bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data
Authors: Sandmann Sarah , de Graaf Aniek O. , Karimi Mohsen , van der Reijden Bert A. , Hellström-Lindberg Eva , Jansen Joop H. , Dugas Martin
Published: February 2017

Valid variant calling results are crucial for the use of next-generation sequencing in clinical routine. However, there are numerous variant calling tools that usually differ in algorithms, filtering strategies, recommendations and thus, also in the output. We evaluated eight open-source tools regarding their ability to call single nucleotide variants and short indels with allelic frequencies as low as 1% in non-matched next-generation sequencing data: GATK HaplotypeCaller, Platypus, VarScan, LoFreq, FreeBayes, SNVer, SAMtools and VarDict. We analysed two real datasets from patients with myelodysplastic syndrome, covering 54 Illumina HiSeq samples and 111 Illumina NextSeq samples. Mutations were validated by re-sequencing on the same platform, on a different platform and expert based review. In addition we considered two simulated datasets with varying coverage and error profiles, covering 50 samples each. In all cases an identical target region consisting of 19 genes (42,322 bp) was analysed. Altogether, no tool succeeded in calling all mutations. High sensitivity was always accompanied by low precision. Influence of varying coverages- and background noise on variant calling was generally low. Taking everything into account, VarDict performed best. However, our results indicate that there is a need to improve reproducibility of the results in the context of multithreading.
Correction: Corrigendum: Evidence of Cnidarians sensitivity to sound after exposure to low frequency underwater sources
Authors: Solé Marta , Lenoir Marc , Fortuño José Manuel , Durfort Mercè , van der Schaar Mike , André Michel
Published: February 2017

Scientific Reports 6: Article number: 37979; published online: 21 December 2016; updated: 23 February 2017 The original version of this Article contained errors. The Title, “Evidence of Cnidarians sensitivity to sound after exposure to low frequency noise underwater sources” now reads: “Evidence of Cnidarians sensitivity to sound after exposure to low frequency underwater sources”
Evidence for risk extrapolation in decision making by tadpoles
Authors: Crane Adam L. , Ferrari Maud C. O.
Published: February 2017

Through time, the activity patterns, morphology, and development of both predators and prey change, which in turn alter the relative vulnerability of prey to their coexisting predators. Recognizing these changes can thus allow prey to make optimal decisions by projecting risk trends into the future. We used tadpoles (Lithobates sylvaticus) to test the hypothesis that tadpoles can extrapolate information about predation risk from past information. We exposed tadpoles to an odour that represented either a temporally consistent risk or an increasing risk. When tested for their response to the odour, the initial antipredator behaviour of tadpoles did not differ, appearing to approach the limit of their maximum response, but exposure to increasing risk induced longer retention of these responses. When repeating the experiment using lower risk levels, heightened responses occurred for tadpoles exposed to increasing risk, and the strongest responses were exhibited by those that received an abrupt increase compared to a steady increase. Our results indicate that tadpoles can assess risk trends through time and adjust their antipredator responses in a way consistent with an extrapolated trend. This is a sophisticated method for prey to avoid threats that are becoming more (or less) dangerous over part of their lifespan.
Silencing salusin-β attenuates cardiovascular remodeling and hypertension in spontaneously hypertensive rats
Authors: Ren Xing-Sheng , Ling Li , Zhou Bing , Han Ying , Zhou Ye-Bo , Chen Qi , Li Yue-Hua , Kang Yu-Ming , Zhu Guo-Qing
Published: February 2017

Salusin-β is a bioactive peptide involved in vascular smooth muscle cell proliferation, vascular fibrosis and hypertension. The present study was designed to determine the effects of silencing salusin-β on hypertension and cardiovascular remodeling in spontaneously hypertensive rats (SHR). Thirteen-week-old male SHR and normotensive Wistar-Kyoto rats (WKY) were subjected to intravenous injection of PBS, adenoviral vectors encoding salusin-β shRNA (Ad-Sal-shRNA) or a scramble shRNA. Salusin-β levels in plasma, myocardium and mesenteric artery were increased in SHR. Silencing salusin-β had no significant effect on blood pressure in WKY, but reduced blood pressure in SHR. It reduced the ratio of left ventricle weight to body weight, cross-sectional areas of cardiocytes and perivascular fibrosis, and decreased the media thickness and the media/lumen ratio of arteries in SHR. Silencing salusin-β almost normalized plasma norepinephrine and angiotensin II levels in SHR. It prevented the upregulation of angiotensin II and AT1 receptors, and reduced the NAD(P)H oxidase activity and superoxide anion levels in myocardium and mesenteric artery of SHR. Knockdown of salusin-β attenuated cell proliferation and fibrosis in vascular smooth muscle cells from SHR. These results indicate that silencing salusin-β attenuates hypertension and cardiovascular remodeling in SHR.
Regulation of photosensitisation processes by an RNA aptamer
Authors: Thoa Tran Thi Thanh , Minagawa Noriko , Aigaki Toshiro , Ito Yoshihiro , Uzawa Takanori
Published: February 2017

One of the most powerful attributes of proteins is their ability to bind to and modulate the chemistry of cofactors and prosthetic groups. Here, we demonstrated the ability of an artificial nucleic acid (an aptamer) to similarly control the functionality of a non-biological element. Specifically, we selected an RNA aptamer that binds tris(bipyridine) ruthenium (II), Ru(bpy)32+, an inorganic complex that has attracted intense interest due to its photoredox chemistry, including its ability to split water by visible light. We found that a newly discovered aptamer strongly and enantioselectively binds Λ-Ru(bpy)32+ (Kd = 65 nM) and, in doing so, selectively suppresses deactivation via energy transfer, thereby elongating the lifetime of its photo-excited state by four-fold. The ability of the aptamer to enhance this important aspect of Ru(bpy)32+ chemistry illustrates a broader point concerning the potential power of combining in vitro-created biomolecules with non-biological reactants to perform enhanced chemical reactions.
An endoparasitoid wasp influences host DNA methylation
Authors: Kumar Sunil , Kim Yonggyun
Published: February 2017

Parasitism by endoparasitoid wasps changes the expression of various host genes, and alters host immune and developmental processes. However, it is not clearly understood how parasitism changes host gene expression in a whole genome scale. This study focused on an epigenetic control of Cotesia plutellae, an endoparasitoid wasp, against its host, Plutella xylostella. Two DNA methyltransferases (DNMT-1 and DNMT-2) are encoded in the genome of P. xylostella. In addition, methyl-binding domain proteins (MBDs) and DNA demethylation factor, ten-eleven translation protein (TET) are encoded. DNA methylation of P. xylostella genomic DNA was confirmed by restriction digestion with Gla I specific to 5-methylcytosine. DNA methylation intensity in parasitized (P) larvae was decreased compared to that in nonparasitized (NP) larvae, especially at late parasitic stage, at which expression levels of both DNMT-1 and DNMT-2 were also decreased. DNA demethylation of P. xylostella was confirmed in both NP and P larvae by restriction digestion with PvuRts1I recognizing 5-hydroxymethyl cytosine. Parasitism also suppressed expression levels of TET and MBDs. Treatment of 5-aza-2′-deoxycytidine (AZA) reduced DNA methylation intensity of NP larvae, causing suppression of hemocyte-spreading behavior and delay of immature development. RNA interference of DNMT-1 or DNMT-2 mimicked the adverse effects of AZA.
Relapsing-remitting multiple sclerosis patients display an altered lipoprotein profile with dysfunctional HDL
Authors: Jorissen Winde , Wouters Elien , Bogie Jeroen F. , Vanmierlo Tim , Noben Jean-Paul , Sviridov Denis , Hellings Niels , Somers Veerle , Valcke Roland , Vanwijmeersch Bart , Stinissen Piet , Mulder Monique T. , Remaley Alan T. , Hendriks Jerome J. A.
Published: February 2017

Lipoproteins modulate innate and adaptive immune responses. In the chronic inflammatory disease multiple sclerosis (MS), reports on lipoprotein level alterations are inconsistent and it is unclear whether lipoprotein function is affected. Using nuclear magnetic resonance (NMR) spectroscopy, we analysed the lipoprotein profile of relapsing-remitting (RR) MS patients, progressive MS patients and healthy controls (HC). We observed smaller LDL in RRMS patients compared to healthy controls and to progressive MS patients. Furthermore, low-BMI (BMI ≤ 23 kg/m2) RRMS patients show increased levels of small HDL (sHDL), accompanied by larger, triglyceride (TG)-rich VLDL, and a higher lipoprotein insulin resistance (LP-IR) index. These alterations coincide with a reduced serum capacity to accept cholesterol via ATP-binding cassette (ABC) transporter G1, an impaired ability of HDL3to suppress inflammatory activity of human monocytes, and modifications of HDL3’s main protein component ApoA-I. In summary, lipoprotein levels and function are altered in RRMS patients, especially in low-BMI patients, which may contribute to disease progression in these patients.
Ultrafast electron and hole transfer dynamics of a solar cell dye containing hole acceptors on mesoporous TiO2 and Al2O3
Authors: Scholz Mirko , Flender Oliver , Boschloo Gerrit , Oum Kawon , Lenzer Thomas
Published: February 2017

The solar cell dye E6 with built-in hole acceptors efficiently separates charges after photoexcitation.
Colloidal capsules: nano- and microcapsules with colloidal particle shells
Authors: Bollhorst Tobias , Rezwan Kurosch , Maas Michael
Published: February 2017

This review provides a comprehensive overview of the synthesis strategies and the progress made so far of bringing colloidal capsules closer to technical and biomedical applications.
Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data
Authors: Latino Diogo A. R. S. , Wicker Jörg , Gütlein Martin , Schmid Emanuel , Kramer Stefan , Fenner Kathrin
Published: February 2017

Eawag-Soil offers an extensive collection of data on pesticide soil degradation pathways and half-lives for diverse uses, including QSBR development.
Nanotechnology for sustainable food production: promising opportunities and scientific challenges
Authors: Rodrigues Sónia M. , Demokritou Philip , Dokoozlian Nick , Hendren Christine Ogilvie , Karn Barbara , Mauter Meagan S. , Sadik Omowunmi A. , Safarpour Maximilian , Unrine Jason M. , Viers Josh , Welle Paul , White Jason C. , Wiesner Mark R. , Lowry Gregory V.
Published: February 2017

Unique properties of nanomaterials can be leveraged to increase the sustainability of food production and distribution.
Catalyst accessibility to chemical reductants in metal–organic frameworks
Authors: Roy Souvik , Pascanu Vlad , Pullen Sonja , González Miera Greco , Martín-Matute Belén , Ott Sascha
Published: February 2017

This study of catalyst accessibility inside metal–organic frameworks demonstrates that pore dimensions, catalyst loadings, concentration of reductant, and reaction times all influence the proportion of catalysts within MOFs that engage in redox chemistry.
Metal-free nitroxyl radical-mediated β-C(sp3)–H amination of saturated ketones with heteroaryl halides: multiple roles of TEMPO
Authors: Qian Ping , Deng Yu , Mei Haibo , Han Jianlin , Pan Yi
Published: February 2017

The first metal-free nitroxyl-radical-mediated β-amination of saturated ketones by using heteroaryl halides as amide precursors has been developed.
Robust high-connected rare-earth MOFs as efficient heterogeneous catalysts for CO2conversion
Authors: Wei Na , Zuo Rong-Xia , Zhang Yu-Yang , Han Zheng-Bo , Gu Xue-Jun
Published: February 2017

Two series of chemically and thermally stable rare-earth MOFs with a 12-connected hcp topology exhibit high catalytic activity towards the cycloaddition of CO2and epoxides under mild conditions.
A thermoregulated phase-separable chiral Pt nanocatalyst for recyclable asymmetric hydrogenation of α-ketoesters
Authors: Xue Xiuru , Wang Yanhua , Han Fu-She
Published: February 2017

Asymmetric hydrogenation of α-ketoesters catalyzed by a recyclable chiral Pt nanocatalyst system possessing thermoregulated phase-separation property is presented.
Structure–property–activity relationships in a pyridine containing azine-linked covalent organic framework for photocatalytic hydrogen evolution
Authors: Haase Frederik , Banerjee Tanmay , Savasci Gökcen , Ochsenfeld Christian , Lotsch Bettina V.
Published: February 2017

Organic solids such as covalent organic frameworks (COFs), porous polymers and carbon nitrides have garnered attention as a new generation of photocatalysts that offer tunability of their optoelectronic properties both at the molecular level and at the nanoscale. Owing to their inherent porosity and well-ordered nanoscale architectures, COFs are an especially attractive platform for the rational design of new photocatalysts for light-induced hydrogen evolution. In this report, our previous design strategy of altering the nitrogen content in an azine-linked COF platform to tune photocatalytic hydrogen evolution is extended to a pyridine-based photocatalytically active framework, where nitrogen substitution in the peripheral aryl rings reverses the polarity compared to the previously studied materials. We demonstrate how simple changes at the molecular level translate into significant differences in atomic-scale structure, nanoscale morphology and optoelectronic properties, which greatly affect the photocatalytic hydrogen evolution efficiency. In an effort to understand the complex interplay of such factors, we carve out the conformational flexibility of the PTP-COF precursor and the vertical radical anion stabilization energy as important descriptors to understand the performance of the COF photocatalysts.
Correction: Mapping metabolites from rough terrain: laser ablation electrospray ionization on non-flat samples
Authors: Bartels Benjamin , Kulkarni Purva , Danz Norbert , Böcker Sebastian , Saluz Hans Peter , Svatoš Aleš
Published: February 2017

Correction for ‘Mapping metabolites from rough terrain: laser ablation electrospray ionization on non-flat samples’ by Benjamin Bartels et al., RSC Adv., 2017, 7, 9045–9050.
Hybrid energy storage of battery-type nickel hydroxide and supercapacitor-type graphene: redox additive and charge storage mechanism
Authors: Sirisinudomkit Pichamon , Iamprasertkun Pawin , Krittayavathananon Atiweena , Pettong Tanut , Dittanet Peerapan , Kidkhunthod Pinit , Sawangphruk Montree
Published: February 2017

Charge storage mechanism byin situX-ray absorption spectroscopy.
Evaluation of flow schemes for near-neutral pH electrolytes in solar-fuel generators
Authors: Singh Meenesh R. , Xiang Chengxiang , Lewis Nathan S.
Published: February 2017

Operating conditions and design principles for the efficient operation of solar-fuel generators with active flow of near-neutral pH electrolytes.
Possibilités et limites du traitement de la dysharmonie dents-arcades par chirurgie maxillo-faciale
Authors: Paulus Christian
Published: February 2017

Introduction : La dysharmonie dents-arcades autrefois appelée « dysharmonie dento-maxillaire » ou « macrodontie/microdontie relative » correspond à une disproportion de volume entre les dents et les bases osseuses. En présence d’un volume dentaire trop important par rapport à la longueur d’arcade, un traitement avec extraction peut être proposé. Les techniques de « distraction osseuse » mises au point par Ilizarov dans les années 1950 permettent actuellement d’augmenter la longueur d’arcade au maxillaire et à la mandibule. Matériels et méthodes : Les auteurs décriront la mise en œuvre orthodontico-chirurgicale de cette augmentation de longueur d’arcade depuis l’établissement du plan thérapeutique jusqu’à l’obtention d’une longueur d’arcade suffisante ainsi que l’intérêt thérapeutique devant l’encombrement dentaire, la vestibuloversion et les troubles des fonctions orofaciales. Discussion : La distraction est un moyen thérapeutique intéressant à envisager dans la prise en charge de la dysharmonie dents-arcades, qui permet de gagner la longueur d’arcade nécessaire à l’objectif thérapeutique fixé.
Prise en compte de la forme des dents dans un contexte d’hyperdivergence faciale
Authors: Sorel Olivier , Naaim Mohamed , Chataigner Pierre-Alexandre , Brézulier Damien , Bertaud Valérie
Published: February 2017

Introduction : Le sujet de cette étude est la prise en compte de la forme des dents dans le contexte de l’hyperdivergence faciale. Nous avons voulu vérifier l’idée communément acceptée que le patient hyperdivergent a des dents longues. Discussion : Notre étude n’établit pas de lien entre la forme des dents et l’hyperdivergence faciale confirmant ainsi les données de la littérature. Nous nous sommes posé la question de la caractérisation des formes dentaires. Nous retrouvons trois types de formes : rectangulaire, triangulaire et ovoïde. Ces formes sont diversement appréciées. Une prise en charge individualisée de l’harmonie des formes des dents permet d’envisager leur remodelage par réduction amélaire proximale. Les conditions anatomiques de ce remodelage privilégient les formes ovoïdes et triangulaires qui sont moins appréciées et qui, après réduction, tendent vers la forme rectangulaire qui est la plus appréciée. Matériels et méthodes : Nous avons établi sur la base d’un tableur un outil de calcul qui permet le diagnostic quantitatif dimensionnel ainsi qu’une approche qualitative des formes par le dessin. Cette démarche permet d’appréhender les zones à remanier et de prévisualiser les objectifs de traitement. L’aboutissement est la création de l’harmonie tant sur le plan des formes, des proportions et des positions que sur le plan fonctionnel et parodontal.
Synthesis of Optically Active Oxazolines by an Organocatalytic Isocyanoacetate Aldol Reaction with α-Keto Esters
Authors: Chen Jiean , Huang Yong , Wang Fei
Published: February 2017

An enantioselective [3+2] cyclization is reported for the construction of a chiral oxazoline skeleton in moderate yield and up to 97% ee. The reactivity and stereochemical discrimination originate from the noncovalent interaction and orientation of a bifunctional catalyst. The novel combination of an α-keto ester and an α-isocyanoacetate establishes an oxazoline which could be a potential chiral ligand for metal-mediated catalysis, and also could be easily converted into an optically active β-hydroxy-α-amino acid.
Observational Case Series Evaluation of the Granisetron Transdermal Patch System (Sancuso) for the Management of Nausea/Vomiting of Pregnancy
Authors: Le Tran , Adler Michael , Ouillette Holly , Berens Pamela , Smith Judith
Published: February 2017

Objective The objective of this study was to observe the efficacy of antiemetic therapy (no emesis/retching episodes and no rescue medication use) when granisetron is administered via a transdermal patch system (TDS) in women who are 6 to 14 weeks pregnant when compared with oral ondansetron by evaluating the frequency of the use of rescue medications for control of nausea/vomiting of pregnancy (NVP).

Methods This was an observational case series study to observe the potential benefits of granisetron TDS compared with oral ondansetron for management of NVP in pregnant patients during the first trimester. Dates of data collection were September 1, 2014, through December 31, 2015. There was no direct contact with patient. The oral ondansetron and granisetron TDS patients were matched by age, 4:1. The proportion of patients who received rescue antiemetics was calculated from those patients who continued to experience NVP. Risk factors for NVP were identified and compared between groups. Descriptive statistics were used to describe study results.

Results Patients were prescribed rescue antiemetics in 0/3 patients in the granisetron TDS group compared with 2/12 patients in the oral ondansetron group.

Conclusion Prospective efficacy studies on the use of granisetron TDS for management of NVP are needed to confirm this clinical observation.
Aspekte beruflicher und sozialer Wiedereingliederung aus Sicht kardiovaskulär erkrankter Rehabilitanden in besonderen beruflichen Problemlagen – Ergebnisse einer qualitativen Erhebung
Authors: Schulz-Behrendt C. , Salzwedel A. , Rabe S. , Ortmann K. , Völler H.
Published: February 2017

Untersucht wurden subjektive bio-psycho-soziale Auswirkungen chronischer Herz- und Gefäßerkrankungen, Bewältigungsstrategien und Formen sozialer Unterstützung bei Rehabilitanden in besonderen beruflichen Problemlagen (BBPL).

Für die qualitative Untersuchung wurden 17 Patienten (48,9±7,0 Jahre, 13 männl.) mit BBPL (SIMBO-C>30) in leitfadengestützten Interviews befragt. Die Auswertung erfolgte softwaregestützt nach dem inhaltsanalytischen Ansatz von Mayring.

Im Rahmen der Krankheitsauswirkungen benannten die Patienten soziale, einschließlich beruflicher Aspekte mit 62% der Aussagen deutlich häufiger als physische oder psychische Faktoren (9 bzw. 29%). Angewandte Bewältigungsstrategien und erfahrene Unterstützungsleistungen richteten sich jedoch überwiegend auf körperliche Einschränkungen (70 bzw. 45%).

Obgleich soziale Krankheitsauswirkungen für die befragten Rehabilitanden subjektiv bedeutsam waren, gelang die Entwicklung geeigneter Bewältigungsstrategien nur unzureichend.
Accumulation rate of bound states of dipoles generated by point charges in strained graphene
Authors: Dorsch Florian
Published: February 2017

We consider strained graphene, modelled by the two-dimensional massive Dirac operator, with potentials corresponding to charge distributions with vanishing total charge, non-vanishing dipole moment and finitely many point charges of subcritical coupling constants located in the graphene sheet. We show that the bound state energies accumulate exponentially fast at the edges of the spectral gap by determining the leading order of the accumulation rate.
Simulation of liquid jet atomization coupled with forced perturbation
Authors: Yang Xiaochuan , Turan Ali
Published: February 2017

In this paper, the physical coupling processes between atomization and forced perturbation are considered. The effect of perturbation frequency and amplitude has been numerically investigated via a tree-based adaptive algorithm incorporating a time-dependent incompressible two-phase Navier-Stokes solver to simulate the atomization process. An open source code Gerris is validated using theoretical, numerical, and experimental results to demonstrate the generic capability and accuracy regarding atomization both in the low- and high-speed regimes. For a low speed jet, the breakup length and droplet diameter are examined to study the effect on breakup behaviour. For the high speed case, the frequency response of the jet is essentially classified into three distinct regimes. The jet shows a strong response for the low frequency and a correspondingly weak response for the high frequency. Perturbation amplitude also affects the atomization significantly.
Effect of Si on DC arc plasma generation from Al-Cr and Al-Cr-Si cathodes used in oxygen
Authors: Zhirkov I. , Landälv L. , Göthelid E. , Ahlgren M. , Eklund P. , Rosen J.
Published: February 2017

Al2O3 alloyed with Cr is an important material for the tooling industry. It can be synthesized from an arc discharge using Al-Cr cathodes in an oxygen atmosphere. Due to formation of Al-rich oxide islands on the cathode surface, the arc process stability is highly sensitive to oxygen pressure. For improved stability, the use of Al0.70Cr0.25Si0.05 cathodes has previously been suggested, where Si may reduce island formation. Here, we have investigated the effect of Si by comparing plasma generation and thin film deposition from Al0.7Cr0.3 and Al0.7Cr0.25Si0.05 cathodes. Plasma ion composition, ion energies, ion charge states, neutral species, droplet formation, and film composition have been characterized at different O2 flow rates for arc currents of 60 and 90 A. Si and related compounds are detected in plasma ions and in plasma neutrals. Scanning electron microscopy and energy dispersive X-ray analysis show that the cathode composition and the film composition are the same, with Si present in droplets as well. The effect of Si on the process stability, ion energies, and ion charge states is found to be negligible compared to that of the arc current. The latter is identified as the most relevant parameter for tuning the properties of the reactive discharge. The present work increases the fundamental understanding of plasma generation in a reactive atmosphere, and provides input for the choice of cathode composition and process parameters in reactive DC arc synthesis.
Genetic relations and indirect response to selection based on indices for scrotal circumference, visual scores and weight gain in beef cattle
Authors: Boligon A. A. , Farias P. P. , Roso V. M. , Santana M. L. , Bignardi A. B. , Souza F. R. P.
Published: February 2017

Genetic improvement in beef cattle involves evaluation for fertility, growth, carcass and visual scores traits. In general, genetic and economic parameters of these traits are considered for selection index construction. The present study was conducted to establish the magnitude of genetic and phenotypic correlations between visual scores of conformation, precocity and muscling at weaning and at yearling, birth to weaning weight gain, weaning to yearling weight gain and yearling scrotal circumference, and between these traits with selection indices applied in this population. In addition, the expected gains were obtained in such traits by taking under consideration the adopted selection criteria based on indices. Positive and high genetic correlations were estimated between weaning traits (visual scores and weight gain), ranging from 0.70 ± 0.02 to 0.97 ± 0.01. In genetic terms, the same visual scores, but evaluated in two ages (weaning and yearling) showed positive and high associations, with values of 0.90 ± 0.01 (conformation), 0.88 ± 0.01 (precocity) and 0.84 ± 0.02 (muscling). Genetic associations between yearling visual scores with scrotal circumference and weaning to yearling weight gain ranging from 0.36 ± 0.02 to 0.53 ± 0.01. Using the weaning index, are expected genetic gains ranging from 0.26% to 0.70%/year of the phenotypic mean of each weaning trait. Using the yearling index, annual genetic gains estimated for weaning traits (ranging from 0.25% to 0.63% of the phenotypic mean of the trait) were lower than that obtained at yearling (ranging from 0.27% to 0.98% of the phenotypic mean of the trait). Selection for one of traits obtained at weaning should result, by correlated response, in gain for the others. Also, the choice of animals with higher breeding values for weaning visual scores, beyond anticipate the selection process, should lead to favourable changes in these traits at yearling. Selection for better body composition at yearling (higher scores) should provide increase in scrotal circumference and weight gain. The use of higher values of the indices should result in positively correlated response, but in different magnitudes for each trait used in these indices. However, in both weaning and yearling, higher genetic gains to visual scores are expected in the same period, when the selection is based on the values of these indices.
Optical detection of nanometric thermal fluctuations to measure the stiffness of rigid superparamagnetic microrods
Authors: Gerbal Fabien , Wang Yuan
Published: February 2017

Significance

Under the influence of thermal forces, microscopic rod-shaped objects immersed in a fluid exhibit fluctuations: They deform mechanically. The energy provided by the thermal forces being well known, the measure of these fluctuations provides a convenient means of probing the rigidity of many biological filaments (DNA, microtubules, etc.) or synthetic microrods such as carbon nanotubes. However, only relatively flexible items could be studied by this technique: If they are too rigid, the fluctuations are too small to be detected. We substantially improved the method and measured the rigidity of rods 1,000 times stiffer than in previous studies. The method could henceforth be applied to numerous harder microscopic objects.
Chirality-induced spin polarization places symmetry constraints on biomolecular interactions
Authors: Kumar Anup , Capua Eyal , Kesharwani Manoj K. , Martin Jan M. L. , Sitbon Einat , Waldeck David H. , Naaman Ron
Published: February 2017

Significance

Chiral molecules are the building blocks of life. Although artificially, it is difficult to separate two different enantiomers of the same molecules; in nature, this process is efficient. This work proposes a mechanism for understanding this efficiency. In many bioprocesses, the interactions between molecules result from electron reorganization in the molecules, like that which occurs when an external electric field is applied. We show that the charge reorganization in chiral molecules is accompanied by a polarization of the spins associated with the displaced charge. The symmetry constraints imposed by the spin polarization may help account for the enantioselectivity. Calculations indicate that this contribution to the interaction energy for two molecules of the same handedness can be comparable with the available thermal energy.
Recapitulation of physiological spatiotemporal signals promotes in vitro formation of phenotypically stable human articular cartilage
Authors: Ng Johnathan J. , Wei Yiyong , Zhou Bin , Bernhard Jonathan , Robinson Samuel , Burapachaisri Aonnicha , Guo X. Edward , Vunjak-Novakovic Gordana
Published: February 2017

Significance

Despite significant efforts, stable and organized human cartilage has not been grown from human mesenchymal stem cells in vitro. We report the formation of organized cartilage discs that resemble the articular cartilage from self-assembling human mesenchymal stem cells by implementing spatiotemporal regulation in vitro that mimics native development. Selective application of chondrogenic and hypertrophic induction regimens enabled the maintenance of functional hyaline cartilage and progressive deep-zone mineralization. We demonstrate that this simple biomimetic approach helped mature the cartilage discs and enabled them to remain stable and organized following implantation. These findings highlight the limitations of current isotropic culture, and could greatly accelerate the development of new therapeutic modalities for cartilage repair from a patient’s own cells.
Pedagogy, modernity and nationalism in the Caucasus in the age of reaction, 1880–1905
Authors: Blauvelt Timothy K. , Vacharadze Anton
Published: February 2017

The head of the Caucasus Educational District (CED), K.P. Yanovskiy, epitomized the liberal minded reformers in the Russian Empire who saw the reform of pedagogy – introducing modern sciences, languages, critical thinking and emphasis on the individual – as a means to bring modernity and civilization while respecting ethnic, linguistic and religious diversity. The CED became a sort of refuge for liberal reformers among educational administrators, beyond the grasp of conservative elements in St. Petersburg. Yet under their administration, language education policies for local nationalities in the Caucasus shifted from encouraging local languages to demanding instruction in Russian, and Yanovskiy and his colleagues in the CED came to be viewed in the narratives of nationalists as instruments of russification and assimilation. Using archival sources and other contemporary materials, this article examines the intersection of reform and nationalism in the question of language pedagogy in schools in the Caucasus at a time of state-directed centralization in the Russian Empire and seeks to understand the often complex motives behind the changes in policy and their unintended consequences.
The budding yeast Polo-like kinase localizes to distinct populations at centrosomes during mitosis
Authors: Botchkarev Vladimir V. , Garabedian Mikael V. , Lemos Brenda , Paulissen Eric , Haber James E.
Published: February 2017

The budding yeast Polo-like kinase Cdc5 is a key regulator of many mitotic events. Cdc5 coordinates its functions spatially and temporally by changing its localization during the cell cycle: Cdc5 is imported into the nucleus in G2 phase and released to the cytoplasm in anaphase, where it accumulates at the bud neck. Cdc5 also localizes to the spindle pole bodies (SPBs) from S phase until the end of mitosis. Whether Cdc5 changes its SPB population during the cell cycle is not known. We find that Cdc5 localizes to distinct SPB subpopulations, depending on the mitotic stage. Cdc5 localizes to the nuclear side of the SPBs during metaphase and early anaphase and to the cytoplasmic surface of the SPBs during late anaphase. Cdc14 is necessary to relocalize Cdc5 from the nuclear SPB plaque. Accumulation of Cdc5 at the daughter SPB in late anaphase is controlled by Bfa1. We also show that Cdc5 and Bfa1 are found in spatially distinct locations at the SPBs during G2/M arrest after DNA damage. Collectively our data reveal that Cdc5 is a dynamic component of the SPBs during mitosis and provide new insight into its regulation during both late mitotic events and DNA damage–induced G2/M arrest.
swga: a primer design toolkit for selective whole genome amplification
Authors: Clarke Erik L , Sundararaman Sesh A , Seifert Stephanie N , Bushman Frederic D , Hahn Beatrice H , Brisson Dustin
Published: February 2017

Motivation

Population genomic analyses are often hindered by difficulties in obtaining sufficient numbers of genomes for analysis by DNA sequencing. Selective whole-genome amplification (SWGA) provides an efficient approach to amplify microbial genomes from complex backgrounds for sequence acquisition. However, the process of designing sets of primers for this method has many degrees of freedom and would benefit from an automated process to evaluate the vast number of potential primer sets.

Results

Here, we present swga, a program that identifies primer sets for SWGA and evaluates them for efficiency and selectivity. We used swga to design and test primer sets for the selective amplification of Wolbachia pipientis genomic DNA from infected Drosophila melanogaster and Mycobacterium tuberculosis from human blood. We identify primer sets that successfully amplify each against their backgrounds and describe a general method for using swga for arbitrary targets. In addition, we describe characteristics of primer sets that correlate with successful amplification, and present guidelines for implementation of SWGA to detect new targets.

Availability and Implementation

Source code and documentation are freely available on https://www.github.com/eclarke/swga. The program is implemented in Python and C and licensed under the GNU Public License.

Supplementary information

Supplementary data are available at Bioinformatics online.
An analysis of patient-provider secure messaging at two Veterans Health Administration medical centers: message content and resolution through secure messaging
Authors: Shimada Stephanie L , Petrakis Beth Ann , Rothendler James A , Zirkle Maryan , Zhao Shibei , Feng Hua , Fix Gemmae M , Ozkaynak Mustafa , Martin Tracey , Johnson Sharon A , Tulu Bengisu , Gordon Howard S , Simon Steven R , Woods Susan S
Published: February 2017

Objective: We sought to understand how patients and primary care teams use secure messaging (SM) to communicate with one another by analyzing secure message threads from 2 Department of Veterans Affairs facilities.

Methods: We coded 1000 threads of SM communication sampled from 40 primary care teams.

Results: Most threads (94.5%) were initiated by patients (90.4%) or caregivers (4.1%); only 5.5% were initiated by primary care team members proactively reaching out to patients. Medication renewals and refills (47.2%), scheduling requests (17.6%), medication issues (12.9%), and health issues (12.7%) were the most common patient-initiated requests, followed by referrals (7.0%), administrative issues (6.5%), test results (5.4%), test issues (5.2%), informing messages (4.9%), comments about the patient portal or SM (4.1%), appreciation (3.9%), self-reported data (2.8%), life issues (1.5%), and complaints (1.5%). Very few messages were clinically urgent (0.7%) or contained other potentially challenging content. Message threads were mostly short (2.7 messages), comprising an average of 1.35 discrete content types. A substantial proportion of issues (24.2%) did not show any evidence of being resolved through SM. Time to response and extent of resolution via SM varied by message content. Proactive SM use by teams varied, but was most often for test results (32.7%), medication-related issues (21.8%), medication renewals (16.4%), or scheduling issues (18.2%).

Conclusions: The majority of messages were transactional and initiated by patients or caregivers. Not all content categories were fully addressed over SM. Further education and training for both patients and clinical teams could improve the quality and efficiency of SM communication.
Emergency Department Pain Management in Children With Appendicitis in a Biethnic Population
Authors: Jacob Ron , Krauss Baruch , Twito Gal , Leiba Ronit , Shavit Itai
Published: February 2017

Objectives:

Our goal was to examine factors associated with the administration of emergency department analgesia (any analgesia, opioid analgesia) in patients with acute appendicitis in a tertiary children’s hospital in Israel, and to examine ethnic differences.

Methods:

A retrospective cohort study of children evaluated in the emergency department, who had International Classification Of Disease—Ninth Revision (ICD-9) diagnosis of acute appendicitis. Regression analysis was used to test the effect of multiple variables on the provision of analgesia. Medications were administered according to a nurse-driven pain protocol. Multivariate regression was performed to estimate the strength of association between ethnicity and provision of analgesia. The effect of patient-nurse ethnicity concordance was assessed.

Results:

During the 6-year study period, there were 715 children with acute appendicitis, 457 Jews and 258 Arabs. Overall, 289 (40.4%) received some form of analgesia, and 139 (19.4%) received opioid analgesia. Univariate analysis revealed that higher pain score (P<0.001) and higher triage acuity (P<0.001) were associated with administration of any type of analgesia and of opioid analgesia. When adjusted for age, weight, sex, triage category, pain score, and 24-hour time of arrival, Jewish and Arab patients had similar likelihood of receiving analgesia of any type 41.8% (95% confidence interval [CI], 40.3%-43.3%) versus 40.7% (95% CI, 38.7%-42.8%), and receiving opioid analgesia 26.1% (95% CI, 24.4%-27.8%) versus 25.3% (95% CI, 22.9%-27.7%). Similar proportions of Jewish and Arab patients received analgesia from Jewish and Arab nurses.

Conclusions:

Low rates of analgesia and opioid administration were found with no ethnic differences.
Glenohumeral osteoarthritis and the young patient: current options for treatment
Authors: Dialectos Adam , Namdari Surena
Published: February 2017

Glenohumeral arthritis in young patients is a challenging clinical problem without a gold standard for either nonoperative or operative treatment. These patients often have high activity levels and high expectations, are employed, and have a long life expectancy. There are few studies that specifically examine treatment outcomes in young patients. While many treatment options can yield short-term success, eventual failures at mid-term and long-term follow-up are expected. Because of these factors, treatment decisions are particularly complex.
Low-Cost 3D Printing Orbital Implant Templates in Secondary Orbital Reconstructions
Authors: Callahan Alison B. , Campbell Ashley A. , Petris Carisa , Kazim Michael
Published: February 2017

Purpose:

Despite its increasing use in craniofacial reconstructions, three-dimensional (3D) printing of customized orbital implants has not been widely adopted. Limitations include the cost of 3D printers able to print in a biocompatible material suitable for implantation in the orbit and the breadth of available implant materials. The authors report the technique of low-cost 3D printing of orbital implant templates used in complex, often secondary, orbital reconstructions.

Methods:

A retrospective case series of 5 orbital reconstructions utilizing a technique of 3D printed orbital implant templates is presented. Each patient’s Digital Imaging and Communications in Medicine data were uploaded and processed to create 3D renderings upon which a customized implant was designed and sent electronically to printers open for student use at our affiliated institutions. The mock implants were sterilized and used intraoperatively as a stencil and mold. The final implant material was chosen by the surgeons based on the requirements of the case.

Results:

Five orbital reconstructions were performed with this technique: 3 tumor reconstructions and 2 orbital fractures. Four of the 5 cases were secondary reconstructions. Molded Medpor Titan (Stryker, Kalamazoo, MI) implants were used in 4 cases and titanium mesh in 1 case. The stenciled and molded implants were adjusted no more than 2 times before anchored in place (mean 1). No case underwent further revision.

Conclusions:

The technique and cases presented demonstrate 1) the feasibility and accessibility of low-cost, independent use of 3D printing technology to fashion patient-specific implants in orbital reconstructions, 2) the ability to apply this technology to the surgeon’s preference of any routinely implantable material, and 3) the utility of this technique in complex, secondary reconstructions.
Biologics for asthma and allergy
Authors: Walsh Garry M.
Published: February 2017

Purpose of review

The development of monoclonal antibody-based biologics targeted at inhibition of the Th2 cytokines interleukin-4, interleukin-5 and interleukin-13 represent potentially effective treatments for asthma and allergic diseases. This short review is based on English-language original articles in PubMed or MedLine that reported significant clinical findings on the evidence demonstrating the effectiveness or otherwise of the targeting of interleukin-4, interleukin-5 or interleukin-13 in asthma or allergic disease.

Recent findings

Asthma exhibits marked heterogeneity both clinically and at the molecular phenotypic level requiring specifically targeted treatments to block the key pathways of the disease. It is becoming apparent that significant clinical effects with anticytokine-based biologic therapies are more likely in carefully selected patient populations that take asthma phenotypes into account. Biologics aimed at interleukin-4/13, interleukin-5 or immunoglobulin E are potentially effective treatments for patients with difficult to treat allergic disease. The development of reproducible and straightforward discriminatory biomarkers may aid identification of those patients most likely to benefit from treatment with these expensive interventions.

Overall these biologics-based therapies are effective treatments for difficult to treat asthma and allergic disease with a safety profile comparable with placebo in the majority of published studies.
Detailed Follow‐up Study of Pediatric Orofacial Granulomatosis Patients
Authors: Haaramo Anu , Alapulli Heikki , Aine Liisa , Saarnisto Ulla , Tuokkola Jetta , Ruuska Tarja , Sipponen Taina , Pitkäranta Anne , Kolho Kaija‐Leena
Published: February 2017

Objectives:

Orofacial granulomatosis (OFG) is a chronic inflammatory condition affecting the orofacial area. Its connection to Crohn disease (CD) is debated. Our aim was to describe a cohort of pediatric patients with OFG in detail, study the long‐term behavior of OFG, and evaluate factors predicting CD in patients with OFG.

Methods:

We invited patients diagnosed with OFG at 2 university hospitals, Finland for a follow‐up appointment. Patients (n = 29) were examined by a dentist and an otorhinolaryngologist using a structural schema. Orofacial findings were also recorded using digital photographing. Patients filled in questionnaires about general health and special diets. Patients’ nutrition was evaluated from food records. The findings were compared between patients with OFG only and OFG with CD.

Results:

Patients with CD had more findings in the orofacial area (total score for orofacial findings median 11) compared to patients with OFG only (total score median 7.5). There was no statistically significant difference in the type of lesions between these groups, except the upper lip was more often affected in patients with CD (n = 11) than in patients with OFG only (n = 0). Most of the patients had normal otorhinolaryngological findings. All patients with elevated anti–Saccharomyces cerevisiae antibody A levels had CD (n = 6) and they presented with more orofacial findings (total score) than patients with normal levels of anti–S cerevisiae antibody A (P = 0.0311).

Conclusions:

Long‐term follow‐up of pediatric‐onset patients with OFG shows good prognosis. Patients with OFG do not seem to have otorhinolaryngological comorbidity. Anti–S cerevisiae antibody A may serve as a factor to indicate the possible presence of underlying CD in patients with OFG, but further studies are requested.
Suboptimal Prenatal Syphilis Testing Among Commercially Insured Women in the United States, 2013
Authors: Neblett Fanfair Robyn , Tao Guoyu , Owusu-Edusei Kwame , Gift Thomas L. , Bernstein Kyle T.
Published: February 2017

United States surveillance data demonstrate that congenital syphilis cases are increasing. We performed an analysis of commercially insured pregnant females using MarketSan to determine syphilis screening rates at different prenatal stages; 85% of pregnant women in this population had a syphilis test performed at least once during the prenatal period.
A Case of Postmortem Canine Depredation
Authors: Chute Dennis J. , Bready Robert J.
Published: February 2017

We report the case of postmortem animal depredation that produced initial confusion for investigators who responded to the scene. A decomposing elderly woman was found in her presumed home with bilateral upper extremity amputations and craniocerebral trauma. This raised suspicion of foul play. Subsequent investigations together with autopsy led the medical examiner to conclude that the cause of death was natural disease and that those injuries found on her body were produced by at least one of the dogs who shared the premises. We linked the canine culprit to the postmortem trauma and positively identified the remains by collecting material defecated by the animal and by using radiologic and dental comparison techniques.