Analysis of interspecies adherence of oral bacteria using a membrane binding assay coupled with polymerase chain reaction-denaturing gradient gel electrophoresis profiling.

Information on co-adherence of different oral bacterial species is important for understanding interspecies interactions within oral microbial community. Current knowledge on this topic is heavily based on pariwise coaggregation of known, cultivable species. In this study, we employed a membrane binding assay coupled with polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) to systematically analyze the co-adherence profiles of oral bacterial species, and achieved a more profound knowledge beyond pairwise coaggregation. Two oral bacterial species were selected to serve as "bait": Fusobacterium nucleatum (F. nucleatum) whose ability to adhere to a multitude of oral bacterial species has been extensively studied for pairwise interactions and Streptococcus mutans (S. mutans) whose interacting partners are largely unknown. To enable screening of interacting partner species within bacterial mixtures, cells of the "bait" oral bacterium were immobilized on nitrocellulose membranes which were washed and blocked to prevent unspecific binding. The "prey" bacterial mixtures (including known species or natural saliva samples) were added, unbound cells were washed off after the incubation period and the remaining cells were eluted using 0.2 mol x L(-1) glycine. Genomic DNA was extracted, subjected to 16S rRNA PCR amplification and separation of the resulting PCR products by DGGE. Selected bands were recovered from the gel, sequenced and identified via Nucleotide BLAST searches against different databases. While few bacterial species bound to S. mutans, consistent with previous findings F. nucleatum adhered to a variety of bacterial species including uncultivable and uncharacterized ones. This new approach can more effectively analyze the co-adherence profiles of oral bacteria, and could facilitate the systematic study of interbacterial binding of oral microbial species

Origin of the Temperature Oscillation in Turbulent Thermal Convection

We report an experimental study of the three-dimensional spatial structure of the low frequency temperature oscillations in a cylindrical Rayleigh-B\'{e}nard convection cell. It is found that thermal plumes are not emitted periodically, but randomly and continuously, from the top and bottom plates. We further found that the oscillation of the temperature field does not originate from the boundary layers, but rather is a result of the horizontal motion of the hot ascending and cold descending fluids being modulated by the twisting and sloshing motion of the bulk flow field.Comment: 5 figure

Overview of the TREC 2014 Federated Web Search Track

The TREC Federated Web Search track facilitates research in topics related to federated web search, by providing a large realistic data collection sampled from a multitude of online search engines. The FedWeb 2013 challenges of Resource Selection and Results Merging challenges are again included in FedWeb 2014, and we additionally introduced the task of vertical selection. Other new aspects are the required link between the Resource Selection and Results Merging, and the importance of diversity in the merged results. After an overview of the new data collection and relevance judgments, the individual participants’ results for the tasks are introduced, analyzed, and compared

Alligning Vertical Collection Relevance with User Intent

Selecting and aggregating different types of content from multiple vertical search engines is becoming popular in web search. The user vertical intent, the verticals the user expects to be relevant for a particular information need, might not correspond to the vertical collection relevance, the verticals containing the most relevant content. In this work we propose different approaches to define the set of relevant verticals based on document judgments. We correlate the collection-based relevant verticals obtained from these approaches to the real user vertical intent, and show that they can be aligned relatively well. The set of relevant verticals defined by those approaches could therefore serve as an approximate but reliable ground-truth for evaluating vertical selection, avoiding the need for collecting explicit user vertical intent, and vice versa

FedWeb Greatest Hits: Presenting the New Test Collection for Federated Web Search

This paper presents 'FedWeb Greatest Hits', a large new test collection for research in web information retrieval. As a combination and extension of the datasets used in the TREC Federated Web Search Track, this collection opens up new research possibilities on federated web search challenges, as well as on various other problems

Blocking interaction between SHP2 and PD‐1 denotes a novel opportunity for developing PD‐1 inhibitors

Small molecular PD‐1 inhibitors are lacking in current immuno‐oncology clinic. PD‐1/PD‐L1 antibody inhibitors currently approved for clinical usage block interaction between PD‐L1 and PD‐1 to enhance cytotoxicity of CD8+ cytotoxic T lymphocyte (CTL). Whether other steps along the PD‐1 signaling pathway can be targeted remains to be determined. Here, we report that methylene blue (MB), an FDA‐approved chemical for treating methemoglobinemia, potently inhibits PD‐1 signaling. MB enhances the cytotoxicity, activation, cell proliferation, and cytokine‐secreting activity of CTL inhibited by PD‐1. Mechanistically, MB blocks interaction between Y248‐phosphorylated immunoreceptor tyrosine‐based switch motif (ITSM) of human PD‐1 and SHP2. MB enables activated CTL to shrink PD‐L1 expressing tumor allografts and autochthonous lung cancers in a transgenic mouse model. MB also effectively counteracts the PD‐1 signaling on human T cells isolated from peripheral blood of healthy donors. Thus, we identify an FDA‐approved chemical capable of potently inhibiting the function of PD‐1. Equally important, our work sheds light on a novel strategy to develop inhibitors targeting PD‐1 signaling axis

Experimental Progress on Layered Topological Semimetals

We review recent experimental progresses on layered topological materials, mainly focusing on transitional metal dichalcogenides with various lattice types including 1T, Td and 1T' structural phases. Their electronic quantum states are interestingly rich, and many appear to be topological nontrivial, such as Dirac/Weyl semimetallic phase in multilayers and quantum spin hall insulator phase in monolayers. The content covers recent major advances from material synthesis, basic characterizations, angle-resolved photoemission spectroscopy measurements, transport and optical responses. Following those, we outlook the exciting future possibilities enabled by the marriage of topological physics and two dimensional van der Waals layered heterostructures.Comment: 2D Materials (2019

Modeling the IPv6 Internet AS-level Topology

To measure the IPv6 internet AS-level topology, a network topology discovery system, called Dolphin, was developed. By comparing the measurement result of Dolphin with that of CAIDA's Scamper, it was found that the IPv6 Internet at AS level, similar to other complex networks, is also scale-free but the exponent of its degree distribution is 1.2, which is much smaller than that of the IPv4 Internet and most other scale-free networks. In order to explain this feature of IPv6 Internet we argue that the degree exponent is a measure of uniformity of the degree distribution. Then, for the purpose on modeling the networks, we propose a new model based on the two major factors affecting the exponent of the EBA model. It breaks the lower bound of degree exponent which is 2 for most models. To verify the validity of this model, both theoretical and experimental analyses have been carried out. Finally, we demonstrate how this model can be successfully used to reproduce the topology of the IPv6 Internet.Comment: 15 pages, 5 figure

Pyrolyzing soft template-containing poly(ionic liquid) into hierarchical N-doped porous carbon for electroreduction of carbon dioxide

Heteroatom-doped carbon materials have demonstrated great potential in the electrochemical reduction reaction of CO2 (CO2RR) due to their versatile structure and function. However, rational structure control remains one challenge. In this work, we reported a unique carbon precursor of soft template-containing porous poly(ionic liquid) (PIL) that was directly synthesized via free-radical self-polymerization of ionic liquid monomer in a soft template route. Variation of the carbonization temperature in a direct pyrolysis process without any additive yielded a series of carbon materials with facile adjustable textural properties and N species. Significantly, the integration of soft-template in the PIL precursor led to the formation of hierarchical porous carbon material with a higher surface area and larger pore size than that from the template-free precursor. In CO2RR to CO, the champion catalyst gave a Faraday efficiency of 83.0% and a current density of 1.79 mA?cm?2 at ?0.9 V vs. reversible hydrogen electrode (vs. RHE). The abundant graphite N species and hierarchical pore structure, especially the unique hierarchical small-/ultra-micropores were revealed to enable better CO2RR performance