bluuebunny/crossref_metadata_2025 huggingface dataset:
Developing and piloting a well-being program for hospital-based physicians
Authors: Debets Maarten P. M. , Lombarts KikiM. J. M. H. , Hugenholtz Nathalie I. R. , Scheepers Renée A.
Published: July 2020

Background Demanding working conditions in medical practice pressurise the well-being of physicians across all career stages, likely harming patients and healthcare systems. Structural solutions to harmful working conditions are necessary as well as interventions to support physicians in contemporary practice. We report on developing and piloting a team-based program for physicians to improve their working conditions and well-being.

Approach Program development steps involved: a preparatory phase, needs assessment, and program design. The program consisted of (1) a feedback tool addressing working conditions and well-being, and an intervention including (2a) a facilitated team dialogue and (2b) a team training on communication and collaborative job crafting. In the program’s pilot, 377 physicians from 48 teams in 14 Dutch hospitals used the feedback tool. Four teams participated in the team dialogue. Two teams performed the team training.

Evaluation Physicians indicated that the program was a useful format to gain insight into their working conditions and well-being, and possibly to improve their well-being collaboratively.

Reflection We provide seven critical reflections on developing and piloting our program, accompanied by recommendations for developing well-being interventions. Our development approach, program components, and recommendations may support physicians and other healthcare professionals in demanding work environments.
The Mechanical Response of Wet Volcanic Sand to Impact Loading, Effects of Water Content and Initial Compaction
Authors: Varley L. , Rutherford M. E. , Zhang L. , Pellegrino A.
Published: July 2020

The effects of water content and initial compaction on the dynamic response of volcanic sand from Mount Etna were investigated by a series of experiments on a long Split Hopkinson Pressure Bar apparatus capable of generating stress pulses of duration exceeding one millisecond. The dynamic stress–strain characteristics were determined until large final compressive strains were achieved. An experimental protocol for the preparation of samples characterised by different initial porosity and moisture content was defined in order to reproduce, in a laboratory environment, granular volcanic aggregates representative of naturally occurring soils in different initial density and water content states. It was found that, for limited amounts of water content, the dynamic response of the investigated volcanic wet sand is more compliant than in dry conditions. Conversely, highly saturated samples exhibit a steep increase in stiffness occurring at strains when the dynamic compressive behaviour becomes dominated by the response of the nearly incompressible water. The presence of water has negligible effect on the mechanical behaviour when the samples are loaded at quasi static strain rates. The grain size distribution and morphology of samples tested in different conditions were evaluated and compared by means of edge detection analysis techniques applied to high contrast images.
Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-Tissue Network Analysis
Authors: Hu Jihong , Zeng Tao , Xia Qiongmei , Huang Liyu , Zhang Yesheng , Zhang Chuanchao , Zeng Yan , Liu Hui , Zhang Shilai , Huang Guangfu , Wan Wenting , Ding Yi , Hu Fengyi , Yang Congdang , Chen Luonan , Wang Wen
Published: July 2020

Significantly increasing crop yield is a major and worldwide challenge for food supply and security. It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide. Yet, the gene regulatory mechanism underpinning this ultrahigh yield has been a mystery. Here, we systematically collected the transcriptome data for seven key tissues at different developmental stages using rice cultivated both at Taoyuan as the case group and at another regular rice planting place Jinghong as the control group. We identified the top 24 candidate high-yield genes with their network modules from these well-designed datasets by developing a novel computational systems biology method, i.e., dynamic cross-tissue (DCT) network analysis. We used one of the candidate genes, OsSPL4, whose function was previously unknown, for gene editing experimental validation of the high yield, and confirmed that OsSPL4 significantly affects panicle branching and increases the rice yield. This study, which included extensive field phenotyping, cross-tissue systems biology analyses, and functional validation, uncovered the key genes and gene regulatory networks underpinning the ultrahigh yield of rice. The DCT method could be applied to other plant or animal systems if different phenotypes under various environments with the common genome sequences of the examined sample. DCT can be downloaded from https://github.com/ztpub/DCT.
Shift Work Sleep Disorder and Night Shift Work Significantly Impair Erectile Function
Authors: Rodriguez Katherine M. , Kohn Taylor P. , Kohn Jaden R. , Sigalos John T. , Kirby E. Will , Pickett Stephen M. , Pastuszak Alexander W. , Lipshultz Larry I.
Published: July 2020

Objectives

Here we examine the association between shift work sleep disorder (SWSD) and erectile dysfunction (ED) in shift workers.

Methods

Men presenting to a single andrology clinic between January 2014 and July 2017 completed validated questionnaires: International Index of Erectile Function (IIEF), Patient Health Questionnaire-9 (PHQ-9), and the nonvalidated SWSD Questionnaire. Men were also asked about shift work schedule, comorbidities, phosphodiesterase 5 (PDE5) inhibitor use, and testosterone use. Serum total testosterone values were determined for each visit. Linear regression was performed controlling for testosterone use, testosterone levels, PDE5 inhibitor use, age, and comorbidities to determine the effect of SWSD on ED as assessed using the IIEF.

Results

Of the 754 men completing questionnaires, 204 reported nonstandard shift work (begins before 7 am or after 6 pm, regularly extends out of that frame, or rotates frequently) and 48 were found to have SWSD using a screening questionnaire. Nonstandard shift work alone did not result in worse IIEF-EF scores (P = .31), but those who worked nonstandard shifts and had SWSD demonstrated IIEF-EF scores 2.8 points lower than men without SWSD (P < .01). When assessing for the type of shift work performed, men who worked night shifts had IIEF-EF scores 7.6 points lower than men who worked during the day or evening (P < .01). Testosterone use improved IIEF-EF scores for men with SWSD by 2.9 points, ameliorating the effect of SWSD on ED. However, baseline testosterone levels were not associated with worse erectile function in this cohort.

Conclusion

Men with SWSD have worse erectile function, with men who work night shifts having even poorer erectile function. These findings suggest that circadian rhythm disturbance may significantly impact erectile function. While testosterone therapy may partly reverse the effects of SWSD, shift work is a potential risk factor for ED and should be assessed for as part of the evaluation of men with ED.
Using the ArcGIS Collector Mobile App for Settlement Survey Data Collection in Armenia
Authors: Lindsay Ian , Kong Ningning Nicole
Published: July 2020

Recent years have seen the rapid adoption of digital site recording strategies following the proliferation of GPS-enabled mobile devices and data collection apps. Much of the emerging literature on digital—or paperless—archaeology, however, has focused on excavation contexts, with fewer discussions of mobile-GIS solutions on archaeological survey. This article discusses the design and implementation of a site survey workflow based on Esri's ArcGIS Collector mobile app in the context of Project ArAGATS's Kasakh Valley Archaeology Survey in northwestern Armenia. The Collector app provides a simple, map-centric user interface that allows surveyors with little-to-no GIS experience to record site locations, enter attribute data on customized digital forms, and attach photographs. With a network connection, the Collector app instantly uploads site information as GIS data to the project geodatabase and refreshes the data across surveyors’ mobile devices. Although the Collector app lacks certain GIS features and requires an institutional Esri license, we found that the native integration with our project GIS and broad access to visualization and recording tools in the app made in-field decision-making and interpretation more collaborative and inclusive across the survey team.
The Philosophy of Accidentality
Authors: VARGAS MANUEL
Published: July 2020

In mid-twentieth-century Mexican philosophy, there was a peculiar nationalist existentialist project focused on the cultural conditions of agency. This article revisits some of those ideas, including the idea that there is an important but underappreciated experience of one's relationship to norms and social meanings. This experience—something called accidentality—casts new light on various forms of social subordination and socially scaffolded agency, including cultural alienation, biculturality, and double consciousness.
Autocratic Stability in the Shadow of Foreign Threats
Authors: DI LONARDO LIVIO , SUN JESSICA S. , TYSON SCOTT A.
Published: July 2020

Autocrats confront a number of threats to their power, some from within the regime and others from foreign actors. To understand how these threats interact and affect autocratic survival, we build a model where an autocratic leader can be ousted by a domestic opposition and a foreign actor. We concentrate on the impact that foreign threats have on the stability of autocratic leadership and show that the presence of foreign threats increases the probability an autocrat retains power. Focusing on two cases, one where a foreign actor and the domestic opposition have aligned interests and one where their interests are misaligned, we elucidate two distinct mechanisms. First, when interests are aligned, autocrats are compelled to increase domestic security to alleviate international pressure. Second, when interests are misaligned, autocrats exploit the downstream threat of foreign intervention to deter domestic threats. We also show that autocrats have incentives to cultivate ideological views hostile to broader interests among politically influential domestic actors.
A REASSESSMENT OF LEATHERWORK FROM THE SUTTON HOO SHIP BURIAL
Authors: Volken Marquita , Mould Quita , Cameron Esther
Published: July 2020

The seventh-century ship burial at Sutton Hoo Mound 1, excavated in 1939, contained an impressive display of gold, silver and bronze objects, weapons and other offerings. Organic materials such as wood, textiles and leather were also present. The leather items were studied, and the results published in 1983, when two pairs of shoes were identified from the extremely fragmented remains that survived. Recently, a reassessment of the leather fragments revised the identification to two bags and a single pair of shoes. Multiple reconstruction techniques, developed over the last twenty years, were used to examine the leather fragments and associated metal fittings to provide a new understanding of the leather items and how they had been placed in the burial.
Phạm Quỳnh, borrowed language, and the ambivalences of colonial discourse
Authors: Vu Yen N.
Published: July 2020

Phạm Quỳnh (1893–1945), twentieth century Vietnamese intellectual and politician, is a contentious figure in Vietnamese colonial history in terms of his collaboration with the French administration. Much of the mixed opinions on his role, though gleaned from his essays and political positions, have not yet been connected to the ambiguities of the colonial reforms concurrent with his budding career. Informed by Homi Bhabha's framework of ‘mimicry’, this study offers a reading of Phạm Quỳnh's attachment to language, both tongue and discourse, to nuance his character and reveal the ambiguous articulations of French colonial policy in Vietnam.
Feeding strategies and body condition of juvenile European flounderPlatichthys flesusin a nursery habitat
Authors: Mendes C. , Ramos S. , Elliott M. , Bordalo A. A.
Published: July 2020

Estuarine habitats are major nurseries for the European flounderPlatichthys flesus, with different year classes sharing food and space resources. Hence, an understanding of feeding strategies that optimize resource use and maintain carrying capacity is fundamental for sustainable and successful ecosystem management. The main feeding areas of juvenile European flounder (including 0-group and 1-group age classes) in the Lima estuary (northern Portugal) nursery ground were investigated by integrating stomach content analyses with stable isotopic values (δ13C and δ15N) and fish condition indices (Fulton K and RNA:DNA ratio). The 0-group flounder that were associated with the upstream section of the estuary presented the lowest δ13C value (−25.58 ± 1.86‰), while 1-group flounder exhibited a higher δ13C value (−22.59 ± 2.51‰), indicating use of the more saline areas of the estuary (lower and middle sections). The two age groups did not differ in terms of δ15N (0-group: 13.93 ± 0.29‰; 1-group: 13.50 ± 0.96‰), indicating similar trophic levels. The low salinity upper estuary was the main feeding area of 0-group flounder (74%), while 1-group flounder fed along the estuary both upstream (52%) and downstream (48%). Juvenile flounder showed high individual condition based on the Fulton K index (0-group: 1.05 ± 0.08; 1-group: 1.07 ± 0.05) and RNA:DNA (0-group: 1.70 ± 0.70; 1-group: 1.41 ± 0.47). These indices deal with fish health, and hence indicate nursery habitat quality. It is concluded that in this temperate nursery habitat, different feeding strategies sustained the condition of the European flounder juveniles, compared with other flounder populations.
Essence, Explanation, and Modality
Authors: Wallner Michael , Vaidya Anand
Published: July 2020

Recently, Kit Fine's (1994) view that modal truths aretrue in virtue of,grounded in, orexplained byessentialist truths has been under attack. In what follows we offer two responses to the wave of criticism against his view. While the first response is pretty straightforward, the second is based on the distinction between, what we call,Reductive Finean EssentialismandNon-Reductive Finean Essentialism. Engaging the work of Bob Hale onNon-Reductive Finean Essentialism, we aim to show that the arguments against Fine's view are unconvincing, while we acknowledge the presence of a deep standoff between the two views.
Generalized monoidal effects and handlers
Authors: PIETERS RUBEN P. , RIVAS EXEQUIEL , SCHRIJVERS TOM
Published: July 2020

Algebraic effects and handlers are a convenient method for structuring monadic effects with primitive effectful operations and separating the syntax from the interpretation of these operations. However, the scope of conventional handlers is limited as not all side effects are monadic in nature. This paper generalizes the notion of algebraic effects and handlers from monads to generalized monoids, which notably covers applicative functors and arrows as well as monads. For this purpose, we switch the category theoretical basis from free algebras to free monoids. In addition, we show how lax monoidal functors enable the reuse of handlers and programs across different computation classes, for example, handling applicative computations with monadic handlers. We motivate and present these handler interfaces in the context of build systems. Tasks in a build system are represented by a free computation and their interpretation as a handler. This use case is based on the work of Mokhov et al. [(2018). PACMPL2(ICFP), 79:1–79:29.].
Progressive right ventricular outflow tract fibrosis after repair of tetralogy of Fallot
Authors: Karur Gauri R. , Mawad Wadi , Grosse-Wortmann Lars
Published: July 2020

Objectives:

The objective of this study was to determine the evolution of fibrosis over time and its association with clinical status.

Methods:

Children with repaired tetralogy of Fallot who had undergone at least two cardiac magnetic resonance examinations including T1 mapping at least 1 year apart were included.

Results:

Thirty-seven patients (12.7 ± 2.6 years, 61% male) were included. Right ventricular free wall T1 increased (913 ± 208 versus 1023 ± 220 ms; p = 0.02). Baseline cardiac magnetic resonance parameters did not predict a change in imaging markers or exercise tolerance. The right ventricular free wall per cent change correlated with left ventricular T1% change (r = 0.51, p = 0.001) and right ventricular mass Z-score change (r = 0.51, p = 0.001). T1 in patients with late gadolinium enhancement did not differ from the rest.

Conclusion:

Increasing right ventricular free wall T1 indicates possible progressive fibrotic remodelling in the right ventricular outflow tract in this pilot study in children and adolescents with repaired tetralogy of Fallot. The value of T1 mapping both at baseline and during serial assessments will need to be investigated in larger cohorts with longer follow-up.
Sleep Early After Trauma
Authors: Azza Yasmine , Wilhelm Ines , Kleim Birgit
Published: July 2020

Abstract. Posttraumatic stress disorder (PTSD) is characterized by intrusive re-experiencing of emotional memories of a traumatic event. Such memories are formed after exposure to trauma in the context of a cascading stress response including high levels of emotional arousal and stress hormone release. Sleep could be a key modulator of early memory formation and re-consolidation processes. Initial studies have investigated this association in this early time period, that is, hours and days after trauma exposure, and its role in modulating trauma memories and PTSD. The time is thus ripe to integrate findings from these studies. The current review consolidated evidence from five experimental and seven naturalistic studies on the association between trauma, sleep, and the development of intrusive emotional memories and PTSD, respectively. Together, the studies point to a potential protective role of sleep after trauma for the development of intrusive memories and PTSD. Findings regarding key sleep architecture features are more mixed and require additional investigation. The findings are important for prevention and intervention science.
In Vegetation Growth Studies, What You Measure Matters
Authors: Rehnberg Morgan
Published: July 2020

Different satellite-based metrics for global vegetation coverage tell complementary, but not identical, stories.
Vegetation Affects Timing and Location of Wetland Methane Emissions
Authors: Bansal Sheel , Johnson Olivia F. , Meier Jacob , Zhu Xiaoyan
Published: July 2020

Common assumptions about how vegetation affects wetland methane (CH4) flux include acting as conduits for CH4release, providing carbon substrates for growth and activity of methanogenic organisms, and supplying oxygen to support CH4oxidation. However, these effects may change through time, especially in seasonal wetlands that experience drying and rewetting, or change across space, dependent on proximity to vegetation. In a mesocosm study, we assessed the impacts ofTyphaon CH4flux using clear flux chamber measurements directly overTyphaplants (“whole‐plant”), adjacent toTyphaplants (where roots were present but no stems; “plant‐adjacent”), and plant‐free soils (“control”). During the establishment phase of the study (first 30 days), the whole‐plant treatment had ~5 times higher CH4flux rates (51.78 ± 8.16 mg‐C m−2day−1) than plant‐adjacent or control treatments, which was primarily due to plant‐mediated transport, with little contribution from diffusive‐only flux. However, porewater CH4concentrations were relatively low directly below whole‐plant and in neighboring plant‐adjacent treatments, while controls accumulated a highly concentrated reservoir of porewater CH4. When the water table was drawn down to simulate seasonal drying, reserve porewater CH4from control soil was released as a pulse, equaling the earlier higher CH4emissions from whole‐plants. Plant‐adjacent treatments, which had neither plant‐mediated CH4transport nor a concentrated reservoir of porewater CH4, had low CH4flux throughout the study. Our findings indicate that in seasonal wetlands, vegetation affects the timing and location of CH4emissions. These results have important mechanistic and methodological implications for understanding the role of vegetation on wetland CH4flux.
Association between adjuvant chemotherapy and survival in patients with rectal cancer and pathological complete response after neoadjuvant chemoradiotherapy and resection
Authors: He Fang , Ju Huai-Qiang , Ding Yi , Jiang Zhiqiang , Li Zhenhui , Huang Bo , Wang Xiuhong , Zhao Yuanyuan , Li Yong , Qi Bin , Luo Wenguang , Zhang Zijian , Pei Qian , Chen Haiyang , Liu Shuai , Pang Xiaolin , Zheng Jian , Wang Jianping , Ajani Jaffer A. , Wan Xiang-Bo
Published: July 2020

Background

For patients with locally advanced rectal cancer (LARC), it is unclear whether neoadjuvant chemoradiotherapy-induced pathologic complete response (pCR) individuals would further benefit from adjuvant chemotherapy (ACT).

Methods

The pCR individuals who received different ACT cycles were paired by propensity score matching. Overall survival (OS), disease-free survival (DFS), local recurrence-free survival (LRFS), and distant metastasis-free survival (DMFS) were calculated by Kaplan–Meier and log-rank test.

Results

In total, 1041 pCR individuals were identified from 5567 LARC cases. Specifically, 303 pCR cases had no ACT treatment, and 738 pCR patients received fluoropyrimidine-based ACT (median, 4 cycles) treatment. After 1:3 propensity score matching, 297 cases without ACT treatment were matched to 712 cases who received ACT treatment. Kaplan–Meier analysis showed that pCR individuals treated with or without ACT had the similar 3-year outcome (OS, DFS, LRFS and DMFS) (all P > 0.05). Moreover, the pCR patients received different ACT cycle(s) (0 vs. 1–4 cycles, 0 vs. ≥5 cycles) had comparable 3-year OS, DFS, LRFS and DMFS (all P > 0.05). In stratified analysis, ACT treatment did not improve 3-year survival (OS, DFS, LRFS and DMFS) for the baseline high-risk (cT3–4/cN1–2) subgroup patients (all P > 0.05).

Conclusion

ACT, which did not improve survival, is unnecessary to neoadjuvant treatment-induced pCR LARC patients.

Trial registration

2019ZSLYEC-136 (24-6-2019).
Contributions of de novo variants to systemic lupus erythematosus
Authors: Almlöf Jonas Carlsson , Nystedt Sara , Mechtidou Aikaterini , Leonard Dag , Eloranta Maija-Leena , Grosso Giorgia , Sjöwall Christopher , Bengtsson Anders A. , Jönsen Andreas , Gunnarsson Iva , Svenungsson Elisabet , Rönnblom Lars , Sandling Johanna K. , Syvänen Ann-Christine
Published: July 2020

By performing whole-genome sequencing in a Swedish cohort of 71 parent-offspring trios, in which the child in each family is affected by systemic lupus erythematosus (SLE, OMIM 152700), we investigated the contribution of de novo variants to risk of SLE. We found de novo single nucleotide variants (SNVs) to be significantly enriched in gene promoters in SLE patients compared with healthy controls at a level corresponding to 26 de novo promoter SNVs more in each patient than expected. We identified 12 de novo SNVs in promoter regions of genes that have been previously implicated in SLE, or that have functions that could be of relevance to SLE. Furthermore, we detected three missense de novo SNVs, five de novo insertion-deletions, and three de novo structural variants with potential to affect the expression of genes that are relevant for SLE. Based on enrichment analysis, disease-affecting de novo SNVs are expected to occur in one-third of SLE patients. This study shows that de novo variants in promoters commonly contribute to the genetic risk of SLE. The fact that de novo SNVs in SLE were enriched to promoter regions highlights the importance of using whole-genome sequencing for identification of de novo variants.
A crop type dataset for consistent land cover classification in Central Asia
Authors: Remelgado Ruben , Zaitov Sherzod , Kenjabaev Shavkat , Stulina Galina , Sultanov Murod , Ibrakhimov Mirzakhayot , Akhmedov Mustakim , Dukhovny Victor , Conrad Christopher
Published: July 2020

Land cover is a key variable in the context of climate change. In particular, crop type information is essential to understand the spatial distribution of water usage and anticipate the risk of water scarcity and the consequent danger of food insecurity. This applies to arid regions such as the Aral Sea Basin (ASB), Central Asia, where agriculture relies heavily on irrigation. Here, remote sensing is valuable to map crop types, but its quality depends on consistent ground-truth data. Yet, in the ASB, such data are missing. Addressing this issue, we collected thousands of polygons on crop types, 97.7% of which in Uzbekistan and the remaining in Tajikistan. We collected 8,196 samples between 2015 and 2018, 213 in 2011 and 26 in 2008. Our data compile samples for 40 crop types and is dominated by “cotton” (40%) and “wheat”, (25%). These data were meticulously validated using expert knowledge and remote sensing data and relied on transferable, open-source workflows that will assure the consistency of future sampling campaigns.
The structural basis of the genetic code: amino acid recognition by aminoacyl-tRNA synthetases
Authors: Kaiser Florian , Krautwurst Sarah , Salentin Sebastian , Haupt V. Joachim , Leberecht Christoph , Bittrich Sebastian , Labudde Dirk , Schroeder Michael
Published: July 2020

Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. We extensively characterize how these enzymes distinguish all natural amino acids based on the computational analysis of crystallographic structure data. The results of this meta-analysis show that the correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric effects.
Climate smart Dry Chain Technology for safe storage of quinoa seeds
Authors: Bakhtavar Muhammad Amir , Afzal Irfan
Published: July 2020

Quinoa (Chenopodium quinoa) is a climate resilient crop having superior nutritional profile compared to other cereal grains and may help to ensure future food security. Commercial cultivation of quinoa is dependent upon availability of quality seed. Adoption of Dry Chain Technology: drying before storage and maintaining seed dryness through hermetic packaging, may prevent quinoa seed deterioration. Quinoa seeds were dried to 8, 10, 12 and 14% initial seed moisture content (SMC) and stored in conventional (Paper, polypropylene, cloth and jute) and hermetic Super Bags for 6, 12 and 18 months. Seed stored in Super Bag at 8% initial SMC maintained low seed moisture and higher germination. Total soluble sugars and α-amylase activity were higher while EC, reducing sugars and MDA contents were low for the seeds stored in hermetic bag at 8% initial SMC. Seed stored in traditional packaging materials irrespective of initial seed moisture contents, gained moisture due to ambient high relative humidity which resulted in seed deterioration as indicated by increased reducing sugars, MDA contents and seed leachates conductivity and reduced vigor, viability, soluble sugars. The Dry Chain Technology preserves seed quality by maintaining low seed moisture and reducing deteriorative physiological and biochemical changes in the quinoa seed.
Narrow genetic base shapes population structure and linkage disequilibrium in an industrial oilseed crop, Brassica carinata A. Braun
Authors: Khedikar Yogendra , Clarke Wayne E. , Chen Lifeng , Higgins Erin E. , Kagale Sateesh , Koh Chu Shin , Bennett Rick , Parkin Isobel A. P.
Published: July 2020

Ethiopian mustard (Brassica carinataA. Braun) is an emerging sustainable source of vegetable oil, in particular for the biofuel industry. The present study exploited genome assemblies of the Brassica diploids,Brassica nigraandBrassica oleracea,to discover over 10,000 genome-wide SNPs using genotype by sequencing of 620B. carinatalines. The analyses revealed a SNP frequency of one every 91.7 kb, a heterozygosity level of 0.30, nucleotide diversity levels of 1.31 × 10−05, and the first five principal components captured only 13% molecular variation, indicating low levels of genetic diversity among theB. carinatacollection. Genome bias was observed, with greater SNP density found on the B subgenome. The 620 lines clustered into two distinct sub-populations (SP1 and SP2) with the majority of accessions (88%) clustered in SP1 with those from Ethiopia, the presumed centre of origin. SP2 was distinguished by a collection of breeding lines, implicating targeted selection in creating population structure. Two selective sweep regions on B3 and B8 were detected, which harbour genes involved in fatty acid and aliphatic glucosinolate biosynthesis, respectively. The assessment of genetic diversity, population structure, and LD in the globalB. carinatacollection provides critical information to assist future crop improvement.
Anti-biofilm efficacy of a medieval treatment for bacterial infection requires the combination of multiple ingredients
Authors: Furner-Pardoe Jessica , Anonye Blessing O. , Cain Ricky , Moat John , Ortori Catherine A. , Lee Christina , Barrett David A. , Corre Christophe , Harrison Freya
Published: July 2020

Novel antimicrobials are urgently needed to combat drug-resistant bacteria and to overcome the inherent difficulties in treating biofilm-associated infections. Studying plants and other natural materials used in historical infection remedies may enable further discoveries to help fill the antibiotic discovery gap. We previously reconstructed a 1,000-year-old remedy containing onion, garlic, wine, and bile salts, known as ‘Bald’s eyesalve’, and showed it had promising antibacterial activity. In this current paper, we have found this bactericidal activity extends to a range of Gram-negative and Gram-positive wound pathogens in planktonic culture and, crucially, that this activity is maintained against Acinetobacter baumannii, Stenotrophomonas maltophilia, Staphylococcus aureus, Staphylococcus epidermidis and Streptococcus pyogenes in a soft-tissue wound biofilm model. While the presence of garlic in the mixture can explain the activity against planktonic cultures, garlic has no activity against biofilms. We have found the potent anti-biofilm activity of Bald’s eyesalve cannot be attributed to a single ingredient and requires the combination of all ingredients to achieve full activity. Our work highlights the need to explore not only single compounds but also mixtures of natural products for treating biofilm infections and underlines the importance of working with biofilm models when exploring natural products for the anti-biofilm pipeline.
BDNF belongs to the nurse-like cell secretome and supports survival of B chronic lymphocytic leukemia cells
Authors: Talbot Hugo , Saada Sofiane , Barthout Elodie , Gallet Paul-François , Gachard Nathalie , Abraham Julie , Jaccard Arnaud , Troutaud Danielle , Lalloué Fabrice , Naves Thomas , Fauchais Anne-Laure , Jauberteau Marie-Odile
Published: July 2020

Evading apoptosis and sustained survival signaling pathways are two central hallmarks of B-cell chronic lymphocytic leukemia (B-CLL) cells. In this regard, nurse-like cells (NLC), the monocyte-derived type 2 macrophages, deliver stimulatory signals via B-cell activating factor (BAFF), a proliferation-inducing ligand (APRIL), and the C-X-C Motif Chemokine Ligand 12 (CXCL12). Previously, we demonstrated that brain-derived neurotrophic factor (BDNF) protects B-CLL cells from spontaneous apoptosis by activating the oncogenic complex NTSR2-TrkB (neurotensin receptor 2-tropomyosin-related kinase receptor B), only overexpressed in B-CLL cells, inducing anti-apoptotic protein Bcl-2 (B-cell lymphoma 2) expression and Src kinase survival signaling pathways. Herein, we demonstrate that BDNF belongs to the NLC secretome and promotes B-CLL survival. This was demonstrated in primary B-CLL co-cultured with their autologous NLC, compared to B-CLL cells cultured alone. Inhibition of BDNF in co-cultures, enhances B-CLL apoptosis, whereas its exogenous recombinant activates pro-survival pathways in B-CLL cultured alone (i.e. Src activation and Bcl-2 expression), at a higher level than those obtained by the exogenous recombinant cytokines BAFF, APRIL and CXCL12, the known pro-survival cytokines secreted by NLC. Together, these results showed that BDNF release from NLC trigger B-CLL survival. Blocking BDNF would support research strategies against pro-survival cytokines to limit sustained B-CLL cell survival.
SO2 and HCHO over the major cities of Kazakhstan from 2005 to 2016: influence of political, economic and industrial changes
Authors: Darynova Zhuldyz , Amouei Torkmahalleh Mehdi , Abdrakhmanov Talgat , Sabyrzhan Serik , Sagynov Sultan , Hopke Philip K. , Kushta Jonilda
Published: July 2020

Satellite observations of the Ozone Monitoring Instrument (OMI) for tropospheric sulfur dioxide (SO2) and formaldehyde (HCHO) column mass densities (CMD) are analyzed for the period 2005–2016 over the atmosphere of Kazakhstan. Regarding SO2 the major hot spots relate to regions with high population and large industrial facilities. Such an example is the city of Ekibastuz that hosts the biggest thermal power plants in the country and exhibits the higher SO2 CMD at national level. The annual average CMD in Ekibastuz reaches 2.5 × 10−5 kg/m2, whereas for the rest of the country respective values are 6 times lower. Other hotspots, mostly urban conglomerates such as Almaty and Nur-Sultan, experience high CMDs of SO2 in particular years, such as 2008. One of the main reasons for this behavior is the financial crisis of 2008, forcing the application of alternate heating sources based on cheap low-quality coal. Regarding HCHO, an oxygenated Volatile Organic Compound (VOC), the main hot spot is noticed over the city Atyrau, the oil capital of the country where two massive oil fields are located. The highest HCHO CMD (9 × 1015 molecules/cm2) appears in the summertime due to secondary production as a result of the photo-oxidation of VOCs emitted by industrial sectors, oil refinery plants and vehicles. Strongly elevated HCHO amounts are also observed in Nur-Sultan in 2012 that could be due to the residential coal combustion and vehicle exhaust under poor winter dispersion conditions. Significant reductions in HCHO observed between 2012 and 2015 can be attributed to two significant measures implemented in the country in 2013 that aimed at the improvement of air quality: the introduction of the emission trading system (ETS) for greenhouse gases and Euro-4 standards for new vehicles entering the national vehicle fleet.
Photoelectrochemical and crystalline properties of a GaN photoelectrode loaded with α-Fe2O3 as cocatalyst
Authors: Velazquez-Rizo Martin , Iida Daisuke , Ohkawa Kazuhiro
Published: July 2020

Nitrides are of particular interest in energy applications given their suitability to photocatalytically generate H2 from aqueous solutions. However, one of the drawbacks of nitrides is the decomposition they suffer when used in photoelectrochemical cells. Here, we report the improvement of the catalytic performance and chemical stability of a GaN electrode when it is decorated with Fe2O3 particles compared with an undecorated electrode. Our results show a higher reaction rate in the Fe2O3/GaN electrode, and that photocorrosion marks take more than 20 times longer to appear on it. We also characterized the crystalline properties of the Fe2O3 particles with transmission electron microscopy. The results show that the Fe2O3 particles keep an epitaxial relationship with GaN that follows the Fe2O3$$\{{0003}\}||$${0003}||GaN$$\{{0001}\}$${0001} and Fe2O3$$[{11{\bar{ 2}}0}]||$$[112¯0]||GaN$$[{1{\bar{ 1}}00}]$$[11¯00] symmetry constraints. We also characterized an Fe2O3 (thin film)/GaN electrode, however it did not present any catalytic improvement compared with a bare GaN electrode. The epitaxial relationship found between the Fe2O3 thin film and GaN exhibited the Fe2O3$$\{{11{\bar{ 2}}0}\}||$${112¯0}||GaN$$\{{0002}\}$${0002} and Fe2O3$$[ {3{\bar{ 3}}00} ]||$$[33¯00]||GaN$$[{11{\bar{ 2}}0}]$$[112¯0] symmetry constraints.
Physiological impact and comparison of mutant screening methods in piwil2 KO founder Nile tilapia produced by CRISPR/Cas9 system
Authors: Jin Ye Hwa , Liao Baoshan , Migaud Herve , Davie Andrew
Published: July 2020

The application of genome engineering techniques to understand the mechanisms that regulate germ cell development opens promising new avenues to develop methods to control sexual maturation and mitigate associated detrimental effects in fish. In this study, the functional role of piwil2 in primordial germ cells (PGCs) was investigated in Nile tilapia using CRISPR/Cas9 and the resultant genotypes were further explored. piwil2 is a gonad-specific and maternally deposited gene in Nile tilapia eggs which is known to play a role in repression of transposon elements and is therefore thought to be important for maintaining germline cell fate. A functional domain of piwil2, PIWI domain, was targeted by injecting Cas9 mRNA and sgRNAs into Nile tilapia embryos at 1 cell stage. Results showed 54% of injected mutant larvae had no or less putative PGCs compared to control fish, suggesting an essential role of piwil2 in survival of PGCs. The genotypic features of the different phenotypic groups were explored by next generation sequencing (NGS) and other mutant screening methods including T7 endonuclease 1 (T7E1), CRISPR/Cas-derived RNA-guided engineered nuclease (RGEN), high resolution melt curve analysis (HRMA) and fragment analysis. Linking phenotypes to genotypes in F0 was hindered by the complex mosacism and wide indel spectrum revealed by NGS and fragment analysis. This study strongly suggests the functional importance of piwil2 in PGCs survival. Further studies should focus on reducing mosaicism when using CRISPR/Cas9 system to facilitate direct functional analysis in F0.
Evaluation of PCR conditions for characterizing bacterial communities with full-length 16S rRNA genes using a portable nanopore sequencer
Authors: Fujiyoshi So , Muto-Fujita Ai , Maruyama Fumito
Published: July 2020

MinION (Oxford Nanopore Technologies), a portable nanopore sequencer, was introduced in 2014 as a new DNA sequencing technology. MinION is now widely used because of its low initial start-up costs relative to existing DNA sequencers, good portability, easy-handling, real-time analysis and long-read output. However, differences in the experimental conditions used for 16S rRNA-based PCR can bias bacterial community assessments in samples. Therefore, basic knowledge about reliable experimental conditions is needed to ensure the appropriate use of this technology. Our study concerns the reliability of techniques for obtaining accurate and quantitative full-length 16S rRNA amplicon sequencing data for bacterial community structure assessment using MinION. We compared five PCR conditions using three independent mock microbial community standard DNAs and established appropriate, standardized, better PCR conditions among the trials. We then sequenced two mock communities and six environmental samples using Illumina MiSeq for comparison. Modifying the PCR conditions improved the sequencing quality; the optimized conditions were 35 cycles of 95 °C for 1 min, 60 °C for 1 min and 68 °C for 3 min. Our results provide important information for researchers to determine bacterial community using MinION accurately.
Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion
Authors: Stanton David W. G. , Alberti Federica , Plotnikov Valery , Androsov Semyon , Grigoriev Semyon , Fedorov Sergey , Kosintsev Pavel , Nagel Doris , Vartanyan Sergey , Barnes Ian , Barnett Ross , Ersmark Erik , Döppes Doris , Germonpré Mietje , Hofreiter Michael , Rosendahl Wilfried , Skoglund Pontus , Dalén Love
Published: July 2020

The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of 14C and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52– 2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species.
Coccolithophore community response to ocean acidification and warming in the Eastern Mediterranean Sea: results from a mesocosm experiment
Authors: D’Amario Barbara , Pérez Carlos , Grelaud Michaël , Pitta Paraskevi , Krasakopoulou Evangelia , Ziveri Patrizia
Published: July 2020

Mesocosm experiments have been fundamental to investigate the effects of elevated CO2and ocean acidification (OA) on planktic communities. However, few of these experiments have been conducted using naturally nutrient-limited waters and/or considering the combined effects of OA and ocean warming (OW). Coccolithophores are a group of calcifying phytoplankton that can reach high abundances in the Mediterranean Sea, and whose responses to OA are modulated by temperature and nutrients. We present the results of the first land-based mesocosm experiment testing the effects of combined OA and OW on an oligotrophic Eastern Mediterranean coccolithophore community. Coccolithophore cell abundance drastically decreased under OW and combined OA and OW (greenhouse, GH) conditions.Emiliania huxleyicalcite mass decreased consistently only in the GH treatment; moreover, anomalous calcifications (i.e. coccolith malformations) were particularly common in the perturbed treatments, especially under OA. Overall, these data suggest that the projected increase in sea surface temperatures, including marine heatwaves, will cause rapid changes in Eastern Mediterranean coccolithophore communities, and that these effects will be exacerbated by OA.
Properties enhancement of carboxymethyl cellulose with thermo-responsive polymer as solid polymer electrolyte for zinc ion battery
Authors: Dueramae Isala , Okhawilai Manunya , Kasemsiri Pornnapa , Uyama Hiroshi , Kita Rio
Published: July 2020

A novel polymer host from carboxymethyl cellulose (CMC)/poly(N-isopropylacrylamide) (PNiPAM) was developed for a high safety solid polymer electrolyte (SPE) in a zinc ion battery. Effects of the PNiPAM loading level in the range of 0–40% by weight ( wt%) on the chemical, mechanical, thermal, and morphological properties of the CMC/PNiPAMx films (where x is the wt% of PNiPAM) were symmetrically investigated. The obtained CMC/PNiPAMx films showed a high compatibility between the polymers. The CMC/PNiPAM20 blend showed the greatest tensile strength and modulus at 37.9 MPa and 2.1 GPa, respectively. Moreover, the thermal degradation of CMC was retarded by the addition of PNiPAM. Scanning electron microscopy images of CMC/PNiPAM20 revealed a porous structure that likely supported Zn2+ movement in the SPEs containing zinc triflate, resulting in the high Zn2+ ion transference number (0.56) and ionic conductivity (1.68 × 10–4 S cm−1). Interestingly, the presence of PNiPAM in the CMC/PNiPAMx blends showed a greater stability during charge–discharge cyclic tests, indicating the ability of PNiPAM to suppress dendrite formation from causing a short circuit. The developed CMC/PNiPAM20 based SPE is a promising material for high ionic conductivity and stability in a Zn ion battery.
Evolutionary trends of the conserved neurocranium shape in angel sharks (Squatiniformes, Elasmobranchii)
Authors: López-Romero Faviel A. , Stumpf Sebastian , Pfaff Cathrin , Marramà Giuseppe , Johanson Zerina , Kriwet Jürgen
Published: July 2020

Elasmobranchii (i.e., sharks, skates, and rays) forms one of the most diverse groups of marine predators. With a fossil record extending back into the Devonian, several modifications in their body plan illustrate their body shape diversity through time. The angel sharks, whose fossil record dates back to the Late Jurassic, some 160 Ma, have a dorsoventrally flattened body, similar to skates and rays. Fossil skeletons of this group show that the overall morphology was well established earlier in its history. By examining the skull shape of well-preserved fossil material compared to extant angel sharks using geometric morphometric methods, within a phylogenetic framework, we were able to determine the conservative skull shape among angel sharks with a high degree of integration. The morphospace occupation of extant angel sharks is rather restricted, with extensive overlap. Most of the differences in skull shape are related to their geographic distribution patterns. We found higher levels of disparity in extinct forms, but lower ones in extant species. Since angel sharks display a highly specialized prey capture behaviour, we suggest that the morphological integration and biogeographic processes are the main drivers of their diversity, which might limit their capacity to display higher disparities since their origin.
Fourfold daily growth rate in multicellular marine alga Ulva meridionalis
Authors: Hiraoka Masanori , Kinoshita Yutaro , Higa Motoki , Tsubaki Shuntaro , Monotilla Alvin P. , Onda Ayumu , Dan Akinori
Published: July 2020

Microalgae with high growth rates have been considered as promising organisms to replace fossil resources with contemporary primary production as a renewable source. However, their microscopic size makes it hard to be harvested for industrial applications. In this regard, multicellular macroalgae are more suitable for harvesting. Here, we show that Ulva meridionalis has the highest growth rate ever reported for a multicellular autotrophic plant. Contrasted to the known bloom-forming species U. prolifera growing at an approximately two-fold growth rate per day in optimum conditions, U. meridionalis grows at a daily rate of over fourfold. The high growth ability of this multicellular alga would provide the most effective method for CO2 fixation and biomass production.