bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New Quantum Cuckoo Search Algorithm for Multiple Sequence Alignment
Authors: Kartous Widad , Layeb Abdesslem , Chikhi Salim 
Published: June 2014

AbstractMultiple sequence alignment (MSA) is one of the major problems that can be encountered in the bioinformatics field. MSA consists in aligning a set of biological sequences to extract the similarities between them. Unfortunately, this problem has been shown to be NP-hard. In this article, a new algorithm was proposed to deal with this problem; it is based on a quantum-inspired cuckoo search algorithm. The other feature of the proposed approach is the use of a randomized progressive alignment method based on a hybrid global/local pairwise algorithm to construct the initial population. The results obtained by this hybridization are very encouraging and show the feasibility and effectiveness of the proposed solution.
Comparison of statistical methods for finding network motifs
Authors: Albieri Vanna , Didelez Vanessa 
Published: June 2014

AbstractThere has been much recent interest in systems biology for investigating the structure of gene regulatory systems. Such networks are often formed of specific patterns, or network motifs, that are interesting from a biological point of view. Our aim in the present paper is to compare statistical methods specifically with regard to the question of how well they can detect such motifs. One popular approach is by network analysis with Gaussian graphical models (GGMs), which are statistical models associated with undirected graphs, where vertices of the graph represent genes and edges indicate regulatory interactions. Gene expression microarray data allow us to observe the amount of mRNA simultaneously for a large number of genes
The Genetic Control of Apomixis: Asexual Seed Formation
Authors: Hand Melanie L , Koltunow Anna M G 
Published: June 2014

Abstract
Apomixis (asexual seed formation) is the result of a plant gaining the ability to bypass the most fundamental aspects of sexual reproduction: meiosis and fertilization. Without the need for male fertilization, the resulting seed germinates a plant that develops as a maternal clone. This dramatic shift in reproductive process has been documented in many flowering plant species, although no major seed crops have been shown to be capable of apomixis. The ability to generate maternal clones and therefore rapidly fix desirable genotypes in crop species could accelerate agricultural breeding strategies. The potential of apomixis as a next-generation breeding technology has contributed to increasing interest in the mechanisms controlling apomixis. In this review, we discuss the progress made toward understanding the genetic and molecular control of apomixis. Research is currently focused on two fronts. One aims to identify and characterize genes causing apomixis in apomictic species that have been developed as model species. The other aims to engineer or switch the sexual seed formation pathway in non-apomictic species, to one that mimics apomixis. Here we describe the major apomictic mechanisms and update knowledge concerning the loci that control them, in addition to presenting candidate genes that may be used as tools for switching the sexual pathway to an apomictic mode of reproduction in crops.
The Role of Phase Stability in Ductile, Ordered B2 Intermetallics
Authors: Morris James R. , Ye Yiying , Krcmar Maja , Fu Chong Long 
Published: June 2014

AbstractWe discuss the underlying atomistic mechanism for experimentally observed large tensile ductility in various strongly ordered B2 intermetallic compounds. First-principles calculations demonstrate that all of the compounds exhibit little energy differences between the B2, B27 and B33 phases. These calculations relate observations of ductility in YAg, YCu and ZrCo to shape-memory materials including NiTi. One transformation pathway between the B2 and B33 phases establishes a connection between this phase competition, and stacking faults on the {011}B2 plane. The low energy of such a stacking fault will lead to splitting of the b=<100> dislocations into b/2 partials, observed in ZrCo, TiCo, and in the B19' phase of NiTi. Calculations demonstrate that this pathway is competitive with the traditional pathway for NiTi.
Peracetic Acid as an Alternative Disinfection Technology for Wet Weather Flows
Authors: Coyle Elizabeth E. , Ormsbee Lindell E. , Brion Gail M. 
Published: June 2014

ABSTRACT: Rain‐induced wet weather flows (WWFs) consist of combined sewer overflows, sanitary sewer overflows, and stormwater, all of which introduce pathogens to surface waters when discharged. When people come into contact with the contaminated surface water, these pathogens can be transmitted resulting in severe health problems. As such, WWFs should be disinfected. Traditional disinfection technologies are typically cost‐prohibitive, can yield toxic byproducts, and space for facilities is often limited, if available. More cost‐effective alternative technologies, requiring less space and producing less harmful byproducts are currently being explored. Peracetic acid (PAA) was investigated as one such alternative and this research has confirmed the feasibility and applicability of using PAA as a disinfectant for WWFs. Peracetic acid doses ranging from 5 mg/L to 15 mg/L over contact times of 2 to 10 minutes were shown to be effective and directly applicable to WWF disinfection.
Tryptophan Catabolism Restricts IFN-γ–Expressing Neutrophils and Clostridium difficile Immunopathology
Authors: El-Zaatari Mohamad , Chang Yu-Ming , Zhang Min , Franz Matthew , Shreiner Andrew , McDermott Andrew J. , van der Sluijs Koenraad F. , Lutter René , Grasberger Helmut , Kamada Nobuhiko , Young Vincent B. , Huffnagle Gary B. , Kao John Y. 
Published: June 2014

Abstract
The interplay between Clostridium difficile and the host’s metabolome is believed to influence the severity of infection. However, the mechanism for this phenomenon remains unclear. In this study, we model one of these metabolic pathways by focusing on tryptophan metabolism in the host. We found that inhibition of tryptophan catabolism in IDO1-knockout mice led to increased mucosal destruction, cecal hemorrhage, and increased production of IFN-γ in response to C. difficile infection, but no significant change in mucosal effector or regulatory T cell numbers or IL-10 mRNA expression. The increased immunopathology in infected IDO1-knockout mice was associated with a lower C. difficile burden and an increased percentage of IFN-γ–expressing neutrophils. We further demonstrated the ability of kynurenine to induce apoptosis in bone marrow–derived neutrophils, whereas the presence of tryptophan reversed this effect, providing a possible mechanism for the increased neutrophil accumulation in IDO1−/− mice. We conclude that C. difficile induces tryptophan catabolism in cecal lamina propria cells, which restricts C. difficile–associated immunopathology and the accumulation of IFN-γ–expressing neutrophils. This might represent a self-regulatory mechanism for neutrophils, via the IFN-γ–IDO1 pathway, to restrict their own accumulation during infection. These findings have important clinical implications because IDO inhibitors are used to treat cancer in clinical trials (in patients particularly susceptible to getting C. difficile infection), and treatment with IDO1 inhibitors may exacerbate the severity of C. difficile colitis.
PILRα Negatively Regulates Mouse Inflammatory Arthritis
Authors: Sun Yonglian , Caplazi Patrick , Zhang Juan , Mazloom Anita , Kummerfeld Sarah , Quinones Gabriel , Senger Kate , Lesch Justin , Peng Ivan , Sebrell Andrew , Luk Wilman , Lu Yanmei , Lin Zhonghua , Barck Kai , Young Judy , Del Rio Mariela , Lehar Sophie , Asghari Vida , Lin WeiYu , Mariathasan Sanjeev , DeVoss Jason , Misaghi Shahram , Balazs Mercedesz , Sai Tao , Haley Benjamin , Hass Philip E. , Xu Min , Ouyang Wenjun , Martin Flavius , Lee Wyne P. , Zarrin Ali A. 
Published: June 2014

Abstract
Paired Ig-like type 2 receptor (PILR)α inhibitory receptor and its counterpart PILRβ activating receptor are coexpressed on myeloid cells. In this article, we report that PILRα, but not PILRβ, is elevated in human rheumatoid arthritis synovial tissue and correlates with inflammatory cell infiltration. Pilrα−/− mice produce more pathogenic cytokines during inflammation and are prone to enhanced autoimmune arthritis. Correspondingly, engaging PILRα with anti-PILRα mAb ameliorates inflammation in mouse arthritis models and suppresses the production of proinflammatory cytokines. Our studies suggest that PILRα mediates an important inhibitory pathway that can dampen inflammatory responses.
Human NK Cells Licensed by Killer Ig Receptor Genes Have an Altered Cytokine Program That Modifies CD4+ T Cell Function
Authors: Lin Lin , Ma Chao , Wei Bo , Aziz Najib , Rajalingam Raja , Yusung Susy , Erlich Henry A. , Trachtenberg Elizabeth A. , Targan Stephan R. , McGovern Dermot P. B. , Heath James R. , Braun Jonathan 
Published: June 2014

Abstract
NK cells are innate immune cells known for their cytolytic activities toward tumors and infections. They are capable of expressing diverse killer Ig-like receptors (KIRs), and KIRs are implicated in susceptibility to Crohn’s disease (CD), a chronic intestinal inflammatory disease. However, the cellular mechanism of this genetic contribution is unknown. In this study, we show that the “licensing” of NK cells, determined by the presence of KIR2DL3 and homozygous HLA-C1 in host genome, results in their cytokine reprogramming, which permits them to promote CD4+ T cell activation and Th17 differentiation ex vivo. Microfluidic analysis of thousands of NK single cells and bulk secretions established that licensed NK cells are more polarized to proinflammatory cytokine production than unlicensed NK cells, including production of IFN-γ, TNF-α, CCL-5, and MIP-1β. Cytokines produced by licensed NK augmented CD4+ T cell proliferation and IL-17A/IL-22 production. Ab blocking indicated a primary role for IFN-γ, TNF-α, and IL-6 in the augmented T cell–proliferative response. In conclusion, NK licensing mediated by KIR2DL2/3 and HLA-C1 elicits a novel NK cytokine program that activates and induces proinflammatory CD4+ T cells, thereby providing a potential biologic mechanism for KIR-associated susceptibility to CD and other chronic inflammatory diseases.
Autotaxin Produced by Stromal Cells Promotes LFA-1–Independent and Rho-Dependent Interstitial T Cell Motility in the Lymph Node Paracortex
Authors: Katakai Tomoya , Kondo Naoyuki , Ueda Yoshihiro , Kinashi Tatsuo 
Published: June 2014

Abstract
T cells exhibit high-speed migration within the paracortical T zone of lymph nodes (LNs) as they scan cognate Ags displayed by dendritic cells in the tissue microenvironment supported by the network of stromal cells. Although intranodal T cell migration is controlled in part by chemokines and LFA-1/ICAM-1, the mechanisms underlying their migratory activity independent of these factors remain to be elucidated. In this study, we show that LN stromal cells constitutively express autotaxin (ATX), an ectoenzyme that is important for the generation of lysophosphatidic acid (LPA). Importantly, CCL21+ stromal cells in the T zone produced and immobilized ATX on their cell surface. Two-photon imaging using LN tissue slices revealed that pharmacological inhibition of ATX or LPA receptors significantly reduced T cell migration, and this was further exacerbated by blockage of Gαi signaling or LFA-1. Therefore, T cell motility mediated by the ATX–LPA axis was independent of Gαi and LFA-1. LPA induced slow intermittent movement of T cells in vitro in a LFA-1–independent manner and enhanced CCL21-induced migration. Moreover, LPA and CCL21 cooperatively augmented RhoA activity in T cells, which was necessary for efficient intranodal T cell migration via the downstream ROCK–myosin II pathway. Taken together, T zone stromal cells control optimal migratory behavior of T cells via multiple signaling cues mediated by chemokines and ATX/LPA.
Trust in Physicians and Hospitals During the COVID-19 Pandemic in a 50-State Survey of US Adults
Authors: Perlis Roy H. , Ognyanova Katherine , Uslu Ata , Lunz Trujillo Kristin , Santillana Mauricio , Druckman James N. , Baum Matthew A. , Lazer David 
Published: July 2024

ImportanceTrust in physicians and hospitals has been associated with achieving public health goals, but the increasing politicization of public health policies during the COVID-19 pandemic may have adversely affected such trust.ObjectiveTo characterize changes in US adults’ trust in physicians and hospitals over the course of the COVID-19 pandemic and the association between this trust and health-related behaviors.Design, Setting, and ParticipantsThis survey study uses data from 24 waves of a nonprobability internet survey conducted between April 1, 2020, and January 31, 2024, among 443 455 unique respondents aged 18 years or older residing in the US, with state-level representative quotas for race and ethnicity, age, and gender.Main Outcome and MeasureSelf-report of trust in physicians and hospitals; self-report of SARS-CoV-2 and influenza vaccination and booster status. Survey-weighted regression models were applied to examine associations between sociodemographic features and trust and between trust and health behaviors.ResultsThe combined data included 582 634 responses across 24 survey waves, reflecting 443 455 unique respondents. The unweighted mean (SD) age was 43.3 (16.6) years; 288 186 respondents (65.0%) reported female gender; 21 957 (5.0%) identified as Asian American, 49 428 (11.1%) as Black, 38 423 (8.7%) as Hispanic, 3138 (0.7%) as Native American, 5598 (1.3%) as Pacific Islander, 315 278 (71.1%) as White, and 9633 (2.2%) as other race and ethnicity (those who selected “Other” from a checklist). Overall, the proportion of adults reporting a lot of trust for physicians and hospitals decreased from 71.5% (95% CI, 70.7%-72.2%) in April 2020 to 40.1% (95% CI, 39.4%-40.7%) in January 2024. In regression models, features associated with lower trust as of spring and summer 2023 included being 25 to 64 years of age, female gender, lower educational level, lower income, Black race, and living in a rural setting. These associations persisted even after controlling for partisanship. In turn, greater trust was associated with greater likelihood of vaccination for SARS-CoV-2 (adjusted odds ratio [OR], 4.94; 95 CI, 4.21-5.80) or influenza (adjusted OR, 5.09; 95 CI, 3.93-6.59) and receiving a SARS-CoV-2 booster (adjusted OR, 3.62; 95 CI, 2.99-4.38).Conclusions and RelevanceThis survey study of US adults suggests that trust in physicians and hospitals decreased during the COVID-19 pandemic. As lower levels of trust were associated with lesser likelihood of pursuing vaccination, restoring trust may represent a public health imperative.
Colossal Near‐Field Radiative Heat Transfer Mediated by Coupled Polaritons with an Ultrahigh Dynamic Range
Authors: Zhang Wenbin , Wang Boxiang , Jin Shenghao , Zhou Jiahao , Gong Zhen , Zhao Changying 
Published: July 2024

AbstractNear‐field radiative heat transfer (NFRHT) can exceed the blackbody limit by several orders of magnitude owing to the tunneling evanescent waves. Exploiting this near‐field enhancement holds significant potential for emerging technologies. It has been suggested that coupled polaritons can give rise to orders of magnitude enhancement of NFRHT. However, a thorough experimental verification of this phenomenon is still missing. Here this work experimentally shows that NFRHT mediated by coupled polaritons in millimeter‐size graphene/SiC/SiO2 composite devices in planar plate configuration can realize about 302.8 ±  35.2‐fold enhancement with respect to the blackbody limit at a gap distance of 87  ±  0.8 nm. The radiative thermal conductance and effective gap heat transfer coefficient can reach unprecedented values of 0.136 WK−1 and 5440 Wm−2K−1. Additionally, a scattering‐type scanning near‐field optical measurement, in conjunction with full‐wave numerical simulations, provides further evidence for the coupled polaritonic characteristics of the devices. Notably, this work experimentally demonstrates dynamic regulation of NFRHT can be achieved by modulating the bias voltage, leading to an ultrahigh dynamic range of ≈4.115. This work ambiguously elucidates the important role of coupled polaritons in NFRHT, paving the way for the manipulation of nanoscale heat transport, energy conversion, and thermal computing via the strong coupling effect.
Highly Robust and Self‐Adhesive Soft Strain Gauge via Interface Design Engineering
Authors: Li Jianhao , Dai Qingqing , Wang Ze , Yi Yaozhen , Shen Yan , Yao Zhongwen , Niu Shichao , Han Zhiwu , Ren Luquan 
Published: July 2024

AbstractHighly robust soft strain gauges are rapidly emerging as a promising candidate in the fields of vital signs and machine conditions monitoring. However, it is still a key challenge to achieve high‐performance strain sensing in these sensors with mechanical/electrical robustness for long‐term usage. The multilayer structural design of sensors enhances sensing performance while the interfacial connection of heterogeneous materials between different layers is weak. Herein, inspired by the efficient perception mechanism of scorpion slit sensilla with tough interface interconnections, the synergy of ultra‐high electrical performance and mechanical robustness is successfully achieved via interface design engineering. The developed multilayer soft strain gauge (MSSG) exhibits a strain sensitivity beyond 105, a lower detection limit of 8.3 µm, a frequency resolution within 0.1 Hz, and cyclic stability over 63 000 strain cycles. Also, the tough interface improves the level of heterogeneous integration in the MSSG which allows to endure different stresses. Furthermore, an MSSG‐based wireless strain monitoring system is developed that enables applications on different complex dynamic surfaces, including accurate identification of human throat activity and monitoring of rolling bearing conditions.
Photocontrolled Reversible Solid‐Fluid Transitions of Azopolymer Nanocomposites for Intelligent Nanomaterials
Authors: Liang Shuofeng , Yuan Chenrui , Nie Chen , Liu Yazhi , Zhang Dachuan , Xu Wen‐Cong , Liu Chengwei , Xu Guofeng , Wu Si 
Published: July 2024

AbstractIntelligent polymer nanocomposites are multicomponent and multifunctional materials that show immense potential across diverse applications. However, to exhibit intelligent traits such as adaptability, reconfigurability and dynamic properties, these materials often require a solvent or heating environment to facilitate the mobility of polymer chains and nanoparticles, rendering their applications in everyday settings impractical. Here intelligent azopolymer nanocomposites that function effectively in a solvent‐free, room‐temperature environment based on photocontrolled reversible solid‐fluid transitions via switching flow temperatures (Tfs) are shown. A range of nanocomposites is synthesized through the grafting of Au nanoparticles, Au nanorods, quantum dots, or superparamagnetic nanoparticles with photoresponsive azopolymers. Leveraging the reversible cis‐trans photoisomerization of azo groups, the azopolymer nanocomposites transition between solid (Tf above room temperature) and fluid (Tf below room temperature) states. Such photocontrolled reversible solid‐fluid transitions empower the rewriting of nanopatterns, correction of nanoscale defects, reconfiguration of complex multiscale structures, and design of intelligent optical devices. These findings highlight Tf‐switchable polymer nanocomposites as promising candidates for the development of intelligent nanomaterials operative in solvent‐free, room‐temperature conditions.
FeCl3/K2S2O8/Et3SiH System‐Mediated α‐Methylation of β‐Ketosulfones with DMF
Authors: Chang Meng‐Yang , Yang Chi‐Ru 
Published: July 2024

AbstractFeCl3/K2S2O8/Et3SiH system‐mediated α‐methylation of β‐ketosulfones with N,N‐dimethylformamide (DMF) was developed. In the overall process, DMF takes up the role of one methyl group in the generation of α‐methyl β‐ketosulfones via single carbon−carbon (C−C) bond formation under reflux conditions. Herein, a plausible reaction mechanism is proposed.
Exfoliated 2D Nanosheet‐Based Conjugated Polymer Composites with P‐N Heterojunction Interfaces for Highly Efficient Electrocatalytic Hydrogen Evolution
Authors: Tsai Cheng‐Yu , Li Hsu‐Sheng , Kuchayita Kumasser Kusse , Huang Hsin‐Chih , Su Wei‐Nien , Cheng Chih‐Chia 
Published: July 2024

AbstractWe have achieved a significant breakthrough in the preparation and development of two‐dimensional nanocomposites with P‐N heterojunction interfaces as efficient cathode catalysts for electrochemical hydrogen evolution reaction (HER) and iodide oxidation reaction (IOR). P‐type acid‐doped polyaniline (PANI) and N‐type exfoliated molybdenum disulfide (MoS2) nanosheets can form structurally stable composites due to formation of P‐N heterojunction structures at their interfaces. These P‐N heterojunctions facilitate charge transfer from PANI to MoS2 structures and thus significantly enhance the catalytic efficiency of MoS2 in the HER and IOR. Herein, by combining efficient sodium‐functionalized chitosan‐assisted MoS2 exfoliation, electropolymerization of PANI on nickel foam (NF) substrate, and electrochemical activation, controllable and scalable Na‐Chitosan/MoS2/PANI/NF electrodes are successfully constructed as non‐noble metal‐based electrochemical catalysts. Compared to a commercial platinum/carbon (Pt/C) catalyst, the Na‐Chitosan/MoS2/PANI/NF electrode exhibits significantly lower resistance and overpotential, a similar Tafel slope, and excellent catalytic stability at high current densities, demonstrating excellent catalytic performance in the HER under acidic conditions. More importantly, results obtained from proton exchange membrane fuel cell devices confirm the Na‐Chitosan/MoS2/PANI/NF electrode exhibits a low turn‐on voltage, high current density, and stable operation at 2 V. Thus, this system holds potential as a replacement for Pt/C with feasibility for applications in energy‐related fields.
Lineage diversification and rampant hybridization among subspecies explain taxonomic confusion in the endemic Hawaiian fern Polypodium pellucidum
Authors: Mendez‐Reneau Jonas I. , Richards Joseph L. , Hobbie Julia , Bollich Emily , Kooyers Nicholas J. , Sigel Erin M. 
Published: July 2024

AbstractPremisePolypodium pellucidum, a fern endemic to the Hawaiian Islands, encompasses five ecologically and morphologically variable subspecies, suggesting a complex history involving both rapid divergence and rampant hybridization.MethodsWe employed a large target‐capture data set to investigate the evolution of genetic, morphological, and ecological variation in P. pellucidum. With a broad sampling across five Hawaiian Islands, we deciphered the evolutionary history of P. pellucidum, identified nonhybrid lineages and intraspecific hybrids, and inferred the relative influence of geography and ecology on their distributions.ResultsPolypodium pellucidum is monophyletic, dispersing to the Hawaiian archipelago 11.53–7.77 Ma and diversifying into extant clades between 5.66 and 4.73 Ma. We identified four nonhybrid clades with unique morphologies, ecological niches, and distributions. Additionally, we elucidated several intraspecific hybrid combinations and evidence for undiscovered or extinct “ghost” lineages contributing to extant hybrid populations.ConclusionsWe provide a foundation for revising the taxonomy of P. pellucidum to account for cryptic lineages and intraspecific hybrids. Geologic succession of the Hawaiian Islands through cycles of volcanism, vegetative succession, and erosion has determined the available habitats and distribution of ecologically specific, divergent clades within P. pellucidum. Intraspecific hybrids have likely arisen due to ecological and or geological transitions, often persisting after the local extinction of their progenitors. This research contributes to our understanding of the evolution of Hawai'i's diverse fern flora and illuminated cryptic taxa to allow better‐informed conservation efforts.