gebhart/patrepeval huggingface dataset:
Nucleosomes are well positioned in exons and carry characteristic histone modifications (2009)

The genomes of higher organisms are packaged in nucleosomes with functional histone modifications. Until now, genome-wide nucleosome and histone modification studies have focused on transcription start sites (TSSs) where nucleosomes in RNA polymerase II (RNAPII) occupied genes are well positioned and have histone modifications that are characteristic of expression status. Using public data, we here show that there is a higher nucleosome-positioning signal in internal human exons and that this positioning is independent of expression. We observed a similarly strong nucleosome-positioning signal in internal exons of Caenorhabditis elegans. Among the 38 histone modifications analyzed in man, H3K36me3, H3K79me1, H2BK5me1, H3K27me1, H3K27me2, and H3K27me3 had evidently higher signals in internal exons than in the following introns and were clearly related to exon expression. These observations are suggestive of roles in splicing. Thus, exons are not only characterized by their coding capacity, but also by their nucleosome organization, which seems evolutionarily conserved since it is present in both primates and nematodes.
High quality color images with continuous ink jets (2003)

The halftone method used generates shades of color by controlling the number of ink drops deposited in each pixel. Since only about 22 drops are actually available during the time allowed for the printing of one pixel (25 ms), only 22 density steps plus white can be generated. The diffuse reflection density is shown as a function of the number of drops deposited in each pixel. The curve was obtained using cyan ink on baryte paper and depends on many parameters, especially paper quality. The 23 density steps obtainable by the halftone method will give rise to contouring which degrades image quality. This is especially true at the lowest density levels, where, e.g. the step between zero and one drop per pixel is very noticeable. The problem can be solved by using a variation of an error diffusion or dither algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Spatial regulation of the actin cytoskeleton by HSF-1 during aging (2018)

There are many studies suggesting an age-associated decline in the actin cytoskeleton, and this has been adopted as common knowledge in the field of aging biology. However, a direct identification of this phenomenon in aging multicellular organisms has not been performed. Here, we express LifeAct::mRuby in a tissue-specific manner to interrogate cytoskeletal organization as a function of age. We show for the first time in Caenorhabditis elegans that the organization and morphology of the actin cytoskeleton deteriorate at advanced age in the muscles, intestine, and hypodermis. Moreover, hsf-1 is essential for regulating cytoskeletal integrity during aging, so that knockdown of hsf-1 results in premature aging of actin and its overexpression protects actin cytoskeletal integrity in the muscles, the intestine, and the hypodermis. Finally, hsf-1 overexpression in neurons alone is sufficient to protect cytoskeletal integrity in nonneuronal cells.
Heteroleptic tris-cyclometalated iridium(iii) complexes supported by an o-carboranyl-pyridine ligand (2013)

Heteroleptic tris-cyclometalated Ir(III) complexes supported by the o-carboranyl-pyridine (CBpy) as a novel C^N chelating ligand were synthesized and characterized. While the CBpy ligand contributes to the electronic stabilization of complexes, their photophysical properties are dominated by 2-arylpyridine ligands.
Canine model of convection-enhanced delivery of liposomes containing CPT-11 monitored with real-time magnetic resonance imaging (2008)

Convection-enhanced delivery of liposomal Gd/CPT-11 is associated with minimal adverse effects in a large animal model, and further assessment for use in clinical patients is warranted. Future studies investigating real-time monitored CED in spontaneous gliomas in canines are feasible and will provide a unique, clinically relevant large animal translational model for testing this and other therapeutic strategies.
Conformational trapping in a membrane environment: a regulatory mechanism for protein activity? (1996)

Functional regulation of proteins is central to living organisms. Here it is shown that a nonfunctional conformational state of a polypeptide can be kinetically trapped in a lipid bilayer environment. This state is a metastable structure that is stable for weeks just above the phase transition temperature of the lipid. When the samples are incubated for several days at 68 degrees C, 50% of the trapped conformation converts to the minimum-energy functional state. This result suggests the possibility that another mechanism for functional regulation of protein activity may be available for membrane proteins: that cells may insert proteins into membranes in inactive states pending the biological demand for protein function.
Preparation and Characterization of Porous Si-Coated SiC Fiber Media (2004)

Electrically conductive porous Si/SiC fiber media were prepared by infiltration of liquid silicon into porous carbon fiber preforms. The series rule of mixture for the effective electrical conductivity was applied to the disc shaped samples to estimate their silicon content, effective electrical conductivity and porosity. The electrical conductivity was estimated by assuming the disc sample as a plate of equivalent geometry, i.e., same thickness, electrode distance and volume. As the volumetric content of silicon in a sample increases from 0.026% to 0.97%, the estimated electrical conductivity increases from 0.17 S/cm to 2.09 S/cm. The porosity of the samples measured by Archimedes principle was in the range of 75~83% and 1~4% less than the one estimated by the series rule of mixture for the effective electrical conductivity.
CD74 in antigen presentation, inflammation, and cancers of the gastrointestinal tract (2009)

CD74 is a protein whose initial role in antigen presentation was recognized two decades ago. Recent studies have revealed that it has additional functions as a receptor for macrophage migration inhibitory factor and as a receptor for an important human pathogen, Helicobacter pylori (H pylori). The role of CD74 as a receptor is important because after binding of migration inhibitory factor or H pylori, NF-kappaB and Erk1/2 activation occurs, along with the induction of proinflammatory cytokine secretion. This review provides an up-to-date account of the functions of CD74 and how it might be involved in inflammation and cancer within the gastrointestinal tract.
Differential effects of the proteasome inhibitor bortezomib on apoptosis and angiogenesis in human prostate tumor xenografts. (2003)

Bortezomib (Velcade, PS-341) is a dipeptide boronate inhibitor of the 26S proteasome developed for use in cancer therapy. Here we examined the effects of bortezomib on apoptosis and angiogenesis in derivatives of two popular human prostate cancer cell lines (LNCaP-Pro5 and PC3M-Pro4). Bortezomib strongly inhibited proliferation in both cell lines in vitro, but the PC3M-Pro4 cells were significantly more sensitive than the LNCaP-Pro5 cells to bortezomib-induced apoptosis. The compound also significantly inhibited the growth of LNCaP-Pro5 and LNCaP-Pro4 tumor xenografts, but the mechanisms involved in tumor growth inhibition differed in the two models. Bortezomib-treated LNCaP-Pro5 tumors displayed reduced microvessel densities and vascular endothelial cell growth factor secretion and high levels of endothelial cell apoptosis consistent with angiogenesis inhibition. In contrast, PC3M-Pro4 tumors were poorly vascularized at baseline, and bortezomib failed to induce significant changes in microvessel density, angiogenic factor secretion, or endothelial cell death in this model. Rather, growth inhibition in the PC3M-Pro4 tumors was associated with direct increases in tumor cell death. Together, our results confirm that bortezomib is active in preclinical models of human prostate cancer, but its effects on apoptosis versus angiogenesis are cell type dependent.
Jointly Learning Energy Expenditures and Activities Using Egocentric Multimodal Signals (2017)

Physiological signals such as heart rate can provide valuable information about an individuals state and activity. However, existing work on computer vision has not yet explored leveraging these signals to enhance egocentric video understanding. In this work, we propose a model for reasoning on multimodal data to jointly predict activities and energy expenditures. We use heart rate signals as privileged self-supervision to derive energy expenditure in a training stage. A multitask objective is used to jointly optimize the two tasks. Additionally, we introduce a dataset that contains 31 hours of egocentric video augmented with heart rate and acceleration signals. This study can lead to new applications such as a visual calorie counter.
Analysis of Mice with Single and Multiple Copies of Transgenes Reveals a Novel Arrangement for the λ 5-V preB1 Locus Control Region (1999)

The murine lambda5-VpreB1 locus encodes two proteins that form part of the pre-B-cell receptor and play a key role in B-lymphocyte development. We have identified a locus control region (LCR) which is responsible for coordinate activation of both genes in pre-B cells. Analysis of mice with single and multiple copies of transgenes shows a clear difference in the expression behavior of the genes depending on the transgene copy number. While expression of both lambda5 and VpreB1 in single- and two-copy integrations requires the presence of a set of DNase I hypersensitive sites located 3' of the lambda5 gene, small fragments containing the genes have LCR activity when arranged in multiple-copy tandem arrays, indicating that additional components of the LCR are located within or close to the genes. The complete LCR is capable of driving efficient copy-dependent expression of a lambda5 gene in pre-B cells even when it is integrated into centomeric gamma-satellite DNA. The finding that activation of expression of the locus by positively acting factors is fully dominant over the silencing effect of heterochromatin has implications for models for chromatin-mediated gene silencing during B-cell development.
Coherent Analog Low Power, Small Size 400/200/100Gb/s Receiver Based on Bipolar SiGe Technology (2018)

We demonstrate first to our knowledge analog coherent engine (ACE). Simulations show power consumption under 2W for 400Gb/s ACE. Combination of ACE with CMOS direct detection unit is good candidate for short reach communications.
Longterm drug therapy for rheumatoid arthritis in seven rheumatology private practices: II. Second line drugs and prednisone. (1992)

The probability of continuation of 1,077 courses of 2nd line drugs taken by 532 patients with rheumatoid arthritis treated in 7 rheumatology private practices was examined. This probability was that 50% of courses were continued over 10 months for oral gold, 20 months for hydroxychloroquine, 21 months for penicillamine, 25 months for parenteral gold, 27 months for azathioprine, and more than 60 months for methotrexate (MTX). MTX and prednisone were the only drugs continued by more than 50% of patients after 60 months, while about 20% of courses of other 2nd line drugs other than oral gold were estimated to be continued at 60 months. Estimated drug continuation did not differ significantly according to age, duration of disease, or whether the drug was the first, second, or 3rd 2nd line drug used. Some patients took each 2nd line drug for more than 5 years, suggesting a favorable experience, but most courses were not continued beyond 2 years.
Transcriptomic Identification of Floral Transition and Development-Associated Genes in Styrax japonicus (2019)

Styrax japonicus (S. japonicus) is an important flowering tree species in temperate regions, and it is regarded as a nectariferous plant. However, there have been few studies to date analyzing floral development in this species. In order to understand gene expression dynamics during S. japonicus flower development, we; therefore, prepared cDNA libraries from three distinct stages of S. japonicus. Illumina sequencing generated 31,471 differentially expressed unigenes during flower development. We additionally conducted pathway enrichment analyses using the GO and KEGG database in order to assess the functions of genes differentially expressed during different stages of the floral development process, revealing these genes to be associated with pathways including phytohormone signaling, Transcription factor, protein kinase, and circadian rhythms. In total, 4828 TF genes, 8402 protein kinase genes, and 78 DEGs related to hormone pathways were identified in flower development stages. Six genes were selected for confirmation of expression levels using quantitative real-time PCR. The gene expression data presented herein represent the most comprehensive dataset available regarding the flowering of S. japonicus, thus offering a reference for future studies of the flowering of this and other Styracaceae species.
BBN at TREC7: Using Hidden Markov Models for Information Retrieval. (1998)

We present a new method for information retrieval using hidden Markov models (HMMs) and relate our experience with this system on the TREC-7 ad hoc task. We develop a general framework for incorporating multiple word generation mechanisms within the same model. We then demonstrate that an extremely simple realization of this model substantially outperforms tf:idf ranking on both the TREC-6 and TREC-7 ad hoc retrieval tasks. We go on to present several algorithmic re nements, including a novel method for performing blind feedback in the HMM framework. Together, these methods form a state-of-the-art retrieval system that ranked among the best on the TREC-7 ad hoc retrieval task, and showed extraordinary performance in development experiments on TREC-6. 1
DEVELOPMENT OF A DRIVING DATA RECORDER FOR COMMERCIAL VEHICLES AND ITS APPLICATIONS (1984)

Generally, data loggers are used for the purpose of investigating on the driving conditions of vehicles which are under some research and development works. Hino Motors, Ltd., in co-operation with Sawafuji Electric Co., Ltd., has developed an in-vehicle data logger, however, which can easily be installed by customers on vehicles for use in actual operation in the field. Through the production of printed digital data, graphs, and tables, the logger provides useful information on fuel economy for both drivers and managers of fleets, as well as valuable information regarding maintenance schedules. The logger, named the Hino Driving Data Recorder, has been delivered to all Hino-dealers in Japan and is receiving very positive feedback from customers. Specifications and details of this data recorder and actual examples of its applications on buses are described in this paper.
Patients' shifting goals for deep brain stimulation and informed consent (2018)

These data illustrate how patients' primary goals for DBS shift early in stimulation and highlight the important differences between symptom and behavioral goals. Changes in the rank order of symptom goals were related to changes in symptom severity, whereas subtler shifts in behavioral goals were unrelated to improvements after DBS. This observation suggests that DBS does not affect goals that may be more reflective of core personal values. The findings provide empiric data that can help improve the informed consent process.
Statistical Hypoglycemia Prediction (2008)

Statistical linear prediction gives significant lead time before hypoglycemic events with an explicit, tunable trade-off between longer lead times and fewer missed events versus fewer false alarms.
Artificial intelligence versus logistic regression statistical modelling to predict cardiac complications after noncardiac surgery (1994)

The traditional approach to developing models predictive of cardiac events has been to perform logistic regression (LR) analysis on a variety of potential predictors. An alternative to use an artificial intelligence system called a neural network (NN) which simulates biological intelligence. To evaluate the potential applicability of the latter method, we compared the ability of LR and NN techniques to predict cardiac events after noncardiac surgery. A total of 200 patients (training group) underwent cardiac risk assessment before major noncardiac surgery using 17 clinical parameters and 7 quantitative indices based on dipyridamole-thallium imaging. There were 21 post-operative myocardial infarctions and/or cardiac deaths. Data from the training group were used to develop two predictive models: one based on backward stepwise LR multivariate statistical analysis and the other one using a neural network. Both models were then validated on a second group of 160 consecutive patients also referred for preoperative risk stratification (validation group). The NN consisted of 14 input, 29 hidden, and 1 output neurons and used a back-propagation algorithm (learning rate 0.2, training tolerance 0.5, sigmoid transfer function). The sensitivity, specificity, positive and negative predictive accuracies for the prediction of postoperative events in the validation group of 160 patients were, respectively, 67% (6/9), 82% (124/151), 18% (6/33), and 98% (124/127) for LR, and 67% (6/9), 96% (145/151), 50% (6/12), and 98% (145/148) for the NN, with a difference in specificity which attained statistical significance (p < 0.01). Artificial intelligence may provide a useful alternative to conventional LR statistical analysis for the purpose of preoperative cardiac risk assessment.
Biologically Motivated Audio-Visual Cue Integration for Object (2008)

Auditory and visual cues are important sensor inputs for biological and artificial systems. They provide crucial information for navigating environments, recognizing categories, animals and people. How to combine effectively these two sensory channels is still an open issue. As a step towards this goal, this paper presents a comparison between three different multi-modal integration strategies, for audiovisual object category detection. We consider a high-level and a low-level cue integration approach, both biologically motivated, and we compare them with a mid-level cue integration scheme. All the three integration methods are based on the least square support vector machine algorithm, and state of the art audio and visual feature representations. We conducted experiments on two audio-visual object categories, dogs and guitars, presenting different visual and auditory characteristics. Results show that the high-level integration scheme consistently performs better than single cue methods, and of the other two integration schemes. These findings confirm results from the neuroscience. This suggests that the high-level integration scheme is the most suitable approach for multi-modal cue integration for artificial cognitive systems.
Inflammation and oxidative stress in vertebrate host–parasite systems (2008)

Innate, inflammation-based immunity is the first line of vertebrate defence against micro-organisms. Inflammation relies on a number of cellular and molecular effectors that can strike invading pathogens very shortly after the encounter between inflammatory cells and the intruder, but in a non-specific way. Owing to this non-specific response, inflammation can generate substantial costs for the host if the inflammatory response, and the associated oxygen-based damage, get out of control. This imposes strong selection pressure that acts to optimize two key features of the inflammatory response: the timing of activation and resolution (the process of downregulation of the response). In this paper, we review the benefits and costs of inflammation-driven immunity. Our aim is to emphasize the importance of resolution of inflammation as a way of maintaining homeostasis against oxidative stress and to prevent the 'horror autotoxicus' of chronic inflammation. Nevertheless, host immune regulation also opens the way to pathogens to subvert host defences. Therefore, quantifying inflammatory costs requires assessing (i) short-term negative effects, (ii) delayed inflammation-driven diseases, and (iii) parasitic strategies to subvert inflammation.
Olfactory marker protein (OMP) gene deletion causes altered physiological activity of olfactory sensory neurons. (1996)

Olfactory marker protein (OMP) is an abundant, phylogentically conserved, cytoplasmic protein of unknown function expressed almost exclusively in mature olfactory sensory neurons. To address its function, we generated OMP-deficient mice by gene targeting in embryonic stem cells. We report that these OMP-null mice are compromised in their ability to respond to odor stimull, providing insight to OMP function. The maximal electroolfactogram response of the olfactory neuroepithelium to several odorants was 20-40% smaller in the mutants compared with controls. In addition, the onset and recovery kinetics following isoamyl acetate stimulation are prolonged in the null mice. Furthermore, the ability of the mutants to respond to the second odor pulse of a pair is impaired, over a range of concentrations, compared with controls. These results imply that neural activity directed toward the olfactory bulb is also reduced. The bulbar phenotype observed in the OMP-null mouse is consistent with this hypothesis. Bulbar activity of tyrosine hydroxylase, the rate limiting enzyme of catecholamine biosynthesis, and content of the neuropeptide cholecystokinin are reduced by 65% and 50%, respectively. This similarity to postsynaptic changes in gene expression induced by peripheral olfactory deafferentation or naris blockade confirms that functional neural activity is reduced in both the olfactory neuroepithelium and the olfactory nerve projection to the bulb in the OMP-null mouse. These observations provide strong support for the conclusion that OMP is a novel modulatory component of the odor detection/signal transduction cascade.
THE ANTIGENIC COMPLEX OF STREPTOCOCCUS HÆMOLYTICUS (1928)

1. Hydrochloric acid extracts of Streptococcus hæmolyticus contain type-specific, as well as non-type-specific, substances. The precipitates formed by these crude extracts with homologous antibacterial serum are flocculent, while those obtained with heterologous serum are usually disc-like. 2. The type-specific substance may be detected by the use of anti-bacterial sera absorbed with heterologous strains of hemolytic streptococci. Such absorbed sera are type-specific: they are precipitated only by extracts of strains of the homologous type. 3. Any heterologous strain of hemolytic streptococcus absorbs the antibodies for all other heterologous strains, but homologous strains absorb type-specific antibodies as well. Numerous repeated absorptions with heterologous hemolytic streptococci tend to lower the titer of the type-specific antibody. A possible explanation of this fact is suggested. 4. Three strains did not yield a type-specific substance; and it seems probable that they had lost this function because of long continued cultivation in artificial media. 5. Classification based on the precipitin test with absorbed serum agrees with that previously determined by agglutination and protection tests. The method is, therefore, applicable to the problem of classification of the hemolytic streptococci.