gebhart/patrepeval huggingface dataset:
<title>Storing temporal sequences of patterns in neural networks</title> (1993)

This paper presents neural network models for storing terminating and cyclic temporal sequences of patterns under synchronous, sequential and asynchronous dynamics. We use fully interconnected neural networks with asymmetric weight connections for synchronous and sequential dynamics and a layered neural network with feedback for asynchronous dynamics. The network were successfully implemented and the number of patterns that could be stored and recalled was approximately 12% of the size of the patterns in the network.
Short Communication: Identification of Genes Differentially Expressed in Osteoclast-like Cells (2005)

Homeostasis of the skeletal system is maintained by a balance between bone formation and resorption. The receptor activator of NF-kappaB ligand (RANKL) induces the differentiation of bone-resorbing cells, osteoclasts. To identify genes regulated during osteoclast differentiation, we constructed a subtraction cDNA library using a mouse RAW264 macrophage cell line that differentiates into osteoclast-like multinucleated cells after treatment with RANKL. Northern blot analysis showed that RANKL treatment upregulated expression of 17 genes. Among these were the genes for five H(+)-ATPase subunits, two chemokines, and the osteoclast marker cathepsin K. In addition, a mouse homolog of human dendritic cell (DC)-specific transmembrane protein (DCSTAMP), whose function in osteoclastogenesis was recently revealed, was also included in the induced genes. Characterization of these inducible genes will provide an insight into the biology of osteoclasts and the mechanism of bone-related diseases.
Protein tyrosine phosphatases in the JAK/STAT pathway (2008)

The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway is crucial in controlling cellular activities in response to extracellular cytokines. Dysfunctions of the JAK/STAT pathway result in various hematopoietic and immune disorders. The central events in regulating this pathway are tyrosine phosphorylation and dephosphorylation of the signaling components, which are carried out by protein tyrosine kinases and protein tyrosine phosphatases (PTP), respectively. Here, we review recent advances in the regulatory roles of PTPs, in particular, SHP2 phosphatase, in the JAK/STAT signaling pathway.
The Size-Dependent Structural Phase Behaviors of Supported Bimetallic (Pt−Ru) Nanoparticles (2003)

We describe in this report the preparation, structural characterization, and phase behaviors exhibited by supported metallic and bimetallic nanoparticles. Homometallic nanoparticles of either Pt or Ru were synthesized by the reduction of various precursors ((CH3)2Pt(COD), H2PtCl6, and RuCl3) onto different carbon supports: Vulcan XC-72 (VXC) and Shawinigan Acetylene Black (SAB). The choice of precursor has a large structural influence on the reductive condensation of the Pt metal particles. All of the various precursors and supports produced particles with very similar size distributions, with the exception of (CH3)2Pt(COD), which formed a complex distribution of small (20 Å) and large (>50 Å) particles. The centerpiece of this study is the characterization of the growth behaviors seen in the synthesis of binary Pt−Ru nanoparticles. These heterometallic particles were synthesized via a seeded reductive condensation of one metal precursor onto pre-supported nanoparticles of a second metal; the latter serve as nucleating sites for the growth of the binary phase. As shown via data from X-ray photoelectron spectroscopy (XPS), electron microscopy, and energy-dispersive X-ray analysis (EDX), this growth technique yields fully alloyed metallic nanoparticles, albeit ones of varying size and compositional distributions depending on the specific conditions used. Generally we found that the particles had a wide composition distribution. The nature of this distribution and the correlations between the nanoparticle sizes, compositions, and structures embedded in it were characterized in depth by scanning transmission electron microscopy (STEM). These results are used to establish an apparent size correlated binary phase diagram of the bimetallic (Pt−Ru) nanoparticles. The structural properties of the supported bimetallic nanoclusters are different from that of the bulk, as evidenced by the presence of strongly persistent metastable structures that are not found in the bulk phase diagram.
Combined effect of tumor necrosis factor-related apoptosis-inducing ligand and ionizing radiation in breast cancer therapy (2000)

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a potent endogenous activator of the cell death pathway and functions by activating the cell surface death receptors 4 and 5 (DR4 and DR5). TRAIL is nontoxic in vivo and preferentially kills neoplastically transformed cells over normal cells by an undefined mechanism. Radiotherapy is a common treatment for breast cancer as well as many other cancers. Here we demonstrate that ionizing radiation can sensitize breast carcinoma cells to TRAIL-induced apoptosis. This synergistic effect is p53-dependent and may be the result of radiation-induced up-regulation of the TRAIL-receptor DR5. Importantly, TRAIL and ionizing radiation have a synergistic effect in the regression of established breast cancer xenografts. Changes in tumor cellularity and extracellular space were monitored in vivo by diffusion-weighted magnetic resonance imaging (diffusion MRI), a noninvasive technique to produce quantitative images of the apparent mobility of water within a tissue. Increased water mobility was observed in combined TRAIL- and radiation-treated tumors but not in tumors treated with TRAIL or radiation alone. Histological analysis confirmed the loss of cellularity and increased numbers of apoptotic cells in TRAIL- and radiation-treated tumors. Taken together, our results provide support for combining radiation with TRAIL to improve tumor eradication and suggest that efficacy of apoptosis-inducing cancer therapies may be monitored noninvasively, using diffusion MRI.
Energy Dissipation in Gigahertz Oscillators from Multiwalled Carbon Nanotubes (2003)

Using atomistic models and molecular dynamics simulations, interlayer corrugation and resistant force in a biwalled carbon nanotube are shown to be strongly dependent upon the morphology combination of the bitube. Consequently, energy dissipation in a commensurate (e.g., armchair/armchair or zigzag/zigzag) bitube oscillator is found to be much larger than that in an incommensurate (e.g., zigzag/armchair) oscillator, resulting in a decay of oscillation amplitude within a few nanoseconds in the commensurate bitube and several tens of nanoseconds in the incommensurate bitube.
Two‐chain structure of the interleukin 1 receptor (1988)

By crosslinking radioiodinated recombinant human IL1 alpha to mouse EL4 thymoma cells we have identified in addition to the known IL1-binding proteins of 80 kDa, a second IL1-binding protein of about 40 kDa. This second binding protein could be demonstrated most easily when crosslinking to higher protein complexes was inhibited. This finding suggests that the IL1 receptor, similar to the receptor for other cytokines such as interleukin 2, is composed of a heterodimer, of which both polypeptides contribute to ligand binding.
Automatic calibration of low-cost digital cameras (2003)

Recent developments of digital cameras in terms of the size of charge-coupled device (CCD) arrays and reduced costs are leading to their applications in traditional as well as new photogrammetric, surveying, and mapping functions. Digital cameras, intended to replace conventional film-based mapping cameras, are becoming available along with many smaller formats capable of precise measurement applications. All such cameras require careful calibration to determine their metric characteristics, which are essential to carrying out photogrammetric activities. We introduce a new approach for incorporating straight lines in a bundle adjustment for calibrating off-the-shelf, low-cost digital cameras. The optimal configuration for successfully deriving the distortion parameters is considered when establishing the required test field. Moreover, a framework for automatic extraction of the straight lines in the images is presented and tested. The developed calibration procedure can be used as an efficient tool to investigate the most appropriate model that compensates for various distortions associated with the camera being calibrated. Experiments performed to compare line-based with traditional point-based self-calibration methods prove the feasibility of the suggested approach.
Neural Network Ensembles, Cross Validation, and Active Learning (1994)

Learning of continuous valued functions using neural network ensembles (committees) can give improved accuracy, reliable estimation of the generalization error, and active learning. The ambiguity is defined as the variation of the output of ensemble members averaged over unlabeled data, so it quantifies the disagreement among the networks. It is discussed how to use the ambiguity in combination with cross-validation to give a reliable estimate of the ensemble generalization error, and how this type of ensemble cross-validation can sometimes improve performance. It is shown how to estimate the optimal weights of the ensemble members using unlabeled data. By a generalization of query by committee, it is finally shown how the ambiguity can be used to select new training data to be labeled in an active learning scheme. 1 INTRODUCTION It is well known that a combination of many different predictors can improve predictions. In the neural networks community &amp;quot;ensembles&amp;quot; of neural networks h...
Increased therapeutic efficacy with rt-PA and anti-CD18 antibody treatment of stroke in the rat (1999)

The combination of antileukocyte adhesion antibody and thrombolytic therapy may increase the therapeutic window for the treatment of stroke.
Purification of a membrane-associated protein complex required for protein translocation across the endoplasmic reticulum. (1980)

The capacity of microsomal membranes to translocate nascent presecretory proteins across their lipid bilayer can be largely abolished by extracting them with high ionic strength buffers. It can be reconstituted by adding the salt extract back to the depleted membranes [Warren, G. & Doberstein, B. (1978) Nature (London) 273, 569-571]. Utilizing hydrophobic chromatography, we purified to homogeneity a protein component of the salt extract that reconstitutes the translocation activity of the extracted membranes. This component behaves as a homogeneous species upon gel filtration, ion-exchange chromatography, adsorption chromatography, and sucrose-gradient centrifugation. When examined by polyacrylamide gel electrophoresis in NaDodSO4, six polypeptides with apparent Mr of 72,000, 68,000, 54,000, 19,000, 14,000, and 9000 are observed in about equal and constant stoichiometry, suggesting that they are subunits of a complex. The sedimentation coefficient of 11S is in good agreement with the sum of the Mr of the subunits. The Mr 68,000 and 9000 subunits label intensely with N-[3H]ethylmaleimide. Thus, the reported sulfhydryl group requirement of the translocation activity in the unfractionated extract [Jackson, R. C., Walter, P. & Blobel, G. (1980) Nature (London), 286, 174-176] may be localized to either or both the Mr 68,000 and 9000 subunits of the purified complex.
Discordant Phenotypes in Fraternal Twins Having an Identical Mutation in Exon ORF15 of the RPGR Gene (2008)

The clinical observation of different retinal phenotypes in a family with the same mutation in exon ORF15 of RPGR implicates the potential importance of modifier genes for the phenotypic expression of this form of X-linked retinal disease.
New Developments in Therapeutic Ultrasound-Assisted Coronary Angioplasty. (1999)

Ultrasound at high energy, as distinct from the low energy used in ultrasound imaging, has found many uses in varied branches of medicine and surgery. Clinical trials of catheter-delivered, high-energy, low-frequency (kHz) ultrasound over the past 6 years have shown the safety of this modality in the treatment of coronary artery disease and have identified a number of indications in which its use, as an adjunct to conventional percutaneous transluminal coronary angioplasty (PTCA) techniques, may offer therapeutic advantages. Thrombus-mediated conditions--such as myocardial infarction, chronic total occlusion, and atherosclerosis in small vessels--appear to derive particular benefit from ultrasound treatment. Recent developments in these fields are reviewed.
<title>Instrumentation development in support of fiber grating sensor arrays</title> (1993)

This paper discusses the use of fiber gratings as sensing devices and the measurement limitations imposed by conventional laboratory instrumentation. Work that is currently in progress on instrumentation development to alleviate some of these limitations to yield practical, robust systems is discussed. Research activities concerning 2 system configurations are addressed in some detail: (1) sensor arrays in a system based on broadband optical transmitters with narrowband optical receivers using conventional optical filters or acoustically-tuned, integrated optic filters, and (2) sensor arrays in a system based on narrowband, optical transmitters with laser diodes or fiber lasers that make use of fiber gratings as wavelength tuning elements in conjunction with simple, broadband optical receivers.
Direct methods for estimation of structure and motion from three views (1996)

We describe a new direct method for estimating structure and motion from image intensities of multiple views. We extend the direct methods of [7] to three views. Adding the third view enables us to solve for motion, and compute a dense depth map of the scene, directly from image spatio-temporal derivatives in a linear manner without first having to find point correspondences or compute optical flow. We describe the advantages and limitations of this method which are then verified through simulation and experiments with real images. Copyright c fl Massachusetts Institute of Technology, 1996 This report describes research done at the Artificial Intelligence Laboratory of the Massachusetts Institute of Technology. Support for this research was provided in part by the Advanced Research Projects Agency of the Department of Defense under Office of Naval Research contract N00014-94-01-0994. G.P.S. is supported by Alphatech/ DARPA &amp;quot;Automatic Target Recognition&amp;quot; project 95009-5381 and TASC/ DAR...
Development of Reverse Transcription-PCR Assays Specific for Detection of Equine Encephalitis Viruses (2000)

Specific and sensitive reverse transcription-PCR (RT-PCR) assays were developed for the detection of eastern, western, and Venezuelan equine encephalitis viruses (EEE, WEE, and VEE, respectively). Tests for specificity included all known alphavirus species. The EEE-specific RT-PCR amplified a 464-bp region of the E2 gene exclusively from 10 different EEE strains from South and North America with a sensitivity of about 3,000 RNA molecules. In a subsequent nested PCR, the specificity was confirmed by the amplification of a 262-bp fragment, increasing the sensitivity of this assay to approximately 30 RNA molecules. The RT-PCR for WEE amplified a fragment of 354 bp from as few as 2,000 RNA molecules. Babanki virus, as well as Mucambo and Pixuna viruses (VEE subtypes IIIA and IV), were also amplified. However, the latter viruses showed slightly smaller fragments of about 290 and 310 bp, respectively. A subsequent seminested PCR amplified a 195-bp fragment only from the 10 tested strains of WEE from North and South America, rendering this assay virus specific and increasing its sensitivity to approximately 20 RNA molecules. Because the 12 VEE subtypes showed too much divergence in their 26S RNA nucleotide sequences to detect all of them by the use of nondegenerate primers, this assay was confined to the medically important and closely related VEE subtypes IAB, IC, ID, IE, and II. The RT-PCR-seminested PCR combination specifically amplified 342- and 194-bp fragments of the region covering the 6K gene in VEE. The sensitivity was 20 RNA molecules for subtype IAB virus and 70 RNA molecules for subtype IE virus. In addition to the subtypes mentioned above, three of the enzootic VEE (subtypes IIIB, IIIC, and IV) showed the specific amplicon in the seminested PCR. The practicability of the latter assay was tested with human sera gathered as part of the febrile illness surveillance in the Amazon River Basin of Peru near the city of Iquitos. All of the nine tested VEE-positive sera showed the expected 194-bp amplicon of the VEE-specific RT-PCR-seminested PCR.
Avaliação da maturação das fístulas arteriovenosas para hemodiálise pelo eco-Doppler colorido (2008)

CONTEXTO: Quando se confecciona uma fístula arteriovenosa para hemodiálise (FAVH) autógena, é necessário que se aguarde a dilatação da veia em questão e o desenvolvimento de volume de fluxo mínimo, fenômeno chamado de maturação. Ainda hoje se discute qual o tempo necessário para ocorrer essa maturação. OBJETIVO: Avaliar a maturação de FAVH utilizando-se critérios ecográficos. MÉTODO: Entre maio de 2004 e 2005, 40 pacientes foram selecionados prospectivamente, sendo 23 homens (57,5%), com média de idade de 17,5±51,3 anos, com indicação de confecção de uma FAVH. Utilizou-se o aparelho Logic III® com transdutor de 10 MHz para a avaliação no pré-operatório e nos 7º, 14º, 21º e 28º dias de pós-operatório. Os critérios para a maturação após a cirurgia foram: veia com diâmetro médio maior que 4 mm e volume de fluxo maior que 400 mL/min. RESULTADOS: O diâmetro médio pré-operatório foi de 3,24±1,43 e 3,71±1,37 mm para fístulas de punho e de cotovelo, respectivamente. O diâmetro final foi de 5,01±0,87 mm para as FAVH de punho (p = 0,006) e de 6,15±1,16 mm para as FAVH de cotovelo (p = 0,95). O volume de fluxo no 7º dia pós-operatório foi de 493,63±257,49 mL/min e 976,33±332,90 mL/min para as FAVH de punho e cotovelo, respectivamente. Ao final do estudo, foi calculado o valor de 556,81±288,42 mL/min nas FAVH de punho (p &lt; 0,05) e de 1031,62±614,812 mL/min nas FAVH de cotovelo. Baseados nos dois critérios, a maturação ocorreu em 57,1% das fístulas de punho e em 100% das fístulas de cotovelo após a 1ª semana. Após 4 semanas, 67,9% das fístulas de punho e 100% das fístulas de cotovelo apresentaram maturação. CONCLUSÃO: A maioria das FAVH de cotovelo apresentou diâmetro e fluxo adequados para punção logo após a 1ª semana de pós-operatório. Para as FAVH de punho, houve melhora progressiva dos padrões de maturação com o passar das semanas, sugerindo que essas FAVH devem ser puncionadas preferencialmente após a 4ª semana de pós-operatório.
Wide-stripe AlGaInP laser diodes with current-blocking region near facets grown on misoriented substrates (1991)

Wide-stripe high-power AlGaInP laser diodes (λL = 659 nm) with a current-blocking region (CBR) near the facets have been successfully fabricated for the first time by MOCVD using (100) GaAs substrates with a misorientation of 7° towards the (011) direction. The laser diodes show linear light output against current characteristics, in contrast with those fabricated using (100) substrates. Maximum continuous-wave light output power is achieved with 410 mW at 20°C.
TAF4b and Jun/Activating Protein-1 Collaborate to Regulate the Expression of Integrin α6 and Cancer Cell Migration Properties (2010)

The TAF4b subunit of the transcription factor IID, which has a central role in transcription by polymerase II, is involved in promoter recognition by selective recruitment of activators. The activating protein-1 (AP-1) family members participate in oncogenic transformation via gene regulation. Utilizing immunoprecipitation of endogenous protein complexes, we documented specific interactions between Jun family members and TATA box binding protein-associated factors (TAF) in colon HT29 adenocarcinoma cells. Particularly, TAF4b and c-Jun were found to colocalize and interact in the nucleus of advanced carcinoma cells and in cells with epithelial-to-mesenchymal transition (EMT) characteristics. TAF4b was found to specifically regulate the AP-1 target gene involved in EMT integrin alpha6, thus altering related cellular properties such as migration potential. Using a chromatin immunoprecipitation approach in colon adenocarcinoma cell lines, we further identified a synergistic role for TAF4b and c-Jun and other AP-1 family members on the promoter of integrin alpha6, underlining the existence of a specific mechanism related to gene expression control. We show evidence for the first time of an interdependence of TAF4b and AP-1 family members in cell type-specific promoter recognition and initiation of transcription in the context of cancer progression and EMT.
The N-terminal region of the 37-kDa translocated fragment of Pseudomonas exotoxin A aborts translocation by promoting its own export after microsomal membrane insertion. (1993)

The 37-kDa C-terminal fragment of Pseudomonas exotoxin A (PE; termed PE37 and composed of aa 280-613 of PE) translocates to the cell cytosol to cause cell death. PE37 requires a C-terminal endoplasmic reticulum retention sequence to be cytotoxic, indicating that the toxin may translocate to the cytosol from the endoplasmic reticulum. We show here that the N-terminal region of nascent PE37 can be inserted into the membrane of canine pancreatic microsomes by the preprocecropin signal sequence but then is exported or released from microsomes. The 34 N-terminal amino acids of the toxin fragment are sufficient to arrest translocation and prevent the microsomal accumulation of nascent chains that otherwise are sequestered into microsomes. These data support a role for the N-terminal region of PE37 in the translocation of the toxin from the endoplasmic reticulum to the cytosol in mammalian cells.
The Complete Nucleotide Sequence of the Group II RNA Coliphage GA1 (1986)

The complete nucleotide sequence of the RNA coliphage GA, a group II phage, is presented. The entire genome comprises 3466 bases. Three large open reading frames were identified, which correspond to the maturation protein gene (390 amino acids), the coat protein gene (129 amino acids) and the replicase beta-subunit protein gene (531 amino acids). In addition, untranslated regions occur at the 5' (135 bases) and 3' (122 bases) ends of the molecule. Two intercistronic untranslated regions occur between the cistrons for the maturation and coat proteins, and between the coat and beta-subunit proteins. We have compared the nucleotide sequence of GA RNA with the published sequence of MS2 RNA, and show that they are related. The comparative structures of two important regulatory regions are presented; the coat protein binding site which is involved in translational repression of the replicase beta-subunit protein gene, and a hairpin in a region proximal to the lysis protein gene.