bluuebunny/crossref_metadata_2025 huggingface dataset:
Challenges to achieving appropriate and equitable access to Caesarean section: ethnographic insights from rural Pakistan
Authors: Mumtaz Zubia , Bhatti Afshan , Salway Sarah
Published: October 2019

Access to Caesarean section (C-section) remains inadequate for some groups of women while others have worryingly high rates. Understanding differential receipt demands exploration of the socio-cultural, and political economic, characteristics of the health systems that produce them. This extensive institutional ethnography investigated under- and over-receipt of C-section in two rural districts in Pakistan – Jhelum and Layyah. Data were collected between November and July 2013 using semi-structured interviews from a randomly selected sample of 11 physicians, 38 community midwives, 18 Lady Health Visitors and nurses and 15 Traditional Birth Attendants. In addition, 78 mothers, 35 husbands and 23 older women were interviewed. The understandings of birth by C-section held by women and their family members were heavily shaped by gendered constructions of womanhood, patient–provider power differentials and financial constraints. They considered C-section an expensive and risky procedure, which often lacked medical justification, and was instead driven by profit motive. Physicians saw C-section as symbolizing obstetric skill and status and a source of legitimate income. Physician views and practices were also shaped by the wider health care system characterized by private practice, competition between providers and a lack of regulation and supervision. These multi-layered factors have resulted in both unnecessary intervention, and missed opportunities for appropriate C-sections. The data indicate a need for synergistic action at patient, provider and system levels. Recommendations include: improving physician communication with patients and family so that the need for C-section is better understood as a life-saving procedure, challenging negative attitudes and promoting informed decision-making by mothers and their families, holding physicians accountable for their practice and introducing price caps and regulations to limit financial incentives associated with C-sections. The current push for privatization of health care in low-income countries also needs scrutiny given its potential to encourage unnecessary intervention.
Carers’ involvement in telecare provision by local councils for older people in England: perspectives of council telecare managers and stakeholders
Authors: Steils Nicole , Woolham John , Fisk Malcolm , Porteus Jeremy , Forsyth Kirsty
Published: October 2019

This paper explores telecare manager and other ‘stakeholder’ perspectives on the nature, extent and impact of family and other unpaid/informal carers’ involvement in the provision of telecare equipment and services for older people. Data used in the paper are derived from a larger study on telecare provision by local councils in England. The paper aims to add to the growing evidence about carers’ engagement with electronic assistive technology and telecare, and considers this in the context of typologies of professionals’ engagement with carers. How carers are involved in telecare provision is examined primarily from the perspectives of senior managers responsible for telecare services who responded to an online survey and/or were interviewed in 2016 as part of a wider study. The perspectives of three unpaid carers were captured in a separate strand of the main study, which comprised more detailed case study interviews within four selected councils. Thematic and comparative analysis of both qualitative and quantitative survey data revealed the varied involvements and responsibilities that carers assumed during the telecare provision process, the barriers that they needed to overcome and their integration in local council strategies. Findings are discussed in the context of Twigg and Atkin's typology of carer support. They suggest that carers are mainly perceived as ‘resources’ and involvement is largely taken for granted. There are instances in which carers can be seen as ‘co-workers’: this is mainly around responding to alerts generated by the telecare user or by monitored devices, but only in those councils that fund response services. Though some participants felt that telecare devices could replace or ‘supersede’ hands-on care that involved routine monitoring of health and wellbeing, it was also acknowledged that its use might also place new responsibilities on carers. Furthermore, the study found that meeting carers’ own rights as ‘co-clients’ was little acknowledged.
On the expressive power of user-defined effects: Effect handlers, monadic reflection, delimited control
Authors: FORSTER YANNICK , KAMMAR OHAD , LINDLEY SAM , PRETNAR MATIJA
Published: October 2019

We compare the expressive power of three programming abstractions for user-defined computational effects: Plotkin and Pretnar’s effect handlers, Filinski’s monadic reflection, and delimited control. This comparison allows a precise discussion about the relative expressiveness of each programming abstraction. It also demonstrates the sensitivity of the relative expressiveness of user-defined effects to seemingly orthogonal language features. We present three calculi, one per abstraction, extending Levy’s call-by-push-value. For each calculus, we present syntax, operational semantics, a natural type-and-effect system, and, for effect handlers and monadic reflection, a set-theoretic denotational semantics. We establish their basic metatheoretic properties: safety, termination, and, where applicable, soundness and adequacy. Using Felleisen’s notion of a macro translation, we show that these abstractions can macro express each other, and show which translations preserve typeability. We use the adequate finitary set-theoretic denotational semantics for the monadic calculus to show that effect handlers cannot be macro expressed while preserving typeability either by monadic reflection or by delimited control. Our argument fails with simple changes to the type system such as polymorphism and inductive types. We supplement our development with a mechanised Abella formalisation.
Germ plasm-related structures in marine medaka gametogenesis; novel sites of Vasa localization and the unique mechanism of germ plasm granule arising
Authors: Reunov Arkadiy A. , Au Doris W. T. , Alexandrova Yana N. , Chiang Michael W. L. , Wan Miles T. , Yakovlev Konstantin V. , Reunova Yulia A. , Komkova Alina V. , Cheung Napo K. M. , Peterson Drew R. , Adrianov Andrey V.
Published: October 2019

Germ plasm, a cytoplasmic factor of germline cell differentiation, is suggested to be a perspective tool forin vitromeiotic differentiation. To discriminate between the: (1) germ plasm-related structures (GPRS) involved in meiosis triggering; and (2) GPRS involved in the germ plasm storage phase, we investigated gametogenesis in the marine medakaOryzias melastigma. The GPRS of the mitosis-to-meiosis period are similar in males and females. In both sexes, five events typically occur: (1) turning of the primary Vasa-positive germ plasm granules into the Vasa-positive intermitochondrial cement (IMC); (2) aggregation of some mitochondria by IMC followed by arising of mitochondrial clusters; (3) intramitochondrial localization of IMC-originated Vasa; followed by (4) mitochondrial cluster degradation; and (5) intranuclear localization of Vasa followed by this protein entering the nuclei (gonial cells) and synaptonemal complexes (zygotene–pachytene meiotic cells). In post-zygotene/pachytene gametogenesis, the GPRS are sex specific; the Vasa-positive chromatoid bodies are found during spermatogenesis, but oogenesis is characterized by secondary arising of Vasa-positive germ plasm granules followed by secondary formation and degradation of mitochondrial clusters. A complex type of germ plasm generation, ‘the follicle cell assigned germ plasm formation’, was found in late oogenesis. The mechanisms discovered are recommended to be taken into account for possible reconstruction of those underin vitroconditions.
Context-specific regulation of surface and soluble IL7R expression by an autoimmune risk allele
Authors: Al-Mossawi Hussein , Yager Nicole , Taylor Chelsea A. , Lau Evelyn , Danielli Sara , de Wit Jelle , Gilchrist James , Nassiri Isar , Mahe Elise A. , Lee Wanseon , Rizvi Laila , Makino Seiko , Cheeseman Jane , Neville Matt , Knight Julian C. , Bowness Paul , Fairfax Benjamin P.
Published: October 2019

IL-7 is a key factor in T cell immunity and common variants at IL7R, encoding its receptor, are associated with autoimmune disease susceptibility. IL7R mRNA is induced in stimulated monocytes, yet a function for IL7R in monocyte biology remains unexplored. Here we characterize genetic regulation of IL7R at the protein level in healthy individuals, and find that monocyte surface and soluble IL7R (sIL7R) are markedly induced by lipopolysaccharide. In monocytes, both surface IL7R and sIL7R expression strongly associate with allelic carriage of rs6897932, a disease-associated IL7R polymorphism. Monocytes produce more sIL7R than CD4 + T cells, and the amount is additionally correlated with the expression of DDX39A, encoding a splicing factor. Synovial fluid-derived monocytes from patients with spondyloarthritis are enriched for IL7R+ cells with a unique transcriptional profile that overlaps with IL-7-induced gene sets. Our data thus suggest a previously unappreciated function for monocytes in IL-7 biology and IL7R-associated diseases.
Photoactivation of silicon rhodamines via a light-induced protonation
Authors: Frei Michelle S. , Hoess Philipp , Lampe Marko , Nijmeijer Bianca , Kueblbeck Moritz , Ellenberg Jan , Wadepohl Hubert , Ries Jonas , Pitsch Stefan , Reymond Luc , Johnsson Kai
Published: October 2019

Photoactivatable fluorophores are important for single-particle tracking and super-resolution microscopy. Here we present a photoactivatable fluorophore that forms a bright silicon rhodamine derivative through a light-dependent protonation. In contrast to other photoactivatable fluorophores, no caging groups are required, nor are there any undesired side-products released. Using this photoactivatable fluorophore, we create probes for HaloTag and actin for live-cell single-molecule localization microscopy and single-particle tracking experiments. The unusual mechanism of photoactivation and the fluorophore’s outstanding spectroscopic properties make it a powerful tool for live-cell super-resolution microscopy.
Sound-driven single-electron transfer in a circuit of coupled quantum rails
Authors: Takada Shintaro , Edlbauer Hermann , Lepage Hugo V. , Wang Junliang , Mortemousque Pierre-André , Georgiou Giorgos , Barnes Crispin H. W. , Ford Christopher J. B. , Yuan Mingyun , Santos Paulo V. , Waintal Xavier , Ludwig Arne , Wieck Andreas D. , Urdampilleta Matias , Meunier Tristan , Bäuerle Christopher
Published: October 2019

Surface acoustic waves (SAWs) strongly modulate the shallow electric potential in piezoelectric materials. In semiconductor heterostructures such as GaAs/AlGaAs, SAWs can thus be employed to transfer individual electrons between distant quantum dots. This transfer mechanism makes SAW technologies a promising candidate to convey quantum information through a circuit of quantum logic gates. Here we present two essential building blocks of such a SAW-driven quantum circuit. First, we implement a directional coupler allowing to partition a flying electron arbitrarily into two paths of transportation. Second, we demonstrate a triggered single-electron source enabling synchronisation of the SAW-driven sending process. Exceeding a single-shot transfer efficiency of 99%, we show that a SAW-driven integrated circuit is feasible with single electrons on a large scale. Our results pave the way to perform quantum logic operations with flying electron qubits.
Direct imaging of light-element impurities in graphene reveals
triple-coordinated oxygen
Authors: Hofer Christoph , Skákalová Viera , Görlich Tobias , Tripathi Mukesh , Mittelberger Andreas , Mangler Clemens , Monazam Mohammad Reza Ahmadpour , Susi Toma , Kotakoski Jani , Meyer Jannik C.
Published: October 2019

Along with hydrogen, carbon, nitrogen and oxygen are the arguably most
important elements for organic chemistry. Due to their rich variety of possible
bonding configurations, they can form a staggering number of compounds. Here, we
present a detailed analysis of nitrogen and oxygen bonding configurations in a
defective carbon (graphene) lattice. Using aberration-corrected scanning
transmission electron microscopy and single-atom electron energy loss spectroscopy,
we directly imaged oxygen atoms in graphene oxide, as well as nitrogen atoms
implanted into graphene. The collected data allows us to compare nitrogen and oxygen
bonding configurations, showing clear differences between the two elements. As
expected, nitrogen forms either two or three bonds with neighboring carbon atoms,
with three bonds being the preferred configuration. Oxygen, by contrast, tends to
bind with only two carbon atoms. Remarkably, however, triple-coordinated oxygen with
three carbon neighbors is also observed, a configuration that is exceedingly rare in
organic compounds.
Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea
Authors: Hua Zheng-Shuang , Wang Yu-Lin , Evans Paul N. , Qu Yan-Ni , Goh Kian Mau , Rao Yang-Zhi , Qi Yan-Ling , Li Yu-Xian , Huang Min-Jun , Jiao Jian-Yu , Chen Ya-Ting , Mao Yan-Ping , Shu Wen-Sheng , Hozzein Wael , Hedlund Brian P. , Tyson Gene W. , Zhang Tong , Li Wen-Jun
Published: October 2019

Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.
Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition
Authors: Travin Dmitrii Y. , Watson Zoe L. , Metelev Mikhail , Ward Fred R. , Osterman Ilya A. , Khven Irina M. , Khabibullina Nelli F. , Serebryakova Marina , Mergaert Peter , Polikanov Yury S. , Cate Jamie H. D. , Severinov Konstantin
Published: October 2019

Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display outstanding diversity of mechanisms of action while sharing common structural features. Here, we report the discovery of a new LAP biosynthetic gene cluster in the genome of Rhizobium Pop5, which encodes the precursor peptide and modification machinery of phazolicin (PHZ) – an extensively modified peptide exhibiting narrow-spectrum antibacterial activity against some symbiotic bacteria of leguminous plants. The cryo-EM structure of the Escherichia coli 70S-PHZ complex reveals that the drug interacts with the 23S rRNA and uL4/uL22 proteins and obstructs ribosomal exit tunnel in a way that is distinct from other compounds. We show that the uL4 loop sequence determines the species-specificity of antibiotic action. PHZ expands the known diversity of LAPs and may be used in the future as biocontrol agent for agricultural needs.
5-Fluorouracil treatment induces characteristic T>G mutations in human cancer
Authors: Christensen Sharon , Van der Roest Bastiaan , Besselink Nicolle , Janssen Roel , Boymans Sander , Martens John W. M. , Yaspo Marie-Laure , Priestley Peter , Kuijk Ewart , Cuppen Edwin , Van Hoeck Arne
Published: October 2019

5-Fluorouracil (5-FU) is a chemotherapeutic drug commonly used for the treatment of solid cancers. It is proposed that 5-FU interferes with nucleotide synthesis and incorporates into DNA, which may have a mutational impact on both surviving tumor and healthy cells. Here, we treat intestinal organoids with 5-FU and find a highly characteristic mutational pattern that is dominated by T>G substitutions in a CTT context. Tumor whole genome sequencing data confirms that this signature is also identified in vivo in colorectal and breast cancer patients who have received 5-FU treatment. Taken together, our results demonstrate that 5-FU is mutagenic and may drive tumor evolution and increase the risk of secondary malignancies. Furthermore, the identified signature shows a strong resemblance to COSMIC signature 17, the hallmark signature of treatment-naive esophageal and gastric tumors, which indicates that distinct endogenous and exogenous triggers can converge onto highly similar mutational signatures.
Dissecting splicing decisions and cell-to-cell variability with designed sequence libraries
Authors: Mikl Martin , Hamburg Amit , Pilpel Yitzhak , Segal Eran
Published: October 2019

Most human genes are alternatively spliced, allowing for a large expansion of the proteome. The multitude of regulatory inputs to splicing limits the potential to infer general principles from investigating native sequences. Here, we create a rationally designed library of >32,000 splicing events to dissect the complexity of splicing regulation through systematic sequence alterations. Measuring RNA and protein splice isoforms allows us to investigate both cause and effect of splicing decisions, quantify diverse regulatory inputs and accurately predict (R2 = 0.73–0.85) isoform ratios from sequence and secondary structure. By profiling individual cells, we measure the cell-to-cell variability of splicing decisions and show that it can be encoded in the DNA and influenced by regulatory inputs, opening the door for a novel, single-cell perspective on splicing regulation.
Realisation of high-fidelity nonadiabatic CZ gates with superconducting qubits
Authors: Li Shaowei , Clark Juno , Wang Shiyu , Wu Yulin , Gong Ming , Yan Zhiguang , Rong Hao , Deng Hui , Zha Chen , Guo Cheng , Sun Lihua , Peng Chengzhi , Zhu Xiaobo , Pan Jian-Wei
Published: October 2019

Entangling gates with error rates reaching the threshold for quantum error correction have been reported for CZ gates using adiabatic longitudinal control based on the interaction between the |11〉 and |20〉 states. Here, we design and implement nonadiabatic CZ gates, which outperform adiabatic gates in terms of speed and fidelity, with gate times reaching

$$1.25/(2\sqrt 2 g_{01,10})$$

1.25
∕

(

2

2

g

01
,
10

)

, and fidelities reaching 99.54 ± 0.08%. Nonadiabatic gates are found to have proportionally less incoherent error than adiabatic gates thanks to their fast gate times, which leave more room for further improvements in the design of the control pules to eliminate coherent errors. We also show that state leakage can be reduced to below 0.2% with optimisation. Furthermore, the gate optimisation process is highly feasible: experimental optimisation can be expected to take less than four hours. Finally, the gate design process can be extended to CCZ gates, and our preliminary results suggest that this process would be feasible as well, if we can measure the CCZ fidelity separate from the initialisation and readout errors in experimental optimisation.
ModelBricks—modules for reproducible modeling improving model annotation and provenance
Authors: Cowan Ann E. , Mendes Pedro , Blinov Michael L.
Published: October 2019

Most computational models in biology are built and intended for “single-use”; the lack of appropriate annotation creates models where the assumptions are unknown, and model elements are not uniquely identified. Simply recreating a simulation result from a publication can be daunting; expanding models to new and more complex situations is a herculean task. As a result, new models are almost always created anew, repeating literature searches for kinetic parameters, initial conditions and modeling specifics. It is akin to building a brick house starting with a pile of clay. Here we discuss a concept for building annotated, reusable models, by starting with small well-annotated modules we call ModelBricks. Curated ModelBricks, accessible through an open database, could be used to construct new models that will inherit ModelBricks annotations and thus be easier to understand and reuse. Key features of ModelBricks include reliance on a commonly used standard language (SBML), rule-based specification describing species as a collection of uniquely identifiable molecules, association with model specific numerical parameters, and more common annotations. Physical bricks can vary substantively; likewise, to be useful the structure of ModelBricks must be highly flexible—it should encapsulate mechanisms from single reactions to multiple reactions in a complex process. Ultimately, a modeler would be able to construct large models by using multiple ModelBricks, preserving annotations and provenance of model elements, resulting in a highly annotated model. We envision the library of ModelBricks to rapidly grow from community contributions. Persistent citable references will incentivize model creators to contribute new ModelBricks.
Compendiums of cancer transcriptomes for machine learning applications
Authors: Lim Su Bin , Tan Swee Jin , Lim Wan-Teck , Lim Chwee Teck
Published: October 2019

There are massive transcriptome profiles in the form of microarray. The challenge is that they are processed using diverse platforms and preprocessing tools, requiring considerable time and informatics expertise for cross-dataset analyses. If there exists a single, integrated data source, data-reuse can be facilitated for discovery, analysis, and validation of biomarker-based clinical strategy. Here, we present merged microarray-acquired datasets (MMDs) across 11 major cancer types, curating 8,386 patient-derived tumor and tumor-free samples from 95 GEO datasets. Using machine learning algorithms, we show that diagnostic models trained from MMDs can be directly applied to RNA-seq-acquired TCGA data with high classification accuracy. Machine learning optimized MMD further aids to reveal immune landscape across various carcinomas critically needed in disease management and clinical interventions. This unified data source may serve as an excellent training or test set to apply, develop, and refine machine learning algorithms that can be tapped to better define genomic landscape of human cancers.
Risk of African swine fever virus introduction into the United States through smuggling of pork in air passenger luggage
Authors: Jurado Cristina , Mur Lina , Pérez Aguirreburualde María Sol , Cadenas-Fernández Estefanía , Martínez-López Beatriz , Sánchez-Vizcaíno José Manuel , Perez Andrés
Published: October 2019

African swine fever causes substantial economic losses in the swine industry in affected countries. Traditionally confined to Africa with only occasional incursions into other regions, ASF began spreading into Caucasian countries and Eastern Europe in 2007, followed by Western Europe and Asia in 2018. Such a dramatic change in the global epidemiology of ASF has resulted in concerns that the disease may continue to spread into disease-free regions such as the US. In this study, we estimated the risk of introduction of ASF virus into the US through smuggling of pork in air passenger luggage. Results suggest that the mean risk of ASFV introduction into the US via this route has increased by 183.33% from the risk estimated before the disease had spread into Western Europe or Asia. Most of the risk (67.68%) was associated with flights originating from China and Hong Kong, followed by the Russian Federation (26.92%). Five US airports accounted for >90% of the risk. Results here will help to inform decisions related to the design of ASF virus surveillance strategies in the US.
Normal mammary gland development after MMTV-Cre mediated conditional PAK4 gene depletion
Authors: Rabieifar Parisa , Zhuang Ting , Costa Tânia D. F. , Zhao Miao , Strömblad Staffan
Published: October 2019

p21-activated kinases (PAKs) are serine/threonine kinases functioning as downstream effectors of the small GTPases Rac1 and Cdc42. Members of the PAK family are overexpressed in human breast cancer, but their role in mammary gland development is not fully explored. Here we examined the functional role of PAK4 in mammary gland development by creating a mouse model of MMTV-Cre driven conditional PAK4 gene depletion in the mammary gland. The PAK4 conditional knock-out mice were born healthy, with no observed developmental deficits. Mammary gland whole-mounts revealed no defects in ductal formation or elongation of the mammary tree through the fat pad. PAK4 gene depletion also did not alter proliferation and invasion of the mammary epithelium in young virgin mice. Moreover, adult mice gave birth to healthy pups with normal body weight upon weaning. This implies that MMTV-Cre induced gene depletion of PAK4 in mice does not impair normal mammary gland development and thereby provides an in vivo model that can be explored for examination of the potential function of PAK4 in breast cancer.
Nanoscale graphene Hall sensors for high-resolution ambient magnetic imaging
Authors: Collomb David , Li Penglei , Bending Simon J.
Published: October 2019

A major challenge to routine non-invasive, nanoscale magnetic imaging is the development of Hall sensors that are stable under ambient conditions and retain low minimum detectable fields down to nanoscale dimensions. To address these issues we have fabricated and characterised chemical vapour deposition (CVD) graphene Hall sensors with wire widths between 50 nm and 1500 nm, in order to exploit the high carrier mobility and tuneability of this material. The measured Hall voltage noise is in good agreement with theoretical models and we demonstrate that minimum detectable fields at fixed drive current are lowest in the vicinity of the charge neutrality point. Our best performing deep sub-micron sensors, based on a wire width of 85 nm, display the excellent room temperature resolution of 59 µT/√Hz at a dc drive current of 12 µA and measurement frequency of 531 Hz. We observe a weak increase in minimum detectable field as the active sensor area is reduced while the Hall offset field is largely independent of size. These figures-of-merit significantly surpass prior results on larger probes in competing materials systems, with considerable scope for further optimisation. Our results clearly demonstrate the feasibility of using CVD graphene to realise very high spatial resolution nanosensors for quantitative room temperature magnetic imaging.
Choline supported poly(ionic liquid) graft copolymers as novel delivery systems of anionic pharmaceuticals for anti-inflammatory and anti-coagulant therapy
Authors: Bielas Rafał , Mielańczyk Anna , Skonieczna Magdalena , Mielańczyk Łukasz , Neugebauer Dorota
Published: October 2019

New type of carriers based on grafted poly(ionic liquid)s was designed for delivery of ionically attached salicylates (Sal). Choline derived ionic liquid monomeric units were successfully introduced with various content in the side chains by the controlled radical polymerization. Properly high amounts of ionic pharmaceutics in the polymer systems were achieved by the well-fitted length and grafting degree of the side chains. In aqueous solution the graft copolymers were self-assembled into the spherical superstructures with sizes up to 73 nm. Delivery studies showed “burst” release within 4 h, after that it was slower yielding ~70% of released drug within 80 h. Proposed nanocarriers supported low toxicity against human cells (NHDF and BEAS-2B), anti-inflammation activity evaluated with the use of pro-inflammatory interleukins (IL-6 and IL-8) and antibacterial activities towards E. coli. Adjustment of ionic drug content by structural parameters of graft copolymers, including grafting degree and graft length, are advantageous to tailor nanocarriers with self-assembly properties in aqueous media. Effective release process by ionic exchange and biological activity with low toxicity are promising for further development of this type of drug delivery (DDS).
Volcanic glass properties from 1459 C.E. volcanic event in South Pole ice core dismiss Kuwae caldera as a potential source
Authors: Hartman Laura H. , Kurbatov Andrei V. , Winski Dominic A. , Cruz-Uribe Alicia M. , Davies Siwan M. , Dunbar Nelia W. , Iverson Nels A. , Aydin Murat , Fegyveresi John M. , Ferris David G. , Fudge T. J. , Osterberg Erich C. , Hargreaves Geoffrey M. , Yates Martin G.
Published: October 2019

A large volcanic sulfate increase observed in ice core records around 1450 C.E. has been attributed in previous studies to a volcanic eruption from the submarine Kuwae caldera in Vanuatu. Both EPMA–WDS (electron microprobe analysis using a wavelength dispersive spectrometer) and SEM–EDS (scanning electron microscopy analysis using an energy dispersive spectrometer) analyses of five microscopic volcanic ash (cryptotephra) particles extracted from the ice interval associated with a rise in sulfate ca. 1458 C.E. in the South Pole ice core (SPICEcore) indicate that the tephra deposits are chemically distinct from those erupted from the Kuwae caldera. Recognizing that the sulfate peak is not associated with the Kuwae volcano, and likely not a large stratospheric tropical eruption, requires revision of the stratospheric sulfate injection mass that is used for parameterization of paleoclimate models. Future work is needed to confirm that a volcanic eruption from Mt. Reclus is one of the possible sources of the 1458 C.E. sulfate anomaly in Antarctic ice cores.
Arsenite exposure suppresses adipogenesis, mitochondrial biogenesis and thermogenesis via autophagy inhibition in brown adipose tissue
Authors: Bae Jiyoung , Jang Yura , Kim Heejeong , Mahato Kalika , Schaecher Cameron , Kim Isaac M. , Kim Eunju , Ro Seung-Hyun
Published: October 2019

Arsenite, a trivalent form of arsenic, is an element that occurs naturally in the environment. Humans are exposed to high dose of arsenite through consuming arsenite-contaminated drinking water and food, and the arsenite can accumulate in the human tissues. Arsenite induces oxidative stress, which is linked to metabolic disorders such as obesity and diabetes. Brown adipocytes dissipating energy as heat have emerging roles for obesity treatment and prevention. Therefore, understanding the pathophysiological role of brown adipocytes can provide effective strategies delineating the link between arsenite exposure and metabolic disorders. Our study revealed that arsenite significantly reduced differentiation of murine brown adipocytes and mitochondrial biogenesis and respiration, leading to attenuated thermogenesis via decreasing UCP1 expression. Oral administration of arsenite in mice resulted in heavy accumulation in brown adipose tissue and suppression of lipogenesis, mitochondrial biogenesis and thermogenesis. Mechanistically, arsenite exposure significantly inhibited autophagy necessary for homeostasis of brown adipose tissue through suppression of Sestrin2 and ULK1. These results clearly confirm the emerging mechanisms underlying the implications of arsenite exposure in metabolic disorders.
Replicating Arabidopsis Model Leaf Surfaces for Phyllosphere Microbiology
Authors: Soffe Rebecca , Bernach Michal , Remus-Emsermann Mitja N. P. , Nock Volker
Published: October 2019

Artificial surfaces are commonly used in place of leaves in phyllosphere microbiology to study microbial behaviour on plant leaf surfaces. These surfaces enable a reductionist approach to be undertaken, to enable individual environmental factors influencing microorganisms to be studied. Commonly used artificial surfaces include nutrient agar, isolated leaf cuticles, and reconstituted leaf waxes. Recently, replica surfaces mimicking the complex topography of leaf surfaces for phyllosphere microbiology studies are appearing in literature. Replica leaf surfaces have been produced in agar, epoxy, polystyrene, and polydimethylsiloxane (PDMS). However, none of these protocols are suitable for replicating fragile leaves such as of the model plant Arabidopsis thaliana. This is of importance, as A. thaliana is a model system for molecular plant genetics, molecular plant biology, and microbial ecology. To overcome this limitation, we introduce a versatile replication protocol for replicating fragile leaf surfaces into PDMS. Here we demonstrate the capacity of our replication process using optical microscopy, atomic force microscopy (AFM), and contact angle measurements to compare living and PDMS replica A. thaliana leaf surfaces. To highlight the use of our replica leaf surfaces for phyllosphere microbiology, we visualise bacteria on the replica leaf surfaces in comparison to living leaf surfaces.
Altered levels of circulating nuclear and mitochondrial DNA in patients with Papillary Thyroid Cancer
Authors: Perdas Ewelina , Stawski Robert , Kaczka Krzysztof , Nowak Dariusz , Zubrzycka Maria
Published: October 2019

Papillary thyroid cancer is the most common thyroid cancer type. However, diagnostics based on fine needle biopsy cannot make a definitive diagnosis in 25% of thyroid nodules. Additionally, approximately 70% to 80% of thyroid lobectomies performed just for diagnostic purposes are benign. Despite this, biopsy still remains the main method of evaluation of thyroid nodules. Cell-free DNA (cf-DNA) measurement could give a new diagnostic opportunities which may reduce the number of unnecessary thyroid procedures. In this study, using a qPCR, we have examined the nuclear cf-DNA and mitochondrial cf-DNA in the plasma of 32 patients. We have found that the level of nuclear cf-DNA is almost 2-fold increased (median 3 089 vs. 1 872, p = 0.022), whereas mitochondrial cf-DNA content was significantly decreased in respect to healthy controls (median 44 992 vs. 92 220, p = 0.010). The ROC curve analysis showed high specificity for nuclear cf-DNA and mitochondrial cf-DNA, which may serve as a useful tool to decrease the number of unneeded surgeries. Our study reports the first epidemiological evidence for lower mitochondrial cf-DNA content in the patient group, what suggests that apart from nuclear cf-DNA also mitochondrial cf-DNA is affected by disease development.
Global gene expression analysis of Escherichia coli K-12 DH5α after exposure to 2.4 GHz wireless fidelity radiation
Authors: Said-Salman Ilham H. , Jebaii Fatima A. , Yusef Hoda H. , Moustafa Mohamed E.
Published: October 2019

This study investigated the non-thermal effects of Wi-Fi radiofrequency radiation of 2.4 GHz on global gene expression in Escherichia coli K-12 DH5α. High-throughput RNA-sequencing of 2.4 GHz exposed and non-exposed bacteria revealed that 101 genes were differentially expressed (DEGs) at P ≤ 0.05. The up-regulated genes were 52 while the down-regulated ones were 49. QRT-PCR analysis of pgaD, fliC, cheY, malP, malZ, motB, alsC, alsK, appB and appX confirmed the RNA-seq results. About 7% of DEGs are involved in cellular component organization, 6% in response to stress stimulus, 6% in biological regulation, 6% in localization, 5% in locomotion and 3% in cell adhesion. Database for annotation, visualization and integrated discovery (DAVID) functional clustering revealed that DEGs with high enrichment score included genes for localization of cell, locomotion, chemotaxis, response to external stimulus and cell adhesion. Kyoto encyclopedia of genes and genomes (KEGG) pathways analysis showed that the pathways for flagellar assembly, chemotaxis and two-component system were affected. Go enrichment analysis indicated that the up-regulated DEGs are involved in metabolic pathways, transposition, response to stimuli, motility, chemotaxis and cell adhesion. The down-regulated DEGs are associated with metabolic pathways and localization of ions and organic molecules. Therefore, the exposure of E. coli DH5α to Wi-Fi radiofrequency radiation for 5 hours influenced several bacterial cellular and metabolic processes.
The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2
Authors: Harkey Thomas , Govind Kumar Vivek , Hettige Jeevapani , Tabari Seyed Hamid , Immadisetty Kalyan , Moradi Mahmoud
Published: October 2019

YidC, a bacterial member of the YidC/Alb3/Oxa1 insertase family, mediates membrane protein assembly and insertion. Cytoplasmic loops are known to have functional significance in membrane proteins such as YidC. Employing microsecond-level molecular dynamics (MD) simulations, we show that the crystallographically unresolved C2 loop plays a crucial role in the structural dynamics of Bacillus halodurans YidC2. We have modeled the C2 loop and used all- atom MD simulations to investigate the structural dynamics of YidC2 in its apo form, both with and without the C2 loop. The C2 loop was found to stabilize the entire protein and particularly the C1 region. C2 was also found to stabilize the alpha-helical character of the C-terminal region. Interestingly, the highly polar or charged lipid head groups of the simulated membranes were found to interact with and stabilize the C2 loop. These findings demonstrate that the crystallographically unresolved loops of membrane proteins could be important for the stabilization of the protein despite the apparent lack of structure, which could be due to the absence of the relevant lipids to stabilize them in crystallographic conditions.
A Deep Learning Approach to Denoise Optical Coherence Tomography Images of the Optic Nerve Head
Authors: Devalla Sripad Krishna , Subramanian Giridhar , Pham Tan Hung , Wang Xiaofei , Perera Shamira , Tun Tin A. , Aung Tin , Schmetterer Leopold , Thiéry Alexandre H. , Girard Michaël J. A.
Published: October 2019

Optical coherence tomography (OCT) has become an established clinical routine for the in vivo imaging of the optic nerve head (ONH) tissues, that is crucial in the diagnosis and management of various ocular and neuro-ocular pathologies. However, the presence of speckle noise affects the quality of OCT images and its interpretation. Although recent frame-averaging techniques have shown to enhance OCT image quality, they require longer scanning durations, resulting in patient discomfort. Using a custom deep learning network trained with 2,328 ‘clean B-scans’ (multi-frame B-scans; signal averaged), and their corresponding ‘noisy B-scans’ (clean B-scans + Gaussian noise), we were able to successfully denoise 1,552 unseen single-frame (without signal averaging) B-scans. The denoised B-scans were qualitatively similar to their corresponding multi-frame B-scans, with enhanced visibility of the ONH tissues. The mean signal to noise ratio (SNR) increased from 4.02 ± 0.68 dB (single-frame) to 8.14 ± 1.03 dB (denoised). For all the ONH tissues, the mean contrast to noise ratio (CNR) increased from 3.50 ± 0.56 (single-frame) to 7.63 ± 1.81 (denoised). The mean structural similarity index (MSSIM) increased from 0.13 ± 0.02 (single frame) to 0.65 ± 0.03 (denoised) when compared with the corresponding multi-frame B-scans. Our deep learning algorithm can denoise a single-frame OCT B-scan of the ONH in under 20 ms, thus offering a framework to obtain superior quality OCT B-scans with reduced scanning times and minimal patient discomfort.
A New Coracoclavicular Guider for Minimally Invasive Anatomic Coracoclavicular Reconstruction with Two TightRope Systems in Acute Acromioclavicular Joint Dislocation
Authors: Zhao Yi , Tan Lei , Tang Wan , Yu Tiecheng
Published: October 2019

High-grade injuries of complete acromioclavicular (AC) joint disruption (types IV - VI) are typically treated surgically. Since the coracoclavicular (CC) ligament is most often used for stabilizing the AC joint, most reconstruction techniques to treat dislocation of this joint rely upon CC interval fixation. A TightRope system is usually used to augment the CC ligament to treat acute AC dislocations with arthroscopic assistance. The conventional arthroscopic technique employing one TightRope system is associated with some complications, including anterior subluxation of the clavicle and clavicular bony avulsion as a consequence of rotational movements. As an alternative, two TightRope systems can be used to anatomically reconstruct the CC ligament to avoid these complications. We present a new CC guider with which the surgeon can replicate the native CC ligament complex orientation using two TightRope systems via two minimally invasive incisions without arthroscopic assistance. This procedure relies upon the accommodation and stable placement of the clavicle and coracoid bone tunnels for the two TightRope systems in place of the trapezoid and conoid of the CC ligament. We retrospectively reviewed the outcomes for 16 patients with acute dislocation of the AC joint that had been treated by a single surgeon using a double-button fixation system. An independent reviewer conducted functional testing of these patients, including the use of Disability of Arm, Shoulder and Hand (DASH), Constant and visual analog scale (VAS) scores. Standard radiographs were used for assessing the CC distance for the impacted shoulder relative to that of the unaffected contralateral shoulderThe new CC guider leads to an excellent cosmetic result. Our clinical results show that this technique can be easily performed and is similarly invasive to other current arthroscopic techniques.
Author Correction: Towards a reliable assessment of Asian elephant population parameters: the application of photographic spatial capture–recapture sampling in a priority floodplain ecosystem
Authors: Goswami Varun R. , Yadava Mahendra K. , Vasudev Divya , Prasad Parvathi K. , Sharma Pragyan , Jathanna Devcharan
Published: October 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Structural transformation of sulfidized zerovalent iron and its impact on long-term reactivity
Authors: Mangayayam Marco C. , Perez Jeffrey Paulo H. , Dideriksen Knud , Freeman Helen M. , Bovet Nicolas , Benning Liane G. , Tobler Dominique J.
Published: October 2019

This study elucidates the structural changes of sulfidized zerovalent iron (S-nZVI) in anoxic groundwater, presents a compelling evidence on the structural robustness of the material and explains how S-nZVI long-term reactivity is achieved.
Characterizing colloidal metals in drinking water by field flow fractionation
Authors: Trueman Benjamin F. , Anaviapik-Soucie Tim , L'Hérault Vincent , Gagnon Graham A.
Published: October 2019

We show that lead is associated with natural organic matter and colloidal iron at the tap. Removing these species during treatment could reduce lead exposure.
Multiple morphologies and functionality of nanowires made from earth-abundant zinc phosphide
Authors: Escobar Steinvall Simon , Tappy Nicolas , Ghasemi Masoomeh , Zamani Reza R. , LaGrange Thomas , Stutz Elias Z. , Leran Jean-Baptiste , Zamani Mahdi , Paul Rajrupa , Fontcuberta i Morral Anna
Published: October 2019

Semiconductors made of earth-abundant elements, such as zinc phosphide, have the potential to substitute less abundant, highly functional compound semiconductors such as InAs or InP.
Synthesis of 3-(tri/difluoromethyl)-1H-1,2,4-triazol-5(4H)-ones via the cyclization of hydrazinecarboxamides with tri/difluoroacetic anhydride
Authors: You Yi , Chen Yueji , You Chenhui , Wang Junwen , Weng Zhiqiang
Published: October 2019

A method for the synthesis of 3-(tri/difluoromethyl)-1H-1,2,4-triazol-5(4H)-ones via the cyclization of hydrazinecarboxamides with tri/difluoroacetic anhydride was developed.
Forcing single-chain nanoparticle collapse through hydrophobic solvent interactions in comb copolymers
Authors: Liu Cheyenne H. , Dugas Logan D. , Bowman Jared I. , Chidanguro Tamuka , Storey Robson F. , Simon Yoan C.
Published: October 2019

We demonstrate that we can tune the chain collapse of comb copolymers into single-chain nanoparticles upon UV irradiation through solvency control.
Synergistically optimized thermoelectric properties of Ag1+xIn5Se8 alloys
Authors: Shen Xingchen , Zhang Bin , Chen Qiuyi , Tan Huan , Zhang Xiao , Wang Guoyu , Lu Xu , Zhou Xiaoyuan
Published: October 2019

A synergistic strategy yields a peak zT value of 0.67 at 883 K and an average zT value of 0.34 from 323 to 883 K for Ag1.03In5Se8, and the latter is a record high value for AgIn5Se8 based compounds so far.
Tunable upconversion emission in NaLuF4–glass-ceramic fibers doped with Er3+ and Yb3+
Authors: Gorni G. , Velázquez Jose J. , Kochanowicz M. , Dorosz D. , Balda R. , Fernández J. , Durán A. , Pascual M. J.
Published: October 2019

Novel glass-ceramic optical fibers containing NaLuF4 nanocrystals doped with 0.5ErF3 and 2YbF3 (mol%) have been prepared by the rod-in-tube method and controlled crystallization.
A label-free RTP sensor based on aptamer/quantum dot nanocomposites for cytochrome c detection
Authors: Li Dongxia , Guo Junping , Zhao Liang , Zhang Guoxian , Yan Guiqin
Published: October 2019

In this study, the nanocomposites from polyethyleneimine-capped Mn-doped ZnS QDs (PEI-QDs) and Cyt c binding aptamer (CBA) were prepared and used as Cyt c RTP sensors..
Cytotoxic effect, generation of reactive oxygen/nitrogen species and electrochemical properties of Cu(ii) complexes in comparison to half-sandwich complexes of Ru(ii) with aminochromone derivatives
Authors: Mucha Paulina , Hikisz Pawel , Gwoździński Krzysztof , Krajewska Urszula , Leniart Andrzej , Budzisz Elzbieta
Published: October 2019

New Cu(ii)/Ru(ii) complexes with 6-aminoflavone/chromone derivatives as ligands were synthesized and characterized. Their cytotoxicity, pro-oxidative and redox properties were investigated.
Highly selective hydrogenation of amides catalysed by a molybdenum pincer complex: scope and mechanism
Authors: Leischner Thomas , Artús Suarez Lluis , Spannenberg Anke , Junge Kathrin , Nova Ainara , Beller Matthias
Published: October 2019

A series of molybdenum pincer complexes has been shown for the first time to be active in the catalytic hydrogenation of amides.
NiMoS on alumina-USY zeolites for hydrotreating lignin dimers: effect of support acidity and cleavage of C–C bonds
Authors: Salam Muhammad Abdus , Arora Prakhar , Ojagh Houman , Cheah You Wayne , Olsson Louise , Creaser Derek
Published: October 2019

NiMoS on alumina, USY and mixed alumina-USY supports was studied in a batch reactor to assess the effect of support acidity in valorizing lignin dimers by hydrodeoxygenation (HDO).
Tunable adhesion and slip on a bio-mimetic sticky soft surface
Authors: Bandyopadhyay Saumyadwip , Sriram S. M. , Parihar Vartika , Das Gupta Sunando , Mukherjee Rabibrata , Chakraborty Suman
Published: October 2019

By tuning the extent of submergence of the rose petal structures with silicone oil, we could alter the adhesion characteristics of the surface on demand, while retaining its slippery characteristics for a wide range of the pertinent parameters.
Multi-charged bis(p-calixarene)/pillararene functionalized gold nanoparticles for ultra-sensitive sensing of butyrylcholinesterase
Authors: Li Pei-yu , Chen Yong , Chen Chang-hui , Liu Yu
Published: October 2019

A novel supramolecular assembly based on BSC4A/CP5A modified AuNPs for colorimetric sensing of both succinylcholine (SuCh) and butyrylcholinesterase (BChE).