gebhart/patrepeval huggingface dataset:
Asynchrony begets momentum, with an application to deep learning (2016)

Asynchronous methods are widely used in deep learning, but have limited theoretical justification when applied to non-convex problems. We show that running stochastic gradient descent (SGD) in an asynchronous manner can be viewed as adding a momentum-like term to the SGD iteration. Our result does not assume convexity of the objective function, so it is applicable to deep learning systems. We observe that a standard queuing model of asynchrony results in a form of momentum that is commonly used by deep learning practitioners. This forges a link between queuing theory and asynchrony in deep learning systems, which could be useful for systems builders. For convolutional neural networks, we experimentally validate that the degree of asynchrony directly correlates with the momentum, confirming our main result. An important implication is that tuning the momentum parameter is important when considering different levels of asynchrony. Furthermore, our theory suggests ways of counter-acting the adverse effects of asynchrony. We see that a simple mechanism like using negative algorithmic momentum can be beneficial under high asynchrony. Since asynchronous methods have better hardware efficiency, this result may shed light on when asynchronous execution is more efficient for deep learning systems.
Ultrafast Excited-State Dynamics of DNA Fluorescent Intercalators:  New Insight into the Fluorescence Enhancement Mechanism (2006)

The excited-state dynamics of the DNA bisintercalator YOYO-1 and of two derivatives has been investigated using ultrafast fluorescence up-conversion and time-correlated single photon counting. The free dyes in water exist in two forms: nonaggregated dyes and intramolecular H-type aggregates, the latter form being only very weakly fluorescent because of excitonic interaction. The excited-state dynamics of the nonaggregated dyes is dominated by a nonradiative decay with a time constant of the order of 5 ps associated with large amplitude motion around the monomethine bridge of the cyanine chromophores. The strong fluorescence enhancement observed upon binding of the dyes to DNA is due to both the inhibition of this nonradiative deactivation of the nonaggregated dyes and the dissociation of the aggregates and thus to the disruption of the excitonic interaction. However, the interaction between the two chromophoric moieties in DNA is sufficient to enable ultrafast hopping of the excitation energy as revealed by the decay of the fluorescence anisotropy. Finally, these dyes act as solvation probes since a dynamic fluorescence Stokes shift was observed both in bulk water and in DNA. Very similar time scales were found in bulk water and in DNA.
Activation of Murine Lung Mast Cells by the Adenosine A3 Receptor (2003)

Adenosine has been implicated to play a role in asthma in part through its ability to influence mediator release from mast cells. Most physiological roles of adenosine are mediated through adenosine receptors; however, the mechanisms by which adenosine influences mediator release from lung mast cells are not understood. We established primary murine lung mast cell cultures and used real-time RT-PCR and immunofluorescence to demonstrate that the A(2A), A(2B), and A(3) adenosine receptors are expressed on murine lung mast cells. Studies using selective adenosine receptor agonists and antagonists suggested that activation of A(3) receptors could induce mast cell histamine release in association with increases in intracellular Ca(2+) that were mediated through G(i) and phosphoinositide 3-kinase signaling pathways. The function of A(3) receptors in vivo was tested by exposing mice to the A(3) receptor agonist, IB-MECA. Nebulized IB-MECA directly induced lung mast cell degranulation in wild-type mice while having no effect in A(3) receptor knockout mice. Furthermore, studies using adenosine deaminase knockout mice suggested that elevated endogenous adenosine induced lung mast cell degranulation by engaging A(3) receptors. These results demonstrate that the A(3) adenosine receptor plays an important role in adenosine-mediated murine lung mast cell degranulation.
Osteoinduction within porous polysulfone implants at extraosseous sites using demineralized allogeneic bone matrix (1983)

The objective of this study was to determine if bone induction could occur in implants of porous polysulfone (PPSF) impregnated with particles of demineralized allogeneic bone matrix (DABM). DABM-PPSF composites were fabricated by inserting DABM particles into PPSF specimens. The porous implants were produced by sintering polysulfone particles (850-1180 micron in diameter). DABM particles were prepared by demineralizing rat cortical bone in 0.6N HCl at 4 degrees C for 18-24 h. A composite DABM-PPSF specimen and three "controls" were implanted subcutaneously at abdominal sites in 30 adult Sprague-Dawley rats. The three controls were whole DABM (4 X 4 X 1 mm), particulate DABM (1 X 1 X 1 mm), and porous polysulfone (5 X 5 X 1 mm). Microradiographic and histological evaluation of DABM-PPSF composites revealed chondrogenesis within the pores of the specimens at 10 days, followed by ossification and fatty marrow production at 21 and 43 days. This histological sequence was similar to that seen with DABM controls. The tissue response to porous polysulfone did not prevent the osteoinductive process. These results suggest that an osteoinductive material such as DABM may be useful in augmenting the implantation of porous implants at osseous sites in which the potential for bone regeneration is limited.
Blocking immunoinhibitory receptor LILRB2 reprograms tumor-associated myeloid cells and promotes antitumor immunity (2018)

Tumor-associated myeloid cells maintain immunosuppressive microenvironments within tumors. Identification of myeloid-specific receptors to modulate tumor-associated macrophage and myeloid-derived suppressor cell (MDSC) functions remains challenging. The leukocyte immunoglobulin-like receptor B (LILRB) family members are negative regulators of myeloid cell activation. We investigated how LILRB targeting could modulate tumor-associated myeloid cell function. LILRB2 antagonism inhibited receptor-mediated activation of SHP1/2 and enhanced proinflammatory responses. LILRB2 antagonism also inhibited AKT and STAT6 activation in the presence of M-CSF and IL-4. Transcriptome analysis revealed that LILRB2 antagonism altered genes involved in cell cytoskeleton remodeling, lipid/cholesterol metabolism, and endosomal sorting pathways, as well as changed differentiation gene networks associated with inflammatory myeloid cells as opposed to their alternatively activated phenotype. LILRB2 blockade effectively suppressed granulocytic MDSC and Treg infiltration and significantly promoted in vivo antitumor effects of T cell immune checkpoint inhibitors. Furthermore, LILRB2 blockade polarized tumor-infiltrating myeloid cells from non-small cell lung carcinoma tumor tissues toward an inflammatory phenotype. Our studies suggest that LILRB2 can potentially act as a myeloid immune checkpoint by reprogramming tumor-associated myeloid cells and provoking antitumor immunity.
Bactericidal/Permeability-Increasing Protein Preserves Leukocyte Functions After Major Liver Resection (2000)

The results of this study show that patients undergoing major liver resection have an increased activation of leukocytes compared with those undergoing other major abdominal surgery. This enhanced activation may contribute to the increased risk of infection in these patients. Administration of the endotoxin-neutralizing agent rBPI21 to hemihepatectomy patients was shown to reduce plasma LBP levels, to preserve leukocyte functions partially, and to reduce leukocyte activation to the level of other, nonhepatic abdominal surgery.
Virtual environments in scientific visualization (2003)

A virtual environment is defined. The rationale for the use of virtual environments in scientific visualization is then examined, and the role of virtual environments in scientific visualization is discussed. It is noted that virtual environments are extremely well suited for the exploration of phenomena. One generic example is the investigation of complex high-dimensional databases, for example a three-dimensional unsteady velocity vector field.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Estimating Forage Mass with a Commercial Capacitance Meter, Rising Plate Meter, and Pasture Ruler (2001)

Accurate assessment of forage mass in pastures is key to budgeting forage in grazing systems. Our objective was to determine the accuracy of an electronic capacitance meter, a rising plate meter, and a pasture ruler in measuring forage mass and to determine the cost of measurement inaccuracy. Forage mass was estimated in grazed pastures on farms in Pennsylvania, Maryland, and West Virginia in 1998 and 1999. Forage mass estimated by each method was compared with forage mass estimated by hand‐clipped samples. None of these indirect methods were accurate or precise, and error levels ranged from 26 to 33% of the mean forage mass measured on the pastures. The computer model DAFOSYM (Dairy Forage System Model) was used to simulate farm performance and the resulting effects of inaccuracies in estimating forage mass on pasture. A representative grazing dairy farm was developed, and the costs and returns from low‐input and conventional managements were calculated. Different scenarios were then simulated, including under‐ or overestimating forage yield on pastures by 10 or 20%. All scenarios simulated resulted in lower returns compared with the optimum farm, with decreases in net return ranging from $8 to $198 ha −1 yr −1 . Underestimating forage mass resulted in less hay and silage being harvested, more pasture being consumed, and more forage purchased compared with the optimum scenario. The opposite occurred for overestimation of forage mass. Our results indicate that achieving greater accuracy (to within 10% of actual pasture yield) in estimating pasture yields will improve forage budgeting and increase net returns.
Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis (2014)

Nannochloropsis spp. are a group of oleaginous microalgae that harbor an expanded array of lipid-synthesis related genes, yet how they are transcriptionally regulated remains unknown. Here a phylogenomic approach was employed to identify and functionally annotate the transcriptional factors (TFs) and TF binding-sites (TFBSs) in N. oceanica IMET1. Among 36 microalgae and higher plants genomes, a two-fold reduction in the number of TF families plus a seven-fold decrease of average family-size in Nannochloropsis, Rhodophyta and Chlorophyta were observed. The degree of similarity in TF-family profiles is indicative of the phylogenetic relationship among the species, suggesting co-evolution of TF-family profiles and species. Furthermore, comparative analysis of six Nannochloropsis genomes revealed 68 "most-conserved" TFBS motifs, with 11 of which predicted to be related to lipid accumulation or photosynthesis. Mapping the IMET1 TFs and TFBS motifs to the reference plant TF-"TFBS motif" relationships in TRANSFAC enabled the prediction of 78 TF-"TFBS motif" interaction pairs, which consisted of 34 TFs (with 11 TFs potentially involved in the TAG biosynthesis pathway), 30 TFBS motifs and 2,368 regulatory connections between TFs and target genes. Our results form the basis of further experiments to validate and engineer the regulatory network of Nannochloropsis spp. for enhanced biofuel production.
Photoredox Catalytic Trifluoromethylation and Perfluoroalkylation of Arenes Using Trifluoroacetic and Related Carboxylic Acids (2020)

Trifluoroacetic acid (TFA) is among the most attractive trifluoromethylation reagents with respect to its low prices, ease of handling, and availability in large quantities. However, because of its exceedingly high oxidation potential, harsh conditions are required for the direct oxidation of TFA to the trifluoroacetate radical, which after prompt CO2 extrusion, affords the desired CF3 radical. Therefore, mild and efficient protocols for the direct conversion of TFA to the CF3 radical are still in high demand. Here, we report a mild and practical method that allows for the direct C–H trifluoromethylation, perfluoroalkylation, and chlorodifluoromethylation of (hetero)arenes using TFA and the related carboxylic acids. A diverse array of arenes and heteroarenes were successfully transformed into valued fluoroalkylated compounds. The combination of photoredox catalysis and a diaryl sulfoxide provides a platform for the facile generation of fluoroalkyl radicals from the corresponding fluoroalkyl carboxylic acids under mild conditions.
Detection of Mycobacterium tuberculosis DNA in clinical samples by using a simple lysis method and polymerase chain reaction (1993)

We have evaluated the polymerase chain reaction for detection of Mycobacterium tuberculosis in clinical samples from patients with tuberculous infection. Two simple methods for mycobacterial DNA release have been compared: sonication and lysis with nonionic detergents and proteinase K. The more effective method was the enzymatic technique. By using this protocol with 75 specimens we detected M. tuberculosis DNA in all of the samples, whereas only 48 and 71 samples were positive by acid-fast staining and culture, respectively.
Towards Robust File System Checkers (2018)

File systems may become corrupted for many reasons despite various protection techniques. Therefore, most file systems come with a checker to recover the file system to a consistent state. However, existing checkers are commonly assumed to be able to complete the repair without interruption, which may not be true in practice. In this work, we demonstrate via fault injection experiments that checkers of widely used file systems (EXT4, XFS, BtrFS, and F2FS) may leave the file system in an uncorrectable state if the repair procedure is interrupted unexpectedly. To address the problem, we first fix the ordering issue in the undo logging of e2fsck and then build a general logging library (i.e., rfsck-lib) for strengthening checkers. To demonstrate the practicality, we integrate rfsck-lib with existing checkers and create two new checkers: rfsck-ext, a robust checker for Ext-family file systems, and rfsck-xfs, a robust checker for XFS file systems, both of which require only tens of lines of modification to the original versions. Both rfsck-ext and rfsck-xfs are resilient to faults in our experiments. Also, both checkers incur reasonable performance overhead (i.e., up to 12%) compared to the original unreliable versions. Moreover, rfsck-ext outperforms the patched e2fsck by up to nine times while achieving the same level of robustness.
De-Icing Effectiveness of External Electric Heaters for Propeller Blades (1948)

Note presenting an investigation in the icing research tunnel to determine the icing protection provided by external rubber-clad blade heaters at several icing, heating, and propeller operating conditions. Data are presented to show the effect of propeller speed, ambient-air temperature, liquid-water concentration, heating-power density, duration of heating, and total cycle times on the power requirements and de-icing performance of the blade heaters.
Expression of colony-stimulating factor-1 in the human uterus and placenta (1992)

Previous studies in the mouse have strongly implicated colony-stimulating factor-1 (CSF-1) in the regulation of placental development. In this study of human pregnancy, we detected CSF-1 in serum, endometrium, placenta, chorion, amnion, and amniotic fluid, with significant increases in serum and endometrial samples from the first trimester compared to levels in nonpregnant controls. CSF-1 mRNA was demonstrated in all of these tissues, except amnion, with a significant increase within the first trimester endometrial samples over nonpregnant control values. In addition to the major 4.0-kilobase mRNA, other species of CSF-1 mRNA were detected, which were shown to be due to alternative splicing within exon 6 and the alternative use of exon 9 or 10. In the endometrium, CSF-1 was localized to glandular epithelial and endothelial cells. In first trimester placenta, CSF-1 was in the cytotrophoblasts lining the villous core and in the cytotrophoblastic shell. During the second trimester, CSF-1 was localized to villous mesenchymal cells. By the third trimester, CSF-1 was only detected in cells lining the villous vessels. The detection of CSF-1 during gestation strongly supports a role for CSF-1 in the regulation of placental function in humans by autocrine and/or paracrine mechanisms.
Evolution of phase separation in In-rich InGaN alloys (2010)

Evolution of phase separation in InxGa1−xN alloys (x∼0.65) grown on AlN/sapphire templates by metal organic chemical vapor deposition has been probed. It was found that growth rate, GR, is a key parameter and must be high enough (&gt;0.5 μm/h) in order to grow homogeneous and single phase InGaN alloys. Our results implied that conditions far from thermodynamic equilibrium are needed to suppress phase separation. Both structural and electrical properties were found to improve significantly with increasing GR. The improvement in material quality is attributed to the suppression of phase separation with higher GR. The maximum thickness of the single phase epilayer tmax (i.e., maximum thickness that can be grown without phase separation) was determined via in situ interference pattern monitoring and found to be a function of GR. As GR increases, tmax also increases. The maximum value of tmax for In0.65Ga0.35N alloy was found to be ∼1.1 μm at GR&gt;1.8 μm/h.
Relativistic norm-conserving pseudopotentials (1982)

The simple procedure to extract pseudopotentials from ab initio atomic calculations introduced by Hamann, Schl\"uter, and Chiang is extended to handle the case of heavy atoms. The solutions of the full core Dirac equation are used as references, following a recent suggestion by Kleinman. As an example, results for the atoms of group IV (C, Si, Ge, Sn, Pb) are presented.
Regulating intravenous fluid flow: Controller versus clamps (1979)

The ability of nine intravenous infusion set clamps and of an electronic rate controller to maintain a constant rate of infusion was studied. Nine sets were tested in vitro, four while being used by hospitalized patients, and three by a volunteer who performed a standard series of movements. Maintenance of infusion rate was checked by a device which recorded the rate in drops/minute. All but two i.v. administration sets showed a gradual fate decline of 1.5% or more over the 4.5-minute in vitro testing period. The electronic i.v. controller maintained a constant in vitro infusion rate. In seven hospitalized patients, the infusion rates with the four sets tested varied greatly and with no particular pattern. The i.v. controller maintained a constant infusion rate in five of the seven patients; in one patient, rate was constant except for two one-minute periods. The other patient was thought to have had a faulty i.v. infusion site. Under controlled movement conditions, all three of the sets tested failed to maintain an even flow rate but the i.v. controller’s flow rate was constant. The clamps supplied with i.v. administration sets cannot be expected to maintain a constant infusion rate. In most clinical situations requiring a constant infusion rate, an electronic i.v. rate controller can be used.
Detecting Problematic Control-Plane Protocol Interactions in Mobile Networks (2015)

The control-plane protocols in 3G/4G mobile networks communicate with each other, and provide a rich set of control functions, such as radio resource control, mobility support, connectivity management, to name a few. Despite their significance, the problem of verifying protocol correctness remains largely unaddressed. In this paper, we examine control-plane protocol interactions in mobile networks. We propose CNetVerifier, a two-phase signaling diagnosis tool to detect problematic interactions in both design and practice. CNetVerifier first performs protocol screening based on 3GPP standards via domain-specific model checking, and then conducts phone-based empirical validation in operational 3G/4G networks. With CNetVerifier, we have uncovered seven types of troublesome interactions, along three dimensions of cross (protocol) layers, cross (circuit-switched and packet-switched) domains, and cross (3G and 4G) systems. Some are caused by necessary yet problematic cooperation (i.e., protocol interactions are needed but they misbehave), whereas others are due to independent yet unnecessary coupled operations (i.e., protocols interactions are not required but actually coupled). These instances span both design defects in 3GPP standards and operational slips by carriers and vendors. They all result in performance penalties or functional incorrectness. We deduce root causes, present empirical results, propose solutions, and summarize learned lessons.
XANES study of carbon based nanotubes (2005)

Single-walled carbon nanotubes (SWNTs), double-walled carbon nanotubes (DWNTs) and multi-walled carbon nanotubes (MWNTs) have been investigated using X-ray Absorption Near Edge Spectroscopy (XANES) after different thermal annealing procedures performed in ultra high vacuum. Carbon K-edge spectra show that the contaminants present on the surface of MWNTs are more sensitive to thermal treatments than those for DWNTs and SWNTs. In addition, multiple-scattering features in the XANES region shift towards low energies going from single to multi-walled nanotubes, addressing a different interaction between layers in these different nanotube systems.
A 6-basepair insert in the reverse transcriptase gene of human immunodeficiency virus type 1 confers resistance to multiple nucleoside inhibitors. (1998)

While many point mutations in the HIV-1 reverse transcriptase (RT) confer resistance to antiretroviral drugs, inserts or deletions in this gene have not been previously characterized. In this report, 14 RT inhibitor-treated patients were found to have HIV-1 strains possessing a 6-basepair insert between codons 69 and 70 of the RT gene. Known drug resistance mutations were also observed in these strains, with T215Y appearing in all strains. Genotypic analysis indicated that the inserts had substantial nucleotide variability that resulted in relatively restricted sets of amino acid sequences. Linkage of patients' treatment histories with longitudinal sequencing data showed that insert strains appeared during drug regimens containing ddI or ddC, with prior or concurrent AZT treatment. Drug susceptibility tests of recombinant patient isolates showed reduced susceptibility to nearly all nucleoside RT inhibitors. Site- directed mutagenesis studies confirmed the role of the inserts alone in conferring reduced susceptibility to most RT inhibitors. The addition of AZT-associated drug resistance mutations further increased the range and magnitude of resistance. These results establish that inserts, like point mutations, are selected in vivo during antiretroviral therapy and provide resistance to multiple nucleoside analogs.