bluuebunny/crossref_metadata_2025 huggingface dataset:
Formation of the Low‐Energy “Finger” Ion Spectral Structure Near the Inner Edge of the Plasma Sheet
Authors: Wang Y. B. , Kistler L. M. , Mouikis C. G. , Zhang J. C. , Lu J. Y. , Welling D. , Rastaetter L. , Bingham S. , Jin Y. W. , Wang L. , Miyoshi Y.
Published: November 2020

We present a case study of the H+, He+, and O+ low‐energy “finger” structure observed by the Van Allen Probe A Helium, Oxygen, Proton, and Electron (HOPE) spectrometer on 26 October 2016. This structure, whose characteristic energy is from approximately tens of eV to a few keV, looks like a “finger” that is rich in O+ and He+, faint in H+ on an energy‐time spectrogram. By using the Space Weather Modeling Framework (SWMF) and Weimer05 electric fields, combined with a dipole or more self‐consistent magnetohydrodynamic (MHD) magnetic field, backward tracing of O+ reveals that the structure is formed by ions with a long drift time from the plasma sheet during the magnetic storm main phase to the inner region with trajectories dominated by eastward drift motion, and the formation depends on the convection electric field model. The heavy ion dominance of the feature is explained by charge exchange losses along the long slow drift paths.
Shear Instability and Turbulence Within a Submesoscale Front Following a Storm
Authors: Carpenter Jeffrey R. , Rodrigues Arthur , Schultze Larissa K. P. , Merckelbach Lucas M. , Suzuki Nobuhiro , Baschek Burkard , Umlauf Lars
Published: November 2020

Narrow baroclinic fronts are observed in the surface mixed layer (SML) of the Baltic Sea following an autumn storm. The fronts are subjected to hydrodynamic instabilities that lead to submesoscale and turbulent motions while restratifying the SML. We describe observations from an ocean glider that combines currents, stratification, and turbulence microstructure in a high horizontal resolution (150–300 m) to analyze such fronts. The observations show that SML turbulence is strongly modulated by frontal activity, acting as both source and sink for turbulent kinetic energy. In particular, a direct route to turbulent dissipation within the front is linked to shear instability caused by elevated nongeostrophic shear. The turbulent dissipation of frontal kinetic energy is large enough that it could be a significant influence in the evolution of the front and demonstrates that small‐scale turbulence can act as a significant sink of submesoscale kinetic energy.
Imprints of Sunspot Cycles on Normal and Abnormal Geomagnetic Fields: Case Study From Equatorial and Low‐Latitude Sites of India
Authors: Chandrasekhar N. Phani , Roy Arka
Published: November 2020

The quiet time characteristics of equatorial electrojet (EEJ), counter electrojet (CEJ), and solar quiet (Sq) day geomagnetic field over two decades (1980–2002) are established using Principal component analysis (PCA) from equatorial (Ettaiyapuram) and off‐equatorial (Hyderabad) Magnetic Observatories, India, over sunspot cycles 21–23. The patterns of normal field shows that the diurnal amplitudes were strong during equinox compared to other seasons. Varying contributions of abnormal field in different Lloyd's seasons were evident in different phases of sunspot cycle. The diurnal amplitudes have reduced from the 21st to the 23rd sunspot maxima following the trend of weakening of sunspot cycle. Analysis of seasonal means shows evening CEJs were more pronounced when compared to morning and afternoon in different phases of sunspot cycle. The abnormal field variations have a strong correlation with the occurrence of afternoon CEJs during solar minima; a correlation of seasonal occurrences of CEJs with phases of sunspot cycles is revealed.
International Coordination and Support for SmallSat‐Enabled Space Weather Activities
Authors: Nieves‐Chinchilla Teresa , Lal Bhavya , Robinson Robert , Caspi Amir , Jackson David R. , Moretto Jørgensen Therese , Spann James
Published: November 2020

Advances in space weather science and small satellite (SmallSat) technology have proceeded in parallel over the past two decades, but better communication and coordination are needed among the respective worldwide communities contributing to this rapid progress. We identify six areas where improved international coordination is especially desirable, including (1) orbital debris mitigation; (2) spectrum management; (3) export control regulations; (4) access to timely and low‐cost launch opportunities; (5) inclusive data policies; and (6) education. We argue the need for internationally coordinated policies and programs to promote the use of SmallSats for space weather research and forecasting while realizing maximum scientific and technical advances through the integration of these two increasingly important endeavors.
Vascular endothelial growth factor encoded by Parapoxviruses can regulate metabolism and survival of triple negative breast cancer cells
Authors: Bose Dipayan , Banerjee Sagarika , Singh Rajnish Kumar , Wise Lyn M. , Robertson Erle S.
Published: November 2020

Dysbiotic microbiomes are linked to many pathological outcomes including different metabolic disorders like diabetes, atherosclerosis and even cancer. Breast cancer is the second leading cause of cancer associated death in women, and triple negative breast cancer (TNBC) is the most aggressive type with major challenges for intervention. Previous reports suggested that Parapoxvirus signatures are one of the predominant dysbiotic viral signatures in TNBC. These viruses encode several genes that are homologs of human genes. In this study, we show that the VEGF homolog encoded by Parapoxviruses, can induce cell proliferation, and alter metabolism of breast cancer and normal breast cells, through alteration of MAPK-ERK and PI3K-AKT signaling. In addition, the activity of the transcription factor FoxO1 was altered by viral-encoded VEGF through activation of the PI3K-AKT pathway, leading to reprogramming of cellular metabolic gene expression. Therefore, this study provides new insights into the function of viral-encoded VEGFs, which promoted the growth of the breast cancer cells and imparted proliferative phenotype with altered metabolism in normal breast cells.
A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes
Authors: Ganapathiraju Madhavi K. , Subramanian Sandeep , Chaparala Srilakshmi , Karunakaran Kalyani B.
Published: November 2020

A palindrome in DNA is like a palindrome in language, but when read backwards, it is a complement of the forward sequence; effectively, the two halves of a sequence complement each other from its midpoint like in a double strand of DNA. Palindromes are distributed throughout the human genome and play significant roles in gene expression and regulation. Palindromic mutations are linked to many human diseases, such as neuronal disorders, mental retardation, and various cancers. In this work, we computed and analyzed the palindromic sequences in the human genome and studied their conservation in personal genomes using 1000 Genomes data. We found that ~30% of the palindromes exhibit variation, some of which are caused by rare variants. The analysis of disease/trait-associated single-nucleotide polymorphisms in palindromic regions showed that disease-associated risk variants are 14 times more likely to be present in palindromic regions than in other regions. The catalog of palindromes in the reference genome and 1000 Genomes is being made available here with details on their variations in each individual genome to serve as a resource for future and retrospective whole-genome studies identifying statistically significant palindrome variations associated with diseases or traits and their roles in disease mechanisms.
Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2
Authors: Arizti-Sanz Jon , Freije Catherine A. , Stanton Alexandra C. , Petros Brittany A. , Boehm Chloe K. , Siddiqui Sameed , Shaw Bennett M. , Adams Gordon , Kosoko-Thoroddsen Tinna-Solveig F. , Kemball Molly E. , Uwanibe Jessica N. , Ajogbasile Fehintola V. , Eromon Philomena E. , Gross Robin , Wronka Loni , Caviness Katie , Hensley Lisa E. , Bergman Nicholas H. , MacInnis Bronwyn L. , Happi Christian T. , Lemieux Jacob E. , Sabeti Pardis C. , Myhrvold Cameron
Published: November 2020

The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We identify the optimal conditions to allow RPA-based amplification and Cas13-based detection to occur in a single step, simplifying assay preparation and reducing run-time. We improve HUDSON to rapidly inactivate viruses in nasopharyngeal swabs and saliva in 10 min. SHINE’s results can be visualized with an in-tube fluorescent readout — reducing contamination risk as amplification reaction tubes remain sealed — and interpreted by a companion smartphone application. We validate SHINE on 50 nasopharyngeal patient samples, demonstrating 90% sensitivity and 100% specificity compared to RT-qPCR with a sample-to-answer time of 50 min. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.
Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers
Authors: Okazaki Keito , Anzawa Hayato , Liu Zun , Ota Nao , Kitamura Hiroshi , Onodera Yoshiaki , Alam Md. Morshedul , Matsumaru Daisuke , Suzuki Takuma , Katsuoka Fumiki , Tadaka Shu , Motoike Ikuko , Watanabe Mika , Hayasaka Kazuki , Sakurada Akira , Okada Yoshinori , Yamamoto Masayuki , Suzuki Takashi , Kinoshita Kengo , Sekine Hiroki , Motohashi Hozumi
Published: November 2020

Transcriptional dysregulation, which can be caused by genetic and epigenetic alterations, is a fundamental feature of many cancers. A key cytoprotective transcriptional activator, NRF2, is often aberrantly activated in non-small cell lung cancers (NSCLCs) and supports both aggressive tumorigenesis and therapeutic resistance. Herein, we find that persistently activated NRF2 in NSCLCs generates enhancers at gene loci that are not normally regulated by transiently activated NRF2 under physiological conditions. Elevated accumulation of CEBPB in NRF2-activated NSCLCs is found to be one of the prerequisites for establishment of the unique NRF2-dependent enhancers, among which the NOTCH3 enhancer is shown to be critical for promotion of tumor-initiating activity. Enhancer remodeling mediated by NRF2-CEBPB cooperativity promotes tumor-initiating activity and drives malignancy of NRF2-activated NSCLCs via establishment of the NRF2-NOTCH3 regulatory axis.
Inferring the molecular and phenotypic impact of amino acid variants with MutPred2
Authors: Pejaver Vikas , Urresti Jorge , Lugo-Martinez Jose , Pagel Kymberleigh A. , Lin Guan Ning , Nam Hyun-Jun , Mort Matthew , Cooper David N. , Sebat Jonathan , Iakoucheva Lilia M. , Mooney Sean D. , Radivojac Predrag
Published: November 2020

Identifying pathogenic variants and underlying functional alterations is challenging. To this end, we introduce MutPred2, a tool that improves the prioritization of pathogenic amino acid substitutions over existing methods, generates molecular mechanisms potentially causative of disease, and returns interpretable pathogenicity score distributions on individual genomes. Whilst its prioritization performance is state-of-the-art, a distinguishing feature of MutPred2 is the probabilistic modeling of variant impact on specific aspects of protein structure and function that can serve to guide experimental studies of phenotype-altering variants. We demonstrate the utility of MutPred2 in the identification of the structural and functional mutational signatures relevant to Mendelian disorders and the prioritization of de novo mutations associated with complex neurodevelopmental disorders. We then experimentally validate the functional impact of several variants identified in patients with such disorders. We argue that mechanism-driven studies of human inherited disease have the potential to significantly accelerate the discovery of clinically actionable variants.
Assembling custom side chains on proteoglycans to interrogate their function in living cells
Authors: Wang Wenshuang , Han Naihan , Xu Yingying , Zhao Yunxue , Shi Liran , Filmus Jorge , Li Fuchuan
Published: November 2020

Proteoglycans (PGs) are composed of a core protein and one or more chains of glycosaminoglycans (GAGs). The highly heterogeneous GAG chains play an irreplaceable role in the functions of PGs. However, the lack of an approach to control the exact structure of GAG chains conjugated to PGs tremendously hinders functional studies of PGs. Herein, by using glypican-3 as a model, we establish an aldehyde tag-based approach to assemble PGs with specific GAG chains on the surface of living cells. We show that the engineered glypican-3 can regulate Wnt and Hedgehog signaling like the wild type. Furthermore, we also present a method for studying the interaction of PGs with their target glycoproteins by combining the assembly of PGs carrying specific GAG chains with metabolic glycan labeling, and most importantly, we obtain evidence of GPC3 directly interacting with Frizzled. In conclusion, this study provides a very useful platform for structural and functional studies of PGs with specific GAG chains.
Post-lockdown SARS-CoV-2 nucleic acid screening in nearly ten million residents of Wuhan, China
Authors: Cao Shiyi , Gan Yong , Wang Chao , Bachmann Max , Wei Shanbo , Gong Jie , Huang Yuchai , Wang Tiantian , Li Liqing , Lu Kai , Jiang Heng , Gong Yanhong , Xu Hongbin , Shen Xin , Tian Qingfeng , Lv Chuanzhu , Song Fujian , Yin Xiaoxv , Lu Zuxun
Published: November 2020

Stringent COVID-19 control measures were imposed in Wuhan between January 23 and April 8, 2020. Estimates of the prevalence of infection following the release of restrictions could inform post-lockdown pandemic management. Here, we describe a city-wide SARS-CoV-2 nucleic acid screening programme between May 14 and June 1, 2020 in Wuhan. All city residents aged six years or older were eligible and 9,899,828 (92.9%) participated. No new symptomatic cases and 300 asymptomatic cases (detection rate 0.303/10,000, 95% CI 0.270–0.339/10,000) were identified. There were no positive tests amongst 1,174 close contacts of asymptomatic cases. 107 of 34,424 previously recovered COVID-19 patients tested positive again (re-positive rate 0.31%, 95% CI 0.423–0.574%). The prevalence of SARS-CoV-2 infection in Wuhan was therefore very low five to eight weeks after the end of lockdown.
Author Correction: The structure of a red-shifted photosystem I reveals a red site in the core antenna
Authors: Toporik Hila , Khmelnitskiy Anton , Dobson Zachary , Riddle Reece , Williams Dewight , Lin Su , Jankowiak Ryszard , Mazor Yuval
Published: November 2020

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-19953-w
Machine learning to predict early TNF inhibitor users in patients with ankylosing spondylitis
Authors: Lee Seulkee , Eun Yeonghee , Kim Hyungjin , Cha Hoon-Suk , Koh Eun-Mi , Lee Jaejoon
Published: November 2020

We aim to generate an artificial neural network (ANN) model to predict early TNF inhibitor users in patients with ankylosing spondylitis. The baseline demographic and laboratory data of patients who visited Samsung Medical Center rheumatology clinic from Dec. 2003 to Sep. 2018 were analyzed. Patients were divided into two groups: early-TNF and non-early-TNF users. Machine learning models were formulated to predict the early-TNF users using the baseline data. Feature importance analysis was performed to delineate significant baseline characteristics. The numbers of early-TNF and non-early-TNF users were 90 and 505, respectively. The performance of the ANN model, based on the area under curve (AUC) for a receiver operating characteristic curve (ROC) of 0.783, was superior to logistic regression, support vector machine, random forest, and XGBoost models (for an ROC curve of 0.719, 0.699, 0.761, and 0.713, respectively) in predicting early-TNF users. Feature importance analysis revealed CRP and ESR as the top significant baseline characteristics for predicting early-TNF users. Our model displayed superior performance in predicting early-TNF users compared with logistic regression and other machine learning models. Machine learning can be a vital tool in predicting treatment response in various rheumatologic diseases.
Optimized split nitrogen fertilizer increase photosynthesis, grain yield, nitrogen use efficiency and water use efficiency under water-saving irrigation
Authors: Zhang Zhen , Zhang Yongli , Shi Yu , Yu Zhenwen
Published: November 2020

This study aims to investigate optimization of the basal-top-dressing nitrogen ratio for improving winter wheat grain yield, nitrogen use efficiency, water use efficiency and physiological parameters under supplemental irrigation. A water-saving irrigation (SI) regime was established and sufficient irrigation (UI) was used as a control condition. The split-nitrogen regimes used were based on a identical total nitrogen application rate of 240 kg ha−1 but were split in four different proportions between sowing and the jointing stage; i.e. 10:0 (N1), 7:3 (N2), 5:5 (N3) and 3:7 (N4). Compared with the N1, N2 and N4 treatments, N3 treatment increased grain yield, nitrogen and water use efficiencies by 5.27–17.75%, 5.68–18.78% and 5.65–31.02%, respectively, in both years. The yield advantage obtained with the optimized split-nitrogen fertilizer application may be attributable to greater flag leaf photosynthetic capacity and grain-filling capacity. Furthermore, the N3 treatment maintained the highest nitrogen and water use efficiencies. Moreover, we observed that water use efficiency of SI compared with UI increased by 9.75% in 2016 and 10.79% in 2017, respectively. It can be concluded that SI along with a 5:5 basal-top-dressing nitrogen ratio should be considered as an optimal fertigation strategy for both high grain yield and efficiency in winter wheat.
Author Correction: Quasi-probability information in a coupled two-qubit system interacting non-linearly with a coherent cavity under intrinsic decoherence
Authors: Mohamed Abdel‑Baset A. , Eleuch Hichem
Published: November 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Neutrophil to lymphocyte ratio and breast cancer risk: analysis by subtype and potential interactions
Authors: Gago‑Dominguez Manuela , Matabuena Marcos , Redondo Carmen M. , Patel Sandip Pravin , Carracedo Angel , Ponte Sara Miranda , Martínez María Elena , Castelao J. Esteban
Published: November 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Two-year outcomes of intravitreal aflibercept in a Swiss routine treat and extend regimen for patients with neovascular age-related macular degeneration
Authors: Ebneter Andreas , Michels Stephan , Pruente Christian , Imesch Pascal , Eilenberger Felix , Oesch Susanne , Thomet-Hunziker Isabelle P. , Hatz Katja
Published: November 2020

The aim of this observational study was to assess the use and outcome of intravitreal aflibercept in a treat and extend regimen in treatment-naïve neovascular AMD patients in routine practice. This both retrospective and prospective study was conducted in four larger Swiss retina clinics (ASTERIA study). The primary endpoint was the mean change in best-corrected visual acuity (BCVA) in ETDRS letters from baseline to 12 months. Between December 2017 and August 2018, 160 patients were included. For patients with available data, the mean change in BCVA was + 8.4 (± 14.4) letters at month 12 (n = 139) and + 5.0 (± 11.4) letters at month 24 (n = 95). A mean number of 8.3 (± 2.4) injections were administered within the first year and 5.4 (± 2.9) injections during the second year. On average, the observed treatment interval at month 12 was 63.3 (± 22.0) days and increased to 69.1 (± 28.6) days at month 24. For 37% of the patients, a treatment interval ≥ 12 weeks was attained at month 24. In conclusion,  intravitreal aflibercept in a Swiss real-life treat and extend regimen resulted in comparable anatomic and functional outcomes as were observed in the prospective registration trials of aflibercept for nAMD treatment.
Role of RPTPβ/ζ in neuroinflammation and microglia-neuron communication
Authors: Fernández-Calle Rosalía , Galán-Llario Milagros , Gramage Esther , Zapatería Begoña , Vicente-Rodríguez Marta , Zapico José M. , de Pascual-Teresa Beatriz , Ramos Ana , Ramos-Álvarez M. Pilar , Uribarri María , Ferrer-Alcón Marcel , Herradón Gonzalo
Published: November 2020

Pleiotrophin (PTN) is a cytokine that is upregulated in different neuroinflammatory disorders. Using mice with transgenic PTN overexpression in the brain (Ptn-Tg), we have found a positive correlation between iNos and Tnfα mRNA and Ptn mRNA levels in the prefrontal cortex (PFC) of LPS-treated mice. PTN is an inhibitor of Receptor Protein Tyrosine Phosphatase (RPTP) β/ζ, which is mainly expressed in the central nervous system. We aimed to test if RPTPβ/ζ is involved in the modulation of neuroinflammatory responses using specific inhibitors of RPTPβ/ζ (MY10 and MY33-3). Treatment with MY10 potentiated LPS-induced microglial responses in the mouse PFC. Surprisingly, MY10 caused a decrease in LPS-induced NF-κB p65 expression, suggesting that RPTPβ/ζ may be involved in a novel mechanism of potentiation of microglial activation independent of the NF-κB p65 pathway. MY33-3 and MY10 limited LPS-induced nitrites production and iNos increases in BV2 microglial cells. SH-SY5Y neuronal cells were treated with the conditioned media from MY10/LPS-treated BV2 cells. Conditioned media from non-stimulated and from LPS-stimulated BV2 cells increased the viability of SH-SY5Y cultures. RPTPβ/ζ inhibition in microglial cells disrupted this neurotrophic effect of microglia, suggesting that RPTPβ/ζ plays a role in the neurotrophic phenotype of microglia and in microglia-neuron communication.
Early prediction of macrocrack location in concrete, rocks and other granular composite materials
Authors: Tordesillas Antoinette , Kahagalage Sanath , Ras Charl , Nitka Michał , Tejchman Jacek
Published: November 2020

Heterogeneous quasibrittle composites like concrete, ceramics and rocks comprise grains held together by bonds. The question on whether or not the path of the crack that leads to failure can be predicted from known microstructural features, viz. bond connectivity, size, fracture surface energy and strength, remains open. Many fracture criteria exist. The most widely used are based on a postulated stress and/or energy extremal. Since force and energy share common transmission paths, their flow bottleneck may be the precursory failure mechanism to reconcile these optimality criteria in one unified framework. We explore this in the framework of network flow theory, using microstructural data from 3D discrete element models of concrete under uniaxial tension. We find the force and energy bottlenecks emerge in the same path and provide an early and accurate prediction of the ultimate macrocrack path $${\mathcal {C}}$$
C
. Relative to all feasible crack paths, the Griffith’s fracture surface energy and the Francfort–Marigo energy functional are minimum in $${\mathcal {C}}$$
C
; likewise for the critical strain energy density if bonds are uniformly sized. Redundancies in transmission paths govern prefailure dynamics, and predispose $${\mathcal {C}}$$
C
to cascading failure during which the concomitant energy release rate and normal (Rankine) stress become maximum along $${\mathcal {C}}$$
C
.
Author Correction: CCT α is a novel biomarker for diagnosis of laryngeal squamous cell cancer
Authors: Yang Jingpu , Zhang Zhuping , Zhao Yin , Cheng Jinzhang , Zhao Chang , Wang Zonggui
Published: November 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Comprehensive genomic profile of Chinese lung cancer patients and mutation characteristics of individuals resistant to icotinib/gefitinib
Authors: Shang Yanhong , Li Xiaofang , Liu Weiwei , Shi Xiaoliang , Yuan Shaohua , Huo Ran , Fang Guotao , Han Xiao , Zhang Jingnan , Wang Kunjie , Dou Zhengyue , Zhang Yan , Zang Aimin , Zhang Lin
Published: November 2020

Lung cancer is the leading causes of cancer-related death worldwide. Precise treatment based on next-generation sequencing technology has shown advantages in the diagnosis and treatment of lung cancer. This cohort study included 371 lung cancer patients. The lung cancer subtype was related to the smoking status and sex of the patients. The most common mutated genes were TP53 (62%), EGFR (55%), and KRAS (11%). The mutation frequencies of EGFR, TP53, PIK3CA, NFE2L2, KMT2D, FGFR1, CCND1, and CDKN2A were significantly different between lung adenocarcinoma and lung squamous cell carcinoma. We identified the age-associated mutations in ALK, ERBB2, KMT2D, RBM10, NRAS, NF1, PIK3CA, MET, PBRM1, LRP2, and CDKN2B; smoking-associated mutations in CDKN2A, FAT1, FGFR1, NFE2L2, CCNE1, CCND1, SMARCA4, KEAP1, KMT2C, and STK11; tumor stage-associated mutations in ARFRP1, AURKA, and CBFB; and sex-associated mutations in EGFR. Tumor mutational burden (TMB) is associated with tumor subtype, age, sex, and smoking status. TMB-associated mutations included CDKN2A, LRP1B, LRP2, TP53, and EGFR. EGFR amplification was commonly detected in patients with acquired lcotinib/gefitinib resistance. DNMT3A and NOTCH4 mutations may be associated with the benefit of icotinib/gefitinib treatment.
Analyzing long-term impacts of ungulate herbivory on forest-recruitment dynamics at community and species level contrasting tree densities versus maximum heights
Authors: Nopp-Mayr Ursula , Reimoser Susanne , Reimoser Friedrich , Sachser Frederik , Obermair Leopold , Gratzer Georg
Published: November 2020

Herbivores are constitutive elements of most terrestrial ecosystems. Understanding effects of herbivory on ecosystem dynamics is thus a major, albeit challenging task in community ecology. Effects of mammals on plant communities are typically explored by comparing plant densities or diversity in exclosure experiments. This might over-estimate long-term herbivore effects at community levels as early life stage mortality is driven by a multitude of factors. Addressing these challenges, we established a set of 100 pairs of ungulate exclosures and unfenced control plots (25 m2) in mixed montane forests in the Alps in 1989 covering a forest area of 90 km2. Investigations ran until 2013. Analogous to the gap-maker–gap-filler approach, dynamically recording the height of the largest trees per tree species in paired plots with and without exclosures might allow for assessing herbivore impacts on those individuals with a high probability of attaining reproductive stages. We thus tested if recording maximum heights of regenerating trees would better reflect effects of ungulate herbivory on long-term dynamics of tree regeneration than recording of stem density, and if species dominance patterns would shift over time. For quantifying the effects of ungulate herbivory simultaneously at community and species level we used principle response curves (PRC). PRCs yielded traceable results both at community and species level. Trajectories of maximum heights yielded significant results contrary to trajectories of total stem density. Response patterns of tree species were not uniform over time: e.g., both Norway spruce and European larch switched in their response to fencing. Fencing explained about 3% of the variance of maximum tree heights after nine years but increased to about 10% after 24 years thus confirming the importance of long-term surveys. Maximum height dynamics of tree species, addressed in our study, can thus reflect local dominance of tree species via asymmetric plant competition. Such effects, both within and among forest patches, can accrue over time shaping forest structure and composition.
Regional and network neural activity reflect men’s preference for greater socioeconomic status during impression formation
Authors: Barth Denise M. , Mattan Bradley D. , Dang Tzipporah P. , Cloutier Jasmin
Published: November 2020

Evidence from social psychology suggests that men compared to women more readily display and pursue control over human resources or capital. However, studying how status and gender shape deliberate impression formation is difficult due to social desirability concerns. Using univariate and multivariate fMRI analyses (n = 65), we examined how gender and socioeconomic status (SES) may influence brain responses during deliberate but private impression formation. Men more than women showed greater activity in the VMPFC and NAcc when forming impressions of high-SES (vs. low-SES) targets. Seed partial least squares (PLS) analysis showed that this SES-based increase in VMPFC activity was associated with greater co-activation across an evaluative network for the high-SES versus low-SES univariate comparison. A data-driven task PLS analysis also showed greater co-activation in an extended network consisting of regions involved in salience detection, attention, and task engagement as a function of increasing target SES. This co-activating network was most pronounced for men. These findings provide evidence that high-SES targets elicit neural responses indicative of positivity, reward, and salience during impression formation among men. Contributions to a network neuroscience understanding of status perception and implications for gender- and status-based impression formation are discussed.
Adverse impact of renin–angiotensin system blockade on the clinical course in hospitalized patients with severe COVID-19: a retrospective cohort study
Authors: Lim Jeong-Hoon , Cho Jang-Hee , Jeon Yena , Kim Ji Hye , Lee Ga Young , Jeon Soojee , Noh Hee Won , Lee Yong-Hoon , Lee Jaehee , Chang Hyun-Ha , Jung Hee-Yeon , Choi Ji-Young , Park Sun-Hee , Kim Chan-Duck , Kim Yong-Lim , Kim Shin-Woo
Published: November 2020

The association between angiotensin-converting enzyme inhibitor (ACE-I) or angiotensin II receptor blocker (ARB) and the risk of mortality in hospitalized patients with severe coronavirus disease 2019 (COVID-19) was investigated. This retrospective cohort study was performed in all hospitalized patients with COVID-19 in tertiary hospitals in Daegu, Korea. Patients were classified based on whether they received ACE-I or ARB before COVID-19 diagnosis. The analysis of the primary outcome, in-hospital mortality, was performed using the Cox proportional hazards regression model. Of 130 patients with COVID-19, 30 (23.1%) who received ACE-I or ARB exhibited an increased risk of in-hospital mortality (adjusted hazard ratio, 2.20; 95% confidence interval [CI], 1.10–4.38; P = 0.025). ACE-I or ARB was also associated with severe complications, such as acute respiratory distress syndrome (ARDS) (adjusted odds ratio [aOR], 2.58; 95% CI, 1.02–6.51; P = 0.045) and acute kidney injury (AKI) (aOR, 3.06; 95% CI, 1.15–8.15; P = 0.026). Among the patients with ACE-I or ARB therapy, 8 patients (26.7%) used high equivalent doses of ACE-I or ARB and they had higher in-hospital mortality and an increased risk of ARDS and AKI (all, P < 0.05). ACE-I or ARB therapy in patients with severe COVID-19 was associated with the occurrence of severe complications and increased in-hospital mortality. The potentially harmful effect of ACE-I or ARB therapy may be higher in patients who received high doses.
Focal stimulation of the temporoparietal junction improves rationality in prosocial decision-making
Authors: Li Flora , Ball Sheryl , Zhang Xiaomeng , Smith Alec
Published: November 2020

We tested the hypothesis that modulation of neurocomputational inputs to value-based decision-making affects the rationality of economic choices. The brain’s right temporoparietal junction (rTPJ) has been functionally associated with both social behavior and with domain-general information processing and attention. To identify the causal function of rTPJ in prosocial decisions, we administered focal high definition transcranial direct current stimulation (HD-tDCS) while participants allocated money between themselves and a charity in a modified dictator game. Anodal stimulation led to improved rationality as well as increased charitable giving and egalitarianism, resulting in more consistent and efficient choices and increased sensitivity to the price of giving. These results are consistent with the theory that anodal stimulation of the rTPJ increases the precision of value computations in social decision-making. Our results demonstrate that theories of rTPJ function should account for the multifaceted role of the rTPJ in the representation of social inputs into value-based decisions.
Effectiveness of the European Natura 2000 network to sustain a specialist wintering waterbird population in the face of climate change
Authors: Marchowski Dominik , Ławicki Łukasz , Fox Anthony D. , Nielsen Rasmus D. , Petersen Ib K. , Hornman Menno , Nilsson Leif , Haas Fredrik , Wahl Johannes , Kieckbusch Jan , Nehls Hans W. , Calbrade Neil , Hearn Richard , Meissner Włodzimierz , Fitzgerald Niamh , Luigujoe Leho , Zenatello Marco , Gaudard Clemence , Koschinski Sven
Published: November 2020

Analysis of coordinated Greater Scaup (Aythya marila) count data from the last 30 years showed a 38.1% decrease in wintering numbers in North-West Europe, from 309,000 during 1988–1991 to c.192,300 individuals during 2015–2018. Annual trends in wintering numbers differed throughout the range. Numbers decreased in the UK, Ireland, and in the Netherlands, while numbers were stable in Denmark. Germany, Poland, Sweden, and Estonia showed increasing numbers, suggesting a shift in the distribution of the species within its wintering grounds towards the east and north. Higher temperatures in northern and eastern areas were correlated with the range shift of the wintering distribution. Deaths from bycatch drowning of Scaup in fishing gear have significantly decreased in recent decades in the Netherlands, where currently the greatest threat is considered the deterioration of food resources. The increasing concentration of wintering Scaup in coastal Poland and Germany (where lack of effective implementation of conservation measures fail to protect the species from the impacts of bycatch and declining food quality) pose major threats to the entire population.
A primordial 15N-depleted organic component detected within the carbonaceous chondrite Maribo
Authors: Vollmer Christian , Leitner Jan , Kepaptsoglou Demie , Ramasse Quentin M. , King Ashley J. , Schofield Paul F. , Bischoff Addi , Araki Tohru , Hoppe Peter
Published: November 2020

We report on the detection of primordial organic matter within the carbonaceous chondrite Maribo that is distinct from the majority of organics found in extraterrestrial samples. We have applied high-spatial resolution techniques to obtain C-N isotopic compositions, chemical, and structural information of this material. The organic matter is depleted in 15N relative to the terrestrial value at around δ15N ~ -200‰, close to compositions in the local interstellar medium. Morphological investigations by electron microscopy revealed that the material consists of µm- to sub-µm-sized diffuse particles dispersed within the meteorite matrix. Electron energy loss and synchrotron X-ray absorption near-edge structure spectroscopies show that the carbon functional chemistry is dominated by aromatic and C=O bonding environments similar to primordial organics from other carbonaceous chondrites. The nitrogen functional chemistry is characterized by C-N double and triple bonding environments distinct from what is usually found in 15N-enriched organics from aqueously altered carbonaceous chondrites. Our investigations demonstrate that Maribo represents one of the least altered CM chondrite breccias found to date and contains primordial organic matter, probably originating in the interstellar medium.
Effects of precipitation and temperature on precipitation use efficiency of alpine grassland in Northern Tibet, China
Authors: Zhang Xiaoke , Du Xindong , Zhu Zhangming
Published: November 2020

Precipitation use efficiency (PUE) is crucial in understanding the coupling between ecosystem carbon and water cycling. In this study, we used a time series (2000–2013) dataset of net primary productivity (NPP) based on the Carnegie–Ames–Stanford Approach (CASA) model together with precipitation to reveal the spatial and temporal patterns of alpine grassland PUE in Northern Tibet. The mean annual PUE values of alpine meadow, alpine meadow steppe, alpine steppe, alpine desert steppe, and alpine desert were 0.48, 0.39, 0.36, 0.29 and 0.23 gc m−2 mm−1, respectively. The spatial patterns of PUE of alpine grassland demonstrated an initial increase in the arid region and a subsequent decrease in the humid region along the precipitation gradient and peaked at approximately 500 mm. To evaluate the temporal patterns, the sensitivity $$Slope$$

Slope

and the Pearson correlation coefficient $${R}_{xy}$$

R

xy

between the PUE and climatic factors were calculated. The inter-annual variability of PUE exhibited a significant negative correlation with annual precipitation (P < 0.05), which implies that NPP had a lower sensitivity to precipitation in most regions. The relationship between PUE and the mean annual temperature is different for different regions. Our findings have an important role in understanding the impacts of precipitation availability on climate change and in the scientific management of the alpine grassland ecosystems.
Validation of deep learning natural language processing algorithm for keyword extraction from pathology reports in electronic health records
Authors: Kim Yoojoong , Lee Jeong Hyeon , Choi Sunho , Lee Jeong Moon , Kim Jong-Ho , Seok Junhee , Joo Hyung Joon
Published: November 2020

Pathology reports contain the essential data for both clinical and research purposes. However, the extraction of meaningful, qualitative data from the original document is difficult due to the narrative and complex nature of such reports. Keyword extraction for pathology reports is necessary to summarize the informative text and reduce intensive time consumption. In this study, we employed a deep learning model for the natural language process to extract keywords from pathology reports and presented the supervised keyword extraction algorithm. We considered three types of pathological keywords, namely specimen, procedure, and pathology types. We compared the performance of the present algorithm with the conventional keyword extraction methods on the 3115 pathology reports that were manually labeled by professional pathologists. Additionally, we applied the present algorithm to 36,014 unlabeled pathology reports and analysed the extracted keywords with biomedical vocabulary sets. The results demonstrated the suitability of our model for practical application in extracting important data from pathology reports.
Enhanced cognitive demodulation with artificial intelligence
Authors: Ren Hang , Shin Sang-Hee , Lucyszyn Stepan
Published: November 2020

The low-cost ‘THz Torch’ wireless link technology is still in its infancy. Until very recently, inherent limitations with available hardware has resulted in a modest operational figure of merit performance (Range $$\times$$
×
Bit Rate). However, a breakthrough was reported here by the authors, with the introduction of ‘Cognitive Demodulation’. This bypassed the thermal time constant constraints normally associated with both the thermal emitter and sensor; allowing step-change increases in both Range and Bit Rate with direct electronic modulation. This paper concentrates on advancements to the bit error rate (BER) performance. Here, separate techniques are introduced to the demodulation software that, when combined, result in enhanced Cognitive Demodulation. A factor of more than 100 improvement in BER was demonstrated within the laboratory and approximately a 60-fold improvement in a non-laboratory environment; both at the maximum Range and Bit Rate of 2 m and 125 bps, respectively, demonstrated recently. Moreover, demodulation speed is increased by almost a factor of 10,000; allowing for real-time demodulation while easing future computational hardware requirements. In addition to these software advancements, the paper demonstrates important improvements in hardware that has brought the technology out of the laboratory, with field trials being performed within an office corridor.
Non-contact monitoring of the depth temperature profile for medical laser scanning technologies
Authors: Kosir Jure , Vella Daniele , Jezersek Matija
Published: November 2020

Medical treatments such as high-intensity focused ultrasound, hyperthermic laser lipolysis or radiofrequency are employed as a minimally invasive alternatives for targeted tissue therapies. The increased temperature of the tissue triggers various thermal effects and leads to an unavoidable damage. As targeted tissues are generally located below the surface, various approaches are utilized to prevent skin layers from overheating and irreparable thermal damages. These procedures are often accompanied by cooling systems and protective layers accounting for a non-trivial detection of the subsurface temperature peak. Here, we show a temperature peak estimation method based on infrared thermography recording of the surface temperature evolution coupled with a thermal-diffusion-based model and a time-dependent data matching algorithm. The performance of the newly developed method was further showcased by employing hyperthermic laser lipolysis on an ex-vivo porcine fat tissue. Deviations of the estimated peak temperature remained below 1 °C, as validated by simultaneous measurement of depth temperature field within the tissue. Reconstruction of the depth profile shows a good reproducibility of the real temperature distribution with a small deviation of the peak temperature position. A thermal camera in combination with the time-dependent matching bears the scope for non-contact monitoring of the depth temperature profile as fast as 30 s. The latest demand for miniaturization of thermal cameras provides the possibility to embed the model in portable thermal scanners or medical laser technologies for improving safety and efficiency.
ROCK inhibitors beneficially alter the spatial configuration of TGFβ2-treated 3D organoids from a human trabecular meshwork (HTM)
Authors: Ota Chiaki , Ida Yosuke , Ohguro Hiroshi , Hikage Fumihito
Published: November 2020

To elucidate molecular pharmacology of Rho-associated coiled-coil containing protein kinase inhibitors (ROCK-i, Ripasudil and Y27632) on their efficiency for aqueous outflow, 2D or 3D cultures of a human trabecular meshwork (HTM) were prepared in the presence of TGFβ2. Those were examined by transendothelial electrical resistance (TEER, 2D), electronic microscopy (EM, 2D and 3D), expression of the extracellular matrix (ECM) including collagen1 (COL1), COL4 and COL6, and fibronectin (FN) by immunolabeling and/or quantitative PCR (3D), and solidity of 3D organoids by a micro-squeezer. TGFβ2 significantly increased the TEER values in 2D cultures, and the ECM expression indicated that the 3D organoids assumed a more densely packed shape. ROCK-i greatly reduced the TGFβ2-induced enhancement of TEER and the immunolabeled ECM expression of the 3D organoids. In contrast, the mRNA expression of COL1 was increased, and those of COL4 and FN were unchanged. EM revealed that TGFβ2 caused the HTM cells to become more compact and abundant ECM deposits within the 3D organoids were observed. These were significantly inhibited by ROCK-i. The dense solids caused by the presence of TGFβ2 were significantly suppressed by ROCK-i. Current study indicates that ROCK-i cause beneficial effects toward the spatial configuration of TGFβ2-induced HTM 3D organoids.
Chronic exposure to TNF reprograms cell signaling pathways in fibroblast-like synoviocytes by establishing long-term inflammatory memory
Authors: Gangishetti Umesh , Ramirez-Perez Sergio , Jones Kyle , Arif Abul , Drissi Hicham , Bhattaram Pallavi
Published: November 2020

Fibroblast-like synoviocytes (FLS) play a critical role in the pathogenesis of rheumatoid arthritis (RA). Chronic inflammation induces transcriptomic and epigenetic modifications that imparts a persistent catabolic phenotype to the FLS, despite their dissociation from the inflammatory environment. We analyzed high throughput gene expression and chromatin accessibility data from human and mouse FLS from our and other studies available on public repositories, with the goal of identifying the persistently reprogrammed signaling pathways driven by chronic inflammation. We found that the gene expression changes induced by short-term tumor necrosis factor-alpha (TNF) treatment were largely sustained in the FLS exposed to chronic inflammation. These changes that included both activation and repression of gene expression, were accompanied by the remodeling of chromatin accessibility. The sustained activated genes (SAGs) included established pro-inflammatory signaling components known to act at multiple levels of NF-kappaB, STAT and AP-1 signaling cascades. Interestingly, the sustained repressed genes (SRGs) included critical mediators and targets of the BMP signaling pathway. We thus identified sustained repression of BMP signaling as a unique constituent of the long-term inflammatory memory induced by chronic inflammation. We postulate that simultaneous targeting of these activated and repressed signaling pathways may be necessary to combat RA persistence.
Two-dimensional Talbot effect of the optical vortices and their spatial evolution
Authors: Ikonnikov Denis A. , Myslivets Sergey A. , Volochaev Mikhail N. , Arkhipkin Vasily G. , Vyunishev Andrey M.
Published: November 2020

We report on the experimental and theoretical study of the near-field diffraction of optical vortices (OVs) at a two-dimensional diffraction grating. The Talbot effect for the optical vortices in the visible range is experimentally observed and the respective Talbot carpets for the optical vortices are experimentally obtained for the first time. It is shown that the spatial configuration of the light field behind the grating represents a complex three-dimensional lattice of beamlet-like optical vortices. A unit cell of the OV lattice is reconstructed using the experimental data and the spatial evolution of the beamlet intensity and phase singularities of the optical vortices is demonstrated. In addition, theself-healingeffect for the optical vortices, which consists in flattening of the central dip in the annular intensity distribution, i.e., restoring the image of the object plane predicted earlier is observed. The calculated results agree well with the experimental ones. The results obtained can be used to create and optimize the 3D OV lattices for a wide range of application areas.
Portable device for presbyopia correction with optoelectronic lenses driven by pupil response
Authors: Mompeán Juan , Aragón Juan L. , Artal Pablo
Published: November 2020

A novel portable device has been developed and built to dynamically, and automatically, correct presbyopia by means of a couple of opto-electronics lenses driven by pupil tracking. The system is completely portable providing with a high range of defocus correction up to 10 D. The glasses are controlled and powered by a smartphone. To achieve a truly real-time response, image processing algorithms have been implemented in OpenCL and ran on the GPU of the smartphone. To validate the system, different visual experiments were carried out in presbyopic subjects. Visual acuity was maintained nearly constant for a range of distances from 5 m to 20 cm.