bluuebunny/crossref_metadata_2025 huggingface dataset:
Tropical Belt Width Proportionately More Sensitive to Aerosols Than Greenhouse Gases
Authors: Zhao Xueying , Allen Robert J. , Wood Tom , Maycock Amanda C.
Published: March 2020

The tropical belt has widened during the last several decades, and both internal variability and anthropogenic forcings have contributed. Although greenhouse gases and stratospheric ozone depletion have been implicated as primary anthropogenic drivers of tropical expansion, the possible role of other drivers remains uncertain. Here, we analyze the tropical belt width response to idealized perturbations in multiple models. Our results show that absorbing black carbon (BC) aerosol drives tropical expansion, and scattering sulfate aerosol drives contraction. BC, especially from Asia, is more efficient per unit radiative forcing than greenhouse gases in driving tropical expansion, particularly in the Northern Hemisphere. Tropical belt expansion (contraction) is associated with an increase (decrease) in extratropical static stability induced by absorbing (scattering) aerosol. Although a formal attribution is difficult, scaling the normalized expansion rates to the historical time period suggests that BC is the largest driver of the Northern Hemisphere tropical widening but with relatively large uncertainty.
Fate of Forearc Lithosphere at Arc‐Continent Collision Zones: Evidence From Local Earthquake Tomography of the Sunda‐Banda Arc Transition, Indonesia
Authors: Supendi P. , Nugraha A. D. , Widiyantoro S. , Abdullah C. I. , Rawlinson N. , Cummins P. R. , Harris C. W. , Roosmawati N. , Miller M. S.
Published: March 2020

A new 3‐D seismic P wave velocity model of the Sunda‐Banda Arc Transition from local earthquake tomography reveals (i) northward subduction of oceanic lithosphere, associated with the convergence of Australia and Sundaland, as a high‐velocity zone extending down to ~200 km depth; (ii) two distinct low‐velocity zones, one immediately above the slab, which is likely a zone of partial melt, and one in the 0–40 km depth range, which is probably a magma chamber associated with active volcanoes above; and (iii) a northerly dipping high‐velocity zone that bisects the two low‐velocity anomalies, which we interpret as an underthrust forearc sliver of continental origin. Based on He3/He4 measurements from volcanic outflows, it is possible that the magma supply is contaminated by interaction with this forearc sliver as it ascends from the melt region below.
Different Responses of Tropical Cyclone Tracks Over the Western North Pacific and North Atlantic to Two Distinct Sea Surface Temperature Warming Patterns
Authors: Zhao Jiuwei , Zhan Ruifen , Wang Yuqing
Published: March 2020

How future tropical cyclone (TC) activity could change under global warming is enormously important to society, which has been widely assessed using state‐of‐the‐art climate models. However, these models were predominantly based on projection of an El Niño‐like warming pattern. Recent studies suggested that a La Niña‐like warming pattern is also possible. Here we compare the responses of TC track density (TCTD) over the western North Pacific and North Atlantic to the two distinct global warming patterns. We find that the La Niña‐like warming pattern reduces western North Pacific TCTD except in the South China Sea and along China coast and increases NA TCTD, while the El Niño‐like warming pattern generally reduces TCTD in both basins. This is due to different responses of large‐scale dynamic/thermodynamic conditions to the distinct zonal sea surface temperature gradients associated with the two warming patterns. These results help better understand potential future change in TC tracks.
Advection by the North Equatorial Current of a Cold Wake due to Multiple Typhoons in the Western Pacific: Measurements From a Profiling Float Array
Authors: Johnston T. M. Shaun , Rudnick Daniel L. , Brizuela Noel , Moum James N.
Published: March 2020

Cold wakes of previous tropical cyclones (TCs) affect the development of subsequent TCs, but few subsurface data sets have sufficient persistence and spatial coverage to follow a cold wake as it is advected by currents. For >2 months in 2018, an array of eight floats obtained >20,000 temperature profiles from the surface to <200 m every <40 min before, during, and after Super Typhoons Mangkhut, Trami, Kong‐Rey, and Yutu. Two floats were in/near Mangkhut's eye, experienced gale force winds during Trami and Kong‐Rey, drifted over 1,000 km westward with the North Equatorial Current, and tracked the advection of the weakly stratified, cold wake produced by the sequence of TCs. Sea surface temperature shows the westward advection of the cumulative cold wake. While causation cannot be established, since atmospheric measurements were not made, Yutu weakened as it passed over the cold wake. The stratification and the energy needed to mix the water column in the cold wake decreased with each TC. One float directly in the path of Yutu showed that mixing to 125–150 m was likely, corresponding to a cooling of 0.5–1°C under the eye. Sea surface temperature in the cold wake cooled by 1°C within a 150 km radius of Yutu's eye, where the effect on air‐sea heat fluxes is maximal. A cold wake can remain weakly stratified for many weeks during a sequence of TCs. These results also suggest that an advected cold wake from previous TCs may contribute many weeks later to the arrested development of a subsequent TC at a distant location.
A New Improved Estimation of Agulhas Leakage Using Observations and Simulations of Lagrangian Floats and Drifters
Authors: Daher Houraa , Beal Lisa M. , Schwarzkopf Franziska U.
Published: March 2020

A new estimate of Agulhas leakage transport is calculated using profiling floats and drifters. Since Richardson's seminal estimate of 15 Sv in 2007, the number of floats and drifters passing through the Agulhas Current has quadrupled. Within uncertainties we find the same leakage percentages as Richardson, with 34% of drifters leaking at the surface and 21% of floats leaking at 1,000 m depth. We find that the drifters tend to follow a northward leakage pathway via the Benguela Current compared to the northwestward leakage pathway of the floats along the Agulhas Ring corridor. We simulate the isobaric and profiling behavior of the floats and drifters using two high resolution models and two offline Lagrangian tracking tools, quantifying for the first time the sampling biases associated with the observations. We find that the isobaric bias cannot be robustly simulated but likely causes an underestimate of observed leakage by one or two Sverdrups. The profiling behavior of the floats causes no significant bias in the leakage. Fitting a simulated vertical leakage profile to the observed leakage percentages from the floats and drifters and using the mean Agulhas transport observed by a moored array at 34°S we find an improved Agulhas leakage transport of 21.3 Sv, with an estimated error of 4.7 Sv. Our new leakage transport is higher primarily because we account for leakage at depths down to 2,000 m, while Richardson considered only the top 1,000 m of the water column.
Analyses Through the Metastatistical Extreme Value Distribution Identify Contributions of Tropical Cyclones to Rainfall Extremes in the Eastern United States
Authors: Miniussi Arianna , Villarini Gabriele , Marani Marco
Published: March 2020

Tropical cyclones (TCs) generate extreme precipitation with severe impacts across large coastal and inland areas, calling for accurate frequency estimation methods. Statistical approaches that take into account the physical mechanisms responsible for these extremes can help reduce the estimation uncertainty. Here we formulate a mixed‐population Metastatistical Extreme Value Distribution explicitly incorporating non‐TC and TC‐induced rainfall and evaluate its implications on long series of daily rainfall for six major U.S. urban areas impacted by these storms. We find statistically significant differences between the distributions of TC‐ and non‐TC‐related precipitation; moreover, including mixtures of distributions improves the estimation of the probability of extreme precipitation where TCs occur more frequently. These improvements are greater when rainfall aggregated over durations longer than one day are considered.
Impact of Current‐Wind Interaction on Vertical Processes in the Southern Ocean
Authors: Song Hajoon , Marshall John , McGillicuddy Dennis J. , Seo Hyodae
Published: March 2020

Momentum input from westerly winds blowing over the Southern Ocean can be modulated by mesoscale surface currents and result in changes in large‐scale ocean circulation. Here, using an eddy‐resolving 1/20 degree ocean model configured near Drake Passage, we evaluate the impact of current‐wind interaction on vertical processes. We find a reduction in momentum input from the wind, reduced eddy kinetic energy, and a modification of Ekman pumping rates. Wind stress curl resulting from current‐wind interaction leads to net upward motion, while the nonlinear Ekman pumping term associated with horizontal gradients of relative vorticity induces net downward motion. The spatially averaged mixed layer depth estimated using a density criteria is shoaled slightly by current‐wind interaction. Current‐wind interaction, on the other hand, enhances the stratification in the thermocline below the mixed layer. Such changes have the potential to alter biogeochemical processes including nutrient supply, biological productivity, and air‐sea carbon dioxide exchange.
A direct comparison of selective BH3-mimetics reveals BCL-XL, BCL-2 and MCL-1 as promising therapeutic targets in neuroblastoma
Authors: Bierbrauer Annika , Jacob Maureen , Vogler Meike , Fulda Simone
Published: March 2020

Background

Despite advances in the treatment of neuroblastoma, patients with high-risk disease still have dismal survival prognosis. Neuroblastoma cells display elevated expression of the antiapoptotic BCL-2 proteins, suggesting that BH3-mimetics may be a promising treatment option. Here, we investigated the role of BCL-2, BCL-XL and MCL-1 in neuroblastoma.

Methods

A panel of neuroblastoma cell lines and primary patient-derived cells were exposed to BH3-mimetics targeting BCL-2 (ABT-199), BCL-XL (A1331852) or MCL-1 (S63845). In addition, protein expression and interaction patterns were analysed using Western blotting and immunoprecipitation.

Results

All tested BH3-mimetics were able to induce apoptosis in neuroblastoma cell lines, indicating that not only BCL-2 but also BCL-XL and MCL-1 may be promising therapeutic targets. Primary patient-derived cells displayed highest sensitivity to A1331852, highlighting the important role of BCL-XL in neuroblastoma. Further analysis into the molecular mechanisms of apoptosis revealed that A1331852 and S63845 displaced proapoptotic proteins like BIM and BAK from their antiapoptotic targets, subsequently leading to the activation of BAX and BAK and caspase-dependent apoptosis.

Conclusions

By using selective BH3-mimetics, this study demonstrates that BCL-2, BCL-XL, and MCL-1 are all relevant therapeutic targets in neuroblastoma. A1331852 and S63845 induce rapid apoptosis that is initiated following a displacement of BAK from BCL-XL or MCL-1, respectively.
A programmable chemical computer with memory and pattern recognition
Authors: Parrilla-Gutierrez Juan Manuel , Sharma Abhishek , Tsuda Soichiro , Cooper Geoffrey J. T. , Aragon-Camarasa Gerardo , Donkers Kevin , Cronin Leroy
Published: March 2020

Current computers are limited by the von Neumann bottleneck, which constrains the throughput between the processing unit and the memory. Chemical processes have the potential to scale beyond current computing architectures as the processing unit and memory reside in the same space, performing computations through chemical reactions, yet their lack of programmability limits them. Herein, we present a programmable chemical processor comprising of a 5 by 5 array of cells filled with a switchable oscillating chemical (Belousov–Zhabotinsky) reaction. Each cell can be individually addressed in the ‘on’ or ‘off’ state, yielding more than 2.9 × 1017 chemical states which arise from the ability to detect distinct amplitudes of oscillations via image processing. By programming the array of interconnected BZ reactions we demonstrate chemically encoded and addressable memory, and we create a chemical Autoencoder for pattern recognition able to perform the equivalent of one million operations per second.
Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes
Authors: Schmidt Hanno , Collier Travis C. , Hanemaaijer Mark J. , Houston Parker D. , Lee Yoosook , Lanzaro Gregory C.
Published: March 2020

A number of recent papers report that standing genetic variation in natural populations includes ubiquitous polymorphisms within target sites for Cas9-based gene drive (CGD) and that these “drive resistant alleles” (DRA) preclude the successful application of CGD for managing these populations. Here we report the results of a survey of 1280 genomes of the mosquitoes Anopheles gambiae, An. coluzzii, and Aedes aegypti in which we determine that ~90% of all protein-encoding CGD target genes in natural populations include at least one target site with no DRAs at a frequency of ≥1.0%. We conclude that the abundance of conserved target sites in mosquito genomes and the inherent flexibility in CGD design obviates the concern that DRAs present in the standing genetic variation of mosquito populations will be detrimental to the deployment of this technology for population modification strategies.
Female copulation song is modulated by seminal fluid
Authors: Kerwin Peter , Yuan Jiasheng , von Philipsborn Anne C.
Published: March 2020

In most animal species, males and females communicate during sexual behavior to negotiate reproductive investments. Pre-copulatory courtship may settle if copulation takes place, but often information exchange and decision-making continue beyond that point. Here, we show that female Drosophila sing by wing vibration in copula. This copulation song is distinct from male courtship song and requires neurons expressing the female sex determination factor DoublesexF. Copulation song depends on transfer of seminal fluid components of the male accessory gland. Hearing female copulation song increases the reproductive success of a male when he is challenged by competition, suggesting that auditory cues from the female modulate male ejaculate allocation. Our findings reveal an unexpected fine-tuning of reproductive decisions during a multimodal copulatory dialog. The discovery of a female-specific acoustic behavior sheds new light on Drosophila mating, sexual dimorphisms of neuronal circuits and the impact of seminal fluid molecules on nervous system and behavior.
Tomographic mapping of the nanoscale water-filled pore structure in corroded borosilicate glass
Authors: Perea Daniel E. , Schreiber Daniel K. , Ryan Joseph V. , Wirth Mark G. , Deng Lu , Lu Xiaonan , Du Jincheng , Vienna John D.
Published: March 2020

Cryo-based atom probe tomography has been applied to directly reveal the water-solid interface and hydrated corrosion layers making up the nanoscale porous structure of a corroded borosilicate glass in its native aqueous environment. The analysis includes morphology and compositional mapping of the inner gel/glass interface, isolation of a tomographic sub-volume of the tortuous water-filled gel, and comparison of the gel structure with simulations. The nanoscale porous structure is qualitatively consistent with that of the molecular dynamics simulation, enabling in greater confidence in both interrogations. Comparison of the gel/glass interface between desiccated and cryogenically preserved samples reveals consistently abrupt B dissolution behavior and quantitative differences in the apparent H ingress into the glass. These comparisons give some guidance to future experimental approaches to understanding glass corrosion behavior. More broadly, the cryogenic preservation and 3D visualization of the native water/solid structure in 3D at the nanoscale has direct relevance to a wide range of materials systems beyond glass science.
Structural and functional brain abnormalities in children with schizotypal disorder: a pilot study
Authors: Wang Ya , Harding Ian H. , Testa Renee , Tonge Bruce , Jones Harvey , Seal Marc , Ross Nola , Chan Raymond C. K. , van Beurden Florian , Abu-Akel Ahmad , Skafidas Efstratios , Pantelis Christos
Published: March 2020

Schizotypal disorder lies in the schizophrenia spectrum and is widely studied in adult populations. Schizotypal disorder in children (SDc) is less well described. This study examined brain morphological and functional connectivity abnormalities in SDc (12 SDc and 9 typically developing children), focusing on the default mode and executive control brain networks. Results indicated that SDc is associated with reduced grey matter volume (GMV) in superior and medial frontal gyri, and increased resting-state functional connectivity between the superior frontal gyrus and inferior parietal lobule, compared to typically developing children (cluster-level FWE-corrected p < 0.05). The brain structure abnormality (GMV in left superior frontal gyrus) was correlated with clinical symptoms in SDc (r = −0.66, p = 0.026) and functional connectivity abnormality was correlated with extra-dimensional shifting impairments in all participants (r = 0.62, p = 0.011), suggesting their contribution to the underlying mechanisms of clinical presentation. These preliminary results motivate further work to characterize the neural basis of SDc and its significance as a risk factor for later psychosis.
Economic evaluation of ion-exchange processes for nutrient removal and recovery from municipal wastewater
Authors: Huang Xiangjun , Guida Samuela , Jefferson Bruce , Soares Ana
Published: March 2020

Ion exchange (IEX) processes are a promising alternative to remove and recover nutrients from municipal wastewater. To assess the feasibility and viability of IEX processes for full-scale application, this study aimed at providing an evaluation of performance and economics on upscaling these processes for two different configurations in a 10,000 population equivalent wastewater treatment plant (WWTP) and compared them with a traditional biological nutrient removal (BNR) plant. The IEX processes were designed based on existing pilot-scale data, and after aerobic or anaerobic carbon removal stages. The nutrients were recovered from spent regenerants in the form of (NH4)2SO4 and hydroxyapatite Ca5(PO4)3(OH), allowing regenerant reuse. The 40-year whole life cost (WLC) of IEX coupled with traditional activated sludge processes was estimated to be ~£7.4 M, and WLC of IEX coupled with anaerobic membrane process was estimated to be £6.1 M, which was, respectively, 17% and 27% less than the traditional BNR based WWTP. Furthermore, ~98 tonnes of (NH4)2SO4 and 3.4 tonnes of Ca3(PO4)2 could be recovered annually. The benefits of lower costs, reduction in greenhouse gas emissions and nutrient recovery aligned with circular economy, illustrated that IEX processes are attractive for nutrient removal and recovery from municipal wastewater.
Bayesian Optimization for Materials Design with Mixed Quantitative and Qualitative Variables
Authors: Zhang Yichi , Apley Daniel W. , Chen Wei
Published: March 2020

Although Bayesian Optimization (BO) has been employed for accelerating materials design in computational materials engineering, existing works are restricted to problems with quantitative variables. However, real designs of materials systems involve both qualitative and quantitative design variables representing material compositions, microstructure morphology, and processing conditions. For mixed-variable problems, existing Bayesian Optimization (BO) approaches represent qualitative factors by dummy variables first and then fit a standard Gaussian process (GP) model with numerical variables as the surrogate model. This approach is restrictive theoretically and fails to capture complex correlations between qualitative levels. We present in this paper the integration of a novel latent-variable (LV) approach for mixed-variable GP modeling with the BO framework for materials design. LVGP is a fundamentally different approach that maps qualitative design variables to underlying numerical LV in GP, which has strong physical justification. It provides flexible parameterization and representation of qualitative factors and shows superior modeling accuracy compared to the existing methods. We demonstrate our approach through testing with numerical examples and materials design examples. The chosen materials design examples represent two different scenarios, one on concurrent materials selection and microstructure optimization for optimizing the light absorption of a quasi-random solar cell, and another on combinatorial search of material constitutes for optimal Hybrid Organic-Inorganic Perovskite (HOIP) design. It is found that in all test examples the mapped LVs provide intuitive visualization and substantial insight into the nature and effects of the qualitative factors. Though materials designs are used as examples, the method presented is generic and can be utilized for other mixed variable design optimization problems that involve expensive physics-based simulations.
Large-scale acoustic-driven neuronal patterning and directed outgrowth
Authors: Cohen Sharon , Sazan Haim , Kenigsberg Avraham , Schori Hadas , Piperno Silvia , Shpaisman Hagay , Shefi Orit
Published: March 2020

Acoustic manipulation is an emerging non-invasive method enabling precise spatial control of cells in their native environment. Applying this method for organizing neurons is invaluable for neural tissue engineering applications. Here, we used surface and bulk standing acoustic waves for large-scale patterning of Dorsal Root Ganglia neurons and PC12 cells forming neuronal cluster networks, organized biomimetically. We showed that by changing parameters such as voltage intensity or cell concentration we were able to affect cluster properties. We examined the effects of acoustic arrangement on cells atop 3D hydrogels for up to 6 days and showed that assembled cells spontaneously grew branches in a directed manner towards adjacent clusters, infiltrating the matrix. These findings have great relevance for tissue engineering applications as well as for mimicking architectures and properties of native tissues.
Author Correction: Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing
Authors: Das Sarbashis , Pettersson B. M. Fredrik , Behra Phani Rama Krishna , Mallick Amrita , Cheramie Martin , Ramesh Malavika , Shirreff Lisa , DuCote Tanner , Dasgupta Santanu , Ennis Don G. , Kirsebom Leif. A.
Published: March 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Rooting behaviour and soil properties in different bamboo species of Western Himalayan Foothills, India
Authors: Kaushal R. , Singh Indra , Thapliyal S. D. , Gupta A. K. , Mandal D. , Tomar J. M. S. , Kumar Ambrish , Alam N. M. , Kadam D. , Singh D. V. , Mehta H. , Dogra Pradeep , Ojasvi P. R. , Reza S. , Durai J.
Published: March 2020

Due to extensive root system, connected rhizome bamboos are considered suitable for improving soil properties within a short period, though most of the claims are anecdotal and need to be supported with quantified data. The study evaluates seven bamboo species viz., Bambusa balcooa, Bambusa bambos, Bambusa vulgaris, Bambusa nutans, Dendrocalamus hamiltonii, Dendrocalamus stocksii and Dendrocalamus strictus for their rooting pattern and impact on soil health properties. Coarse and fine root intensity was maximum in B. vulgaris. Coarse root biomass ranged from 0.6 kg m−3 in B. nutans to 2.0 kg m−3 in B. vulgaris and B. bambos. Fine root biomass ranged from 1.1 kg m−3 in B. nutans to 4.5 kg m−3 in D. hamiltonii. Contribution of fine roots in terms of intensity and biomass was much higher than coarse roots. Fine root biomass showed declining trend with increase in soil depth in all the species. During sixth year, the litter fall ranged from 8.1 Mg ha−1 in D. stocksii to 12.4 Mg ha−1 in D. hamiltonii. Among soil physical properties significant improvement were recorded in hydraulic conductivity, water stable aggregates and mean weight diameter. Soil pH, organic carbon and available phosphorus under different species did not reveal any significant changes, while significant reduction was observed in total nitrogen and potassium. Significant positive correlation was observed between WSA and iron content. Soil microbial population and enzyme activities were higher in control plot. Considering root distribution, biomass, soil hydraulic conductivity and water stable aggregates, B. bambos, B. vulgaris and D. hamiltonii are recommended for rehabilitation of degraded lands prone to soil erosion.
Structural, Magnetic, and Dielectric properties of Sr4Fe6O13 ferrite prepared of small crystallites
Authors: Azab A. A. , Mansour A. M. , Turky G. M.
Published: March 2020

A stable Sr4Fe6O13 was prepared as small crystallites by auto-combustion of a sol-gel in air followed by annealing the later at pertinent temperatures. A green sample, as annealed at elevated temperatures, yields a single Sr4Fe6O13 phase of tailored magnetic properties. The structural, morphological, magnetic and electrical properties were investigated by X-ray diffraction, transmission electron microscopy, vibrating sample magnetometer, and broadband dielectric spectrometer. Hard magnetic Sr4Fe6O13 properties arise with saturation magnetization Ms = 12.4 emu/g, coercivity Hc = 3956.7 Oe and squareness 0.512. Studies made at low temperatures reveals Ms decreasing on increasing temperature from 17.5 emu/g at 85 K down to 12.4 emu/g at 305 K, while Hc rises from 1483 Oe at 85 K to 1944 Oe at 305 K. The ac-conductivity follows the Jonscher relation. The dc-conductivity at high temperatures/low frequencies exhibits a plateau and it depends linearly on a characteristic frequency according to the Barton-Nakajima-Namikawa) relation.
Screening ginseng saponins in progenitor cells identifies 20(R)-ginsenoside Rh2 as an enhancer of skeletal and cardiac muscle regeneration
Authors: Kim Ah Ra , Kim Seon-Wook , Lee Ba-Wool , Kim Kuk-Hwa , Kim Woong-Hee , Seok Hong , Lee Ji-Hyung , Um JungIn , Yim Soon-Ho , Ahn Youngkeun , Jin Suk-Won , Jung Da-Woon , Oh Won Keun , Williams Darren R.
Published: March 2020

Aging is associated with increased prevalence of skeletal and cardiac muscle disorders, such as sarcopenia and cardiac infarction. In this study, we constructed a compendium of purified ginsenoside compounds fromPanax ginsengC.A. Meyer, which is a traditional Korean medicinal plant used to treat for muscle weakness. Skeletal muscle progenitor cell-based screening identified three compounds that enhance cell viability, of which 20(R)-ginsenoside Rh2showed the most robust response. 20(R)-ginsenoside Rh2increased viability in myoblasts and cardiomyocytes, but not fibroblasts or disease-related cells. The cellular mechanism was identified as downregulation of cyclin-dependent kinase inhibitor 1B (p27Kip1) via upregulation of Akt1/PKB phosphorylation at serine 473, with the orientation of the 20 carbon epimer being crucially important for biological activity. In zebrafish and mammalian models, 20(R)-ginsenoside Rh2enhanced muscle cell proliferation and accelerated recovery from degeneration. Thus, we have identified 20(R)-ginsenoside Rh2as a p27Kip1inhibitor that may be developed as a natural therapeutic for muscle degeneration.
ecTMB: a robust method to estimate and classify tumor mutational burden
Authors: Yao Lijing , Fu Yao , Mohiyuddin Marghoob , Lam Hugo Y. K.
Published: March 2020

Tumor Mutational Burden (TMB) is a measure of the abundance of somatic mutations in a tumor, which has been shown to be an emerging biomarker for both anti-PD-(L)1 treatment and prognosis; however, multiple challenges still hinder the adoption of TMB as a biomarker. The key challenges are the inconsistency of tumor mutational burden measurement among assays and the lack of a meaningful threshold for TMB classification. Here we describe a new method, ecTMB (Estimation and Classification of TMB), which uses an explicit background mutation model to predict TMB robustly and to classify samples into biologically meaningful subtypes defined by tumor mutational burden.
Prevalence of HPV infection among sexually active adolescents and young adults in Brazil: The POP-Brazil Study
Authors: Wendland Eliana Marcia , Villa Luisa Lina , Unger Elizabeth R. , Domingues Carla Magda , Benzaken Adele Schwartz ,   POP-Brazil Study Group, Maranhão Ana Goretti Kalume , Kops Natalia Luiza , Bessel Marina , Caierão Juliana , Hohenberger Glaucia Fragoso , Horvath Jaqueline , Tavares Giovana , Mello Barbara Pereira , Santos Aniusca Vieira dos , Berto Maiquidieli Dal , Bica Claudia , Pereira Gerson Fernandes Mendes , Moreno Flavia
Published: March 2020

For Brazil, there are no nationwide data on HPV prevalence against which the impact of the HPV immunization program can be measured in the future. Therefore, we aim to evaluate the prevalence of genital HPV infection among adolescents and young adults in Brazil. A cross-sectional, multicentric, nationwide survey was conducted between September 2016 and November 2017. Sexually active unvaccinated women and men aged 16 to 25 years old were recruited from 119 public primary care units, including all 26 state capitals and the Federal District. All participants answered a face-to-face interview and provided biological samples for genital HPV analysis. We used an automated DNA extraction method and HPV genotyping was performed using the Linear Array genotyping test (Roche). Of 7,694 participants, 53.6% (95% CI 51.4–55.8) were positive for any HPV type. The prevalence of high-risk HPV types was significantly higher in women (38.6% vs. 29.2%, P < 0·001). The HPV types included in the quadrivalent vaccine were detected in 1002 (14.8%) specimens, with a different pattern of HPV infection between sexes. Characteristics associated with overall HPV detection included female gender, self-declaration of race as brown/pardo, lower socioeconomic class, single or dating, current smoking and having 2 or more sex partners in the past year. We found a high prevalence of HPV, with significant differences between regions. Our data provide information that may be considered when developing HPV prevention policies and constitute a baseline against which the impact of the HPV immunization program in Brazil can be measured in future years.
Malignancy and IgG4-related disease: the incidence, related factors and prognosis from a prospective cohort study in China
Authors: Tang Hanqi , Yang Huaxia , Zhang Panpan , Wu Di , Zhang Shangzhu , Zhao Jiuliang , Peng Linyi , Chen Hua , Fei Yunyun , Zhang Xuan , Zhao Yan , Zeng Xiaofeng , Zhang Fengchun , Zhang Wen
Published: March 2020

This prospective cohort study aims to investigate the incidence, related factors and prognosis of IgG4-related disease (IgG4-RD) with malignancies in the Chinese cohort. We prospectively analyzed the IgG4-RD patients recruited in Peking Union Medical College Hospital from January 2011 to August 2018 and identified patients diagnosed with IgG4-RD complicating malignancies. Data regarding demographics, clinical features, treatment and prognosis of IgG4-RD patients complicating malignancies were collected and compared to those of age- and sex-matched controls. Among the 587 Chinese patients with IgG4-RD, 17 malignancies were identified. Ten of them developed malignancy after the diagnosis of IgG4-RD, given a standard incidence ratio (SIR) of 2.78 (95%CI 1.33–5.12). Multivariate logistic analysis indicated that autoimmune pancreatitis (OR = 6.230, 95%CI 1.559–24.907, p = 0.010) was positively associated with malignancy, whereas eosinophilia (OR = 0.094, 95%CI 0.010–0.883, p = 0.039) was negatively related with malignancies. During a median follow-up period of 61.4 ± 26.4 months, all patients with IgG4-RD and malignancies survived. We conclude that an increased incidence of malignancy was found in Chinese IgG4-RD cohort. Autoimmune pancreatitis is a potential risk factor, whereas eosinophilia is a possible protective factor for complicating malignancies.
Probing dynamical cortical gating of attention with concurrent TMS-EEG
Authors: Okazaki Yuka O. , Mizuno Yuji , Kitajo Keiichi
Published: March 2020

Attention facilitates the gating of information from the sending brain area to the receiving areas, with this being achieved by dynamical changes in effective connectivity, which refers to the directional influences between cortical areas. To probe the effective connectivity and cortical excitability modulated by covertly shifted attention, transcranial magnetic stimulation (TMS) was used to directly perturb the right retinotopic visual cortex with respect to attended and unattended locations, and the impact of this was tracked from the stimulated area to other areas by concurrent use of electroencephalography (EEG). TMS to the contralateral visual hemisphere led to a stronger evoked potential than stimulation to the ipsilateral hemisphere. Moreover, stronger beta- and gamma-band effective connectivities assessed as time-delayed phase synchronizations between stimulated areas and other areas were observed when TMS was delivered to the contralateral hemisphere. These effects were more enhanced when they preceded more prominent alpha lateralization, which is known to be associated with attentional gating. Our results indicate that attention-regulated cortical feedforward effective connectivity can be probed by TMS-EEG with direct cortical stimulation, thereby bypassing thalamic gating. These results suggest that cortical gating of the feedforward input is achieved by regulating the effective connectivity in the phase dynamics between cortical areas.
Impact of global structure on diffusive exploration of organelle networks
Authors: Brown Aidan I. , Westrate Laura M. , Koslover Elena F.
Published: March 2020

We investigate diffusive search on planar networks, motivated by tubular organelle networks in cell biology that contain molecules searching for reaction partners and binding sites. Exact calculation of the diffusive mean first-passage time on a spatial network is used to characterize the typical search time as a function of network connectivity. We find that global structural properties — the total edge length and number of loops — are sufficient to largely determine network exploration times for a variety of both synthetic planar networks and organelle morphologies extracted from living cells. For synthetic networks on a lattice, we predict the search time dependence on these global structural parameters by connecting with percolation theory, providing a bridge from irregular real-world networks to a simpler physical model. The dependence of search time on global network structural properties suggests that network architecture can be designed for efficient search without controlling the precise arrangement of connections. Specifically, increasing the number of loops substantially decreases search times, pointing to a potential physical mechanism for regulating reaction rates within organelle network structures.
Identifying predictive features of autism spectrum disorders in a clinical sample of adolescents and adults using machine learning
Authors: Küpper Charlotte , Stroth Sanna , Wolff Nicole , Hauck Florian , Kliewer Natalia , Schad-Hansjosten Tanja , Kamp-Becker Inge , Poustka Luise , Roessner Veit , Schultebraucks Katharina , Roepke Stefan
Published: March 2020

Diagnosing autism spectrum disorders (ASD) is a complicated, time-consuming process which is particularly challenging in older individuals. One of the most widely used behavioral diagnostic tools is the Autism Diagnostic Observation Schedule (ADOS). Previous work using machine learning techniques suggested that ASD detection in children can be achieved with substantially fewer items than the original ADOS. Here, we expand on this work with a specific focus on adolescents and adults as assessed with the ADOS Module 4. We used a machine learning algorithm (support vector machine) to examine whether ASD detection can be improved by identifying a subset of behavioral features from the ADOS Module 4 in a routine clinical sample of N = 673 high-functioning adolescents and adults with ASD (n = 385) and individuals with suspected ASD but other best-estimate or no psychiatric diagnoses (n = 288). We identified reduced subsets of 5 behavioral features for the whole sample as well as age subgroups (adolescents vs. adults) that showed good specificity and sensitivity and reached performance close to that of the existing ADOS algorithm and the full ADOS, with no significant differences in overall performance. These results may help to improve the complicated diagnostic process of ASD by encouraging future efforts to develop novel diagnostic instruments for ASD detection based on the identified constructs as well as aiding clinicians in the difficult question of differential diagnosis.
The effect of metallic substrates on the optical properties of monolayer MoSe2
Authors: Grzeszczyk M. , Molas M. R. , Nogajewski K. , Bartoš M. , Bogucki A. , Faugeras C. , Kossacki P. , Babiński A. , Potemski M.
Published: March 2020

Atomically thin materials, like semiconducting transition metal dichalcogenides (S-TMDs), are highly sensitive to the environment. This opens up an opportunity to externally control their properties by changing their surroundings. Photoluminescence and reflectance contrast techniques are employed to investigate the effect of metallic substrates on optical properties of MoSe2 monolayer (ML). The optical spectra of MoSe2 MLs deposited on Pt, Au, Mo and Zr have distinctive metal-related lineshapes. In particular, a substantial variation in the intensity ratio and the energy separation between a negative trion and a neutral exciton is observed. It is shown that using metals as substrates affects the doping of S-TMD MLs. The explanation of the effect involves the Schottky barrier formation at the interface between the MoSe2 ML and the metallic substrates. The alignment of energy levels at the metal/semiconductor junction allows for the transfer of charge carriers between them. We argue that a proper selection of metallic substrates can be a way to inject appropriate types of carriers into the respective bands of S-TMDs.
Ecological interactions are a primary driver of population dynamics in wine yeast microbiota during fermentation
Authors: Bagheri Bahareh , Bauer Florian Franz , Cardinali Gianluigi , Setati Mathabatha Evodia
Published: March 2020

Spontaneous wine fermentation is characterized by yeast population evolution, modulated by complex physical and metabolic interactions amongst various species. The contribution of any given species to the final wine character and aroma will depend on its numerical persistence during the fermentation process. Studies have primarily evaluated the effect of physical and chemical factors such as osmotic pressure, pH, temperature and nutrient availability on mono- or mixed-cultures comprising 2–3 species, but information about how interspecies ecological interactions in the wine fermentation ecosystem contribute to population dynamics remains scant. Therefore, in the current study, the effect of temperature and sulphur dioxide (SO2) on the dynamics of a multi-species yeast consortium was evaluated in three different matrices including synthetic grape juice, Chenin blanc and Grechetto bianco. The population dynamics were affected by temperature and SO2, reflecting differences in stress resistance and habitat preferences of the different species and influencing the production of most volatile aroma compounds. Evidently at 15 °C and in the absence of SO2 non-Saccharomyces species were dominant, whereas at 25 °C and when 30 mg/L SO2 was added S. cerevisiae dominated. Population growth followed similar patterns in the three matrices independently of the conditions. The data show that fermentation stresses lead to an individual response of each species, but that this response is strongly influenced by the interactions between species within the ecosystem. Thus, our data suggest that ecological interactions, and not only physico-chemical conditions, are a dominant factor in determining the contribution of individual species to the outcome of the fermentation.
Severe maternal morbidity by mode of delivery in women with twin pregnancy and planned vaginal delivery
Authors: Korb Diane , Deneux-Tharaux Catherine , Goffinet François , Schmitz Thomas
Published: March 2020

Planned vaginal delivery in twin pregnancies has three potential outcomes: vaginal or cesarean delivery of both twins, or cesarean for the second twin. Our objective was to assess the association between delivery mode and severe acute maternal morbidity (SAMM) in women with twin pregnancies and planned vaginal deliveries. We limited this planned secondary analysis of the JUMODA cohort, a national prospective population-based study of twin deliveries, to women with planned vaginal delivery at or after 24 weeks of gestation who gave birth to two live fetuses at hospital. The association between delivery mode and SAMM was estimated from multivariate Poisson regression models. Of 5,055 women with planned vaginal delivery, 4,007 (79.3%) delivered both twins vaginally, 134 (2.6%) had cesarean for the second twin and 914 (18.1%) cesarean for both twins. Compared to vaginal delivery of both twins, the risk of SAMM was significantly higher after cesarean for the second twin (9.0% versus 4.5%; aRR 2.22, 95% CI 1.27–3.88) and for both twins (9.4% versus 4.5%, aRR 1.56, 95% CI 1.16–2.10). In twin pregnancies with planned vaginal delivery, cesarean deliveries for the second twin and for both twins are associated with higher risks of SAMM than vaginal delivery.
Hollow Polyaniline Microsphere/Fe3O4 Nanocomposite as an Effective Adsorbent for Removal of Arsenic from Water
Authors: Dutta Soumi , Manna Kunal , Srivastava Suneel Kumar , Gupta Ashok Kumar , Yadav Manoj Kumar
Published: March 2020

Polyaniline hollow microsphere (PNHM)/Fe3O4magnetic nanocomposites have been synthesized by a novel strategy and characterized. Subsequently, PNHM/Fe3O4-40 (Fe3O4content: 40 wt.%) was used as an adsorbent for the removal of arsenic (As) from the contaminated water. Our investigations showed 98–99% removal of As(III) and As(V) in the presence of PNHM/Fe3O4-40 following pseudo-second-order kinetics (R2 > 0.97) and equilibrium isotherm data fitting well with Freundlich isotherm (R2 > 0.98). The maximum adsorption capacity of As(III) and As(V) correspond to 28.27 and 83.08 mg g−1, respectively. A probable adsorption mechanism based on X-ray photoelectron spectroscopy analysis was also proposed involving monodentate-mononuclear/bidentate-binuclear As-Fe complex formation via legend exchange. In contrast to NO3−and SO42−ions, the presence of PO43−and CO32−co-ions in contaminated water showed decrease in the adsorption capacity of As(III) due to the competitive adsorption. The regeneration and reusability studies of spent PNHM/Fe3O4-40 adsorbent showed ~83% of As(III) removal in the third adsorption cycle. PNHM/Fe3O4-40 was also found to be very effective in the removal of arsenic (<10 μg L−1) from naturally arsenic-contaminated groundwater sample.
Practical and environment-friendly indirect electrochemical reduction of indigo and dyeing
Authors: Yi Changhai , Tan Xiaodong , Bie Bihan , Ma Haitao , Yi Hong
Published: March 2020

Indigo has been widely used as a dye in the industrial dyeing due to its good color fastness in dyeing cellulose fibers. However, excess reducing agent, “insurance powder (Na2S2O4)”, was always used in the actual production of the factory, sparking serious pollution (water pollution and air pollution). Herein, we developed a practical and environment-friendly indirect electrochemical reduction of indigo, and applied this method for cloth dyeing. The electrochemical device was designed in the combination of source of electro-catalytic reduction and dyeing. The iron-triethanolamine-calcium gluconate (Fe-TEOA-Ca) complex played a role of key intermediate, and ultrasonic wave was found to speed up the indirect electro-catalytic process. The electrochemical performance of intermedia was improved by calcium ion addition. Washed with oxalic acid solution, the dyed fabric could achieve the level of color fastness in industry standard. Generally speaking, our method leads to a green route for indigo reduction using electrochemistry, which may change the crafting process of indigo dyeing in industry.
Involvement of the Nucleus Accumbens in Chocolate-induced Cataplexy
Authors: Su Jingyang , Li Zhi , Yamashita Akira , Kusumoto-Yoshida Ikue , Isomichi Takuto , Hao Liying , Kuwaki Tomoyuki
Published: March 2020

Happiness is key for both mental and physical well-being. To further understand the brain mechanisms involved, we utilized the cataplexy that occurs in narcoleptic animal models as a quantitative behavioral measure because it is triggered by actions associated with happiness, such as laughter in humans and palatable foods in mice. Here we report that the rostral part of the nucleus accumbens (NAc) shell is strongly activated during the beginning of chocolate-induced cataplexy in orexin neuron-ablated mice. We made a local lesion in the NAc using ibotenic acid and observed the animals’ behavior. The number of cataplexy bouts was negatively correlated to the lesion size. We also examined the hedonic response to palatable food by measuring the number of tongue protrusions in response to presentation of honey, which was also found to be negatively correlated to the lesion size. Next, we used clozapine N-oxide to either activate or inactivate the NAc through viral DREADD expression. As expected, the number of cataplexy bouts increased with activation and decreased with inactivation, and saline control injections showed no changes. Hedonic response in the DREADD experiment varied and showed both increases and decreases across mice. These results demonstrated that the rostral part of the NAc plays a crucial role in triggering cataplexy and hedonic orofacial movements. Since the NAc is also implicated in motivated behavior, we propose that the NAc is one of the key brain structures involved in happiness and is a driving force for positive emotion-related behaviors.
Neuroprotection with rasagiline in patients with macula-off retinal detachment: A randomized controlled pilot study
Authors: Yu Siqing , Framme Carsten , Menke Marcel Nico , Berger Lieselotte Erika , Zinkernagel Martin Sebastian , Munk Marion Rohit , Wolf Sebastian , Ebneter Andreas
Published: March 2020

We aimed to evaluate the neuroprotective efficacy of rasagiline in pseudophakic patients who had surgery for macula-off rhegmatogenous retinal detachment (RRD). This was a 6-month, prospective, randomized, double-blind, placebo-controlled pilot study. Patients presenting with acute macula-off RRD were recruited and randomized 1:1 to receive rasagiline 1 mg/day or placebo for 7 days. Best-corrected visual acuity (BCVA) and optical coherence tomography were acquired 1 day before as well as 2 days, 3 weeks, 3 months and 6 months after surgery. We screened 26 patients with RRD whereof 23 were eventually included and randomized. The primary outcome was final BCVA. Secondary outcomes included central retinal thickness (CRT) and adverse events (AE). We evaluated photoreceptor cells (prc) recovery through morphological measurements. The baseline characteristics were comparable between groups. BCVA significantly improved in both groups (letters gained: rasagiline 61.5 ± 18.1 vs placebo 55.3 ± 29.2, p = 0.56), but no significant inter-group difference was found at any visit. CRT was stable 3 weeks after surgery onwards, with no inter-group difference. No treatment-emergent AE occurred. Significant prc restoration was observed from 3 weeks to 6 months after surgery, without inter-group difference at either visit. Ellipsoid zone integrity (β = 0.517, p = 0.008) and foveal bulge (β = 0.387, p = 0.038) were significant predictors of good final BCVA. In conclusion, perioperative oral treatment with rasagiline 1 mg/day for 7 days did not show significant benefits on visual or anatomical outcomes in macula-off RRD patients.