gebhart/patrepeval huggingface dataset:
A novel Stochastic Clustering Auction for task allocation in multi-robot teams (2010)

It will be shown that the global cost of the task allocations obtained with fast greedy algorithms can be improved upon by using a class of auction methods called Stochastic Clustering Auctions (SCAs). SCAs use stochastic transfers or swaps between the task clusters assigned to each team member, allow both uphill and downhill cost movements, and rely on simulated annealing. The choice of a key annealing parameter and turning the uphill movements on and off enables the converged solution of a SCA to slide in the region between the global optimal performance and the performance associated with a random allocation. The first SCA, called GSSCA, was based on a Gibbs Sampler, which constrained the stochastic cluster reallocations to simple single transfers or swaps. This paper presents a new and more efficient SCA, called SWSCA, based on the generalized Swendsen-Wang method that enables more complex and efficient movements between clusters by connecting tasks that appear to be synergistic and then stochastically reassigning these connected tasks. For centralized auctioning, extensive numerical experiments are used to compare the performance of SWSCA with GSSCA in terms of costs and computational and communication requirements. Distributed SWSCA is then compared with centralized SWSCA using communication links between robots that were motivated by a generic topology called a “scale free network”.
ChemInform Abstract: New Organometallic Solutions to Problems in Polyene Natural and Unnatural Product Synthesis (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Synthesis and Reactions of Optically Active Phosphine‐Boranes. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Figure Legends from ERK and p38 MAPK Activities Determine Sensitivity to PI3K/mTOR Inhibition via Regulation of MYC and YAP (2023)

&lt;p&gt;Legends for Supplementary Figures S1-S4.&lt;/p&gt;
Homoepitaxial Diamond Grown in a Liquid Metal Solvent (2022)

A single-crystal diamond substrate (SCDS) with a (100) surface orientation was submerged in liquid gallium containing a small amount of dissolved silicon, and exposed to a mixture of methane and hydrogen at 1 atm and 900 ºC. New growth diamonds were found that are single crystal square pyramids with (111) facets and that are homoepitaxial to the substrate, as proven by scanning and transmission electron microscopy, and small angle X-ray scattering and diffraction. Raman spectroscopy with 13C-labeling prove that the methane as well as the SCDS are the carbon source for the newly grown diamond. This approach opens up new ways for growing diamond in liquid metal systems.
Network Formation in an Orthogonally Self-Assembling System (2011)

Many supramolecular motifs self-assemble into nanorods, forming the basis of the mechanical properties of supramolecular polymers. When integrated as end-caps in a bifunctional telechelic polymer, the motifs can phase segregate into the same or into another nanorod. In the latter case, a functional cross-link is formed by the bridging chain that strengthens the polymer network. This study introduces a supramolecular polymeric system that consists of two different nanorod forming supramolecular motifs. When end-capped to monofunctional polymers, these supramolecular motifs self-assemble in an orthogonal fashion in two separate types of noncross-linked nanorods, resulting in a viscous liquid lacking macroscopic properties. The addition of 15 mol % of an α,ω-telechelic polymer containing both supramolecular motifs, each on one end, transforms this viscous sticky liquid to a solid material with elastomeric properties due to network formation between the two types of nanorods.
Similar evolutionary trajectories in an environmental Cryptococcus neoformans isolate after human and murine infection (2023)

A pet cockatoo was the suspected source of <i>Cryptococcus neoformans</i> recovered from an immunocompromised patient with cryptococcosis based on molecular analyses available in 2000. Here, we report whole genome sequence analysis of the clinical and cockatoo strains. Both are closely related MATα strains belonging to the VNII lineage, confirming that the human infection likely originated from pet bird exposure. The two strains differ by 61 single nucleotide polymorphisms, including eight nonsynonymous changes involving seven genes. To ascertain whether changes in these genes are selected for during mammalian infection, we passaged the cockatoo strain in mice. Remarkably, isolates obtained from mouse tissue possess a frameshift mutation in one of the seven genes altered in the human sample (LQVO5_000317), a gene predicted to encode an SWI-SNF chromatin-remodeling complex protein. In addition, both cockatoo and patient strains as well as mouse-passaged isolates obtained from brain tissue had a premature stop codon in a homologue of ZFC3 (LQVO5_004463), a predicted single-zinc finger containing protein, which is associated with larger capsules when deleted and reverted to a full-length protein in the mouse-passaged isolates obtained from lung tissue. The patient strain and mouse-passaged isolates show variability in virulence factors, with differences in capsule size, melanization, rates of nonlytic expulsion from macrophages, and amoeba predation resistance. Our results establish that environmental strains undergo genomic and phenotypic changes during mammalian passage, suggesting that animal virulence can be a mechanism for genetic change and that the genomes of clinical isolates may provide a readout of mutations acquired during infection.
Ultra-precision geometrical measurement technique based on a statistical random phase clock combined with acoustic-optical deflection (2010)

Mask writers and large area measurements systems are key systems for production of large liquid crystal displays (LCD) and image devices. With position tolerances in the sub-µm range over square meter sized masks, the metrology challenges are indeed demanding. Most systems used for this type of measurement rely on a microscope camera imaging system, provided with a charge coupled device, a complementary metal-oxide–semiconductor sensor or a time delay and integration sensor to transform the optical image to a digital gray-level image. From this image, processing algorithms are used to extract information such as location of edges. The drawback of this technique is the vast amount of data captured but never used. This paper presents a new approach for ultra-high-precision lateral measurement at nm-levels of chrome/glass patterns separated by centimeters, so called registration marks, on masks used for the LCD manufacturing. Registration specifications demand a positioning accuracy <200 nm and critical dimensions, i.e. chrome line widths, which need to be accurate in the 80 nm range. This accuracy has to be achieved on glass masks of 2.4 × 1.6 m2 size. Our new measurement method is based on nm-precise lateral scanning of a focused laser beam combined with statistical random phase sampling of the reflected signal. The precise scanning is based on an extremely accurate time measuring device controlling an acousto optic deflector crystal. The method has been successfully applied in measuring the 4 µm pitch of reference gratings at standard deviations σ of 0.5 nm and registration marks separated by several cm at standard deviations of 23 nm.
New Locally Decodable Codes and Private Information Retrieval Schemes. (2006)

A q query Locally Decodable Code (LDC) encodes an n-bit message x as an N-bit codeword C(x), such that one can probabilistically recover any bit xi of the message by querying only q bits of the codeword C(x), even after some constant fraction of codeword bits has been corrupted. We give new constructions of three query LDCs of vastly shorter length than that of previous constructions. Specifically, given any Mersenne prime p = 2 t − 1, we design three query LDCs of length N = exp � n 1/t �, for every n. Based on the largest known Mersenne prime, this translates to a length of less than exp n 10−7� compared to exp � n1/2 � in the previous constructions. It has often been conjectured that there are infinitely many Mersenne�primes. Under this conjecture, our constructions yield three query locally decodable codes of length N = exp n O
Thermally Stable Nanocrystalline γ‐Alumina Layers with Highly Ordered 3D Mesoporosity. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Carnitine and acetylcarnitine modulate mesenchymal differentiation of adult stem cells (2013)

Cellular metabolic activity, especially mitochondrial metabolism, plays a vital role in regulating cell proliferation and differentiation. Metabolism could therefore be an important factor to consider when using engineering technologies to stimulate tissue development and repair. The small metabolite carnitine and its derivative acetylcarnitine affect the activities of several pathways in mitochondrial metabolism, but their influence on cell differentiation has not yet been thoroughly studied. To elucidate the effects of these two small molecules on mesenchymal tissue engineering, we used adult stem cells as a platform in both monolayer and 3D hydrogel culture systems. We investigated the impact of these two small molecules on the differentiation of adult stem cells and analysed gene expression, cell proliferation and extracellular matrix deposition. We found that the molecules reduced adipogenesis but stimulated osteogenesis and chondrogenesis in both culture systems. Our results suggest that carnitine and acetylcarnitine could affect the differentiation rate of adult stem cells by regulating mitochondrial metabolism. The effects of these two small molecules give rise to the possibility of employing such metabolites in tissue-engineering systems to enhance cell differentiation and tissue development.
S6K1 activation is not required for muscle hypertrophy (2011)

The substrate docking site (PIF-pocket) in the kinase domain of the phosphoinositol-dependent protein kinase (PDK1) is required for the activation of S6K1. Since activation of S6K1 is thought to be important for muscle hypertrophy following resistance exercise (RE), we hypothesized that the PIF-pocket is required for muscle hypertrophy. Methods Using transgenic mice with a knockin mutation in the PIF-pocket (PDK1 PIF) we determined skeletal muscle hypertrophy, S6K1 phosphorylation and activity after 7 days of plantaris overload (OVL), insulin treatment, and an acute bout of RE. Results Following OVL, the plantaris of the PDK1 PIF mice hypertrophied as normal (wt=26.6±2.6%, PIF=28.8±2.95%). The response to an acute bout of RE followed the same pattern as insulin. S6S240/244, S6K1T389 and T229 phosphorylation were increased by 1575%, 466% and 310% respectively in control mice 1 hour after RE and this response was completely lost in the PDK1 PIF mice. Discussion These data suggest that, as with insulin, an acute bout of RE requires the PIF-pocket of PDK1 for phosphorylation and activation of S6K1 and that the activation of S6K1 is not required for skeletal muscle hypertrophy.
Cellular Distribution of Secreted Phospholipase A2 in Lungs of IPF Patients and Its Inhibition in Bleomycin-Induced Pulmonary Fibrosis in Mice (2023)

Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease with a very poor prognosis as it has a 2.5 to 5 years mean survival after proper diagnosis. Even nintedanib and pirfenidone cannot halt the progression, though they slow the progression of IPF. Hence, there is a need to understand the novel pathophysiology. Phospholipase A2 (PLA2) could be the ideal candidate to study in IPF, as they have a role in both inflammation and fibrosis. In the present study, we have shown the expression profile of various secretory Phospholipase A2 (PLA2) isoforms by analyzing publicly available transcriptome data of single cells from the lungs of healthy individuals and IPF patients. Among 11 members of sPLA2, PLA2G2A is found to be increased in the fibroblasts and mesothelial cells while PLA2G5 is found to be increased in the fibroblasts of IPF patients. We identified a subset of fibroblasts expressing high PLA2G2A with moderate expression of PLA2G5 and which are specific to IPF only; we named it as PLA2G2A+ IPF fibroblast. Pathway analysis revealed that these PLA2G2A+ IPF fibroblast have upregulation of both inflammatory and fibrosis-related pathways like the TGF-β signaling pathway, IL-17 signaling, the arachidonic acid metabolism pathway and ECM-receptor interaction. In addition to this, we found elevated levels of sPLA2-IIA in plasma samples of IPF patients in our cohort. PLA2G3, PLA2G10 and PLA2G12B are found in to be increased in certain epithelial cells of IPF patients. Thus, these findings indicate that these five isoforms have a disease-dominant role along with innate immune roles as these isoforms are found predominantly in structural cells of IPF patients. Further, we have targeted sPLA2 in mice model of bleomycin-induced lung fibrosis by pBPB, a known sPLA2 inhibitor. pBPB treatment attenuated lung fibrosis induced by bleomycin along with a reduction in TGF-β and deposition of extracellular matrix in lung. Thus, these findings indicate that these sPLA2 isoforms especially PLA2G2A may serve as a therapeutic target in lung fibrosis.
ChemInform Abstract: An Asymmetric Synthesis of MK‐0417. Observations on Oxazaborolidine‐ Catalyzed Reductions. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Spatially Consistent Geometric D2D Small-Scale Fading Model for Multiple Frequencies (2019)

The 3rd generation partnership project (3GPP) new radio (NR) channel model introduced spatial consistency and a correlation model for multiple frequencies. Future extensions of this model will incorporate mobility at both ends of the link. These features are essential for many emerging wireless technologies in the 5G era. However, the existing small-scale-fading (SSF) model does not integrate these features coherently. To solve this problem, we propose a new SSF model that seamlessly integrates with the remaining NR model and allows the simultaneous simulation of all three features. We demonstrate this integration by showing that the output of the new SSF model agrees well with large-scale fading (LSF) parameter distributions provided by 3GPP. This enables the simulation of new wireless technology proposals that were difficult to realize with existing geometry-based stochastic channel models (GSCMs).
Differential Expression of CD8+ T Cell Cytotoxic Effector Molecules in Blood and Gastrointestinal Mucosa in HIV-1 Infection (2018)

We previously reported that CD8<sup>+</sup> T cells in human gastrointestinal mucosa exhibit reduced perforin expression and weak or impaired cytotoxic capacity compared with their counterparts in blood. Nevertheless, these cells degranulate and express cytokines and chemokines in response to cognate Ag. In addition to weak expression of perforin, earlier studies suggested differential regulation of perforin and granzymes (Gzms), with GzmA and B expressed by significantly higher percentages of mucosal CD8<sup>+</sup> T cells than perforin. However, this topic has not been fully explored. The goal of this study was to elucidate the expression and coexpression patterns of GzmA, B, and K in conjunction with perforin in rectosigmoid CD8<sup>+</sup> T cells during HIV-1 infection. We found that expression of both perforin and GzmB, but not GzmA or GzmK, was reduced in mucosa compared with blood. A large fraction of rectosigmoid CD8<sup>+</sup> T cells either did not express Gzms or were single-positive for GzmA. Rectosigmoid CD8<sup>+</sup> T cells appeared skewed toward cytokine production rather than cytotoxic responses, with cells expressing multiple cytokines and chemokines generally lacking in perforin and Gzm expression. These data support the interpretation that perforin and Gzms are differentially regulated, and display distinct expression patterns in blood and rectosigmoid T cells. These studies may help inform the development of strategies to combat HIV-1 and other mucosal pathogens.
Poly-N-acetyllactosamine Extension inN-Glycans and Core 2- and Core 4-branchedO-Glycans Is Differentially Controlled by i-Extension Enzyme and Different Members of the β1,4-Galactosyltransferase Gene Family (2000)

Poly-N-acetyllactosamines are attached to N-glycans, O-glycans, and glycolipids and serve as underlying glycans that provide functional oligosaccharides such as sialyl Lewis(X). Poly-N-acetyllactosaminyl repeats are synthesized by the alternate addition of beta1,3-linked GlcNAc and beta1,4-linked Gal by i-extension enzyme (iGnT) and a member of the beta1,4-galactosyltransferase (beta4Gal-T) gene family. In the present study, we first found that poly-N-acetyllactosamines in N-glycans are most efficiently synthesized by beta4Gal-TI and iGnT. We also found that iGnT acts less efficiently on acceptors containing increasing numbers of N-acetyllactosamine repeats, in contrast to beta4Gal-TI, which exhibits no significant change. In O-glycan biosynthesis, N-acetyllactosamine extension of core 4 branches was found to be synthesized most efficiently by iGnT and beta4Gal-TI, in contrast to core 2 branch synthesis, which requires iGnT and beta4Gal-TIV. Poly-N-acetyllactosamine extension of core 4 branches is, however, less efficient than that of N-glycans or core 2 branches. Such inefficiency is apparently due to competition between a donor substrate and acceptor in both galactosylation and N-acetylglucosaminylation, since a core 4-branched acceptor contains both Gal and GlcNAc terminals. These results, taken together, indicate that poly-N-acetyllactosamine synthesis in N-glycans and core 2- and core 4-branched O-glycans is achieved by iGnT and distinct members of the beta4Gal-T gene family. The results also exemplify intricate interactions between acceptors and specific glycosyltransferases, which play important roles in how poly-N-acetyllactosamines are synthesized in different acceptor molecules.
Surface profile dependence of the photon coupling efficiency and enhanced fluorescence in the grating-coupled surface plasmon resonance (2010)

The fluorescence excited by the enhanced electric field of grating-coupled surface plasmon resonance was detected on biochips. The enhancement of the electric field on a metallic grating surface was calculated using the finite difference time domain method for rectangular, trapezoidal, and sinusoidal models to clarify the grating-surface profile dependence of the enhanced fluorescence. The computational results showed that the enhancement in the trapezoidal model was stronger than that in the other models, and that the groove depth dependence of the enhancement in the trapezoidal model agreed well with the experimental data. The grating surface profile, including the groove depth, was found to be an important parameter of the grating structure for it to couple effectively with light.
Surface modification of biodegradable electrospun nanofiber scaffolds and their interaction with fibroblasts (2007)

Biodegradable polymers, such as poly(glycolic acid) (PGA), poly(L-lactic acid) (PLLA) and poly(lactic-co-glycolic acid) (PLGA), were dissolved individually in the proper solvents and then subjected to electrospinning process to make nanofibrous scaffolds. Their surfaces were then chemically modified using oxygen plasma treatment and in situ grafting of hydrophilic acrylic acid (AA). The fiber thickness, pore size and porosity were estimated to 200-800 nm, 2-30 microm and 94-96%, respectively, and these properties were insignificant in the PGA, PLLA and PLGA nanofibrous scaffolds. The ultimate tensile strength of PGA was about 2.5 MPa on average and that of PLGA and PLLA was less than 2 MPa. The elongation-at-break was 100-130% for the three nanofibrous scaffolds. When the surface properties of AA-grafted scaffolds were examined, higher ratios of oxygen to carbon, lower contact angles and the presence of carboxylic (-COOH) groups were identified. The properties were significantly different from those of the unmodified nanofibrous scaffolds. Fibroblasts once seeded on the scaffolds were spreading over large surface area on the AA-grafted surface as compared to the unmodified PGA, PLLA and PLGA nanofibrous scaffolds. Cultured for up to 6 days, the fibroblast proliferation was found to be much better on the surface-modified nanofibrous scaffolds. The present study showed that, with the use of plasma treatment and AA grafting, the hydrophilic functional groups could be successfully adapted on the surface of electrospun nanofibrous scaffolds. Those surface-modified scaffolds made significant improvement on cell attachment and proliferation in vitro.
[The use of anti-A and anti-B monoclonal antibodies in forensic medicine]. (1989)

Anti-A and anti-B monoclonal antibodies (MCA) may be used in the analysis of liquid blood, blood and saliva traces in order to detect ABO blood group antigens A and B using common methods of evidence investigation. Use of MCA and isohaemagglutinins anti-A and anti-B in absorbtion-elution reaction during the analysis of minute saliva traces enhances the possibility of establishing the origin of the saliva at the expense of nonsecretor.
Implementation of the Ebola Virus Persistence in Ocular Tissues and Fluids (EVICT) study: Lessons learned for vision health systems strengthening in Sierra Leone (2021)

The EVICT Study showed that cataract surgery with a protocol-driven approach was safe and vision-restorative for EVD survivors, which provided guidance for EVD ophthalmic surgical care. Ophthalmologic care remains a key aspect of the public health response for EVD outbreaks but requires a meticulous, yet partnered approach with international and local in-country partners. Future efforts may build on this framework for clinical care and to improve our understanding of ophthalmic sequelae, develop treatment paradigms for EVD survivors, and strengthen vision health systems in resource-limited settings.
Novel polymer materials for optical waveguides and their applications to polymer CWDM devices (2004)

We have developed several novel polymer materials for optical waveguides. In the first part of this paper, we described two examples of our developed materials, one is low loss optical waveguide materials for optical communications at near infrared wavelength region, the other is low loss and high heat resistant materials for optical interconnections in the electronic devices at around 850 nm wavelength region, which can resist to the lead-free solder reflowing process. In the second part, we demonstrated two kinds of novel low cost polymer coarse wavelength division multiplexing (CWDM) devices, one is the polymer arrayed waveguide grating (AWG) device and the other is the polymer CWDM device using the polymer diffraction grating. The structures and performances of these devices were described in detail.