gebhart/patrepeval huggingface dataset:
Immunoliposomal Systems Targeting Primary Effusion Lymphoma: In Vitro Study (2010)

ILp could be proposed as effective carriers for oligonucleotide transfer in BCBL-1 cells. In vitro experimental results encourage us to further test the in vivo therapeutic potential of ILp for specific delivery of antitumoral agents.
Cycloalkano‐2H‐pyrrole as a Stable Intermediate in the Conversion of β‐Cycloalkenyl‐α‐azidoacrylates to Cycloalkano‐1H pyrroles (1993)

A quantitative 1,5-electrocyclization takes place on thermolysis of the 2-vinylcycloalkenyl-α-azidoacrylate 1 to form the substituted cycloalkano-2H-pyrroles 2. Products of a reaction of vinyl azide or -nitrene with the unsaturated side chains were not observed.
A TEM horn antenna design and measurement (2008)

The semi-rigid cable for radio frequency band as a feeding network structure that effectively excited tapered triangle-shape TEM horn antenna geometry is proposed. The semi-rigid cable to parallel waveguide transition then to feed triangle-shape parallel plate transmission line as a TEM horn antenna. The designed triangle-shape TEM horn antenna has the merits such as wideband, simple feeding network, low profile compact size with fairly good antenna performances such as return loss, peak gain and radiation patterns.
Intraoperative spectral domain optical coherence tomography for vitreoretinal surgery (2010)

We demonstrate in vivo human retinal imaging using an intraoperative microscope-mounted optical coherence tomography system (MMOCT). Our optomechanical design adapts an Oculus Binocular Indirect Ophthalmo Microscope (BIOM3), suspended from a Leica ophthalmic surgical microscope, with spectral domain optical coherence tomography (SD-OCT) scanning and relay optics. The MMOCT enables wide-field noncontact real-time cross-sectional imaging of retinal structure, allowing for SD-OCT augmented intrasurgical microscopy for intraocular visualization. We experimentally quantify the axial and lateral resolution of the MMOCT and demonstrate fundus imaging at a 20Hz frame rate.
ImageNet/ResNet-50 Training in 224 Seconds. (2018)

Scaling the distributed deep learning to a massive GPU cluster level is challenging due to the instability of the large mini-batch training and the overhead of the gradient synchronization. We address the instability of the large mini-batch training with batch-size control and label smoothing. We address the overhead of the gradient synchronization with 2D-Torus all-reduce. Specifically, 2D-Torus all-reduce arranges GPUs in a logical 2D grid and performs a series of collective operation in different orientations. These two techniques are implemented with Neural Network Libraries (NNL). We have successfully trained ImageNet/ResNet-50 in 122 seconds without significant accuracy loss on ABCI cluster.
Neutral Sphingomyelinase 2 (nSMase2)-dependent Exosomal Transfer of Angiogenic MicroRNAs Regulate Cancer Cell Metastasis (2013)

The release of humoral factors between cancer cells and the microenvironmental cells is critical for metastasis; however, the roles of secreted miRNAs in non-cell autonomous cancer progression against microenvironmental cells remain largely unknown. Here, we demonstrate that the neutral sphyngomyelinase 2 (nSMase2) regulates exosomal microRNA (miRNA) secretion and promotes angiogenesis within the tumor microenvironment as well as metastasis. We demonstrate a requirement for nSMase2-mediated cancer cell exosomal miRNAs in the regulation of metastasis through the induction of angiogenesis in inoculated tumors. In addition, miR-210, released by metastatic cancer cells, was shown to transport to endothelial cells and suppress the expression of specific target genes, which resulted in enhanced angiogenesis. These findings suggest that the horizontal transfer of exosomal miRNAs from cancer cells can dictate the microenviromental niche for the benefit of the cancer cell, like "on demand system" for cancer cells.
Detection of Somatic DNA Recombination in the Transgenic Mouse Brain (1991)

A DNA construct containing the bacterial beta-galactosidase gene (lacZ) was used to study somatic DNA recombination in the transgenic mouse brain. Recombination-positive areas of the adult brain were stained blue with X-gal, a substrate of beta-galactosidase. Blue-colored cells appeared soon after birth, and continued to emerge in postnatal tissue. Staining was prominent in sensory as opposed to motor regions of the brain, and was present in more than 70 discrete areas of the nervous system. The possibility of DNA rearrangement is discussed with respect to the development of the central nervous system.
Effect of recombinant and purified hematopoietic growth factors on human megakaryocyte colony formation. (1988)

The effect of a number of purified or recombinant hematopoietic growth factors, including recombinant erythropoietin (rEpo), thrombocytopoiesis stimulating factor (TSF), recombinant interleukin 1 alpha (rIL-1 alpha), recombinant granulocyte colony-stimulating factor (rG-CSF), macrophage colony-stimulating factor (CSF-1), recombinant interleukin 3 (rIL-3), and recombinant granulocyte-macrophage colony-stimulating factor (rGM-CSF), on megakaryocyte (MK) colony formation by normal human marrow cells in a serum-depleted assay system was determined. Neither rEpo, TSF, CSF-1, rIL-1 alpha, nor rG-CSF alone augmented MK colony formation. Both rGM-CSF and rIL-3 at optimal doses increased MK colony formation eightfold and tenfold, respectively, above baseline values. Addition of increasing amounts of either rGM-CSF or rIL-3 led to progressively greater numbers of MK colonies formed until plateau levels were reached. Both rGM-CSF and rIL-3 also led to a dose-related increase in the number of cells per MK colony formed in culture. These molecules were equivalent stimulators of MK colony formation when their effects at optimal concentrations were compared. The effects of rGM-CSF and rIL-3 were additive at suboptimal concentrations of rIL-3 in that colony formation by a combination of the two growth factors approximated the sum of colony formation by each growth factor alone. These data suggest that rGM-CSF and rIL-3 alone and in combination are important regulators of in vitro megakaryocytopoiesis at the progenitor cell level.
Relation of circulating interleukin‐6 to left ventricular remodeling in patients with reperfused anterior myocardial infarction (2004)

Circulating IL-6 levels correlated closely with LV geometric changes during the remodeling process in patients with reperfused MI. Our study addresses the usefulness of another marker for LV remodeling after MI.
Protective efficacy of adenovirus/protein vaccines against SIV challenges in rhesus monkeys (2015)

Preclinical studies of viral vector-based HIV-1 vaccine candidates have previously shown partial protection against neutralization-resistant virus challenges in rhesus monkeys. In this study, we evaluated the protective efficacy of adenovirus serotype 26 (Ad26) vector priming followed by purified envelope (Env) glycoprotein boosting. Rhesus monkeys primed with Ad26 vectors expressing SIVsmE543 Env, Gag, and Pol and boosted with AS01B-adjuvanted SIVmac32H Env gp140 demonstrated complete protection in 50% of vaccinated animals against a series of repeated, heterologous, intrarectal SIVmac251 challenges that infected all controls. Protective efficacy correlated with the functionality of Env-specific antibody responses. Comparable protection was also observed with a similar Ad/Env vaccine against repeated, heterologous, intrarectal SHIV-SF162P3 challenges. These data demonstrate robust protection by Ad/Env vaccines against acquisition of neutralization-resistant virus challenges in rhesus monkeys.
Playing Atari with Deep Reinforcement Learning (2013)

We present the first deep learning model to successfully learn control policies directly from high-dimensional sensory input using reinforcement learning. The model is a convolutional neural network, trained with a variant of Q-learning, whose input is raw pixels and whose output is a value function estimating future rewards. We apply our method to seven Atari 2600 games from the Arcade Learning Environment, with no adjustment of the architecture or learning algorithm. We find that it outperforms all previous approaches on six of the games and surpasses a human expert on three of them.
An optimized electroporation protocol applicable to a wide range of cell lines. (1994)

A number of transfection methods for mammalian cells are available; however, many cell lines may appear resistant to efficient transfection, or at best, necessitate lengthy optimization procedures in recommended protocols. We describe here an electroporation protocol that yields highly efficient gene transfer (20%-100% of surviving cells) in all 19 cell lines tested so far, including lymphoid, myeloid, glial, fibroblast and COS cells. Unlike earlier electroporation protocols, adaptation of this protocol to a cell line of interest only requires the optimization of a single parameter, i.e., the voltage, and can be performed within a day. Furthermore, it is also superior to transfection protocols for other methods (calcium phosphate precipitation, lipofection, DEAE-dextran transfection and transferrinfection) in terms of reproducibility, economy and average transfection efficiency for a wide variety of cell lines.
Sequence of the Spacer in the Recombination Signal Sequence Affects V(D)J Rearrangement Frequency and Correlates with Nonrandom Vκ Usage In Vivo (1998)

Functional variable (V), diversity (D), and joining (J) gene segments contribute unequally to the primary repertoire. One factor contributing to this nonrandom usage is the relative frequency with which the different gene segments rearrange. Variation from the consensus sequence in the heptamer and nonamer of the recombination signal sequence (RSS) is therefore considered a major factor affecting the relative representation of gene segments in the primary repertoire. In this study, we show that the sequence of the spacer is also a determinant factor contributing to the frequency of rearrangement. Moreover, the effect of the spacer on recombination rates of various human Vkappa gene segments in vitro correlates with their frequency of rearrangement in vivo in pre-B cells and with their representation in the peripheral repertoire.
MOLECULAR EVENTS IN THE PATHOGENESIS OF HEPADNAVIRUS-ASSOCIATED HEPATOCELLULAR CARCINOMA (1994)

Chronic hepadnavirus infection is associated with hepatocellular carcinoma (HCC) in natural hosts such as humans, woodchucks, and Beechey ground squirrels. Several possible oncogenic mechanisms have been identified, including a potential role of the hepadnavirus x (hbx) gene, which transactivates transcription regulated by certain cis-acting sequences, e.g. regulatory sequences of the hepatitis B virus (HBV) and heterologous regulatory sequences of other viruses and cellular genes. The oncogenic potential of hbx is suggested by the observation of HCCs in hbx transgenic mice, the oncogenic transformation of cells expressing hbx in culture, and the transactivation of oncogenes c-myc and c-jun by hbx. Cis-activation of cellular oncogenes N-myc and c-myc by viral promoter insertion has been a common finding in woodchuck hepatitis virus (WHV)-associated HCCs of woodchucks. No such cis-activation of any cellular gene has been shown in virus-associated HCCs of ground squirrels or humans. Amplification and overexpression of the c-myc gene has been a common finding in HCCs of ground squirrels, and is rare in woodchuck or human HCCs. Point mutations in the p53 gene and allelic deletion of p53 have been common findings in human HCCs, but have not been found in HCCs in woodchucks and have been found rarely in ground squirrels. How each of these genetic changes in the different hosts contributes to HCC remains to be determined, but apparently different changes in different HCCs of hepadnavirus-infected hosts suggest that several separate genetic events may contribute to the development of HCC. These events may differ in each host, and some may not result from a direct virus-specific mechanism. Chronic hepadnavirus infection is often associated with chronic necroinflammatory liver disease and cirrhosis, a pathologic process common to several other risk factors for HCC. This suggests that this pathologic process (necroinflammatory disease) may be hepatocarcinogenic regardless of the inciting agent. Thus hepadnavirus infection may play an important role in the development of HCC by causing chronic hepatitis and HCC with the same mechanisms by which other risk factors for HCC cause chronic necroinflammatory liver disease and HCC.
Computational Study on the Performance of the Impeller in Centrifugal Pump (2000)

This paper reports the impeller performance of centrifugal pump, modified HES65-250. Developed CFD code uses SIMPLE algorithm, power-law scheme, standard turbulence model in curvilinear coordinate system. The calculations are conducted for 5 cases, from 0.6 to 1.4 of flow rate ratio with 0.2 increment. The flow characteristics inside of impeller are analysed. The results show that reversal flows exist at the inlet of impeller which have small rotary stagnation pressure. The obtained results are compared with the experimental data at impeller exit and shows good qualitative agreement.
Global, regional, and national prevalence of overweight and obesity in children and adults during 1980–2013: a systematic analysis for the Global Burden of Disease Study 2013 (2014)

BACKGROUND: In 2010, overweight and obesity were estimated to cause 3·4 million deaths, 3·9% of years of life lost, and 3·8% of disability-adjusted life-years (DALYs) worldwide. The rise in obesity has led to widespread calls for regular monitoring of changes in overweight and obesity prevalence in all populations. Comparable, up-to-date information about levels and trends is essential to quantify population health effects and to prompt decision makers to prioritise action. We estimate the global, regional, and national prevalence of overweight and obesity in children and adults during 1980-2013. METHODS: We systematically identified surveys, reports, and published studies (n=1769) that included data for height and weight, both through physical measurements and self-reports. We used mixed effects linear regression to correct for bias in self-reports. We obtained data for prevalence of obesity and overweight by age, sex, country, and year (n=19,244) with a spatiotemporal Gaussian process regression model to estimate prevalence with 95% uncertainty intervals (UIs). FINDINGS: Worldwide, the proportion of adults with a body-mass index (BMI) of 25 kg/m(2) or greater increased between 1980 and 2013 from 28·8% (95% UI 28·4-29·3) to 36·9% (36·3-37·4) in men, and from 29·8% (29·3-30·2) to 38·0% (37·5-38·5) in women. Prevalence has increased substantially in children and adolescents in developed countries; 23·8% (22·9-24·7) of boys and 22·6% (21·7-23·6) of girls were overweight or obese in 2013. The prevalence of overweight and obesity has also increased in children and adolescents in developing countries, from 8·1% (7·7-8·6) to 12·9% (12·3-13·5) in 2013 for boys and from 8·4% (8·1-8·8) to 13·4% (13·0-13·9) in girls. In adults, estimated prevalence of obesity exceeded 50% in men in Tonga and in women in Kuwait, Kiribati, Federated States of Micronesia, Libya, Qatar, Tonga, and Samoa. Since 2006, the increase in adult obesity in developed countries has slowed down. INTERPRETATION: Because of the established health risks and substantial increases in prevalence, obesity has become a major global health challenge. Not only is obesity increasing, but no national success stories have been reported in the past 33 years. Urgent global action and leadership is needed to help countries to more effectively intervene. FUNDING: Bill & Melinda Gates Foundation.
Restoring punctuation and capitalization in transcribed speech (2009)

Adding punctuation and capitalization greatly improves the readability of automatic speech transcripts. We discuss an approach for performing both tasks in a single pass using a purely text-based n-gram language model. We study the effect on performance of varying the n-gram order (from n = 3 to n = 6) and the amount of training data (from 58 million to 55 billion tokens). Our results show that using larger training data sets consistently improves performance, while increasing the n-gram order does not help nearly as much.
Effect of nonresonant frequencies on the enhancement of quantum beat amplitudes in rovibrational states of Li2: The role of state spacing (2002)

Optical phase manipulation of nonresonant frequencies is investigated as a method of achieving optimal population transfer during resonant impulsive stimulated Raman scattering. Wave packets containing quantum beats between an initially prepared rovibrational level in the A(1Σu+) electronic state of Li2 and states populated via a resonance-enhanced rotational Raman process are created using a shaped ultrafast pulse centered near 800 nm. Study of these wave packets allows a quantitative comparison of population transfer as a function of applied phases in the ultrafast pulse. Two cases are explored to determine the ability to enhance population transfer: one with a wide state spacing [A(νA=11, JA=28)-A(11,30) at 50.1 cm−1] and one with a narrow spacing [A(11,8)-A(11,10) at 16.6 cm−1]. In both cases, several different phase masks are applied to the wave packet preparation pulse to enhance the population transferred to the newly formed state of interest. One phase mask involves the application of a −90° phase shift to the nonresonant optical frequencies that lie between the resonant transition frequencies, resulting in an optimal phase relationship between pairs of nonresonant frequencies contributing to the Stokes–Raman excitation. Another extends the phase modification to the nonresonant frequencies lying outside the two resonant transitions to allow constructive enhancement from a larger range of frequencies. Significant population enhancements, up to a factor of ∼12, of the newly formed A(11,30) and A(11,10) states are demonstrated. In addition, the dependence on the state spacing and therefore the extent to which nonresonant frequencies affect the population transferred in the stimulated Raman process are demonstrated.
Matched molecular pair-based data sets for computer-aided medicinal chemistry (2014)

<ns4:p>Matched molecular pairs (MMPs) are widely used in medicinal chemistry to study changes in compound properties including biological activity, which are associated with well-defined structural modifications. Herein we describe up-to-date versions of three MMP-based data sets that have originated from in-house research projects. These data sets include activity cliffs, structure-activity relationship (SAR) transfer series, and second generation MMPs based upon retrosynthetic rules. The data sets have in common that they have been derived from compounds included in the ChEMBL database (release 17) for which high-confidence activity data are available. Thus, the activity data associated with MMP-based activity cliffs, SAR transfer series, and retrosynthetic MMPs cover the entire spectrum of current pharmaceutical targets. Our data sets are made freely available to the scientific community.</ns4:p>
Structure and functions of nucleolin (1999)

Nucleolin is an abundant protein of the nucleolus. Nucleolar proteins structurally related to nucleolin are found in organisms ranging from yeast to plants and mammals. The association of several structural domains in nucleolin allows the interaction of nucleolin with different proteins and RNA sequences. Nucleolin has been implicated in chromatin structure, rDNA transcription, rRNA maturation, ribosome assembly and nucleo-cytoplasmic transport. Studies of nucleolin over the last 25 years have revealed a fascinating role for nucleolin in ribosome biogenesis. The involvement of nucleolin at multiple steps of this biosynthetic pathway suggests that it could play a key role in this highly integrated process.
Identification of palmitoylation sites on CD4, the human immunodeficiency virus receptor. (1992)

We report that the cell surface glycoprotein CD4 expressed in HeLa cells can be metabolically labeled with [3H]palmitic acid. Analysis of the 3H-label after hydrolysis of the protein indicated that it was incorporated predominantly as palmitic acid. Comparison of the amount of [3H]palmitate incorporated into CD4 with that incorporated into a protein known to contain one molecule of esterified palmitate suggested that one to two molecules of palmitate were added to CD4. The fatty acid was readily cleaved from CD4 by treatment with weak base suggesting a thioester linkage. Mutations of each of 2 cysteine residues, Cys394 and Cys397, in CD4 at the junction of the transmembrane and cytoplasmic domains reduced labeling with [3H]palmitic acid, and mutation of both cysteines eliminated labeling. These results indicate that both cysteines are esterified to palmitate. Modification with palmitate was not required for expression of CD4 on the cell surface or for binding of p56lck to its cytoplasmic domain.
Optimal capacity placement for path restoration in STM or ATM mesh-survivable networks (1998)

The total transmission capacity required by a transport network to satisfy demand and protect it from failures contributes significantly to its cost, especially in long-haul networks. Previously, the spare capacity of a network with a given set of working span sizes has been optimized to facilitate span restoration. Path restorable networks can, however, be even more efficient by defining the restoration problem from an end to end rerouting viewpoint. We provide a method for capacity optimization of path restorable networks which is applicable to both synchronous transfer mode (STM) and asynchronous transfer mode (ATM) virtual path (VP)-based restoration. Lower bounds on spare capacity requirements in span and path restorable networks are first compared, followed by an integer program formulation based on flow constraints which solves the spare and/or working capacity placement problem in either span or path restorable networks. The benefits of path and span restoration, and of jointly optimizing working path routing and spare capacity placement, are then analyzed.
Serum Circulating Human mRNA Profiling and Its Utility for Oral Cancer Detection (2006)

The utility of serum transcriptome diagnostics is successfully demonstrated for OSCC detection. This novel concept could be developed as an adjunctive tool for disease diagnosis.