bluuebunny/crossref_metadata_2025 huggingface dataset:
Antibiotics in the clinical pipeline as of December 2022
Authors: Butler Mark S. , Henderson Ian R. , Capon Robert J. , Blaskovich Mark A. T.
Published: June 2023

The need for new antibacterial drugs to treat the increasing global prevalence of drug-resistant bacterial infections has clearly attracted global attention, with a range of existing and upcoming funding, policy, and legislative initiatives designed to revive antibacterial R&D. It is essential to assess whether these programs are having any real-world impact and this review continues our systematic analyses that began in 2011. Direct-acting antibacterials (47), non-traditional small molecule antibacterials (5), and β-lactam/β-lactamase inhibitor combinations (10) under clinical development as of December 2022 are described, as are the three antibacterial drugs launched since 2020. Encouragingly, the increased number of early-stage clinical candidates observed in the 2019 review increased in 2022, although the number of first-time drug approvals from 2020 to 2022 was disappointingly low. It will be critical to monitor how many Phase-I and -II candidates move into Phase-III and beyond in the next few years. There was also an enhanced presence of novel antibacterial pharmacophores in early-stage trials, and at least 18 of the 26 phase-I candidates were targeted to treat Gram-negative bacteria infections. Despite the promising early-stage antibacterial pipeline, it is essential to maintain funding for antibacterial R&D and to ensure that plans to address late-stage pipeline issues succeed.
Patterns in soil microbial diversity across Europe
Authors: Labouyrie Maëva , Ballabio Cristiano , Romero Ferran , Panagos Panos , Jones Arwyn , Schmid Marc W. , Mikryukov Vladimir , Dulya Olesya , Tedersoo Leho , Bahram Mohammad , Lugato Emanuele , van der Heijden Marcel G. A. , Orgiazzi Alberto
Published: June 2023

Factors driving microbial community composition and diversity are well established but the relationship with microbial functioning is poorly understood, especially at large scales. We analysed microbial biodiversity metrics and distribution of potential functional groups along a gradient of increasing land-use perturbation, detecting over 79,000 bacterial and 25,000 fungal OTUs in 715 sites across 24 European countries. We found the lowest bacterial and fungal diversity in less-disturbed environments (woodlands) compared to grasslands and highly-disturbed environments (croplands). Highly-disturbed environments contain significantly more bacterial chemoheterotrophs, harbour a higher proportion of fungal plant pathogens and saprotrophs, and have less beneficial fungal plant symbionts compared to woodlands and extensively-managed grasslands. Spatial patterns of microbial communities and predicted functions are best explained when interactions among the major determinants (vegetation cover, climate, soil properties) are considered. We propose guidelines for environmental policy actions and argue that taxonomical and functional diversity should be considered simultaneously for monitoring purposes.
Integrated quantum optical phase sensor in thin film lithium niobate
Authors: Stokowski Hubert S. , McKenna Timothy P. , Park Taewon , Hwang Alexander Y. , Dean Devin J. , Celik Oguz Tolga , Ansari Vahid , Fejer Martin M. , Safavi-Naeini Amir H.
Published: June 2023

The quantum noise of light, attributed to the random arrival time of photons from a coherent light source, fundamentally limits optical phase sensors. An engineered source of squeezed states suppresses this noise and allows phase detection sensitivity beyond the quantum noise limit (QNL). We need ways to use quantum light within deployable quantum sensors. Here we present a photonic integrated circuit in thin-film lithium niobate that meets these requirements. We use the second-order nonlinearity to produce a squeezed state at the same frequency as the pump light and realize circuit control and sensing with electro-optics. Using 26.2 milliwatts of optical power, we measure (2.7 ± 0.2)% squeezing and apply it to increase the signal-to-noise ratio of phase measurement. We anticipate that photonic systems like this, which operate with low power and integrate all of the needed functionality on a single die, will open new opportunities for quantum optical sensing.
Transcriptional control of pancreatic cancer immunosuppression by metabolic enzyme CD73 in a tumor-autonomous and -autocrine manner
Authors: Tang Tianyu , Huang Xing , Lu Minghao , Zhang Gang , Han Xu , Liang Tingbo
Published: June 2023

Cancer cell metabolism contributes to the establishment of an immunosuppressive tumor microenvironment. Aberrant expression of CD73, a critical enzyme in ATP metabolism, on the cell surface results in the extracellular accumulation of adenosine, which exhibits direct inhibitory effects on tumor-infiltrating lymphocytes. However, little is known about the influence of CD73 on negative immune regulation-associated signaling molecules and transduction pathways inside tumor cells. This study aims to demonstrate the moonlighting functions of CD73 in immunosuppression in pancreatic cancer, an ideal model characterized by complex crosstalk among cancer metabolism, immune microenvironment, and immunotherapeutic resistance. The synergistic effect of CD73-specific drugs in combination with immune checkpoint blockade is observed in multiple pancreatic cancer models. Cytometry by time-of-flight analysis shows that CD73 inhibition reduces tumor-infiltrating Tregs in pancreatic cancer. Tumor cell-autonomous CD73 is found to facilitate Treg recruitment, in which CCL5 is identified as a significant downstream effector of CD73 using integrated proteomic and transcriptomic analyses. CD73 transcriptionally upregulates CCL5 through tumor cell-autocrine adenosine–Adora2a signaling-mediated activation of the p38–STAT1 axis, recruiting Tregs to pancreatic tumors and causing an immunosuppressive microenvironment. Together, this study highlights that CD73–adenosine metabolism transcriptionally controls pancreatic cancer immunosuppression in a tumor-autonomous and -autocrine manner.
Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates
Authors: Chen Xinhong , Wolfe Damien A. , Bindu Dhanesh Sivadasan , Zhang Mengying , Taskin Naz , Goertsen David , Shay Timothy F. , Sullivan Erin E. , Huang Sheng-Fu , Ravindra Kumar Sripriya , Arokiaraj Cynthia M. , Plattner Viktor M. , Campos Lillian J. , Mich John K. , Monet Deja , Ngo Victoria , Ding Xiaozhe , Omstead Victoria , Weed Natalie , Bishaw Yeme , Gore Bryan B. , Lein Ed S. , Akrami Athena , Miller Cory , Levi Boaz P. , Keller Annika , Ting Jonathan T. , Fox Andrew S. , Eroglu Cagla , Gradinaru Viviana
Published: June 2023

Delivering genes to and across the brain vasculature efficiently and specifically across species remains a critical challenge for addressing neurological diseases. We have evolved adeno-associated virus (AAV9) capsids into vectors that transduce brain endothelial cells specifically and efficiently following systemic administration in wild-type mice with diverse genetic backgrounds, and in rats. These AAVs also exhibit superior transduction of the CNS across non-human primates (marmosets and rhesus macaques), and in ex vivo human brain slices, although the endothelial tropism is not conserved across species. The capsid modifications translate from AAV9 to other serotypes such as AAV1 and AAV-DJ, enabling serotype switching for sequential AAV administration in mice. We demonstrate that the endothelial-specific mouse capsids can be used to genetically engineer the blood-brain barrier by transforming the mouse brain vasculature into a functional biofactory. We apply this approach to Hevin knockout mice, where AAV-X1-mediated ectopic expression of the synaptogenic protein Sparcl1/Hevin in brain endothelial cells rescued synaptic deficits.
Fertilization controls tiller numbers via transcriptional regulation of a MAX1-like gene in rice cultivation
Authors: Cui Jinying , Nishide Noriko , Mashiguchi Kiyoshi , Kuroha Kana , Miya Masayuki , Sugimoto Kazuhiko , Itoh Jun-Ichi , Yamaguchi Shinjiro , Izawa Takeshi
Published: June 2023

Fertilization controls various aspects of cereal growth such as tiller number, leaf size, and panicle size. However, despite such benefits, global chemical fertilizer use must be reduced to achieve sustainable agriculture. Here, based on field transcriptome data from leaf samples collected during rice cultivation, we identify fertilizer responsive genes and focus on Os1900, a gene orthologous to Arabidopsis thaliana MAX1, which is involved in strigolactone biosynthesis. Elaborate genetic and biochemical analyses using CRISPR/Cas9 mutants reveal that Os1900 together with another MAX1-like gene, Os5100, play a critical role in controlling the conversion of carlactone into carlactonoic acid during strigolactone biosynthesis and tillering in rice. Detailed analyses of a series of Os1900 promoter deletion mutations suggest that fertilization controls tiller number in rice through transcriptional regulation of Os1900, and that a few promoter mutations alone can increase tiller numbers and grain yields even under minor-fertilizer conditions, whereas a single defective os1900 mutation does not increase tillers under normal fertilizer condition. Such Os1900 promoter mutations have potential uses in breeding programs for sustainable rice production.
Reassessment of growth-climate relations indicates the potential for decline across Eurasian boreal larch forests
Authors: Li Wenqing , Manzanedo Rubén D. , Jiang Yuan , Ma Wenqiu , Du Enzai , Zhao Shoudong , Rademacher Tim , Dong Manyu , Xu Hui , Kang Xinyu , Wang Jun , Wu Fang , Cui Xuefeng , Pederson Neil
Published: June 2023

Larch, a widely distributed tree in boreal Eurasia, is experiencing rapid warming across much of its distribution. A comprehensive assessment of growth on warming is needed to comprehend the potential impact of climate change. Most studies, relying on rigid calendar-based temperature series, have detected monotonic responses at the margins of boreal Eurasia, but not across the region. Here, we developed a method for constructing temporally flexible and physiologically relevant temperature series to reassess growth-temperature relations of larch across boreal Eurasia. Our method appears more effective in assessing the impact of warming on growth than previous methods. Our approach indicates widespread and spatially heterogeneous growth-temperature responses that are driven by local climate. Models quantifying these results project that the negative responses of growth to temperature will spread northward and upward throughout this century. If true, the risks of warming to boreal Eurasia could be more widespread than conveyed from previous works.
ALPL-1 is a target for chimeric antigen receptor therapy in osteosarcoma
Authors: Mensali Nadia , Köksal Hakan , Joaquina Sandy , Wernhoff Patrik , Casey Nicholas P. , Romecin Paola , Panisello Carla , Rodriguez René , Vimeux Lene , Juzeniene Asta , Myhre Marit R. , Fåne Anne , Ramírez Carolina Castilla , Maggadottir Solrun Melkorka , Duru Adil Doganay , Georgoudaki Anna-Maria , Grad Iwona , Maturana Andrés Daniel , Gaudernack Gustav , Kvalheim Gunnar , Carcaboso Angel M. , de Alava Enrique , Donnadieu Emmanuel , Bruland Øyvind S. , Menendez Pablo , Inderberg Else Marit , Wälchli Sébastien
Published: June 2023

Osteosarcoma (OS) remains a dismal malignancy in children and young adults, with poor outcome for metastatic and recurrent disease. Immunotherapies in OS are not as promising as in some other cancer types due to intra-tumor heterogeneity and considerable off-target expression of the potentially targetable proteins. Here we show that chimeric antigen receptor (CAR) T cells could successfully target an isoform of alkaline phosphatase, ALPL-1, which is highly and specifically expressed in primary and metastatic OS. The target recognition element of the second-generation CAR construct is based on two antibodies, previously shown to react against OS. T cells transduced with these CAR constructs mediate efficient and effective cytotoxicity against ALPL-positive cells in in vitro settings and in state-of-the-art in vivo orthotopic models of primary and metastatic OS, without unexpected toxicities against hematopoietic stem cells or healthy tissues. In summary, CAR-T cells targeting ALPL-1 show efficiency and specificity in treating OS in preclinical models, paving the path for clinical translation.
Pluripotency-independent induction of human trophoblast stem cells from fibroblasts
Authors: Naama Moriyah , Rahamim Moran , Zayat Valery , Sebban Shulamit , Radwan Ahmed , Orzech Dana , Lasry Rachel , Ifrah Annael , Jaber Mohammad , Sabag Ofra , Yassen Hazar , Khatib Areej , Epsztejn-Litman Silvina , Novoselsky-Persky Michal , Makedonski Kirill , Deri Noy , Goldman-Wohl Debra , Cedar Howard , Yagel Simcha , Eiges Rachel , Buganim Yosef
Published: June 2023

Human trophoblast stem cells (hTSCs) can be derived from embryonic stem cells (hESCs) or be induced from somatic cells by OCT4, SOX2, KLF4 and MYC (OSKM). Here we explore whether the hTSC state can be induced independently of pluripotency, and what are the mechanisms underlying its acquisition. We identify GATA3, OCT4, KLF4 and MYC (GOKM) as a combination of factors that can generate functional hiTSCs from fibroblasts. Transcriptomic analysis of stable GOKM- and OSKM-hiTSCs reveals 94 hTSC-specific genes that are aberrant specifically in OSKM-derived hiTSCs. Through time-course-RNA-seq analysis, H3K4me2 deposition and chromatin accessibility, we demonstrate that GOKM exert greater chromatin opening activity than OSKM. While GOKM primarily target hTSC-specific loci, OSKM mainly induce the hTSC state via targeting hESC and hTSC shared loci. Finally, we show that GOKM efficiently generate hiTSCs from fibroblasts that harbor knockout for pluripotency genes, further emphasizing that pluripotency is dispensable for hTSC state acquisition.
Pregnane X receptor agonist nomilin extends lifespan and healthspan in preclinical models through detoxification functions
Authors: Fan Shengjie , Yan Yingxuan , Xia Ying , Zhou Zhenyu , Luo Lingling , Zhu Mengnan , Han Yongli , Yao Deqiang , Zhang Lijun , Fang Minglv , Peng Lina , Yu Jing , Liu Ying , Gao Xiaoyan , Guan Huida , Li Hongli , Wang Changhong , Wu Xiaojun , Zhu Huanhu , Cao Yu , Huang Cheng
Published: June 2023

Citrus fruit has long been considered a healthy food, but its role and detailed mechanism in lifespan extension are not clear. Here, by using the nematode C. elegans, we identified that nomilin, a bitter-taste limoloid that is enriched in citrus, significantly extended the animals’ lifespan, healthspan, and toxin resistance. Further analyses indicate that this ageing inhibiting activity depended on the insulin-like pathway DAF-2/DAF-16 and nuclear hormone receptors NHR-8/DAF-12. Moreover, the human pregnane X receptor (hPXR) was identified as the mammalian counterpart of NHR-8/DAF-12 and X-ray crystallography showed that nomilin directly binds with hPXR. The hPXR mutations that prevented nomilin binding blocked the activity of nomilin both in mammalian cells and in C. elegans. Finally, dietary nomilin supplementation improved healthspan and lifespan in D-galactose- and doxorubicin-induced senescent mice as well as in male senescence accelerated mice prone 8 (SAMP8) mice, and induced a longevity gene signature similar to that of most longevity interventions in the liver of bile-duct-ligation male mice. Taken together, we identified that nomilin may extend lifespan and healthspan in animals via the activation of PXR mediated detoxification functions.
Template-jumping prime editing enables large insertion and exon rewriting in vivo
Authors: Zheng Chunwei , Liu Bin , Dong Xiaolong , Gaston Nicholas , Sontheimer Erik J. , Xue Wen
Published: June 2023

Targeted insertion of large DNA fragments holds promise for genome engineering and gene therapy. Prime editing (PE) effectively inserts short (<50 bp) sequences. Employing paired prime editing guide RNAs (pegRNAs) has enabled PE to better mediate relatively large insertions in vitro, but the efficiency of larger insertions (>400 bp) remains low and in vivo application has not been demonstrated. Inspired by the efficient genomic insertion mechanism of retrotransposons, we develop a template-jumping (TJ) PE approach for the insertion of large DNA fragments using a single pegRNA. TJ-pegRNA harbors the insertion sequence as well as two primer binding sites (PBSs), with one PBS matching a nicking sgRNA site. TJ-PE precisely inserts 200 bp and 500 bp fragments with up to 50.5 and 11.4% efficiency, respectively, and enables GFP (~800 bp) insertion and expression in cells. We transcribe split circular TJ-petRNA in vitro via a permuted group I catalytic intron for non-viral delivery in cells. Finally, we demonstrate that TJ-PE can rewrite an exon in the liver of tyrosinemia I mice to reverse the disease phenotype. TJ-PE has the potential to insert large DNA fragments without double-stranded DNA breaks and facilitate mutation hotspot exon rewriting in vivo.
Absence of critical thickness for polar skyrmions with breaking the Kittel’s law
Authors: Gong Feng-Hui , Tang Yun-Long , Wang Yu-Jia , Chen Yu-Ting , Wu Bo , Yang Li-Xin , Zhu Yin-Lian , Ma Xiu-Liang
Published: June 2023

The period of polar domain (d) in ferroics was commonly believed to scale with corresponding film thicknesses (h), following the classical Kittel’s law of d ∝ $$\sqrt{h}$$

h

. Here, we have not only observed that this relationship fails in the case of polar skyrmions, where the period shrinks nearly to a constant value, or even experiences a slight increase, but also discovered that skyrmions have further persisted in [(PbTiO3)2/(SrTiO3)2]10 ultrathin superlattices. Both experimental and theoretical results indicate that the skyrmion periods (d) and PbTiO3 layer thicknesses in superlattice (h) obey the hyperbolic function of d = Ah + $$\frac{{{\mbox{B}}}}{h}$$

B

h

other than previous believed, simple square root law. Phase-field analysis indicates that the relationship originates from the different energy competitions of the superlattices with PbTiO3 layer thicknesses. This work exemplified the critical size problems faced by nanoscale ferroelectric device designing in the post-Moore era.
A synthetic dataset of Danish residential electricity prosumers
Authors: Yuan Rui , Pourmousavi S. Ali , Soong Wen L. , Black Andrew J. , Liisberg Jon A. R. , Lemos-Vinasco Julian
Published: June 2023

Conventional residential electricity consumers are becoming prosumers who not only consume electricity but also produce it. This shift is expected to occur over the next few decades at a large scale, and it presents numerous uncertainties and risks for the operation, planning, investment, and viable business models of the electricity grid. To prepare for this shift, researchers, utilities, policymakers, and emerging businesses require a comprehensive understanding of future prosumers’ electricity consumption. Unfortunately, there is a limited amount of data available due to privacy concerns and the slow adoption of new technologies such as battery electric vehicles and home automation. To address this issue, this paper introduces a synthetic dataset containing five types of residential prosumers’ imported and exported electricity data. The dataset was developed using real traditional consumers’ data from Denmark, PV generation data from the global solar energy estimator (GSEE) model, electric vehicle (EV) charging data generated using package, a residential energy storage system (ESS) operator and a generative adversarial network (GAN) based model to produce synthetic data. The quality of the dataset was assessed and validated through qualitative inspection and three methods: empirical statistics, metrics based on information theory, and evaluation metrics based on machine learning techniques.
Carbon Monitor Europe near-real-time daily CO2 emissions for 27 EU countries and the United Kingdom
Authors: Ke Piyu , Deng Zhu , Zhu Biqing , Zheng Bo , Wang Yilong , Boucher Olivier , Arous Simon Ben , Zhou Chuanlong , Andrew Robbie M. , Dou Xinyu , Sun Taochun , Song Xuanren , Li Zhao , Yan Feifan , Cui Duo , Hu Yifan , Huo Da , Chang Jean-Pierre , Engelen Richard , Davis Steven J. , Ciais Philippe , Liu Zhu
Published: June 2023

With the urgent need to implement the EU countries pledges and to monitor the effectiveness of Green Deal plan, Monitoring Reporting and Verification tools are needed to track how emissions are changing for all the sectors. Current official inventories only provide annual estimates of national CO2 emissions with a lag of 1+ year which do not capture the variations of emissions due to recent shocks including COVID lockdowns and economic rebounds, war in Ukraine. Here we present a near-real-time country-level dataset of daily fossil fuel and cement emissions from January 2019 through December 2021 for 27 EU countries and UK, which called Carbon Monitor Europe. The data are calculated separately for six sectors: power, industry, ground transportation, domestic aviation, international aviation and residential. Daily CO2 emissions are estimated from a large set of activity data compiled from different sources. The goal of this dataset is to improve the timeliness and temporal resolution of emissions for European countries, to inform the public and decision makers about current emissions changes in Europe.
Bioinformatics and system biology approach to identify potential common pathogenesis for COVID-19 infection and osteoarthritis
Authors: Chen Ziyi , Wang Wenjuan , Jue Hao , Hua Yinghui
Published: June 2023

A growing of evidence has showed that patients with osteoarthritis (OA) had a higher coronavirus 2019 (COVID-19) infection rate and a poorer prognosis after infected it. Additionally, scientists have also discovered that COVID-19 infection might cause pathological changes in the musculoskeletal system. However, its mechanism is still not fully elucidated. This study aims to further explore the sharing pathogenesis of patients with both OA and COVID-19 infection and find candidate drugs. Gene expression profiles of OA (GSE51588) and COVID-19 (GSE147507) were obtained from the Gene Expression Omnibus (GEO) database. The common differentially expressed genes (DEGs) for both OA and COVID-19 were identified and several hub genes were extracted from them. Then gene and pathway enrichment analysis of the DEGs were performed; protein–protein interaction (PPI) network, transcription factor (TF)-gene regulatory network, TF-miRNA regulatory network and gene-disease association network were constructed based on the DEGs and hub genes. Finally, we predicted several candidate molecular drugs related to hub genes using DSigDB database. The receiver operating characteristic curve (ROC) was applied to evaluate the accuracy of hub genes in the diagnosis of both OA and COVID-19. In total, 83 overlapping DEGs were identified and selected for subsequent analyses. CXCR4, EGR2, ENO1, FASN, GATA6, HIST1H3H, HIST1H4H, HIST1H4I, HIST1H4K, MTHFD2, PDK1, TUBA4A, TUBB1 and TUBB3 were screened out as hub genes, and some showed preferable values as diagnostic markers for both OA and COVID-19. Several candidate molecular drugs, which are related to the hug genes, were identified. These sharing pathways and hub genes may provide new ideas for further mechanistic studies and guide more individual-based effective treatments for OA patients with COVID-19 infection.
Using machine learning to detect coronaviruses potentially infectious to humans
Authors: Gonzalez-Isunza Georgina , Jawaid M. Zaki , Liu Pengyu , Cox Daniel L. , Vazquez Mariel , Arsuaga Javier
Published: June 2023

Establishing the host range for novel viruses remains a challenge. Here, we address the challenge of identifying non-human animal coronaviruses that may infect humans by creating an artificial neural network model that learns from spike protein sequences of alpha and beta coronaviruses and their binding annotation to their host receptor. The proposed method produces a human-Binding Potential (h-BiP) score that distinguishes, with high accuracy, the binding potential among coronaviruses. Three viruses, previously unknown to bind human receptors, were identified: Bat coronavirus BtCoV/133/2005 and Pipistrellus abramus bat coronavirus HKU5-related (both MERS related viruses), and Rhinolophus affinis coronavirus isolate LYRa3 (a SARS related virus). We further analyze the binding properties of BtCoV/133/2005 and LYRa3 using molecular dynamics. To test whether this model can be used for surveillance of novel coronaviruses, we re-trained the model on a set that excludes SARS-CoV-2 and all viral sequences released after the SARS-CoV-2 was published. The results predict the binding of SARS-CoV-2 with a human receptor, indicating that machine learning methods are an excellent tool for the prediction of host expansion events.
Colour opponency is widespread across the mouse subcortical visual system and differentially targets GABAergic and non-GABAergic neurons
Authors: Feord R. C. , Gomoliszewska A. , Pienaar A. , Mouland J. W. , Brown T. M.
Published: June 2023

Colour vision plays many important roles in animal behaviour but the brain pathways processing colour remain surprisingly poorly understood, including in the most commonly used laboratory mammal, mice. Indeed, particular features of mouse retinal organisation present challenges in defining the mechanisms underlying colour vision in mice and have led to suggestions that this may substantially rely on ‘non-classical’ rod-cone opponency. By contrast, studies using mice with altered cone spectral sensitivity, to facilitate application of photoreceptor-selective stimuli, have revealed widespread cone-opponency across the subcortical visual system. To determine the extent to which such findings are truly reflective of wildtype mouse colour vision, and facilitate neural circuit mapping of colour-processing pathways using intersectional genetic approaches, we here establish and validate stimuli for selectively manipulating excitation of the native mouse S- and M-cone opsin classes. We then use these to confirm the widespread appearance of cone-opponency (> 25% of neurons) across the mouse visual thalamus and pretectum. We further extend these approaches to map the occurrence of colour-opponency across optogenetically identified GABAergic (GAD2-expressing) cells in key non-image forming visual centres (pretectum and intergeniculate leaflet/ventral lateral geniculate; IGL/vLGN). Strikingly, throughout, we find S-ON/M-OFF opponency is specifically enriched in non-GABAergic cells, with identified GABAergic cells in the IGL/VLGN entirely lacking this property. Collectively, therefore, we establish an important new approach for studying cone function in mice, confirming a surprisingly extensive appearance of cone-opponent processing in the mouse visual system and providing new insight into functional specialisation of the pathways processing such signals.
Effect of the 2020 hypersensitivity pneumonitis guideline on the pathologic diagnosis of interstitial pneumonia
Authors: Ozasa Mutsumi , Bychkov Andrey , Zaizen Yoshiaki , Tabata Kazuhiro , Uegami Wataru , Yamano Yasuhiko , Kataoka Kensuke , Johkoh Takeshi , Mukae Hiroshi , Kondoh Yasuhiro , Fukuoka Junya
Published: June 2023

It was reported that the 2020 guideline for hypersensitivity pneumonitis (HP) might result in the overdiagnosis of fibrotic HP (fHP). fHP and other types of interstitial pneumonias have several overlapping characteristics, and a high diagnostic concordance rate of fHP is rarely obtained. Therefore, we investigated the impact of the 2020 HP guideline on the pathological diagnosis of cases previously diagnosed as interstitial pneumonia. We identified 289 fibrotic interstitial pneumonia cases from 2014 to 2019 and classified them into four categories according to the 2020 HP guideline: typical, probable, and indeterminate for fHP and alternative diagnosis. The original pathological diagnosis of 217 cases were compared to their classification as either typical, probable, or indeterminate for fHP according to the 2020 guideline. The clinical data, including serum data and pulmonary function tests, were compared among the groups. Diagnoses changed from non-fHP to fHP for 54 (25%) of the 217 cases, of which, 8 were typical fHP and 46 were probable fHP. The ratio of typical and probable fHP cases to the total number of VATS cases was significantly lower when using transbronchial lung cryobiopsy (p < 0.001). The clinical data of these cases bore a more remarkable resemblance to those diagnosed as indeterminate for fHP than to those diagnosed as typical or probable. The pathological criteria in the new HP guidelines increase the diagnosis of fHP. However, it is unclear whether this increase leads to overdiagnosis, and requires further investigation. Transbronchial lung cryobiopsy may not be helpful when using the new criteria to impart findings for fHP diagnosis.
The mere presence of a smartphone reduces basal attentional performance
Authors: Skowronek Jeanette , Seifert Andreas , Lindberg Sven
Published: June 2023

The smartphone has become an indispensable part of everyday life. It enables endless possibilities and offers persistent access to a multiplicity of entertainment, information, and social contacts. The development towards a greater use and a persistent presence of the smartphone does not only lead to advantages, but also raises potential for negative consequences and a negative influence on attention. In this research, the hypothesis of the mere smartphone presence leading to cognitive costs and a lower attention is being tested. The smartphone may use limited cognitive resources and consequently lead to a lower cognitive performance. To investigate this hypothesis, participants aged 20–34 perform a concentration and attention test in the presence and absence of a smartphone. The results of the conducted experiment imply that the mere presence of a smartphone results in lower cognitive performance, which supports the hypothesis of the smartphone presence using limited cognitive resources. The study as well as the subsequent results and the resulting practical implications are presented and discussed in this paper.
Comparison and fusion prediction model for lung adenocarcinoma with micropapillary and solid pattern using clinicoradiographic, radiomics and deep learning features
Authors: Wang Fen , Wang Cheng-Long , Yi Yin-Qiao , Zhang Teng , Zhong Yan , Zhu Jia-Jia , Li Hai , Yang Guang , Yu Tong-Fu , Xu Hai , Yuan Mei
Published: June 2023

To investigate whether the combination scheme of deep learning score (DL-score) and radiomics can improve preoperative diagnosis in the presence of micropapillary/solid (MPP/SOL) patterns in lung adenocarcinoma (ADC). A retrospective cohort of 514 confirmed pathologically lung ADC in 512 patients after surgery was enrolled. The clinicoradiographic model (model 1) and radiomics model (model 2) were developed with logistic regression. The deep learning model (model 3) was constructed based on the deep learning score (DL-score). The combine model (model 4) was based on DL-score and R-score and clinicoradiographic variables. The performance of these models was evaluated with area under the receiver operating characteristic curve (AUC) and compared using DeLong's test internally and externally. The prediction nomogram was plotted, and clinical utility depicted with decision curve. The performance of model 1, model 2, model 3 and model 4 was supported by AUCs of 0.848, 0.896, 0.906, 0.921 in the Internal validation set, that of 0.700, 0.801, 0.730, 0.827 in external validation set, respectively. These models existed statistical significance in internal validation (model 4 vs model 3, P = 0.016; model 4 vs model 1, P = 0.009, respectively) and external validation (model 4 vs model 2, P = 0.036; model 4 vs model 3, P = 0.047; model 4 vs model 1, P = 0.016, respectively). The decision curve analysis (DCA) demonstrated that model 4 predicting the lung ADC with MPP/SOL structure would be more beneficial than the model 1and model 3 but comparable with the model 2. The combined model can improve preoperative diagnosis in the presence of MPP/SOL pattern in lung ADC in clinical practice.
An improved preparation method for a CuO/CeO2-coated monolith for the CO–PrOx reaction
Authors: Meißner Jan , Ahrens Lara , Pasel Joachim , Schwedt Alexander , Wohlrab Sebastian , Mayer Joachim , Peters Ralf
Published: June 2023

In this study, we present a method for directly coating monoliths with a CeO2/CuO catalyst using the urea-nitrate combustion method. The catalyst was characterized by means of XRD, SEM/EDX, and EPR measurements. Experimental results are described, when this catalyst was used for the preferential oxidation of CO. The catalytic activity for the CO–PrOx-reaction was measured by recording CO conversion as a function of the reaction temperature in a hydrogen-rich gas mixture in the presence and absence of water vapor. In a long-term test of over 310 h, the catalyst’s long-term stability was demonstrated. Direct coating is shown to be a promising approach by which a larger amount of catalyst can be deposited onto the monolith in a single step than would be possible with washcoats.
Ultra-effective modified clinoptilolite adsorbent for selective thorium removal from radioactive residue
Authors: Alotaibi Abdulrahman Masoud , Ismail Aznan Fazli , Aziman Eli Syafiqah
Published: June 2023

This study investigated the efficacy of using phosphate-modified zeolite (PZ) as an adsorbent for removing thorium from aqueous solutions. The effects of various factors such as contact time, adsorbent mass, initial thorium concentration, and pH value of the solution on the removal efficiency were analyzed using the batch technique to obtain optimum adsorption condition. The results revealed that the optimal conditions for thorium adsorption were a contact time of 24 h, 0.03 g of PZ adsorbent, pH 3, and a temperature of 25 °C. Isotherm and kinetics parameters of the thorium adsorption on PZ were also determined, with equilibrium studies showing that the experimental data followed the Langmuir isotherm model. The maximum adsorption capacity (Qo) for thorium was found to be 17.3 mg/g with the Langmuir isotherm coefficient of 0.09 L/mg. Using phosphate anions to modify natural zeolite increased its adsorption capacity. Furthermore, adsorption kinetics studies demonstrated that the adsorption of thorium onto PZ adsorbent fitted well with the pseudo-second-order model. The applicability of the PZ adsorbent in removing thorium from real radioactive waste was also investigated, and nearly complete thorium removal was achieved (> 99%) from the leached solution obtained from cracking and leaching processes of rare earth industrial residue under optimized conditions. This study elucidates the potential of PZ adsorbent for efficient removal of thorium from rare earth residue via adsorption, leading to a reduction in waste volume for ultimate disposition.
RNA activation in ticks
Authors: Kwofie Kofi Dadzie , Hernandez Emmanuel Pacia , Anisuzzaman  , Kawada Hayato , Koike Yuki , Sasaki Sana , Inoue Takahiro , Jimbo Kei , Mikami Fusako , Ladzekpo Danielle , Umemiya-Shirafuji Rika , Yamaji Kayoko , Tanaka Tetsuya , Matsubayashi Makoto , Alim Md Abdul , Dadzie Samuel Kweku , Iwanaga Shiroh , Tsuji Naotoshi , Hatta Takeshi
Published: June 2023

RNA activation (RNAa) is a burgeoning area of research in which double-stranded RNAs (dsRNAs) or small activating RNAs mediate the upregulation of specific genes by targeting the promoter sequence and/or AU-rich elements in the 3′- untranslated region (3’-UTR) of mRNA molecules. So far, studies on the phenomenon have been limited to mammals, plants, bacteria, Caenorhabditis elegans, and recently, Aedes aegypti. However, it is yet to be applied in other arthropods, including ticks, despite the ubiquitous presence of argonaute 2 protein, which is an indispensable requirement for the formation of RNA-induced transcriptional activation complex to enable a dsRNA-mediated gene activation. In this study, we demonstrated for the first time the possible presence of RNAa phenomenon in the tick vector, Haemaphysalis longicornis (Asian longhorned tick). We targeted the 3ʹ-UTR of a novel endochitinase-like gene (HlemCHT) identified previously in H. longicornis eggs for dsRNA-mediated gene activation. Our results showed an increased gene expression in eggs of H. longicornis endochitinase-dsRNA-injected (dsHlemCHT) ticks on day-13 post-oviposition. Furthermore, we observed that eggs of dsHlemCHT ticks exhibited relatively early egg development and hatching, suggesting a dsRNA-mediated activation of the HlemCHT gene in the eggs. This is the first attempt to provide evidence of RNAa in ticks. Although further studies are required to elucidate the detailed mechanism by which RNAa occurs in ticks, the outcome of this study provides new opportunities for the use of RNAa as a gene overexpression tool in future studies on tick biology, to reduce the global burden of ticks and tick-borne diseases.
Porphyromonas gingivalis-odontogenic infection is the potential risk for progression of nonalcoholic steatohepatitis-related neoplastic nodule formation
Authors: Sakamoto Shinnichi , Nagasaki Atsuhiro , Shrestha Madhu , Shintani Tomoaki , Watanabe Atsushi , Furusho Hisako , Chayama Kazuaki , Takata Takashi , Miyauchi Mutsumi
Published: June 2023

Porphyromonas gingivalis (P.g.), a major periodontal pathogen is a known risk factor for various systemic diseases. However, the relationship between P.g. and nonalcoholic steatohepatitis (NASH)-related hepatocellular carcinoma (HCC) is unclear. Thus, we aimed to elucidate whether P.g.-odontogenic infection promotes NASH-related HCC development/progression and to clarify its mechanism. Using high-fat diet (HFD)-induced NASH mouse model, P.g. was infected odontogenically. After 60 weeks of infection, tumor profiles were examined. Chow diet (CD) groups were also prepared at 60 weeks. Nodule formation was only seen in HFD-mice. P.g.-odontogenic infection significantly increased the mean nodule area (P = 0.0188) and tended to promote histological progression score after 60 weeks (P = 0.0956). Interestingly, P.g. was detected in the liver. HFD-P.g. (+) showed numerous TNF-α positive hepatic crown-like structures and 8-OHdG expression in the non-neoplastic liver. In P.g.-infected hepatocytes, phosphorylation of integrin β1 signaling molecules (FAK/ERK/AKT) was upregulated in vitro. In fact, total AKT in the liver of HFD-P.g. (+) was higher than that of HFD-P.g. (−). P.g.-infected hepatocytes showed increased cell proliferation and migration, and decreased doxorubicin-mediated apoptosis. Integrin β1 knockdown inhibited these phenotypic changes. P.g.-odontogenic infection may promote the progression of neoplastic nodule formation in an HFD-induced NASH mouse model via integrin signaling and TNF-α induced oxidative DNA damage.
Emerging investigator series: aqueous photooxidation of live bacteria with hydroxyl radicals under cloud-like conditions: insights into the production and transformation of biological and organic matter originating from bioaerosols
Authors: Liu Yushuo , Lee Patrick K. H. , Nah Theodora
Published: June 2023

In this study, we investigate what happens when live bacteria are exposed to hydroxyl radicals under cloud-like conditions.
Carbon dots using a household cleaning liquid as a dopant for iron detection in hydroponic systems
Authors: Hjort Robert G. , Pola Cícero C. , Casso-Hartmann Lisseth , Vanegas Diana C. , McLamore Eric , Gomes Carmen L.
Published: June 2023

Carbon dots for iron sensing in hydroponic systems. Iron (Fe) is a required micronutrient in plants for the production of chlorophyll and transport of oxygen.
A computational study of the thortveitite structure of zinc pyrovanadate, Zn2V2O7, under pressure
Authors: Reza S. , Maaza M. , Islam M. S.
Published: June 2023

The ambient (α) phase of Zn2V2O7 shows polymorphic structures that are pressure dependent. All polymorphs exhibit stability, anisotropy, malleability, and indirect band gap semiconductivity.
Cu(ii)-catalyzed C–N coupling of 2-aminobenzothiazoles with boronic acids at room temperature
Authors: Radhika Sankaran , Chandravarkar Aravind , Anilkumar Gopinathan
Published: June 2023

A Cu(ii)-catalyzed, effective C–N coupling of 2-aminobenzothiazoles with boronic acids in acetonitrile under open vessel chemistry was achieved.
Design and implementation of a wireless CAN module for marine engines using ZigBee protocol
Authors: Siemuri Akpojoto , Glocker Tobias , Mekkanen Mike , Kauhaniemi Kimmo , Mantere Timo , Elmusrati Mohammed
Published: June 2023

This paper describes the design and implementation of a wireless control area network (CAN bus) protocol for communication between the smart NOx (nitrogen oxide) sensor on diesel engines and the engine control unit (ECU). In this research, the approach taken is based on a case study of Wärtsilä's smart NOx sensor on a W4L20 diesel engine with the objective of replacing the wired CAN protocol with a wireless CAN communication node. In the current setup, the smart NOx sensor is connected to the engine control unit (ECU) with a wired CAN bus connection. The XBee module, which uses the ZigBee (IEEE 802.15.4) technology was used in the design and implementation of the wireless CAN prototype. With the emergence of 5G networks and the era of IoT, the topic of wireless industrial automation becomes essential in the modern industry. In addition to the great advantages and opportunities that the use of wireless nodes has in automation systems, there are many real challenges. The practical design challenges have been addressed in this paper.
Green integrated cooperative spectrum sensing for cognitive satellite terrestrial networks
Authors: Yao Rugui , Yu Yongsong , Wang Peng , Fan Ye , Li Xudong , Zuo Xiaoya , Qi Nan , Miridakis Nikolaos I. , Tsiftsis Theodoros A.
Published: June 2023

In this paper, a two‐way relay‐aided cognitive satellite terrestrial network (TR‐CSTN) model is proposed, where primary users are located at the edge of the base station. In the TR‐CSTN, one of satellite terminal users (STUs) is selected by the fusion center as the TR to forward information between two edge primary users with power of the TR. Meanwhile, these edge primary users share the licensed frequency band with the selected TR to send information to the satellite. Then, given the limited spectrum utilization and energy efficiency (EE) of the communication system, the cooperative spectrum sensing is employed to realize green communication. Specifically, the fusion center threshold, energy detection threshold, sensing duration and number of STUs are jointly optimized to enhance EE. Furthermore, considering that the node's energy shortage results in a short network lifetime, absolute EE gets improved. In detail, a power allocation scheme named normalized power aided Lévy flight trajectory‐based whale optimization algorithm (NP‐LWOA) is provided, which fulfills effective energy compensation among STUs to prolong the network lifetime notably. Finally, numerical results confirm the theoretical analysis and show the effectiveness of the TR‐CSTN and the NP‐LWOA in efficiently achieving the concept of green communication compared with other methods.
A robust routing strategy based on deep reinforcement learning for mega satellite constellations
Authors: Chu Ke , Cheng Sixi , Zhu Lidong
Published: June 2023

For mega satellite constellations, it has been a great challenge to achieve global routing and guarantee the performance of inter‐satellite transmission. To address the problem, a robust routing strategy based on deep reinforcement learning is proposed in this letter. The proposed method is applicable to degraded transmission performance, which exhibits better conformity to real‐world scenarios. Moreover, the age of information (AoI) of packets are utilized as one of the multi‐optimization targets to ensure the effectiveness of message transmission throughout the network. Numerical simulations show the outstanding average AoI performance of the proposed method and its greater robustness to jamming compared to existing methods. Meanwhile, it is also more effective for utilizing resources.
Periodic average magnitude difference function for remote heart rate monitoring
Authors: Zhang Chi , Wei Shaoming , Dong Ge , Zeng Yajun
Published: June 2023

With the increasing attention on remote monitoring of human heart rate by radar, there is a need to develop a method that can estimate heart rate quickly and reliably. In this study, a new estimation method using a periodic average magnitude difference function (PAMDF) is proposed to estimate the heart rate from the radar signal. PAMDF advances the classical average magnitude difference function (AMDF) with the help of maximum likelihood (ML) theory. It operates in the time domain and estimates the heart rate by calculating the signal magnitude difference between all heartbeat periods. The proposed technique is more accurate than AMDF and has a similar performance to the ML estimation, while maintaining the low complexity advantage of AMDF. The algorithm was validated using radar data from two publicly available datasets.
SE‐Former: Incorporating sentence embeddings into Transformer for low‐resource NMT
Authors: Wang Dongsheng , Wang Shaoyong
Published: June 2023

Recently, pre‐trained language models (PLM), such as Roberta and SimCSE, demonstrate strengths in many natural language understanding (NLU) tasks. However, there are few works on applying PLM to neural machine translation (NMT). Motivated by alleviating the data scarcity issue of low‐resource NMT, here incorporating sentence embeddings from SimCSE into the Transformer network is explored and SE‐Former model is proposed. In this model an embed‐fusion module is designed to utilize the output of SimCSE for NMT. Specifically, the outputs of encoder and SimCSE are fed into embed‐fusion module, attention network learns the relationship of sentence embedding and corresponding word embeddings. After addition, concatenation and linear transformation operations, the tensor fused with sentence embedding is obtained. The size of tensor output by embed‐fusion module is the same as original encoder. Finally, embed‐fusion module is connected to Transformer decoder. On IWSLT En‐Es, En‐Zh and En‐Fr tasks, SE‐Former obtains 42.13, 29.32 and 39.21 bilingual evaluation understudy (BLEU) points, respectively. Experimental results show the superiority of this method.
On‐line identification of power transformer short‐circuit parameters based on instantaneous phasor
Authors: Han Meiyu , Zhao Rende , Zhang Yunjian , Zhang Yinqing
Published: June 2023

Among the various faults of power transformers, winding faults are particularly common. It is known that short‐circuit parameters can reflect the winding condition, so the on‐line identification of short‐circuit parameters is of great significance for monitoring the power transformer health. An instantaneous phasor extraction method based on Second‐Order Generalised Integrator Frequency‐Locked Loop is introduced, and then an on‐line identification algorithm of power transformer short‐circuit parameters based on an instantaneous phasor is proposed. In this algorithm, multi second‐order generalised integrator frequency‐locked loop is used to extract the fundamental instantaneous phasors of the voltage and current signals on the primary and secondary sides of the transformer. After that, the short‐circuit parameters are calculated from the phasor equation of the transformer. The effectiveness of the proposed algorithm has been verified with experimental results.