bluuebunny/crossref_metadata_2025 huggingface dataset:
The relationship between live weight and the intake of bulky foods in pigs
Authors: Whittemore E.C. , Emmans G. C. , Kyriazakis I.
Published: May 2017

Data from pigs between 12 and 120 kg live weight were used to develop a relationship between the capacity for food bulk and live weight. High bulk foods, intended to limit growth, were offered for 21 days to pigs of 12, 36 (600 g sugar-beet pulp per kg (SBP60)) and 108 (800 g sugar-beet pulp per kg (SBP80)) kg live weight. Control pigs were given a low bulk food C at all weights. After 21 days the pigs were slaughtered and measurements made on the gastro-intestinal tract (GIT). In two additional treatment groups SBP60was offered from a weight of either 36 kg or 72 kg before SBP80was offered at 108 kg. Daily live-weight gain, after allowing for the effects of a change of gut fill, was less at all weights on the high bulk foods than on C. At all weights the high bulk foods caused a significant increase in the weights of the stomach, large intestine, caecum and gut fill. Effects on the weight of the small intestine were small. Previous nutrition had no significant effect on the adapted performance, or on the size of the GIT, of pigs given SBP80at 108 kg but pre-feeding SBP60significantly increased initial consumption of SBP80. Constrained intake was not directly proportional to live weight beyond 40 kg. The absolute capacity for bulk (Cap, kg water-holding capacity per day) was related to live weight (W, kg) by the quadratic function Cap = (0·192.W) - (0·000299.W2). The value of Cap is predicted to reach a maximum when W = 321 kg. The combined weights of the large intestine and caecum (WLIC) changed with W in ways that were similar to the way in which Cap changed. In addition the ratio of Cap to WLIC was close to constant. The combined weight of the large intestine and the caecum may determine the capacity for food bulk in pigs.
Meat quality and composition of three muscles from French cull cows and young bulls
Authors: Dransfield E. , Martin J.-F. , Bauchart D. , Abouelkaram S. , Lepetit J. , Culioli J. , Jurie C. , Picard B.
Published: May 2017

The quality of grilled steaks was assessed by experienced panellists in longissimus thoracis (LT), semitendinosus (St) and triceps brachii (TB) muscles of Aubrac, Charolais, Limousin and Salers breeds raised in two production systems: 15-, 19- and 24-month-old bulls and 4-, 6- and 8-year-old cull cows.

Scores for sensory ‘initial tenderness’, ‘overall tenderness’, ‘juiciness’, ‘residue after mastication’ and ‘flavour intensity’ for all 497 meats were pooled to derive three eating quality classes.

Meats from the bulls and cows and from the four breeds were evenly distributed among the three eating quality classes. The highest quality class, representing one third of all the meats, contained 45% of the LT, 35% of the TB and 21% of the St muscles and one third of the meats from the 8-year-old cull cows. The meats in this class tended to have finer fibres, a greater proportion of slow oxidative fibres, slower post-mortem glycolysis, lower connective tissue and higher fat contents than those in the lower classes.

Lipid content accounted for proportionately 0·56 of the variation in flavour intensity and pH at 3 h post mortem, 0·52 of the variation in tenderness due to muscle and slaughter age.

Considering both young bulls and cull cows together, tenderness was highest in the meats from 15-month-old bulls and low in the meats from the intermediate age groups, and flavour and juiciness was highest in the meats from the oldest animals from each production system.
The effect of choice feeding complete diets on the performance of weaned pigs
Authors: Lawlor P. G. , Lynch P. B. , Caffrey P. J. , O’Doherty J. V.
Published: May 2017

Post-weaning growth rate in pigs is frequently poor and variable. Choice feeding may offer the opportunity to rectify this. In experiment 1, 24 mixed sex groups of 16 pigs weaned with an average weight of 6·8 kg were blocked on weaning weight and assigned at random to the following treatments: (A) starter diet (18·3 g/kg lysine and 16·6 MJ digestible energy (DE) per kg) for 11 days followed by link diet (15·0 g/kg lysine and 15·3 MJ DE per kg) to 27 days; (B) starter diet and link diet offered in a free choice to 27 days; and (C) starter diet and weaner diet (13·0 g/kg lysine and 14·3 MJ DE per kg) offered in a free choice to 27 days. In experiment 2, 66 pigs were weaned at 6·3 kg, blocked as individuals on sex and weight and were randomly assigned to treatments as in experiment 1. In experiment 3, 24 single sex groups of 16 pigs were formed from pigs weaned at 7·8 kg. The groups were blocked on the basis of weaning weight and randomly assigned to the following treatments: (A) starter diet for 11 days followed by link diet to 26 days, (B) starter diet and link diet offered in a free choice to 26 days and (C) starter diet and link diet offered in a free choice to 26 days with feeder position rotated twice weekly. In experiments 1 and 3 pigs were offered a common weaner diet (14·1 g/kg lysine and 14·4 MJ DE per kg) following the experimental period. In experiment 1, daily gain was 406, 410 and 397 g/day (s.e. 6·6; P > 0·05) and food coversion efficiency (FCE) was 1·24, 1·21 and 1·27 g/g (s.e. 0·01; P < 0·01) during the period from day 0 to 27 for treatments A, B and C, respectively. The proportion of the diet selected as starter diet was 0·20, 0·50 and 0·47 (s.e. 0·023; P < 0·001) for treatments A, B and C, respectively. Within-pen variation in pig weight was similar for all treatments at day 14, 27 and 56 (P > 0·05), respectively. In experiment 2, daily gain was 403, 436 and 394 g/day (s.e. 13·0; P = 0·07) and FCE was 1·19, 1·16 and 1·24 g/g (s.e. 0·02; P < 0·05) during the period from day 0 to 26 for treatments A, B and C, respectively. The proportion of the diet selected as starter diet was 0·20, 0·57 and 0·53 (s.e. 0·024; P < 0·001) for treatments A, B and C, respectively. In experiment 3, daily gain was 465, 486 and 488 g/day (s.e.9·4; P > 0·05) and FCE was 1·14, 1·11 and 1·07 g/g (s.e. 0·015; P < 0·01) during the period from day 0 to 26 for treatments A, B and C, respectively. The proportion of the diet selected as starter diet was 0·21, 0·49 and 0·55 (s.e. 0·022; P < 0·001) for treatments A, B and C, respectively. Pig weight at day 49 was 36·4, 37·1 and 37·3 kg (s.e. 0·27; P = 0·09). It was concluded from these experiments that choice feeding did improve pig performance when a choice of starter and link diet was offered.
The nutritive value of five pasture species occurring in the summer grazing ranges of the Pyrenees
Authors: Marinas A. , García-González R. , Fondevila M.
Published: May 2017

Five species of alpine pasture plants from the Pyrenees representing 3 botanical groups: grasses (Festuca eskia, Nardus stricta), forbs (Anthyllis vulneraria, Galium verum) and shrubs (Echinospartum horridum), were collected monthly from June to September and analysed for nitrogen (N) content, cell wall composition, in vitro enzymatic digestibility (DMDe) and volume of gas produced by microbial fermentation. Among the dicotyledenous varieties, A. vulneraria and G. verum showed the highest nutritive value whilst that of E. horridum was low due to high lignin content. Grasses showed moderate nutritive values in June rapidly decreasing thereafter. Nitrogen content and organic matter digestibility (OMDg) of A. vulneraria remained relatively constant through the sampling period whereas it abruptly decreased for remaining species from July. Gas production significantly differed among species during the first 48 h of microbial fermentation but not at later stages of fermentation. Collection date did not affect gas production before 24 h of incubation but significant differences were found thereafter with samples from June and July being more degraded than from August and September. Principal component analysis associated OMDg positively with N content and gas production and negatively with fibre content. Lignin proportion did not significantly correlate with gas production or with OMDg, suggesting that the degree of lignification is not the only factor affecting microbial fermentation but other factors such as lignin tissue locations may be involved. A. vulneraria has been revealed as very good forage with a high potential in extensive animal production systems. Both OMDg and DMDe methods seem more accurate than chemical analyses for evaluating forages at different stages of maturity.
Effect of nutrition in early pregnancy on the periparturient relaxation of immunity to gastro-intestinal parasitism in prolific ewes
Authors: Valderrábano J. , Uriarte J.
Published: May 2017

The rôle of body reserves stored during early pregnancy on the periparturient breakdown of resistance to nematode parasites was investigated. From the 35th day of pregnancy, 46 ewes were distributed in four groups and given access to a lucerne pelleted diet. Two groups were given food at maintenance (M and C) and the other two were offered food either ad libitum (H) or at 0·70 their maintenance requirements (L) in order to achieve three well differentiated levels of body reserves by the 90th day of pregnancy when backfat thickness reached a mean value of 10·6, 7·5, 7·4 and 5·0 mm for H, M, C, and L treatments respectively. After the 90th day of pregnancy all animals were given food at 50 g/kg live weight per day. All ewes in groups H, M and L received 5000 infective larvae per week (40% Teladorsagia circumcincta, 40% Trichostrongylus colubriformis, 20% Haemonchus contortus) from 5 weeks before to 3 weeks after lambing. The animals in group C remained as uninfected controls.

Host resistance, as measured by faecal egg counts, was significantly affected by the nutritional treatment established during early pregnancy, showing a mean excretion of 546, 766 and 1007 eggs per gram (e.p.g. ) for H, M, and L treatments, respectively, until 3 weeks post lambing. This response was accompanied by a significant effect on circulating eosinophils and better fed ewes showed a higher concentration with a maximum mean value of 10·1, 6·9, 5·5 and 4·0 cells per mm3 for H, M, L and C treatments, respectively, 2 weeks post infection. The effect of the worm infection per se was evident in that the lambs of the M treatment ewes grew at 0·90 of the rate of those in the control treatment (189 v. 213 g/day). Ad libitum feeding in early pregnancy appeared to sufficiently compensate for this depressive effect, with the H ewes producing lambs that grew at a rate similar to those of the C ewes (213 v. 213 g/day).

The results support the view that fat mass stored by ewes in early pregnancy is involved in the expression of immunity against gastro-intestinal nematode infection around parturition. Furthermore, the depressive effect of ewes’ infection on lambs’ growth rate can be overcome by increasing the plane of nutrition of their dams. These results have clear implications for grazing animals, particularly their nutritional management in early pregnancy and provide a simple management strategy in sustainable management systems.
An in vivo strategy to counteract post-administration anticoagulant activity of azido-Warfarin
Authors: Ursuegui Sylvain , Recher Marion , Krężel Wojciech , Wagner Alain
Published: May 2017

Drugs, usually long acting and metabolically stable molecules, might be the source of adverse effects triggered by complex drug interactions, anaphylaxis and drug-induced coagulopathy. To circumvent this growing drug safety issue, we herein investigate the opportunity offered by bio-orthogonal chemistry for in vivo drug neutralization. We design a small-molecule anticoagulant drug (Warfarin) containing an azide group that acts as a safety pin. It allows drug deactivation and restoration of physiological coagulation via in vivo click reaction with a suitable cyclooctyne-based neutralizing agent. In this strategy, the new molecule formed by reaction of the drug and the antidote is deprived of biological activity and prone to fast renal clearance. This ‘Click & Clear’ approach lays ground for new strategies in designing drugs with switchable biophysical properties.
Extended fisheries recovery timelines in a changing environment
Authors: Britten Gregory L. , Dowd Michael , Kanary Lisa , Worm Boris
Published: May 2017

Rebuilding depleted fish stocks is an international policy goal and a 2020 Aichi target under the Convention on Biological Diversity. However, stock productivity may shift with future climate change, with unknown consequences for sustainable harvesting, biomass targets and recovery timelines. Here we develop a stochastic modelling framework to characterize variability in the intrinsic productivity parameter (r) and carrying capacity (K) for 276 global fish stocks worldwide. We use models of dynamic stock productivity fitted via Bayesian inference to forecast rebuilding timelines for depleted stocks. In scenarios without fishing, recovery probabilities are reduced by 19%, on average, relative to models assuming static productivity. Fishing at 90% of the maximum sustainable rate depresses recovery probabilities by 42%, on average, relative to static models. This work reveals how a changing environmental context can delay the rebuilding of depleted fish stocks, and provides a framework to account for the potential impacts of environmental change on the productivity of wildlife populations more broadly.
Concerted regulation of retinal pigment epithelium basement membrane and barrier function by angiocrine factors
Authors: Benedicto Ignacio , Lehmann Guillermo L. , Ginsberg Michael , Nolan Daniel J. , Bareja Rohan , Elemento Olivier , Salfati Zelda , Alam Nazia M. , Prusky Glen T. , Llanos Pierre , Rabbany Sina Y. , Maminishkis Arvydas , Miller Sheldon S. , Rafii Shahin , Rodriguez-Boulan Enrique
Published: May 2017

The outer blood-retina barrier is established through the coordinated terminal maturation of the retinal pigment epithelium (RPE), fenestrated choroid endothelial cells (ECs) and Bruch’s membrane, a highly organized basement membrane that lies between both cell types. Here we study the contribution of choroid ECs to this process by comparing their gene expression profile before (P5) and after (P30) the critical postnatal period when mice acquire mature visual function. Transcriptome analyses show that expression of extracellular matrix-related genes changes dramatically over this period. Co-culture experiments support the existence of a novel regulatory pathway: ECs secrete factors that remodel RPE basement membrane, and integrin receptors sense these changes triggering Rho GTPase signals that modulate RPE tight junctions and enhance RPE barrier function. We anticipate our results will spawn a search for additional roles of choroid ECs in RPE physiology and disease.
An apicobasal gradient of Rac activity determines protrusion form and position
Authors: Couto Africa , Mack Natalie Ann , Favia Lucrezia , Georgiou Marios
Published: May 2017

Each cell within a polarized epithelial sheet must align and correctly position a wide range of subcellular structures, including actin-based dynamic protrusions. Using in vivo inducible transgenes that can sense or modify Rac activity, we demonstrate an apicobasal gradient of Rac activity that is required to correctly form and position distinct classes of dynamic protrusion along the apicobasal axis of the cell. We show that we can modify the Rac activity gradient in genetic mutants for specific polarity proteins, with consequent changes in protrusion form and position and additionally show, using photoactivatable Rac transgenes, that it is the level of Rac activity that determines protrusion form. Thus, we demonstrate a mechanism by which polarity proteins can spatially regulate Rac activity and the actin cytoskeleton to ensure correct epithelial cell shape and prevent epithelial-to-mesenchymal transitions.
Plasmonic computing of spatial differentiation
Authors: Zhu Tengfeng , Zhou Yihan , Lou Yijie , Ye Hui , Qiu Min , Ruan Zhichao , Fan Shanhui
Published: May 2017

Optical analog computing offers high-throughput low-power-consumption operation for specialized computational tasks. Traditionally, optical analog computing in the spatial domain uses a bulky system of lenses and filters. Recent developments in metamaterials enable the miniaturization of such computing elements down to a subwavelength scale. However, the required metamaterial consists of a complex array of meta-atoms, and direct demonstration of image processing is challenging. Here, we show that the interference effects associated with surface plasmon excitations at a single metal–dielectric interface can perform spatial differentiation. And we experimentally demonstrate edge detection of an image without any Fourier lens. This work points to a simple yet powerful mechanism for optical analog computing at the nanoscale.
Mistranslation can enhance fitness through purging of deleterious mutations
Authors: Bratulic Sinisa , Toll-Riera Macarena , Wagner Andreas
Published: May 2017

Phenotypic mutations are amino acid changes caused by mistranslation. How phenotypic mutations affect the adaptive evolution of new protein functions is unknown. Here we evolve the antibiotic resistance protein TEM-1 towards resistance on the antibiotic cefotaxime in an Escherichia coli strain with a high mistranslation rate. TEM-1 populations evolved in such strains endow host cells with a general growth advantage, not only on cefotaxime but also on several other antibiotics that ancestral TEM-1 had been unable to deactivate. High-throughput sequencing of TEM-1 populations shows that this advantage is associated with a lower incidence of weakly deleterious genotypic mutations. Our observations show that mistranslation is not just a source of noise that delays adaptive evolution. It could even facilitate adaptive evolution by exacerbating the effects of deleterious mutations and leading to their more efficient purging. The ubiquity of mistranslation and its effects render mistranslation an important factor in adaptive protein evolution.
Impact of simultaneous exposure to arboviruses on infection and transmission by Aedes aegypti mosquitoes
Authors: Rückert Claudia , Weger-Lucarelli James , Garcia-Luna Selene M. , Young Michael C. , Byas Alex D. , Murrieta Reyes A. , Fauver Joseph R. , Ebel Gregory D.
Published: May 2017

The recent emergence of both chikungunya and Zika viruses in the Americas has significantly expanded their distribution and has thus increased the possibility that individuals may become infected by more than one Aedes aegypti-borne virus at a time. Recent clinical data support an increase in the frequency of coinfection in human patients, raising the likelihood that mosquitoes could be exposed to multiple arboviruses during one feeding episode. The impact of coinfection on the ability of relevant vector species to transmit any of these viruses (that is, their vector competence) has not been determined. Thus, we here expose Ae. aegypti mosquitoes to chikungunya, dengue-2 or Zika viruses, both individually and as double and triple infections. Our results show that these mosquitoes can be infected with and can transmit all combinations of these viruses simultaneously. Importantly, infection, dissemination and transmission rates in mosquitoes are only mildly affected by coinfection.
Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification
Authors: Liu Fan , Lössl Philip , Scheltema Richard , Viner Rosa , Heck Albert J. R.
Published: May 2017

We describe optimized fragmentation schemes and data analysis strategies substantially enhancing the depth and accuracy in identifying protein cross-links using non-restricted whole proteome databases. These include a novel hybrid data acquisition strategy to sequence cross-links at both MS2 and MS3 level and a new algorithmic design XlinkX v2.0 for data analysis. As proof-of-concept we investigated proteome-wide protein interactions in E. coli and HeLa cell lysates, respectively, identifying 1,158 and 3,301 unique cross-links at ∼1% false discovery rate. These protein interaction repositories provide meaningful structural information on many endogenous macromolecular assemblies, as we showcase on several protein complexes involved in translation, protein folding and carbohydrate metabolism.
Self-assembly of a supramolecular hexagram and a supramolecular pentagram
Authors: Jiang Zhilong , Li Yiming , Wang Ming , Song Bo , Wang Kun , Sun Mingyu , Liu Die , Li Xiaohong , Yuan Jie , Chen Mingzhao , Guo Yuan , Yang Xiaoyu , Zhang Tong , Moorefield Charles N. , Newkome George R. , Xu Bingqian , Li Xiaopeng , Wang Pingshan
Published: May 2017

Five- and six-pointed star structures occur frequently in nature as flowers, snow-flakes, leaves and so on. These star-shaped patterns are also frequently used in both functional and artistic man-made architectures. Here following a stepwise synthesis and self-assembly approach, pentagonal and hexagonal metallosupramolecules possessing star-shaped motifs were prepared based on the careful design of metallo-organic ligands (MOLs). In the MOL design and preparation, robust ruthenium–terpyridyl complexes were employed to construct brominated metallo-organic intermediates, followed by a Suzuki coupling reaction to achieve the required ensemble. Ligand LA (VRu2+X, V=bisterpyridine, X=tetraterpyridine, Ru=Ruthenium) was initially used for the self-assembly of an anticipated hexagram upon reaction with Cd2+ or Fe2+; however, unexpected pentagonal structures were formed, that is, [Cd5LA5]30+ and [Fe5LA5]30+. In our redesign, LB [V(Ru2+X)2] was synthesized and treated with 60° V-shaped bisterpyridine (V) and Cd2+ to create hexagonal hexagram [Cd12V3LB3]36+ along with traces of the triangle [Cd3V3]6+. Finally, a pure supramolecular hexagram [Fe12V3LB3]36+ was successfully isolated in a high yield using Fe2+ with a higher assembly temperature.
Brønsted acid-catalysed enantioselective construction of axially chiral arylquinazolinones
Authors: Wang Yong-Bin , Zheng Sheng-Cai , Hu Yu-Mei , Tan Bin
Published: May 2017

The axially chiral arylquinazolinone acts as a privileged structural scaffold, which is present in a large number of natural products and biologically active compounds as well as in chiral ligands. However, a direct catalytic enantioselective approach to access optically pure arylquinazolinones has been underexplored. Here we show a general and efficient approach to access enantiomerically pure arylquinazolinones in one-pot fashion catalysed by chiral phosphoric acids. A variety of axially chiral arylquinazolinones were obtained in high yields with good to excellent enantioselectivities under mild condition. Furthermore, we disclosed a method for atroposelective synthesis of alkyl-substituted arylquinazolinones involving Brønsted acid-catalysed carbon–carbon bond cleavage strategy. Finally, the asymmetric total synthesis of eupolyphagin bearing a cyclic arylquinazolinone skeleton was accomplished with an overall yield of 32% in six steps by utilizing the aforementioned methodology.
Hif-1α regulates macrophage-endothelial interactions during blood vessel development in zebrafish
Authors: Gerri Claudia , Marín-Juez Rubén , Marass Michele , Marks Alora , Maischein Hans-Martin , Stainier Didier Y R.
Published: May 2017

Macrophages are known to interact with endothelial cells during developmental and pathological angiogenesis but the molecular mechanisms modulating these interactions remain unclear. Here, we show a role for the Hif-1α transcription factor in this cellular communication. We generated hif-1aa;hif-1ab double mutants in zebrafish, hereafter referred to as hif-1α mutants, and find that they exhibit impaired macrophage mobilization from the aorta-gonad-mesonephros (AGM) region as well as angiogenic defects and defective vascular repair. Importantly, macrophage ablation is sufficient to recapitulate the vascular phenotypes observed in hif-1α mutants, revealing for the first time a macrophage-dependent angiogenic process during development. Further substantiating our observations of vascular repair, we find that most macrophages closely associated with ruptured blood vessels are Tnfα-positive, a key feature of classically activated macrophages. Altogether, our data provide genetic evidence that Hif-1α regulates interactions between macrophages and endothelial cells starting with the mobilization of macrophages from the AGM.
Symbiont community stability through severe coral bleaching in a thermally extreme lagoon
Authors: Smith E. G. , Vaughan G. O. , Ketchum R. N. , McParland D. , Burt J. A.
Published: May 2017

Coral reefs are threatened by climate change as coral-algal symbioses are currently living close to their upper thermal limits. The resilience of the algal partner plays a key role in determining the thermal tolerance of the coral holobiont and therefore, understanding the acclimatory limits of present day coral-algal symbioses is fundamental to forecasting corals’ responses to climate change. This study characterised the symbiont community in a highly variable and thermally extreme (Max = 37.5 °C, Min = 16.8 °C) lagoon located in the southern Persian/Arabian Gulf using next generation sequencing of ITS2 amplicons. Despite experiencing extreme temperatures, severe bleaching and many factors that would be expected to promote the presence of, or transition to clade D dominance, the symbiont communities of the lagoon remain dominated by the C3 variant, Symbiodinium thermophilum. The stability of this symbiosis across multiple genera with different means of symbiont transmission highlights the importance of Symbiodinium thermophilum for corals living at the acclimatory limits of modern day corals. Corals in this extreme environment did not undergo adaptive bleaching, suggesting they are living at the edge of their acclimatory potential and that this valuable source of thermally tolerant genotypes may be lost in the near future under climate change.
An ultra-high gain and efficient amplifier based on Raman amplification in plasma
Authors: Vieux G. , Cipiccia S. , Grant D. W. , Lemos N. , Grant P. , Ciocarlan C. , Ersfeld B. , Hur M. S. , Lepipas P. , Manahan G. G. , Raj G. , Reboredo Gil D. , Subiel A. , Welsh G. H. , Wiggins S. M. , Yoffe S. R. , Farmer J. P. , Aniculaesei C. , Brunetti E. , Yang X. , Heathcote R. , Nersisyan G. , Lewis C. L. S. , Pukhov A. , Dias J. M. , Jaroszynski D. A.
Published: May 2017

Raman amplification arising from the excitation of a density echelon in plasma could lead to amplifiers that significantly exceed current power limits of conventional laser media. Here we show that 1–100 J pump pulses can amplify picojoule seed pulses to nearly joule level. The extremely high gain also leads to significant amplification of backscattered radiation from “noise”, arising from stochastic plasma fluctuations that competes with externally injected seed pulses, which are amplified to similar levels at the highest pump energies. The pump energy is scattered into the seed at an oblique angle with 14 J sr−1, and net gains of more than eight orders of magnitude. The maximum gain coefficient, of 180 cm−1, exceeds high-power solid-state amplifying media by orders of magnitude. The observation of a minimum of 640 J sr−1 directly backscattered from noise, corresponding to ≈10% of the pump energy in the observation solid angle, implies potential overall efficiencies greater than 10%.
Mapping few-femtosecond slices of ultra-relativistic electron bunches
Authors: Plath Tim , Lechner Christoph , Miltchev Velizar , Amstutz Philipp , Ekanayake Nagitha , Lazzarino Leslie Lamberto , Maltezopoulos Theophilos , Bödewadt Jörn , Laarmann Tim , Roßbach Jörg
Published: May 2017

Free-electron lasers are unique sources of intense and ultra-short x-ray pulses that led to major scientific breakthroughs across disciplines from matter to materials and life sciences. The essential element of these devices are micrometer-sized electron bunches with high peak currents, low energy spread, and low emittance. Advanced FEL concepts such as seeded amplifiers rely on the capability of analyzing and controlling the electron beam properties with few-femtosecond time resolution. One major challenge is to extract tomographic slice parameters instead of projected electron beam properties. Here, we demonstrate that a radio-frequency deflector in combination with a dipole spectrometer not only allows for single-shot extraction of a seeded FEL pulse profile, but also provides information on the electron slice emittance and energy spread. The seeded FEL power profile can be directly related to the derived slice emittance as a function of intra-bunch coordinate with a resolution down to a few femtoseconds.
Droplet Digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data
Authors: Taylor Sean C. , Laperriere Genevieve , Germain Hugo
Published: May 2017

Quantitative PCR (qPCR) has become the gold standard technique to measure cDNA and gDNA levels but the resulting data can be highly variable, artifactual and non-reproducible without appropriate verification and validation of both samples and primers. The root cause of poor quality data is typically associated with inadequate dilution of residual protein and chemical contaminants that variably inhibit Taq polymerase and primer annealing. The most susceptible, frustrating and often most interesting samples are those containing low abundant targets with small expression differences of 2-fold or lower. Here, Droplet Digital PCR (ddPCR) and qPCR platforms were directly compared for gene expression analysis using low amounts of purified, synthetic DNA in well characterized samples under identical reaction conditions. We conclude that for sample/target combinations with low levels of nucleic acids (Cq ≥ 29) and/or variable amounts of chemical and protein contaminants, ddPCR technology will produce more precise, reproducible and statistically significant results required for publication quality data. A stepwise methodology is also described to choose between these complimentary technologies to obtain the best results for any experiment.
Textured NiSe2 Film: Bifunctional Electrocatalyst for Full Water Splitting at Remarkably Low Overpotential with High Energy Efficiency
Authors: Swesi Abdurazag T. , Masud Jahangir , Liyanage Wipula P. R. , Umapathi Siddesh , Bohannan Eric , Medvedeva Julia , Nath Manashi
Published: May 2017

Herein we have shown that electrodeposited NiSe2 can be used as a bifunctional electrocatalyst under alkaline conditions to split water at very low potential by catalyzing both oxygen evolution and hydrogen evolution reactions at anode and cathode, respectively, achieving a very high electrolysis energy efficiency exceeding 80% at considerably high current densities (100 mA cm−2). The OER catalytic activity as well as electrolysis energy efficiency surpasses any previously reported OER electrocatalyst in alkaline medium and energy efficiency of an electrolyzer using state-of-the-art Pt and RuO2 as the HER and OER catalyst, respectively. Through detailed electrochemical and structural characterization, we have shown that the enhanced catalytic activity is attributed to directional growth of the electrodeposited film that exposes a Ni-rich lattice plane as the terminating plane, as well as increased covalency of the selenide lattice which decreases the Ni(II) to Ni(III) oxidation potential. Thereby, the high efficiency along with extended stability makes NiSe2 as the most efficient water electrolyzer known to-date.
Bioturbation as a key driver behind the dominance of Bacteria over Archaea in near-surface sediment
Authors: Chen Xihan , Andersen Thorbjørn Joest , Morono Yuki , Inagaki Fumio , Jørgensen Bo Barker , Lever Mark Alexander
Published: May 2017

The factors controlling the relative abundances of Archaea and Bacteria in marine sediments are poorly understood. We determined depth distributions of archaeal and bacterial 16S rRNA genes by quantitative PCR at eight stations in Aarhus Bay, Denmark. Bacterial outnumber archaeal genes 10–60-fold in uppermost sediments that are irrigated and mixed by macrofauna. This bioturbation is indicated by visual observations of sediment color and faunal tracks, by porewater profiles of dissolved inorganic carbon and sulfate, and by distributions of unsupported 210Pb and 137Cs. Below the depth of bioturbation, the relative abundances of archaeal genes increase, accounting for one third of 16S rRNA genes in the sulfate zone, and half of 16S rRNA genes in the sulfate-methane transition zone and methane zone. Phylogenetic analyses reveal a strong shift in bacterial and archaeal community structure from bioturbated sediments to underlying layers. Stable isotopic analyses on organic matter and porewater geochemical gradients suggest that macrofauna mediate bacterial dominance and affect microbial community structure in bioturbated sediment by introducing fresh organic matter and high-energy electron acceptors from overlying seawater. Below the zone of bioturbation, organic matter content and the presence of sulfate exert key influences on bacterial and archaeal abundances and overall microbial community structure.
A Bioactive Chemical Markers Based Strategy for Quality Assessment of Botanical Drugs: Xuesaitong Injection as a Case Study
Authors: Yang Zhenzhong , Shao Qing , Ge Zhiwei , Ai Ni , Zhao Xiaoping , Fan Xiaohui
Published: May 2017

Current chemical markers based quality assessment methods largely fail to reflect intrinsic chemical complexity and multiple mechanisms of action of botanical drugs (BD). The development of novel quality markers is greatly needed. Here we propose bioactive chemical markers (BCM), defined as a group of chemo-markers that exhibit similar pharmacological activities comparable to the whole BD, which can therefore be used to effectively assess the quality of BD. As a proof-of-concept, a BCM-based strategy was developed and applied to Xuesaitong Injection (XST) for assessing the efficacy and consistency of different batches. Firstly, systemic characterization of chemical profile of XST revealed a total number of 97 compounds. Secondly, notoginsenoside R1, ginsenoside Rg1, Re, Rb1 and Rd were identified as BCM of XST on treating cardiovascular and cerebrovascular diseases according to Adjusted Efficacy Score following an in vivo validation. Analytical method for quantification of BCM was then developed to ensure the efficacy of XST. Finally, chemical fingerprinting was developed and used to evaluate the batch-to-batch consistency. Our present case study on XST demonstrates that BCM-based strategy offers a rational approach for quality assessment of BD and provides a workflow for chemistry, manufacturing, and controls (CMC) study of BD required by regulatory authority.
Autocatalytic Time-Dependent Evolution of Metastable Two-Component Supramolecular Assemblies to Self-Sorted or Coassembled State
Authors: Fukui Tomoya , Takeuchi Masayuki , Sugiyasu Kazunori
Published: May 2017

Despite substantial effort devoted in the history of supramolecular chemistry, synthetic supramolecular systems still lag behind biomolecular systems in terms of complexity and functionality. This is because biomolecular systems function in a multicomponent molecular network under out-of-equilibrium conditions. Here we report two-component supramolecular assemblies that are metastable and thus show time-dependent evolution. We found that the systems undergo either self-sorting or coassembly in time depending on the combination of components. Interestingly, this outcome, which had been previously achievable only under specific conditions, emerged from the two-component systems as a result of synergistic or reciprocal interplay between the coupled equilibria. We believe that this study sheds light on the similarity between synthetic and biomolecular systems and promotes better understanding of their intricate kinetic behaviors.
Classification of Paediatric Inflammatory Bowel Disease using Machine Learning
Authors: Mossotto E. , Ashton J. J. , Coelho T. , Beattie R. M. , MacArthur B. D. , Ennis S.
Published: May 2017

Paediatric inflammatory bowel disease (PIBD), comprising Crohn’s disease (CD), ulcerative colitis (UC) and inflammatory bowel disease unclassified (IBDU) is a complex and multifactorial condition with increasing incidence. An accurate diagnosis of PIBD is necessary for a prompt and effective treatment. This study utilises machine learning (ML) to classify disease using endoscopic and histological data for 287 children diagnosed with PIBD. Data were used to develop, train, test and validate a ML model to classify disease subtype. Unsupervised models revealed overlap of CD/UC with broad clustering but no clear subtype delineation, whereas hierarchical clustering identified four novel subgroups characterised by differing colonic involvement. Three supervised ML models were developed utilising endoscopic data only, histological only and combined endoscopic/histological data yielding classification accuracy of 71.0%, 76.9% and 82.7% respectively. The optimal combined model was tested on a statistically independent cohort of 48 PIBD patients from the same clinic, accurately classifying 83.3% of patients. This study employs mathematical modelling of endoscopic and histological data to aid diagnostic accuracy. While unsupervised modelling categorises patients into four subgroups, supervised approaches confirm the need of both endoscopic and histological evidence for an accurate diagnosis. Overall, this paper provides a blueprint for ML use with clinical data.
Proximity Effect induced transport Properties between MBE grown (Bi1−xSbx)2Se3 Topological Insulators and Magnetic Insulator CoFe2O4
Authors: Huang Shun-Yu , Chong Cheong-Wei , Tung Yi , Chen Tzu-Chin , Wu Ki-Chi , Lee Min-Kai , Huang Jung-Chun-Andrew , Li Z. , Qiu H.
Published: May 2017

In this study, we investigate the proximity effect in topological insulator (TI) and magnetic insulator bilayer system. (Bi1−xSbx)2Se3/CoFe2O4 (CFO) heterostructure was fabricated using molecular beam epitaxy and pulsed laser deposition system respectively. As revealed from the magnetoresistance measurement, the weak anti-localization (WAL) is strongly suppressed by proximity effect in (Bi1−xSbx)2Se3/CFO interface. Modified Hikama-Larkin-Nagaoka equation was used to fit the WAL results so that the size of surface state gap can be extracted successfully. The temperature-dependent resistance of the heterostructures at small and large perpendicular magnetic fields were also measured and analyzed. The results indicate that the surface band gap can be induced in TI and continuously enlarged up to 9 T, indicating the gradual alignment of the magnetic moment in CFO under perpendicular magnetic field. The approaches and results accommodated in this work show that CFO can effectively magnetize (Bi1−xSbx)2Se3 and the heterostructures are promising for TI-based spintronic device applications.
Probing the Roles of Calcium-Binding Sites during the Folding of Human Peptidylarginine Deiminase 4
Authors: Liu Yi-Liang , Lee Chien-Yun , Huang Yu-Ni , Chen Hui-Yi , Liu Guang-Yaw , Hung Hui-Chih
Published: May 2017

Our recent studies of peptidylarginine deiminase 4 (PAD4) demonstrate that its non-catalytic Ca2+-binding sites play a crucial role in the assembly of the correct geometry of the enzyme. Here, we examined the folding mechanism of PAD4 and the role of Ca2+ ions in the folding pathway. Multiple mutations were introduced into the calcium-binding sites, and these mutants were termed the Ca1_site, Ca2_site, Ca3_site, Ca4_site and Ca5_site mutants. Our data indicate that during the unfolding process, the PAD4 dimer first dissociates into monomers, and the monomers then undergo a three-state denaturation process via an intermediate state formation. In addition, Ca2+ ions assist in stabilizing the folding intermediate, particularly through binding to the Ca3_site and Ca4_site to ensure the correct and active conformation of PAD4. The binding of calcium ions to the Ca1_site and Ca2_site is directly involved in the catalytic action of the enzyme. Finally, this study proposes a model for the folding of PAD4. The nascent polypeptide chains of PAD4 are first folded into monomeric intermediate states, then continue to fold into monomers, and ultimately assemble into a functional and dimeric PAD4 enzyme, and cellular Ca2+ ions may be the critical factor governing the interchange.
Elevated baseline potassium level within reference range is associated with worse clinical outcomes in hospitalised patients
Authors: Park Sehoon , Baek Seon Ha , Lee Sung Woo , Lee Anna , Chin Ho Jun , Na Ki Young , Kim Yon Su , Chae Dong-Wan , Han Jin Suk , Kim Sejoong
Published: May 2017

The clinical significance of elevated baseline serum potassium (K+) levels in hospitalised patients is rarely described. Hence, we performed a retrospective study assessing the significance of elevated K+ levels in a one-year admission cohort. Adult patients without hypokalaemia or end-stage renal disease were included. Adverse outcomes were all-cause mortality, hospital-acquired acute kidney injury, and events of arrhythmia. In total, 17,777 patients were included in the study cohort, and a significant difference (P < 0.001) was observed in mortality according to baseline serum K+ levels. The adjusted hazard ratios (HRs) and associated 95% confidence intervals (CIs) of all-cause mortality for K+ levels above the reference range of 3.6–4.0 mmol/L were as follows: 4.1–4.5 mmol/L, adjusted HR 1.075 (95% CI 0.981–1.180); 4.6–5.0 mmol/L, adjusted HR 1.261 (1.105–1.439); 5.1–5.5 mmol/L, adjusted HR 1.310 (1.009–1.700); >5.5 mmol/L, adjusted HR 2.119 (1.532–2.930). Moreover, the risks of in-hospital acute kidney injury and arrhythmia were higher in patients with serum K+ levels above 4.0 mmol/L and 5.5 mmol/L, respectively. In conclusion, increased serum K+ levels, including mild elevations may be related to worse prognosis. Close monitoring and prompt correction of underlying causes or hyperkalaemia itself is warranted for admitted patients.
Potential decline in carbon carrying capacity under projected climate-wildfire interactions in the Sierra Nevada
Authors: Liang Shuang , Hurteau Matthew D. , Westerling Anthony LeRoy
Published: May 2017

Ecosystem carbon carrying capacity (CCC) is determined by prevailing climate and natural disturbance regimes, conditions that are projected to change significantly. The interaction of changing climate and its effects on disturbance regimes is expected to affect forest regeneration and growth, which may diminish forest carbon (C) stocks and uptake. We modeled landscape C dynamics over 590 years along the latitudinal gradient of the U.S. Sierra Nevada Mountains under climate and area burned by large wildfires projected by late 21stcentury. We assumed climate and wildfire stabilize at late-21stcentury conditions (2090–2100) to facilitate analysis of lags between warming and changing CCC. We show that compared with historical (1980–2010) climate and wildfire conditions, projected scenarios would drive a significant decrease of up to 73% in mean total ecosystem carbon (TEC) by the end of the 590-year simulation. Tree regeneration failure due to intensified growing season dryness and increased area burned would substantially decrease forested area, transitioning the system from C sink to source. Our results demonstrate the potential for a lower CCC in the system due to extensive vegetation type conversion from forest to non-forest types, and suggest a decline in the contribution of Sierra Nevada forests to U.S. C sink.
Local cryotherapy minimally impacts the metabolome and transcriptome of human skeletal muscle
Authors: Sarver Dylan C. , Sugg Kristoffer B. , Disser Nathaniel P. , Enselman Elizabeth R. Sibilsky , Awan Tariq M. , Mendias Christopher L.
Published: May 2017

Cryotherapy is commonly used in the treatment of skeletal muscle injuries. However, the data to support the use of cryotherapy is inconclusive, and the biochemical etiology of cryotherapy in human skeletal muscle remains largely unknown. We therefore sought to determine how a clinically-relevant dose of cryotherapy would impact the transcriptome and metabolome of skeletal muscle. Eight healthy male subjects (age 24.7 ± 4.5 years, BMI 22.2 ± 1.6) received a 15 minute bout of local cryotherapy, delivered via ice cup massage over the anterolateral thigh. This resulted in an 85% decrease in skin temperature and a predicted 27% reduction in intramuscular temperature. The contralateral side served as a non-treated control. Two hours after cryotherapy, muscle biopsies were obtained to analyze changes in the transcriptome, metabolome, and activation of p38 MAPK, ERK1/2, Akt, and p70S6K proteins. No changes were detected in the transcriptome between control and cooled muscles. Cryotherapy reduced levels of hexose sugars and hypoxanthine by 1.3%, but no statistically different changes were observed in 60 additional metabolites. Overall, no differences in phosphorylated p38 MAPK, ERK1/2, Akt, and p70S6K were observed. A clinically relevant dose of cryotherapy produced negligible acute biochemical and molecular changes in the skeletal muscle of human subjects.
The study of complexation between dicationic surfactants and the DNA duplex using structural and spectroscopic methods
Authors: Andrzejewska W. , Wilkowska M. , Chrabąszczewska M. , Kozak M.
Published: May 2017

Dicationic (also known as gemini or dimeric) bis-alkylimidazolium surfactants belong to a group of non-viral transfection systems proposed for the successful introduction of different types of nucleic acids (i.e., siRNA, DNA oligomers, and plasmid DNA) into living cells.
N-Sulfonyl α-imino ester-derived chiral oxaziridines: catalytic asymmetric synthesis and application as a modular chiral organic oxidant
Authors: Tanaka Naoya , Tsutsumi Ryosuke , Uraguchi Daisuke , Ooi Takashi
Published: May 2017

A novel class of chiral N-sulfonyl oxaziridines is catalytically prepared and introduced for use as highly reactive and enantiospecific oxidants.
Fe2O3 nanoparticles anchored on 2D kaolinite with enhanced antibacterial activity
Authors: Long Mei , Zhang Yi , Shu Zhan , Tang Aidong , Ouyang Jing , Yang Huaming
Published: May 2017

Fe2O3 nanoparticles with different dispersion states on the surface of modified kaolinite were controlled for enhancing antibacterial activity.
Laser triggered phase transition in photothermal liquid crystals
Authors: Ciancone Mathieu , Camerel Franck
Published: May 2017

Laser irradiation allows rapid high temperature phase transition directly from room temperature in pure liquid crystalline materials built around photothermal cores with a high spatial control and responsivness.
MnOx-decorated carbonized porous silicon nanowire electrodes for high performance supercapacitors
Authors: Ortaboy Sinem , Alper John P. , Rossi Francesca , Bertoni Giovanni , Salviati Giancarlo , Carraro Carlo , Maboudian Roya
Published: May 2017

The highest energy and power densities ever reported in silicon-based pseudo-capacitor electrodes are obtained showing excellent electrochemical performances.