bluuebunny/crossref_metadata_2025 huggingface dataset:
Carrier transport theory for twisted bilayer graphene in the metallic regime
Authors: Sharma Gargee , Yudhistira Indra , Chakraborty Nilotpal , Ho Derek Y. H. , Ezzi M. M. Al , Fuhrer Michael S. , Vignale Giovanni , Adam Shaffique
Published: September 2021

Understanding the normal-metal state transport in twisted bilayer graphene near magic angle is of fundamental importance as it provides insights into the mechanisms responsible for the observed strongly correlated insulating and superconducting phases. Here we provide a rigorous theory for phonon-dominated transport in twisted bilayer graphene describing its unusual signatures in the resistivity (including the variation with electron density, temperature, and twist angle) showing good quantitative agreement with recent experiments. We contrast this with the alternative Planckian dissipation mechanism that we show is incompatible with available experimental data. An accurate treatment of the electron-phonon scattering requires us to go well beyond the usual treatment, including both intraband and interband processes, considering the finite-temperature dynamical screening of the electron-phonon matrix element, and going beyond the linear Dirac dispersion. In addition to explaining the observations in currently available experimental data, we make concrete predictions that can be tested in ongoing experiments.
Chiral Brønsted acid-controlled intermolecular asymmetric [2 + 2] photocycloadditions
Authors: Sherbrook Evan M. , Genzink Matthew J. , Park Bohyun , Guzei Ilia A. , Baik Mu-Hyun , Yoon Tehshik P.
Published: September 2021

Control over the stereochemistry of excited-state photoreactions remains a significant challenge in organic synthesis. Recently, it has become recognized that the photophysical properties of simple organic substrates can be altered upon coordination to Lewis acid catalysts, and that these changes can be exploited in the design of highly enantioselective catalytic photoreactions. Chromophore activation strategies, wherein simple organic substrates are activated towards photoexcitation upon binding to a Lewis acid catalyst, rank among the most successful asymmetric photoreactions. Herein, we show that chiral Brønsted acids can also catalyze asymmetric excited-state photoreactions by chromophore activation. This principle is demonstrated in the context of a highly enantio- and diastereoselective [2+2] photocycloaddition catalyzed by a chiral phosphoramide organocatalyst. Notably, the cyclobutane products arising from this method feature a trans-cis stereochemistry that is complementary to other enantioselective catalytic [2+2] photocycloadditions reported to date.
Possible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics
Authors: Dyson Louise , Hill Edward M. , Moore Sam , Curran-Sebastian Jacob , Tildesley Michael J. , Lythgoe Katrina A. , House Thomas , Pellis Lorenzo , Keeling Matt J.
Published: September 2021

Viral reproduction of SARS-CoV-2 provides opportunities for the acquisition of advantageous mutations, altering viral transmissibility, disease severity, and/or allowing escape from natural or vaccine-derived immunity. We use three mathematical models: a parsimonious deterministic model with homogeneous mixing; an age-structured model; and a stochastic importation model to investigate the effect of potential variants of concern (VOCs). Calibrating to the situation in England in May 2021, we find epidemiological trajectories for putative VOCs are wide-ranging and dependent on their transmissibility, immune escape capability, and the introduction timing of a postulated VOC-targeted vaccine. We demonstrate that a VOC with a substantial transmission advantage over resident variants, or with immune escape properties, can generate a wave of infections and hospitalisations comparable to the winter 2020-2021 wave. Moreover, a variant that is less transmissible, but shows partial immune-escape could provoke a wave of infection that would not be revealed until control measures are further relaxed.
Settling the matter of the role of vibrations in the stability of high-entropy carbides
Authors: Esters Marco , Oses Corey , Hicks David , Mehl Michael J. , Jahnátek Michal , Hossain Mohammad Delower , Maria Jon-Paul , Brenner Donald W. , Toher Cormac , Curtarolo Stefano
Published: September 2021

High-entropy ceramics are attracting significant interest due to their exceptional chemical stability and physical properties. While configurational entropy descriptors have been successfully implemented to predict their formation and even to discover new materials, the contribution of vibrations to their stability has been contentious. This work unravels the issue by computationally integrating disorder parameterization, phonon modeling, and thermodynamic characterization. Three recently synthesized carbides are used as a testbed: (HfNbTaTiV)C, (HfNbTaTiW)C, and (HfNbTaTiZr)C. It is found that vibrational contributions should not be neglected when precursors or decomposition products have different nearest-neighbor environments from the high-entropy carbide.
Coherent control of asymmetric spintronic terahertz emission from two-dimensional hybrid metal halides
Authors: Cong Kankan , Vetter Eric , Yan Liang , Li Yi , Zhang Qi , Xiong Yuzan , Qu Hongwei , Schaller Richard D. , Hoffmann Axel , Kemper Alexander F. , Yao Yongxin , Wang Jigang , You Wei , Wen Haidan , Zhang Wei , Sun Dali
Published: September 2021

Next-generation terahertz (THz) sources demand lightweight, low-cost, defect-tolerant, and robust components with synergistic, tunable capabilities. However, a paucity of materials systems simultaneously possessing these desirable attributes and functionalities has made device realization difficult. Here we report the observation of asymmetric spintronic-THz radiation in Two-Dimensional Hybrid Metal Halides (2D-HMH) interfaced with a ferromagnetic metal, produced by ultrafast spin current under femtosecond laser excitation. The generated THz radiation exhibits an asymmetric intensity toward forward and backward emission direction whose directionality can be mutually controlled by the direction of applied magnetic field and linear polarization of the laser pulse. Our work demonstrates the capability for the coherent control of THz emission from 2D-HMHs, enabling their promising applications on the ultrafast timescale as solution-processed material candidates for future THz emitters.
Roles of insolation forcing and CO2 forcing on Late Pleistocene seasonal sea surface temperatures
Authors: Lee Kyung Eun , Clemens Steven C. , Kubota Yoshimi , Timmermann Axel , Holbourn Ann , Yeh Sang-Wook , Bae Si Woong , Ko Tae Wook
Published: September 2021

Late Pleistocene changes in insolation, greenhouse gas concentrations, and ice sheets have different spatially and seasonally modulated climatic fingerprints. By exploring the seasonality of paleoclimate proxy data, we gain deeper insight into the drivers of climate changes. Here, we investigate changes in alkenone-based annual mean and Globigerinoides ruber Mg/Ca-based summer sea surface temperatures in the East China Sea and their linkages to climate forcing over the past 400,000 years. During interglacial-glacial cycles, there are phase differences between annual mean and seasonal (summer and winter) temperatures, which relate to seasonal insolation changes. These phase differences are most evident during interglacials. During glacial terminations, temperature changes were strongly affected by CO2. Early temperature minima, ~20,000 years before glacial terminations, except the last glacial period, coincide with the largest temperature differences between summer and winter, and with the timing of the lowest atmospheric CO2 concentration. These findings imply the need to consider proxy seasonality and seasonal climate variability to estimate climate sensitivity.
Nanoscale lattice dynamics in hexagonal boron nitride moiré superlattices
Authors: Moore S. L. , Ciccarino C. J. , Halbertal D. , McGilly L. J. , Finney N. R. , Yao K. , Shao Y. , Ni G. , Sternbach A. , Telford E. J. , Kim B. S. , Rossi S. E. , Watanabe K. , Taniguchi T. , Pasupathy A. N. , Dean C. R. , Hone J. , Schuck P. J. , Narang P. , Basov D. N.
Published: September 2021

Twisted two-dimensional van der Waals (vdW) heterostructures have unlocked a new means for manipulating the properties of quantum materials. The resulting mesoscopic moiré superlattices are accessible to a wide variety of scanning probes. To date, spatially-resolved techniques have prioritized electronic structure visualization, with lattice response experiments only in their infancy. Here, we therefore investigate lattice dynamics in twisted layers of hexagonal boron nitride (hBN), formed by a minute twist angle between two hBN monolayers assembled on a graphite substrate. Nano-infrared (nano-IR) spectroscopy reveals systematic variations of the in-plane optical phonon frequencies amongst the triangular domains and domain walls in the hBN moiré superlattices. Our first-principles calculations unveil a local and stacking-dependent interaction with the underlying graphite, prompting symmetry-breaking between the otherwise identical neighboring moiré domains of twisted hBN.
A synergistic exploitation to produce high-voltage quasi-solid-state lithium metal batteries
Authors: Wu Junru , Wang Xianshu , Liu Qi , Wang Shuwei , Zhou Dong , Kang Feiyu , Shanmukaraj Devaraj , Armand Michel , Rojo Teofilo , Li Baohua , Wang Guoxiu
Published: September 2021

The current Li-based battery technology is limited in terms of energy contents. Therefore, several approaches are considered to improve the energy density of these energy storage devices. Here, we report the combination of a heteroatom-based gel polymer electrolyte with a hybrid cathode comprising of a Li-rich oxide active material and graphite conductive agent to produce a high-energy “shuttle-relay” Li metal battery, where additional capacity is generated from the electrolyte’s anion shuttling at high voltages. The gel polymer electrolyte, prepared via in situ polymerization in an all-fluorinated electrolyte, shows adequate ionic conductivity (around 2 mS cm−1 at 25 °C), oxidation stability (up to 5.5 V vs Li/Li+), compatibility with Li metal and safety aspects (i.e., non-flammability). The polymeric electrolyte allows for a reversible insertion of hexafluorophosphate anions into the conductive graphite (i.e., dual-ion mechanism) after the removal of Li ions from Li-rich oxide (i.e., rocking-chair mechanism).
Modified Bose-Einstein condensation in an optical quantum gas
Authors: Vretenar Mario , Toebes Chris , Klaers Jan
Published: September 2021

Open quantum systems can be systematically controlled by making changes to their environment. A well-known example is the spontaneous radiative decay of an electronically excited emitter, such as an atom or a molecule, which is significantly influenced by the feedback from the emitter’s environment, for example, by the presence of reflecting surfaces. A prerequisite for a deliberate control of an open quantum system is to reveal the physical mechanisms that determine its state. Here, we investigate the Bose-Einstein condensation of a photonic Bose gas in an environment with controlled dissipation and feedback. Our measurements offer a highly systematic picture of Bose-Einstein condensation under non-equilibrium conditions. We show that by adjusting their frequency Bose-Einstein condensates naturally try to avoid particle loss and destructive interference in their environment. In this way our experiments reveal physical mechanisms involved in the formation of a Bose-Einstein condensate, which typically remain hidden when the system is close to thermal equilibrium.
Wilson loop and Wilczek-Zee phase from a non-Abelian gauge field
Authors: Sugawa Seiji , Salces-Carcoba Francisco , Yue Yuchen , Putra Andika , Spielman I. B.
Published: September 2021

Quantum states can acquire a geometric phase called the Berry phase after adiabatically traversing a closed loop, which depends on the path not the rate of motion. The Berry phase is analogous to the Aharonov–Bohm phase derived from the electromagnetic vector potential, and can be expressed in terms of an Abelian gauge potential called the Berry connection. Wilczek and Zee extended this concept to include non-Abelian phases—characterized by the gauge-independent Wilson loop—resulting from non-Abelian gauge potentials. Using an atomic Bose–Einstein condensate, we quantum-engineered a non-Abelian SU(2) gauge field, generated by a Yang monopole located at the origin of a 5-dimensional parameter space. By slowly encircling the monopole, we characterized the Wilczek–Zee phase in terms of the Wilson loop, that depended on the solid-angle subtended by the encircling path: a generalization of Stokes’ theorem. This observation marks the observation of the Wilson loop resulting from a non-Abelian point source.
Harnessing 3D collagen hydrogel-directed conversion of human GMSCs into SCP-like cells to generate functionalized nerve conduits
Authors: Zhang Qunzhou , Nguyen Phuong , Burrell Justin C. , Zeng Jincheng , Shi Shihong , Shanti Rabie M. , Kulischak Grace , Cullen D. Kacy , Le Anh D.
Published: September 2021

Achieving a satisfactory functional recovery after severe peripheral nerve injuries (PNI) remains one of the major clinical challenges despite advances in microsurgical techniques. Nerve autografting is currently the gold standard for the treatment of PNI, but there exist several major limitations. Accumulating evidence has shown that various types of nerve guidance conduits (NGCs) combined with post-natal stem cells as the supportive cells may represent a promising alternative to nerve autografts. In this study, gingiva-derived mesenchymal stem cells (GMSCs) under 3D-culture in soft collagen hydrogel showed significantly increased expression of a panel of genes related to development/differentiation of neural crest stem-like cells (NCSC) and/or Schwann cell precursor-like (SCP) cells and associated with NOTCH3 signaling pathway activation as compared to their 2D-cultured counterparts. The upregulation of NCSC-related genes induced by 3D-collagen hydrogel was abrogated by the presence of a specific NOTCH inhibitor. Further study showed that GMSCs encapsulated in 3D-collagen hydrogel were capable of transmigrating into multilayered extracellular matrix (ECM) wall of natural NGCs and integrating well with the aligned matrix structure, thus leading to biofabrication of functionalized NGCs. In vivo, implantation of functionalized NGCs laden with GMSC-derived NCSC/SCP-like cells (designated as GiSCs), significantly improved the functional recovery and axonal regeneration in the segmental facial nerve defect model in rats. Together, our study has identified an approach for rapid biofabrication of functionalized NGCs through harnessing 3D collagen hydrogel-directed conversion of GMSCs into GiSCs.
The think aloud paradigm reveals differences in the content, dynamics and conceptual scope of resting state thought in trait brooding
Authors: Raffaelli Quentin , Mills Caitlin , de Stefano Nadia-Anais , Mehl Matthias R. , Chambers Kate , Fitzgerald Surya A. , Wilcox Ramsey , Christoff Kalina , Andrews Eric S. , Grilli Matthew D. , O’Connor Mary-Frances , Andrews-Hanna Jessica R.
Published: September 2021

Although central to well-being, functional and dysfunctional thoughts arise and unfold over time in ways that remain poorly understood. To shed light on these mechanisms, we adapted a “think aloud” paradigm to quantify the content and dynamics of individuals’ thoughts at rest. Across two studies, external raters hand coded the content of each thought and computed dynamic metrics spanning duration, transition probabilities between affective states, and conceptual similarity over time. Study 1 highlighted the paradigm’s high ecological validity and revealed a narrowing of conceptual scope following more negative content. Study 2 replicated Study 1’s findings and examined individual difference predictors of trait brooding, a maladaptive form of rumination. Across individuals, increased trait brooding was linked to thoughts rated as more negative, past-oriented and self-focused. Longer negative and shorter positive thoughts were also apparent as brooding increased, as well as a tendency to shift away from positive conceptual states, and a stronger narrowing of conceptual scope following negative thoughts. Importantly, content and dynamics explained independent variance, accounting for a third of the variance in brooding. These results uncover a real-time cognitive signature of rumination and highlight the predictive and ecological validity of the think aloud paradigm applied to resting state cognition.
Evaluation of prophylactic efficacy of cinnamaldehyde in murine model against Paradendryphiella arenariae mycotoxin tenuazonic acid-induced oxidative stress and organ toxicity
Authors: Kumari Ankita , Singh Karuna
Published: September 2021

Cinnamaldehyde (Cin) is a natural product obtained from cinnamon and is reported to have a potential anti-fungal, anti-oxidant, anti-inflammatory and anticancer effect. The present study investigated the possible protective role of Cin against tenuazonic acid-induced mycotoxicity in the murine model. Tenuazonic acid (TeA), a toxin produced by Alternaria is a common contaminant in tomato and tomato-based products. Here, Swiss male mice were administered with TeA isolated from Paradendryphiella arenariae (MW504999) (source-tomato) through injection (238 µg/kg BW) and ingestion (475 µg/kg BW) routes for 2 weeks. Thereafter, the prophylaxis groups were treated with Cin (210 mg/kg BW). The experiment was carried out for 8 weeks. The treated groups were compared to the oral and intra-peritoneal experimental groups that received the toxin solely for 8 weeks. Haematological, histopathological and biochemical aspects of the experimental and the control mice were analysed. Sub-chronic intoxication of mice with TeA showed elevated malondialdehyde (MDA), reduced catalase (CAT) and superoxide dismutase (SOD) production; abnormal levels of aspartate transaminase (AST) and alanine transaminase (ALT). Treatment with Cin reversed TeA-induced alterations of antioxidant defense enzyme activities and significantly prevented TeA-induced organ damage. Thus, cinnamaldehyde showed therapeutic effects and toxicity reduction in TeA induced mycotoxicosis.
Verification method of Monte Carlo codes for transport processes with arbitrary accuracy
Authors: Martelli Fabrizio , Tommasi Federico , Sassaroli Angelo , Fini Lorenzo , Cavalieri Stefano
Published: September 2021

In this work, we present a robust and powerful method for the verification, with arbitrary accuracy, of Monte Carlo codes for simulating random walks in complex media. Such random walks are typical of photon propagation in turbid media, scattering of particles, i.e., neutrons in a nuclear reactor or animal/humans’ migration. Among the numerous applications, Monte Carlo method is also considered a gold standard for numerically “solving” the scalar radiative transport equation even in complex geometries and distributions of the optical properties. In this work, we apply the verification method to a Monte Carlo code which is a forward problem solver extensively used for typical applications in the field of tissue optics. The method is based on the well-known law of average path length invariance when the entrance of the entities/particles in a medium obeys to a simple cosine law, i.e., Lambertian entrance, and annihilation of particles inside the medium is absent. By using this law we achieve two important points: (1) the invariance of the average path length guarantees that the expected value is known regardless of the complexity of the medium; (2) the accuracy of a Monte Carlo code can be assessed by simple statistical tests. We will show that we can reach an arbitrary accuracy of the estimated average pathlength as the number of simulated trajectories increases. The method can be applied in complete generality versus the scattering and geometrical properties of the medium, as well as in presence of refractive index mismatches in the optical case. In particular, this verification method is reliable to detect inaccuracies in the treatment of boundaries of finite media. The results presented in this paper, obtained by a standard computer machine, show a verification of our Monte Carlo code up to the sixth decimal digit. We discuss how this method can provide a fundamental tool for the verification of Monte Carlo codes in the geometry of interest, without resorting to simpler geometries and uniform distribution of the scattering properties.
Use of timelapse photography to determine flower opening time and pattern in banana (Musa spp.) for efficient hand pollination
Authors: Waniale Allan , Swennen Rony , Mukasa Settumba B. , Tugume Arthur K. , Kubiriba Jerome , Tushemereirwe Wilberforce K. , Uwimana Brigitte , Gram Gil , Amah Delphine , Tumuhimbise Robooni
Published: September 2021

Sterility and low seed set in bananas is the main challenge to their conventional genetic improvement. The first step to seed set in a banana breeding program depends on pollination at the right time to ensure effective fertilization. This study aimed at determining bract opening time (BOT) to enhance efficient pollination and seed set in bananas. A Nikon D810 digital camera was set-up to take pictures of growing banana inflorescences at five-minute intervals and time-lapse movies were developed at a speed of 30 frames per second to allow real-time monitoring of BOT. Genotypes studied included wild banana (1), Mchare (2), Matooke (4), Matooke hybrid (1), and plantain (1). Events of bract opening initiated by bract lift for female flowers (P < 0.01) started at 16:32 h and at 18:54 h for male flowers. Start of bract rolling was at 18:51 h among female flowers (P < 0.001) and 20:48 h for male flowers. Bracts ended rolling at 02:33 h and 01:16 h for female and flowers respectively (P < 0.05). Total time of bract opening (from lift to end of rolling) for female flowers was significantly longer than that of male flowers (P < 0.001). On average, the number of bracts subtending female flowers opening increased from one on the first day, to between one and four on the fourth day. The number regressed to one bract on day eight before start of opening of bracts subtending male flowers. There was a longer opening interval between bracts subtending female and male flowers constituting spatial and temporal separation. Bract rolling increased from partial to complete rolling from proximal to the distal end of the inflorescence among female flower. On the other hand, bracts subtending male flowers completely rolled. Differences in BOT of genotypes with the same reference time of assessment may be partly responsible for variable fertility. Hand pollination time between 07:00 and 10:00 h is slightly late thus an early feasible time should be tried.
A differential DNA methylome signature of pulmonary immune cells from individuals converting to latent tuberculosis infection
Authors: Karlsson Lovisa , Das Jyotirmoy , Nilsson Moa , Tyrén Amanda , Pehrson Isabelle , Idh Nina , Sayyab Shumaila , Paues Jakob , Ugarte-Gil Cesar , Méndez-Aranda Melissa , Lerm Maria
Published: September 2021

Tuberculosis (TB), caused byMycobacterium tuberculosis,spreads via aerosols and the first encounter with the immune system is with the pulmonary-resident immune cells. The role of epigenetic regulations in the immune cells is emerging and we have previously shown that macrophages capacity to killM. tuberculosisis reflected in the DNA methylome. The aim of this study was to investigate epigenetic modifications in alveolar macrophages and T cells in a cohort of medical students with an increased risk of TB exposure, longitudinally. DNA methylome analysis revealed that a unique DNA methylation profile was present in healthy subjects who later developed latent TB during the study. The profile was reflected in a different overall DNA methylation distribution as well as a distinct set of differentially methylated genes (DMGs). The DMGs were over-represented in pathways related to metabolic reprogramming of macrophages and T cell migration and IFN-γ production, pathways previously reported important in TB control. In conclusion, we identified a unique DNA methylation signature in individuals, with no peripheral immune response toM. tuberculosisantigen who later developed latent TB. Together the study suggests that the DNA methylation status of pulmonary immune cells can reveal who will develop latent TB infection.
Origins of the change in mechanical strength of silicon/gold nanocomposites during irradiation
Authors: Chen Elton Y. , Hopper Cameron P. , Santhapuram Raghuram R. , Dingreville Rémi , Nair Arun K.
Published: September 2021

Silicon-based layered nanocomposites, comprised of covalent-metal interfaces, have demonstrated elevated resistance to radiation. The amorphization of the crystalline silicon sublayer during irradiation and/or heating can provide an additional mechanism for accommodating irradiation-induced defects. In this study, we investigated the mechanical strength of irradiated Si-based nanocomposites using atomistic modeling. We first examined dose effects on the defect evolution mechanisms near silicon-gold crystalline and amorphous interfaces. Our simulations reveal the growth of an emergent amorphous interfacial layer with increasing dose, a dominant factor mitigating radiation damage. We then examined the effect of radiation on the mechanical strength of silicon-gold multilayers by constructing yield surfaces. These results demonstrate a rapid onset strength loss with dose. Nearly identical behavior is observed in bulk gold, a phenomenon that can be rooted to the formation of radiation-induced stacking fault tetrahedra which dominate the dislocation emission mechanism during mechanical loading. Taken together, these results advance our understanding of the interaction between radiation-induced point defects and metal-covalent interfaces.
Graphene-based autonomous pyroelectric system for near-field energy conversion
Authors: Latella Ivan , Ben-Abdallah Philippe
Published: September 2021

In the close vicinity of a hot solid, at distances smaller than the thermal wavelength, a strong electromagnetic energy density exists because of the presence of evanescent field. Here we introduce a many-body conversion principle to harvest this energy using graphene-based pyroelectric conversion devices made with an active layer encapsulated between two graphene field-effect transistors which are deposited on the source and on the cold sink. By tuning the bias voltage applied to the gates of these transistors, the thermal state and the spontaneous polarization of the active layer can be controlled at kHz frequencies. We demonstrate that the power density generated by these conversion systems can reach $$130\,{\rm mW\,cm}^{-2}$$

130

mW

cm

-
2

using pyroelectric Ericsson cycles, a value which surpasses the current production capacity of near-field thermophotovoltaic conversion devices by more than three orders of magnitude with low grade heat sources ($$T<500\,{\rm K}$$

T
<
500

K

) and small temperature differences ($$\Delta T\sim 100\,K$$

Δ
T
∼
100

K

).
Assessment of distribution center locations using a multi-expert subjective–objective decision-making approach
Authors: Keshavarz-Ghorabaee Mehdi
Published: September 2021

Distribution is a strategic function of logistics in different companies. Establishing distribution centers (DCs) in appropriate locations helps companies to reach long-term goals and have better relations with their customers. Assessment of possible locations for opening new DCs can be considered as an MCDM (Multi-Criteria Decision-Making) problem. In this study, a decision-making approach is proposed to assess DC locations. The proposed approach is based on Stepwise Weight Assessment Ratio Analysis II (SWARA II), Method based on the Removal Effects of Criteria (MEREC), Weighted Aggregated Sum Product Assessment (WASPAS), simulation, and the assignment model. The assessment process is performed using the subjective and objective criteria weights determined based on multiple experts’ judgments. The decision matrix, subjective weights and objective weights are modeled based on the triangular probability distribution to assess the possible alternatives. Then, using simulation and the assignment model, the final aggregated results are determined. A case of DC locations assessment is addressed to show the applicability of the proposed approach. A comparative analysis is also made to verify the results. The analyses of this study show that the proposed approach is efficient in dealing with the assessment of DC locations, and the final results are congruent with those of existing MCDM methods.
The effect of air pollution on the transcriptomics of the immune response to respiratory infection
Authors: Croft Daniel P. , Burton David S. , Nagel David J. , Bhattacharya Soumyaroop , Falsey Ann R. , Georas Steve N. , Hopke Philip K. , Johnston Carl J. , Kottmann R. Matthew , Litonjua Augusto A. , Mariani Thomas J. , Rich David Q. , Thevenet-Morrison Kelly , Thurston Sally W. , Utell Mark J. , McCall Matthew N.
Published: September 2021

Combustion related particulate matter air pollution (PM) is associated with an increased risk of respiratory infections in adults. The exact mechanism underlying this association has not been determined. We hypothesized that increased concentrations of combustion related PM would result in dysregulation of the innate immune system. This epidemiological study includes 111 adult patients hospitalized with respiratory infections who underwent transcriptional analysis of their peripheral blood. We examined the association between gene expression at the time of hospitalization and ambient measurements of particulate air pollutants in the 28 days prior to hospitalization. For each pollutant and time lag, gene-specific linear models adjusting for infection type were fit using LIMMA (Linear Models For Microarray Data), and pathway/gene set analyses were performed using the CAMERA (Correlation Adjusted Mean Rank) program. Comparing patients with viral and/or bacterial infection, the expression patterns associated with air pollution exposure differed. Adjusting for the type of infection, increased concentrations of Delta-C (a marker of biomass smoke) and other PM were associated with upregulation of iron homeostasis and protein folding. Increased concentrations of black carbon (BC) were associated with upregulation of viral related gene pathways and downregulation of pathways related to antigen presentation. The pollutant/pathway associations differed by lag time and by type of infection. This study suggests that the effect of air pollution on the pathogenesis of respiratory infection may be pollutant, timing, and infection specific.
Genetic diversity of candidate loci linked to Mycobacterium tuberculosis resistance to bedaquiline, delamanid and pretomanid
Authors: Gómez-González Paula J. , Perdigao Joao , Gomes Pedro , Puyen Zully M. , Santos-Lazaro David , Napier Gary , Hibberd Martin L. , Viveiros Miguel , Portugal Isabel , Campino Susana , Phelan Jody E. , Clark Taane G.
Published: September 2021

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the deadliest infectious diseases worldwide. Multidrug and extensively drug-resistant strains are making disease control difficult, and exhausting treatment options. New anti-TB drugs bedaquiline (BDQ), delamanid (DLM) and pretomanid (PTM) have been approved for the treatment of multi-drug resistant TB, but there is increasing resistance to them. Nine genetic loci strongly linked to resistance have been identified (mmpR5, atpE, and pepQ for BDQ; ddn, fgd1, fbiA, fbiB, fbiC, and fbiD for DLM/PTM). Here we investigated the genetic diversity of these loci across >33,000 M. tuberculosis isolates. In addition, epistatic mutations in mmpL5-mmpS5 as well as variants in ndh, implicated for DLM/PTM resistance in M. smegmatis, were explored. Our analysis revealed 1,227 variants across the nine genes, with the majority (78%) present in isolates collected prior to the roll-out of BDQ and DLM/PTM. We identified phylogenetically-related mutations, which are unlikely to be resistance associated, but also high-impact variants such as frameshifts (e.g. in mmpR5, ddn) with likely functional effects, as well as non-synonymous mutations predominantly in MDR-/XDR-TB strains with predicted protein destabilising effects. Overall, our work provides a comprehensive mutational catalogue for BDQ and DLM/PTM associated genes, which will assist with establishing associations with phenotypic resistance; thereby, improving the understanding of the causative mechanisms of resistance for these drugs, leading to better treatment outcomes.
Nano-imaging confirms improved apatite precipitation for high phosphate/silicate ratio bioactive glasses
Authors: Jaimes Altair T. Contreras , Kirste Gloria , de Pablos-Martín Araceli , Selle Susanne , de Souza e Silva Juliana Martins , Massera Jonathan , Karpukhina Natalia , Hill Robert G. , Brauer Delia S.
Published: September 2021

Bioactive glasses convert to a biomimetic apatite when in contact with physiological solutions; however, the number and type of phases precipitating depends on glass composition and reactivity. This process is typically followed by X-ray diffraction and infrared spectroscopy. Here, we visualise surface mineralisation in a series of sodium-free bioactive glasses, using transmission electron microscopy (TEM) with energy-dispersive X-ray spectroscopy (EDXS) and X-ray nano-computed tomography (nano-CT). In the glasses, the phosphate content was increased while adding stoichiometric amounts of calcium to maintain phosphate in an orthophosphate environment in the glass. Calcium fluoride was added to keep the melting temperature low. TEM brought to light the presence of phosphate clustering and nearly crystalline calcium fluoride environments in the glasses. A combination of analytical methods, including solid-state NMR, shows how with increasing phosphate content in the glass, precipitation of calcium fluoride during immersion is superseded by fluorapatite precipitation. Nano-CT gives insight into bioactive glass particle morphology after immersion, while TEM illustrates how compositional changes in the glass affect microstructure at a sub-micron to nanometre-level.
Cell aging related genes can be used to characterize clinical prognoses and further stratify diffuse gliomas
Authors: Yang Yang , Chen Xin , Sun Jianjun , Chen Suhua , Yang Chenlong , Ma Qianquan , Yang Jun
Published: September 2021

Increasing evidence has indicated that senescent cells are associated with the glioma development. Thus, we aimed to explore the relationship between the cellular senescence gene profile and the clinical prognosis of diffuse glioma. In total, 699 gliomas from The Cancer Genome Atlas (TCGA) dataset were used as the training cohort and 693 gliomas from the Chinese Glioma Genome Atlas (CGGA) dataset were used as the validation cohort. Bioinformatics statistical methods are used to develop the risk signature and to study the prognostic value of the risk signature. We identified a 14-gene risk signature and its risk score was an independent prognostic factor (P < 0.001) in the validation dataset. The risk signature had better prognostic value than traditional factors for the 3- and 5-year survival rate. Importantly, the risk signature could further stratify gliomas in specific subgroups of World Health Organization (WHO) classification by the survival rate. Furthermore, the mRNA levels of genes involved in the cell cycle, cell division and other processes were significantly correlated with the risk score. Our study highlighted a 14-gene risk signature for further stratifying the outcomes of patients with gliomas with definite WHO subgroups. These results indicate the potential clinical implications of cell aging-related genes in gliomas.
Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey
Authors: Sato Masaaki , Inoue Nariaki , Nambu Ryogen , Furuichi Naoki , Imaizumi Tomohito , Ushio Masayuki
Published: September 2021

Since the early 1970s, many artificial reefs (ARs) have been deployed in Japanese coastal waters to create fisheries grounds. Recently, researchers began to use environmental DNA (eDNA) methods for biodiversity monitoring of aquatic species. A metabarcoding approach using internal standard DNAs [i.e., quantitative MiSeq sequencing (qMiSeq)] makes it possible to monitor eDNA concentrations of multiple species simultaneously. This method can improve the efficiency of monitoring AR effects on fishes. Our study investigated distributions of marine fishes at ARs and surrounding stations in the open oceanographic environment of Tateyama Bay, central Japan, using qMiSeq and echo sounder survey. Using the qMiSeq with 12S primers, we found higher quantities of fish eDNAs at the ARs than at surrounding stations and different fish species compositions between them. Comparisons with echo sounder survey also showed positive correlations between fish eDNA concentration and echo intensity, which indicated a highly localized signal of eDNA at each sampling station. These results suggest that qMiSeq is a promising technique to complement conventional methods to monitor distributions of multiple fish species.
Presence of distinctive microbiome in the first-pass meconium of newborn infants
Authors: Turunen Jenni , Tejesvi Mysore V. , Paalanne Niko , Hekkala Jenni , Lindgren Outi , Kaakinen Mika , Pokka Tytti , Kaisanlahti Anna , Reunanen Justus , Tapiainen Terhi
Published: September 2021

We critically evaluated the fetal microbiome concept in 44 neonates with placenta, amniotic fluid, and first-pass meconium samples. Placental histology showed no signs of inflammation. Meconium samples were more often bacterial culture positive after vaginal delivery. In next-generation sequencing of the bacterial 16S gene, before and after removal of extracellular and PCR contaminant DNA, the median number of reads was low in placenta (48) and amniotic fluid (46) and high in meconium samples (14,556 C-section, 24,860 vaginal). In electron microscopy, meconium samples showed extracellular vesicles. Utilizing the analysis of composition of microbiomes (ANCOM) against water, meconium samples had a higher relative abundance of Firmicutes, Lactobacillus, Streptococcus, and Escherichia-Shigella. Our results did not support the existence of the placenta and amniotic fluid microbiota in healthy pregnancies. The first-pass meconium samples, formed in utero, appeared to harbor a microbiome that may be explained by perinatal colonization or intrauterine colonization via bacterial extracellular vesicles.
New chemical biopsy tool for spatially resolved profiling of human brain tissue in vivo
Authors: Bogusiewicz Joanna , Burlikowska Katarzyna , Łuczykowski Kamil , Jaroch Karol , Birski Marcin , Furtak Jacek , Harat Marek , Pawliszyn Janusz , Bojko Barbara
Published: September 2021

It is extremely challenging to perform chemical analyses of the brain, particularly in humans, due to the restricted access to this organ. Imaging techniques are the primary approach used in clinical practice, but they only provide limited information about brain chemistry. Solid-phase microextraction (SPME) has been presented recently as a chemical biopsy tool for the study of animal brains. The current work demonstrates for the first time the use of SPME for the spatially resolved sampling of the human brain in vivo. Specially designed multi-probe sampling device was used to simultaneously extract metabolites from the white and grey matter of patients undergoing brain tumor biopsies. Samples were collected by inserting the probes along the planned trajectory of the biopsy needle prior to the procedure, which was followed by metabolomic and lipidomic analyses. The results revealed that studied brain structures were predominantly composed of lipids, while the concentration and diversity of detected metabolites was higher in white than in grey matter. Although the small number of participants in this research precluded conclusions of a biological nature, the results highlight the advantages of the proposed SPME approach, as well as disadvantages that should be addressed in future studies.
Experimental evolution supports the potential of neonicotinoid-pyrethroid combination for managing insecticide resistance in malaria vectors
Authors: Zoh Marius Gonse , Bonneville Jean-Marc , Tutagata Jordan , Laporte Frederic , Fodjo Behi K. , Mouhamadou Chouaibou S. , Sadia Christabelle Gba , McBeath Justin , Schmitt Frederic , Horstmann Sebastian , Reynaud Stephane , David Jean-Philippe
Published: September 2021

The introduction of neonicotinoids for managing insecticide resistance in mosquitoes is of high interest as they interact with a biochemical target not previously used in public health. In this concern, Bayer developed a combination of the neonicotinoid clothianidin and the pyrethroid deltamethrin (brand name Fludora Fusion) as a new vector control tool. Although this combination proved to be efficient against pyrethroid-resistant mosquitoes, its ability to prevent the selection of pyrethroid and neonicotinoid resistance alleles was not investigated. In this context, the objective of this work was to study the dynamics and the molecular mechanisms of resistance ofAn. gambiaeto the separated or combined components of this combination. A field-derivedAn. gambiaeline carrying resistance alleles to multiple insecticides at low frequencies was used as a starting for 33 successive generations of controlled selection. Resistance levels to each insecticide and target site mutation frequencies were monitored throughout the selection process. Cross resistance to other public health insecticides were also investigated. RNA-seq was used to compare gene transcription variations and polymorphisms across all lines. This study confirmed the potential of this insecticide combination to impair the selection of resistance as compared to its two separated components. Deltamethrin selection led to the rapid enrichment of the kdr L1014F target-site mutation. Clothianidin selection led to the over-transcription of multiple cytochrome P450s including some showing high homology with those conferring neonicotinoid resistance in other insects. A strong selection signature associated with clothianidin selection was also observed on a P450 gene cluster previously associated with resistance. Within this cluster, the geneCYP6M1showed the highest selection signature together with a transcription profile supporting a role in clothianidin resistance. Modelling the impact of point mutations selected by clothianidin on CYP6M1 protein structure showed that selection retained a protein variant with a modified active site potentially enhancing clothianidin metabolism. In the context of the recent deployment of neonicotinoids for mosquito control and their frequent usage in agriculture, the present study highlights the benefit of combining them with other insecticides for preventing the selection of resistance and sustaining vector control activities.
Boosting proximity spin–orbit coupling in graphene/WSe2 heterostructures via hydrostatic pressure
Authors: Fülöp Bálint , Márffy Albin , Zihlmann Simon , Gmitra Martin , Tóvári Endre , Szentpéteri Bálint , Kedves Máté , Watanabe Kenji , Taniguchi Takashi , Fabian Jaroslav , Schönenberger Christian , Makk Péter , Csonka Szabolcs
Published: September 2021

Van der Waals heterostructures composed of multiple few layer crystals allow the engineering of novel materials with predefined properties. As an example, coupling graphene weakly to materials with large spin–orbit coupling (SOC) allows to engineer a sizeable SOC in graphene via proximity effects. The strength of the proximity effect depends on the overlap of the atomic orbitals, therefore, changing the interlayer distance via hydrostatic pressure can be utilized to enhance the interlayer coupling between the layers. In this work, we report measurements on a graphene/WSe2 heterostructure exposed to increasing hydrostatic pressure. A clear transition from weak localization to weak antilocalization is visible as the pressure increases, demonstrating the increase of induced SOC in graphene.
Photoluminescence as a probe of phosphorene properties
Authors: Molas Maciej R. , Macewicz Łukasz , Wieloszyńska Aleksandra , Jakóbczyk Paweł , Wysmołek Andrzej , Bogdanowicz Robert , Jasinski Jacek B.
Published: September 2021

Here, we provide a detailed evaluation of photoluminescence (PL) as a comprehensive tool for phosphorene characterization with the emphasis on a prominent quantitative role of PL in providing fingerprint-like features due to its extreme sensitivity to the band structure details, anisotropy, disorder, external fields, etc. Factors such as number of layers, dimensionality, structural and chemical disorder, and environmental factors and their effect on phosphorene’s PL signal are reviewed and discussed. Applications of PL in monitoring phosphorene and its modifications, as well as potential impacts on the fields of chemical and biosensing, nanomedicine, and solar energy harvesting, are also elaborated.
Statistical uncertainty quantification to augment clinical decision support: a first implementation in sleep medicine
Authors: Kang Dae Y. , DeYoung Pamela N. , Tantiongloc Justin , Coleman Todd P. , Owens Robert L.
Published: September 2021

Machine learning has the potential to change the practice of medicine, particularly in areas that require pattern recognition (e.g. radiology). Although automated classification is unlikely to be perfect, few modern machine learning tools have the ability to assess their own classification confidence to recognize uncertainty that might need human review. Using automated single-channel sleep staging as a first implementation, we demonstrated that uncertainty information (as quantified using Shannon entropy) can be utilized in a “human in the loop” methodology to promote targeted review of uncertain sleep stage classifications on an epoch-by-epoch basis. Across 20 sleep studies, this feedback methodology proved capable of improving scoring agreement with the gold standard over automated scoring alone (average improvement in Cohen’s Kappa of 0.28), in a fraction of the scoring time compared to full manual review (60% reduction). In summary, our uncertainty-based clinician-in-the-loop framework promotes the improvement of medical classification accuracy/confidence in a cost-effective and economically resourceful manner.
A genotyping assay to determine geographic origin and transmission potential of Plasmodium falciparum malaria cases
Authors: Molina-Cruz Alvaro , Raytselis Nadia , Withers Roxanne , Dwivedi Ankit , Crompton Peter D. , Traore Boubacar , Carpi Giovanna , Silva Joana C. , Barillas-Mury Carolina
Published: September 2021

As countries work towards malaria elimination, it is important to monitor imported cases to prevent reestablishment of local transmission. The Plasmodium falciparum Pfs47 gene has strong geographic population structure, because only those parasites with Pfs47 haplotypes compatible with the mosquito vector species in a given continent are efficiently transmitted. Analysis of 4,971 world-wide Pfs47 sequences identified two SNPs (at 707 and 725 bp) as sufficient to establish the likely continent of origin of P. falciparum isolates. Pfs47 sequences from Africa, Asia, and the New World presented more that 99% frequency of distinct combinations of the SNPs 707 and 725 genotypes. Interestingly, Papua New Guinea Pfs47 sequences have the highest diversity in SNPs 707 and 725. Accurate and reproducible High-Resolution Melting (HRM) assays were developed to genotype Pfs47 SNPs 707 and 725 in laboratory and field samples, to assess the geographic origin and risk of local transmission of imported P. falciparum malaria cases.