bluuebunny/crossref_metadata_2025 huggingface dataset:
Network-based prediction of COVID-19 epidemic spreading in Italy
Authors: Pizzuti Clara , Socievole Annalisa , Prasse Bastian , Van Mieghem Piet
Published: November 2020

Initially emerged in the Chinese city Wuhan and subsequently spread almost worldwide causing a pandemic, the SARS-CoV-2 virus follows reasonably well the Susceptible–Infectious–Recovered (SIR) epidemic model on contact networks in the Chinese case. In this paper, we investigate the prediction accuracy of the SIR model on networks also for Italy. Specifically, the Italian regions are a metapopulation represented by network nodes and the network links are the interactions between those regions. Then, we modify the network-based SIR model in order to take into account the different lockdown measures adopted by the Italian Government in the various phases of the spreading of the COVID-19. Our results indicate that the network-based model better predicts the daily cumulative infected individuals when time-varying lockdown protocols are incorporated in the classical SIR model.
Structural performance envelopes in load space
Authors: Dharmasaroja A. , Armstrong C.G. , Murphy A. , Robinson T.T. , Iorga N.L. , Barron J.R.
Published: November 2020

Visualising the loads that a structure can tolerate provides a key insight into the structural design process, especially for materials and structures that are governed by complex failure criteria. This paper proposes a general method for efficient construction of performance envelopes in load space, and demonstrates the approach with two examples. The performance envelope identifies all possible failure modes, all the redundant and non-redundant structural constraints, and the limiting failure mode in a particular direction in load space. Once the envelope has been constructed, the structural reserve factors can be calculated extremely quickly. In design such envelopes are most useful for structural analysis processes which involve a very large number of load cases, and where the cost of constructing an envelope for a given feature is relatively modest.
Numerical simulation, clustering, and prediction of multicomponent polymer precipitation
Authors: Inguva Pavan , Mason Lachlan R. , Pan Indranil , Hengardi Miselle , Matar Omar K.
Published: November 2020

Multicomponent polymer systems are of interest in organic photovoltaic and drug delivery applications, among others where diverse morphologies influence performance. An improved understanding of morphology classification, driven by composition-informed prediction tools, will aid polymer engineering practice. We use a modified Cahn–Hilliard model to simulate polymer precipitation. Such physics-based models require high-performance computations that prevent rapid prototyping and iteration in engineering settings. To reduce the required computational costs, we apply machine learning (ML) techniques for clustering and consequent prediction of the simulated polymer-blend images in conjunction with simulations. Integrating ML and simulations in such a manner reduces the number of simulations needed to map out the morphology of polymer blends as a function of input parameters and also generates a data set which can be used by others to this end. We explore dimensionality reduction, via principal component analysis and autoencoder techniques, and analyze the resulting morphology clusters. Supervised ML using Gaussian process classification was subsequently used to predict morphology clusters according to species molar fraction and interaction parameter inputs. Manual pattern clustering yielded the best results, but ML techniques were able to predict the morphology of polymer blends with ≥90% accuracy.
Efficacy of five herbicide treatments for control ofPyrus calleryana
Authors: Vogt James T. , Coyle David R. , Jenkins David , Barnes Chris , Crowe Christopher , Horn Scott , Bates Chip , Roesch Francis A.
Published: November 2020

Callery pear (Pyrus calleryanaDecne.) is rapidly spreading in the United States, gaining attention in the last two decades as a serious invasive pest. Recommended control methods include foliar, basal bark, cut stump, and hack-and-squirt application of herbicides, but there are few published studies with replicated data on efficacy. Four readily available herbicidal active ingredients and a combination of two active ingredients were tested for control efficacy againstP. calleryanain old-field areas and loblolly pine (Pinus taedaL.) understory. Basal bark applications (triclopyr, triclopyr + aminopyralid), foliar applications (glyphosate, imazapyr), and a soil application (hexazinone) effectively killedP. calleryanawith the exception of hexazinone at one site, where rainfall may not have been optimal. Foliar application of glyphosate provided the most consistent control. Our results demonstrate efficacy of registered herbicide formulations forP. calleryanacontrol in two geographic locations and two habitat types. The need for development of integrated pest management programs forP. calleryanais discussed.
Influences on adolescent help-seeking for mental health problems
Authors: Pearson Sarah , Hyde Chelsea
Published: November 2020

Seeking help for mental health concerns is critical for improving wellbeing and preventing the development of mental health disorders, yet many adolescents with mental health problems fail to seek professional help. It is well established that young people with mental health problems face a variety of barriers to help-seeking; however, little is known about the ways in which these barriers interact to impact upon the help-seeking process. Guided by the reasoned action approach, this study investigated the predictive relationship between factors that influence help-seeking. Results revealed that mental health knowledge significantly predicted help-seeking intentions, while attitudes did not. Gender differences were identified for help source preferences. The current study contributes to knowledge on the relationship between key variables that influence the adolescent help-seeking process. Findings highlight the importance of mental health knowledge in predicting help-seeking intentions and provide support for interventions that focus on improving mental health literacy in adolescents.
Twenty-year trends in vegetable consumption by preparation method and eating location for Korean population from 1998 to 2017
Authors: Kim Sang Young , Freeland-Graves Jeanne H. , Kim Hyun Ja
Published: November 2020

Vegetables are an important source for the essential vitamins and minerals that are necessary for optimal health. This research investigated changes in vegetable intake over time in the Korean population from 1998 to 2017, focusing on preparation methods of vegetables and location of consumption. This cross-sectional study is based on the Korea National Health and Nutrition Examination Survey (KNHANES) that was established in 1998 to assess the health and nutritional status of the South Korean population. This research utilised information from 1998 to 2017 which is the extent of all available KNHANES data. Vegetable consumption was grouped, according to preparation methods and common eating locations. Both crude and age-standardised means of vegetable intake were derived via a 24-h dietary recall. All participants who completed a 24-h dietary recall survey were selected for the analyses. This included 109 220 individuals (49 069 men and 60 151 women) over the course of 20 years of the KNHANES. Total vegetable intake decreased over time (Pfor trends < 0·001), specifically, steamed and salted vegetables (Pfor trends < 0·001). In contrast, Koreans consumed noticeably more raw vegetables from 1998 to 2017 (Pfor trends < 0·001). Vegetable intake at home significantly declined (Pfor trends < 0·001), while that eaten at restaurants or outside the home increased greatly (Pfor trends < 0·001). Over 20 years, Koreans have ingested decreasing amounts of vegetables, but the intake of raw vegetables has escalated. However, the location of vegetable consumption has changed, with an increase at both restaurants and outside the home (approximately 70·0 %).
Assessment of eating habits and lifestyle during the coronavirus 2019 pandemic in the Middle East and North Africa region: a cross-sectional study
Authors: Cheikh Ismail Leila , Osaili Tareq M. , Mohamad Maysm N. , Al Marzouqi Amina , Jarrar Amjad H. , Zampelas Antonis , Habib-Mourad Carla , Omar Abu Jamous Dima , Ali Habiba I. , Al Sabbah Haleama , Hasan Hayder , AlMarzooqi Latifa Mohammed Rashid , Stojanovska Lily , Hashim Mona , Shaker Obaid Reyad R. , ElFeky Samar , Saleh Sheima T. , Shawar Zahieh A. M. , Al Dhaheri Ayesha S.
Published: November 2020

Coronavirus disease 2019 (COVID-19) has rapidly spread globally, forcing countries to apply lockdowns and strict social distancing measures. The aim of this study was to assess eating habits and lifestyle behaviours among residents of the Middle East and North Africa (MENA) region during the lockdown. A cross-sectional study among adult residents of the MENA region was conducted using an online questionnaire designed on Google Forms during April 2020. A total of 2970 participants from eighteen countries participated in the present study. During the pandemic, over 30 % reported weight gain, 6·2 % consumed five or more meals per d compared with 2·2 % before the pandemic (P < 0·001) and 48·8 % did not consume fruits on a daily basis. Moreover, 39·1 % did not engage in physical activity, and over 35 % spent more than 5 h/d on screens. A significant association between the frequency of training during the pandemic and the reported change in weight was found (P < 0·001). A significantly higher percentage of participants reported physical and emotional exhaustion, irritability and tension either all the time or a large part of the time during the pandemic (P < 0·001). Although a high percentage of participants reported sleeping more hours per night during the pandemic, 63 % had sleep disturbances. The study highlights that the lockdown due to the COVID-19 pandemic caused a variety of lifestyle changes, physical inactivity and psychological problems among adults in the MENA region.
An ‘Institution-First’ Conception of Public Integrity
Authors: Kirby Nikolas
Published: November 2020

There is an emerging drive to define a new praiseworthy governance goal: a goal that not only implies addressing corruption but going further to establish institutions that are truly worthy of trust. That goal is ‘public integrity’. However, most current accounts of public integrity adopt an ‘officer-first’ approach: defining public integrity primarily as a quality of individual public officers, and only derivatively, if at all, as a quality of public institutions themselves. This article argues that this approach is flawed. Analysing the current debate, it identifies the need to define a role-specific sense of praiseworthy behaviour for public officers. However, it is only possible to define this role-specific sense of praiseworthy behaviour by referring to a public officer's contribution to the overall moral ideal of her institution. Assuming that this ideal itself is a form of public integrity, it then follows that such institutional integrity must be defined ‘first’ in order to then define a public officer's praiseworthy contribution to it second. Substantively, this article argues that ‘public institutional integrity’ is an institution's robust disposition to pursue its purpose efficiently, within the constraints of legitimacy, consistent with its commitments. ‘Public officer integrity’ is the robust disposition of an officer to support the integrity of her institution, within the course of her duties, to the best of her abilities.
Conversionary Protestants Do Not Cause Democracy
Authors: Nikolova Elena , Polansky Jakub
Published: November 2020

In The Missionary Roots of Liberal Democracy, Robert D. Woodberry (2012) claims that conversionary Protestantism influenced the emergence of stable democracies around the world. While his historical analysis is exhaustive, the accompanying empirical evidence suffers from severe inconsistencies. This letter replicates Woodberry's analysis using twenty-six alternative democracy measures and extends the time period over which the democracy measures are averaged. These two simple modifications lead to the breakdown of Woodberry's results. We find no significant relationship between Protestant missions and the development of democracy, which raises concerns about the robustness and broader applicability of Woodberry's findings. The letter discusses some alternative explanations for Woodberry's results, which can inform future research on this topic.
Impacts of climate change on potential geographical cultivation areas of longan (Dimocarpus longan) in China
Authors: Li H.Q. , Liu X. L. , Wang J. H. , Fu Y. Y. , Sun X.P. , Xing L. G.
Published: November 2020

Longan is an economically important sub-tropical fruit tree native to southern China and southeast Asia. Its production has been affected significantly by climate change, but the underlying reasons remain unclear. Herein, the potential growing areas of longan were simulated by the Maxent model under current and future conditions. The results showed excellent prediction performance, with an area under curve of >0.9 for model training and validation. The key environmental variables identified were mean temperature of the coldest quarter, minimum temperature of the coldest month, annual mean temperature and mean temperature of the driest quarter. The optimum suitable areas of longan were found to be concentrated mainly in south-western, southern and eastern China, with a slight increase in optimum suitable areas under two different emission scenarios of three global climatic models. However, its future potential growing areas were predicted to differ among provinces or cities. Suitable growing areas in Sichuan, Jiangxi, Guangxi and Chongqing will first increase and then remain approximately unchanged between the 2050s and 2070s; those in Yunnan, Guangdong and Hainan will remain approximately unchanged from the present to the 2070s; those in Fujian and Guizhou will fluctuate slightly from the present to the 2050s and then increase to the 2070s; those in Taiwan will first decrease and then increase. In summary, the major future production areas of longan will be Guangdong, Hainan and Guangxi provinces, followed by Chongqing, Yunnan, Fujian and Taiwan. Thus, this study serves as a useful guide for the management of longan.
Bacterial starter cultures induce suitable changes in milk fatty acid profiles at different fermentation conditions
Authors: Bahrami Gholamreza , Mostafaie Ali , Kiani Amir , Chalabi Maryam
Published: November 2020

This study aimed to compare the effect of different ratios of Streptococcus thermophilus to Lactobacillus bulgaricus (3 : 1, 1 : 1, and 1 : 3) under the various stressful temperatures (37 and 45°C) on the fatty acid profiles quality of Kermanshahi roghan (yogurt by-product) and sour cream to obtain a formula for producing a kind of animal fat healthier than milk and cream. Stresses such as fermentation play an important role in bacterial behavior and consequently in food quality. Our findings presented a significant difference between roghan and sour cream fatty acid levels only at 37°C. Furthermore, starter culture 3 : 1 was the best starter for producing products with a higher quality of fatty acid profile at 37°C, and a 1 : 1 S. thermophilus to L. bulgaricus ratio was optimal at 45°C. It seems that bacteria adapt to harsh growth conditions by changing the fatty acid profiles, and these changes warrant consideration in the production of a kind of animal fat with the best fatty acid profiles. In conclusion, the roghan fatty acid profile is more suitable than sour cream only at 37°C.
What are the barriers to the SHAI being completed within a ME/CFS service?
Authors: Fanous Marianne , Ryninks Kirsty , Daniels Jo
Published: November 2020

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating condition, characterised by unexplained and excessive fatigue, muscle pain and sleep disturbances. Health anxiety is common in ME/CFS and accurate measurement is essential in facilitating therapeutic gains. However, there are clinical concerns over the utility of the Short Health Anxiety Inventory (SHAI) in measuring health anxiety in this population. This study aims to use qualitative responses from two ex-service users and specialist health clinicians to explore the barriers to completing the SHAI within a specialist ME/CFS service. Qualitative responses from a focus group consisting of 15 specialist health professionals including occupational therapists, physiotherapists, dieticians, cognitive behavioural therapists, counsellors, clinical psychologists and assistant psychologists were transcribed and analysed for themes. Patient voices were represented by two former service users through individual semi-structured interviews on the telephone, which were recorded, transcribed and later analysed thematically. Clinicians and service user involvement agreed on core difficulties with the utility of the SHAI in the ME/CFS population. The timing of the SHAI being administered pre-diagnosis, the language of the SHAI and lack of context around the questionnaire were identified as barriers that were likely to contribute to the SHAI not being completed by service users. Sensitive and accurate measurement is required in order to retain patient engagement, which could further facilitate appropriate assessment and treatment of health anxiety and ME/CFS. Findings suggest that adaption of the SHAI is vital for use with ME/CFS.

Key learning aims

(1)

To understand the different barriers to completing the SHAI in a ME/CFS service.

(2)

To understand the implications of administering the SHAI to ME/CFS service users.

(3)

To learn from multi-disciplinary ME/CFS health professionals about perceived difficulties in administering the SHAI.
Data Sets Are Foundational to Research. Why Don’t We Cite Them?
Authors: Vannan Suresh , Downs Robert , Meier Walt , Wilson Bruce , Gerasimov Irina
Published: November 2020

The lack of clear references to and descriptions of data sets in published literature limits the usefulness of data, as well as the reproducibility and credibility of scientific findings.
Magma Source Evolution Following Subduction Initiation: Evidence From the Element Concentrations, Stable Isotope Ratios, and Water Contents of Volcanic Glasses From the Bonin Forearc (IODP Expedition 352)
Authors: Coulthard Daniel A. , Reagan Mark K. , Shimizu Kenji , Bindeman Ilya N. , Brounce Maryjo , Almeev Renat R. , Ryan Jeffrey , Chapman Timothy , Shervais John , Pearce Julian A.
Published: November 2020

International Ocean Discovery Program Expedition 352 to the Bonin forearc drilled the sequence of volcanic rocks erupted in the immediate aftermath of subduction initiation along the western margin of the Pacific Plate. Pristine volcanic glasses collected during this expedition were analyzed for major and trace elements, halogens, sulfur, and H and O isotopes with goals of characterizing the fluids and melts of subducted materials that were involved in generating the nascent upper plate crust. Incompatible trace element compositions of the oldest lavas (forearc basalts [FAB]) are similar to those of the most depleted mid‐ocean ridge basalts globally. Most FAB were generated by decompression melting during seafloor spreading in a near‐trench, supra‐subduction zone environment with only minor involvement of diverse and generally dilute water‐rich fluids from the subducting plate. Boninite series glasses are enriched in incompatible trace elements mobilized from the subducting plate, but strongly depleted in other elements, such as the middle‐heavy rare‐earth elements. These traits are attributed to generation of boninites largely by flux melting involving water‐rich melts first derived from the leading edge of subducted basaltic crust and then from both subducted crust and sediment. These melts were generated at low pressures as the shallow, embryonic slab extracted heat from hot asthenosphere near the trench. The progressive depletion of the mantle source for the FAB‐through‐boninite sequence suggests that the asthenospheric mantle remained trapped above the nascent subducting plate for the first several million years of subduction beneath the Philippine Sea Plate.
Impacts of the 2014–2015 Warm‐Water Anomalies on Nutrients, Chlorophyll‐a and Hydrographic Conditions in the Coastal Zone of Northern Baja California
Authors: Delgadillo‐Hinojosa F. , Félix‐Bermúdez A. , Torres‐Delgado E. V. , Durazo R. , Camacho‐Ibar V. , Mejía A. , Ruiz M. C. , Linacre L.
Published: November 2020

We report the seasonal variability of temperature, nutrients, and total and size‐fractionated chlorophyll‐a (Chl‐a) in nearshore waters off northern Baja California (nBC), under conditions of the marine heatwave and El Niño that occurred in the northeastern Pacific during 2014–2015. Compared with the mean annual cycle (2008–2015), our study period was characterized by warmer waters, nitrate‐impoverished, and with very low Chl‐a concentration, which was closely associated with strong stratification and reduced upwelling conditions off nBC. Temperature anomalies were >2.0°C by the end of 2014 when the marine heatwave prevailed, decreased during the spring‐early summer upwelling season of 2015, and returned to >2.5°C by the end of 2015 when El Niño appeared along the coast of nBC. As in 2008–2012 and closely coupled with upwelling, a seasonal cycle of total Chl‐a was recorded under these abnormally warm conditions. However, relative to the mean annual cycle, total Chl‐a and nitrate concentrations were significantly reduced (19%–55% and 40%–81%, respectively), with negative anomalies throughout the study period. Moreover, the seasonal evolution of the size‐fractionated Chl‐a concentration showed that smaller cells (<5 μm) systematically contributed with the largest fraction (>60%) of the total Chl‐a. Our findings indicate that the sequential occurrence of the marine heatwave in 2014 and El Niño in 2015 had a significant and sustained impact limiting the nitrate supply and reducing the total Chl‐a in nearshore waters off nBC. In conclusion, our data reveal that a shift toward an oligotrophic state occurred in coastal waters off nBC during the warm period of 2014–2015.
Amorphization of S, Cl‐Salts Induced by Martian Dust Activities
Authors: Wang Alian , Yan Yuanchao , Dyar Darby M. , Houghton Jen L. , Farrell William M. , Jolliff Bradley L. , McLennan Scott M. , Shi Erbin , Qu Hongkun
Published: November 2020

A high proportion of noncrystalline (X‐ray‐amorphous) components has been found in all samples analyzed by CheMin on theCuriosity roverat Gale crater on Mars, and such X‐ray‐amorphous components probably occur at all sites that have been investigated thus far by landers and rovers. The amorphous material at Gale crater is rich in volatiles (S, Cl, and H2O), as indicated by other science payload elements (APXS, SAM). We demonstrate here that amorphization of S and Cl salts can be induced by energetic electrons and free radicals generated in a medium‐strength electrostatic discharge (ESD) process during Martian dust activities such as dust storms, dust devils, and grain saltation. Furthermore, we found that the amorphization is commonly accompanied by dehydration of the salts and oxidation of Cl, S, and Fe species. On the basis of experimentally observed rates of the above phase transformations and the mission‐observed dust activities and wind speeds on Mars, we anticipate that similar phase transformations could occur on Mars within a time frame of years to hundreds of years. Considering the high frequency, long duration, and large areal coverage of Martian dust activities, our study suggests that the ESD induced by Martian dust activities may have contributed to some the S‐ and Cl‐rich portion of X‐ray amorphous materials observed in surface soils at Gale crater. Furthermore, dust activities in the Amazonian period may have generated and deposited a significant quantity of S‐ and Cl‐rich amorphous materials all over Mars.
Comparison of decayed, missing, filled teeth index between thalassemia major patients and control group in Iran: a systematic review and meta-analysis
Authors: Moosazadeh Mahmood , Gorji Nadia Elyassi , Nasiri Pegah , Shafaroudi Ali Malekzadeh
Published: November 2020

Introduction

Scientific evidence of the association between Decayed, Missing, and Filled Teeth (DMFT) and thalassemia are conflicting and difficult to establish conclusions. Therefore, this study aimed to determine the relationship between dental caries (using the DMFT index) and thalassemia major using meta-analysis.

Methods

Databases were searched using such keywords as “Thalassemia,” “Caries,” “decay,” “DMFT,” “Iran,” and OR operators, AND, and NOT. After the elimination of duplicate documentation, the articles which met the inclusion criteria were selected. Quality assessment was performed based on the Newcastle-Ottawa Quality Checklist. Thereafter, the standardized mean difference of the DMFT index was estimated.

Results

In eight studies, the mean DMFT was compared between patients with thalassemia major and the control group. In six studies, the mean of this index was higher in patients with thalassemia major than in the control group and in all six of the studies, the differences were statistically significant. The mean standardized difference of DMFT, D, M, and F were reported as 1.36 (0.41, 2.30), 2.63 (0.42, 4.84), 1.65 (−0.14, 3.45), and 0.02 (−1.67, 1.72), respectively.

Conclusion

The results of this meta-analysis indicated that DMFT index was more inappropriate in patients with thalassemia, as compared to the control group which represents the higher incidence of dental caries among patients with thalassemia compared to the control group.
Accuracy and stability of electronic apex locator length measurements in root canals with wide apical foramen: an ex vivo study
Authors: Shacham Maayan , Levin Avi , Shemesh Avi , Lvovsky Alex , Ben Itzhak Joe , Solomonov Michael
Published: November 2020

The aim of the current study was to determine the accuracy of electronic apex locator (EAL) measurements when using files of different sizes in roots with wide apical foramina while considering a new parameter ofstabilityof EAL reading. Ten teeth with straight roots were subjected to a sequential widening of the apical foramen to 0.6, 0.7, and 0.8 mm. The roots were embedded after each enlargement stage in an alginate mold and subjected to EAL readings. Measurements were done using sequential K-file sizes and the self-adjusting file (SAF). Measurement stability was introduced as a new additional parameter. As the difference between the file size used and the apical diameter of the canal decreases, the results obtained were more accurate and stable. The stability and accuracy of the measurements coincided with each other in a statistically significant manner. Within the limitations of the present ex vivo study, it may be concluded that in straight canals with wide apical foramina of 0.6–0.8 mm, both SS K-files which fit snugly to the walls of apical foramen and the SAF file may offer both accurate and stable EAL measurements.
Exosomes and breast cancer drug resistance
Authors: Dong Xingli , Bai Xupeng , Ni Jie , Zhang Hao , Duan Wei , Graham Peter , Li Yong
Published: November 2020

Drug resistance is a daunting challenge in the treatment of breast cancer (BC). Exosomes, as intercellular communicative vectors in the tumor microenvironment, play an important role in BC progression. With the in-depth understanding of tumor heterogeneity, an emerging role of exosomes in drug resistance has attracted extensive attention. The functional proteins or non-coding RNAs contained in exosomes secreted from tumor and stromal cells mediate drug resistance by regulating drug efflux and metabolism, pro-survival signaling, epithelial–mesenchymal transition, stem-like property, and tumor microenvironmental remodeling. In this review, we summarize the underlying associations between exosomes and drug resistance of BC and discuss the unique biogenesis of exosomes, the change of exosome cargo, and the pattern of release by BC cells in response to drug treatment. Moreover, we propose exosome as a candidate biomarker in predicting and monitoring the therapeutic drug response of BC and as a potential target or carrier to reverse the drug resistance of BC.
Multi-year incubation experiments boost confidence in model projections of long-term soil carbon dynamics
Authors: Jian Siyang , Li Jianwei , Wang Gangsheng , Kluber Laurel A. , Schadt Christopher W. , Liang Junyi , Mayes Melanie A.
Published: November 2020

Global soil organic carbon (SOC) stocks may decline with a warmer climate. However, model projections of changes in SOC due to climate warming depend on microbially-driven processes that are usually parameterized based on laboratory incubations. To assess how lab-scale incubation datasets inform model projections over decades, we optimized five microbially-relevant parameters in the Microbial-ENzyme Decomposition (MEND) model using 16 short-term glucose (6-day), 16 short-term cellulose (30-day) and 16 long-term cellulose (729-day) incubation datasets with soils from forests and grasslands across contrasting soil types. Our analysis identified consistently higher parameter estimates given the short-term versus long-term datasets. Implementing the short-term and long-term parameters, respectively, resulted in SOC loss (–8.2 ± 5.1% or –3.9 ± 2.8%), and minor SOC gain (1.8 ± 1.0%) in response to 5 °C warming, while only the latter is consistent with a meta-analysis of 149 field warming observations (1.6 ± 4.0%). Comparing multiple subsets of cellulose incubations (i.e., 6, 30, 90, 180, 360, 480 and 729-day) revealed comparable projections to the observed long-term SOC changes under warming only on 480- and 729-day. Integrating multi-year datasets of soil incubations (e.g., > 1.5 years) with microbial models can thus achieve more reasonable parameterization of key microbial processes and subsequently boost the accuracy and confidence of long-term SOC projections.
Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury
Authors: Floriddia Elisa M. , Lourenço Tânia , Zhang Shupei , van Bruggen David , Hilscher Markus M. , Kukanja Petra , Gonçalves dos Santos João P. , Altınkök Müge , Yokota Chika , Llorens-Bobadilla Enric , Mulinyawe Sara B. , Grãos Mário , Sun Lu O. , Frisén Jonas , Nilsson Mats , Castelo-Branco Gonçalo
Published: November 2020

Mature oligodendrocytes (MOLs) show transcriptional heterogeneity, the functional consequences of which are unclear. MOL heterogeneity might correlate with the local environment or their interactions with different neuron types. Here, we show that distinct MOL populations have spatial preference in the mammalian central nervous system (CNS). We found that MOL type 2 (MOL2) is enriched in the spinal cord when compared to the brain, while MOL types 5 and 6 (MOL5/6) increase their contribution to the OL lineage with age in all analyzed regions. MOL2 and MOL5/6 also have distinct spatial preference in the spinal cord regions where motor and sensory tracts run. OL progenitor cells (OPCs) are not specified into distinct MOL populations during development, excluding a major contribution of OPC intrinsic mechanisms determining MOL heterogeneity. In disease, MOL2 and MOL5/6 present different susceptibility during the chronic phase following traumatic spinal cord injury. Our results demonstrate that the distinct MOL populations have different spatial preference and different responses to disease.
Impacts of irrigated agriculture on food–energy–water–CO2 nexus across metacoupled systems
Authors: Xu Zhenci , Chen Xiuzhi , Liu Jianguo , Zhang Yu , Chau Sophia , Bhattarai Nishan , Wang Ye , Li Yingjie , Connor Thomas , Li Yunkai
Published: November 2020

Irrigated agriculture has important implications for achieving the United Nations Sustainable Development Goals. However, there is a lack of systematic and quantitative analyses of its impacts on food–energy–water–CO2 nexus. Here we studied impacts of irrigated agriculture on food–energy–water–CO2 nexus across food sending systems (the North China Plain (NCP)), food receiving systems (the rest of China) and spillover systems (Hubei Province, affected by interactions between sending and receiving systems), using life cycle assessment, model scenarios, and the framework of metacoupling (socioeconomic-environmental interactions within and across borders). Results indicated that food supply from the NCP promoted food sustainability in the rest of China, but the NCP consumed over four times more water than its total annual renewable water, with large variations in food–energy–water–CO2 nexus across counties. Although Hubei Province was seldom directly involved in the food trade, it experienced substantial losses in water and land due to the construction of the South-to-North Water Transfer Project which aims to alleviate water shortages in the NCP. This study suggests the need to understand impacts of agriculture on food–energy–water–CO2 nexus in other parts of the world to achieve global sustainability.
Self-attenuation of extreme events in Navier–Stokes turbulence
Authors: Buaria Dhawal , Pumir Alain , Bodenschatz Eberhard
Published: November 2020

Turbulent fluid flows are ubiquitous in nature and technology, and are mathematically described by the incompressible Navier-Stokes equations. A hallmark of turbulence is spontaneous generation of intense whirls, resulting from amplification of the fluid rotation-rate (vorticity) by its deformation-rate (strain). This interaction, encoded in the non-linearity of Navier-Stokes equations, is non-local, i.e., depends on the entire state of the flow, constituting a serious hindrance in turbulence theory and even establishing regularity of the equations. Here, we unveil a novel aspect of this interaction, by separating strain into local and non-local contributions utilizing the Biot-Savart integral of vorticity in a sphere of radius R. Analyzing highly-resolved numerical turbulent solutions to Navier-Stokes equations, we find that when vorticity becomes very large, the local strain over small R surprisingly counteracts further amplification. This uncovered self-attenuation mechanism is further shown to be connected to local Beltramization of the flow, and could provide a direction in establishing the regularity of Navier-Stokes equations.
Computationally predicting clinical drug combination efficacy with cancer cell line screens and independent drug action
Authors: Ling Alexander , Huang R. Stephanie
Published: November 2020

Evidence has recently emerged that many clinical cancer drug combinations may derive their efficacy from independent drug action (IDA), where patients only receive benefit from the single most effective drug in a drug combination. Here we present IDACombo, an IDA based method to predict the efficacy of drug combinations using monotherapy data from high-throughput cancer cell line screens. We show that IDACombo predictions closely agree with measured drug combination efficacies both in vitro (Pearson’s correlation = 0.93 when comparing predicted efficacies to measured efficacies for >5000 combinations) and in a systematically selected set of clinical trials (accuracy > 84% for predicting statistically significant improvements in patient outcomes for 26 first line therapy trials). Finally, we demonstrate how IDACombo can be used to systematically prioritize combinations for development in specific cancer settings, providing a framework for quickly translating existing monotherapy cell line data into clinically meaningful predictions of drug combination efficacy.
Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses
Authors: Mick Eran , Kamm Jack , Pisco Angela Oliveira , Ratnasiri Kalani , Babik Jennifer M. , Castañeda Gloria , DeRisi Joseph L. , Detweiler Angela M. , Hao Samantha L. , Kangelaris Kirsten N. , Kumar G. Renuka , Li Lucy M. , Mann Sabrina A. , Neff Norma , Prasad Priya A. , Serpa Paula Hayakawa , Shah Sachin J. , Spottiswoode Natasha , Tan Michelle , Calfee Carolyn S. , Christenson Stephanie A. , Kistler Amy , Langelier Charles
Published: November 2020

SARS-CoV-2 infection is characterized by peak viral load in the upper airway prior to or at the time of symptom onset, an unusual feature that has enabled widespread transmission of the virus and precipitated a global pandemic. How SARS-CoV-2 is able to achieve high titer in the absence of symptoms remains unclear. Here, we examine the upper airway host transcriptional response in patients with COVID-19 (n = 93), other viral (n = 41) or non-viral (n = 100) acute respiratory illnesses (ARIs). Compared with other viral ARIs, COVID-19 is characterized by a pronounced interferon response but attenuated activation of other innate immune pathways, including toll-like receptor, interleukin and chemokine signaling. The IL-1 and NLRP3 inflammasome pathways are markedly less responsive to SARS-CoV-2, commensurate with a signature of diminished neutrophil and macrophage recruitment. This pattern resembles previously described distinctions between symptomatic and asymptomatic viral infections and may partly explain the propensity for pre-symptomatic transmission in COVID-19. We further use machine learning to build 27-, 10- and 3-gene classifiers that differentiate COVID-19 from other ARIs with AUROCs of 0.981, 0.954 and 0.885, respectively. Classifier performance is stable across a wide range of viral load, suggesting utility in mitigating false positive or false negative results of direct SARS-CoV-2 tests.
XPC deficiency increases risk of hematologic malignancies through mutator phenotype and characteristic mutational signature
Authors: Yurchenko Andrey A. , Padioleau Ismael , Matkarimov Bakhyt T. , Soulier Jean , Sarasin Alain , Nikolaev Sergey
Published: November 2020

Recent studies demonstrated a dramatically increased risk of leukemia in patients with a rare genetic disorder, Xeroderma Pigmentosum group C (XP-C), characterized by constitutive deficiency of global genome nucleotide excision repair (GG-NER). The genetic mechanisms of non-skin cancers in XP-C patients remain unexplored. In this study, we analyze a unique collection of internal XP-C tumor genomes including 6 leukemias and 2 sarcomas. We observe a specific mutational pattern and an average of 25-fold increase of mutation rates in XP-C versus sporadic leukemia which we presume leads to its elevated incidence and early appearance. We describe a strong mutational asymmetry with respect to transcription and the direction of replication in XP-C tumors suggesting association of mutagenesis with bulky purine DNA lesions of probably endogenous origin. These findings suggest existence of a balance between formation and repair of bulky DNA lesions by GG-NER in human body cells which is disrupted in XP-C patients.
Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep
Authors: Dong Xiyang , Rattray Jayne E. , Campbell D. Calvin , Webb Jamie , Chakraborty Anirban , Adebayo Oyeboade , Matthews Stuart , Li Carmen , Fowler Martin , Morrison Natasha M. , MacDonald Adam , Groves Ryan A. , Lewis Ian A. , Wang Scott H. , Mayumi Daisuke , Greening Chris , Hubert Casey R. J.
Published: November 2020

At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers. In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Depth distributions of hydrocarbon-oxidizing archaea revealed that they are not necessarily associated with sulfate reduction, which is especially surprising for anaerobic ethane and butane oxidizers. Overall, these findings link subseafloor microbiomes to various biochemical mechanisms for the anaerobic degradation of deeply-sourced thermogenic hydrocarbons.
Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells
Authors: Huang Deli , Tran Jenny Tuyet , Olson Alex , Vollbrecht Thomas , Tenuta Mary , Guryleva Mariia V. , Fuller Roberta P. , Schiffner Torben , Abadejos Justin R. , Couvrette Lauren , Blane Tanya R. , Saye Karen , Li Wenjuan , Landais Elise , Gonzalez-Martin Alicia , Schief William , Murrell Ben , Burton Dennis R. , Nemazee David , Voss James E.
Published: November 2020

HIV broadly neutralizing antibodies (bnAbs) can suppress viremia and protect against HIV infection. However, their elicitation is made difficult by low frequencies of appropriate precursor B cell receptors and the complex maturation pathways required to generate bnAbs from these precursors. Antibody genes can be engineered into B cells for expression as both a functional antigen receptor on cell surfaces and as secreted antibody. Here, we show that HIV bnAb-engineered primary mouse B cells can be adoptively transferred and vaccinated in immunocompetent mice resulting in the expansion of durable bnAb memory and long-lived plasma cells. Somatic hypermutation after immunization indicates that engineered cells have the capacity to respond to an evolving pathogen. These results encourage further exploration of engineered B cell vaccines as a strategy for durable elicitation of HIV bnAbs to protect against infection and as a contributor to a functional HIV cure.
FIS1 encodes a GA2-oxidase that regulates fruit firmness in tomato
Authors: Li Ren , Sun Shuai , Wang Haijing , Wang Ketao , Yu Hong , Zhou Zhen , Xin Peiyong , Chu Jinfang , Zhao Tongmin , Wang Huanzhong , Li Jiayang , Cui Xia
Published: November 2020

Fruit firmness is a target trait in tomato breeding because it facilitates transportation and storage. However, it is also a complex trait and uncovering the molecular genetic mechanisms controlling fruit firmness has proven challenging. Here, we report the map-based cloning and functional characterization of qFIRM SKIN 1 (qFIS1), a major quantitative trait locus that partially determines the difference in compression resistance between cultivated and wild tomato accessions. FIS1 encodes a GA2-oxidase, and its mutation leads to increased bioactive gibberellin content, enhanced cutin and wax biosynthesis, and increased fruit firmness and shelf life. Importantly, FIS1 has no unfavorable effect on fruit weight or taste, making it an ideal target for breeders. Our study demonstrates that FIS1 mediates gibberellin catabolism and regulates fruit firmness, and it offers a potential strategy for tomato breeders to produce firmer fruit.
d-Orbital steered active sites through ligand editing on heterometal imidazole frameworks for rechargeable zinc-air battery
Authors: Jiang Yi , Deng Ya-Ping , Liang Ruilin , Fu Jing , Gao Rui , Luo Dan , Bai Zhengyu , Hu Yongfeng , Yu Aiping , Chen Zhongwei
Published: November 2020

The implementation of pristine metal-organic frameworks as air electrode may spark fresh vitality to rechargeable zinc-air batteries, but successful employment is rare due to the challenges in regulating their electronic states and structural porosity. Here we conquer these issues by incorporating ligand vacancies and hierarchical pores into cobalt-zinc heterometal imidazole frameworks. Systematic characterization and theoretical modeling disclose that the ligand editing eases surmountable energy barrier for *OH deprotonation by its efficacy to steer metal d-orbital electron occupancy. As a stride forward, the selected cobalt-zinc heterometallic alliance lifts the energy level of unsaturated d-orbitals and optimizes their adsorption/desorption process with oxygenated intermediates. With these merits, cobalt-zinc heterometal imidazole frameworks, as a conceptually unique electrode, empowers zinc-air battery with a discharge-charge voltage gap of 0.8 V and a cyclability of 1250 h at 15 mA cm–2, outperforming the noble-metal benchmarks.
Highly accurate long-read HiFi sequencing data for five complex genomes
Authors: Hon Ting , Mars Kristin , Young Greg , Tsai Yu-Chih , Karalius Joseph W. , Landolin Jane M. , Maurer Nicholas , Kudrna David , Hardigan Michael A. , Steiner Cynthia C. , Knapp Steven J. , Ware Doreen , Shapiro Beth , Peluso Paul , Rank David R.
Published: November 2020

The PacBio®HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10–25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemblers, variant callers, and haplotyping algorithms. We present deep coverage HiFi datasets for five complex samples including the two inbred model genomesMus musculusandZea mays, as well as two complex genomes, octoploidFragaria × ananassaand the diploid anuranRana muscosa. Additionally, we release sequence data from a mock metagenome community. The datasets reported here can be used without restriction to develop new algorithms and explore complex genome structure and evolution. Data were generated on the PacBio Sequel II System.
Ecological drivers of genetic connectivity for African malaria vectors Anopheles gambiae and An. arabiensis
Authors: Hemming-Schroeder Elizabeth , Zhong Daibin , Machani Maxwell , Nguyen Hoan , Thong Sarah , Kahindi Samuel , Mbogo Charles , Atieli Harrysone , Githeko Andrew , Lehmann Tovi , Kazura James W. , Yan Guiyun
Published: November 2020

Anopheles gambiaeandAn. arabiensisare major malaria vectors in sub-Saharan Africa. Knowledge of how geographical factors drive the dispersal and gene flow of malaria vectors can help in combatting insecticide resistance spread and planning new vector control interventions. Here, we used a landscape genetics approach to investigate population relatedness and genetic connectivity ofAn. gambiaeandAn. arabiensisacross Kenya and determined the changes in mosquito population genetic diversity after 20 years of intensive malaria control efforts. We found a significant reduction in genetic diversity inAn. gambiae, but not inAn. arabiensisas compared to prior to the 20-year period in western Kenya. Significant population structure among populations was found for both species. The most important ecological driver for dispersal and gene flow ofAn. gambiaeandAn. arabiensiswas tree cover and cropland, respectively. These findings highlight that human induced environmental modifications may enhance genetic connectivity of malaria vectors.