bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework
Authors: Heuts B. M. H. , Arza-Apalategi S. , Frölich S. , Bergevoet S. M. , van den Oever S. N. , van Heeringen S. J. , van der Reijden B. A. , Martens J. H. A.
Published: November 2022

Advanced computational methods exploit gene expression and epigenetic datasets to predict gene regulatory networks controlled by transcription factors (TFs). These methods have identified cell fate determining TFs but require large amounts of reference data and experimental expertise. Here, we present an easy to use network-based computational framework that exploits enhancers defined by bidirectional transcription, using as sole input CAGE sequencing data to correctly predict TFs key to various human cell types. Next, we applied this Analysis Algorithm for Networks Specified by Enhancers based on CAGE (ANANSE-CAGE) to predict TFs driving red and white blood cell development, and THP-1 leukemia cell immortalization. Further, we predicted TFs that are differentially important to either cell line- or primary- associated MLL-AF9-driven gene programs, and in primary MLL-AF9 acute leukemia. Our approach identified experimentally validated as well as thus far unexplored TFs in these processes. ANANSE-CAGE will be useful to identify transcription factors that are key to any cell fate change using only CAGE-seq data as input.
A randomized multicenter evaluation of the efficacy of 0.15% hyaluronic acid versus 0.05% cyclosporine A in dry eye syndrome
Authors: Lee Ji Eun , Kim Sangyoon , Lee Hyung Keun , Chung Tae-Young , Kim Jae Yong , Choi Chul Young , Chung So Hyang , Kim Dong Hyun , Kim Kyoung Woo , Chung Jin Kwon , Hwang Kyu Yeon , Hwang Ho Sik , Kim Jin Hyoung , Hyon Joon Young
Published: November 2022

Hyaluronic acid (HA) and cyclosporine A (CsA) eyedrops are commonly prescribed in dry eye syndrome (DES). The effectiveness of each preparation in DES is well-known, yet the superiority of one over another has been studied little. We assessed the efficacy and tolerability of 0.15% HA compared to combinations of 0.05% CsA plus 0.5% carboxymethylcellulose (CMC), and 0.15% HA plus 0.05% CsA in patients with moderate to severe DES. Total 438 patients with moderate to severe DES were recruited and randomized for one of the three treatments for 12 weeks. Effectiveness was assessed at baseline, 4- and 12-weeks. The primary endpoint was change in corneal staining score. The secondary endpoints were tear break-up time (TBUT), strip meniscometry (SM) score, ocular surface disease index (OSDI) score, and tolerability questionnaire. The change in corneal staining score for 0.15% HA from the baseline was non-inferior to that of 0.05% CsA. Corneal staining score, TBUT, SM score, and OSDI score improved in all groups without statistically significant intergroup differences. Better tolerability and lower prevalence of adverse drug reactions were seen in 0.15% HA. Our findings suggest that 0.15% HA may be equivalently effective and safer than 0.05% CsA in treating moderate to severe DES.
The dominant mesopredator and savanna formations shape the distribution of the rare northern tiger cat (Leopardus tigrinus) in the Amazon
Authors: de Oliveira Tadeu G. , Fox-Rosales Lester A. , Paemelaere Evi A. D. , de Barros Ferraz Katia Maria Paschoaletto Micchi
Published: November 2022

Understanding the distribution patterns of threatened species is central to conservation. The Amazonian distribution of the northern tiger cat (N-tiger cat, Leopardus tigrinus) and its interspecific relationship with the ocelot, its potential intraguild killer, are intriguing. Here, we combined presence/absence records with species distribution models (SDMs) to determine N-tiger cat occurrence in the Amazon. We also modeled ocelot density from 46 published estimates. The N-tiger cat’s presence in the Amazon was negatively influenced by ocelot density and net primary productivity and positively influenced by savannas and precipitation in the driest month. The best-fitting model predicted highly patchy N-tiger cat occurrence over an area of 236,238.67 km2, almost exclusively in savanna enclaves. Additionally, 312,348 camera trap-days at 49 sites in the Amazon revealed no N-tiger cats. The ocelot densities were significantly higher in areas with denser vegetation cover and warmer habitats, with predicted densities ≥ 0.6 ind/km2 throughout most of the biome. The lowest ocelot densities (≤ 0.06 ind/km2) were observed along the predicted range of N-tiger cats. Our findings highlight that the N-tiger cat’s presence in the Amazon is restricted to savannas and highly influenced by ocelot density, emphasizing the importance of including species interactions in SDMs.
Crystal structure thermal evolution and novel orthorhombic phase of methylammonium lead bromide, CH3NH3PbBr3
Authors: Abia Carmen , López Carlos A. , Cañadillas-Delgado Laura , Fernández-Diaz María T. , Alonso José A.
Published: November 2022

Methylammonium (MA) lead trihalide perovskites, CH3NH3PbX3 (X = I, Br, Cl), have emerged as a new class of light-absorbing materials for photovoltaic applications, reaching efficiencies of 23% when implemented in solar cell heterojunctions. In particular, MAPbBr3 is a promising member with a large bandgap that gives rise to a high open circuit voltage. Here we present a structural study from neutron diffraction (ND) data of an undeuterated MAPbBr3 specimen, carried out to follow its crystallographic behaviour in the 2–298 K temperature range. Besides the known crystallographic phases, i.e. the high-temperature Pm$$\overline{3}$$

3
¯

m cubic structure, the intermediate I4/mcm tetragonal symmetry and the low-temperature Pnma orthorhombic phase, we additionally identified, from a detailed sequential ND analysis, a novel intermediate phase within the 148.5–154.0 K temperature range as an orthorhombic Imma structure, early associated with a coexistence of phases. Moreover, our ND data allowed us to unveil the configuration of the organic MA units and their complete localization within the mentioned temperature range, thus improving the crystallographic description of this compound. The evolution with temperature of the H-bonds between the organic molecule and the inorganic cage is also followed. A deep knowledge of the crystal structure and, in particular, the MA conformation inside the perovskite cage seems essential to establish structure–property correlations that may drive further improvements.
Engineered living photosynthetic biocomposites for intensified biological carbon capture
Authors: In-na Pichaya , Sharp Elliot B. , Caldwell Gary S. , Unthank Matthew G. , Perry Justin J. , Lee Jonathan G. M.
Published: November 2022

Carbon capture and storage is required to meet Paris Agreement targets. Photosynthesis is nature’s carbon capture technology. Drawing inspiration from lichen, we engineered 3D photosynthetic cyanobacterial biocomposites (i.e., lichen mimics) using acrylic latex polymers applied to loofah sponge. Biocomposites had CO2 uptake rates of 1.57 ± 0.08 g CO2 g−1biomass d−1. Uptake rates were based on the dry biomass at the start of the trial and incorporate the CO2 used to grow new biomass as well as that contained in storage compounds such as carbohydrates. These uptake rates represent 14–20-fold improvements over suspension controls, potentially scaling to capture 570 tCO2 t−1biomass yr−1, with an equivalent land consumption of 5.5–8.17 × 106 ha, delivering annualized CO2 removal of 8–12 GtCO2, compared with 0.4–1.2 × 109 ha for forestry-based bioenergy with carbon capture and storage. The biocomposites remained functional for 12 weeks without additional nutrient or water supplementation, whereupon experiments were terminated. Engineered and optimized cyanobacteria biocomposites have potential for sustainable scalable deployment as part of humanity’s multifaceted technological stand against climate change, offering enhanced CO2 removal with low water, nutrient, and land use penalties.
Monopole directional antenna bioinspired in elliptical leaf with golden ratio for WLAN and 4G applications
Authors: Froes Eduarda , Silva Junior Paulo F. , Santana Ewaldo E. C. , Sousa Junior Carlos M. , Silva Paulo H. F. , Cruz Carlos A. M. , Aquino Vivianne S. , Castro Luis S. O. , Freire Raimundo C. S. , Pinto Mauro S. S.
Published: November 2022

In this work, it is proposed the development a new monopole directional antenna, bioinspired in elliptical leaf, with cut by golden ratio, for 4G band application, by the use of the technique of the cut of the radiating element for the increasing of the antenna perimeter, being the first work to use this technique in a bioinspired antenna, promotes resonance frequency turned, and reconfiguring of the antenna parameters as bandwidth, radiation pattern and gain, with the use of the reflector near to the group plane, without the insertion of active devices as the pin diode or change in radiating element. The shape antenna is generated by Gielis formula, built in FR4 substrate, with cuts calculated by golden ratio. To compare the results of the bioinspired monopole on the elliptical sheet, a square-shaped monopole antenna was designed, simulated and measured, the structures were designed in the MATLAB software version 2015(b) and the simulations were performed in the Ansys software version 2016. In the results compared between the square monopole and the bioinspired antenna in the elliptical sheet, it can be seen that the measured bioinspired antenna, compared to the square monopole, presented a bandwidth reduction of 77.27%, a more compact structure, with a reduction of 98%, covering the wireless local area network, and long-time evolution 4G at 2.5 GHz. The proposed technique uses a reflector on the ground plane, to change the parameters of the monopole planar antenna, of omnidirectional radiation pattern to a directional, maintaining the characteristics of the broadband, half-power beamwidth great than 100°, with high current density, and similar gain of a directional antenna. From the results, it has been observed that the elliptical leaf monopole antenna shows broadband characteristics, with a half-power beamwidth of 128°, wideband, the bandwidth of 500 MHz, a gain of 6.28 dBi, a current density of 13.01 A/m2, and circular polarization.
Site-specific CRISPR-based mitochondrial DNA manipulation is limited by gRNA import
Authors: Schmiderer Ludwig , Yudovich David , Oburoglu Leal , Hjort Martin , Larsson Jonas
Published: November 2022

Achieving CRISPR Cas9-based manipulation of mitochondrial DNA (mtDNA) has been a long-standing goal and would be of great relevance for disease modeling and for clinical applications. In this project, we aimed to deliver Cas9 into the mitochondria of human cells and analyzed Cas9-induced mtDNA cleavage and measured the resulting mtDNA depletion with multiplexed qPCR. In initial experiments, we found that measuring subtle effects on mtDNA copy numbers is challenging because of high biological variability, and detected no significant Cas9-caused mtDNA degradation. To overcome the challenge of being able to detect Cas9 activity on mtDNA, we delivered cytosine base editor Cas9-BE3 to mitochondria and measured its effect (C →  T mutations) on mtDNA. Unlike regular Cas9-cutting, this leaves a permanent mark on mtDNA that can be detected with amplicon sequencing, even if the efficiency is low. We detected low levels of C → T mutations in cells that were exposed to mitochondrially targeted Cas9-BE3, but, surprisingly, these occurred regardless of whether a guide RNA (gRNA) specific to the targeted site, or non-targeting gRNA was used. This unspecific off-target activity shows that Cas9-BE3 can technically edit mtDNA, but also strongly indicates that gRNA import to mitochondria was not successful. Going forward mitochondria-targeted Cas9 base editors will be a useful tool for validating successful gRNA delivery to mitochondria without the ambiguity of approaches that rely on quantifying mtDNA copy numbers.
Identification of mutations in SARS-CoV-2 PCR primer regions
Authors: Mentes Anikó , Papp Krisztián , Visontai Dávid , Stéger József ,   VEO Technical Working Group, Csabai István , Papp Krisztián , Visontai Dávid , Stéger József , Cochrane Guy , Rahman Nadim , Cummins Carla , Yuan David Yu , Selvakumar Sandeep , Mansurova Milena , O’Cathail Colman , Sokolov Alexey , Thorne Ross , Koopmans Marion , Nieuwenhuijse David , Oude-Munnink Bas , Worp Nathalie , Amid Clara , Csabai István , Medgyes-Horváth Anna , Pipek Orsolya Anna
Published: November 2022

Due to the constantly increasing number of mutations in the SARS-CoV-2 genome, concerns have emerged over the possibility of decreased diagnostic accuracy of reverse transcription-polymerase chain reaction (RT-PCR), the gold standard diagnostic test for SARS-CoV-2. We propose an analysis pipeline to discover genomic variations overlapping the target regions of commonly used PCR primer sets. We provide the list of these mutations in a publicly available format based on a dataset of more than 1.2 million SARS-CoV-2 samples. Our approach distinguishes among mutations possibly having a damaging impact on PCR efficiency and ones anticipated to be neutral in this sense. Samples are categorized as “prone to misclassification” vs. “likely to be correctly detected” by a given PCR primer set based on the estimated effect of mutations present. Samples susceptible to misclassification are generally present at a daily rate of 2% or lower, although particular primer sets seem to have compromised performance when detecting Omicron samples. As different variant strains may temporarily gain dominance in the worldwide SARS-CoV-2 viral population, the efficiency of a particular PCR primer set may change over time, therefore constant monitoring of variations in primer target regions is highly recommended.
Trophic provisioning and parental trade-offs lead to successful reproductive performance in corals after a bleaching event
Authors: Rodrigues Lisa J. , Padilla-Gamiño Jacqueline L.
Published: November 2022

Warming ocean temperatures are severely compromising the health and resilience of coral reefs worldwide. Coral bleaching can affect coral physiology and the energy available for corals to reproduce. Mechanisms associated with reproductive allocation in corals are poorly understood, especially after a bleaching event occurs. Using isotopic labeling techniques, we traced the acquisition and allocation of carbon from adults to gametes by autotrophy and heterotrophy in previously bleached and non-bleachedMontipora capitataandPorites compressacorals. Experiments revealed that both species: (1) relied only on autotrophy to allocate carbon to gametes, while heterotrophy was less relied upon as a carbon source; (2) experienced a trade-off with less carbon available for adult tissues when provisioning gametes, especially when previously bleached; and (3) used different strategies for allocating carbon to gametes. Over time,M. capitataallocated 10% more carbon to gametes despite bleaching by limiting the allocation of carbon to adult tissues, with 50–80% less carbon allocated to bleached compared to non-bleached colonies. Over the same time period,P. compressamaintained carbon allocation to adult tissues, before allocating carbon to gametes. Our study highlights the importance of autotrophy for carbon allocation from adult corals to gametes, and species-specific differences in carbon allocation depending on bleaching susceptibility.
Anemia, iron deficiency, and thalassemia among the Thai population inhabiting at the Thailand-Lao PDR-Cambodia triangle
Authors: Karnpean Rossarin , Vanichakulthada Nawinda , Suwannaloet Wanwisa , Thongrung Ruttiya , Singsanan Sanita , Prakobkaew Nattapol , Fucharoen Goonnapa , Fucharoen Supan
Published: November 2022

Anemia is a major public health problem in many areas of Southeast Asia. Ascertaining anemia and defining its underlying causes is essential for providing appropriate care, management, and establishment of a control program. Limited studies on these have been carried out on people living at the borders of Thailand, Lao PDR, and Cambodia. This cross-sectional study was done in four areas along the borders of Thailand, Lao PDR, and Cambodia. Blood specimens were collected from subjects aged 15–18 years in four districts including Kantharalak, Si Sa Ket province (n = 36), Nam Khun (n = 109), Nam Yuen (n = 98), and Na Chaluai (n = 128), Ubon Ratchathani province, Thailand. RBC parameters were recorded, and serum ferritin (SF) level was measured. Diagnosis of thalassemia and hemoglobinopathies was based on hemoglobin (Hb) and DNA analyses. Measurement of C-reactive protein was performed to exclude false-negative result of iron deficiency. The prevalence of anemia was found to be 25.1%. ID accounted for only 10.5%. Various types of thalassemia were identified in 67.7% of the subjects. The overall prevalence of thalassemia included 3.5% α0-thalassemia, 0.8% β-thalassemia, 47.7% Hb E, and 53.6% α+-thalassemia. The proportions of ID, thalassemia and combined ID and thalassemia among anemic subjects were 6.5%, 66.6%, and 20.4%, respectively. The results indicate that thalassemia and hemoglobinopathies rather than ID are major causes of anemia in Thailand-Lao PDR-Cambodia triangle. This information should prove useful for implementing an anemia control program in the regions.
SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding
Authors: Dudouet Pierre , Colson Philippe , Aherfi Sarah , Levasseur Anthony , Beye Mamadou , Delerce Jeremy , Burel Emilie , Lavrard Philippe , Bader Wahiba , Lagier Jean-Christophe , Fournier Pierre-Edouard , La Scola Bernard , Raoult Didier
Published: November 2022

At the time of a new and unprecedented viral pandemic, many questions are being asked about the genomic evolution of SARS-CoV-2 and the emergence of different variants, leading to therapeutic and immune evasion and survival of this genetically highly labile RNA virus. The nasopharyngeal persistence of infectious virus beyond 17 days proves its constant interaction with the human immune system and increases the intra-individual mutational possibilities. We performed a prospective high-throughput sequencing study (ARTIC Nanopore) of SARS-CoV-2 from so-called "persistent" patients, comparing them with a non-persistent population, and analyzing the quasi-species present in a single sample at time t. Global intra-individual variability in persistent patients was found to be higher than in controls (mean 5.3%, Standard deviation 0.9 versus 4.6% SD 0.3, respectively, p < 0.001). In the detailed analysis, we found a greater difference between persistent and non-persistent patients with non-severe COVID 19, and between the two groups infected with clade 20A. Furthermore, we found minority N501Y and P681H mutation clouds in all patients, with no significant differences found both groups. The question of the SARS-CoV-2 viral variants’ genesis remains to be further investigated, with the need to prevent new viral propagations and their consequences, and quasi-species analysis could be an important key to watch out.
Genome-wide identification, phylogenetic, and expression analysis under abiotic stress conditions of Whirly (WHY) gene family in Medicago sativa L.
Authors: Ruan Qian , Wang Yizhen , Xu Haoyu , Wang Baoqiang , Zhu Xiaolin , Wei Bochuang , Wei Xiaohong
Published: November 2022

The WHY family is a group of plant-specific transcription factors, that can bind to single-stranded DNA molecules and play a variety of functions in plant nuclei and organelles, participating in the regulation of plant leaf senescence. It has been identified and analyzed in many species, however, the systematic identification and analysis of the WHY genes family have not yet been reported in alfalfa (Medicago sativa L.). Therefore, to explore the function of alfalfa the WHY genes, and 10 MsWHY genes were identified and further characterized their evolutionary relationship and expression patterns by analyzing the recently published genome of alfalfa. Comprehensive analysis of the chromosome location, physicochemical properties of the protein, evolutionary relationship, conserved motifs, and responses to abiotic stresses of the WHY gene family in alfalfa using bioinformatics methods. The results showed that 10 MsWHY genes were distributed on 10 chromosomes, and collinearity analysis showed that many MsWHYs might be derived from segmental duplications, and these genes are under purifying selection. Based on phylogenetic analyses, the WHY gene family of alfalfa can be divided into four subfamilies: I-IV subfamily, and approximately all the WHY genes within the same subfamily share similar gene structures. The 10 MsWHY gene family members contained 10 motifs, of which motif 2 and motif 4 are the conserved motifs shared by these genes. Furthermore, the analysis of cis-regulatory elements indicated that regulatory elements related to transcription, cell cycle, development, hormone, and stress response are abundant in the promoter sequence of the MsWHY genes. Real-time quantitative PCR demonstrated that MsWHYs gene expression is induced by drought, salt, and methyl jasmonate. The present study serves as a basic foundation for future functional studies on the alfalfa WHY family.
Ornamental roses for conservation of leafcutter bee pollinators
Authors: Sinu Palatty Allesh , Jamal Mubarak , Shaji Greeshma , Hariraveendra M. , Viswan Gopika , Abhiram Krishnan P. , Das Ankita , Aneha K. , Pooja A. R. , Salikity Spandana , Arathy V.
Published: November 2022

Pollinator conservation is a global priority. Efforts are taken to restore pollinators by improving flower resources, a crucial driver of pollinator diversity and population growth. It helped gardening and landscaping supply chains, which introduced lists of bee-friendly plants and bee hotels, yet, desirable results seem distant. One shortcoming of the present schemes is that they lack a cohesive planning for nesting opportunities and nesting provisions for wild solitary bees, the crucial pollinators of crop and wild plants. We tested whether the world’s popular ornamental plant, rose (Rosa chinensis Jacq.)—a hitherto unlisted bee-friendly plant—can aid in conserving leafcutter bees, which require fresh leaves for constructing nest cells. We surveyed 2360 rose plants in 136 sites in rural and urban places and lowlands and highlands of south (8°N–12°N) and northeastern India (26°N–27°N) for the characteristic notches the bees leave on foraged leaves. We reared brood constructed with rose and non-rose leaves to examine the brood success rate. About a quarter of all the roses surveyed had the notches of leafcutter bees on the leaves. However, the proportion of cut roses varied considerably among sites. Bees used roses much higher in urban areas and lowlands than in rural areas and highlands. The selection of plants was negatively associated with pesticide application. The brood success rate was 100% for the brood that was constructed by the leaves of rose and non-rose plants. Rose flowers do not support bees, but rose leaves indeed do. We recommend rose plants in leafcutter bee conservation and restoration schemes, particularly in urban environment.
Paeoniflorin drives the immunomodulatory effects of mesenchymal stem cells by regulating Th1/Th2 cytokines in oral lichen planus
Authors: Zhang Zhihui , Zhang Yan , Zhao Zhongfang , Li Pei , Chen Danyang , Wang Wei , Han Ying , Zou Shiqi , Jin Xin , Zhao Jianling , Liu Hongwei , Wang Xiao , Zhu Weili
Published: November 2022

Lichen planus (LP) is a chronic inflammatory disease. Oral lichen planus (OLP) mainly appears as oral mucosal reticular or ulcerative lesions with an unknown etiology. We aimed to explore the immunomodulatory effect of paeoniflorin (PF) in mesenchymal stem cells (MSCs) and the potential involvement of Th1/Th2 cytokines in OLP. The effects of paeoniflorin on the proliferation and migration of MSCs were detected by Cell Counting Kit-8 (CCK8) and Transwell assays. MSCs were subjected to osteogenic, adipogenic and neurogenic induction followed by Alizarin red, oil red O, real-time PCR and immunofluorescence assays. We found that paeoniflorin promoted the proliferation, migration and multilineage differentiation of MSCs from OLP lesions (OLP-MSCs) in vitro. Paeoniflorin pretreatment increased the inhibitory effect of OLP-MSCs on peripheral blood mononuclear cells. Furthermore, paeoniflorin-pretreated OLP-MSCs simultaneously decreased Th1 cytokine levels and increased Th2 cytokine levels in T lymphocyte cocultures. Finally, paeoniflorin-pretreated OLP-MSCs also promoted the Th1/Th2 balance both in vitro and in the serum of mice that received skin allografts. In conclusion, paeoniflorin enhanced MSC immunomodulation and changed the inflammatory microenvironment via T lymphocytes, suggesting that the improvement of OLP-MSCs is a promising therapeutic approach for OLP.
Characteristics and local risk factors of community-acquired and health-care-associated Staphylococcus aureus pneumonia
Authors: Lee Li-Na , Chou Wen-Ru , Wang Jann-Yuan , Kuo Yen-Liang , Chang Chi-Yueh , Lee Yi-Chien , Tung Shao-Hsien , Tsao Wen-Ching , Chao Ke-Yun , Liu Wei-Lun
Published: November 2022

This study aims at identifying characteristics, risk factors and mortality of community-acquired (CAP) and health-care-associated pneumonia (HCAP) by Staphylococcus aureus (S. aureus). We retrieved adults with S. aureus CAP or HCAP diagnosed by blood or pleural effusion culture in 2.6 years, and compared with those of Streptococcus pneumoniae (S. pneumoniae) CAP or HCAP diagnosed by blood or respiratory culture, or urine antigen. We found 18 patients with CAP and 9 HCAP due to S. aureus (female 33%, 66.6 ± 12.4 years-old), and 48 patients with CAP and 15 HCAP due to S pneumoniae (female 41%, 69.5 ± 17.5 years). Diabetes mellitus (52% vs. 24%, p = 0.019), hemodialysis (11% vs. 0%, p = 0.046), skin lesions (44% vs. 0%, p < 0.001), cavitary nodules (37% vs. 1.6%, p < 0.001) and pleural effusions (48% vs. 18%, p = 0.007) were more common in staphylococcal than pneumococcal group. Three patients with staphylococcal pneumonia had acute myocardial infarction. Pneumonia severity index (139 ± 52 vs. 109 ± 43, p = 0.005) and 30-day mortality (41% vs. 9.5%, p = 0.001) were higher in staphylococcal group. Multivariate analysis showed underlying disease (especially cancer and cirrhosis), risk class 4/5, altered mentality, shock and bilateral pneumonia were risk factors for 30-day mortality.
Element-specific visualization of dynamic magnetic coupling in a Co/Py bilayer microstructure
Authors: Feggeler Thomas , Meckenstock Ralf , Spoddig Detlef , Schöppner Christian , Zingsem Benjamin , Schaffers Taddäus , Ohldag Hendrik , Wende Heiko , Farle Michael , Ney Andreas , Ollefs Katharina
Published: November 2022

We present the element-specific and time resolved visualization of uniform ferromagnetic resonance excitations of a Permalloy (Py) disk–Cobalt (Co) stripe bilayer microstructure. The transverse high frequency component of the resonantly excited magnetization is sampled in the ps regime by a combination of ferromagnetic resonance (FMR) and scanning transmission X-ray microscopy (STXM-FMR) recording snapshots of the local magnetization precession of Py and Co with nanometer spatial resolution. The approach allows us to individually image the resonant dynamic response of each element, and we find that angular momentum is transferred from the Py disk to the Co stripe and vice versa at their respective resonances. The integral (cavity) FMR spectrum of our sample shows an unexpected additional third resonance. This resonance is observed in the STXM-FMR experiments as well. Our microscopic findings suggest that it is governed by magnetic exchange between Py and Co, showing for the Co stripe a difference in relative phase of the magnetization due to stray field influence.
Modulation of mouse laryngeal inflammatory and immune cell responses by low and high doses of mainstream cigarette smoke
Authors: Easwaran Meena , Martinez Joshua D. , Kim Juyong Brian , Erickson-DiRenzo Elizabeth
Published: November 2022

Cigarette smoking is a major risk factor for laryngeal diseases. Despite well-documented cigarette smoke (CS) induced laryngeal histopathological changes, the underlying immunopathological mechanisms remain largely unexplored. The goal of this study was to evaluate inflammatory and immune cell responses in a CS-exposed larynx. Specifically, we used a 4-week subacute whole-body CS inhalation mouse model to assess these responses in the laryngeal mucosa upon exposure to low (LD; 1 h/day) and high dose (HD; 4 h/day) CS. Laryngeal tissues were harvested and evaluated using a 254-plex NanoString inflammation panel and neutrophil/macrophage/T-cell immunohistochemistry (IHC). NanoString global and differential gene expression analysis revealed a unique expression profile only in the HD group, with 26 significant differentially expressed genes (DEGs). StringDB KEGG pathway enrichment analysis revealed the involvement of these DEGs with pro-inflammatory pathways including TNF/TNFα and IL-17. Furthermore, inflammatory responses remained inhibited in conjunction with predicted activated states of anti-inflammatory regulators like PPARγ and NFE2L2 upon Ingenuity Pathway Analysis (IPA). Subglottic T-cell levels remained significantly inhibited as corroborated by IPA predictions. Overall, our key findings are consistent with HD exposures being anti-inflammatory and immunosuppressive. Furthermore, the identification of important regulatory genes and enriched pathways may help improve clinical interventions for CS-induced laryngeal diseases.
Effect of the high voltage waveform on the ionic wind produced by a needle-to-plate dielectric barrier discharge
Authors: Moreau Eric , Defoort Etienne
Published: November 2022

Although corona discharges are used in many industrial applications because of their ability to produce chemical species, the ionic wind they induce is less known and often ignored. Therefore, the present study aims at investigating the ionic wind produced by a corona discharge ignited between a high voltage needle and a grounded plate electrode covered by a dielectric material. More specifically, the work focuses on the influence of the high voltage waveform on the temporal behavior of the ionic wind. The results highlight that the high voltage waveform plays a key role on the dynamics of the flow produced inside the discharge. On the one hand, for the sine, triangle and sawtooth waveforms, there is a flow acceleration during both the positive and the negative half-cycles, the positive discharge being more effective in velocity production. On the other hand, for the square waveform, the increase in velocity occurs during the rises and falls of the voltage, because of the strengthening of the electric field due to the ions remaining from the previous half-cycle at the wall of the dielectric material.
Ultrafast inactivation of SARS-CoV-2 with 266 nm lasers
Authors: Sun Kexiong , Niu Gang , Zhang Yanfang , Yang Juan , Zhang Danna , Wu Han , Shao Xinyu , Ma Xiuquan
Published: November 2022

Disinfection eliminates pathogenic microorganisms and ensures a biosafe environment for human beings. The rapid spread of COVID-19 is challenging traditional disinfection methods in terms of reducing harmful side effects and conducting faster processes. Spraying large-scale chemical disinfectants is harmful to individuals and the environment, while UV lamp and light-emitting diode (LED) disinfection still requires a long exposure time due to the low irradiance and highly divergent beam characteristics. Given that a laser maintains a high irradiance over a long distance, we studied the effectiveness of lasers as a new disinfection method, and the results show the capability for ultrafast inactivation of SARS-CoV-2 virus with a 266 nm laser. This work confirms UV lasers as a good candidate for disinfection.
Assessing the feasibility of mapping the tibialis anterior muscle with navigated transcranial magnetic stimulation in neuro-oncologic patients
Authors: Eibl Thomas , Schrey Michael , Weigel Jens , Liebert Adrian , Lange Rüdiger , Städt Michael , Eff Florian , Holtmannspötter Markus , Steiner Hans-Herbert
Published: November 2022

Mapping the lower extremity with navigated transcranial magnetic stimulation (nTMS) still remains challenging for the investigator. Clinical factors influencing leg mapping with nTMS have not been fully investigated yet. The aim of the study was to identify factors which influence the possibility of eliciting motor evoked potentials (MEPs) from the tibialis anterior muscle (TA). Patient records, imaging, nTMS examinations and tractography were retrospectively evaluated. 48 nTMS examinations were performed in 46 brain tumor patients. Reproducible MEPs were recorded in 20 patients (41.67%). Younger age (p = 0.044) and absence of perifocal edema (p = 0.035, Cramer’s V = 0.34, OR = 0.22, 95% CI = 0.06–0.81) facilitated mapping the TA muscle. Leg motor deficit (p = 0.49, Cramer’s V = 0.12, OR = 0.53, 95%CI = 0.12–2.36), tumor entity (p = 0.36, Cramer’s V = 0.22), tumor location (p = 0.52, Cramer’s V = 0.26) and stimulation intensity (p = 0.158) were no significant factors. The distance between the tumor and the pyramidal tract was higher (p = 0.005) in patients with successful mapping of the TA. The possibility to stimulate the leg motor area was associated with no postoperative aggravation of motor deficits in general (p = 0.005, Cramer’s V = 0.45, OR = 0.63, 95%CI = 0.46–0.85) but could not serve as a specific predictor of postoperative lower extremity function. In conclusion, successful mapping of the TA muscle for neurosurgical planning is influenced by young patient age, absence of edema and greater distance to the CST, whereas tumor entity and stimulation intensity were non-significant.
A mitophagy-related gene signature associated with prognosis and immune microenvironment in colorectal cancer
Authors: Zhang Cong , Zeng Cailing , Xiong Shaoquan , Zhao Zewei , Wu Guoyu
Published: November 2022

Colorectal cancer (CRC) is a heterogeneous disease and one of the most prevalent malignancies worldwide. Previous research has demonstrated that mitophagy is crucial to developing colorectal cancer. This study aims to examine the association between mitophagy-related genes and the prognosis of CRC patients. Gene expression profiles and clinical information of CRC patients were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Univariate Cox regression and the least absolute shrinkage and selection operator (LASSO) regression analysis were applied to establish a prognostic signature using mitophagy related genes. Kaplan–Meier and receiver operating characteristic (ROC) curves were used to analyze patient survival and predictive accuracy. Meanwhile, we also used the Genomics of Drug Sensitivity in Cancer (GDSC) database and Tumor Immune Dysfunction and Exclusion (TIDE) algorithm to estimate the sensitivity of chemotherapy, targeted therapy and immunotherapy. ATG14 overexpression plasmid was used to regulate the ATG14 expression level in HCT116 and SW480 cell lines, and cell counting kit-8, colony formation and transwell migration assay were performed to validate the function of ATG14 in CRC cells. A total of 22 mitophagy-driven genes connected with CRC survival were identified, and then a novel prognostic signature was established based on 10 of them (AMBRA1, ATG14, MAP1LC3A, MAP1LC3B, OPTN, VDAC1, ATG5, CSNK2A2, MFN1, TOMM22). Patients were divided into high-risk and low-risk groups based on the median risk score, and the survival of patients in the high-risk group was significantly shorter in both the training cohort and two independent cohorts. ROC curve showed that the area under the curves (AUC) of 1-, 3- and 5-year survival were 0.66, 0.66 and 0.64, respectively. Multivariate Cox regression analysis confirmed the independent prognostic value of the signature. Then we constructed a Nomogram combining the risk score, age and M stage, which had a concordance index of survival prediction of 0.77 (95% CI 0.71–0.83) and more robust predictive accuracy. Results showed that CD8+ T cells, regulatory T cells and activated NK cells were significantly more enriched in the high-risk group. Furthermore, patients in the high-risk group are more sensitive to targeted therapy or chemotherapy, including bosutinib, elesclomol, lenalidomide, midostaurin, pazopanib and sunitinib, while the low-risk group is more likely to benefit from immunotherapy. Finally, in vitro study confirmed the oncogenic significance of ATG14 in both HCT116 and SW480 cells, whose overexpression increased CRC cell proliferation, colony formation, and migration. In conclusion, we developed a novel mitophagy-related gene signature that can be utilized not only as an independent predictive biomarker but also as a tool for tailoring personalizing treatment for CRC patients, and we confirmed ATG14 as a novel oncogene in CRC.
Evolution of direct reciprocity in group-structured populations
Authors: Murase Yohsuke , Hilbe Christian , Baek Seung Ki
Published: November 2022

People tend to have their social interactions with members of their own community. Such group-structured interactions can have a profound impact on the behaviors that evolve. Group structure affects the way people cooperate, and how they reciprocate each other’s cooperative actions. Past work has shown that population structure and reciprocity can both promote the evolution of cooperation. Yet the impact of these mechanisms has been typically studied in isolation. In this work, we study how the two mechanisms interact. Using a game-theoretic model, we explore how people engage in reciprocal cooperation in group-structured populations, compared to well-mixed populations of equal size. In this model, the population is subdivided into groups. Individuals engage in pairwise interactions within groups while they also have chances to imitate strategies outside the groups. To derive analytical results, we focus on two scenarios. In the first scenario, we assume a complete separation of time scales. Mutations are rare compared to between-group comparisons, which themselves are rare compared to within-group comparisons. In the second scenario, there is a partial separation of time scales, where mutations and between-group comparisons occur at a comparable rate. In both scenarios, we find that the effect of population structure depends on the benefit of cooperation. When this benefit is small, group-structured populations are more cooperative. But when the benefit is large, well-mixed populations result in more cooperation. Overall, our results reveal how group structure can sometimes enhance and sometimes suppress the evolution of cooperation.
Nutritional value and antioxidant capacity of organic and conventional vegetables of the genus Allium
Authors: Czech Anna , Szmigielski Marek , Sembratowicz Iwona
Published: November 2022

There are indications that organically grown plants are safer for health and have higher antioxidant content than conventional ones. Vegetables of the genus Allium L. are a valuable source of health-promoting substances, including compounds with antioxidant properties. The aim of the study was to compare the antioxidant potential and nutritional value of four species of Allium L. vegetables obtained from organic and conventional production: garlic, leek and red and yellow onion. Their proximate and mineral composition were determined, as well as the content of bioactive substances and antioxidant potential. The study showed that the cultivation method significantly influenced the parameters tested. Comparison of organic vegetables with conventional ones in terms of content of dry matter, crude protein and crude fibre revealed no general trend indicating the superiority of one method over the other. However, all organic vegetables analysed were more abundant in minerals (Ca, Mg, Fe, Zn, Cu and Mn) and bioactive compounds. They also exhibited higher antioxidant capacity as measured by the FRAP and DPPH. tests. Their consumption (especially organic garlic and leek) may therefore strengthen the body's natural antioxidant defences and is beneficial for health.
Isotope effects observed in diluted D2O/H2O mixtures identify HOD-induced low-density structures in D2O but not H2O
Authors: Stefaniuk Anna , Gawinkowski Sylwester , Golec Barbara , Gorski Aleksander , Szutkowski Kosma , Waluk Jacek , Poznański Jarosław
Published: November 2022

Normal and heavy water are solvents most commonly used to study the isotope effect. The isotope effect of a solvent significantly influences the behavior of a single molecule in a solution, especially when there are interactions between the solvent and the solute. The influence of the isotope effect becomes more significant in D2O/H2O since the hydrogen bond in H2O is slightly weaker than its counterpart (deuterium bond) in D2O. Herein, we characterize the isotope effect in a mixture of normal and heavy water on the solvation of a HOD molecule. We show that the HOD molecule affects the proximal solvent molecules, and these disturbances are much more significant in heavy water than in normal water. Moreover, in D2O, we observe the formation of low-density structures indicative of an ordering of the solvent around the HOD molecule. The qualitative differences between HOD interaction with D2O and H2O were consistently confirmed with Raman spectroscopy and NMR diffusometry.
Exciton-polarons in the presence of strongly correlated electronic states in a MoSe2/WSe2 moiré superlattice
Authors: Campbell Aidan J. , Brotons-Gisbert Mauro , Baek Hyeonjun , Vitale Valerio , Taniguchi Takashi , Watanabe Kenji , Lischner Johannes , Gerardot Brian D.
Published: November 2022

Two-dimensional moiré materials provide a highly tunable platform to investigate strongly correlated electronic states. Such emergent many-body phenomena can be optically probed in moiré systems created by stacking two layers of transition metal dichalcogenide semiconductors: optically injected excitons can interact with itinerant carriers occupying narrow moiré bands to form exciton-polarons sensitive to strong correlations. Here, we investigate the behaviour of excitons dressed by a Fermi sea localised by the moiré superlattice of a molybdenum diselenide (MoSe2)/tungsten diselenide (WSe2) twisted hetero-bilayer. At a multitude of fractional fillings of the moiré lattice, we observe ordering of both electrons and holes into stable correlated electronic states. Magneto-optical measurements reveal extraordinary Zeeman splittings of the exciton-polarons due to exchange interactions in the correlated hole phases, with a maximum close to the correlated state at one hole per site. The temperature dependence of the Zeeman splitting reveals antiferromagnetic ordering of the correlated holes across a wide range of fractional fillings. Our results illustrate the nature of exciton-polarons in the presence of strongly correlated electronic states and reveal the rich potential of the MoSe2/WSe2 platform for investigations of Fermi–Hubbard and Bose–Hubbard physics.
Relay and higher-order thalamic nuclei show an intertwined functional association with cortical-networks
Authors: Kumar Vinod Jangir , Beckmann Christian F. , Scheffler Klaus , Grodd Wolfgang
Published: November 2022

Almost all functional processing in the cortex strongly depends on thalamic interactions. However, in terms of functional interactions with the cerebral cortex, the human thalamus nuclei still partly constitute a terra incognita. Hence, for a deeper understanding of thalamic-cortical cooperation, it is essential to know how the different thalamic nuclei are associated with cortical networks. The present work examines network-specific connectivity and task-related topical mapping of cortical areas with the thalamus. The study finds that the relay and higher-order thalamic nuclei show an intertwined functional association with different cortical networks. In addition, the study indicates that relay-specific thalamic nuclei are not only involved with relay-specific behavior but also in higher-order functions. The study enriches our understanding of interactions between large-scale cortical networks and the thalamus, which may interest a broader audience in neuroscience and clinical research.
Antigenic mapping reveals sites of vulnerability on α-HCoV spike protein
Authors: Xiang Jiangchao , Su Jie , Lan Qiaoshuai , Zhao Wenwen , Zhou Yu , Xu Youwei , Niu Jun , Xia Shuai , Qi Qilian , Sidhu Sachdev , Lu Lu , Miersch Shane , Yang Bei
Published: November 2022

Understanding the antigenic signatures of all human coronaviruses (HCoVs) Spike (S) proteins is imperative for pan-HCoV epitopes identification and broadly effective vaccine development. To depict the currently elusive antigenic signatures of α-HCoVs S proteins, we isolated a panel of antibodies against the HCoV-229E S protein and characterized their epitopes and neutralizing potential. We found that the N-terminal domain of HCoV-229E S protein is antigenically dominant wherein an antigenic supersite is present and appears conserved in HCoV-NL63, which holds potential to serve as a pan-α-HCoVs epitope. In the receptor binding domain, a neutralizing epitope is captured in the end distal to the receptor binding site, reminiscent of the locations of the SARS-CoV-2 RBD cryptic epitopes. We also identified a neutralizing antibody that recognizes the connector domain, thus representing the first S2-directed neutralizing antibody against α-HCoVs. The unraveled HCoVs S proteins antigenic similarities and variances among genera highlight the challenges faced by pan-HCoV vaccine design while supporting the feasibility of broadly effective vaccine development against a subset of HCoVs.
Hemocytes in Drosophila melanogaster embryos move via heterogeneous anomalous diffusion
Authors: Korabel Nickolay , Clemente Giuliana D. , Han Daniel , Feldman Felix , Millard Tom H. , Waigh Thomas Andrew
Published: November 2022

Drosophila melanogaster hemocytes are highly motile cells that are crucial for successful embryogenesis and have important roles in the organism’s immunological response. Here we measure the motion of hemocytes using selective plane illumination microscopy. Every hemocyte cell in one half of an embryo is tracked during embryogenesis and analysed using a deep learning neural network. We show that the anomalous transport of the cells is well described by fractional Brownian motion that is heterogeneous in both time and space. LanB1 and SCAR mutants disrupt the collective cellular motion and reduce its persistence due to the modification of laminin and actin-based motility respectively. The anomalous motility of the hemocytes oscillated in time with alternating periods of varying persistent motion. Touching hemocytes appear to experience synchronised contact inhibition of locomotion. A quantitative statistical framework is presented for hemocyte motility which provides biological insights.