bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental Assessment of PCR Specificity and Copy Number for Reliable Data Retrieval in DNA Storage
Authors: Organick Lee , Chen Yuan-Jyue , Ang Siena Dumas , Lopez Randolph , Strauss Karin , Ceze Luis
Published: March 2019

Synthetic DNA has been gaining momentum as a potential storage medium for archival data storage1–9. Digital information is translated into sequences of nucleotides and the resulting synthetic DNA strands are then stored for later individual file retrieval via PCR7–9(Fig. 1a). Using a previously presented encoding scheme9and new experiments, we demonstrate reliable file recovery when as few as 10 copies per sequence are stored, on average. This results in density of about 17 exabytes/g, nearly two orders of magnitude greater than prior work has shown6. Further, no prior work has experimentally demonstrated access to specific files in a pool more complex than approximately 106unique DNA sequences9, leaving the issue of accurate file retrieval at high data density and complexity unexamined. Here, we demonstrate successful PCR random access using three files of varying sizes in a complex pool of over 1010unique sequences, with no evidence that we have begun to approach complexity limits. We further investigate the role of file size on successful data recovery, the effect of increasing sequencing coverage to aid file recovery, and whether DNA strands drop out of solution in a systematic manner. These findings substantiate the robustness of PCR as a random access mechanism in complex settings, and that the number of copies needed for data retrieval does not compromise density significantly.
The impact of DNA polymerase and number of rounds of amplification in PCR on 16S rRNA gene sequence data
Authors: Sze Marc A , Schloss Patrick D
Published: March 2019

PCR amplification of 16S rRNA genes is a critical, yet under appreciated step in the generation of sequence data to describe the taxonomic composition of microbial communities. Numerous factors in the design of PCR can impact the sequencing error rate, the abundance of chimeric sequences, and the degree to which the fragments in the product represent their abundance in the original sample (i.e. bias). We compared the performance of high fidelity polymerases and varying number of rounds of amplification when amplifying a mock community and human stool samples. Although it was impossible to derive specific recommendations, we did observe general trends. Namely, using a polymerase with the highest possible fidelity and minimizing the number of rounds of PCR reduced the sequencing error rate, fraction of chimeric sequences, and bias. Evidence of bias at the sequence level was subtle and could not be ascribed to the fragments’ fraction of bases that were guanines or cytosines. When analyzing mock community data, the amount that the community deviated from the expected composition increased with rounds of PCR. This bias was inconsistent for human stool samples. Overall the results underscore the difficulty of comparing sequence data that are generated by different PCR protocols. However, the results indicate that the variation in human stool samples is generally larger than that introduced by the choice of polymerase or number of rounds of PCR.

Importance

A steep decline in sequencing costs drove an explosion in studies characterizing microbial communities from diverse environments. Although a significant amount of effort has gone into understanding the error profiles of DNA sequencers, little has been done to understand the downstream effects of the PCR amplification protocol. We quantified the effects of the choice of polymerase and number of PCR cycles on the quality of downstream data. We found that these choices can have a profound impact on the way that a microbial community is represented in the sequence data. The effects are relatively small compared to the variation in human stool samples, however, care should be taken to use polymerases with the highest possible fidelity and to minimize the number of rounds of PCR. These results also underscore that it is not possible to directly compare sequence data generated under different PCR conditions.
Polymer brush bilayer under stationary shear motion at linear response regime: A theoretical approach
Authors: Edwards Mike John
Published: March 2019

Statistical mechanics is employed to tackle the problem of polymer brush bilayers under stationary shear motion. The article addresses, solely, the linear response regime in which the polymer brush bilayers behave very much similar to the Newtonian fluids. My approach to this long-standing problem split drastically from the work already published Kreer, T.,Soft Matter,12, 3479 (2016). It has been thought for many decades that the interpenetration between the brushes is source of the friction between the brush covered surfaces sliding over each other. Whiles, in the present article I strongly reject that idea. Instead, here, I show that structure of the whole system is responsible for friction between brush covered surfaces and the interpenetration is absolutely insignificant. Two simple reasons for that are the presence of ambient solvent and also flexibility of the chains. The results of this research would blow one’s mind about how the polymer brush bilayers respond at small shear rates.
Chronic Intermittent Ethanol and Lipopolysaccharide Exposure Differentially Alter Iba-1-Derived Microglia Morphology in the Prelimbic Cortex and Nucleus Accumbens Core
Authors: Siemsen BM , Landin JD , McFaddin JA , Hooker KN , Chandler LJ , Scofield MD
Published: March 2019

Accumulating evidence has linked pathological changes associated with chronic alcohol exposure to neuroimmune signaling mediated by microglia. Prior characterization of the microglial structure-function relationship demonstrates that alterations in activity states occur concomitantly with reorganization of cellular architecture. Accordingly, gaining a better understanding of microglial morphological changes associated with ethanol exposure will provide valuable insight into how neuroimmune signaling may contribute to ethanol-induced reshaping of neuronal function. Here we have used Iba-1-staining combined with high-resolution confocal imaging and 3D reconstruction to examine microglial structure in the prelimbic (PL) cortex and nucleus accumbens (NAc) in male Long-Evans rats. Rats were either sacrificed at peak withdrawal following 14 days of exposure to chronic intermittent ethanol (CIE) or 48 hours after exposure to the immune activator lipopolysaccharide (LPS). LPS exposure resulted in dramatic structural reorganization of microglia in the PL cortex; including increased soma volume, overall cellular volume, and branching complexity. In comparison, CIE exposure was associated with a subtle increase in somatic volume and differential effects on microglia processes, which were largely absent in the NAc. These data reveal that microglial activation following a neuroimmune challenge with LPS or exposure to chronic alcohol exhibit distinct morphometric profiles and brain-region dependent specificity.
Functional arrays of human pluripotent stem cell-derived cardiac microtissues
Authors: Thavandiran Nimalan , Hale Christopher , Blit Patrick , Sandberg Mark L. , McElvain Michele E. , Gagliardi Mark , Sun Bo , Witty Alec , Graham George , Mcintosh May , Bakooshli Mohsen A. , Le Hon , Ostblom Joel , McEwen Samuel , Chau Erik , Prowse Andrew , Fernandes Ian , Gilbert Penney M. , Keller Gordon , Tagari Philip , Xu Han , Radisic Milica , Zandstra Peter W. , Nojima Dana , Vargas Hugo , Qu Yusheng , Motani Alykhan , Reagan Jeff
Published: March 2019

To accelerate the cardiac drug discovery pipeline, we set out to develop a platform that would be amenable to standard multiwell-plate manipulations and be capable of quantifying tissue-level functions such as contractile force. We report a 96-well-based array of 3D human pluripotent stem cell (hPSC)-derived cardiac microtissues - termed Cardiac MicroRings (CaMiRi) - in custom printed multiwell plates capable of contractile force measurement. Within each well, two elastomeric microcantilevers are situated above a ramp. The wells are seeded with cell-laden collagen which, in response to the slope of the ramp, self-organizes around tip-gated microcantilevers to form contracting CaMiRi. The contractile force exerted by the CaMiRi is measured and calculated using the deflection of the cantilevers. Platform responses were robust and comparable across wells and we used it to determine an optimal tissue formulation. We validated contractile force response of CaMiRi using selected cardiotropic compounds with known effects. Additionally, we developed automated protocols for CaMiRi seeding, image acquisition, and analysis to enable measurement of contractile force with increased throughput. The unique tissue fabrication properties of the platform, and the consequent effects on tissue function, were demonstrated upon adding hPSC-derived epicardial cells to the system. This platform represents an open-source contractile force screening system useful for drug screening and tissue engineering applications.
Antigen structure affects cellular routing through DC-SIGN
Authors: Jarvis Cassie M. , Zwick Daniel B. , Grim Joseph C. , Prost Lynne R. , Alam Mohammad Murshid , Gardiner Jaye C. , Park Soyeong , Zimdars Laraine L. , Sherer Nathan M. , Kiessling Laura L.
Published: March 2019

Dendritic cell (DC) lectins mediate the recognition, uptake, and processing of antigens, but they can also be co-opted by pathogens for infection. These distinct activities depend upon the routing of antigens within the cell. Antigens directed to endosomal compartments are degraded and the peptides presented on MHC class II molecules thereby promoting immunity. Alternatively, HIV-1 can avoid degradation, as virus engagement with C-type lectin receptors (CLRs), such as DC-SIGN, results in trafficking to surface-accessible invaginated pockets. This process appears to enable infection of T cells intrans. We sought to explore whether antigen fate upon CLR-mediated internalization was affected by antigen physical properties. To this end, we employed the ring-opening metathesis polymerization to generate glycopolymers that each display multiple copies of mannoside ligand for DC-SIGN yet differ in length and size. The rate and extent of glycopolymer internalization depended upon polymer structure—longer polymers were internalized more rapidly and more efficiently than were shorter polymers. The trafficking, however, did not differ, and both short and longer polymers colocalized with transferrin-labeled early endosomes. To explore how DC-SIGN directs larger particles, such as pathogens, we induced aggregation of the polymers to access particulate antigens. Strikingly, these particulate antigens were diverted to the invaginated pockets that harbor HIV-1. Thus, antigen structure has a dramatic effect on DC-SIGN-mediated uptake and trafficking. These findings have consequences for the design of synthetic vaccines. Additionally, the results suggest new strategies for targeting DC reservoirs that harbor viral pathogens.

Significance Statement

Dendritic cells (DCs) express cell-surface proteins (lectins) that bind to carbohydrates displayed on the surface of pathogens. The binding of pathogens to these lectins results in internalization to endosomal compartments where the pathogens are destroyed and an immune response is initiated. HIV-1 can subvert this process – lectin engagement routes HIV-1 to cellular compartments that allow the virus to evade destruction. We synthesized glycopolymers to test whether the size and physical properties of the antigens impact trafficking. Small polymers trafficked to endosomes, as expected. Alternatively, large particulate polymers localized in the non-endosomal compartments occupied by HIV. These data indicate that antigen structure affects routing by DC lectins. Our findings can be exploited to direct cargo to different compartments.
Digital removal of autofluorescence from microscopy images
Authors: Baharlou Heeva , Canete Nicolas P , Bertram Kirstie M , Sandgren Kerrie J , Cunningham Anthony L , Harman Andrew N , Patrick Ellis
Published: March 2019

Autofluorescence is a long-standing problem that has hindered fluorescence microscopy image analysis. To address this, we have developed a method that identifies and removes autofluorescent signals from multi-channel images post acquisition. We demonstrate the broad utility of this algorithm in accurately assessing protein expression in situ through the removal of interfering autofluorescent signals.

Availability and implementation

https://ellispatrick.github.io/AFremover

Contact

ellis.patrick@sydney.edu.au

Supplementary information

Supplementary Figs. 1–13
PCH1 regulates light, temperature, and circadian signaling as a structural component of phytochrome B-photobodies inArabidopsis
Authors: Huang He , McLoughlin Katrice E. , Sorkin Maria L. , Burgie E. Sethe , Bindbeutel Rebecca K. , Vierstra Richard D. , Nusinow Dmitri A.
Published: March 2019

The phytochrome (phy) family of bilin-containing photoreceptors are major regulators of plant photomorphogenesis through their unique ability to photointerconvert between a biologically inactive red light-absorbing Pr state and an active far-red light­absorbing Pfr state. While the initial steps in Pfr signaling are unclear, an early event for the phyB isoform after photoconversion is its redistribution from the cytoplasm into subnuclear foci named photobodies (PBs) that dissipate after Pfr reverts back to Pr by far-red irradiation or by temperature-dependent non-photochemical reversion. Here we present evidence that PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) functions both as an essential structural component of phyB-containing PBs and as a direct regulator of thermal reversion that is sufficient to stabilize phyB as Pfrin vitro.By examining the genetic interaction between a constitutively active phyBY276H-YFP allele(YHB-YFP)and PCH1, we show that the loss of PCH1 prevents YHB from coalescing into PBs without affecting its nuclear localization, whereas overexpression of PCH1 dramatically increases PB levels. Loss of PCH1, presumably by impacting phyB-PB assembly, compromises a number of events elicited inYHB-YFPplants, including their constitutive photomorphogenic phenotype, red light-regulated thermomorphogenesis, and input of phyB into the circadian clock. Conversely, elevated levels of both phyB and PCH1 generate stable, yet far red-light reversible PBs that persisted for days. Collectively, our data demonstrate that the assembly of PCHl-containing PBs is critical for phyB signaling to multiple outputs, and suggest that altering PB dynamics could be exploited to modulate plant responses to light and temperature.

Significance

InArabidopsis, phytochrome B (phyB) perceives light and temperature signals to regulate various fundamental morphogenic processes in plants through its interconversion between its active Pfr and inactive Pr states. Upon photoconversion from Pr to Pfr, phyB forms subnuclear foci called photobodies, whose composition and molecular function(s) are unclear. We show here that the phyB-interacting protein PCH1 is a structural component of phyB-photobodies and protects Pfr from thermal reversion back to Pr thus helping maintain phyB signaling. Loss of PCH1 compromises photobody formation, which disrupts a number of downstream events including photo- and thermal perception and signaling into the circadian clock. These results demonstrate that forming PCHl-dependent phyB-photobodies is an essential step connecting light and temperature to controls on plant morphogenesis.
Modulation of coordinated activity across cortical layers by plasticity of inhibitory synapses onto layer 5 pyramidal neurons
Authors: Lourenço Joana , Stasi Angela Michela De , Deleuze Charlotte , Bigot Mathilde , Pazienti Antonio , Aguirre Andrea , Giugliano Michele , Ostojic Srdjan , Bacci Alberto
Published: March 2019

In the neocortex, synaptic inhibition shapes all forms of spontaneous and sensory-evoked activity. Importantly, inhibitory transmission is highly plastic, but the functional role of inhibitory synaptic plasticity is unknown. In the mouse barrel cortex, activation of layer 2/3 PNs elicited strong feed-forward perisomatic inhibition (FFI) onto layer 5 PNs. We found that FFI involving PV cells was strongly potentiated by postsynaptic PN burst firing. FFI plasticity modified PN excitation-to-inhibition (E/I) ratio, strongly modulated PN gain and altered information transfer across cortical layers. Moreover, our LTPi-inducing protocol modified the firing of layer 5 PNs and altered the temporal association of PN spikes to γ-oscillations both in vitro and in vivo. All these effects were captured by unbalancing the E/I ratio in a feed-forward inhibition circuit model. Altogether, our results indicate that activity-dependent modulation of perisomatic inhibitory strength effectively influences the participation of single principal cortical neurons to cognitive-relevant network activity.

Impact Statement

Long-term potentiation of feed-forward perisomatic inhibition effectively alters the computational properties of single layer 5 pyramidal neurons and their association to network activity.
Na/K-ATPase Activity and Ketone Body Metabolism in Long-term Diabetic Rats
Authors: Buxbaum Engelbert
Published: March 2019

The long-term (34 weeks) effect of streptozotocin induced diabetes was assessed in Wistar rats.

Na+/K+-ATPase activity was measured by ouabain inhibitable86Rb+-uptake into erythrocytes. No difference in the rate of Rb+-uptake, the Kmfor Rb+or the Kifor ouabain was detected between normal and diabetic rats. Thus, the change in Na+/K+-ATPase activity repeatedly described in short-term studies may not translate into a long term physiologically relevant change in ion flux through the sodium pump.

Rats excrete ketone bodies mainly as β-hydroxybutyrate. This compound does not show up with nitroprusside sodium based test sticks, it can however be detected by coupled spectrophotometric assay with hydroxybutyrate dehydrogenase.

Almost half of the diabetic animals reverted to a non-diabetic state during the experiment, followed by at least partial reversal of secondary diabetic damage.

Abbreviations used

PKC

Protein kinase C

DAG

Diacylglycerol

EDTA

Ethylenediamine tetraacetic acid

PIP3

Phosphatidylinositol trisphosphate

PBS

Phosphate buffered saline

i.p.

intraperitoneal

HBA

β-hydroxybutyric acid

STZ

streptozotocin

Enzymes

: Na+/K+-exchanging ATP-phosphohydrolase (Na+/K+-ATPase), E.C. 7.2.2.13; (R)-3-hydroxybutanoate:NAD+oxidoreductase [1.1.1.30] (β-hydroxybutyrate dehydro-genase)
Cryopreservation ofRosa hybridacv. Helmut Schmidt by PVS2 vitrification method usingin vitrofragmented explants (IFEs)
Authors: Mubbarakh Safiah Ahmad , Udain Jasim , James Jessica Jayanthi , Zakaria Rahmad , Subramaniam Sreeramanan
Published: March 2019

This is the first report on cryopreservation via PVS2 vitrification method on roses usingin vitrofragmented explants (IFEs) as the starting material. The aim of this study is to optimize the efficient plant recovery and regeneration system for cryopreservation ofRosa hybridacv. Helmut Schmidt using IFEs. Some important parameters have been optimized in this study are the effect of ascorbic acid (0.3 mM) examined separately and in combination at all steps in cryopreservation procedure (preculture, loading, unloading and growth recovery), loading type, loading duration, and PVS2 duration. The highest growth recovery of 43.33% was obtained when 3-4 mm size IFEs precultured on 0.25 M sucrose media supplemented with full-strength MS for one (1) day, followed by loading treatment supplemented with 1.5 M glycerol + 0.4 M sucrose + 5% DMSO + 0.3 mM ascorbic acid for 20 minutes, dehydration with PVS2 solution for 30 minutes and then treated with unloading solution supplemented with 1.2 M sucrose + 0.3 mM ascorbic acid for 20 minutes. This finding implies that long-term storage ofRosa Hybridacv. Helmut Schmidt by PVS2 vitrification method was successful with essential biomolecules.
Caffeine but not acetaminophen increases 4-km cycling time-trial performance
Authors: Tomazini Fabiano , Mariano Ana Carla S. , Andrade-Souza Victor A. , Sebben Viviane C. , de Maria Carlos A. B. , Coelho Daniel B. , Bertuzzi Romulo , Silva-Cavalcante Marcos D. , Lima-Silva Adriano E.
Published: March 2019

Acetaminophen has been combined with caffeine for therapeutic purpose, but the effect of co-ingestion of acetaminophen and caffeine on exercise performance has not been investigated. The aim of this study was to determine the effect of isolated and combined ingestion of caffeine and acetaminophen on performance during a 4-km cycling time-trial. In a double-blind, crossover design, eleven men, accustomed to cycling recreationally, completed a 4-km cycling time-trial one hour after the ingestion of cellulose (PLA), acetaminophen (20 mg·kg−1body mass, ACT), caffeine (5 mg·kg−1body mass, CAF) or combined acetaminophen and caffeine (20 and 5 mg·kg−1body mass, respectively, ACTCAF). The perception of pain and rating of perceived exertion were recorded every 1-km, and electromyography and oxygen uptake were continually recorded and averaged each 1-km. Plasma lactate concentration was measured before and immediately after the trial. The time and mean power during the 4-km cycling time-trial was significantly improved (P< 0.05) in CAF (407.9 ± 24.5 s, 241.4 ± 16.1 W) compared to PLA (416.1 ± 34.1 s, 234.1 ± 19.2 W) and ACT (416.2 ± 26.6 s, 235.8 ± 19.7 W). However, there was no difference between ACTCAF (411.6 ± 27.7 s, 238.7 ± 18.7 W) and the other conditions (P> 0.05). The perception of pain, rating of perceived exertion, electromyography, oxygen uptake, and plasma lactate were similar across the conditions (P> 0.05). In conclusion, caffeine but not acetaminophen increases power output ultimately increasing performance during a 4-km cycling time-trial.
About samples, giving examples: Optimized Single Molecule Localization Microscopy
Authors: Jimenez Angélique , Friedl Karoline , Leterrier Christophe
Published: March 2019

Super-resolution microscopy has profoundly transformed how we study the architecture of cells, revealing unknown structures and refining our view of cellular assemblies. Among the various techniques, the resolution of Single Molecule Localization Microscopy (SMLM) can reach the size of macromolecular complexes and offer key insights on their nanoscale arrangement in situ. SMLM is thus a demanding technique and taking advantage of its full potential requires specifically optimized procedures. Here we describe how we perform the successive steps of an SMLM workflow, focusing on single-color Stochastic Optical Reconstruction Microscopy (STORM) as well as multicolor DNA Points Accumulation for imaging in Nanoscale Topography (DNA-PAINT) of fixed samples. We provide detailed procedures for careful sample fixation and immunostaining of typical cellular structures: cytoskeleton, clathrin-coated pits, and organelles. We then offer guidelines for optimal imaging and processing of SMLM data in order to optimize reconstruction quality and avoid the generation of artifacts. We hope that the tips and tricks we discovered over the years and detail here will be useful for researchers looking to make the best possible SMLM images, a pre-requisite for meaningful biological discovery.
TheKlebsiella pneumoniaecitrate synthase gene,gltA, influences site specific fitness during infection
Authors: Sun Yuang , Vornhagen Jay , Breen Paul , Forsyth Valerie , Zhao Lili , Mobley Harry L.T. , Bachman Michael A.
Published: March 2019

Klebsiella pneumoniae(Kp), one of the most common causes of healthcare-associated infections, increases patient morbidity, mortality and hospitalization costs. Kp must acquire nutrients from the host for successful infection. However, the host is able to prevent bacterial nutrient acquisition through multiple systems, including the innate immune protein lipocalin 2 (Lcn2) that prevents Kp iron acquisition by sequestering the siderophore enterobactin. To identify novel Kp factors that mediate evasion of nutritional immunity during lung infection, we undertook an InSeq study using a pool of >20,000 transposon mutants administered toLcn2+/+andLcn2-/-mice. Comparing mutant frequencies between mouse genotypes, this genome-wide screen identified the Kp citrate synthase GltA as potentially interacting with Lcn2, and this novel finding was independently validated. Interestingly,in vitrostudies suggest that this interaction is not direct. Given that GltA is involved in oxidative metabolism, we screened the ability of this mutant to use a variety of carbon and nitrogen sources. The results indicated that thegltAmutant has a distinct amino acid auxotrophy and is unable to use a variety of carbon sources. Specifically, we show thatgltAis necessary for growth in bronchioloalveolar lavage fluid, which is amino acid-limited, but dispensable in serum, which is amino acid rich. Deletion ofLcn2from the host leads to increased amino acid levels in bronchioloalveolar lavage fluid, and thus abrogates the loss ofgltAduring pneumonia in theLcn2-/-background. GltA was also required for gut colonization, but dispensable in the bloodstream in a bacteremia model, demonstrating that deletion ofgltAleads to an organ-specific fitness defect. Together, this study is the first to mechanistically describe a role forgltAin Kp infection and provide unique insight into how metabolic flexibility impacts bacterial fitness during infection.

Author Summary

The bacteriaKlebsiella pneumoniae(Kp) is an important cause of infection in healthcare settings. These infections can be difficult to treat, as they frequently occur in chronically ill patients and the bacteria has the ability to acquire multiple antibiotic resistance markers. Kp is a common colonizer of the intestinal tract in hospitalized patients, and can progress to infections of the bloodstream, respiratory and urinary tract. However, the bacterial factors that allow Kp to replicate in these different body sites is unclear. In this study, we found that the Kp citrate synthase, GltA, enables bacterial replication in the lung and intestine by enhancing the ability of Kp to use diverse nutrients, in a mechanism known as metabolic flexibility. Kp lacking GltA require specific amino acids that are abundant in blood, but not other body sites. The work in this study provides novel insight into why Kp is a successful hospital pathogen that can colonize and infect multiple body sites.
Synthesis, crystal structures and characterizations of three new copper(II) complexes including anti-inflammatory diclofenac
Authors: Hamamci Alisir Sevim , Dege Necmi , Tapramaz Recep
Published: March 2019

Three new diclofenac-based copper(II) complexes, namely tetrakis{μ-2-[2-(2,6-dichloroanilino)phenyl]acetato-κ2
O:O′}bis(methanol-κO)copper(II), [Cu2(μ-dicl)4(CH3OH)2] (1), bis{2-[2-(2,6-dichloroanilino)phenyl]acetato-κ2
O,O′}bis(1-vinyl-1H-imidazole-κN
3)copper(II), [Cu(dicl)2(vim)2] (2), and bis{2-[2-(2,6-dichloroanilino)phenyl]acetato-κ2
O,O′}bis(1H-imidazole-κN
3)copper(II), [Cu(dicl)2(im)2] (3) [dicl is diclofenac (C14H10Cl2NO2), vim is 1-vinylimidazole (C5H6N2) and im is imidazole (C3H4N2)], have been synthesized and characterized by elemental analysis, FT–IR spectroscopy, thermal analysis and single-crystal X-ray diffraction. X-ray diffraction analysis shows that complex 1 consists of dimeric units in which the dicl ligand exhibits a bidentate syn,syn-μ2 coordination mode linking two copper(II) centres. Complexes 2 and 3 have mononuclear units with the general formula [Cu(dicl)2
L
2] (L is vim or im) in which the CuII ions are octahedrally coordinated by two L and two dicl chelating ligands. The L and dicl ligands both occupy the trans positions of the coordination octahedron. The different coordination modes of dicl in the title complexes were revealed by Fourier transform IR (FT–IR) spectroscopy. The spin matching between the copper(II) centres in the dimeric [Cu2(μ-dicl)4(CH3OH)2] units was also confirmed by magnetic data to be lower than the spin-only value and electron paramagnetic resonance (EPR) spectra. The thermal properties of the complexes were investigated by thermogravimetric (TG) and differential thermal analysis (DTA) techniques.
Constitutional Principle, the Rule of Law and Political Reality: The European Union (Withdrawal) Act 2018
Authors: Craig Paul
Published: March 2019

The European Union (Withdrawal) Act 2018 is the cornerstone of UK legislation designed to accomplish the legal dimension of Brexit. It brings the entire acquis of EU law into UK law in order to avoid regulatory black holes that would otherwise occur. The Act embodies a twofold legislative strategy: EU law brought into UK law thereby is to be made fit for purpose by exit day, with necessary changes being made by statutory instrument; Parliament can then decide at greater leisure thereafter whether it wishes to retain, amend or repeal this legislation. The burden placed on Parliament is unprecedented, all the more so given the exigencies of time in which the changes are to be made. This article explicates the principal provisions of the 2018 Act, and the concerns as to constitutional principle and the rule of law raised by the legislation. The tensions in the drafting process are made apparent, and uncertainties in the resulting text are revealed.
Occurrence of Different Forms and Implications of Compound Specific Sterols in Continental Sediments of the Northeast South China Sea
Authors: QIU Hong , ZOU Li , ZHANG Minsheng , ZHU Chaoqi , JIA Yonggang
Published: March 2019

The South China Sea (SCS) is one of the most productive and accumulative marginal shelves of organic carbon in the world. To expound the transformation and preservation of organic carbon in the Northeast SCS, where abundant oil and gas resources have been reported, compound specific sterols in free (FR), base hydrolytic (BH), and acid hydrolytic (AH) forms were analyzed in surface and columnar sediments in May, 2016. The results showed that the total contents of sterols detected ranged from 0.15 to 3.74 ppm dry weight in the surface sediments, and gradually decreased from 3.41 to 0.17 ppm dry weight from surface to deep sediments, in which cholesterol (27Δ5) was the most abundant component. Sterols mainly existed in the BH form (54.51%–74.20%), followed by the FR form (25.50%–45.49%) and then the AH form (0–3.77%) in turn, in the surface sediments. BH and FR sterols accounted for 0–49.08% and 50.92%–100% in the columnar sediments, while AH sterols were undetectable. The contents of specific sterols indicated that, the primary source of marine organic carbon was about 5 times as much as that from terrestrial input. More and more FR sterols transformed into BH sterols with increasing sedimentary depth, and BH sterols absolutely dominated in sediment depths under 25 cm. The forms of Sterols C27 were maintained at a relative consistence state, but Sterols C28 to C30 degraded gradually during the sedimentation process. It was suggested that the stability of sterols, based on the chemical structures, might be the primary factor controlling their degradation and preservation in deeper sediments. These results would help to understand the organic carbon (OC) transformation in a hydrate formation area in a marginal sea.
An Assessment of Grant‐based Multilateral Funding Flows from 2014 to 2016
Authors: McArthur John W , Rasmussen Krista
Published: March 2019

This paper presents a global snapshot of how all countries, plus the Bill & Melinda Gates Foundation, allocated approximately $63 billion per year across 54 major multilateral organizations during the 2014–16 period. We assess direct funding to United Nations and non‐UN organizations to examine three key questions. First, how much does each funder contribute to each organization? Second, what is the relative importance of each funder to each organization? Third, how do funding allocations compare to objective benchmarks like share of donor country income, share of world income and share of world population? We find that a small number of countries provide a majority of total funding and a small number of organizations account for a majority of total resources received. Only a handful of countries are the top funders to at least one organization, but a variety of mid‐ and smaller‐sized economies play larger relative roles in some smaller organizations. Estimating funders’ flows across organizations allows for assessment of their revealed preferences among multilateral priorities and enables comparison against objective benchmarks for burden‐sharing. To our knowledge, this is the first study to provide a comprehensive mapping of all countries’ recent annual grant funding across the majority of large multilateral institutions.
Nontuberculous mycobacterium M. avium infection predisposes aged mice to cardiac abnormalities and inflammation
Authors: Headley Colwyn A. , Gerberick Abigail , Mehta Sumiran , Wu Qian , Yu Lianbo , Fadda Paolo , Khan Mahmood , Ganesan Latha Prabha , Turner Joanne , Rajaram Murugesan V. S.
Published: March 2019

Biological aging dynamically alters normal immune and cardiac function, favoring the production of pro‐inflammatory cytokines (IL‐1β, IL‐6, and TNF‐α) and increased instances of cardiac distress. Cardiac failure is the primary reason for hospitalization of the elderly (65+ years). The elderly are also increasingly susceptible to developing chronic bacterial infections due to aging associated immune abnormalities. Since bacterial infections compound the rates of cardiac failure in the elderly, and this phenomenon is not entirely understood, the interplay between the immune system and cardiovascular function in the elderly is of great interest. Using Mycobacterium avium, an opportunistic pathogen, we investigated the effect of mycobacteria on cardiac function in aged mice. Young (2–3 months) and old (18–20 months) C57BL/6 mice were intranasally infected with M. avium strain 104, and we compared the bacterial burden, immune status, cardiac electrical activity, pathology, and function of infected mice against uninfected age‐matched controls. Herein, we show that biological aging may predispose old mice infected with M. avium to mycobacterial dissemination into the heart tissue and this leads to cardiac dysfunction. M. avium infected old mice had significant dysrhythmia, cardiac hypertrophy, increased recruitment of CD45+ leukocytes, cardiac fibrosis, and increased expression of inflammatory genes in isolated heart tissue. This is the first study to report the effect of mycobacteria on cardiac function in an aged model. Our findings are critical to understanding how nontuberculous mycobacterium (NTM) and other mycobacterial infections contribute to cardiac dysfunction in the elderly population.
Peripheral inflammation induces neuroinflammation that alters neurotransmission and cognitive and motor function in hepatic encephalopathy: Underlying mechanisms and therapeutic implications
Authors: Cabrera‐Pastor Andrea , Llansola Marta , Montoliu Carmina , Malaguarnera Michele , Balzano Tiziano , Taoro‐Gonzalez Lucas , García‐García Raquel , Mangas‐Losada Alba , Izquierdo‐Altarejos Paula , Arenas Yaiza M. , Leone Paola , Felipo Vicente
Published: March 2019

Several million patients with liver cirrhosis suffer minimal hepatic encephalopathy (MHE), with mild cognitive and coordination impairments that reduce their quality of life and life span. Hyperammonaemia and peripheral inflammation act synergistically to induce these neurological alterations. We propose that MHE appearance is because of the changes in peripheral immune system, which are transmitted to brain, leading to neuroinflammation that alters neurotransmission leading to cognitive and motor alterations. We summarize studies showing that MHE in cirrhotic patients is associated with alterations in the immune system and that patients died with HE show neuroinflammation in cerebellum, with microglial and astrocytic activation and Purkinje cell loss. We also summarize studies in animal models of MHE on the role of peripheral inflammation in neuroinflammation induction, how neuroinflammation alters neurotransmission and how this leads to cognitive and motor alterations. These studies identify therapeutic targets and treatments that improve cognitive and motor function. Rats with MHE show neuroinflammation in hippocampus and altered NMDA and AMPA receptor membrane expression, which impairs spatial learning and memory. Neuroinflammation in cerebellum is associated with altered GABA transporters and extracellular GABA, which impair motor coordination and learning in a Y maze. These alterations are reversed by treatments that reduce peripheral inflammation (anti‐TNFα, ibuprofen), neuroinflammation (sulphoraphane, p38 inhibitors), GABAergic tone (bicuculline, pregnenolone sulphate) or increase extracellular cGMP (sildenafil or cGMP). The mechanisms identified would also occur in other chronic diseases associated with inflammation, aging and some mental and neurodegenerative diseases. Treatments that improve MHE may also be beneficial to treat these pathologies.
Urban evictions, public housing and the gendered rationalisation of kampung life in Jakarta
Authors: Tilley Lisa , Elias Juanita , Rethel Lena
Published: March 2019

The dispossession of urban communities across class and racial lines is a global phenomenon linked to the expansion of international investment in the development of ‘exemplary’ city space. However, city evictions are also historically informed and gendered processes which are continuous with past colonial and postcolonial urban rationalisation projects. Drawing on testimonies of women evictees in Jakarta, as well as interviews with public housing managers, this article details the gendered nature of the rationalisation of urban life in the context of a contemporary evictions regime. We argue that the rationalisation of urban space serves to sharpen the gender order by placing material constraints on women's roles, limiting their economic activities and defining them as hygiene‐responsible housewives. Further, and in turn, the limited provision of ‘rusunawa’ public housing, which we show to be a gendered spatial and social transition informed by state doctrine on the family, provides the state with justification for dispossession itself. Finally, women's everyday acts of refusal and resistance show not only that kampung forms of social life continue to be preserved in Jakarta, but also that rationalisation itself is a negotiated and contingent process.
Nice to meet you: Encountering introductions and departures in the field
Authors: Gillen Jamie , Nguyen Tuan Anh , Rigg Jonathan
Published: March 2019

This paper advocates for a clearer understanding of the politics of introductions and partings in fieldwork by engaging with the geographical literature on the encounter. Conducting research with people in the field presents investigators with unfamiliar and confusing cultural rituals involving how to present oneself, what to say, and how to physically interact with respondents on meeting them for the first time. This is also true during the moments when bidding farewell to our research participants. These encounters are more than reflections of different manners and understandings of politeness: in this paper we use field research in Vietnam to argue that the first and last impressions of fieldwork must be separated conceptually from other parts of the experience and evaluated as distinctively important encounters in geographer–respondent relationships.
Daratumumab, bortezomib, cyclophosphamide and dexamethasone in newly diagnosed and relapsed multiple myeloma: LYRA study
Authors: Yimer Habte , Melear Jason , Faber Edward , Bensinger William I. , Burke John M. , Narang Mohit , Stevens Don , Gunawardena Sriya , Lutska Yana , Qi Keqin , Ukropec Jon , Qi Ming , Lin Thomas S. , Rifkin Robert M.
Published: March 2019

This United States community study evaluated the combination of daratumumab, bortezomib, cyclophosphamide and dexamethasone (D‐VCd) in newly diagnosed multiple myeloma (NDMM) and relapsed multiple myeloma (RMM). Patients received 4–8 induction cycles of bortezomib 1·5 mg/m2, cyclophosphamide 300 mg/m2 and dexamethasone 40 mg weekly. Intravenous daratumumab 16 mg/kg was administered as approved except for a split‐first dose in Cycle 1. Eligible patients underwent autologous stem cell transplantation. All patients received ≤12 daratumumab maintenance doses monthly. Eighty‐six NDMM and 14 RMM patients received ≥1 treatment dose. In NDMM patients, very good partial response or better (≥VGPR) and overall response rates after 4 induction cycles were 44% (primary endpoint) and 79%, respectively, and 56% and 81% at end of induction. The 12‐month progression‐free survival (PFS) rate was 87%. Efficacy was also observed in RMM patients. Fatigue (59%) and neutropenia (13%) were the most frequent treatment‐emergent adverse event (TEAE) and grade 3/4 TEAE, respectively. Infusion reactions occurred in 54% of patients, primarily during the first dose, and were mild (2% grade 3). The first 2 daratumumab infusions were 4·5 and 3·8 h (median). Overall, D‐VCd was well tolerated, split‐first daratumumab dosing was feasible, the ≥VGPR rate after 4 cycles was 44% and the 1‐year PFS rate was 87%.
Iron overload in congenital haemolytic anaemias: role of hepcidin and cytokines and predictive value of ferritin and transferrin saturation
Authors: Barcellini Wilma , Zaninoni Anna , Gregorini Anna I. , Soverini Giulia , Duca Lorena , Fattizzo Bruno , Giannotta Juri A. , Pedrotti Patrizia , Vercellati Cristina , Marcello Anna P. , Fermo Elisa , Bianchi Paola , Cappellini Maria Domenica
Published: March 2019

Iron overload (IO) is poorly investigated in the congenital haemolytic anaemias (CHAs), a heterogeneous group of rare inherited diseases encompassing abnormalities of the erythrocyte membrane and metabolism, and defects of the erythropoiesis. In this study we systematically evaluated routine iron parameters and cardiac and hepatic magnetic resonance imaging, together with erythropoietin, hepcidin, non‐transferrin bound iron (NTBI), and cytokine serum levels in patients with different CHAs. We found that 40% of patients had a liver iron concentration (LIC) >4 mg Fe/g dry weight. Hepatic IO was associated with ferritin levels (P = 0·0025), transferrin saturation (TfSat, P = 0·002) and NTBI (P = 0·003). Moreover, ferritin >500 μg/l plus TfSat >60% was demonstrated as the best combination able to identify increased LIC, and TfSat alteration as more important in cases with discordant values. Possible confounding factors, such as transfusions, hepatic disease, metabolic syndrome and hereditary haemochromatosis‐associated mutations, had negligible effects on IO. Erythropoietin and hepcidin levels were increased in CHAs compared with controls, correlating with LIC and ferritin, respectively. Regarding cytokines, γ‐interferon (IFN‐γ) was increased, and both interleukin 6 and IFN‐γ levels positively correlated with ferritin and hepcidin levels. Overall, these findings suggest the existence of a vicious cycle between chronic haemolysis, inflammatory response and IO in CHAs.
Hypomethylating agent alters the immune microenvironment in acute myeloid leukaemia (AML) and enhances the immunogenicity of a dendritic cell/AML vaccine
Authors: Nahas Myrna R. , Stroopinsky Dina , Rosenblatt Jacalyn , Cole Leandra , Pyzer Athalia R. , Anastasiadou Eleni , Sergeeva Anna , Ephraim Adam , Washington Abigail , Orr Shira , McMasters Malgorzata , Weinstock Matthew , Jain Salvia , Leaf Rebecca K. , Ghiasuddin Haider , Rahimian Maryam , Liegel Jessica , Molldrem Jeffrey J. , Slack Frank , Kufe Donald , Avigan David
Published: March 2019

Acute myeloid leukaemia (AML) is a lethal haematological malignancy characterized by an immunosuppressive milieu in the tumour microenvironment (TME) that fosters disease growth and therapeutic resistance. Hypomethylating agents (HMAs) demonstrate clinical efficacy in AML patients and exert immunomodulatory activities. In the present study, we show that guadecitabine augments both antigen processing and presentation, resulting in increased AML susceptibility to T cell‐mediated killing. Exposure to HMA results in the activation of the endogenous retroviral pathway with concomitant downstream amplification of critical mediators of inflammation. In an immunocompetent murine leukaemia model, guadecitabine negatively regulates inhibitory accessory cells in the TME by decreasing PD‐1 (also termed PDCD1) expressing T cells and reducing AML‐mediated expansion of myeloid‐derived suppressor cells. Therapy with guadecitabine results in enhanced leukaemia‐specific immunity, as manifested by increased CD4 and CD8 cells targeting syngeneic leukaemia cells. We have previously reported that vaccination with AML/dendritic cell fusions elicits the expansion of leukaemia‐specific T cells and protects against disease relapse. In the present study, we demonstrate that vaccination in conjunction with HMA therapy results in enhanced anti‐leukaemia immunity and survival. The combination of a novel personalized dendritic cell/AML fusion vaccine and an HMA has therapeutic potential, and a clinical trial investigating this combination is planned.
Online Assessment of Preschool Anxiety: description and initial validation of a new diagnostic tool
Authors: Morgan Amy J. , Tamir Elli , Rapee Ronald M. , Lyneham Heidi J. , McLellan Lauren F. , Bayer Jordana K.
Published: March 2019

Background

The Online Assessment of Preschool Anxiety (OAPA) is a newly developed measure that assesses anxiety disorders in preschool children aged 3–6 years. This study aimed to explore the OAPA's initial psychometric properties with a particular focus on examining its construct validity, both convergent and discriminant.

Method

The OAPA was completed online by a community sample of 319 Australian parents of temperamentally inhibited preschool children (M: 5.3 years). Preliminary diagnoses were automatically generated before assessment reports were reviewed by a psychologist. Construct validity was examined by assessing the degree of agreement between the OAPA and existing valid questionnaire measures that were simultaneously administered online.

Results

Nearly half of participants met criteria for a child anxiety disorder according to the OAPA, most commonly social phobia. Findings supported convergent validity with the Revised Preschool Anxiety Scale (an anxiety symptom measure), the Children's Anxiety Life Interference Scale – Preschool Version (a measure of life interference from anxiety), the Emotional Symptoms scale of the Strengths and Difficulties Questionnaire‐Parent Version (a measure of broader internalizing symptoms), as well as an over‐involved/protective parenting scale. Findings also supported initial discriminant validity with the Conduct Problems scale of the Strengths and Difficulties Questionnaire‐Parent Version.

Conclusions

Results of this study provide evidence for the OAPA's preliminary construct validity. With further research into the OAPA's reliability (test–retest and interrater) and confirming construct validity, the OAPA may be a useful instrument for use in research settings and clinical practice.
Vocal nodules management
Authors: Birchall Martin A. , Carding Paul
Published: March 2019

Vocal fold nodules present the voice clinic team with a number of clinical dilemmas which are not as simple as previously thought. The definition, aetiology, prevalence and diagnosis are all poorly understood. Furthermore, treatment evidence for both behavioural and surgical approaches is weak. This paper reviews the published evidence pertaining to all of these aspects. Specific areas of uncertainty that remain include poorly defined nomenclature, the natural history of paediatric vocal nodules, the establishment of criteria to measure successful treatment, optimal configuration of speech therapy regimens and the rationale for surgical intervention. The authors suggest the development of evidence‐based guidelines for UK practice.