bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and magnetic properties on the Fe-B-P-Cu-W nano-crystalline alloy system
Authors: Zhang Yan , Wang Yaocen , Makino Akihiro
Published: October 2017

In the present article, the structural and soft magnetic properties of Fe-B-P-Cu alloy system with W addition have been studied as well as the annealing configurations required for magnetic softness. It is found that the substitution of B by W deteriorates the soft magnetic properties after annealing. The reason of such impact with W addition may lie in the insufficient bonding strength between W and B so that the addition of W is not effective enough to suppress grain growth against the high concentration and high crystallization tendency of Fe during annealing. The addition of 4 at.% W is also found to reduce the saturation magnetization of the nano-crystalline alloy by 14%. It is also found that the addition of P in the Fe-based alloys could help reduce the coercivity upon annealing with high heating rate. The existence of P could also help slightly increase the overall saturation magnetization by enhancing the electron transfer away from Fe in the residual amorphous structure.
Study of magnetic properties of NiZnCu ferrite synthesized by Pechini method and solid-state reactions
Authors: Frajer Gaëlla , Salaün Mathieu , Delette Gérard , Chazal Hervé , Isnard Olivier
Published: October 2017

Ni-Zn-Cu ferrites are exhibiting excellent magnetic properties at large frequencies and are consequently produced as low-loss magnetic materials used for magnetic components in power electronics. Here we present an experimental study of (Ni0.31Zn0.49Cu0.20)0.979Co0.021Fe1.9-dO4 ferrites synthesized by the Pechini type sol-gel method. Their structural and magnetic properties are characterized and compared to the ones of reference ferrites synthesized by classical solid-state reactions. Optimized parameters for Pechini method allow obtaining comparable low magnetic core-losses for both synthesis methods. The cores obtained by this sol-gel method present higher static permeability and lower coercive field than the ones obtained by classical solid-state reactions. Results suggest that the microstructure of ferrites synthesized by Pechini method can be considered as a promising alternative route for the design of low-loss magnetic components.
Structural evolution and atomic dynamics in Ni–Nb metallic glasses: A molecular dynamics study
Authors: Xu T. D. , Wang X. D. , Zhang H. , Cao Q. P. , Zhang D. X. , Jiang J. Z.
Published: October 2017

The composition and temperature dependence of static and dynamic structures in NixNb1−x (x = 50–70 at. %) were systematically studied using molecular dynamics with a new-released semi-empirical embedded atom method potential by Mendelev. The calculated pair correlation functions and the structure factor match well with the experimental data, demonstrating the reliability of the potential within relatively wide composition and temperature ranges. The local atomic structures were then characterized by bond angle distributions and Voronoi tessellation methods, demonstrating that the icosahedral ⟨0,0,12,0⟩ is only a small fraction in the liquid state but increases significantly during cooling and becomes dominant at 300 K. The most abundant clusters are identified as ⟨0,0,12,0⟩ and distorted icosahedron ⟨0,2,8,2⟩. The large fraction of these two clusters hints that the relatively good glass forming ability is near the eutectic point. Unlike Cu–Zr alloys, both the self-diffusion coefficient and shear viscosity are insensitive to compositions upon cooling in Ni–Nb alloys. The breakdown of the Stokes-Einstein relation happens at around 1.6Tg (Tg: glass transition temperature). In the amorphous state, the solid and liquid-like atoms can be distinguished based on the Debye-Waller factor ⟨u2⟩. The insensitivity of the dynamic properties of Ni–Nb alloys to compositions may result from the relatively simple solidification process in the phase diagram, in which only one eutectic point exists in the studied composition range.
Amorphousness induced significant room temperature ferromagnetism of TiO2 thin films
Authors: Wu Chen , Ding Wenyang , Wang Fang , Lu Yunhao , Yan Mi
Published: October 2017

TiO2 films have been grown on Si(100) substrates via pulsed laser deposition. Amorphousness has been achieved for films <30 nm due to the large film-substrate lattice mismatch. With the increased film thickness, crystallization occurs and the amorphous TiO2 evolves into the anatase and rutile phases. Compared with the crystallized phases, the amorphous structure contains more oxygen vacancies (Vo) for large room temperature ferromagnetism. Significant magnetization (up to 180.4 emu/cc) has been achieved for the film in the complete amorphous state. Theoretical calculations indicate that the magnetic moments distribute around the Ti3+ ions induced by Vo in the amorphous structure.
Conditions for optimal efficiency of PCBM-based terahertz modulators
Authors: Yoo Hyung Keun , Lee Hanju , Lee Kiejin , Kang Chul , Kee Chul-Sik , Hwang In-Wook , Lee Joong Wook
Published: October 2017

We demonstrate the conditions for optimal modulation efficiency of active terahertz modulators based on phenyl-C61-butyric acid methyl ester (PCBM)-silicon hybrid structures. Highly efficient active control of the terahertz wave modulation was realized by controlling organic film thickness, annealing temperature, and laser excitation wavelength. Under the optimal conditions, the modulation efficiency reached nearly 100%. Charge distributions measured with a near-field scanning microwave microscanning technique corroborated the fact that the increase of photo-excited carriers due to the PCBM–silicon hybrid structure enables the enhancement of active modulation efficiency.
Quantization improves stabilization of dynamical systems with delayed feedback
Authors: Stepan Gabor , Milton John G. , Insperger Tamas
Published: October 2017

We show that an unstable scalar dynamical system with time-delayed feedback can be stabilized by quantizing the feedback. The discrete time model corresponds to a previously unrecognized case of the microchaotic map in which the fixed point is both locally and globally repelling. In the continuous-time model, stabilization by quantization is possible when the fixed point in the absence of feedback is an unstable node, and in the presence of feedback, it is an unstable focus (spiral). The results are illustrated with numerical simulation of the unstable Hayes equation. The solutions of the quantized Hayes equation take the form of oscillations in which the amplitude is a function of the size of the quantization step. If the quantization step is sufficiently small, the amplitude of the oscillations can be small enough to practically approximate the dynamics around a stable fixed point.
A new ant-eating spider genus Suffascar (Araneae:Zodariidae) endemic to Madagascar: a considerable extension of the dual femoral organ clade
Authors: Henrard Arnaud , Jocqué Rudy
Published: October 2017

The new zodariid genus Suffascar, gen. nov. is described from Madagascar. It is apparently endemic to the island, common and speciose. Twelve new species were discovered and are here described: Suffascar albolineatus, sp. nov., S. fianara, sp. nov., S. fisheri, sp. nov., S. fitzpatrickae, sp. nov., S. gigas, sp. nov., S. griswoldi, sp. nov., S. macromma, sp. nov., S. micromma, sp. nov., S. nonus, sp. nov., S. scutatus, sp. nov., S. sufficiens, sp. nov. and S. tofti, sp. nov. It is well known that Zodariidae with femoral organs are specialised consumers of ants or termites, although the exact role of these glands still remains obscure. Suffascar is part of the ‘dual femoral organ clade’ (DF), which also includes Asceua Thorell, 1887, Suffasia Jocqué, 1991, and Suffrica Henrard & Jocqué, 2015. Using a morphology-based phylogenetic analysis, we test whether zodariids sharing the dual femoral organ are part of the same group as the ‘single femoral organ clade’ (SF) or form a separate monophyletic group. It appears that SF and DF constitute clearly monophyletic entities with a sister-group relation. These groups may be considered as distinct subfamilies and, together, they may turn out to be sister to the Storeninae (which then could be re-established). An analysis that focuses on these questions is underway. http://zoobank.org/urn:lsid:zoobank.org:pub:281E1357-FAEE-4300-B1BB-F0D43E724E91
Simulated fire behaviour in young, postfire lodgepole pine forests
Authors: Nelson Kellen N. , Turner Monica G. , Romme William H. , Tinker Daniel B.
Published: October 2017

Early-seral forests are expanding throughout western North America as fire frequency and annual area burned increase, yet fire behaviour in young postfire forests is poorly understood. We simulated fire behaviour in 24-year-old lodgepole pine (Pinus contorta var. latifolia) stands in Yellowstone National Park, Wyoming, United States using operational models parameterised with empirical fuel characteristics, 50–99% fuel moisture conditions, and 1–60kmhr−1 open winds to address two questions: [1] How does fireline intensity, and crown fire initiation and spread vary among young, lodgepole pine stands? [2] What are the contributions of fuels, moisture and wind on fire behaviour? Sensitivity analysis indicated the greatest contributors to output variance were stand structure mediated wind attenuation, shrub fuel loads and 1000-h fuel moisture for fireline intensity; crown base height for crown fire initiation; and crown bulk density and 1-h fuel moisture for crown fire spread. Simulation results predicted crown fire (e.g. passive, conditional or active types) in over 90% of stands at 50th percentile moisture conditions and wind speeds greater than 3kmhr−1. We conclude that dense canopy characteristics heighten crown fire potential in young, postfire lodgepole pine forests even under less than extreme wind and fuel moisture conditions.
Identification of a tumor-promoter cholesterol metabolite in human breast cancers acting through the glucocorticoid receptor
Authors: Voisin Maud , de Medina Philippe , Mallinger Arnaud , Dalenc Florence , Huc-Claustre Emilie , Leignadier Julie , Serhan Nizar , Soules Régis , Ségala Grégory , Mougel Aurélie , Noguer Emmanuel , Mhamdi Loubna , Bacquié Elodie , Iuliano Luigi , Zerbinati Chiara , Lacroix-Triki Magali , Chaltiel Léonor , Filleron Thomas , Cavaillès Vincent , Al Saati Talal , Rochaix Philippe , Duprez-Paumier Raphaelle , Franchet Camille , Ligat Laetitia , Lopez Fréderic , Record Michel , Poirot Marc , Silvente-Poirot Sandrine
Published: October 2017

Significance

Cholesterol and its transformation into cholesterol-5,6-epoxides (5,6-EC) was long suspected as contributing to breast cancer (BC) pathogenesis, before it was found that 5,6-EC metabolism controls BC development and is deregulated in breast cancers. Herein, we studied in tumor cells and human samples how 5,6-EC metabolism deregulation promotes tumor progression. We have discovered a pathway in BCs producing an oncometabolite derived from 5,6-EC, through the action of the cortisol-inactivating enzyme, and identified the glucocorticoid receptor (GR) as the target mediating its proliferative effects. Inhibition of its production or GR significantly blocked its action on BC progression. Thus, targeting this oncometabolism and GR represents a new opportunity for therapeutic intervention in BCs and potentially other cancers presenting such deregulations.
Down-regulation of the Wnt/β-catenin signaling pathway by Cacnb4
Authors: Rima Mohamad , Daghsni Marwa , Lopez Anaïs , Fajloun Ziad , Lefrancois Lydie , Dunach Mireia , Mori Yasuo , Merle Philippe , Brusés Juan L. , De Waard Michel , Ronjat Michel
Published: October 2017

The β4 isoform of the β-subunits of voltage-gated calcium channel regulates cell proliferation and cell cycle progression. Herein we show that coexpression of the β4-subunit with actors of the canonical Wnt/β-catenin signaling pathway in a hepatoma cell line inhibits Wnt-responsive gene transcription and decreases cell division, in agreement with the role of the Wnt pathway in cell proliferation. β4-subunit–mediated inhibition of Wnt signaling is observed in the presence of LiCl, an inhibitor of glycogen synthase kinase (GSK3) that promotes β-catenin translocation to the nucleus. Expression of β4-subunit mutants that lost the ability to translocate to the nucleus has no effect on Wnt signaling, suggesting that β4-subunit inhibition of Wnt signaling occurs downstream from GSK3 and requires targeting of β4-subunit to the nucleus. β4-subunit coimmunoprecipitates with the TCF4 transcription factor and overexpression of TCF4 reverses the effect of β4-subunit on the Wnt pathway. We thus propose that the interaction of nuclear β4-subunit with TCF4 prevents β-catenin binding to TCF4 and leads to the inhibition of the Wnt-responsive gene transcription. Thereby, our results show that β4-subunit is a TCF4 repressor and therefore appears as an interesting candidate for the regulation of this pathway in neurons where β4-subunit is specifically expressed.
Local and Global Spatial Organization of Interaural Level Difference and Frequency Preferences in Auditory Cortex
Authors: Panniello Mariangela , King Andrew J , Dahmen Johannes C , Walker Kerry M M
Published: October 2017

Despite decades of microelectrode recordings, fundamental questions remain about how auditory cortex represents sound-source location. Here, we used in vivo 2-photon calcium imaging to measure the sensitivity of layer II/III neurons in mouse primary auditory cortex (A1) to interaural level differences (ILDs), the principal spatial cue in this species. Although most ILD-sensitive neurons preferred ILDs favoring the contralateral ear, neurons with either midline or ipsilateral preferences were also present. An opponent-channel decoder accurately classified ILDs using the difference in responses between populations of neurons that preferred contralateral-ear-greater and ipsilateral-ear-greater stimuli. We also examined the spatial organization of binaural tuning properties across the imaged neurons with unprecedented resolution. Neurons driven exclusively by contralateral ear stimuli or by binaural stimulation occasionally formed local clusters, but their binaural categories and ILD preferences were not spatially organized on a more global scale. In contrast, the sound frequency preferences of most neurons within local cortical regions fell within a restricted frequency range, and a tonotopic gradient was observed across the cortical surface of individual mice. These results indicate that the representation of ILDs in mouse A1 is comparable to that of most other mammalian species, and appears to lack systematic or consistent spatial order.
Generational comparisons (F1 versus F3) of vinclozolin induced epigenetic transgenerational inheritance of sperm differential DNA methylation regions (epimutations) using MeDIP-Seq
Authors: Beck Daniel , Sadler-Riggleman Ingrid , Skinner Michael K.
Published: October 2017

Environmentally induced epigenetic transgenerational inheritance of disease and phenotypic variation has been shown to involve DNA methylation alterations in the germline (e.g. sperm). These differential DNA methylation regions (DMRs) are termed epimutations and in part transmit the transgenerational phenotypes. The agricultural fungicide vinclozolin exposure of a gestating female rat has previously been shown to promote transgenerational disease and epimutations in F3 generation (great-grand-offspring) animals. The current study was designed to investigate the actions of direct fetal exposure on the F1 generation rat sperm DMRs compared to the F3 transgenerational sperm DMRs. A protocol involving methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing (Seq) was used in the current study. Bioinformatics analysis of the MeDIP-Seq data was developed and several different variations in the bioinformatic analysis were evaluated. Observations indicate needs to be considered. Interestingly, the F1 generation DMRs were found to be fewer in number and for the most part distinct from the F3 generation epimutations. Observations suggest the direct exposure induced F1 generation sperm DMRs appear to promote in subsequent generations alterations in the germ cell developmental programming that leads to the distinct epimutations in the F3 generation. This may help explain the differences in disease and phenotypes between the direct exposure F1 generation and transgenerational F3 generation. Observations demonstrate a distinction between the direct exposure versus transgenerational epigenetic programming induced by environmental exposures and provide insights into the molecular mechanisms involved in the epigenetic transgenerational inheritance phenomenon.
Bringing the Message Home: Can Writing to Offenders Influence Their Offending?†
Authors: Dawson Paul , Dangerfield Beth
Published: October 2017

The aim of this article was to explore the utility of ‘Nudge’ in a crime reduction context through the design of two letter variants focussing predominantly upon levels of personalization. The study adopted a quasi-experimental design (176 individuals versus 183 comparisons matched on key crime and demographic variables). The study outcomes focussed upon levels of offending, speed of offending, and location of offending—in the 6 months subsequent to receipt of letter. The results were mixed with no clear narrative: some individuals to receive a letter were slightly less likely to offend, others offended quicker, in some there appeared to be a potential delay in their offending and others offended further away from their home area. The results are discussed—in particular—on the wider appropriateness of the Nudge theory within such a complex context as reoffending alongside wider reflections around implementation and evidence-based learning.
Comparison of Extended Depth-of-Focus Prototype Contact Lenses With the 1-Day ACUVUE MOIST MULTIFOCAL After One Week of Wear
Authors: Sha Jennifer , Tilia Daniel , Kho Danny , Diec Jennie , Thomas Varghese , Bakaraju Ravi C.
Published: October 2017

Objectives:

To compare visual performance of extended depth-of-focus (EDOF) prototypes with a new, center-near, commercial, multifocal contact lens.

Methods:

Presbyopic participants (n=57) wore 1-Day ACUVUE MOIST MULTIFOCAL (1DAMM) and an EDOF prototype for one week in a double-masked, prospective, cross-over, randomized clinical trial. Manufacturers' guide was used to select the first pair of lens to be fit based on subjective distance refraction and near addition. After one week, high- and low-contrast visual acuities were measured at distance (6 m), intermediate (70 cm) and near (50 and 40 cm), and stereopsis at 40 cm. Subjective performance was assessed on a 1 to 10 numeric rating scale for vision clarity and lack of ghosting at distance, intermediate and near, vision stability, haloes at night time, overall vision satisfaction, and ocular comfort. Linear mixed models were used for analysis and the level of significance was set at 5%.

Results:

1DAMM was not significantly different from EDOF for high- or low-contrast visual acuity at any distance, or for stereopsis. Subjectively, EDOF was significantly better than 1DAMM for vision clarity at intermediate (P=0.033) and near (P<0.001), overall lack of ghosting (P=0.012), vision stability (P=0.004), and overall vision satisfaction (P=0.005). For all other subjective variables, there were no differences between EDOF and 1DAMM (P>0.05).

Conclusions:

EDOF prototype lenses offer improvements over the newly marketed 1DAMM lenses for several subjective variables.
Lid-Parallel Conjunctival Folds and Their Ability to Predict Dry Eye
Authors: Pult Heiko , Bandlitz Stefan
Published: October 2017

Purpose:

The observation of lid-parallel conjunctival folds (LIPCOF) is reported to be useful in dry eye diagnoses. Around 70% of the European clinicians use this test in a dry eye clinic. This study investigated the sensitivity and specificity of LIPCOF to predict dry eye.

Methods:

Ocular Surface Disease Index (OSDI) outcome, noninvasive break-up time (NIKBUT) using the Keratograph (Oculus, Wetzlar, Germany), and LIPCOF of 148 randomized selected patient reports (88 females; mean age=37.0±12.9 years) from 3 different sites were analyzed. Subjects were divided into dry eye and non-dry eye groups by OSDI only, named symptomatic dry eye (OSDI scores ≥15) and by a composite score (OSDI scores ≥15 and NIKBUTaverage of ≤9 sec).

Results:

Lid-parallel conjunctival folds (temporal, nasal, Sum [=temporal+nasal]) were significantly correlated to OSDI and to NIKBUTaverage (Spearman; r>−0.185, P<0.013). NIKBUTaverage (r=−0.322; P<0.001) was significantly correlated to OSDI scores. Based on the OSDI questionnaire, 37.2% of the subjects were symptomatic and 14.7% were positive for dry eye based on the composite score. Lid-parallel conjunctival folds were a significant discriminator between healthy and dry eye subjects (P≤0.001). The areas under the receiver operating characteristic curve for temporal LIPCOF, nasal LIPCOF, and LIPCOF Sum were 0.716, 0.737, and 0.771, respectively, for the symptomatic dry eye group and 0.771, 0.719, and 0.798, respectively, for the composite dry eye group.

Conclusions:

As LIPCOF demonstrated high predictive ability of dry eye; it appears to be a promising test in the diagnoses of dry eye.
Severe Phenotype of Keratitis–Ichthyosis–Deafness Syndrome With Presumed Ocular Surface Squamous Neoplasia
Authors: Serrano-Ahumada Ana Silvia , Cortes-González Vianney , González-Huerta Luz María , Cuevas Sergio , Aguilar-Lozano Luis , Villanueva-Mendoza Cristina
Published: October 2017

Purpose:

The aim of this study was to describe a case of severe keratitis–ichthyosis–deafness (KID) syndrome with ocular surface squamous neoplasia.

Methods:

The affected patient underwent complete ocular and systemic examinations. The molecular studies included polymerase chain reaction amplification and automated DNA sequencing of the complete gap junction beta-2 (GJB2) gene coding sequence.

Results:

A 30-year-old man presented with generalized erythro-hyperkeratosis and deafness and complaints of decreased visual acuity, tearing, and photophobia. Ophthalmic examination showed corneal erosion, vascularization, and a gray gelatinous lesion partially covering the right cornea, suggestive of squamous neoplasia. The clinical features were characteristic of KID syndrome. This diagnosis was confirmed with a DNA analysis showing the pathogenic variant p.D50N in the GJB2 gene. Presumed squamous neoplasia was treated with topical interferon α2b.

Conclusions:

KID syndrome is a very rare disease that has been reported with an incremental incidence of squamous cell carcinoma of the mucous membranes and skin (12%–15%). Here, we presented a case of severe systemic KID syndrome with ocular surface squamous neoplasia.
Epidemiology of Competition Injuries in Elite European Judo Athletes: A Prospective Cohort Study
Authors: Čierna Dušana , Štefanovský Miloš , Matejová Lenka , Lystad Reidar P.
Published: October 2017

Objective:

To determine the injury incidence rate (IIR) and injury pattern, and to identify risk factors for injury, among elite adult European judo athletes.

Design:

Prospective cohort study.

Setting:

The 2015 Under 23 European Judo Championships, Bratislava, Slovakia.

Participants:

All registered athletes (N = 295).

Independent Variables:

Sex, weight division, and fight outcome.

Main Outcome Measures:

Injury incidence rates were calculated per 1000 athlete-exposures (IIRAE) and per 1000 minutes of exposure (IIRME) with 95% confidence intervals (CI). Subgroups were compared by calculating the injury incidence rate ratio (RR) with a 95% CI.

Results:

The overall IIRAEand IIRMEwere 35.6 (95% CI, 22.8-53.0) and 10.9 (95% CI, 7.0-16.2), respectively. The most frequently injured anatomical region was the head/neck (41%), whereas the most common type of injury was contusion (33%). The risk of injury was almost 4 times greater for defeated athletes compared with winners [RRME3.80 (95% CI, 1.47-9.82)]. Athletes in middleweight divisions had a greater risk of injury compared with their lightweight [RRME3.58 (95% CI, 1.24-10.35)] and heavyweight [RRME2.34 (95% CI, 0.93-5.89)] counterparts. The risk of injury for women was not significantly different from their male counterparts [RRME1.33 (95% CI, 0.61-2.90)].

Conclusions:

Weight division (middle) and fight outcome (losing) are significant risk factors for injury. The IIR in elite adult judo competition is lower than that in taekwondo and karate. Future research is encouraged to investigate the actual severity of judo injuries, and to investigate potentially modifiable risk factors to mitigate the risk of injury in judo.
Abatacept Monotherapy Versus Abatacept Plus Methotrexate for Treatment-Refractory Rheumatoid Arthritis
Authors: Pascart Tristan , Philippe Peggy , Drumez Elodie , Deprez Xavier , Cortet Bernard , Duhamel Alain , Houvenagel Eric , Flipo René-Marc
Published: October 2017

Background:

Methotrexate combination therapy improves abatacept efficacy as a first-line biologic agent for the treatment of rheumatoid arthritis, but it is unclear when abatacept is used later on, particularly after non–TNF inhibitor (TNFi) failure.

Study Question:

The objective of this study was to determine whether treatment response after non–TNFi inadequate response is different in patients with rheumatoid arthritis (RA) treated with abatacept in combination with or not with methotrexate.

Methods:

Patients treated with abatacept monotherapy or in combination with methotrexate after non–TNFi failure were included.

Results:

Data from 46 patients aged 56 years [49–61] with 12 years [8–16] of disease duration were examined. Rituximab was the treatment used in the previous line for 75.0% of the combination therapy group (15/20) and 34.6% (9/26) in the monotherapy group. At 12 months, 38.5% (10/26) of patients were in good-to-moderate EULAR response in the monotherapy group compared with 25.0% (5/20) in the combination therapy group (P = 0.33). Treatment persistence at 12 months was 61.5% (16/26) in the monotherapy group and 35.0% (7/20) in the combination therapy group (P = 0.07).

Conclusions:

Adding methotrexate to abatacept did not improve treatment response in patients with RA after non–TNFi inadequate response.
Procalcitonin and MR-Proadrenomedullin Combination with SOFA and qSOFA Scores for Sepsis Diagnosis and Prognosis: A Diagnostic Algorithm
Authors: Spoto Silvia , Cella Eleonora , de Cesaris Marina , Locorriere Luciana , Mazzaroppi Silvia , Nobile Edoardo , Lanotte Arcangela M. , Pedicino Lucia , Fogolari Marta , Costantino Sebastiano , Dicuonzo Giordano , Ciccozzi Massimo , Angeletti Silvia
Published: October 2017

Purpose:

The third Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) defined sepsis as an organ dysfunction consequent to infection. A Sequential Organ Failure Assessment (SOFA) score at least 2 identifies sepsis. In this study, procalcitonin (PCT) and midregional pro-adrenomedullin (MR-proADM) were evaluated along with SOFA and quick SOFA (qSOFA) scores in patients with sepsis or septic shock.

Methods:

A total of 109 septic patients and 50 patients with noninfectious disease admitted at the Department of Internal Medicine and General Surgery of the University Hospital Campus Bio-Medico of Rome were enrolled. PCT and MR-proADM were measured with immunoluminometric assays (Brahms, Hennigsdorf, Germany). Data were analyzed with receiver-operating characteristic (ROC) curve analysis, likelihood ratios, and Mann–Whitney U test using MedCalc 11.6.1.0 package.

Results:

At ROC curve analysis, PCT showed the highest area under the curve and positive likelihood ratio values of 27.42 in sepsis and 43.62 in septic shock. MR-proADM and SOFA score showed a comparable performance. In septic shock, lactate showed the most accurate diagnostic ability. In sepsis, the best combination was PCT with MR-proADM with a posttest probability of 0.988. Based upon these results, an algorithm for sepsis and septic shock diagnosis has been developed. MR-proADM, SOFA, and qSOFA scores significantly discriminated survivors from nonsurvivors.

Conclusions:

PCT and MR-proADM test combination represent a good tool in sepsis diagnosis and prognosis suggesting their inclusion in the diagnostic algorithm besides SOFA and qSOFA scores. Furthermore, MR-proADM as marker of organ dysfunction, with a turn around time of about 30 min, has the advantage to be more objective and rapid than SOFA score.
Insights Into the Therapeutic Effect of Responsive Neurostimulation Assessed With Scalp EEG Recording: A Case Report
Authors: Bruzzone Maria Jose , Issa Naoum , Rose Sandra , Warnke Peter , Towle Vernon L. , Tao James X. , Wu Shasha
Published: October 2017

The responsive neurostimulation system (RNS) is the first closed-loop neurostimulator approved as an adjunctive treatment for adults with medically refractory focal epilepsy from no more than two seizure foci. In addition to its therapeutic effect, it provides chronic intracranial EEG recordings, with limited storage capacity. Long-term monitoring with scalp EEG recordings can provide additional information regarding seizure patterns, the efficacy of RNS stimulation in aborting individual seizures, and the net effect of RNS on seizure control. We present a 34-year-old woman with medically intractable right temporoparietal lobe epilepsy who failed two resective epilepsy surgeries and MR-guided laser interstitial thermal therapy (MRgLITT), after which RNS was implanted. Long-term scalp EEG performed 16 months after implantation showed continuous right hemisphere slowing and right temporal sharp waves. In addition, RNS stimulation produced bursts of high-voltage, broad-field, surface-negative activity, which allowed correlation of RNS stimulation with scalp EEG patterns. Twenty-seven seizures were captured. Responsive neurostimulation system stimulation did not abort any of the seizures recorded on the scalp EEG. However, the frequency of seizures doubled after RNS stimulation was discontinued and returned to baseline once it was turned back on. This observation supports the neuromodulation effect of RNS.
Medical Error Avoidance in Intraoperative Neurophysiological Monitoring: The Communication Imperative
Authors: Skinner Stan , Holdefer Robert , McAuliffe John J. , Sala Francesco
Published: October 2017

Error avoidance in medicine follows similar rules that apply within the design and operation of other complex systems. The error-reduction concepts that best fit the conduct of testing during intraoperative neuromonitoring are forgiving design (reversibility of signal loss to avoid/prevent injury) and system redundancy (reduction of false reports by the multiplication of the error rate of tests independently assessing the same structure). However, error reduction in intraoperative neuromonitoring is complicated by the dichotomous roles (and biases) of the neurophysiologist (test recording and interpretation) and surgeon (intervention). This “interventional cascade” can be given as follows: test → interpretation → communication → intervention → outcome. Observational and controlled trials within operating rooms demonstrate that optimized communication, collaboration, and situational awareness result in fewer errors. Well-functioning operating room collaboration depends on familiarity and trust among colleagues. Checklists represent one method to initially enhance communication and avoid obvious errors. All intraoperative neuromonitoring supervisors should strive to use sufficient means to secure situational awareness and trusted communication/collaboration. Face-to-face audiovisual teleconnections may help repair deficiencies when a particular practice model disallows personal operating room availability. All supervising intraoperative neurophysiologists need to reject an insular or deferential or distant mindset.
Peer-Led Team Learning Improves Minority Student Retention in STEM Majors
Authors: Sloane Jeremy D. , Snyder Julia J. , Wiles Jason R.
Published: October 2017

The President’s Council of Advisors on Science and Technology issued a report in 2012 calling for a drastic increase in the number of STEM graduates produced in our country over the following decade if we are to remain economically competitive globally (PCAST, 2012). The report cited the disparity between the diversity among the general public versus that of the STEM professional community and recommended measures to ensure that the women and members of underrepresented racial groups, who together comprise 70% of college graduates but only 45% of college STEM graduates, would become better represented in those fields. This call for action echoed calls by the National Academy of Sciences to expand underrepresented minority participation in STEM at the college level (NAS, 2011). In the following study, we examined whether participation in the Peer-Led Team Learning (PLTL) model in introductory biology influenced the rates of recruitment into STEM and retention in STEM for underrepresented minority (URM) students and for non-URM students. Chi-square analyses reveal that there are significant gaps in STEM recruitment and retention rates between URM and non-URM students, but when these students participate in the PLTL model, no differences in STEM recruitment or retention rates were observed. Additionally, we found that STEM retention rates were significantly improved for URM students who engaged in PLTL.
An alignment method for nucleic acid sequences against annotated genomes
Authors: Deforche Koen
Published: October 2017

Motivation

Biological sequence alignment is fundamental to their further interpretation. Current alignment algorithms typically align either nucleic acid or amino acid sequences. Using only nucleic acid sequence similarity, divergent sequences cannot be aligned reliably because of the limited alphabet and genetic saturation. To align divergent coding nucleic acid sequences, one can align using the translated amino acid sequences. This requires the detection of the correct open reading frame, is prone to eventual frame shift errors, and typically requires the treatment of genes separately. It was our motivation to design a nucleic acid sequence alignment algorithm to align a nucleic acid sequence against a (reference) genome sequence, that works equally well for similar and divergent sequences, and produces an optimal alignment considering simultaneously the alignment of all annotated coding sequences.

Results

We define agenome alignment scorefor evaluating the quality of an alignment of a nucleic acid query sequence against a reference genome sequence, for which coding sequence features have been annotated (for example in a GenBank record). The genome alignment score combines the a ne gap score for the nucleic acid sequence with an a ne gap score for all amino acid alignments resulting from coding sequences in open reading frames contained within the query sequence. We present a Dynamic Programming algorithm to compute the optimal global or local alignment using this genomic alignment score and provide a formal proof of correctness. This algorithm allows the alignment of nucleic acid sequences from closely related and highly divergent sequences within the same software and using the same parameters, automatically correcting any eventual frame shift errors and produces at the same time the aligned translated amino acid sequences of all relevant coding sequence features.

Availability

The software is available as a web application athttp://www.genomedetective.com/app/agaand as command-line application athttps://github.com/emweb/aga
Pneumococcal phenotype and interaction with nontypeableHaemophilus influenzaeas determinants of otitis media progression
Authors: Lewnard Joseph A. , Givon-Lavi Noga , Tähtinen Paula A. , Dagan Ron
Published: October 2017

Background

All-cause otitis media (OM) incidence has declined in numerous settings following introduction of pneumococcal conjugate vaccines (PCVs) despite increases in carriage of non-vaccine pneumococcal serotypes escaping immune pressure. To understand the basis for declining incidence, we assessed the intrinsic capacity of pneumococcal serotypes to cause OM independently and in polymicrobial infections involving nontypeableHaemophilus influenzae(NTHi) using samples obtained from middle ear fluid and nasopharyngeal cultures before PCV7/13 rollout.

Methods

Data included OM episodes (11,811) submitted for cultures during a 10-year prospective study in southern Israel and nasopharyngeal samples (1588) from unvaccinated asymptomatic children in the same population. We compared pneumococcal serotype diversity across carriage and disease isolates with and without NTHi co-isolation. We also measured associations between pneumococcal phenotype and rate of progression from colonization to OM in the presence and absence of NTHi.

Results

Whereas pneumococcal serotype diversity in single-species OM is lower than in single-species colonization, serotype diversity does not differ significantly between colonization and OM in mixed-species episodes. Serotypes differed roughly 100-fold in progression rates, and these differences were attenuated in polymicrobial episodes. Vaccine-serotype pneumococci had higher rates of progression than non-vaccine serotypes. While serotype invasiveness was a weak predictor of OM progression rate, efficient capsular metabolic properties—traditionally thought to serve as an advantage in colonization—predicted an enhanced rate of progression to complex OM.

Conclusions

The lower capacity of non-vaccine serotypes to cause OM may partially account for reductions in all-cause OM incidence despite serotype replacement in carriage following rollout of PCVs.
Cnidarian cell type diversity revealed by whole-organism single-cell RNA-seq analysis
Authors: Sebé-Pedrós Arnau , Chomsky Elad , Saudememont Baptiste , Mailhe Marie-Pierre , Pleisser Flora , Renno Justine , Loe-Mie Yann , Lifshitz Aviezer , Mukamel Zohar , Schmutz Sandrine , Nouvault Sophie , Spitz Francois , Tanay Amos , Marlow Heather
Published: October 2017

A hallmark of animal evolution is the emergence and diversification of cell type-specific transcriptional states. But systematic and unbiased characterization of differentiated gene regulatory programs was so far limited to specific tissues in a few model species. Here, we perform whole-organism single cell transcriptomics to map cell types in the cnidarianNematostella vectensis, a non-bilaterian animal that display complex tissue-level bodyplan organization. We uncover high diversity of transcriptional states inNematostella, demonstrating cell type-specific expression for 35% of the genes and 51% of the transcription factors (TFs) detected. We identify eight broad cell clusters corresponding to cell classes such as neurons, muscles, cnidocytes, or digestive cells. These clusters comprise multiple cell modules expressing diverse and specific markers, uncovering in particular a rich repertoire of cells associated with neuronal markers. TF expression and sequence analysis defines the combinatorial code that underlies this cell-specific expression. It also reveals the existence of a complex regulatory lexicon of TF binding motifs encoded at both enhancer and promoters ofNematostellatissue-specific genes. Whole organism single cell RNA-seq is thereby established as a tool for comprehensive study of genome regulation and cell type evolution.
Transcriptomic Dynamics of a non-coding trinucleotide repeat expansion disorder SCA12 in iPSC derived neuronal cells: signatures of interferon induced response
Authors: Kumar Deepak , Dhapola Parashar , Hussain Ashaq , Kutum Rintu , Srivastava Achal K. , Mukerji Mitali , Mukherjee Odity , Faruq Mohammed
Published: October 2017

Spinocerebellar ataxia type-12 (SCA12) is a neurological disorder that exhibits a unique progressive tremor/ataxia syndrome induced by triplet (CAG) repeat expansion in 5’ UTR ofPPP2R2B. SCA12 is one of the most prominent SCA-subtype in India and till date no appropriate disease models have been described. Our aim was to establish human iPSC derived neuronal cell lines of SCA12 and study transcriptomic level alterations induced by CAG expansion. For translational application, peripheral blood transcriptomics of SCA12 patients was also performed. Lymphoblastoid cell lines of three SCA12 patients were reprogrammed to iPSCs and then re-differentiated into pan-neuronal lineage. RNA-sequencing based comparative transcriptomics was performed for disease and control cell lineages. Microarray based transcriptomic profiling of peripheral blood of SCA12 patients was performed in a case/control (n=15/9) design. We have successfully created human neuronal cell lines of SCA12 patient as exhibited by their molecular profiling. Differential expression analysis of RNA-Seq data has shown enrichment for type-I interferon signaling and other relevant cellular processes in SCA12-neurons. At the splice-isoform level, we observed an upregulation of expanded CAG containing non-coding transcript ofPPP2R2B. Peripheral blood transcriptomics analysis and targeted validation of RNA-Seq data has allowed us to identify inflammatory signatures as potential markers of molecular pathology in SCA12. Our study has allowed us to establish first iPSC based neuronal cell lines of SCA12. We have identified pro-inflammatory signatures in SCA12-neurons suggestive of a dsRNA mediated activation of interferon signaling and that corroborates with the emerging evidence of neuronal atrophy due to neuro-inflammation in common neurodegenerative diseases. This study involved development of an iPSCs derived neuronal cells of SCA12 and look through signatures of neurodegeneration by whole RNA sequencing. This model sheds light upon key role of RNA mediated induced response in Interferon signaling for neurodegeneration.
Identification and characterization ofGypsophila paniculatacolor morphs in Sleeping Bear Dunes National Lakeshore, MI, USA
Authors: Yang Marisa L. , Rice Emma , Leimbach-Maus Hailee , Partridge Charlyn G.
Published: October 2017

Background

Gypsophila paniculata(baby’s breath) is an invasive species found throughout much of the northwest United States and western Canada. Recently, plants exhibiting a different color morphology were identified within the coastal dunes along eastern Lake Michigan. The common baby’s breath (G. paniculata) typically produces stems that are purple in color (purple morph), while the atypical morph has stems that are green-yellow (green-yellow morph). The purpose of this study was to characterize these newly identified morphs and determine if they are genetically distinct species from the common baby’s breath in order to assess whether alternative management strategies should be employed to control these populations.

Methods

We sequenced two chloroplast regions, rbcL and matK, and one nuclear region, ITS2, from the purple morphs and green-yellow morphs collected from Sleeping Bear Dunes National Lakeshore, MI, USA (SBDNL). Sequences were aligned to the reference sequences from otherGypsophilaspecies obtained from the Barcode of Life (BOLD) and GenBank databases. We also collected seeds from wild purple morph and wild green-yellow morph plants in SBDNL. We grew the seeds in a common garden setting and characterized the proportion of green-yellow individuals produced from the two color morphs after five-months of growth.

Results

Phylogenetic analyses based upon rbcL, matK, and ITS2 regions suggest that the two color morphs are not distinct species and they both belong toG. paniculata. Seeds collected from wild green-yellow morphs produced a significantly higher proportion of green-yellow individuals compared to the number produced by seeds collected from wild purple morphs. However, seeds collected from both color morphs produced more purple morphs than green-yellow morphs.

Discussion

Based upon these results, we propose that the two color morphs are variants ofG. paniculata. Given the significant difference in the number of green-yellow morphs produced from the seeds of each morph type, we also suggest that this color difference has some genetic basis. We propose that current management continue to treat the two color morphs in a similar manner in terms of removal to prevent the further spread of this species.
Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities
Authors: Fan Yuhang , Xiao Yandong , Momeni Babak , Liu Yang-Yu
Published: October 2017

Horizontal gene transfer and species coexistence are two focal points in the study of microbial communities. The evolutionary advantage of horizontal gene transfer has not been well-understood and is constantly being debated. Here we propose a simple population dynamics model based on the frequency-dependent interactions between different genotypes to evaluate the influence of horizontal gene transfer on microbial communities. We find that both structural stability and robustness of the microbial community are strongly affected by the gene transfer rate and direction. An optimal gene flux can stablize the ecosystem, helping it recover from disturbance and maintain the species coexistence.
Parental allele-specific genome architecture and transcription during the cell cycle
Authors: Chen Haiming , Liu Sijia , Seaman Laura , Najarian Cyrus , Wu Weisheng , Ljungman Mats , Higgins Gerald , Hero Alfred , Wicha Max , Rajapakse Indika
Published: October 2017

A normal human somatic cell inherits two haploid genomes. Individual chromosomes of each pair have distinct parental origins and parental alleles are known to unequally contribute to cellular function. We integrated chromosome conformation (form) and gene transcription (function) analyses to dissect the dynamics of the maternal and paternal genomes in lymphoblastoid cells during the cell cycle. We found a distinct set of homologous alleles with very different activity often located close to boundaries of euchromatin and heterochromatin domains. We also identified a set of allele-biased topologically associating domains (TADs) that were small sized and had higher gene density. Thousands of genes show allelically biased expression (ABE) with false discovery rate < 0.05, and 98% of them have no allelic switching during G1, S, and G2/M phases. A subset of ABE genes are preferentially localized near TAD boundaries, enriched with chromatin organization transcription factor binding sites, and contained higher number of sequence variants in CCCTC-binding factor sites. Our results extend previous findings of sequence variation as a basis for unequal functional parental genomes. Investigation of haplotype-resolved form-function dynamics may further our understanding of phenotypic traits, genetic diseases, vulnerability to complex disorders, and the development of cancers.
Sexual lineage specific DNA methylation regulates Arabidopsis meiosis
Authors: Walker James , Gao Hongbo , Zhang Jingyi , Aldridge Billy , Vickers Martin , Higgins James D. , Feng Xiaoqi
Published: October 2017

DNA methylation controls eukaryotic gene expression and is extensively reprogrammed to regulate animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive, gene-targeted RNA-directed DNA methylation (RdDM) activity in theArabidopsis thalianamale sexual lineage that regulates gene expression in meiocytes. Loss of sexual lineage-specific RdDM causes mis-splicing of theMPS1/PRD2gene, thereby disrupting meiosis. Our results establish a regulatory paradigm in whichde novomethylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants.