gebhart/patrepeval huggingface dataset:
Studies of H3K4me3 demethylation by KDM5B/Jarid1B/PLU1 reveals strong substrate recognition <i>in vitro</i> and identifies 2,4‐pyridine‐dicarboxylic acid as an <i>in vitro</i> and <i>in cell</i> inhibitor (2012)

Dynamic methylations and demethylations of histone lysine residues are important for gene regulation and are facilitated by histone methyltransferases and histone demethylases (HDMs). KDM5B/Jarid1B/PLU1 is an H3K4me3/me2-specific lysine demethylase belonging to the JmjC domain-containing family of histone demethylases (JHDMs). Several studies have linked KDM5B to breast, prostate and skin cancer, highlighting its potential as a drug target. However, most inhibitor studies have focused on other JHDMs, and inhibitors for KDM5B remain to be explored. Here, we report the expression, purification and characterization of the catalytic core of recombinant KDM5B (ccKDM5B, residues 1-769). We show that ccKDM5B, recombinantly expressed in insect cells, demethylates H3K4me3 and H3K4me2 in vitro. The kinetic characterization showed that ccKDM5B has an apparent Michaelis constant (K(m) (app) ) value of 0.5 μm for its trimethylated substrate H3(1-15)K4me3, a considerably increased apparent substrate affinity than reported for related HDMs. Despite the presence of a PHD domain, the catalytic activity was not affected by additional methylation at the H3K9 position, suggesting that in vitro chromatin cross-talk between H3K4 and H3K9 does not occur for ccKDM5B. Inhibition studies of ccKDM5B showed both in vitro and in cell inhibition of ccKDM5B by 2,4-pyridinedicarboxylic acid (2,4-PDCA) with a potency similar to that reported for the HDM KDM4C. Structure-guided sequence alignment indicated that the binding mode of 2,4-PDCA is conserved between KDM4A/C and KDM5B.
Transferring Rich Feature Hierarchies for Robust Visual Tracking (2015)

Convolutional neural network (CNN) models have demonstrated great success in various computer vision tasks including image classification and object detection. However, some equally important tasks such as visual tracking remain relatively unexplored. We believe that a major hurdle that hinders the application of CNN to visual tracking is the lack of properly labeled training data. While existing applications that liberate the power of CNN often need an enormous amount of training data in the order of millions, visual tracking applications typically have only one labeled example in the first frame of each video. We address this research issue here by pre-training a CNN offline and then transferring the rich feature hierarchies learned to online tracking. The CNN is also fine-tuned during online tracking to adapt to the appearance of the tracked target specified in the first video frame. To fit the characteristics of object tracking, we first pre-train the CNN to recognize what is an object, and then propose to generate a probability map instead of producing a simple class label. Using two challenging open benchmarks for performance evaluation, our proposed tracker has demonstrated substantial improvement over other state-of-the-art trackers.
Strategies for cost effective DNA testing for the thryoglobulin gene in beef cattle. (2001)

GeneSTAR marbling is a DNA diagnostic test available to beef cattle breeders, which tests for the recessive thryoglobulin gene, presently at low frequency in beef cattle populations. Widespread testing is an expensive option given current pricing. This paper investigates low-cost strategies for DNA testing and segregation analysis to give extensive information on the frequency of the thryoglobulin gene in a breed of beef cattle. A genotype priority-testing index (GPTI) is proposed to prioritise animals for genotyping in each genotyping cycle according to the whole-herd information gained by that genotyping. The eventual aim is to increase the frequency of the favourable allele in the participating breeding herds.
CT Artifact Recognition for the Nuclear Technologist (2008)

The goal of this article is to make the PET/CT and SPECT/CT operator aware of common artifacts found in CT. In diagnostic imaging, the ability to render an accurate diagnosis requires the technologist to take steps to optimize image quality and recognize when image quality has been compromised-that is, when there is an image artifact. One way these artifacts occur is through the inability of the CT linear attenuation image to precisely represent the linear attenuation map of a 2-dimensional section through the body. The reasons for this inability are multifold. First, CT is subject to the laws of x-ray quantum physics resulting in noise in all CT images. Moreover, all current CT x-ray systems generate a spectrum of energies. Also, CT scanners use detectors of finite dimension, as are the x-ray focal spots; reconstruct images from a finite number of samples distributed over a finite number of views; and acquire the data for each reconstruction over a finite period.
Crucial Role of Activin A in Tubulogenesis of Endothelial Cells Induced by Vascular Endothelial Growth Factor (2004)

The present study was conducted to elucidate the role of activin A in tubulogenesis of vascular endothelial cells. Activin A was produced in bovine aortic endothelial cells (BAEC). These cells also expressed the type I and type II activin receptors. When added to BAEC cultured in a collagen gel, activin A induced capillary formation. Activin A was as potent as vascular endothelial growth factor (VEGF) and markedly enhanced VEGF-induced tubulogenesis. To examine the role of endogenous activin A, we added follistatin, an inhibitor of activin A. Follistatin nearly completely blocked the VEGF-induced tubulogenesis, and the effect of follistatin was reproduced by transfection of the dominant-negative type II activin receptor gene. In BAEC, activin A increased the expression of VEGF and the VEGF receptors, Flt-1 and Flk-1. On the other hand, VEGF increased the production of activin A. Finally, addition of follistatin, which blocks the action of endogenous activin A, reduced the expression of Flt-1 and Flk-1. These results indicate that an autocrine factor activin A amplifies the effect of VEGF by up-regulating VEGF and its receptors. This effect of activin A is critical in the VEGF-induced tubulogenic morphogenesis in BAEC.
Introduction (1999)

The opening of most archives in the former USSR starting in the late 1980s not only dramatically altered the nature of the historical study of Russia and the Soviet Union but has pushed historians to begin what promises to be a long and fruitful reevaluation of the country's imperial and Soviet past. The last decade has also witnessed an important revival of local and regional historical research by a new generation of scholars, most of whom are based in graduate history progams at oblast pedagogical universities throughout Russia. Such renewed interest in recovering local histories can be seen in a wide range of ongoing activities, including the organization of municipal and church-based preservation societies; the resurrection of historical societies (most of which existed prior to 1917); the appearance of numerous journals (both semipopular and scholarly) focusing on local history; the creation of new university programs in such areas as oral history; and a still small but growing cohort of young historians engaged in local archival research on a broad array of topics stretching from the medieval period to the Soviet era. Indeed, there is an argument to be made that some of the most exciting and potentially significant historical research currently underway in Russia is taking place not in the centers of Moscow and Petersburg, but in smaller localities like Yaroslavl, Nizhnii Novgorod, Riazan, Smolensk, and elsewhere.
Higher-Harmonic-Control Algorithm for Helicopter Vibration Reduction Revisited (2005)

Peer Reviewed
Deep depletion of abundant serum proteins reveals low‐abundant proteins as potential biomarkers for human ovarian cancer (2009)

Epithelial ovarian cancer (EOC) ranks fifth as a cause of cancer deaths in women. Current diagnostic and monitoring markers have limited reliability for the detection of disease. We have tested the possibility of identifying candidate biomarkers present at low nanogram to picogram levels after removing both the 12 most abundant and 77 moderately abundant proteins from serum samples of EOC patients using antibody affinity columns. We showed that this approach allows the identification of proteins that are expressed at nanogram per liter levels in the serum. Using ICAT/MS/MS analysis, we identified 51 proteins that are differentially expressed by at least twofold. These proteins include leucine-rich alpha-2-glycoprotein, matrix metalloproteinase-9 (MMP-9), inter-alpha-trypsin inhibitor heavy chain H1, insulin-like growth factor-binding protein 6, insulin-like growth factor-binding protein 3, isoform 1 of epidermal growth factor receptor, angiopoietin-like protein 3 (ANGPTL3) and phosphatidylcholine-sterol acyltransferase. We confirmed the differential expression of MMP9 and ANGPTL3 in normal and ovarian cancer sera by ELISA assays. Further robust clinical evaluation of the candidate markers identified is necessary.
1.65-nm Brillouin optical time domain reflectometry employing a Raman fiber amplifier and a lithium niobate phase-modulator (2002)

Brillouin optical time-domain reflectometry (B-OTDR) operated in the 1.60-1.65 /spl mu/m wavelength region is a promising technique for in-line monitoring and preventive maintenance in optical fiber networks. This paper presents strain and optical loss distributions measured in 30- and 100-km-long optical fibers, respectively.
Genetic diagnosis of the preimplantation embryo (1989)

Genetic diagnosis and therapy is well established in the antenatal period. The advancement of uterine and in vitro fertilization allow access to the early blastocyst. Simultaneously, laboratory techniques are being miniaturized to be sufficiently sensitive and specific for diagnosis with only a few cells. Thus genetic diagnosis and therapy may be extended from the antenatal patient to the antegravid patient. This article discusses the techniques of uterine lavage and in vitro fertilization as well as the diagnostic possibilities that this early embryonic period offers.
Ketamine for Rapid Reduction of Suicidal Thoughts in Major Depression: A Midazolam-Controlled Randomized Clinical Trial (2017)

Adjunctive ketamine demonstrated a greater reduction in clinically significant suicidal ideation in depressed patients within 24 hours compared with midazolam, partially independently of antidepressant effect.
Centromere protein B assembles human centromeric alpha-satellite DNA at the 17-bp sequence, CENP-B box. (1992)

We purified 15,000-fold from HeLa cell nuclear extract the centromere antigen that reacts specifically with the 17-bp sequence, designated previously as CENP-B box, in human centromeric alpha-satellite (alphoid) DNA by a two-step procedure including an oligonucleotide affinity column. The purified protein was identified as the centromere protein B (CENP-B) by its mobility on SDS-PAGE (80 kD), and reactivities to a monoclonal antibody raised to CENP-B (bacterial fusion protein) and to anticentromere sera from patients with autoimmune diseases. Direct binding by CENP-B of the CENP-B box sequence in the alphoid DNA has been proved using the purified CENP-B by DNA mobility-shift assay, Southwestern blotting, and DNase I protection analysis. The binding constant of the antigen to the CENP-B box sequence is 6 x 10(8) M-1. DNA mobility-shift assays indicated that the major complex formed between the CENP-B and the DNA contains two DNA molecules, suggesting the importance of the CENP-B/CENP-B box interaction in organization of higher ordered chromatin structures in the centromere and/or kinetochore. Location of DNA binding and dimerization domains in CENP-B was discussed based on the DNA mobility-shift assays performed with a protein fraction containing intact and partial cleavage products of CENP-B.
Numerical analysis of thermal fracturing in subsurface cold water injection by finite element methods (2012)

SUMMARY Integration of poromechanics and fracture mechanics plays an important role in understanding a series of thermal fracturing phenomena in subsurface porous media such as cold water flooding for enhanced oil recovery, produced‐water reinjection for waste disposal, cold water injection for geothermal energy extraction, and CO 2 injection for geosequestration. Thermal fracturing modeling is important to prevent the potential risks when fractures propagate into undesired zones, and it involves the coupling of heat transfer, mass transport, and stress change as well as the fracture propagation. Analytical method, finite element method, and finite difference method as well as boundary element method have been used to perform the thermal fracturing modeling considering different degrees and combinations of coupling. In this paper, extended finite element method is employed for the thermal fracturing modeling in a fully coupled fashion with remeshing avoided, and the stabilized finite element method is employed to account for the convection‐dominated heat transfer in the fracturing process with numerical oscillation circumvented. With the thermal fracturing model, a hypothetical numerical experiment on cold water injection into a deep warm aquifer is conducted. Results show that parameters such as injection rate, injection temperature, aquifer stiffness, and permeability can affect the fracture development in different ways and extended finite element method and stabilized finite element method provide effective tools for thermal fracturing simulation. Copyright © 2012 John Wiley & Sons, Ltd.
Novel role of VMP1 as modifier of the pancreatic tumor cell response to chemotherapeutic drugs (2013)

We hypothesized that inhibiting molecules that mediate the adaptation response to cellular stress can antagonize the resistance of pancreatic cancer cells to chemotherapeutic drugs. Toward this end, here, we investigated how VMP1, a stress-induced autophagy-associated protein, modulate stress responses triggered by chemotherapeutic agents in PDAC. We find that VMP1 is particularly over-expressed in poorly differentiated human pancreatic cancer. Pharmacological studies show that drugs that work, in part, via the endoplasmic reticulum stress response, induce VMP1 expression. Similarly, VMP1 is induced by known endoplasmic reticulum stress activators. Genetic inactivation of VMP1 using RNAi-based antagonize the pancreatic cancer stress response to antitumoral agents. Functionally, we find that VMP1 regulates both autophagy and chemotherapeutic resistance even in the presence of chloroquin, ATG5 or Beclin 1 siRNAs, or a Beclin 1-binding VMP1 mutant. In addition, VMP1 modulates endoplasmic reticulum stress independently of its coupling to the molecular and cellular autophagy machinery. Preclinical studies demonstrate that xenografts expressing an inducible and tractable form of VMP1 show increased resistance to the gemcitabine treatment. These results underscore a novel role for VMP1 as a potential therapeutic target for combinatorial therapies aimed at sensitizing pancreatic cancer cells to chemotherapeutic agents as well as provide novel molecular mechanisms to better understand this phenomenon.
Nanoscale Roughness Effects at the Interface of Lithography and Plasma Etching: Modeling of Line-Edge-Roughness Transfer During Plasma Etching (2009)

We present 3-D modeling results on resist line-edge-roughness (LER) transfer to underlying films during plasma etching. After generating random fractal resist sidewalls with controlled roughness parameters, we model and contrast the nanoscale roughness phenomena for both resist and underlayer sidewalls in a two-layer stack using two different plasma processes in three scenarios: (1) pattern transfer; (2) resist trimming; and (3) resist trimming followed by pattern transfer. In the pattern transfer process, etching is considered ion driven and anisotropic. The protrusions of the rough, trimmed or nontrimmed, resist sidewall act as a shadowing mask for the incident ions. It is found that shadowing of ions is enough to induce the, well known by experiments, striations at the sidewalls of both the underlayer and the resist. Pattern transfer induces a decrease of rms roughness but has no important effects on the correlation length. In the trimming process, the evolution of the resist sidewall is modeled with an isotropic etching process not affecting the underlayer. The trimming process causes a decrease of the rms value of the resist sidewall and an increase of its correlation length and roughness exponent. For sufficiently long trimming times, the change of LER parameters becomes less intense. In the case of trimming followed by pattern transfer, the striations of the underlayer widen with trimming time, and pattern transfer further reduces all LER parameters. The effect of trimming on the rms roughness of the underlayer is important in the case of initially anisotropic resist sidewall. For both trimming and pattern transfer, a stronger relative reduction on rms roughness of both the resist and the underlayer sidewalls is obtained for smaller correlation length and larger rms roughness of the initial resist.
Kinetics of Oxygen Reduction in Aprotic Li–O<sub>2</sub> Cells: A Model-Based Study (2014)

A comprehensive and general kinetic model is developed for the oxygen reduction reaction in aprotic Li-O2 cells. The model is based on the competitive uptake of lithium superoxide by the surface and solution. A demonstrative kinetic study is provided to demystify the origin of curvature in Tafel plots as well as the current dependency and aberrant diversity of the nature and morphology of discharge products in these systems. Our results are general and extend to any system where solubilization of superoxide is favored, such as where phase-transfer catalysts play an important role.
Chitosan coated alginate beads containing poly(<i>N</i>‐isopropylacrylamide) for dual‐stimuli‐responsive drug release (2007)

Chitosan coated alginate beads containing poly(N-isopropylacrylamide) (PNIPAAM), were prepared to be used as a controlled pH/temperature sensitive drug delivery system with improved encapsulation efficiency and delayed release rate. The studied beads were characterized by differential scanning calorimetry, scanning electron microscopy, and Fourier transform infrared spectroscopy. Water uptake and release studies using indomethacin as a model drug were also performed. The drug loading efficiency of the beads with the polyelectrolyte complex coating is significantly higher (84%) than that of the uncoated ones (74%). The equilibrium swelling of the developed materials was found to be pH- and thermo- responsive. For all the conditions it was found that the release profile was slower for the coated beads, indicating that the polyelectrolyte complex coating could slow down the release rate effectively. These results suggest that the studied smart system has potential to be used as an effective pH/temperature sustainable delivery system for biomedical applications.
James Britten, the Catholic Truth Society, and the Defense of Convent Life in Late Victorian England (2011)

The life and work of James Britten, a Roman Catholic layman who helped establish the Catholic Truth Society, is described. Britten's work with the Society aimed to refute slanders against English Catholic sisterhoods.
Topographic Organization in and near Human Visual Area V4 (2007)

The existence and location of a human counterpart of macaque visual area V4 are disputed. To resolve this issue, we used functional magnetic resonance imaging to obtain topographic maps from human subjects, using visual stimuli and tasks designed to maximize accuracy of topographic maps of the fovea and parafovea and to measure the effects of attention on topographic maps. We identified multiple topographic transitions, each clearly visible in > or = 75% of the maps, that we interpret as boundaries of distinct cortical regions. We call two of these regions dorsal V4 and ventral V4 (together comprising human area V4) because they share several defining characteristics with the macaque regions V4d and V4v (which together comprise macaque area V4). Ventral V4 is adjacent to V3v, and dorsal V4 is adjacent to parafoveal V3d. Ventral V4 and dorsal V4 meet in the foveal confluence shared by V1, V2, and V3. Ventral V4 and dorsal V4 represent complementary regions of the visual field, because ventral V4 represents the upper field and a subregion of the lower field, whereas dorsal V4 represents lower-field locations that are not represented by ventral V4. Finally, attentional modulation of spatial tuning is similar across dorsal and ventral V4, but attention has a smaller effect in V3d and V3v and a larger effect in a neighboring lateral occipital region.
Capture of CO<sub>2</sub> from combustion gases in a fluidized bed of CaO (2004)

Abstract Experiments in a pilot‐scale fluidized‐bed reactor have been carried out to investigate the carbonation reaction of CaO, as a potential method for CO 2 capture from combustion flue gases at high‐temperatures. Results show that CO 2 capture efficiencies are very high, while there is a sufficient fraction of CaO in the bed reacting in the fast reaction regime. The total capture capacity of the bed decays with the number of carbonation‐calcination cycles. The experimental CO 2 concentration profiles measured inside the bed during the fast reaction period are interpreted with the KL fluid bed model, by supplying information on sorbent deactivation from laboratory tests. It is concluded that a fluidized bed of CaO can be a suitable reactor to achieve very effective CO 2 capture efficiencies from a combustion flue gas. © 2004 American Institute of Chemical Engineers AIChE J, 50:1614–1622, 2004
Facile Electrochemical Synthesis of Hexagonal Cu<sub>2</sub>O Nanotube Arrays and Their Application (2010)

Large-scale and highly oriented single-crystalline hexagonal Cu(2)O nanotube arrays have been successfully synthesized using a two-step solution approach, which involves the electrodeposition of oriented Cu(2)O nanorods and a subsequent dissolution technique along the c axis to form a tubular structure. Herein, NH(4)Cl was found to be an effectual additive, and it can successfully realize the dissolution process of Cu(2)O from nanorods to nanotubes. The dissolution mechanism of Cu(2)O from nanorods to nanotubes was illustrated in detail. These prepared Cu(2)O nanotube arrays were characterized by SEM, EDS, XRD, XPS, and TEM. The photoluminescence (PL) spectrum of Cu(2)O nanotube arrays was also measured, and it shows there is a greater fraction of copper or oxygen vacancies in these prepared Cu(2)O nanotubes. Finally, the applications of Cu(2)O nanotube arrays for gas sensors were investigated in this paper.
Improved MR Imaging of the Orbit at 1.5 T with Surface Coils (1985)

A method for obtaining localized high-resolution magnetic resonance (MR) images of the eye and orbit is demonstrated. The method uses modified surface receiver coils placed immediately adjacent to the anatomy to detect the MR signal. Surface coils provide enhanced sensitivity for imaging voxels close to the surface of the body while limiting the received patient-generated noise. The resulting improvement in signal-to-noise ratio allows for a reduction in the imaging voxel size to about 0.5 X 0.5 X 5 mm in scan times of 3.4-5 min. At this level of resolution, anatomic detail in the orbital region previously unobservable in MR images is seen.