bluuebunny/crossref_metadata_2025 huggingface dataset:
Human Inborn Errors of Immunity: 2019 Update of the IUIS Phenotypical Classification
Authors: Bousfiha Aziz , Jeddane Leila , Picard Capucine , Al-Herz Waleed , Ailal Fatima , Chatila Talal , Cunningham-Rundles Charlotte , Etzioni Amos , Franco Jose Luis , Holland Steven M , Klein Christoph , Morio Tomohiro , Ochs Hans D. , Oksenhendler Eric , Puck Jennifer , Torgerson Troy R. , Casanova Jean-Laurent , Sullivan Kathleen E. , Tangye Stuart G.
Published: February 2020

Since 2013, the International Union of Immunological Societies (IUIS) expert committee (EC) on Inborn Errors of Immunity (IEI) has published an updated phenotypic classification of IEI, which accompanies and complements their genotypic classification into ten tables. This phenotypic classification is user-friendly and serves as a resource for clinicians at the bedside. There are now 430 single-gene IEI underlying phenotypes as diverse as infection, malignancy, allergy, autoimmunity, and autoinflammation. We herein report the 2019 phenotypic classification, including the 65 new conditions. The diagnostic algorithms are based on clinical and laboratory phenotypes for each of the ten broad categories of IEI.
Broadcasting a file in a communication network
Authors: Goetzmann Kai-Simon , Harks Tobias , Klimm Max
Published: February 2020

We study the problem of distributing a file, initially located at a server, among a set of n nodes. The file is divided into $$m\ge 1$$

m
≥
1

equally sized packets. After downloading a packet, nodes can upload it to other nodes, possibly to multiple nodes in parallel. Each node, however, may receive each packet from a single source node only. The upload and download rates between nodes are constrained by node- and server-specific upload and download capacities. The objective is to minimize the makespan. This problem has been proposed and analyzed first by Mundinger et al. (J Sched 11:105–120, 2008. 10.1007/s10951-007-0017-9) under the assumption that uploads obey the fair sharing principle, that is, concurrent upload rates from a common source are equal at any point in time. Under this assumption, the authors devised an optimal polynomial time algorithm for the case where the upload capacity of the server and the nodes’ upload and download capacities are all equal. In this work, we drop the fair sharing assumption and derive an exact polynomial time algorithm for the case when upload and download capacities per node and among nodes are equal. We further show that the problem becomes strongly NP-hard for equal upload and download capacities per node that may differ among nodes, even for a single packet. For this case, we devise a polynomial time $$\smash {(1+2\sqrt{2})}$$

(
1
+
2

2

)

-approximation algorithm. Finally, we devise two polynomial time algorithms with approximation guarantees of 5 and $$2 + \lceil \log _2 \lceil n/m\rceil \rceil /m$$

2
+
⌈

log
2

⌈
n
/
m
⌉

⌉
/
m

, respectively, for the general case of m packets.
Antioxidants and molecular damage in Nile Tilapia (Oreochromis niloticus) after exposure to microplastics
Authors: Hamed Mohamed , Soliman Hamdy A. M. , Osman Alaa G. M. , Sayed Alaa El-Din H.
Published: February 2020

Recently, research on the biological effects of microplastics (MPs) has grown exponentially. However, effects of MPs on freshwater fishes and the mechanisms of the biological effects of MPs were limited. So, the purpose of the current study was to clarify the effects of microplastics on oxidative stress response, DNA fragmentation, and proteinogram of the early juvenile stage of Nile Tilapia (Oreochromis niloticus). The fishes were assigned into four groups: one control, three MPs-exposed groups as 1 mg/L of MPs, 10 mg/L of MPs, and 100 mg/L of MPs respectively for 15 days and 15 days of recovery. The activities of superoxide dismutase, catalase, total peroxides, and oxidative stress index (OSI), as well as lipid peroxidation and DNA fragmentation, increased in groups exposed to MPs compared to the control group in a dose-dependent manner. In contrast, the activity of total antioxidant capacity decreased in groups exposed to MPs compared to the control group in a dose-dependent manner. The electrophoretic pattern of muscle proteins revealed alteration in the proteinogram in the MPs-exposed groups compared to control. After the recovery period, the activities of superoxide dismutase, catalase, total peroxides, total antioxidant capacity, lipid peroxidation, DNA fragmentation, and the electrophoretic pattern of muscle proteins returned to normal levels in 1 mg/L of MPs-exposed group. Combined with our previous work, these results suggest that MPs cause the overproduction of reactive oxygen species (ROS) and alters the antioxidants parameters, resulting in oxidative stress and DNA damage. The present study fosters a better understanding of the toxic effects of MPs on Tilapia as a freshwater model.
Towards a more robust approach for the restoration of mangroves in Vietnam
Authors: Hai N.T. , Dell B. , Phuong V.T. , Harper R.J.
Published: February 2020

Key message

Globally, mangrove forests are under threat from a range of causes. They also represent a large potential form of climate mitigation and adaptation via reforestation, and this investment may contribute to restoration efforts and reverse mangrove decline. There has been significant (c. 200,000 ha) mangrove reforestation and restoration activity in Vietnam, and these projects provide indicators of the causes of project failure or success, and what is required for more complex restoration of ecosystem services. Failure in mangrove programs can be attributed to lack of understanding of the reasons for the loss of mangroves, poor site and species selection, and lack of incentives to engage local residents in the long-term management of restored areas. Overcoming these impediments and adopting monitoring and reporting procedures that consider both areal success and ecosystem function will provide a more robust approach for future mangrove restoration projects.

Context

Over the last three decades there has been considerable (c. 200,000 ha) state and non-government investment in mangrove programs in Vietnam. The main objectives have been coastal protection and stabilization and the production of forest products, with fisheries, climate mitigation, and adaptation and ecosystem restoration as minor objectives. These have had reportedly varied success in terms of long-term survival rates. Much focus has been on the use of mono-species rather than restoring functioning mangrove ecosystems.

Aims

This paper provides an overview of the status of mangroves in Vietnam and considers the effectiveness of mangrove restoration efforts based on an analysis of these reports. We develop and recommend approaches to make future mangrove restoration programs more effective.

Result

First, we provide an overview of mangrove distribution and mangrove deforestation in Vietnam. Second, we analyse major mangrove projects by investigating their objectives and exploring reasons for their success or failure. Third, we suggest approaches for successful mangrove restoration activities in the context of current international agreements on climate change. Failure in some mangrove restoration programs in Vietnam can be attributed to lack of understanding of the reasons for the loss of mangroves and of site hydrology, poor site and species selection, lack of long-term monitoring and management, and lack of incentives to engage local communities in the long-term management of restored areas. Removal of these impediments will increase restoration success.

Conclusion

The widespread and varied mangrove reforestation and restoration activities in Vietnam allow the analysis of different approaches and identification of the key factors leading to restoration success. These include care with species selection, having clear protocols for monitoring and reporting and implementing a co-management approach that provides incentives for local communities to benefit from the management of restored mangroves.
Evaluation of a Novel Antibiotic Teaching Resource
Authors: Davies Angharad P.
Published: February 2020

Antimicrobial resistance presents a major challenge for healthcare and education of future prescribers is critical. Integrated medical courses allow more limited time for teaching the science of clinical microbiology, which underpins antimicrobial prescribing, making this a difficult topic for students. An innovative educational resource based on a game was created and evaluated in medical student teaching. Most students reported that the game assisted learning. However, testing showed that recall did not improve after using the resource. Student perceptions of resource efficacy may not correlate with test scores. The longer-term positive effect of enhanced student engagement is more difficult to measure.
The diversity of powdery mildew resistance gene loci among wheat germplasm in Southwest China
Authors: Cheng B. , Ding Y. Q. , Gao X. , Cao N. , Xin Z. H. , Zhang L. Y.
Published: February 2020

Knowledge of genetic diversity and genes conferring disease resistance is essential for the effective use of wheat germplasm resistant to powdery mildew in breeding programs in southwest China. In this study, a collection of 140 common wheat varieties was evaluated for their resistance to powdery mildew in four different environments. Thirty-six varieties (25.71%) showed resistance in all four environments, and most of these varieties originated from the Guizhou Province. This collection was also scanned for molecular markers closely linked to the powdery mildew resistance genes. Most of the wheat varieties (79.86%) carried the resistance Pm30 gene locus. Genotyping by sequencing (GBS) was used to screen our collection against the whole genome. Finally, 6864 informative SNP markers were used to construct a consensus tree with 1000 bootstraps, which showed two groups based on their origins and the presence of the Pm21 gene locus. Our results provide useful information for breeding wheat resistant to powdery mildew in China, and they will likely contribute to the identification of new resistance genes in the future.
The Museumification of Treasure Hill: Authenticity, Authority and Art in a Taiwanese Urban Village
Authors: Rogelja Igor
Published: February 2020

This article discusses the “museumification” of an urban village in Taipei into the Treasure Hill Artist Village in the context of wider debates on gentrification and the redevelopment of marginal urban spaces. Populated by soldiers evacuated to Taiwan following the Chinese Civil War, Treasure Hill became a hybrid space, combining welfare provision for elderly veterans with an artist colony, forming part of the Taipei Cultural Foundation. Lauded as a compromise that combined social, cultural and economic aspects of urban regeneration, the mix of high-modernist paternalism and neoliberal place-making resulted in the integration of the space into the existing city bureaucracy as a museum-like institution, with elderly residents and artists becoming exhibits in a living diorama. Although widely understood as “gentrification” at the time, the article argues that the museumification of Treasure Hill was a process led by a coalition of state and spatial experts which has distinct implications for the study of state-led neighbourhood amelioration.
Hearing and Believing: Listening Experiences as Religious Experiences in Nineteenth-Century British Methodism
Authors: Clarke Martin V.
Published: February 2020

This article uses Jeff Astley's concept of ordinary theology (Jeff Astley, Ordinary Theology: Looking, Listening and Learning in Theology (Aldershot: Ashgate, 2002)) to examine and interpret listening experiences from nineteenth-century Methodist sources. It argues that the participatory experiences of singing together with fellow believers were crucial to the development and sustenance of personal faith, and that believers shared accounts of such experiences in ways that they knew would be understood by their readers as indicative of the depth and sincerity of their spirituality. It further contends that the widely recognized importance of hymnody in Methodism demands attention to its practice as well its content, and that while the lyrics of hymns set out Methodist theology and doctrine, the participative experience of communal singing was itself invested with meaning and value by many lay Methodists. Ordinary theology provides a framework through which common features of these accounts are identified and discussed, emphasizing the importance of various forms of life writing in understanding the ways in which religious practice shaped the lives and interactions of individual believers. The article also explores differences between different types of published and unpublished life writing. While examples are drawn from different branches of nineteenth-century Methodism, it is argued that hymnody's potential for creating spiritually intense experiences was commonly recognized and affirmed across them. This article contributes to the wider discussion of the significance of listening experiences by emphasizing music's vital role in the construction and communication of meaning between individuals on matters of deeply personal value.
Between “Eradicate All False Religion” and “Love the Stranger as Yourself”: How Immigration Attitudes Divide Voters of Religious Parties
Authors: Otjes Simon
Published: February 2020

The literature on voting for Christian-democratic parties has emphasized that voters of these parties are still motivated by the old religious cleavages that led to the formation of these parties and that structured the vote for these parties for years. Their strong attachment to religious parties even immunized Christian voters from the temptation of the radical right. Yet what the role the new cultural dimension about immigration, civic integration, and identity plays in structuring the vote for religious parties is unclear. Are voters of religious parties immune to the effect of the party polarization of immigration? This paper shows that the policy positions of religious parties matter for what kind of voter votes for them. This paper shows the importance of immigration attitudes in voting for three different religious parties in the Netherlands by combining eight national election surveys between 1994 and 2017.
A Probabilistic Tremor Location Method
Authors: Li Ka Lok , Gudmundsson Olafur
Published: February 2020

A method to locate tremor with an unclear onset is introduced. The method maps envelopes of cross‐correlated records from pairs of seismographs to signal likelihoods using Bayes' theorem. The likelihood time series are then back projected to obtain likelihoods of source location in space. Assuming that information derived from different station pairs is independent, the joint likelihood for all station pairs is the product of all individual station pair likelihoods. Its peak and spread give the most probable source location and its uncertainty. Robustness of the method has been evaluated with synthetic tests. The method recovers true location within 0.5 km with realistic noise characteristics in synthetic data. Uncertainty estimates are consistent with location deviations for sources inside the seismic network. When applied to real data from Katla and Eyjafjallajökull volcanoes in southern Iceland, their likely tremor source is also recovered within 1 km.
Low Latitude Lightning Activity Responses to Cosmic Ray Forbush Decreases
Authors: Zhang Liang , Tinsley Brian , Zhou Limin
Published: February 2020

The relation between low latitude lightning activity and Forbush decreases (FDs) of galactic cosmic rays was studied, with flash rates observed by the Lightning Image Sensor aboard the Tropical Rainfall Measuring Mission satellite and FDs selected from the events with decreases more than 2% measured by the Mexico City neutron monitor. The effect of spacecraft precession on Lightning Image Sensor data complicates the analysis, but this can be dealt with by the approach we use. Applying a superposed epoch analysis to all of the 70 FD cases, we found the low latitude lightning activity decreases by about 10% after the Forbush minimum, with a 95% confidence level tested by Monte Carlo simulation, and recovers 3 days later. The response is more significant in the Southern Hemisphere. Our result provides evidence for a proposed link between solar activity, cosmic rays, the global atmospheric electric circuit, and cloud microphysics.
Cancer as a disease of old age: changing mutational and microenvironmental landscapes
Authors: Laconi Ezio , Marongiu Fabio , DeGregori James
Published: February 2020

Why do we get cancer mostly when we are old? According to current paradigms, the answer is simple: mutations accumulate in our tissues throughout life, and some of these mutations contribute to cancers. Although mutations are necessary for cancer development, a number of studies shed light on roles for ageing and exposure-dependent changes in tissue landscapes that determine the impact of oncogenic mutations on cellular fitness, placing carcinogenesis into an evolutionary framework. Natural selection has invested in somatic maintenance to maximise reproductive success. Tissue maintenance not only ensures functional robustness but also prevents the occurrence of cancer through periods of likely reproduction by limiting selection for oncogenic events in our cells. Indeed, studies in organisms ranging from flies to humans are revealing conserved mechanisms to eliminate damaged or oncogenically initiated cells from tissues. Reports of the existence of striking numbers of oncogenically initiated clones in normal tissues and of how this clonal architecture changes with age or external exposure to noxious substances provide critical insight into the early stages of cancer development. A major challenge for cancer biology will be the integration of these studies with epidemiology data into an evolutionary theory of carcinogenesis, which could have a large impact on addressing cancer risk and treatment.
Correction: Translationally controlled tumor protein promotes liver regeneration by activating mTORC2/AKT signaling
Authors: Lin Zhibin , Zhang Xuan , Wang Jianlin , Liu Wei , Liu Qi , Ye Yuchen , Dai Bin , Guo Dongnan , Zhang Pengcheng , Yang Peijun , Zhang Ruohan , Wang Lin , Dou Kefeng
Published: February 2020

Reference 26 reads “Hua, J. et al. TCTP and CSN4 control cell cycle progression and development by regulating CULLIN1 neddylation in plants and animals. PLoS Genet. 15, e1007899 (2019).” However, it should read “Betsch, L. et al. TCTP and CSN4 control cell cycle progression and development by regulating CULLIN1 neddylation in plants and animals. PLoS Genet. 15, e1007899 (2019)”.
Sub-picosecond charge-transfer at near-zero driving force in polymer:non-fullerene acceptor blends and bilayers
Authors: Zhong Yufei , Causa’ Martina , Moore Gareth John , Krauspe Philipp , Xiao Bo , Günther Florian , Kublitski Jonas , Shivhare Rishi , Benduhn Johannes , BarOr Eyal , Mukherjee Subhrangsu , Yallum Kaila M. , Réhault Julien , Mannsfeld Stefan C. B. , Neher Dieter , Richter Lee J. , DeLongchamp Dean M. , Ortmann Frank , Vandewal Koen , Zhou Erjun , Banerji Natalie
Published: February 2020

Organic photovoltaics based on non-fullerene acceptors (NFAs) show record efficiency of 16 to 17% and increased photovoltage owing to the low driving force for interfacial charge-transfer. However, the low driving force potentially slows down charge generation, leading to a tradeoff between voltage and current. Here, we disentangle the intrinsic charge-transfer rates from morphology-dependent exciton diffusion for a series of polymer:NFA systems. Moreover, we establish the influence of the interfacial energetics on the electron and hole transfer rates separately. We demonstrate that charge-transfer timescales remain at a few hundred femtoseconds even at near-zero driving force, which is consistent with the rates predicted by Marcus theory in the normal region, at moderate electronic coupling and at low re-organization energy. Thus, in the design of highly efficient devices, the energy offset at the donor:acceptor interface can be minimized without jeopardizing the charge-transfer rate and without concerns about a current-voltage tradeoff.
Quantitative SUMO proteomics identifies PIAS1 substrates involved in cell migration and motility
Authors: Li Chongyang , McManus Francis P. , Plutoni Cédric , Pascariu Cristina Mirela , Nelson Trent , Alberici Delsin Lara Elis , Emery Gregory , Thibault Pierre
Published: February 2020

The protein inhibitor of activated STAT1 (PIAS1) is an E3 SUMO ligase that plays important roles in various cellular pathways. Increasing evidence shows that PIAS1 is overexpressed in various human malignancies, including prostate and lung cancers. Here we used quantitative SUMO proteomics to identify potential substrates of PIAS1 in a system-wide manner. We identified 983 SUMO sites on 544 proteins, of which 62 proteins were assigned as putative PIAS1 substrates. In particular, vimentin (VIM), a type III intermediate filament protein involved in cytoskeleton organization and cell motility, was SUMOylated by PIAS1 at Lys-439 and Lys-445 residues. VIM SUMOylation was necessary for its dynamic disassembly and cells expressing a non-SUMOylatable VIM mutant showed a reduced level of migration. Our approach not only enables the identification of E3 SUMO ligase substrates but also yields valuable biological insights into the unsuspected role of PIAS1 and VIM SUMOylation on cell motility.
Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes
Authors: Roux Simon , Krupovic Mart , Daly Rebecca A. , Borges Adair L. , Nayfach Stephen , Schulz Frederik , Sharrar Allison , Matheus Carnevali Paula B. , Cheng Jan-Fang , Ivanova Natalia N. , Bondy-Denomy Joseph , Wrighton Kelly C. , Woyke Tanja , Visel Axel , Kyrpides Nikos C. , Eloe-Fadrosh Emiley A.
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Reduced holey graphene oxide film and carbon nanotubes sandwich structure as a binder-free electrode material for supercapcitor
Authors: Sammed Khan Abdul , Pan Lujun , Asif Muhammad , Usman Muhammad , Cong Tianze , Amjad Farid , Imran Muhammad Asif
Published: February 2020

A novel carbon nanotubes (CNTs) and reduced holey graphene oxide film (RHGOF) sandwich structure has been fabricated to enhance its electrochemical properties. CNTs are grown by a catalyst assisted chemical vapor deposition technique, interpenetrated between the RHGOF layers. A RHGOF/CNTs hybrid film is used as a binder-free supercapacitor electrode. The grown CNTs in the graphene layers structure act as spacers and bridges to increase the counductivity of RHGOF, while the grown CNTs on the surfaces of the graphene contribute to increase the specific surface area of RHGOF. The results demonstrate that the synthesized porous, flexible and binder free hybrid electrode has advantages of higher ion diffusion rate, longer diffusion length and larger ion accessible surface area as compared to the pristine graphene which results in an extra ordinary galvanostatic charge-discharge specific capacitance of 557 F/g at a current density of 0.5 A/g, with excellent rate capabilities and superior cyclic stabilities.
Surgical necrotizing enterocolitis but not spontaneous intestinal perforation is associated with adverse neurological outcome at school age
Authors: Humberg Alexander , Spiegler Juliane , Fortmann Mats Ingmar , Zemlin Michael , Marissen Janina , Swoboda Isabelle , Rausch Tanja K. , Herting Egbert , Göpel Wolfgang , Härtel Christoph ,   The German Neonatal Network (GNN), Wieg Christian , Kribs Angela , von der Wense Axel , Weller Ursula , Höhn Thomas , Olbertz Dirk M. , Felderhoff-Müser Ursula , Rossi Rainer , Teig Norbert , Heitmann Friedhelm , Schmidtke Susanne , Bohnhorst Bettina , Vochem Matthias , Michel Holger , Möller Jens , Eichhorn Joachim G. , Wintgens Jürgen , Böttger Ralf , Hubert Mechthild , Dördelmann Michael , Hillebrand Georg , Roll Claudia , Jensen Reinhard , Rüdiger Mario , Sandkötter Julia , Schäfer Stefan , Schaible Thomas , Franz Axel , Aydin Malik , Ehlers Silke , Werner Claudius , Orlikowsky Thorsten , Gerleve Hubert , Schneider Katja , Werner Claudius , Böckenholt Kai , Linnemann Knud , Müller Dirk , Gebauer Corinna , Guthmann Florian , Reese Jochen , Haase Roland , Seeliger Stephan , Küster Helmut , Hentschel Roland , Körner Thorsten , Brune Thomas , Müller Andreas , Frank Thomas , Berghäuser Martin Andree , Dawczynski Kristin
Published: February 2020

Gastrointestinal complications during the neonatal period, i.e. necrotizing enterocolitis (NEC) and spontaneous intestinal perforation (SIP), are associated with adverse short-term outcome in very-low-birthweight infants (VLBWI, <1500 g birth weight). However, little is known about the neurological outcome of survivors at school age. We analysed data of 2241 infants followed-up at the age of 6 years. To determine the effect of NEC and SIP on cognitive outcome in consideration of other important confounding factors, we used multivariable logistic regression models. In addition, infants with surgical diagnosis of NEC (n = 43) or SIP (n = 41) were compared to NEC (n = 43) or SIP (n = 41) negative controls using Mahalanobis distance matching. Infants with a history for NEC had a three times increased risk (RR 3.0 [1.8–4.2], p < 0.001) to develop IQ scores <85 while history of surgical SIP did not increase the relative risk for lower IQs at school age (RR 1.0 [0.4–2.1], p = 1.000). In a matched-cohort analysis, we confirmed that infants with surgical NEC had lower mean IQ results than unaffected controls (±SD) (85±17 vs. 94±14, p = 0.023) while no differences were found for history of SIP. Our results reflect that the different aetiology and inflammatory extent of NEC and SIP may lead to disparate neurodevelopment trajectories. Hence, our data suggest a potential role of early gut-brain axis distortion in infants with NEC which needs to be further explored.
Enhanced Field Emission Properties of Au/SnSe Nano-heterostructure: A Combined Experimental and Theoretical Investigation
Authors: Rondiya Sachin R. , Jadhav Chandradip D. , Chavan Padmakar G. , Dzade Nelson Y.
Published: February 2020

We report the field emission properties of two-dimensional SnSe nanosheets (NSs) and Au/SnSe nano-heterostructure (NHS) prepared by a simple and economical route of one-pot colloidal and sputtering technique. Field Emission Scanning Electron Microscope (FESEM) analysis reveal surface protrusions and morphology modification of the SnSe NSs by Au deposition. By decorating the SnSe NSs with Au nanoparticles, significant improvement in field emission characteristics were observed. A significant reduction in the turn-on field from 2.25 V/µm for the SnSe NSs to 1.25 V/µm for the Au/SnSe NHS was observed. Emission current density of 300 µA/cm2 has been achieved at an applied field of 4.00 and 1.91 V/µm for SnSe NSs and Au/SnSe NHS, respectively. Analysis of the emission current as a function of time also demonstrated the robustness of the present Au/SnSe NHS. Consistent with the experimental data, our complementary first-principles DFT calculations predict lower work function for the Au/SnSe NHS compared to the SnSe NSs as the primary origin for improved field emission. The present study has evidently provided a rational heterostructure strategy for improving various field emission related applications via surface and electronic modifications of the nanostructures.
Studies on citrullinated LL-37: detection in human airways, antibacterial effects and biophysical properties
Authors: Al-Adwani Salma , Wallin Cecilia , Balhuizen Melanie D. , Veldhuizen Edwin J. A. , Coorens Maarten , Landreh Michael , Végvári Ákos , Smith Margaretha E. , Qvarfordt Ingemar , Lindén Anders , Gräslund Astrid , Agerberth Birgitta , Bergman Peter
Published: February 2020

Arginine residues of the antimicrobial peptide LL-37 can be citrullinated by peptidyl arginine deiminases, which reduce the positive charge of the peptide. Notably, citrullinated LL-37 has not yet been detected in human samples. In addition, functional and biophysical properties of citrullinated LL-37 are not fully explored. The aim of this study was to detect citrullinated LL-37 in human bronchoalveolar lavage (BAL) fluid and to determine antibacterial and biophysical properties of citrullinated LL-37. BAL fluid was obtained from healthy human volunteers after intra-bronchial exposure to lipopolysaccharide. Synthetic peptides were used for bacterial killing assays, transmission electron microscopy, isothermal titration calorimetry, mass-spectrometry and circular dichroism. Using targeted proteomics, we were able to detect both native and citrullinated LL-37 in BAL fluid. The citrullinated peptide did not kill Escherichia coli nor lysed human red blood cells. Both peptides had similar α-helical secondary structures but citrullinated LL-37 was more stable at higher temperatures, as shown by circular dichroism. In conclusion, citrullinated LL-37 is present in the human airways and citrullination impaired bacterial killing, indicating that a net positive charge is important for antibacterial and membrane lysing effects. It is possible that citrullination serves as a homeostatic regulator of AMP-function by alteration of key functions.
Role of Vitamins A and D in BCR-ABL Arf−/− Acute Lymphoblastic Leukemia
Authors: Annu Kavya , Cline Cynthia , Yasuda Kazuto , Ganguly Samit , Pesch Andrea , Cooper Brittany , Janke Laura , Payton Monique , Mukherjee Kamalika , Surman Sherri L. , Hurwitz Julia L. , Schuetz Erin G.
Published: February 2020

The effects of vitamin A and/or vitamin D deficiency were studied in an Arf−/− BCR-ABL acute lymphoblastic leukemia murine model. Vitamin D sufficient mice died earlier (p = 0.003) compared to vitamin D deficient (VDD) mice. Vitamin A deficient (VAD) mice fared worst with more rapid disease progression and decreased survival. Mice deficient for vitamins A and D (VADD) had disease progression similar to VAD mice. Regulatory T cells, previously shown to associate with poor BCR-ABL leukemia control, were present at higher frequencies among CD4+ splenocytes of vitamin A deficient vs. sufficient mice. In vitro studies demonstrated 1,25-dihydroxyvitamin D (1,25(OH)2VD3) increased the number of BCR-ABL ALL cells only when co-cultured with bone marrow stroma. 1,25(OH)2VD3 induced CXCL12 expression in vivo and in vitro in stromal cells and CXCL12 increased stromal migration and the number of BCR-ABL blasts. Vitamin D plus leukemia reprogrammed the marrow increasing production of collagens, potentially trapping ALL blasts. Vitamin A (all trans retinoic acid, ATRA) treated leukemic cells had increased apoptosis, decreased cells in S-phase, and increased cells in G0/G1. ATRA signaled through the retinoid X receptor to decrease BCR-ABL leukemic cell viability. In conclusion, vitamin A and D deficiencies have opposing effects on mouse survival from BCR-ABL ALL.
Functional characterization of an inducible bidirectional promoter from Fusarium oxysporum f. sp. cubense
Authors: Dash Ashutosh , Gurdaswani Vartika , D’Souza Jacinta S. , Ghag Siddhesh B.
Published: February 2020

Bidirectional promoters (BDPs) are regulatory DNA sequences (~1000 bp long) intervening two genes arranged on opposite strands with their 5′ ends in close proximity. These genes are mostly co-expressed; but, instances of anti-correlation and independent transcription have been observed. In fungal systems, BDPs have shown to provide an improved genetic circuit by assembling and regulating transcription of different genes of a common metabolic pathway. We have identified an intergenic region (1063 bp) from the genome of Fusarium oxysporum f. sp. cubense (Foc), a banana root pathogen. This intergenic region regulates the expression of a gene pair required for the breakdown of hemicellulose. For characterization, it was cloned into pCSN44 vector backbone between two reporter genes, namely β-glucuronidase (GUS) and enhanced green fluorescent protein (EGFP). The newly formed vector was transformed into Foc and tested for its bidirectional expression activity. Using histochemical staining and fluorescence microscopy, the kinetics for both, GUS and EGFP expression were tested under different growth conditions respectively. The activity was differentially regulated by inducers such as xylan, arabinogalactan and pectin. This is the first report on the isolation of the intergenic region with inducible bidirectional promoter activity from Fusarium. Characterization of such BDPs will find applications in genetic engineering, metabolic engineering and synthetic biology using fungal systems.
Physiological and transcriptomic analysis provide novel insight into cobalt stress responses in willow
Authors: Wang Yi-Ming , Yang Qi , Xu Hui , Liu Yan-Jing , Yang Hai-Ling
Published: February 2020

Cobalt (Co) is an essential component of several enzymes and coenzymes in living organisms. Excess Co is highly toxic to plants. The knowledge of molecular response mechanisms to cobalt stress in plants is still limited, especially in woody plants. The responses of weeping willow (Salix babylonica) seedlings to Co stress were studied using morphological and physiochemical measurements and RNA-seq analysis. The physiological and biochemical indexes such as growth rate, the content of chlorophyll and soluble sugar, photosynthesis and peroxidase activity were all changed in willow seedlings under Co stress. The metal ion concentrations in willow including Cu, Zn and Mg were disturbed due to excess Co. Of 2002 differentially expressed genes (DEGs), 1165 were root-specific DEGs and 837 were stem and leaf-specific DEGs. Further analysis of DEGs showed there were multiple complex cascades in the response network at the transcriptome level under Co stress. Detailed elucidation of responses to oxidative stress, phytohormone signaling-related genes and transcription factors (TFs), and detoxification of excess cellular Co ion indicated the various defense mechanisms in plants respond to cobalt stress. Our findings provide new and comprehensive insights into the plant tolerance to excess Co stress.
Installation of authentic BicA and SbtA proteins to the chloroplast envelope membrane is achieved by the proteolytic cleavage of chimeric proteins in Arabidopsis
Authors: Uehara Susumu , Sei Ayane , Sada Misaki , Ito-Inaba Yasuko , Inaba Takehito
Published: February 2020

To improve the photosynthetic performance of C3 plants, installing cyanobacterial bicarbonate transporters to the chloroplast inner envelope membrane (IEM) has been proposed for years. In our previous study, we successfully introduced chimeric cyanobacterial sodium-dependent bicarbonate transporters, BicA or SbtA, to the chloroplast IEM of Arabidopsis. However, the installation of authentic BicA and SbtA to the chloroplast IEM has not been achieved yet. In this study, we examined whether or not tobacco etch virus (TEV) protease targeted within chloroplasts can cleave chimeric proteins and produce authentic bicarbonate transporters. To this end, we constructed a TEV protease that carried the transit peptide and expressed it with chimeric BicA or SbtA proteins containing a TEV cleavage site in planta. Chimeric proteins were cleaved only when the TEV protease was co-expressed. The authentic forms of hemagglutinin-tagged BicA and SbtA were detected in the chloroplast IEM. In addition, cleavage of chimeric proteins at the TEV recognition site seemed to occur after the targeting of chimeric proteins to the chloroplast IEM. We conclude that the cleavage of chimeric proteins within chloroplasts is an efficient way to install authentic bicarbonate transporters to the chloroplast IEM. Furthermore, a similar approach can be applied to other bacterial plasma membrane proteins.
Identification and functional analysis of promoters of heat-shock genes from the fall armyworm, Spodoptera frugiperda
Authors: Chen Xien , Tan Anjiang , Palli Subba Reddy
Published: February 2020

The functional information on heat-shock proteins (Hsp) and heat-shock promoters from an important agricultural insect pest, Spodoptera frugiperda, is still lacking. We conducted a genome-wide identification of Hsp genes and identified a total of 21 genes belonging to four major insect Hsp families (small heat-shock proteins, Hsp60, Hsp70, and Hsp90) in S. frugiperda. Expression of most of S. frugiperda (SfHsp) genes could be detected in Sf9 cells, embryos and larval tissues of S. frugiperda. The heat-inducible activity of heat-shock promoters from several SfHsp genes was tested in Sf9 cells and embryos. The promoter of SfHsp70D showed the high constitutive activity in cell line and embryos, while the activity of SfHsp20.15 and SfHsp20.71 promoters was most dramatically induced in Sf9 cells and embryos. In embryos, the heat-induced activity of SfHsp20.71 and SfHsp70D promoters outperformed commercially used ie1 and ie2 promoters. The heat-induced activity of SfHsp70D and SfHsp19.07 promoters were more robust than ie2 promoter in Sf9 cells. These SfHsp promoters with high basal activity or with heat-induced activity from low basal activity, could be used in S. frugiperda or other lepidopteran insects for many applications including transgenesis and genome editing.
Interaction of the Gulf Stream with small scale topography: a focus on lee waves
Authors: de Marez Charly , Lahaye Noé J. , Gula Jonathan
Published: February 2020

The generation of lee waves in the Gulf Stream along the U.S. seaboard is investigated using high resolution realistic simulations. The model reproduces the surface signature of the waves, which compares favourably with observations from satellite sun glitter images in the region. In particular, a large number of internal waves are observed above the Charleston Bump. These waves match well with the linear theory describing topographically-generated internal waves, which can be used to estimate the associated vertical transport of momentum and energy extracted from the mean flow. Finally, small scale topographic features are shown to have a significant impact on the mean flow in this region of the Gulf Stream, and the specific role of lee waves in this context is outlined.
Incretin accelerates platelet-derived growth factor-BB-induced osteoblast migration via protein kinase A: The upregulation of p38 MAP kinase
Authors: Kawabata Tetsu , Tokuda Haruhiko , Kuroyanagi Gen , Fujita Kazuhiko , Sakai Go , Kim Woo , Matsushima-Nishiwaki Rie , Iida Hiroki , Yata Ken-ichiro , Wang Shujie , Mizoguchi Akira , Otsuka Takanobu , Kozawa Osamu
Published: February 2020

Incretins, including glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP), secreted from enteroendocrine cells after food ingestion, are currently recognized to regulate glucose metabolism through insulin secretion. We previously demonstrated that platelet-derived growth factor-BB (PDGF-BB) induces the migration of osteoblast-like MC3T3-E1 cells through mitogen-activated protein (MAP) kinases, including p38 MAP kinase. In the present study, we investigated whether or not incretins affect the osteoblast migration. The PDGF-BB-induced cell migration was significantly reinforced by GLP-1, GIP or cAMP analogues in MC3T3-E1 cells and normal human osteoblasts. The upregulated migration by GLP-1 or cAMP analogues was suppressed by H89, an inhibitor of protein kinase A. The amplification by GLP-1 of migration induced by PDGF-BB was almost completely reduced by SB203580, a p38 MAP kinase inhibitor in MC3T3-E1 cells and normal human osteoblasts. In addition, GIP markedly strengthened the PDGF-BB-induced phosphorylation of p38 MAP kinase. Exendin-4, a GLP-1 analogue, induced Rho A expression and its translocation from cytoplasm to plasma membranes in osteoblasts at the epiphyseal lines of developing mouse femurs in vivo. These results strongly suggest that incretins accelerates the PDGF-BB-induced migration of osteoblasts via protein kinase A, and the up-regulation of p38 MAP kinase is involved in this acceleration. Our findings may highlight the novel potential of incretins to bone physiology and therapeutic strategy against bone repair.
Prevalence and risk factors of having antibodies to class I and II human leukocyte antigens in older haploidentical allograft candidates
Authors: Cao Le-Qing , Lv Meng , Xu Lan-Ping , Zhang Xiao-Hui , Chen Huan , Chen Yu-Hong , Wang Feng-Rong , Han Wei , Sun Yu-Qian , Yan Chen-Hua , Tang Fei-Fei , Mo Xiao-Dong , Liu Kai-Yan , Huang Xiao-Jun , Chang Ying-Jun
Published: February 2020

The effect of donor-specific anti-human leukocyte antigen (HLA) antibodies (DSAs) has been recognized as a factor in graft failure (GF) in patients who underwent umbilical cord blood transplantation (UBT), matched unrelated donor transplantation (MUDT), or haploidentical stem cell transplantation (haplo-SCT). Presently, we know little about the prevalence of and risk factors for having anti-HLA antibodies among older transplant candidates. Therefore, we analyzed 273 older patients with hematologic disease who were waiting for haplo-SCT. Among all patients, 73 (26.7%) patients had a positive panel-reactive antibody (PRA) result for class I, 38 (13.9%) for class II, and 32 (11.7%) for both. Multivariate analysis showed that females were at a higher risk for having a PRA result for class II (P = 0.001) and for having antibodies against HLA-C and HLA-DQ. Prior pregnancy was a risk factor for having a PRA result for class I (P < 0.001) and for having antibodies against HLA-A, HLA-B and HLA-DQ. Platelet transfusions were risk factors for the following: having a positive PRA result for class I (P = 0.014) and class II (P < 0.001); having antibodies against HLA-A, HLA-B, HLA-C, HLA-DP, HLA-DQ, and HLA-DR; and having higher mean fluorescence intensity (MFI) of PRA for class I (P = 0.042). In addition, previous total transfusions were at high risk for having higher numbers of antibodies to specific HLA loci (P = 0.005), and disease course (7.5 months or more) (P = 0.020) were related to higher MFI of PRAs for class I. Our findings indicated that female sex, prior pregnancy, platelet transfusions and disease courses are independent risk factors for older patients with hematologic disease for having anti-HLA antibodies, which could guide anti-HLA antibody monitoring and be helpful for donor selection.
Author Correction: Circulating Levels of Inflammatory Proteins and Survival in Patients with Gallbladder Cancer
Authors: Liu Zhiwei , Kemp Troy J. , Gao Yu-Tang , Corbel Amanda , McGee Emma E. , Roa Juan Carlos , Wang Bingsheng , Araya Juan Carlos , Shen Ming-Chang , Rashid Asif , Hsing Ann W. , Hildesheim Allan , Ferreccio Catterina , Pfeiffer Ruth M. , Pinto Ligia A. , Koshiol Jill
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Evaluation of in vitro and in vivo antibiotic efficacy against a novel bioluminescent Shigella flexneri
Authors: McCloskey Molly C. , Shaheen Shareef , Rabago Lesley , Hulverson Matthew A. , Choi Ryan , Barrett Lynn K. , Arnold Samuel L. M.
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: The first amber caridean shrimp from Mexico reveals the ancient adaptation of the Palaemon to the mangrove estuary environment
Authors: Du Bao-Jie , Chen Rui , Li Xin-Zheng , Tao Wen-Tao , Bu Wen-Jun , Xiao Jin-Hua , Huang Da-Wei
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Raman spectra and phonon structures of BaGa4Se7 crystal
Authors: Yin Yan , Wang Busheng , E Yiwen , Yao Jiyong , Wang Li , Bai Xuedong , Liu Wuming
Published: February 2020

BaGa4Se7 is a promising nonlinear optical crystal at infrared frequencies and shows interesting terahertz phonon-polaritons and high nonlinear coefficients for terahertz generation. Phonons are the key players in infrared absorptions and the photon-phonon resonance phenomena at terahertz frequencies. Here, we study the phonon structures of BaGa4Se7 crystal, with polarized Raman spectroscopy and theoretical calculations for phonon dispersion curves, density of states and vibration modes. An interesting phonon gap separates the modes with still or vibrating Ba atoms. We also determine the nine strongest Raman peaks’ vibration modes and Raman tensors. Our Raman mode assignments and phonon calculations show consistencies in phonon energies, phonon types, and vibration directions. Above knowledge provides a new case example for phonon gaps, offers a complete picture of the phonon structures of BaGa4Se7, and helps us understand phonon gaps, monoclinic crystals, and its phenomena at infrared and terahertz frequency ranges.
Tetragonality induced superconductivity in anti-ThCr2Si2-type RE2O2Bi (RE = rare earth) with Bi square nets
Authors: Sei Ryosuke , Kawasoko Hideyuki , Matsumoto Kota , Arimitsu Masato , Terakado Kyohei , Oka Daichi , Fukuda Shintaro , Kimura Noriaki , Kasai Hidetaka , Nishibori Eiji , Ohoyama Kenji , Hoshikawa Akinori , Ishigaki Toru , Hasegawa Tetsuya , Fukumura Tomoteru
Published: February 2020

Superconductivity in RE2O2Bi was universally governed by unit cell tetragonality c/a, irrespective of the usually destructive long-range magnetic ordering.
A fast and simple B–C bond formation in metallacarboranes avoiding halometallacarboranes and transition metal catalysts
Authors: Buades Ana B. , Kelemen Zsolt , Arderiu Víctor S. , Zaulet Adnana , Viñas Clara , Teixidor Francesc
Published: February 2020

An electrophilic substitution on metallacarboranes by using a stabilized carbocation that can be made in situ is reported for the first time.
Microrespirometric assessment of the metal–organic framework [Co2(btec)(bipy)(DMF)2]n (“MOF-Co”) to prevent inhibition by arsenic in activated sludge
Authors: Ordaz Alberto , Gil Eva , Hernández-Martínez Gabriel R. , Thalasso Frédéric , Rincón Susana , Zepeda Alejandro
Published: February 2020

This study, for the first time, presents the application of a microrespirometric method to evaluate the effect of MOF-Co and As(iii) on biological processes.
Modifications of the urinary metabolome in young women after cranberry juice consumption were revealed using the UHPLC-Q-orbitrap-HRMS-based metabolomics approach
Authors: Liu Haiyan , Garrett Timothy J. , Su Zhihua , Khoo Christina , Zhao Shaomin , Gu Liwei
Published: February 2020

Cranberry juice altered the urinary metabolome in women compared to apple juice and led to the discovery of potential intake biomarkers.
Protective effects of lactic acid bacteria on gut epithelial barrier dysfunction are Toll like receptor 2 and protein kinase C dependent
Authors: Ren Chengcheng , Zhang Qiuxiang , de Haan Bart J. , Faas Marijke M. , Zhang Hao , de Vos Paul
Published: February 2020

TLR2-signalling lactic acid bacterial strains specifically inhibit PKC-dependent gut epithelial barrier integrity loss but cannot dampen MAPK-dependent epithelial barrier disruption.
Visualising early-stage liquid phase organic crystal growthvialiquid cell electron microscopy
Authors: Cookman Jennifer , Hamilton Victoria , Price Louise S. , Hall Simon R. , Bangert Ursel
Published: February 2020

Here, we show that the development of nuclei and subsequent growth of a molecular organic crystal system can be induced by electron beam irradiation by exploiting the radiation chemistry of the carrier solvent.
Switchable metal-to-half-metal transition at the semi-hydrogenated graphene/ferroelectric interface
Authors: Zhang Yajun , He Xu , Sun Minglei , Wang Jie , Ghosez Philippe
Published: February 2020

Tuning the half-metallicity of low-dimensional materials using an electric field is particularly appealing for spintronic applications but typically requires an ultra-high field, hampering practical applications.
Superatomic molecules with internal electric fields for light harvesting
Authors: Reber Arthur C. , Chauhan Vikas , Bista Dinesh , Khanna Shiv N.
Published: February 2020

Fusing two superatomic clusters with unbalanced donor–acceptor ligands leads to intense internal electric fields analogous to a p–n junction.