gebhart/patrepeval huggingface dataset:
Cold‐inducible RNA‐binding protein (CIRP) regulates target mRNA stabilization in the mouse testis (2012)

Cold‐inducible RNA‐binding protein (CIRP) is an RNA‐binding protein that is expressed in normal testis and down‐regulated after heat stress. Recent studies suggest that CIRP contributes to male fertility problems but the mechanisms are unclear. The purpose of this study was to identify the likely mechanism of CIRP in reproduction. Based on the RNA‐Binding Protein Immunoprecipitation‐Microarray (Chip) Profiling (RIP‐Chip) and biotin pull‐down assays, we found that the mRNAs binding with CIRP in testis were mostly associated with translation regulator activity, antioxidant activity, envelope and reproduction, including important mRNAs related to male infertility. We also discovered that (Un)( n ⩾ 2) was the possible core recognition sequence, and the binding mRNAs increased their stabilization. Our results improve our understanding of the mechanism by which heat stress causes male infertility.
Fundamental controls on fluid flow in carbonates: current workflows to emerging technologies (2014)

Abstract The introduction reviews topics relevant to the fundamental controls on fluid flow in carbonate reservoirs and to the prediction of reservoir performance. The review provides research and industry contexts for papers in this volume only. A discussion of global context and frameworks emphasizes the value yet to be captured from compare and contrast studies. Multidisciplinary efforts highlight the importance of greater integration of sedimentology, diagenesis and structural geology. Developments in analytical and experimental methods, stimulated by advances in the materials sciences, support new insights into fundamental (pore-scale) processes in carbonate rocks. Subsurface imaging methods relevant to the delineation of heterogeneities in carbonates highlight techniques that serve to decrease the gap between seismically resolvable features and well-scale measurements. Methods to fuse geological information across scales are advancing through multiscale integration and proxies. A surge in computational power over the last two decades has been accompanied by developments in computational methods and algorithms. Developments related to visualization and data interaction support stronger geoscience–engineering collaborations. High-resolution and real-time monitoring of the subsurface are driving novel sensing capabilities and growing interest in data mining and analytics. Together, these offer an exciting opportunity to learn more about the fundamental fluid-flow processes in carbonate reservoirs at the interwell scale.
Recent Advances in Biomaterials for 3D Printing and Tissue Engineering (2018)

Three-dimensional printing has significant potential as a fabrication method in creating scaffolds for tissue engineering. The applications of 3D printing in the field of regenerative medicine and tissue engineering are limited by the variety of biomaterials that can be used in this technology. Many researchers have developed novel biomaterials and compositions to enable their use in 3D printing methods. The advantages of fabricating scaffolds using 3D printing are numerous, including the ability to create complex geometries, porosities, co-culture of multiple cells, and incorporate growth factors. In this review, recently-developed biomaterials for different tissues are discussed. Biomaterials used in 3D printing are categorized into ceramics, polymers, and composites. Due to the nature of 3D printing methods, most of the ceramics are combined with polymers to enhance their printability. Polymer-based biomaterials are 3D printed mostly using extrusion-based printing and have a broader range of applications in regenerative medicine. The goal of tissue engineering is to fabricate functional and viable organs and, to achieve this, multiple biomaterials and fabrication methods need to be researched.
Via precise interface engineering towards bioinspired composites with improved 3D printing processability and mechanical properties (2017)

Precise interface engineering in inorganic-organic hybrid materials enhances both the elastic moduli and toughness of a biodegradable composite, which is of relevance for load-bearing applications in bone tissue engineering. Tailor-made MgF<sub>2</sub>-binding peptide-polymer conjugates (MBC) are utilized as precision compatibilizers, having sequence-specific affinity for the surfaces of the inorganic MgF<sub>2</sub> fillers to stabilize these particles and to contribute to the interactions with the continuous polymer matrix. The effects of the coupling agents are investigated in additively biomanufactured scaffolds from composites composed of MBC compatibilized magnesium fluoride nanoparticles (cMgF<sub>2</sub>) and poly(ε-caprolactone). Mechanical properties, degradation behavior, ion release kinetics and in vitro cell viability are positively influenced by the presence of the compatibilized nanoparticles cMgF<sub>2</sub> compared to pure, non-compatibilized MgF<sub>2</sub> (pMgF<sub>2</sub>). Mechanical tensile, compression and indentation experiments with single filaments as well as with scaffolds a reveal strong improvement of both elastic moduli and material toughness.
On Tensors, Sparsity, and Nonnegative Factorizations (2012)

Tensors have found application in a variety of fields, ranging from chemometrics to signal processing and beyond. In this paper, we consider the problem of multilinear modeling of sparse count data. Our goal is to develop a descriptive tensor factorization model of such data, along with appropriate algorithms and theory. To do so, we propose that the random variation is best described via a Poisson distribution, which better describes the zeros observed in the data as compared to the typical assumption of a Gaussian distribution. Under a Poisson assumption, we fit a model to observed data using the negative log-likelihood score. We present a new algorithm for Poisson tensor factorization called CANDECOMP-PARAFAC Alternating Poisson Regression (CP-APR) that is based on a majorization-minimization approach. It can be shown that CP-APR is a generalization of the Lee-Seung multiplicative updates. We show how to prevent the algorithm from converging to non-KKT points and prove convergence of CP-APR under mild conditions. We also explain how to implement CP-APR for large-scale sparse tensors and present results on several data sets, both real and simulated.
Lipid droplet autophagy during energy mobilization lipid homeostasis and protein quality control (2018)

Lipid droplets (LDs) have well-established functions as sites for lipid storage and energy mobilization to meet the metabolic demands of cells. However, recent studies have expanded the roles of LDs to protein quality control. Lipophagy, or LD degradation by autophagy, plays a vital role not only in the mobilization of free fatty acids (FFAs) and lipid homeostasis at LDs, but also in the adaptation of cells to certain forms of stress including lipid imbalance. Recent studies have provided new mechanistic insights about the diverse types of lipophagy, in particular microlipophagy. This review summarizes key findings about the mechanisms and functions of lipophagy and highlights a novel function of LD microlipophagy as a mechanism to maintain endoplasmic reticulum (ER) proteostasis under conditions of lipid imbalance.
Development and Application of Fourier-Transform Infrared Chemical Imaging of Tumour in Human Tissue (2008)

Fourier-transform infrared (FT-IR) based mapping and imaging is a fast emerging technology which is being increasingly applied to investigate tissues in the high-throughput mode. The high resolution close to the cellular level, the possibility to determine the bio-distribution of molecules of interest (proteins, peptides, lipids, carbohydrates) without any pre-treatment and the offer to yield molecular structure information have brought evidence that this technique allows to gain new insights in cancer pathology. Thus, several individual mainly protein and peptide cancer markers ("biomarkers") can be identified from FT-IR tissue images, enabling accurate discrimination between healthy and tumour areas. Optimal data acquisition (spatial resolution, spectral resolution, signal to noise ratio), classification, and validation are necessary to establish practical protocols that can be translated to the qualitative and quantitative clinical routine analysis. Thereby, the development of modern fast infrared imaging systems has strongly supported its acceptance in clinical histopathology. In this review, the necessity of analysis based on global cancer statistics, instrumental setups and developments, experimental state of the art are summarised and applications to investigate different kinds of cancer (e.g., prostate, breast, cervical, colon, oral cavity) are shown and discussed in detail.
Rapid 3-D digitizing and tool path generation for complex shapes (2002)

A system for automatic tool path generation was developed at Sandia National Laboratories for finish machining operations. The system consists of a commercially available 5-axis milling machine controlled by Sandia developed software. This system was used to remove overspray on cast turbine blades. A laser-based, structured-light sensor, mounted on a tool holder, is used to collect 3D data points around the surface of the turbine blade. Using the digitized model of the blade, a tool path is generated which will drive a 0.375" CBN grinding pin around the tip of the blade. A fuzzified digital filter was developed to properly eliminate false sensor readings caused by burrs, holes and overspray. The digital filter was found to successfully generate the correct tool path for a blade with intentionally scanned holes and defects. The fuzzified filter improved the computation efficiency by a factor of 25. For application to general parts, an adaptive scanning algorithm was developed and presented with simulation and experimental results. A right pyramid and an ellipsoid were scanned successfully with the adaptive algorithm in simulation studies. In actual experiments, a nose cone and a turbine blade were successfully scanned. A complex shaped turbine blade was successfully scanned and finish machined using these algorithms.
A Fluorinated Ligand Enables Room-Temperature and Regioselective Pd-Catalyzed Fluorination of Aryl Triflates and Bromides (2015)

A new biaryl monophosphine ligand (AlPhos, L1) allows for the room-temperature Pd-catalyzed fluorination of a variety of activated (hetero)aryl triflates. Furthermore, aryl triflates and bromides that are prone to give mixtures of regioisomeric aryl fluorides with Pd-catalysis can now be converted to the desired aryl fluorides with high regioselectivity. Analysis of the solid-state structures of several Pd(II) complexes, as well as density functional theory (DFT) calculations, shed light on the origin of the enhanced reactivity observed with L1.
Electron emission properties of graphene-oxide-semiconductor planar-type electron emission devices (2016)

Electron emission properties of planar type electron emission device based on graphene-oxide-semiconductor (GOS) structure was investigated. The electron emission efficiency defined as the ratio of anode current to cathode current has no dependence on the graphene electrode thickness, which indicates that the electron scattering within the electrode is perfectly suppressed. A high electron emission current density of 1-100 mA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> with high electron emission efficiency of 0.1-1.0 % was found to be achieved in GOS devices.
A Mathematical Model for a Lithium-Ion Battery/Electrochemical Capacitor Hybrid System (2005)

A one-dimensional model for predicting the performance of a battery/electrochemical capacitor-hybrid system has been developed. Simulation results are presented for a ethylene carbonate/dimethyl carbonate∣carbon battery system and a Maxwell PC 10F carbon double-layer electrochemical capacitor. The current shared between the battery and the electrochemical capacitor at very short times depends on the ohmic resistances of the battery and the capacitor. As the discharge proceeds, the operating conditions such as frequency, duty ratio, and peak pulse discharge current control the current shared among parallel circuits. These parameters also determine the extent of the run time increase of the hybrid system as compared to the battery system. The inclusion of a number of identical series/parallel capacitors is considered in the present model by introducing the parameter, capacitor configuration index. Ragone plots are simulated for a battery-alone and a hybrid system. A substantial improvement in the available energy density is observed while operating hybrid systems under high power densities. Finally, a general optimization approach is presented.
Identification of Genes Associated with the Corticotroph Phenotype in Bronchial Carcinoid Tumors (2002)

The proopiomelanocortin (POMC) gene is occasionally expressed in nonpituitary tumors leading to Cushing's syndrome. Bronchial carcinoid tumors, one of the most frequent source for ectopic ACTH secretion, often display numerous features of the corticotroph phenotype. To identify new markers of corticotroph differentiation in these tumors, we compared the pattern of gene expression in ACTH-secreting (ACTH+) and nonsecreting (ACTH-) bronchial carcinoids by differential display/RT-PCR. Using groups of ACTH+ and ACTH- tumors, we initially selected approximately 300 differentially expressed genes. Fifteen were considered differentially expressed after further characterization by RT-PCR on a larger series of 8 ACTH+ and 12 ACTH- bronchial carcinoids; 11 were restricted to--or overexpressed in--ACTH+ and four in ACTH- tumors. In ACTH+, beside the expected POMC gene, we identified cFos, and KIAA1775, a large expressed sequence tag encoding a putative protocadherin-related protein. On the other hand, the tetraspanin TM4SF5 gene was specifically expressed in ACTH-. Dot blot analysis confirmed the specific expression of KIAA1775 in ACTH+ bronchial carcinoids. However, the expression of most of the differential genes, including KIAA1775, was detected by RT-PCR in pituitary or lung tumors, whether secreting ACTH or not, excepted for TM4SF5, which was only detected in some nonendocrine lung tumors. Our results show that corticotroph differentiation of bronchial carcinoid tumors is accompanied by induction and repression of specific genes. The nature of some of these genes, identified here, underlines the importance of cell-cell or cell-extracellular matrix interactions in the establishment of neoplastic corticotroph phenotype. These genes should help to better characterize ACTH+ bronchial carcinoids as well as other bronchial carcinoid subtypes.
Efficient multi-start strategies for local search algorithms (2011)

Local search algorithms applied to optimization problems often suffer from getting trapped in a local optimum. The common solution for this deficiency is to restart the algorithm when no progress i...
File assignment in parallel I/O systems with minimal variance of service time (2000)

We address the problem of assigning nonpartitioned files in a parallel I/O system where the file accesses exhibit Poisson arrival rates and fixed service times. We present two new file assignment algorithms based on open queuing networks which aim at minimizing simultaneously the load balance across all disks, as well as the variance of the service time at each disk. We first present an off-line algorithm, Sort Partition, which assigns to each disk file with similar access time. Next, we show that, assuming that a perfectly balanced file assignment can be found for a given set of files, Sort Partition will find the one with minimal mean response time. We then present an on-line algorithm, Hybrid Partition, that assigns groups of files with similar service times in successive intervals while guaranteeing that the load imbalance at any point does not exceed a certain threshold. We report on synthetic experiments which exhibit skew in file accesses and sizes and we compare the performance of our new algorithms with the vanilla greedy file allocation algorithm.
<i>Science Advances</i> advancing (2018)

In February 2014, the American Association for the Advancement of Science (AAAS) announced the decision to launch Science Advances as a way to “expand the…content of Science ” ( science.sciencemag.org/content/343/6172/709.full ). The new publication was envisioned as a multidisciplinary, open-access, digital-only journal, edited by a team of scientists actively engaged in research. The first Science Advances papers were published within a year. Now, nearly three-and-a-half years later, Science Advances is soon to publish its 2000th paper—a good time to examine how the journal is fulfilling its founding vision.
Infection with Vpr-Positive Human Immunodeficiency Virus Type 1 Impairs NK Cell Function Indirectly through Cytokine Dysregulation of Infected Target Cells (2008)

Human immunodeficiency virus type 1 (HIV-1) infection has been implicated in impairing various aspects of NK cell function in viremic condition, and several viral factors contribute to these defects. Here, we evaluated the effect of HIV-1 Vpr on NK cell cytolytic function and cytokine (gamma interferon [IFN-gamma]) production in the context of infection and exposure. Our data indicate that NK cells derived from a peripheral blood mononuclear cell culture infected in vitro with HIV-1 vpr(+) virus or exposed to recombinant Vpr protein exhibited reduced target cell killing in conjunction with diminished expression of CD107a and reduced IFN-gamma production compared to their Vpr-negative counterparts. This Vpr-induced NK cell defect is in part through differential regulation of interleukin-12 and transforming growth factor beta production by the infected target cells and concomitant activation of Smad3 signaling pathway. Collectively, these results illustrate the ability of Vpr to impair NK cell-mediated innate immune functions indirectly by dysregulating multiple cytokines in the infected target cells, thus increasing disease severity and affecting the final outcome in HIV-1 infection.
History of cryosurgery (1998)

The use of freezing temperatures for the therapeutic destruction of tissue began in England in 1845-51 when James Arnott described the use of iced salt solutions (about-20 degrees C) to freeze advanced cancers in accessible sites, producing reduction in tumor size and amelioration of pain. Improved freezing techniques were possible early in the 1990s when solidified carbon dioxide came into use and later when liquid nitrogen and nitrous oxide became available. Nevertheless, cryotherapy was a minor technique, used only for the accessible lesions of skin and mucosa. With the development of modern cryosurgical apparatus by Cooper in 1961, a resurgence of interest in cryosurgery was initiated and techniques for diverse clinical conditions, including visceral cancer, evolved, After the initial widespread clinical trials matured in the 1970s, some applications of the technique fell into disuse while others became standard treatment. Late in the 1980s, further improvements in apparatus and imaging techniques have permitted increased clinical use in neoplastic disease, including visceral cancer.
Attribute extraction: An important application in any detailed 3-D interpretation study (1991)

Three-dimensional seismic is playing an increasingly important role in appraisal and development planning. Whereas, at first, 3 D data sets were aimed at analyzing the structural style and the mapping of complex fields, more recently, 3-D seismic has proved its value in defining details at reservoir level. Pore content, reservoir facies and very small faults which may impede fluid movement can often be mapped confidently with 3-D seismic.
Scalar Scattering Theory for Multilayer Optical Coatings (1979)

A scalar theory for scattering from multilayer coatings due to surface roughness is presented. A new model is considered which assumes that the roughness of the top surface of a given layer is due to the roughness introduced by the previously deposited layers and to the variations in thickness of the layer itself. The variations in the layer thickness are assumed to be uncorrelated from one layer to the next, but the roughnesses of the various surfaces are partially correlated. This model is compared to two existing models: one which assumes that the surfaces of the layers are completely uncorrelated and another which assumes that all of the surfaces are identical to that of the substrate. A fourth model is also introduced which assumes that the scattering is due to variations of refractive index within each layer. A matrix formulation for calculating the total integrated scattering and the change in specular reflectance and transmittance is presented. Predictions of the four different models are compared for several multilayer designs.
MAGNETIC FIELD AND CURRENT ARE ZERO INSIDE IDEAL CONDUCTORS (2011)

We prove a theorem on the magnetic energy minimum in a system of perfect, or ideal, conductors. It is analogous to Thomson's theorem on the equilibrium electric fleld and charge distribution in a system of conductors. We flrst prove Thomson's theorem using a variational principle. Our new theorem is then derived by similar methods. We flnd that magnetic energy is minimized when the current distribution is a surface current density with zero interior magnetic fleld; perfect conductors are perfectly diamagnetic. The results agree with currents in superconductors being conflned near the surface. The theorem implies a generalized force that expels current and magnetic fleld from the interior of a conductor that loses its resistivity. Examples of solutions that obey the theorem are presented.
High Anhydrous Proton Conductivity of Imidazole-Loaded Mesoporous Polyimides over a Wide Range from Subzero to Moderate Temperature (2014)

On-board fuel cell technology requires proton conducting materials with high conductivity not only at intermediate temperatures for work but also at room temperature and even at subzero temperature for startup when exposed to the colder climate. To develop such materials is still challenging because many promising candidates for the proton transport on the basis of extended microstructures of water molecules suffer from significant damage by heat at temperatures above 80 °C or by freeze below -5 °C. Here we show imidazole loaded tetrahedral polyimides with mesopores and good stability (Im@Td-PNDI 1 and Im@Td-PPI 2) exhibiting a high anhydrous proton conductivity over a wide temperature range from -40 to 90 °C. Among all anhydrous proton conductors, the conductivity of 2 is the highest at temperatures below 40 °C and comparable with the best materials, His@[Al(OH)(1,4-ndc)]n and [Zn3(H2PO4)6(H2O)3](Hbim), above 40 °C.
A monolithic thin film electrochromic window (1991)

Three closely related thin film solid state ionic devices that are potentially important for applications are: electrochromic smart windows, high energy density thin film rechargeable batteries, and thin film electrochemical sensors. Each usually has at least on mixed ion/electron conductor, an electron-blocking ion conductor, and an ion-blocking electron conductor, and many of the technical issues associated with thin film solid state ionics are common to all three devices. Since the electrochromic window has the added technical requirement of electrically-controlled optical modulation, (over the solar spectrum), and since research at the authors' institution has focused primarily on the window structure, this paper will address the electrochromic window, and particularly a monolithic variable reflectivity electrochromic window, as an illustrative example of some of the challenges and opportunities that are confronting the thin film solid state ionics community. 33 refs.