gebhart/patrepeval huggingface dataset:
Expression of a Murine Cytomegalovirus Early-Late Protein in "Latently" Infected Mice (1995)

Monoclonal antibodies were isolated from the spleen of a latently infected mouse to identify possible antigenic markers for latent murine cytomegalovirus infection. One antibody, AM3, was selected for further study. Characterization of the antigen recognized by AM3 confirmed that it is the early-late phosphoprotein pp50. The antigen was readily detected by immunoautoradiography in the spleens of acutely and latently infected mice. Low levels of the AM3/pp50 transcript were also detected in latently infected tissues by in situ hybridization. Presence of AM3/pp50 mRNA, as well as IE-1 transcripts, was confirmed by reverse transcription-polymerase chain reaction in 3 of 5 latently infected spleens. The expression of both immediate-early and early-late classes of viral genes suggests that persistent infection may be a component of the MCMV life cycle operationally defined as latency and that this gene is not specific for latency.
How to Construct Deep Recurrent Neural Networks (2013)

In this paper, we explore different ways to extend a recurrent neural network (RNN) to a \textit{deep} RNN. We start by arguing that the concept of depth in an RNN is not as clear as it is in feedforward neural networks. By carefully analyzing and understanding the architecture of an RNN, however, we find three points of an RNN which may be made deeper; (1) input-to-hidden function, (2) hidden-to-hidden transition and (3) hidden-to-output function. Based on this observation, we propose two novel architectures of a deep RNN which are orthogonal to an earlier attempt of stacking multiple recurrent layers to build a deep RNN (Schmidhuber, 1992; El Hihi and Bengio, 1996). We provide an alternative interpretation of these deep RNNs using a novel framework based on neural operators. The proposed deep RNNs are empirically evaluated on the tasks of polyphonic music prediction and language modeling. The experimental result supports our claim that the proposed deep RNNs benefit from the depth and outperform the conventional, shallow RNNs.
IN-DROPLET PARTICLE SEPARATION BY TRAVELING WAVE DIELECTROPHORESIS (twDEP) AND EWOD (2006)

This paper describes successful particle separations within a droplet by traveling wave dielectrophoresis (twDEP) and consecutive droplet splitting by electrowetting-on-dielectric (EWOD). This in-droplet method will provide a new functionality of separation and concentration for digital (droplet-based) microfluidics [1], thereby possibly eliminating the necessity of adopting the conventional microchannel-based separation methods.
Computer generated holograms: an historical review (1987)

Since Gabor's first hologram, the meanings of that term have grown with increased use of the invention. Computers expanded applications further, and this paper surveys the methods and techniques of computer generated holograms.
Optical manipulation of silicon microparticles in biological environments (2003)

Manipulation of micron-scale silicon particles has been investigated with optical tweezers implemented using a two-dimensional scanning trap driven with acousto-optic modulators. Spheres of latex, Poly(methyl methacrylate) (PMMA), silica, and silver-coated PMMA have been utilized to calibrate transverse trapping forces. The goal of this work is to non-invasively manipulate 10-20 &mu;m silicon-based devices in and around cells.
Reliability and properties of core materials for all-ceramic dental restorations (2008)

Various core materials have been used as all-ceramic dental restorations. Since many foreign zirconia product systems were introduced to the Japanese dental market in the past few years, the researches and the papers on zirconia for ceramic biomaterials have immediately drawn considerable attention. Recently, most of the manufactures supply zirconia blocks available to multi-unit posterior bridges using CAD/CAM, because zirconia has excellent mechanical properties comparable to metal, due to its microstructures. The properties of conventional zirconia were further improved by the composite in nano-scale such as zirconia/alumina nanocomposite (NANOZR). There are many interesting behaviors such as long-term stability related to low temperature degradation, effect of sandblasting and heat treatment on the microstructure and the strength, bonding to veneering porcelains, bonding to cement, visible light translucency related to esthetic restoration, X-ray opacity, biocompatibility, fracture load of clinical bridge as well as lifetime and clinical survival rates of the restoratives made with zirconia. From the recent material researches on zirconia not only in Japan but also in the world, this review takes into account these interesting properties of zirconia and reliability as core material for all-ceramic dental restorations.
Predicting protein secondary structure by a support vector machine based on a new coding scheme. (2004)

Protein structure prediction is one of the most important problems in modern computational biology. Protein secondary structure prediction is a key step in prediction of protein tertiary structure. There have emerged many methods based on machine learning techniques, such as neural networks (NN) and support vector machine (SVM) etc., to focus on the prediction of the secondary structures. In this paper, a new method was proposed based on SVM. Different from the existing methods, this method takes into account of the physical-chemical properties and structure properties of amino acids. When tested on the most popular dataset CB513, it achieved a Q(3) accuracy of 0.7844, which illustrates that it is one of the top range methods for protein of secondary structure prediction.
Redox states of DsbA in the periplasm of Escherichia coli (1995)

DsbA is a periplasmic, disulfide bond formation factor of E. coli. We studied in vivo redox states of its active site cysteines. When periplasmic contents were prepared from iodoacetic acid-treated cells, according to the previously published procedures, variable but major proportions of DsbA were in the reduced form. We found that this was due to an artificial reduction that occurred after cell disruption; even purified and oxidized DsbA underwent reduction when incubated with cell extracts in the absence of any added reducing agent. Such DsbA-reducing activities were detected in both the periplasmic and the cytoplasmic fractions. To circumvent the artifact, we analyzed redox states of DsbA under denaturing conditions. Now virtually all the DsbA molecules were detected as oxidized or reduced in the dsbB+ background or in the dsbB- background, respectively. Using the improved method, we also examined redox states of DsbA when it was overproduced, and followed the oxidation/reduction pathway that DsbA follows after biosynthesis. It is suggested that newly synthesized DsbA is rapidly oxidized by pre-existing DsbA, while oxidation of mature (functional) DsbA requires DsbB, whose roles might include that of antagonizing the actions of DsbA-reducing enzyme(s).
Molecular characterization of the WC1 antigen expressed specifically on bovine CD4-CD8- gamma delta T lymphocytes (1992)

Although gamma delta T lymphocytes were identified several years ago, the functional importance of these cells remains to be established. gamma delta T cells of ruminants are unique in two respects. First, they are present at much higher levels compared to man and rodents. Second, ruminant CD4-CD8- gamma delta T cells uniquely express a 220 kD surface Ag recognized by a panel of mAb, recently clustered as WC1. WC1 has been most extensively studied in sheep with the use of the mAb T19. Here, we report on the isolation of a full length cDNA clone, encoding the WC1 Ag, from a COS cell cDNA expression library prepared from a bovine gamma delta T cell line. The protein encoded by the pWC1 cDNA clone was reactive with the bovine mAb CC15 and IL.A29, and with T19. The cDNA clone consisted of 4475 bp and contained a single long open reading frame of 1436 amino acids. The pWC1 cDNA clone encoded a type 1 integral membrane protein with an extracellular domain consisting of 11 scavenger receptor cysteine-rich-repeats with homology to CD5 and CD6. Southern blotting suggested that the bovine genome contained multiple sequences highly related to the isolated WC1 cDNA. Furthermore, WC1-like sequences were present in the genomes of all mammals tested including mouse and man. The molecular characterization of the WC1 Ag as reported here provides a starting point for the definition of its role in gamma delta T cell biology.
CSF Aβ 42 levels correlate with amyloid-neuropathology in a population-based autopsy study (2003)

The current study suggests that lower Abeta 42 levels reflect neuropathologic processes implicated in amyloid-related pathologies, such as NP and CAA.
Exenatide and the treatment of patients with Parkinson’s disease (2013)

Cure Parkinson's Trust.
Derivatized Mesoporous Silicon with Dramatically Improved Stability in Simulated Human Blood Plasma (1999)

The stability of derivatized mesoporous silicon in a physiological environment is investigated and potential applications are discussed. It is shown that, while the surface of hydride-terminated mesoporous silicon corrodes very rapidly upon exposure to simulated body fluid (see Figure), the dodecenyl-terminated material is virtually untouched even after a much longer period of time.
Learning structural SVMs with latent variables (2009)

We present a large-margin formulation and algorithm for structured output prediction that allows the use of latent variables. Our proposal covers a large range of application problems, with an optimization problem that can be solved efficiently using Concave-Convex Programming. The generality and performance of the approach is demonstrated through three applications including motiffinding, noun-phrase coreference resolution, and optimizing precision at k in information retrieval.
Curcumin decreases malignant characteristics of glioblastoma stem cells via induction of reactive oxygen species (2017)

Discoveries made in this investigation may lead to a non-toxic intervention designed to prevent recurrence in glioblastoma by targeting glioblastoma stem cells.
Dynamics and Cardiac Arrhythmias (2006)

Cardiac arrhythmias, characterized by single or multiple reentrant circuits, represent a dynamic phenomenon in an excitable medium. In this review, we provide a brief overview of how cardiac action potential duration restitution, conduction velocity restitution, and intracellular calcium cycling regulate the dynamics of action potential excitation and wave propagation in relation to the genesis and maintenance of cardiac arrhythmias.
Acne phototherapy using UV-free high-intensity narrow-band blue light: a three-center clinical study (2001)

Propionibacterium. acnes is a Gram positive, microaerophilic bacterium which takes a part in the pathogenesis of inflammatory acne. P. acnes is capable to produce high amounts endogenic porphyrins with no need of any trigger molecules. Light in the violet-blue range (407-420 nm) has been shown to exhibit a phototoxic effect on Propionibacterium acnes when irradiated in vitro. The purpose of our study was to test the clinical effects of a high intensity narrowband blue light source on papulo pustular acne. A total of 35 patients in 3 centers were treated twice a week with a high intensity metal halide lamp illuminating the entire face (20x20 cm2) or the back with visible light in the 407-420 nm range at an intensity of 90 mW/cm<SUP>2</SUP> (CureLight Ltd.) for a total of 4 weeks. UV is totally cut off. In each treatment the patient was exposed to light for 8-15 minutes. After 8 treatments, 80% of the patients with mild to moderate papulo-pustular acne showed significant improvement at reducing the numbers of non- inflammatory, inflammatory and total facial lesions. Inflammatory lesion count decrease by a mean of 68%. No side effects to the treatment were noticed. In conclusion, full face or back illumination with the high intensity pure blue light we used exhibits a rapid significant decrease in acne lesions counts in 8 biweekly treatments.
Memory: an introduction (2011)

In Chapter 1, we noted that learning focuses on the acquisition of knowledge or a skill, whereas memory refers to our capacity to later recall it. We also noted, however, that the two concepts are intimately, perhaps inextricably, intertwined. Learning necessarily involves memory: To show that you have learned a king's name during a history lesson, you must be able to remember the name. Conversely, memory depends on learning: You can only remember the king's name if you learned it in the first place! In essence, learning and memory are two sides of the same coin – that certain experiences have enduring effects on our behavior – and which term we use depends largely on whether we are emphasizing the initial impact of the experience (learning) or its subsequent effect (memory). Having emphasized the first aspect in the preceding chapters, we now turn our attention to memory.
Synthesis, deprotection, analysis and purification of RNA and ribosomes (1995)

Improvements in the synthesis, deprotection and purification of oligoribonucleotides are described. These advances allow for reduced synthesis and deprotection times, while improving product yield. Coupling times are reduced by half using 5-ethylthio-1H-tetrazole (S-ethyltetrazole) as the activator. Base and 2'-O-t-butyldimethylsilyl deprotection with methylamine (MA) and anhydrous triethylamine/hydrogen fluoride in N-methylpyrrolidinone (TEA.HF/NMP), respectively, requires a fraction of the time necessitated by current standard methods. In addition, the ease of oligoribonucleotide purification and analysis have been significantly enhanced using anion exchange chromatography. These new methods improve the yield and quality of the oligoribonucleotides synthesized. Hammerhead ribozymes synthesized utilizing the described methods exhibited no diminution in catalytic activity.
Life-Threatening Respiratory Tract Disease with Human Bocavirus-1 Infection in a 4-Year-Old Child (2011)

The disease spectrum associated with human bocavirus-1 infection remains to be fully defined. We report a case of bocavirus-1-associated bronchiolitis, leading to severe respiratory failure and extracorporeal membrane oxygenation in a 4-year-old child, and suggest blood testing for human bocavirus-1 in children with severe respiratory tract infection.
Dialysate sodium and sodium gradient in maintenance hemodialysis: a neglected sodium restriction approach? (2011)

Sodium gradient is associated with statistically significant and clinically meaningful differences in IDWG in stable patients on HD.
Alignable epitaxial liftoff of GaAs materials with selective deposition using polyimide diaphragms (1991)

The authors report the selective and alignable deposition of patterned thin-film epitaxial GaAs/GaAlAs devices onto a host substrate such as silicon for low cost, manufacturable hybrid integrated optoelectronic circuits. The authors use a thin polyimide diaphragm as the transparent transfer medium for these patterned epitaxial devices. Each of these devices or a group of these devices on the polyimide is then optically aligned and selectively deposited onto the host substrate. The use of the polyimide transfer diaphragm also allows both the bottom and the top of the device to be processed while under substrate support. Using this technique, a light emitting diode 50*50 mu m in area and 2 mu m thick was grown on a GaAs substrate, lifted off, aligned and selectively deposited onto a silicon host substrate, and electrically contacted and tested.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cis3/Socs3/Ssi3 Plays a Negative Regulatory Role in Stat3 Activation and Intestinal Inflammation (2001)

Immune and inflammatory systems are controlled by multiple cytokines, including interleukins (ILs) and interferons. These cytokines exert their biological functions through Janus tyrosine kinases and signal transducer and activator of transcription (STAT) transcription factors. We recently identified two intrinsic Janus kinase (JAK) inhibitors, JAK binding protein (JAB; also referred to as suppressor of cytokine signaling [SOCS1]/STAT-induced STAT inhibitor [SSI1]) and cytokine-inducible SH2 protein (CIS)3 (or SOCS3/SSI3), which play an essential role in the negative regulation of cytokine signaling. We have investigated the role of STATs and these JAK inhibitors in intestinal inflammation. Among STAT family members, STAT3 was most strongly tyrosine phosphorylated in human ulcerative colitis and Crohn's disease patients as well as in dextran sulfate sodium (DSS)-induced colitis in mice. Development of colitis as well as STAT3 activation was significantly reduced in IL-6-deficient mice treated with DSS, suggesting that STAT3 plays an important role in the perpetuation of colitis. CIS3, but not JAB, was highly expressed in the colon of DSS-treated mice as well as several T cell-dependent colitis models. To define the physiological role of CIS3 induction in colitis, we developed a JAB mutant (F59D-JAB) that overcame the inhibitory effect of both JAB and CIS3 and created transgenic mice. DSS induced stronger STAT3 activation and more severe colitis in F59D-JAB transgenic mice than in their wild-type littermates. These data suggest that hyperactivation of STAT3 results in severe colitis and that CIS3 plays a negative regulatory role in intestinal inflammation by downregulating STAT3 activity.
A microchip for quantitative detection of molecules utilizing luminescent and radioisotope reporter groups. (1994)

Through the marriage of microelectronics and molecular biology, a miniaturized device is presented for ultrasensitive detection of labeled molecules. The novelty of the approach is the direct integration of a charge-coupled device (CCD) and a probe-based assay. Specifically, a CCD detector serves as an active solid support that quantitatively detects and images the distribution of labeled target molecules near the spatially addressable pixels. The device exploits the inherent characteristics of microelectronics that accommodate highly parallel assays, ultrasensitive detection, high throughput, integrated data acquisition and computation. Hence, the technology presented offers substantial practical utility to both research and clinical diagnostic applications that require quantitative analysis of bound molecules. Specifically for probe-based assays such as reverse dot blots, hybridization of radiolabeled or fluorescently labeled, target DNA can be quantitatively assessed within seconds due to the high sensitivity and direct coupling employed.
Small-sized MMIC amplifiers using thin dielectric layers (1995)

Miniaturized MMIC amplifiers utilizing a multilayer structure composed of thin film transmission lines are presented. The fundamental characteristics of the thin film transmission lines for use in microwave active circuits are discussed through calculations by numerical analysis. A two-stage low-noise amplifier, a single-stage wideband amplifier, and a balanced amplifier are designed within very small areas, while good performance is maintained. The results include that a Ka-band single-stage amplifier is fabricated in a 0.8 mm/spl times/0.6 mm area with a gain of 8.0-9.5 dB in the frequency range of 16-26.5 GHz and input/output return losses of better than 8 dB at 26.5 GHz. The proposed amplifier configurations can be applied to high density integration of one-chip MMIC modules.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Altered network hub connectivity after acute LSD administration (2018)

LSD is an ambiguous substance, said to mimic psychosis and to improve mental health in people suffering from anxiety and depression. Little is known about the neuronal correlates of altered states of consciousness induced by this substance. Limited previous studies indicated profound changes in functional connectivity of resting state networks after the administration of LSD. The current investigation attempts to replicate and extend those findings in an independent sample. In a double-blind, randomized, cross-over study, 100 μg LSD and placebo were orally administered to 20 healthy participants. Resting state brain activity was assessed by functional magnetic resonance imaging. <i>Within</i>-network and <i>between</i>-network connectivity measures of ten established resting state networks were compared between drug conditions. Complementary analysis were conducted using resting state networks as sources in seed-to-voxel analyses. Acute LSD administration significantly decreased functional connectivity <i>within</i> visual, sensorimotor and auditory networks and the default mode network. While <i>between</i>-network connectivity was widely increased and all investigated networks were affected to some extent, seed-to-voxel analyses consistently indicated increased connectivity between networks and subcortical (thalamus, striatum) and cortical (precuneus, anterior cingulate cortex) hub structures. These latter observations are consistent with findings on the importance of hubs in psychopathological states, especially in psychosis, and could underlay therapeutic effects of hallucinogens as proposed by a recent model.
Purification of RNA and RNA-protein complexes by an R17 coat protein affinity method (1990)

We describe an affinity chromatography method to isolate specific RNAs and RNA-protein complexes formed in vivo or in vitro. It exploits the highly selective binding of the coat protein of bacteriophage R17 to a short hairpin in its genomic RNA. RNA containing that hairpin binds to coat protein that has been covalently bound to a solid support. Bound RNA-protein complexes can be eluted with excess R17 recognition sites. Using purified RNA, we demonstrate that binding to immobilized coat protein is highly specific and enables one to separate an RNA of interest from a large excess of other RNAs in a single step. Surprisingly, binding of an RNA containing non-R17 sequences to the support requires two recognition sites in tandem; a single site is insufficient. We determine optimal conditions for purification of specific RNAs by comparing specific binding (retention of RNAs with recognition sites) to non-specific binding (retention of RNAs without recognition sites) over a range of experimental conditions. These results suggest that binding of immobilized coat protein to RNAs containing two sites is cooperative. We illustrate the potential utility of the approach in purifying RNA-protein complexes by demonstrating that a U1 snRNP formed in vivo on an RNA containing tandem recognition sites is selectively retained by the coat protein support.