gebhart/patrepeval huggingface dataset:
Edge states in polariton honeycomb lattices (2015)

The experimental study of edge states in atomically-thin layered materials remains a challenge due to the difficult control of the geometry of the sample terminations, the stability of dangling bonds and the need to measure local properties. In the case of graphene, localised edge modes have been predicted in zig-zag and bearded edges, characterised by flat dispersions connecting the Dirac points. Polaritons in semiconductor microcavities have recently emerged as an extraordinary photonic platform to emulate 1D and 2D Hamiltonians, allowing the direct visualization of the wavefunctions in both real- and momentum-space as well as of the energy dispersion of eigenstates via photoluminescence experiments. Here we report on the observation of edge states in a honeycomb lattice of coupled micropillars. The lowest two bands of this structure arise from the coupling of the lowest energy modes of the micropillars, and emulate the π and π* bands of graphene. We show the momentum space dispersion of the edge states associated to the zig-zag and bearded edges, holding unidimensional quasi-flat bands. Additionally, we evaluate polarisation effects characteristic of polaritons on the properties of these states.
Diet‐induced obesity increases the frequency of Pig‐a mutant erythrocytes in male C57BL/6J mice (2016)

Obesity increases the risk of a number of chronic diseases in humans including several cancers. Biological mechanisms responsible for such increased risks are not well understood at present. Increases in systemic inflammation and oxidative stress, endogenous production of mutagenic metabolites, altered signaling in proliferative pathways, and increased sensitivity to exogenous mutagens and carcinogens are some of the potential contributing factors. We hypothesize that obesity creates an endogenously mutagenic environment in addition to increasing the sensitivity to environmental mutagens. To test this hypothesis, we examined two in vivo genotoxicity endpoints. Pig-a mutant frequencies and micronucleus frequencies were determined in blood cells in two independent experiments in 30-week old male mice reared on either a high-fat diet (60% calories from fat) that exhibit an obese phenotype or a normal-fat diet (10% calories from fat) that do not exhibit an obese phenotype. Mice were assayed again at 52 weeks of age in one of the experiments. N-ethyl-N-nitrosourea (ENU) was used as a positive mutation control in one experiment. ENU induced a robust Pig-a mutant and micronucleus response in both phenotypes. Obese, otherwise untreated mice, did not differ from non-obese mice with respect to Pig-a mutant frequencies in reticulocytes or micronucleus frequencies. However, such mice, had significantly higher and sustained Pig-a mutant frequencies (increased 2.5-3.7-fold, p < 0.02) in erythrocytes as compared to non-obese mice (based on measurements collected at 30 weeks or 30 and 52 weeks of age). This suggests that obesity, in the absence of exposure to an exogenous mutagen, is itself mutagenic. Environ. Mol. Mutagen. 57:668-677, 2016. © 2016 Wiley Periodicals, Inc.
Hyperpolarized MRI with silicon micro and nanoparticles: Principles and applications (2021)

Silicon-based micro and nanoparticles are ideally suited for use as biomedical imaging agents because of their biocompatibility, biodegradability, and simple surface chemistry that facilitates drug loading and targeting. A method to hyperpolarize silicon particles using dynamic nuclear polarization (DNP), which increases magnetic resonance (MR) imaging signals by several orders-of-magnitude through enhanced nuclear spin alignment, was developed to allow silicon particles to function as contrast agents for in vivo magnetic resonance imaging. In this review, we describe the application of the DNP technique to silicon particles and nanoparticles for background-free real-time molecular MR imaging. This review provides a summary of the state-of-the-science in silicon particle hyperpolarization with a detailed protocol for hyperpolarizing silicon particles. This information will foster awareness and spur interest in this emerging area of nanoimaging and provide a path to new developments and discoveries to further advance the field. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Therapeutic Approaches and Drug Discovery > Emerging Technologies.
A BSP approach to composite network analysis (2014)

The pervasive availability of personal devices such as smartphones, smartwatches, and in-car navigation systems combined with the widespread acceptance of social networks has resulted in an explosion of data about individuals and their interactions in the society. The presence of multiple social networks such as FaceBook, Twitter, and Google Plus results in fragmentation of an individual's online presence. As such, the notion of interacting multiple networks or composite networks is gaining popularity. In this paper, we present a first-of-a-kind framework to analyze such composite networks in an efficient and scalable manner. We propose to use the BSP programming model to analyze composite networks and show the inportance of analyzing such composite networks as opposed to individual networks separately through preliminary experiments on realworld data.
University Partnership with High School Teachers to Increase Student Awareness of Engineering (2020)

Abstract University Partnership with High School Teachers to Establish a Pipeline of Engineering StudentsMultiple approaches to achieve increases in college enrollment and retention in engineering wereexplored under the first four years of a National Science Foundation funded program. The initialapproach during the first year was to form a team in each of the seven engineering departmentsconsisting of a high school teacher, a faculty member and five undergraduate students. Theobjective was for each team to work with the teacher to develop engineering-based curriculummodules and class demonstrations that the undergraduate team would implement in the teacher’sclassroom. The modules/demonstrations would then be revised as appropriate and offered toother teachers.Assessment during the first year determined that this initial approach was not as effective asdesired due to an inadequate fit between the focus of the specific department and the specificteacher. A new approach was tried the second year. Seven teachers were invited to a daylongworkshop where each student team presented the demonstrations and modules developed duringthe first year. Each teacher filled out a worksheet for each team identifying where in theircurriculum specific activities would fit and also suggesting where that teacher could work withthat specific team for class visits and further module development. This modified approachresulted in improved partnerships with teachers and greater opportunity for each teacher andclass to become more familiar with multiple engineering fields.The successful approach of the second year was expanded for the third and fourth years withgreater than 30 teachers representing more than 20 schools attended the teacher workshop eachyear. This resulted in many more requests from teachers for teams to visit classrooms. Toaccommodate these additional requests, the undergraduate teams were increase from fivestudents to as many as 14 for one team. This addressed another objective of the program,retention. Assessments during the first two years clearly showed that outreach participation andmentoring by college students plus the team and faculty interaction significantly increasedundergraduate excitement in engineering and had a positive effect on retention.The paper provides specific examples of the experiences of the first four years of the program,describes the level of interaction with teachers, describes some of the successfulmodules/demonstrations that have been developed, and presents detailed quantitative assessmentresults.
Infection and Killing of Multiple Myeloma by Adenoviruses (2009)

Oncolytic virotherapy makes use of the natural ability of viruses to infect and kill cancer cells. Adenovirus serotype 5 (Ad5) has been approved for use in humans as a therapy for solid cancers. In this study, we have tested whether Ad5 and low-seroprevalence adenoviruses can be used as oncolytics for multiple myeloma (MM). We show that Ad5 productively infects most myeloma cell lines, replicates to various degrees, and mediates oncolytic cell killing in vitro and in vivo. Comparison of Ad5 with low-seroprevalence Ads on primary marrow samples from MM patients revealed striking differences in the abilities of different adenoviral serotypes to kill normal CD138(-) cells and CD138(+) MM cells. Ad5 and Ad6 from species C and Ad26 and Ad48 from species D all mediated killing of CD138(+) cells with low-level killing of CD138(-) cells. In contrast, Ad11, Ad35, Ad40, and Ad41 mediated weak oncolytic effects in all of the cells. Comparison of cell binding, cell entry, and replication revealed that Ad11 and Ad35 bound MM cells 10 to 100 times better than other serotypes. However, after this efficient interaction, Ad11 and Ad35 viral DNA was not replicated and cell killing did not occur. In contrast, Ad5, Ad6, Ad26, and Ad48 all replicated 10- to 100-fold in MM cells and this correlated with cell killing. These data suggest that Ad5 and other low-seroprevalence adenoviruses may have utility as oncolytic agents against MM and other hematologic malignancies.
Is it time to reconsider how to manage oocytes affected by smooth endoplasmic reticulum aggregates? (2019)

N/A.
Design, Synthesis, and Evaluation of Enhanced DNA Binding New Lipopolythioureas (2006)

Nonviral gene delivery is limited to a large extent by the cationic nature of most of the chemical vector. We have shown that lipopolythioureas interact with DNA. However, lipopolythioureas were not very efficient at transfecting cells, probably due to reduced interaction between the noncationic synthetic lipid and the cell membrane. Here, we report that liposomes made from a new thiourea lipid, DPPC, and a lipid bearing an RGD ligand allowed very efficient entry of the lipopolythioureas into integrin alpha(v)beta(3) expressing cells. In addition, we show that a stable interaction between DNA and lipopolythiourea could be obtain with two thiourea groups. Moreover, the addition of a hydrophilic terminus improves the formulation of these new DNA binding agents.
Active Deep Multi-task Learning for Forecasting Short-Term Loads (2022)

With the increasing adoption of renewable energy generation and electric devices, electric load forecasting, especially short-term load forecasting (STLF), is becoming more and more important. The widespread adoption of smart meters makes it possible to utilize complex machine learning models for both aggregated load and single-home residential load forecasting. Similar homes in nearby locations are likely to have similar load consumption patterns and this similarity can be used to improve the overall forecasting performance. However, most current work on load forecasting focuses on single learning task without exploiting the benefit of joint learning. In this paper, we propose the use of the multi-task learning (MTL) framework with long short-term memory (LSTM) recurrent neural networks for both aggregated and single home STLF. We propose a MTL-based forecasting algorithm for aggregated load forecasting in which single home forecasting is formulated as a single learning task within the MTL framework. This algorithm is extended for single home load forecasting in which load forecasting for a particular home becomes the primary learning task. Experimental results on real-world data sets demonstrate that residential load forecasting for both aggregated load and a single home can be improved within the MTL framework.
Parameter identification method for a polycrystalline viscoplastic selfconsistent model based on analytical derivatives of the direct model equations (2000)

An inverse method for automatic identification of the parameters involved in a polycrystalline viscoplastic selfconsistent (VPSC) model is presented. The parameters of the constitutive viscoplastic law at the single-crystal level, i.e. the critical resolved shear stresses (CRSS) of slip and twinning and the micro-hardening coefficients, can be identified using experimental data at the polycrystal level, i.e. stress-strain curves and deformation-induced textures. The minimization problem is solved by means of a Gauss-Newton scheme and the sensitivity matrix is evaluated by analytical differentiation of the direct model equations. As a particular case, the optimization procedure for the Taylor full constraints (FC) formulation is also presented. The convergence and stability of the identification scheme are analysed using several validation tests for different deformation paths imposed to a polycrystal of hexagonal structure. As an example of application of this inverse method, the relative CRSS of the active deformation systems of a Zircaloy-4 sheet are identified, based on several textures measured for different reductions and rolling directions.
Dynamic imaging of dendritic cell extension into the small bowel lumen in response to epithelial cell TLR engagement (2006)

Cells lining the gastrointestinal tract serve as both a barrier to and a pathway for infectious agent entry.Dendritic cells (DCs) present in the lamina propria under the columnar villus epithelium of the small bowel extend processes across this epithelium and capture bacteria, but previous studies provided limited information on the nature of the stimuli, receptors, and signaling events involved in promoting this phenomenon.Here, we use immunohistochemical as well as dynamic explant and intravital two-photon imaging to investigate this issue.Analysis of CD11c-enhanced green fl uorescent protein (EGFP) or major histocompatibility complex CII-EGFP mice revealed that the number of trans-epithelial DC extensions, many with an unusual "balloon" shape, varies along the length of the small bowel.High numbers of such extensions were found in the proximal jejunum, but only a few were present in the terminal ileum.The extensions in the terminal ileum markedly increased upon the introduction of invasive or noninvasive Salmonella organisms, and chimeric mouse studies revealed the key role of MyD88-dependent Toll-like receptor (TLR) signaling by nonhematopoietic (epithelial) elements in the DC extension response.Collectively, these fi ndings support a model in which epithelial cell TLR signaling upon exposure to microbial stimuli induces active DC sampling of the gut lumen at sites distant from organized lymphoid tissues.
Improving Group Testing via Gradient Descent (2022)

We study the problem of group testing with non-identical, independent priors. So far, the pooling strategies that have been proposed in the literature take the following approach: a hand-crafted test design along with a decoding strategy is proposed, and guarantees are provided on how many tests are sufficient in order to identify all infections in a population. In this paper, we take a different, yet perhaps more practical, approach: we fix the decoder and the number of tests, and we ask, given these, what is the best test design one could use? We explore this question for the Definite Non-Defectives (DND) decoder. We formulate a (non-convex) optimization problem, where the objective function is the expected number of errors for a particular design. We find approximate solutions via gradient descent, which we further optimize with informed initialization. We illustrate through simulations that our method can achieve significant performance improvement over traditional approaches.
Asymptotic Output-Feedback Stabilization of Linear Evolution Equations with Uncertain Inputs via Equivalent Control Method (2018)

The paper studies the problem of minimax control design for linear evolution equations in Hilbert spaces with measurement noise and additive exogenous disturbances. The key result of the paper is an algorithm, generating a control in an output-feedback form, which steers the state of the system as close as possible to a given sliding hyperplane, asymptotically as time goes to infinity. The control is designed in the state space of the minimax filter, and guarantees that the state of the filter will be exactly on the sliding surface, and the state of the plant will belong to an ellipsoid centered at the filter's state vector for large enough time. The optimality of the designed feedback and estimation error is proven. The feedback is represented by means of the unique solution of an algebraic Riccati equation. The theory is then applied to design a minimax control for linear hereditary systems subject to noise and disturbances. This is achieved by projecting the hereditary system onto a finite dimensional subspace of the corresponding state space by means of a finite-volume approximation method, designing feedback in the state space of the resulting finite dimensional system. The solution of the operator Riccati equation is obtained using a (modified) Kleinman-Newton method. The efficacy of the proposed algorithm is illustrated by a numerical example for a time-delay linear systems with constant point delays.
Simultaneous Speckle Contrast and Functional Brain Tissue Imaging System (2010)

We demonstrate simultaneous in vivo reflectance and speckle contrast imaging system, utilizing VCSEL laser diode coherence modulation. By time multiplexing laser modes, VCSEL illumination noise is manipulated to enable a dual mode brain imaging operation.
Recent Progress of Taxonomic Studies on Pathogenic Nocardia and Usefulness of the Bacteria for the Studies on Secondary Metabolites and Antibiotic Resistant Mechanisms (2010)

The present taxonomic situation of pathogenic actinomycetes including Nocardia was clarified, and the impact of genomic sequence information of Nocardia farcinica IFM 10152 on taxonomic work is introduced. The number of cases of nocardiosis is on the rise along with the increasing number of immunocompromised patients in Japan. From 1999 to 2007, 718 strains of pathogenic actinomycetes were received for identification by Medical Mycology Research Center (MMRC), Chiba University. About 75% of these were classified into Nocardia, major species being N. farcinica, N. nova, and N. brasiliensis. Among the strains classified as Nocardia species, there were some unclassifiable strains and taxonomic studies on these led to the proposal of more than 18 new species, resulting in more than 1/4 of all Nocardia species having been proposed by our group. Recently a new Nocardia species, Nocardia mikamii was proposed by American researchers. A new phylogenetic analysis method using gryB and secA1 genes was proposed for the Nocardia and Gordonia strains.Our whole genome analysis of N. farcinica suggests that the bacterium has unique and characteristic gene profiles, and also suggests that N. farcinica is similar to Mycobacterium tuberculosis. N. farcinica also has siderophore (nocobactin) and mce genes which are similar to mycobactin (siderophore) of M. tuberculosis as virulence factors. Nocardia strains were found to be producers of new secondary metabolites including antifungal, antitumor and immunosuppressive activities.We reported novel antibiotic resistance mechanisms such as ribosylation, glucosylation, phosphorylation and degradation of rifampicin, phosphorylation of aminoglycosides, and glucosylation of macrolide antibiotics. Among rifampicin inactivation mechanisms, ribosylation was found to be through the Arr enzyme that catalyzes ADP-ribosylation of rifampicin in a fast-growing Mycobacterium smegmatis. This unique mechanism has also been reported as an antibiotic resistant mechanism in pathogenic Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae and Acinetobacter baumannii.Our cooperative work on the elucidation of high-level resistance to the aminoglycoside antibiotic amikacin in N. farcinica with a research group from CDC, USA, revealed the presence of homozygous mutations in the 16R rRNA genes which are responsible for high-level aminoglycoside antibiotic resistance.
Evaluation of aBacillusdirect-fed microbial candidate on digesta viscosity, bacterial translocation, microbiota composition and bone mineralisation in broiler chickens fed on a rye-based diet (2015)

1. The effects of the dietary inclusion of a Bacillus-based direct-fed microbial (DFM) candidate on digesta viscosity, bacterial translocation, microbiota composition and bone mineralisation were evaluated in broilers consuming rye-based diets. 2. In the present study, control mash rye-based diets (CON) or Bacillus-DFM supplemented diets (TRT) were administered ad libitum to male broilers in three independent experiments. 3. In Experiments 1 and 2 (n = 25/group), liver samples were taken to evaluate bacterial translocation, digesta samples were used for viscosity measurements and the intestinal microbial flora was evaluated from different intestinal sections to enumerate total recovered gram-negative bacteria (TGB), lactic acid bacteria (LAB) and anaerobic bacteria (TAB). Additionally, both tibias were removed for assessment of bone quality. 4. In Experiment 3, each experimental group had 8 replicates of 20 chickens (n = 160/group). Weekly, body weight (BW), feed intake (FI) and feed conversion ratio (FCR) were evaluated. At d 28-of-age, samples were taken to determine bacterial translocation, digesta viscosity and bone quality characteristics. 5. In all experiments, consumption of Bacillus-DFM reduced bacterial translocation to the liver and digesta viscosity. Additionally, DFM supplementation improved BW, bone quality measurements and FCR. Moreover, chickens fed on the Bacillus-DFM diet in Experiments 1 and 2 showed a significant reduction in the number of gram-negative and anaerobic bacteria in the duodenal content compared to control. 6. In summary, chickens fed on a rye-based diet without DFM inclusion showed an increase in bacterial translocation and digesta viscosity, accompanied by reduced performance and bone quality variables relative to the Bacillus-DFM candidate group. Hence, incorporation into the feed of a selected DFM ameliorated the adverse anti-nutritional effects related to utilisation of rye-based diets in broilers chickens.
Effects of rapamycin on growth hormone receptor knockout mice (2018)

It is well documented that inhibition of mTORC1 (defined by Raptor), a complex of mechanistic target of rapamycin (mTOR), extends life span, but less is known about the mechanisms by which mTORC2 (defined by Rictor) impacts longevity. Here, rapamycin (an inhibitor of mTOR) was used in GHR-KO (growth hormone receptor knockout) mice, which have suppressed mTORC1 and up-regulated mTORC2 signaling, to determine the effect of concurrently decreased mTORC1 and mTORC2 signaling on life span. We found that rapamycin extended life span in control normal (N) mice, whereas it had the opposite effect in GHR-KO mice. In the rapamycin-treated GHR-KO mice, mTORC2 signaling was reduced without further inhibition of mTORC1 in the liver, muscle, and s.c. fat. Glucose and lipid homeostasis were impaired, and old GHR-KO mice treated with rapamycin lost functional immune cells and had increased inflammation. In GHR-KO MEF cells, knockdown of Rictor, but not Raptor, decreased mTORC2 signaling. We conclude that drastic reduction of mTORC2 plays important roles in impaired longevity in GHR-KO mice via disruption of whole-body homeostasis.
ChemInform Abstract: Total Synthesis and the Confirmation of the Revised Structures of Botcinins A and B. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.