the planning problem from the workspace of the robot to a higher dimensional space called spacetime where the existing LTL semantics and grammar are sufficient to mathematically formulate the bounded time high level specifications. A discrete path will be generated, that will meet the specifications with all timing constraints and, at the same time, it will optimize some cost function. A continuous trajectory satisfying the continuous dynamics of the robot will be generated from the discrete path using proper control laws.
H.263 to VP6 video transcoder (2007)

VP6 is a video coding standard developed by On2 Technologies. It is the preferred codec in the Flash 8/9 format used by many popular online video services and user generated content sites. The wide adoption of Flash video for video delivery on the Internet has made VP6 one of the most widely used video compression standards on the Internet. With the wide adoption of VP6 comes the need for transcoding other video formats to the VP6 format. This paper presents algorithms to transcode H.263 to the VP6 format. This transcoder has applications in media adaptation including converting older Flash video formats to Flash 8 format. The transcoding algorithms reuse the information from the H.263 decoding stage and accelerate the VP6 encoding stage. Experimental results show that the proposed algorithms are able to reduce the encoding complexity by up to 52% while reducing the PSNR by at most 0.42 dB in the worst case.
Development of optical multi-channel connector for rigid waveguide &#x2014; Fiber optical interconnection (2014)

We propose a newly developed optical multi-channel connector to connect a rigid optical waveguide array and an optical fiber array for an on-board optical interconnection. The prototype of a 24-channel optical card edge connector to connect between a rigid multimode waveguide array fabricated onto a substrate and a multi-mode fiber array is manufactured, and two types of optical connection losses are defined and evaluated by the direction of the optical signal. The optical connection losses from the waveguide to the fiber as transmitting function and from the fiber to the waveguide as receiving function, are less than 0.7 dB and 0.6 dB, respectively.
Functional Group Analysis for Diesel-like Mixing-Controlled Compression Ignition Combustion Blendstocks (2016)

This report addresses the suitability of hydrocarbon and oxygenate functional groups for use as a diesel-like fuel blending component in an advanced, mixing-controlled, compression ignition combustion engine. The functional groups are chosen from those that could be derived from a biomass feedstock, and represent a full range of chemistries. This first systematic analysis of functional groups will be of value to all who are pursuing new bio-blendstocks for diesel-like fuels.
Environmental implications and applications of carbon nanomaterials in water treatment (2013)

Carbon nanomaterials have been proposed as a basis for developing new technologies for photocatalytic oxidation and disinfection, improved membrane processes, adsorbents, and biofilm-resistant surfaces. This study details recent progress towards the development of these proposed applications. We explored the use of carbon nanomaterials such as fullerene C60, single-wall carbon nanotubes (SWCNTs), and multi-wall carbon nanotubes (MWCNTs) for a range of new technologies including, degradation of a probe organic compound by in situ generation of reactive oxygen species (ROS), new strategies for microbial disinfection, and the inhibition of biofilm development on membrane surfaces. The results show that the degradation of 2-chlorophenol by ROS produced microbial inactivation, and the mobility of the nanoparticle aggregates of the carbon nanomaterials all increased as suspensions were fractionated to enrich with smaller aggregates with sonication followed by successive membrane filtration.
Solvent design for catalyst recycling of rhodium/amine catalysts via scCO2 extraction in the reductive hydroformylation of alpha olefins (2022)

Amine modified polyethylene glycol (PEG) derivatives are used as stationary phase to immobilize homogeneous rhodium catalysts during the extraction of alcohols with sc CO 2 .
Personal Attributes Authentication Techniques. (1977)

This research sought to isolate physiological attributes which would be of use in automatic identity verification for access control. The work proceeded in three stages. During the initial phase, over 30 potential physical attributes were evaluated through mathematical modeling, opinion survey, and system analysis. The two best attributes, handprints and a modified electrocardiogram called a 'C-trace'--were selected for in depth study. Data on both attributes was collected on 72 subjects at 3 sessions over 3 months during the 2nd phase. In the 3rd phase, the data was analyzed to determine the type i and ii error rates for identity verification. A type I error is a failure to recognize a legitimate subject, whereas a type II error occurs when an imposter is identified as a legitimate subject. Results were quite encouraging. The handprint achieved a type I error %of 1.4% and a type II of 1.6%. The c-trace performed at a type I of 1.2% and a type II of 1.1%. Arguments which indicate that the handprint results can be improved significantly and the c-trace moderately are given.
Method for the preparation of ethylene-vinyl ether copolymers with a nickel catalyst (2003)

Disclosed is a method for the prepn. of ethylene-vinyl ether copolymers with a nickel catalyst, the copolymers having the general formula -(A)x-(B)y-, where A is -CH2-CH2-, B is -CH2CHOR- with R being a C1-10 hydrocarbyl, preferably a C2-6 alkyl, x (molar fraction of -CH2-CH2-)is 0.6-0.005, preferably 0.7-0.99, y (molar fraction of -CH2CHOR-) is 0.4-0.005, preferably 0.3-0.01. Reaction polymn. of ethylene with vinyl ethers is done in the presence of solvents or diluants, at a pressure of 10-150 bar, temp. of 120-260°, and with a Ni catalytic system having aluminum derivs. as cocatalysts (organo-aluminum compds.), wherein the molar ratio between the co-catalyst and catalyst is 5/1-2000/1.
Illuminating Invisible Grain Boundaries in Coalesced Single-Orientation WS2 Monolayer Films (2021)

Engineering atomic-scale defects is crucial for realizing wafer-scale, single-crystalline transition metal dichalcogenide monolayers for electronic devices. However, connecting atomic-scale defects to larger morphologies poses a significant challenge. Using electron microscopy and ReaxFF reactive force field-based molecular dynamics simulations, we provide insights into WS<sub>2</sub> crystal growth mechanisms, providing a direct link between synthetic conditions and microstructure. Dark-field TEM imaging of coalesced monolayer WS<sub>2</sub> films illuminates defect arrays that atomic-resolution STEM imaging identifies as translational grain boundaries. Electron diffraction and high-resolution imaging reveal that the films have nearly a single orientation with imperfectly stitched domains that tilt out-of-plane when released from the substrate. Imaging and ReaxFF simulations uncover two types of translational mismatch, and we discuss their origin related to relatively fast growth rates. Statistical analysis of >1300 facets demonstrates that microstructural features are constructed from nanometer-scale building blocks, describing the system across sub-Ångstrom to multimicrometer length scales.
Experimental Investigation of Single Micro Tube Steam Engine (2011)

Due to the depletion of fossil fuel resources, more efficient energy conversion technologies are desired. On the other hand, most of the low temperature heat below 300C is wasted, because such heat is spatially distributed in small amounts and its utilization is still expensive. In the present study, a single micro tube oscillating steam engine is investigated. This engine consists of a single tube with heating, insulated and cooling sections and oscillating working fluid. Pressure-volume (P-V) diagrams are experimentally obtained for heating temperatures of 170 and 180 C. The frequency of engine is varied from f = 2 to 14 rps. Mechanical work of 0.6 W is obtained for a 1 mm tube engine at 180 C.
A common allosteric site and mechanism in caspases (2006)

We present a common allosteric mechanism for control of inflammatory and apoptotic caspases. Highly specific thiol-containing inhibitors of the human inflammatory caspase-1 were identified by using disulfide trapping, a method for site-directed small-molecule discovery. These compounds became trapped by forming a disulfide bond with a cysteine residue in the cavity at the dimer interface approximately 15 A away from the active site. Mutational and structural analysis uncovered a linear circuit of functional residues that runs from one active site through the allosteric cavity and into the second active site. Kinetic analysis revealed robust positive cooperativity not seen in other endopeptidases. Recently, disulfide trapping identified a similar small-molecule site and allosteric transition in the apoptotic caspase-7 that shares only a 23% sequence identity with caspase-1. Together, these studies show a general small-molecule-binding site for functionally reversing the zymogen activation of caspases and suggest a common regulatory site for the allosteric control of inflammation and apoptosis.
Nrdp1-Mediated Regulation of ErbB3 Expression by the Androgen Receptor in Androgen-Dependent but not Castrate-Resistant Prostate Cancer Cells (2010)

Patients with advanced prostate cancer (PCa) are initially susceptible to androgen withdrawal (AW), but ultimately develop resistance to this therapy (castration-resistant PCa, CRPC). Here, we show that AW can promote CRPC development by increasing the levels of the receptor tyrosine kinase ErbB3 in androgen-dependent PCa, resulting in AW-resistant cell cycle progression and increased androgen receptor (AR) transcriptional activity. CRPC cell lines and human PCa tissue overexpressed ErbB3, whereas downregulation of ErbB3 prevented CRPC cell growth. Investigation of the mechanism by which AW augments ErbB3, using normal prostate-derived pRNS-1-1 cells, and androgen-dependent PCa lines LNCaP, PC346C, and CWR22 mouse xenografts, revealed that the AR suppresses ErbB3 protein levels, whereas AW relieves this suppression, showing for the first time the negative regulation of ErbB3 by AR. We show that AR activation promotes ErbB3 degradation in androgen-dependent cells, and that this effect is mediated by AR-dependent transcriptional upregulation of neuregulin receptor degradation protein-1 (Nrdp1), an E3 ubiquitin ligase that targets ErbB3 for degradation but whose role in PCa has not been previously examined. Therefore, AW decreases Nrdp1 expression, promoting ErbB3 protein accumulation, and leading to AR-independent proliferation. However, in CRPC sublines of LNCaP and CWR22, which strongly overexpress the AR, ErbB3 levels remain elevated due to constitutive suppression of Nrdp1, which prevents AR regulation of Nrdp1. Our observations point to a model of CRPC development in which progression of PCa to castration resistance is associated with the inability of AR to transcriptionally regulate Nrdp1, and predict that inhibition of ErbB3 during AW may impair CRPC development.
Back-Pressure Routing for Intermittently Connected Networks (2010)

We study a mobile wireless network where groups or clusters of nodes are intermittently connected via mobile "carriers'' (the carriers provide connectivity over time among different clusters of nodes). Over such networks (an instantiation of a delay tolerant network), it is well-known that traditional routing algorithms perform very poorly. In this paper, we propose a two-level Back- Pressure with Source-Routing algorithm (BP+SR) for such networks. The proposed BP+SR algorithm separates routing and scheduling within clusters (fast time-scale) from the communications that occur across clusters (slow time-scale), without loss in network throughput (i.e., BP+SR is throughput-optimal). More importantly, for a source and destination node that lie in different clusters, the traditional back-pressure algorithm results in large queue lengths at each node along its path. This is because the queue dynamics are driven by the slowest time-scale (i.e., that of the carrier nodes) along the path between the source and destination, which results in very large end-to-end delays. On the other-hand, we show that the two-level BP+SR algorithm maintains large queues only at a very few nodes, and thus results in order-wise smaller end-to-end delays. We provide analytical as well as simulation results to confirm our claims.
IEEE Access Special Section Editorial: Security in Wireless Communications and Networking (2018)

Wireless communications and networking have experienced explosive growth during the last years so that security issues are a crucial aspect for networks and system design. Thus, the purpose of this Special Section in IEEE Access was to publish innovative and theoretically-grounded research tackling the fundamental and practical challenges of wireless communications and networking security. This Special Section brought together leading researchers and developers from both industry and academia to discuss and present their views on the current trends, challenges, and state-of-the-art solutions addressing various issues related to security in wireless communications and networking. We received a total of 28 submissions, and after a rigorous review process, 13 articles have been selected for publication, which are briefly discussed next.
Figure S1 from Validation of a Plasma-Based Comprehensive Cancer Genotyping Assay Utilizing Orthogonal Tissue- and Plasma-Based Methodologies (2023)

&lt;p&gt;Genes on the Guardant360 panel.&lt;/p&gt;
Nitric Oxide Generated by Tumor-Associated Macrophages Is Responsible for Cancer Resistance to Cisplatin and Correlated With Syntaxin 4 and Acid Sphingomyelinase Inhibition (2018)

Tumor microenvironment is fundamental for cancer progression and chemoresistance. Among stromal cells tumor-associated macrophages (TAMs) represent the largest population of infiltrating inflammatory cells in malignant tumors, promoting their growth, invasion, and immune evasion. M2-polarized TAMs are endowed with the nitric oxide (NO)-generating enzyme inducible nitric oxide synthase (iNOS). NO has divergent effects on tumors, since it can either stimulate tumor cells growth or promote their death depending on the source of it; likewise the role of iNOS in cancer differs depending on the cell type. The role of NO generated by TAMs has not been investigated. Using different tumor models <i>in vitro</i> and <i>in vivo</i> we found that NO generated by iNOS of M2-polarized TAMs is able to protect tumor cells from apoptosis induced by the chemotherapeutic agent cisplatin (CDDP). Here, we demonstrate that the protective effect of NO depends on the inhibition of acid sphingomyelinase (A-SMase), which is activated by CDDP in a pathway involving the death receptor CD95. Mechanistic insights indicate that NO actions occur <i>via</i> generation of cyclic GMP and activation of protein kinase G (PKG), inducing phosphorylation of syntaxin 4 (synt4), a SNARE protein responsible for A-SMase trafficking and activation. Noteworthy, phosphorylation of synt4 at serine 78 by PKG is responsible for the proteasome-dependent degradation of synt4, which limits the CDDP-induced exposure of A-SMase to the plasma membrane of tumor cells. This inhibits the cytotoxic mechanism of CDDP reducing A-SMase-triggered apoptosis. This is the first demonstration that endogenous NO system is a key mechanism through which TAMs protect tumor cells from chemotherapeutic drug-induced apoptosis. The identification of the pathway responsible for A-SMase activity downregulation in tumors leading to chemoresistance warrants further investigations as a means to identify new anti-cancer molecules capable of specifically inhibiting synt4 degradation.
Supplementary Table 3 from <i>HOXB13</i> G84E Mutation in Finland: Population-Based Analysis of Prostate, Breast, and Colorectal Cancer Risk (2023)

&lt;p&gt;PDF file - 38K, Table includes the results of six tolerance predictors and two protein stability predictors included in Pon-P selected for in silico analysis.&lt;/p&gt;
Will Computes Ever Be Secure (2016)

These days, it feels like news reports about data security breaches are commonplace. It looks like as if the attackers won and securing IT systems is a Sisyphean task.In this talk, I will motivate the challenges of building secure systems and provide insights into the (fundamental) questions if we can build a computer program that decides if a system secure or not.
Animal models of vulnerable plaque (2007)

Pioneering work by pathologists, including Erling Falk and the late Michael Davies, established that structural disruption of atherosclerotic plaques is the main mechanism underlying myocardial infarctions and strokes.1 Key histologic features of disrupted plaques include thinning of the fibrous cap and depletion of structural collagens that provide most of the tensile strength.1 These observations suggest that dysregulated protease activity is responsible for weakening the plaque cap. In this chapter, we consider the evidence that matrix metalloproteinases (MMPs) promote plaque vulnerability and are therefore an appropriate target for plaque-stabilizing therapy.
Sirt6 regulates lifespan in Drosophila melanogaster (2022)

Significance Sirt6 is well known for its role in regulating the aging process, particularly for its ability to extend lifespan in mice when overexpressed. However, the underlying molecular mechanisms responsible for lifespan regulation by Sirt6 are not well understood. Here, we characterized dSirt6 in fruit flies ( Drosophila melanogaster ). We found that dSirt6 functions very similarly to mammalian Sirt6 at the molecular and biochemical levels. Furthermore, overexpressing dSirt6 increased lifespan in flies. dSirt6 overexpression extends lifespan, in part, by opposing the activity of Myc, a master regulator of protein synthesis, which is associated with decreased protein synthesis. These findings have relevance for the treatment of age-related disease by modulating Sirt6 activity.
Effect of Carbide Size Distribution on the Impact Toughness of Tempered Martensitic Steels with Two Different Prior Austenite Grain Sizes Evaluated by Instrumented Charpy Test (2013)

The effect of tempering temperature on the impact toughness of 0.3 mass% carbon martensitic steels with prior austenite grain (PAG) size of about 6 and 60 µm was investigated. Instrumented Charpy impact test (ICIT) was used to evaluate the impact toughness. The tempering temperature of 723 K gives the largest difference in the Charpy impact energy at room temperature between the specimens with two different PAG sizes, where the finer PAG specimen shows higher impact energy at room temperature (RT). The other tempering temperatures do not show a significant difference as compared with that shown among the 723 K tempered specimens. Investigation of the test temperature dependence of Charpy impact energy in the 723 K tempered steels shows a steep transition at around 200 K for the 6 µm PAG specimen, while it shows a continuous slow transition in a wide range of temperatures for the 60 µm PAG specimen. ICIT waveform analysis of these steels shows that the fracture propagation energy mainly controls the temperature dependence of the impact energy, while the fracture initiation energy stays nearly constant against the variation of the test temperature. The carbide size distribution in these two specimens was investigated by secondary electron microscope (SEM) and transmission electron microscope (TEM). The 60 µm PAG specimen shows distribution of coarser carbide than does the 6 µm PAG specimen, which seems to give rise to the observed difference between them in the Charpy impact energy and the other properties of impact fracture.
Interferometric spectrally encoded confocal scanning laser ophthalmoscopy (2010)

We present in vivo human fundus imaging using interferometric spectrally encoded confocal scanning laser ophthalmoscopy (iSECSLO). iSECSLO allows for video-rate fully confocal imaging with the interferometric advantage of optical coherence tomography though single-mode optical fiber.
Engineering Cortical Neuron Polarity with Nanomagnets on a Chip (2015)

Intra- and extracellular signaling play critical roles in cell polarity, ultimately leading to the development of functional cell-cell connections, tissues, and organs. In the brain, pathologically oriented neurons are often the cause for disordered circuits, severely impacting motor function, perception, and memory. Aside from control through gene expression and signaling pathways, it is known that nervous system development can be manipulated by mechanical stimuli (e.g., outgrowth of axons through externally applied forces). The inverse is true as well: intracellular molecular signals can be converted into forces to yield axonal outgrowth. The complete role played by mechanical signals in mediating single-cell polarity, however, remains currently unclear. Here we employ highly parallelized nanomagnets on a chip to exert local mechanical stimuli on cortical neurons, independently of the amount of superparamagnetic nanoparticles taken up by the cells. The chip-based approach was utilized to quantify the effect of nanoparticle-mediated forces on the intracellular cytoskeleton as visualized by the distribution of the microtubule-associated protein tau. While single cortical neurons prefer to assemble tau proteins following poly-L-lysine surface cues, an optimal force range of 4.5-70 pN by the nanomagnets initiated a tau distribution opposed to the pattern cue. In larger cell clusters (groups comprising six or more cells), nanoparticle-mediated forces induced tau repositioning in an observed range of 190-270 pN, and initiation of magnetic field-directed cell displacement was observed at forces above 300 pN. Our findings lay the groundwork for high-resolution mechanical encoding of neural networks in vitro, mechanically driven cell polarization in brain tissues, and neurotherapeutic approaches using functionalized superparamagnetic nanoparticles to potentially restore disordered neural circuits.