bluuebunny/crossref_metadata_2025 huggingface dataset:
Agricultural systems in Bangladesh: the first archaeobotanical results from Early Historic Wari-Bateshwar and Early Medieval Vikrampura
Authors: Rahman Mizanur , Castillo Cristina Cobo , Murphy Charlene , Rahman Sufi Mostafizur , Fuller Dorian Q.
Published: January 2020

The present paper reports the first systematic archaeobotanical evidence from Bangladesh together with direct AMS radiocarbon dates on crop remains. Macro-botanical remains were collected by flotation from two sites, Wari-Bateshwar (WB), an Early Historic archaeological site, dating mainly between 400 and 100 BC, with a later seventh century AD temple complex, and Raghurampura Vikrampura (RV), a Buddhist Monastery (vihara) located within the Vikrampura city site complex and dating to the eleventh and sixteenth centuries AD. Despite being a tropical country, with high rainfall and intensive soil processes, our work demonstrates that conventional archaeobotany, the collection of macro-remains through flotation, has much potential towards putting together a history of crops and agricultural systems in Bangladesh. The archaeobotanical assemblage collected from both sites indicates the predominance of rice agriculture, which would have been practiced in summer. Spikelet bases are of domesticated type rice, while grain metrics suggest the majority of rice was probably subspeciesjaponica.The presence of some wetland weeds suggests at least some of the rice was grown in wet (flooded) systems, but much of it may have been rainfed as inferred from the Southeast Asian weedAcmella paniculata. Other crops include winter cereals, barley and possible oat, and small numbers of summer millets (Pennisetum glaucum,Sorghum bicolor,Setaria italica), a wide diversity of summer and winter pulses (14 spp.), cotton, sesame and mustard seed. Pulse crops included many known from India. Thus, while most crops indicate diffusion of crops from India eastwards, the absence ofindicarice could also indicate some diffusion from Southeast Asia. The later site RV also produced evidence of the rice bean (Vigna umbellata), a domesticate of mainland Southeast Asia. These data provide the first empirical evidence for reconstructing past agriculture in Bangladesh and for the role of connections to both India and mainland Southeast Asia in the development of crop diversity in the Ganges delta region.
Coordinate-wise powers of algebraic varieties
Authors: Dey Papri , Görlach Paul , Kaihnsa Nidhi
Published: January 2020

We introduce and study coordinate-wise powers of subvarieties of $${\mathbb {P}}^n$$

P

n

, i.e. varieties arising from raising all points in a given subvariety of $${\mathbb {P}}^n$$

P

n

to the r-th power, coordinate by coordinate. This corresponds to studying the image of a subvariety of $${\mathbb {P}}^n$$

P

n

under the quotient of $${\mathbb {P}}^n$$

P

n

by the action of the finite group $${\mathbb {Z}}_r^{n+1}$$

Z
r

n
+
1

. We determine the degree of coordinate-wise powers and study their defining equations, in particular for hypersurfaces and linear spaces. Applying these results, we compute the degree of the variety of orthostochastic matrices and determine iterated dual and reciprocal varieties of power sum hypersurfaces. We also establish a link between coordinate-wise squares of linear spaces and the study of real symmetric matrices with a degenerate eigenspectrum.
Jim Tozzi’s Latest on Centralized Regulatory Review
Authors: Miller James C.
Published: January 2020

Jim Tozzi is a legend and a treasure. Who better to reflect upon the history of, the significance of, and the prospects for centralized regulatory review (CRR)?
Communication strategies for designing Facebook advertising campaigns to recruit rural participants to develop healthcare delivery interventions
Authors: Flood-Grady Elizabeth , Hough Deaven , Damiani Rachel E. , Gebru Nioud Mulugeta , Fedele David A. , Leeman Robert F. , Krieger Janice L.
Published: January 2020

Background:

Little is known about designing research recruitment campaigns that connect with underserved, geographically isolated rural populations. A theoretically informed process is needed to assist research teams and practitioners in their evaluation of Facebook’s feasibility as a recruitment tool and development of online materials for recruiting rural adults into healthcare delivery intervention development studies.

Methods:

We drew from research and theory in communication and incorporated process analysis techniques to develop replicable procedures for designing and evaluating Facebook campaigns for rural recruitment. We describe our process and illustrate using two case studies.

Results:

Campaigns received approximately 1000 link clicks from the target rural demographic and successfully enrolled participants using Facebook as a primary method of recruitment. The rural tobacco intervention development study received a total of 477 link clicks, cost only $155.80, and enrolled three (23%) of its 13 participants from Facebook. The rural mental health intervention development study received a total of 518 link clicks, cost only $233.28, and enrolled 178 participants.

Conclusions:

Our process yielded two successful recruitment campaigns. Facebook was an affordable and efficacious strategy for enrolling adults in behavioral research studies on tobacco and mental health. Future work should apply these theoretical techniques to additional study topics and evaluate specific message features associated with recruitment.
The effect of high salt and high protein intake on calcium metabolism,
bone composition and bone resorption in the rat
Authors: Creedon Annette , Cashman Kevin D.
Published: January 2020

The effects of salt (NaCl) supplementation of rat diets (50 g/kg diet),
with normal (200 g/kg) or high (500 g/kg) dietary casein content, were
studied in 3-week-old male rats over a 3-week period. Weight gain was
reduced by dietary salt but was unaffected by dietary casein.
Salt-supplemented rats exhibited a two-and three-fold increase in urinary Mg
and Ca excretion respectively, irrespective of dietary casein content.
Dietary casein had no effect on urinary Ca or Mg. Salt reduced femoral mass
but not femoral mass expressed relative to body weight, but neither variable
was affected by dietary casein. Femoral Mg and P contents and concentrations
were unaffected by dietary salt or casein. While femoral Ca concentration
was unaffected by dietary salt, the Ca content was reduced by salt
supplementation, irrespective of dietary casein content. Neither the content
nor concentration of Ca in femora was affected by dietary casein. Urinary
pyridinoline and deoxypyridinoline levels were increased by salt
supplementation, irrespective of dietary casein content, but were unaffected
by casein. Net Ca absorption was unaffected by dietary salt or casein. In
conclusion, these results show that salt supplementation over the short-term
increased the rate of bone resorption in rats. This was as a consequence of
Na-induced calciuria. On the other hand, a high dietary protein intake had
no effect on Ca metabolism, bone composition or bone resorption, nor did it
augment the Na-induced calciuria or increased rate of bone
resorption.
Intestinal β-carotene 15,15′-dioxygenase activity is markedly enhanced in copper-deficient rats fed on high-iron diets and fructose
Authors: During Alexandrine , Fields Meira , Lewis Charles G. , Smith J. Cecil
Published: January 2020

The purpose of the present work was to examine effects of the Cu–Fe interaction on intestinal β-carotene 15,15′-dioxygenase activity when a wide range of dietary Fe (deficiency to excess) was used in relation to Cu status of rats. The effect of dietary carbohydrates was also examined since they play a role in the Cu–Fe interactionin vivo. Weanling male Sprague-Dawley rats (n72) were divided into twelve dietary groups, which were fed on either low-, normal-, or high-Fe levels (0·9, 9·0, and 90·0 mmol Fe/kg diet respectively) combined with Cu-adequate or -deficient levels (0·94 and 0·09 mmol Cu/kg diet respectively) and with starch or fructose in the diets. The data showed that both Fe concentration and β-carotene 15,15′-dioxygenase activity in small intestinal mucosa were enhanced with increasing dietary Fe and with Cu deficiencyv. Cu adequacy. Dietary fructose did not aggravate the Fe-enhancement, related to Cu deficiency, in the small intestine; however, fructose increased the intestinal dioxygenase activity in rats fed on normal- or high-Fe diets when compared with starch controls. Thus, the highest intestinal dioxygenase activity associated with the lowest hepatic retinol (total) concentration was found in rats fed on the Cu-deficient, high-Fe, fructose-based diet. Finally, a positive linear relationship was found between the dioxygenase activity and Fe concentration in intestinal mucosa. In conclusion, the data indicate that β-carotene 15,15′-dioxygenase activity requires Fe as cofactorin vivoand the enzyme is modulated by the three dietary components: Cu, Fe, and fructose.
Sea-level fluctuations in the late Middle Permian estimated from palaeosols of the Sichuan Basin, SW China
Authors: Li Jun , Han Zhong , Wen Xingyue , Retallack Gregory J. , Huang Chengmin
Published: January 2020

Two upper Middle Permian palaeosols, consisting of coal and pyrite intercalated with a 20 cm thick limestone, were found near Mount Emei in the SW Sichuan Basin, China. The macro- and micromorphology and physico-chemical properties, in conjunction with the mineralogical composition of the palaeosol horizons were investigated. This type of palaeosol is common within the Permian intertidal facies of the Upper Yangtze Craton. The section reflects fluctuations within the range of 0–25 m in relative sea-level, with the depositional environment changing from shallow-marine to littoral, followed by tidal-flat to littoral, and finally to continental volcanic rocks, based on a combination of palaeopedological and carbonate microfacies analyses. Such short-term relative sea-level fluctuations in late Middle Permian times in the SW Sichuan Basin of South China are consistent with the long-term falling trend on a global scale in late Middle Permian times, and may be related to regionally variable subsidence and global cooling. The combination of coastal palaeosol and carbonate microfacies analyses is proposed as an additional tool for estimating the amplitude of sea-level changes.
ANXIETY, CHAOS, AND THE RAJ
Authors: EHRLICH JOSHUA
Published: January 2020

Chaos reigns – at least in the historiography of the Raj. It was once the consensus among historians that British imperial authority in the Indian subcontinent was secure for at least the century-and-a-half before the Second World War. Recently, however, this narrative has drawn a range of challenges. Prominently, Mark Condos and Jon Wilson have held that British imperial authority was chronicallyinsecure. In their view, the irrational anxiety of generations of British officials produced a chaotic administration with minimal social purchase or ideological coherence. Instead of a confident state capable of acting as it chose, these historians have limned a psychologically embattled one incapable of acting except in the abstract, small scale, or short term. Their bold revision succeeds in dispelling the aura of indomitability that has often surrounded the Raj, and in directing attention to its overlooked discontents and weaknesses. Yet their characterization of the British regime asconstantlyandpervasivelyanxious is more an article of faith than a conclusion warranted by evidence. Nor do they explain how, if the regime suffered from permanent ‘chaos’ or ‘insecurity’, it managed to survive for some two hundred years. At the heart of Condos's and Wilson's approach is an effort to bypass texts that results, instead, in misreading them. It is largely by re-emphasizing rigorous textual methods, therefore, that Durba Ghosh offers a compelling alternative approach to the history of state vulnerability and disorder.
Development of a Bio-inspired Wall-Climbing Robot Composed of Spine Wheels, Adhesive Belts and Eddy Suction Cup
Authors: Liu Jinfu , Xu Linsen , Chen Shouqi , Xu Hong , Cheng Gaoxin , Xu Jiajun
Published: January 2020

A novel wall-climbing robot with multiple attachment modes is proposed. For uneven surfaces, the mechanical model of a spine wheel is brought out to grab the surfaces with its multi-spines. For smooth surfaces, an adhesive belt is obtained by the industrial synchronous belt and the polyurethane material to adhere to the surfaces. To avoid the robot overturning, an adsorption device with flexible skirt edge is presented. In addition, the normal force and motor torque are evaluated respectively. Finally, the prototype of the wall-climbing robot is manufactured and tested, and the experimental results show that the robot could climb the wall surface 0–360° with a maximum load of 0.5 kg.
Fishery bycatch is among the most important threats to the European population of Greater ScaupAythya marila
Authors: MARCHOWSKI DOMINIK , JANKOWIAK ŁUKASZ , ŁAWICKI ŁUKASZ , WYSOCKI DARIUSZ , CHYLARECKI PRZEMYSŁAW
Published: January 2020

For Greater ScaupAythya marila, classified as ‘Vulnerable’ on the European Red List of Birds, the south-western Baltic Sea is one of the most important wintering sites in Europe. In this area, a large concentration of gillnet fishery temporally overlaps periods of the most abundant occurrence of foraging diving birds. The aim of the article is to show how bycatch can impact the population of a diving duck. To assess this, we calculate the Potential Biological Removal (PBR) for the studied Greater Scaup population and we model the population change according to age-structured matrix models. Summing all the available recent figures on Greater Scaup bycatch in north-west Europe yields an estimated mean annual total of 3,991 individuals (2% of the flyway population). For a baseline stable population, an age-structured matrix model indicates that at this bycatch level the Greater Scaup population that winters in north-west Europe will decrease by 36% over the next 30 years, qualifying the status of the population as ‘Vulnerable’ according to IUCN criteria. As this population also experiences decline prior to bycatch, this decrease will be 57%, which qualifies the status as ‘Endangered’. PBR as an indicator of population vitality does not work in our case because the PBR-informed allowable bycatch values have a significantly negative impact on the population. Our results indicate unambiguously that fishery bycatch is among the most important threats responsible for the Greater Scaup’s decline. While recent data suggest that some improvement has taken place in the species’ status over the last 10 years, measures to protect Greater Scaup from bycatch are required. The solution should involve the prohibition of gillnet fishing in selected key sites and the use of mitigation techniques in other areas.
BCLM: Forging Ahead: building a new urban history of the Black Country
Authors: Briercliffe Simon
Published: January 2020

The recreation of urban historical space in museums is inevitably a complex, large-scale endeavour bridging the worlds of academic and public history. BCLM: Forging Ahead at the Black Country Living Museum is a £23m project recreating a typical Black Country town post-World War II. This article uses case-studies of three buildings – a Civic Restaurant, a record shop and a pub – to argue that urban-historical research methodology and community engagement can both create a vivid sense of the past, and challenge pervasive prejudices. It also argues that such a collaborative and public project reveals much about the urban and regional nature of industrial areas like the Black Country in this pivotal historical moment.
Agricultural Development and Land Use Change in India: A Scenario Analysis of Trade‐Offs Between UN Sustainable Development Goals (SDGs)
Authors: Hinz R. , Sulser T. B. , Huefner R. , Mason‐D’Croz D. , Dunston S. , Nautiyal S. , Ringler C. , Schuengel J. , Tikhile P. , Wimmer F. , Schaldach R.
Published: January 2020

India has the second largest population in the world and is characterized by a broad diversity in climate, topography, flora, fauna, land use, and socioeconomic conditions. To help ensure food security in the future, agricultural systems will have to respond to global change drivers such as population growth, changing dietary habits, and climate change. However, alterations of how food is produced in the future may conflict with other UN Sustainable Development Goals (SDGs), such as the protection of land resources and climate change mitigation. It is crucial for decision‐makers to understand potential trade‐offs between these goals to find a balance of human needs and environmental impacts. In this paper, we analyze pathways of agricultural productivity, land use, and land‐cover changes in India until 2030 and their impacts on terrestrial biodiversity and carbon storage. The results show that in order to meet future food production demands, agricultural lands are likely to expand, and existing farmlands need to be intensified. However, both processes will result in biodiversity losses. At the same time, the projections reveal carbon stock increases due to intensification processes and decreases due to conversions of natural land into agriculture. On balance, we find that carbon stocks increase with the scenarios of future agricultural productivity as modeled here. In conclusion, we regard further agricultural intensification as a crucial element to help ensure food security and to slow down the expansion of cropland and pasture. At the same time, policies are required to implement this intensification in a way that minimizes biodiversity losses.
Will Melting Sea Ice Expose Marine Animals to New Diseases?
Authors: Crowell Rachel
Published: January 2020

Marine mammals previously separated by Arctic ice may have more opportunities to interact as water routes redefine habitats and species ranges.
Pressure Dependence of Proton Incorporation and Water Solubility in Olivine
Authors: Fei Hongzhan , Katsura Tomoo
Published: January 2020

Hydrous forsterite single crystals were synthesized at 8 GPa and 1250 °C using a multianvil apparatus under various SiO2 activity conditions. Electron microprobe and transmission Fourier‐transform infrared spectroscopy analyses show that the Mg/Si atomic ratio increases with increasing water content. This provides new evidence that protons are mainly stored in Si sites in hydrous forsterite. The contribution of Mg sites for proton incorporation can be significant at ≤2.5 GPa with excess SiO2 but is negligible at higher pressures. Protons in olivine under asthenospheric conditions are therefore mostly maintained in Si sites. A summary of experimental studies suggests that the water solubility of forsterite/olivine equilibrated with excess (Mg,Fe)O is substantially higher than that with excess SiO2; however, this difference decreases with increasing pressure and becomes identical at 12–14 GPa. Owing to the low water solubility of olivine under topmost asthenospheric conditions, the geophysically observed low viscosity and low seismic velocity zones cannot be caused by olivine hydration, and the high conductivity anomaly should not be attributed to free H+‐controlled proton conduction in olivine.
Linkages Between Phytoplankton and Bottom Oxygen in the Chesapeake Bay
Authors: Zheng Guangming , DiGiacomo Paul M.
Published: January 2020

The primary cause of coastal hypoxia is generally attributed to phytoplankton blooms and their subsequent benthic decay. However, direct linkages between phytoplankton and hypoxia have been rarely reported. Here using satellite and field data, we show that such linkages exist in the Chesapeake Bay. For deeper (
10 m) but nonhypoxic stations, bottom dissolved oxygen is significantly correlated with surface algal biomass during the preceding weeks. Optimal correlation exhibits a bimodal seasonal variation with two peaks in April and August, respectively. Significant particulate dislocation effect is also observed: In April, May, August, and September when water column is stratified, the most significant influencer of bottom oxygen is attributable to phytoplankton blooms located down‐estuary; during destratified months of October and November, however, the dislocation effect switches to the opposite direction, that is, phytoplankton from up‐estuary have the biggest impact. We also notice enhanced phytoplankton growth posterior to lower bottom oxygen, and the strongest correlation is during summer when release of recycled ammonium and hypoxia‐induced phosphate is the most intense. These results demonstrate that the decay of phytoplankton exerts a significant impact on bottom oxygen and releases ammonium which sustains further bloom, whereas hypoxia promotes phytoplankton growth by enhancing the efficiency of phosphate recycling. Importantly, the capability of using satellite data to capture these linkages has significant ramifications for improving hypoxia forecasts in coastal systems. It essentially provides a way to characterize and constrain changes in bottom oxygen demand.
Mapping Areas of the Southern Ocean Where Productivity Likely Depends on Dust‐Delivered Iron
Authors: Tatlhego Mokganedi , Bhattachan Abinash , Okin Gregory S. , D'Odorico Paolo
Published: January 2020

The existence of low‐productivity areas in the Southern Ocean has been related to limited supply of bioavailable iron from terrestrial sources of dust. Dust‐delivered iron can be crucial to ocean productivity, though alternative mechanisms have also been identified. To explore the geographic distribution of areas limited in the delivery of iron‐rich atmospheric dust in the austral summer, we calculate forward trajectories from continental sources in the Southern Hemisphere between 2007 and 2015. A statistical comparison between trajectory patterns and maps of chlorophyll‐a, an indicator of ocean productivity, shows a significant positive correlation in ocean areas between 45°S and 65°S, consistent with the dust deposition hypothesis. Likewise, considering the area south of 45°S, while excluding the coastal belt of Antarctica, a positive correlation is also found. These results suggest the existence of two potential sources of bioavailable iron to the Southern Ocean that determine its productivity patterns: aeolian transport from dust sources into the open Southern Ocean and coastal sediment and upwelling in the coastal Antarctic Ocean.
Gravity Wave Activities Associated With Convective Phenomena at a Tropical Location Near Land‐Sea Boundary
Authors: Jana Soumyajyoti , Rakshit Gargi , Maitra Animesh
Published: January 2020

The seasonal analysis of gravity wave activity has been made for the present tropical location, Kolkata (22.5726°N, 88.3639°E) using radiosonde and European Centre for Medium‐Range Weather Forecasts 60 model level data. Gravity wave generated due to intense tropical cyclone Aila has also been investigated using European Centre for Medium‐Range Weather Forecasts 91 model level data over the Indian region. The gravity wave energy calculated from temperature and wind perturbation profiles show a significant enhancement during convective activities as indicated by a low outgoing longwave radiation. The pattern of zonal and meridional wind shears plays an important role in determining the seasonal variation of gravity wave activities. An intrusion of water vapor into the lower stratosphere over the cyclone affected region is detected from European Centre for Medium‐Range Weather Forecasts 91 model level data. The dominant vertical wavelengths of gravity waves in the range of 2.5–3.2 km are found from spectral analysis of wind and temperature perturbations during the tropical cyclone.
Fine Sediment Deposition and Filtration Under Losing and Gaining Flow Conditions: A Particle Tracking Model Approach
Authors: Preziosi‐Ribero Antonio , Packman Aaron I. , Escobar‐Vargas Jorge A. , Phillips Colin B. , Donado Leonardo David , Arnon Shai
Published: January 2020

Fine particle deposition within riverbeds plays a major role in riverine ecology and biogeochemistry by altering hyporheic exchange flux. Moreover, it is ubiquitous within streams and rivers across all flow stages. However, the dynamics of fine particle deposition are still not completely understood in rivers, and continuum models like the advection dispersion equation require modifications to represent the processes accurately. To enhance understanding of fine particle dynamics, we developed a novel numerical particle tracking model that simulates fine particle deposition as a stochastic process under losing, neutral, and gaining streamflow conditions. These flow conditions generate three different velocity profiles by combining the free surface and groundwater flows. In addition, a novel aspect of our model is the storage of filtered particles to estimate concentration fields within the bed. Our simulated results are qualitatively compared with previous laboratory flume experimental results of kaolinite deposition under similar conditions. The model indicates that fine particle deposition patterns and residence time functions depend heavily on the exchange flux between stream and groundwater, as well as bed filtration properties as the deposition of particles occurs at greater depths in the losing stream condition than in the neutral and gaining cases. Therefore, the spatial pattern of particle deposition is a direct result of pore water velocity profiles, while the concentration depends on filtration dynamics within the bed.
Body-Based Jargon Can Be Harassment When It Turns Sexual
Authors: Cartier Kimberly
Published: January 2020

Geology terms based on the human body are extremely common, but they can create a culture where sexualized language in the workplace, a type of harassment, is rampant.
Controlled Explosions Pave the Way for Thwaites Glacier Research
Authors: Kornei Katherine
Published: January 2020

Scientists detonate explosives in West Texas to prepare for fieldwork in West Antarctica.
House Democrats Introduce Ambitious Climate Change Plan
Authors: Showstack Randy
Published: January 2020

Legislation will call for a 100% clean U.S. economy by 2050.
AghaKouchak, Artemyev, Fischer, Macdonald, and van Sebille Receive 2019 James B. Macelwane Medals
Authors:   AGU
Published: January 2020

Amir AghaKouchak, Anton Artemyev, Emily V. Fischer, Francis A. Macdonald, and Erik van Sebille were awarded the 2019 James B. Macelwane Medal at AGU’s Fall Meeting 2020 Honors Ceremony on 11 December 2019 in San Francisco, Calif. The medal is for “significant contributions to the geophysical sciences by an outstanding early career scientist.”
Five Environmental Consequences of Australia’s Fires
Authors: Duncombe Jenessa
Published: January 2020

Australia’s road to recovery may be long: Here’s a developing list of how the fires are affecting glaciers, wildlife, water supplies, and global carbon emissions.
Tumour-derived extracellular vesicles in blood of metastatic cancer patients associate with overall survival
Authors: Nanou Afroditi , Miller M. Craig , Zeune Leonie L. , de Wit Sanne , Punt Cornelis J. A. , Groen Harry J. M. , Hayes Daniel F. , de Bono Johann S. , Terstappen Leon W. M. M.
Published: January 2020

Background

Circulating tumour cells (CTCs) in blood associate with overall survival (OS) of cancer patients, but they are detected in extremely low numbers. Large tumour-derived extracellular vesicles (tdEVs) in castration-resistant prostate cancer (CRPC) patients are present at around 20 times higher frequencies than CTCs and have equivalent prognostic power. In this study, we explored the presence of tdEVs in other cancers and their association with OS.

Methods

The open-source ACCEPT software was used to automatically enumerate tdEVs in digitally stored CellSearch® images obtained from previously reported CTC studies evaluating OS in 190 CRPC, 450 metastatic colorectal cancer (mCRC), 179 metastatic breast cancer (MBC) and 137 non-small cell lung cancer (NSCLC) patients before the initiation of a new treatment.

Results

Presence of unfavourable CTCs and tdEVs is predictive of OS, with respective hazard ratios (HRs) of 2.4 and 2.2 in CRPC, 2.7 and 2.2 in MBC, 2.3 and 1.9 in mCRC and 2.0 and 2.4 in NSCLC, respectively.

Conclusions

tdEVs have equivalent prognostic value as CTCs in the investigated metastatic cancers. CRPC, mCRC, and MBC (but not NSCLC) patients with favourable CTC counts can be further prognostically stratified using tdEVs. Our data suggest that tdEVs could be used in clinical decision-making.
Author Correction: Establishment of a novel human CIC-DUX4 sarcoma cell line, Kitra-SRS, with autocrine IGF-1R activation and metastatic potential to the lungs
Authors: Nakai Sho , Yamada Shutaro , Outani Hidetatsu , Nakai Takaaki , Yasuda Naohiro , Mae Hirokazu , Imura Yoshinori , Wakamatsu Toru , Tamiya Hironari , Tanaka Takaaki , Hamada Kenichiro , Tani Akiyoshi , Myoui Akira , Araki Nobuhito , Ueda Takafumi , Yoshikawa Hideki , Takenaka Satoshi , Naka Norifumi
Published: January 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
PulmonDB: a curated lung disease gene expression database
Authors: Villaseñor-Altamirano Ana B. , Moretto Marco , Maldonado Mariel , Zayas-Del Moral Alejandra , Munguía-Reyes Adrián , Romero Yair , García-Sotelo Jair. S. , Aguilar Luis A. , Aldana-Assad Oscar , Engelen Kristof , Selman Moisés , Collado-Vides Julio , Balderas-Martínez Yalbi I. , Medina-Rivera Alejandra
Published: January 2020

Chronic Obstructive Pulmonary Disease (COPD) and Idiopathic Pulmonary Fibrosis (IPF) have contrasting clinical and pathological characteristics and interesting whole-genome transcriptomic profiles. However, data from public repositories are difficult to reprocess and reanalyze. Here, we present PulmonDB, a web-based database (http://pulmondb.liigh.unam.mx/) and R library that facilitates exploration of gene expression profiles for these diseases by integrating transcriptomic data and curated annotation from different sources. We demonstrated the value of this resource by presenting the expression of already well-known genes of COPD and IPF across multiple experiments and the results of two differential expression analyses in which we successfully identified differences and similarities. With this first version of PulmonDB, we create a new hypothesis and compare the two diseases from a transcriptomics perspective.
Template-based automation of treatment planning in advanced radiotherapy: a comprehensive dosimetric and clinical evaluation
Authors: Cilla Savino , Ianiro Anna , Romano Carmela , Deodato Francesco , Macchia Gabriella , Buwenge Milly , Dinapoli Nicola , Boldrini Luca , Morganti Alessio G. , Valentini Vincenzo
Published: January 2020

Despite the recent advanced developments in radiation therapy planning, treatment planning for head-neck and pelvic cancers remains challenging due to large concave target volumes, multiple dose prescriptions and numerous organs at risk close to targets. Inter-institutional studies highlighted that plan quality strongly depends on planner experience and skills. Automated optimization of planning procedure may improve plan quality and best practice. We performed a comprehensive dosimetric and clinical evaluation of the Pinnacle3 AutoPlanning engine, comparing automatically generated plans (AP) with the historically clinically accepted manually-generated ones (MP). Thirty-six patients (12 for each of the following anatomical sites: head-neck, high-risk prostate and endometrial cancer) were re-planned with the AutoPlanning engine. Planning and optimization workflow was developed to automatically generate “dual-arc” VMAT plans with simultaneously integrated boost. Various dose and dose-volume parameters were used to build three metrics able to supply a global Plan Quality Index evaluation in terms of dose conformity indexes, targets coverage and sparing of critical organs. All plans were scored in a blinded clinical evaluation by two senior radiation oncologists. Dose accuracy was validated using the PTW Octavius-4D phantom together with the 1500 2D-array. Autoplanning was able to produce high-quality clinically acceptable plans in all cases. The main benefit of Autoplanning strategy was the improvement of overall treatment quality due to significant increased dose conformity and reduction of integral dose by 6–10%, keeping similar targets coverage. Overall planning time was reduced to 60–80 minutes, about a third of time needed for manual planning. In 94% of clinical evaluations, the AP plans scored equal or better to MP plans. Despite the increased fluence modulation, dose measurements reported an optimal agreement with dose calculations with a γ-pass-rate greater than 95% for 3%(global)-2 mm criteria. Autoplanning engine is an effective device enabling the generation of VMAT high quality treatment plans according to institutional specific planning protocols.
The composition of the perinatal intestinal microbiota in horse
Authors: Husso A. , Jalanka J. , Alipour M. J. , Huhti P. , Kareskoski M. , Pessa-Morikawa T. , Iivanainen A. , Niku M.
Published: January 2020

The establishment of the intestinal microbiota is critical for the digestive and immune systems. We studied the early development of the rectal microbiota in horse, a hindgut fermenter, from birth until 7 days of age, by qPCR and 16S rRNA gene amplicon sequencing. To evaluate initial sources of the foal microbiota, we characterised dam fecal, vaginal and oral microbiotas. We utilised an amplicon sequence variant (ASV) pipeline to maximise resolution and reproducibility. Stringent ASV filtering based on prevalence and abundance in samples and controls purged contaminants while preserving intestinal taxa. Sampled within 20 minutes after birth, rectal meconium contained small amounts of diverse bacterial DNA, with a profile closer to mare feces than mouth. 24 hours after birth, rectum was colonised by Firmicutes and Proteobacteria, some foals dominated by single genera. At day 7, the rectal genera were still different from adult feces. The mare vaginal microbiota contributed to 24 h and 7 day microbiotas. It contained few lactobacilli, withCorynebacterium,Porphyromonas,CampylobacterandHelcococcusas the most abundant genera. In the oral mucosa,Gemellawas extremely abundant. Our observations indicate that bacteria or bacterial components are present in the intestine immediately after birth, but the newborn microbiota changes rapidly.
Mixed-Dimensional Naphthylmethylammonium-Methylammonium Lead Iodide Perovskites with Improved Thermal Stability
Authors: Chaudhary Bhumika , Koh Teck M. , Febriansyah Benny , Bruno Annalisa , Mathews Nripan , Mhaisalkar Subodh G. , Soci Cesare
Published: January 2020

Metal halide perovskite solar cells, despite achieving high power conversion efficiency (PCE), need to demonstrate high stability prior to be considered for industrialization. Prolonged exposure to heat, light, and moisture is known to deteriorate the perovskite material owing to the breakdown of the crystal structure into its non-photoactive components. In this study, we show that by combining the organic ligand 1-naphthylmethylammonium iodide (NMAI) with methylammonium (MA) to form a mixed dimensional (NMA)2(MA)n−1PbnI3n+1 perovskite the optical, crystallographic and morphological properties of the newly formed mixed dimensional perovskite films under thermal ageing can be retained. Indeed, under thermal ageing at 85 °C, the best performing (NMA)2(MA)n−1PbnI3n+1 perovskites films show a stable morphology, a low PbI2 formation rate and a significantly reduced variation of both MA-specific vibrational modes and fluorescence lifetimes as compared to the pristine MAPbI3 films. These results highlight the role of the bulky NMA+ organic cation in mixed dimensional perovskites to both inhibit the MA+ diffusion and reduce the material defects, which act as non-radiative recombination centres. As a result, the thermal stability of metal halide perovskites has been substantially improved.
Electron Scattering in Conventional Cell Flask Experiments and Dose Distribution Dependency
Authors: Haskins Jeremy S. , Martinez Stephen K. , Engstrom Madison , Murakami Mami , Mori Takashi , Leary Del , Kato Takamitsu A.
Published: January 2020

Electron beam therapy (EBT) is commonly used for treating superficial and subdermal tumors. Previous cellular radiosensitivity research using EBT may be underestimating the contribution from flask wall scattering and the corresponding dose distribution. Single cell suspensions of Chinese hamster ovary (CHO) cells were plated on flasks and irradiated with 3, 4, 7, 9, and 18 MeV energy electron beams from two different institutions, and the spatial locations of surviving colonies were recorded. Gafchromic film dosimetry and Monte Carlo simulations were carried out to determine the spatial electron scattering contribution from the flask walls. Low electron irradiation resulted in an uneven surviving colony distribution concentrated near the periphery of the flasks, while spatial colony formation was statistically uniform at energies above 7 MeV. Our data demonstrates that without proper dosimetric corrections, studies using low energy electrons can lead to misinterpretations of energy dependent cellular radiosensitivity in culture vessels, and radiotherapeutic applications.
Prenatal Testosterone Exposure Disrupts Insulin Secretion And Promotes Insulin Resistance
Authors: Carrasco Albert , Recabarren Mónica P. , Rojas-García Pedro P. , Gutiérrez Mario , Morales Karina , Sir-Petermann Teresa , Recabarren Sergio E.
Published: January 2020

Hyperandrogenemia and metabolic disturbances during postnatal life are strongly linked both to polycystic ovary syndrome and other conditions that arise from prenatal exposure to androgen excess. In an animal model of this condition, we reported that insulin sensitivity (IS) was lower in young female sheep born to testosterone-treated mothers versus sheep born to non-exposed mothers (control). This lower insulin sensitivity remains throughout reproductive life. However, it is unknown whether abnormal postnatal levels of testosterone (T) further decrease IS derived from prenatal exposure to testosterone. Therefore, we assessed the effects of an acute testosterone administration (40 mg) on IS and insulin secretion during an intravenous glucose tolerance test performed at 40 weeks of age (adulthood) in previously ovariectomized sheep at 26 weeks of age (prepuberty), that were either prenatally exposed to testosterone (T-females, n = 6) or not (C-females, n = 6). The incremental area under the curve of insulin was greater in C-females both with or without the acute testosterone treatment (P < 0.05). The ISI-Composite was lower after an acute testosterone treatment, only in T-females. We conclude that prenatal exposure to testosterone disrupts pancreatic insulin secretion in response to glucose and that in this setting further hyperandrogenemia may predispose to lower insulin sensitivity.
Extracellular electron uptake in Methanosarcinales is independent of multiheme c-type cytochromes
Authors: Yee Mon Oo , Rotaru Amelia-Elena
Published: January 2020

The co-occurrence of Geobacter and Methanosarcinales is often used as a proxy for the manifestation of direct interspecies electron transfer (DIET) in the environment. Here we tested eleven new co-culture combinations between methanogens and electrogens. Previously, only the most electrogenic Geobacter paired by DIET with Methanosarcinales methanogens, namely G. metallireducens and G. hydrogenophilus. Here we provide additional support, and show that five additional Methanosarcinales paired with G. metallireducens, while a strict hydrogenotroph could not. We also show that G. hydrogenophilus, which is incapable to grow with a strict hydrogenotrophic methanogen, could pair with a strict non-hydrogenotrophic Methanosarcinales. Likewise, an electrogen outside the Geobacter cluster (Rhodoferrax ferrireducens) paired with Methanosarcinales but not with strict hydrogenotrophic methanogens. The ability to interact with electrogens appears to be conserved among Methanosarcinales, the only methanogens with c-type cytochromes, including multihemes (MHC). Nonetheless, MHC, which are often linked to extracellular electron transfer, were neither unique nor universal to Methanosarcinales and only two of seven Methanosarcinales tested had MHC. Of these two, one strain had an MHC-deletion knockout available, which we hereby show is still capable to retrieve extracellular electrons from G. metallireducens or an electrode suggesting an MHC-independent strategy for extracellular electron uptake.
A continuous evolution system for contracting the host range of bacteriophage T7
Authors: Holtzman Tzvi , Globus Rea , Molshanski-Mor Shahar , Ben-Shem Adam , Yosef Ido , Qimron Udi
Published: January 2020

Bacteriophage T7 is an intracellular parasite that recognizes its host via its tail and tail fiber proteins, known as receptor-binding proteins (RBPs). The RBPs attach to specific lipopolysaccharide (LPS) features on the host. Various studies have shown expansion of the phage’s host range via mutations in the genes encoding the RBPs, whereas only a few have shown contraction of its host range. Furthermore, most experimental systems have not monitored the alteration of host range in the presence of several hosts simultaneously. Here we show that T7 phage grown in the presence of five restrictive strains and one permissive host, each with a different LPS form, gradually avoids recognition of the restrictive strains. Remarkably, avoidance of the restrictive strains was repeated in different experiments using six different permissive hosts. The evolved phages carried mutations that changed their specificity, as determined by sequencing of the genes encoding the RBPs. This system demonstrates a major role for RBPs in narrowing the range of futile infections. The system can be harnessed for host-range contraction in applications such as detection or elimination of a specific bacterial serotype by bacteriophages.
Loss of dominant caterpillar genera in a protected tropical forest
Authors: Salcido Danielle M. , Forister Matthew L. , Garcia Lopez Humberto , Dyer Lee A.
Published: January 2020

Reports of biodiversity loss have increasingly focused on declines in abundance and diversity of insects, but it is still unclear if substantive insect diversity losses are occurring in intact low-latitude forests. We collected 22 years of plant-caterpillar-parasitoid data in a protected tropical forest and found reductions in the diversity and density of insects that appear to be partly driven by a changing climate and weather anomalies. Results also point to the potential influence of variables not directly measured in this study, including changes in land-use in nearby areas. We report a decline in parasitism that represents a reduction in an important ecosystem service: enemy control of primary consumers. The consequences of these changes are in many cases irreversible and are likely to be mirrored in nearby forests; overall declines in the region will have negative consequences for surrounding agriculture. The decline of important tropical taxa and associated ecosystem function illuminates the consequences of numerous threats to global insect diversity and provides additional impetus for research on tropical diversity.
A Comprehensive Transcriptome-Wide Identification and Screening of WRKY Gene Family Engaged in Abiotic Stress in Glycyrrhiza glabra
Authors: Goyal Pooja , Manzoor Malik Muzafar , Vishwakarma Ram A. , Sharma Deepak , Dhar Manoj K. , Gupta Suphla
Published: January 2020

The study reports 147 full-length WRKY genes based on the transcriptome analysis of Glycyrrhiza genus (G. glabra and G. uralensis). Additional motifs in G. glabra included DivIVA (GgWRKY20) and SerS Superfamily (GgWRKY21) at the C-terminal, and Coat family motifs (GgWRKY55) at the N-terminal of the proteins, while Exo70 exo cyst complex subunit of 338 amino acid (GuWRKY9) was present at the N-terminal of G. uralensis only. Plant Zn cluster super-family domain (17 WRKYs) and bZIP domain (2 WRKYs) were common between the two species. Based on the number of WRKY domains, sequence alignment and phylogenesis, the study identified GuWRKY27 comprising of 3 WRKY domains in G. uralensis and a new subgroup-IIf (10 members), having novel zinc finger pattern (C-X4-C-X22-HXH) in G. glabra. Multiple WRKY binding domains (1–11) were identified in the promoter regions of the GgWRKY genes indicating strong interacting network between the WRKY proteins. Tissue-specific expression of 25 GgWRKYs, under normal and treated conditions, revealed 11 of the 18 induction factor triggered response corroborating to response observed in AtWRKYs. The study identified auxin-responsive GgWRKY 55 & GgWRKY38; GA3 responsive GgWRKYs15&59 in roots and GgWRKYs8, 20, 38, 57 &58 in the shoots of the treated plant. GgWRKYs induced under various stresses included GgWRKY33 (cold), GgWRKY4 (senescence), GgWRKYs2, 28 & 33 (salinity) and GgWRKY40 (wounding). Overall, 23 GgWRKYs responded to abiotic stress, and 17 WRKYs were induced by hormonal signals. Of them 13 WRKYs responded to both suggesting inter-connection between hormone signalling and stress response. The present study will help in understanding the transcriptional reprogramming, protein-protein interaction and cross-regulation during stress and other physiological processes in the plant.
Intranasal vaccination with Listeria ivanovii as vector of Mycobacterium tuberculosis antigens promotes specific lung-localized cellular and humoral immune responses
Authors: Jiang Ming-juan , Liu Si-jing , Su Lin , Zhang Xiang , Li Yong-yu , Tang Tian , Wang Chuan
Published: January 2020

We have previously demonstrated that a recombinant Listeria ivanovii (LI) strain expressing the ESAT-6 or Ag85C protein of Mycobacterium tuberculosis (Mtb) as a tuberculosis (TB) vaccine candidates induced antigen-specific cellular immune responses after intravenous immunization of mice. However, whether such recombinant strains could induce desired immune responses in the lung, where TB infection occurs, is not clear. In this paper, C57BL/6 J mice were intranasally vaccinated with attenuated LIΔactAplcB-Rv3875 (Δ refers to gene deletion in the bacterial genome) or LIΔactAplcB-Rv0129c, the two vaccine candidates that utilize LI as an antigen delivery vector. Bacterial load in the target organs, histological changes in the infected organs, the percentage of specific cytokine-secreting T cells in the lung and spleen, IgG levels in the serum and secretory IgA (SIgA) levles in bronchoalveolar lavage (BAL) fluid were determined at specific days post inoculation (dpi). The results showed that both strains were mainly confined to the lung and were eliminated at 10 dpi. The histological damage caused by the infection in the lung was slight and recovered by day 5. Intranasal vaccination of the mice twice at an interval of 4 weeks notably elicited TB antigen-specific CD4+ and CD8+ T cell responses in the lung and SIgA secretion in the pulmonary mucosa, and significantly enhanced the percentage of double-functional CD8+ T cells (IFN-γ+ TNF-α+ CD8+). To our knowledge, this is the first report regarding the used of LI vector vaccines to induce promising lung-localized cellular and humoral immune responses by intranasal vaccination. These data suggest that LI could be a novel and promising live vector to construct an intranasal vaccine against respiratory diseases.