bluuebunny/crossref_metadata_2025 huggingface dataset:
Nucleocytoplasmic Shuttling of Histone Deacetylase 9 Controls Activity-Dependent Thalamocortical Axon Branching
Authors: Alchini Ricardo , Sato Haruka , Matsumoto Naoyuki , Shimogori Tomomi , Sugo Noriyuki , Yamamoto Nobuhiko
Published: July 2017

During development, thalamocortical (TC) axons form branches in an activity-dependent fashion. Here we investigated how neuronal activity is converted to molecular signals, focusing on an epigenetic mechanism involving histone deacetylases (HDACs). Immunohistochemistry demonstrated that HDAC9 was translocated from the nucleus to the cytoplasm of thalamic cells during the first postnatal week in rats. In organotypic co-cultures of the thalamus and cortex, fluorescent protein-tagged HDAC9 also exhibited nuclueocytoplasmic translocation in thalamic cells during culturing, which was reversed by tetrodotoxin treatment. Transfection with a mutant HDAC9 that interferes with the translocation markedly decreased TC axon branching in the culture. Similarly, TC axon branching was significantly decreased by the mutant HDAC9 gene transfer in vivo. However, axonal branching was restored by disrupting the interaction between HDAC9 and myocyte-specific enhancer factor 2 (MEF2). Taken together, the present results demonstrate that the nucleocytoplasmic translocation of HDAC9 plays a critical role in activity-dependent TC axon branching by affecting transcriptional regulation and downstream signaling pathways.
Evaluating the effects of material properties of artificial meniscal implant in the human knee joint using finite element analysis
Authors: Shriram Duraisamy , Praveen Kumar Gideon , Cui Fangsen , Lee Yee Han Dave , Subburaj Karupppasamy
Published: July 2017

Artificial meniscal implants may replace severely injured meniscus and restore the normal functionality of the knee joint. Implant material stiffness and shape influence the longevity of implantations. This study, using 3D finite element analysis, aimed to evaluate the effects of material stiffness variations of anatomically shaped artificial meniscal implant in the knee joint. Finite element simulations were conducted on five different cases including intact knee, medial meniscectomized knee, and the knee joint with the meniscal implant with three distinct material stiffness. Cartilage contact pressures, compression stresses, shear stresses, and implant kinematics (medial-lateral and posterior-anterior displacement) were evaluated for an axial compressive load of 1150 N at full extension. Compared to the meniscectomized knee, the knee joint with the meniscal implant induced lower peak cartilage contact pressure and reduced the cartilage regions loaded with contact pressures greater than the peak cartilage contact pressure induced by the intact knee. Results of the current study also demonstrate that cartilage contact pressures and implant displacement are sensitive to the implant material stiffness. The meniscal implant with a stiffness of 11 MPa restores the intact knee contact mechanics, thereby reducing the risk of physiological damage to the articular cartilage.
Control of crystallization behaviour of supercooled liquid composed of lithium disilicate on platinum substrate
Authors: Tashiro Masanori , Sukenaga Sohei , Shibata Hiroyuki
Published: July 2017

Crystalline lithium disilicate (Li2Si2O5, LS2) materials, which have excellent mechanical properties with high transparency, should be obtained efficiently through the crystallization of supercooled liquid composed of LS2. However, in addition to LS2, a lithium monosilicate (Li2SiO3, LS) phase is also precipitated during the crystallization of the liquid. The precipitation of the LS phase renders it difficult to obtain a single-phase LS2 material. Here, we show that by altering the oxygen partial pressure, it is possible to change the selectivity of the precipitated phase by controlling the interfacial phenomena that occur between the liquid and platinum contact material. During cooling of the supercooled liquid, the type of precipitated phase can be controlled by optimizing the atmosphere and type of contact material. This methodology can be applied for the fabrication of other functional materials and does not require the use of other additives.
The relationship between folding and activity in UreG, an intrinsically disordered enzyme
Authors: Palombo Marta , Bonucci Alessio , Etienne Emilien , Ciurli Stefano , Uversky Vladimir N. , Guigliarelli Bruno , Belle Valérie , Mileo Elisabetta , Zambelli Barbara
Published: July 2017

A growing body of literature on intrinsically disordered proteins (IDPs) led scientists to rethink the structure-function paradigm of protein folding. Enzymes are often considered an exception to the rule of intrinsic disorder (ID), believed to require a unique structure for catalysis. However, recent studies revealed the presence of disorder in several functional native enzymes. In the present work, we address the importance of dynamics for catalysis, by investigating the relationship between folding and activity in Sporosarcina pasteurii UreG (SpUreG), a P-loop GTPase and the first discovered native ID enzyme, involved in the maturation of the nickel-containing urease. The effect of denaturants and osmolytes on protein structure and activity was analyzed using circular dichroism (CD), Site-Directed Spin Labeling (SDSL) coupled to EPR spectroscopy, and enzymatic assays. Our data show that SpUreG needs a “flexibility window” to be catalytically competent, with both too low and too high mobility being detrimental for its activity.
The Effect of Electrical Stimulation of the Calf Muscle on Leg Fluid Accumulation over a Long Period of Sitting
Authors: Vena Daniel , Rubianto Jonathan , Popovic Milos R. , Fernie Geoff R. , Yadollahi Azadeh
Published: July 2017

Leg fluid accumulation during sedentary behaviours such as sitting can lead to leg edema and associated adverse health consequences. This study investigates the use calf muscle electrical stimulation (ES) to reduce seated leg fluid accumulation. Thirteen non-obese, normotensive men (mean age 51 yr.) with sleep apnea were enrolled in the study. Participants first lay supine for 30 minutes to equalize fluid distribution and then sat for 150 minutes. While seated, participants received either active or sham ES of the calf muscles, according to random assignment. Participants returned one-week later to cross over to the other study condition. Leg fluid was measured continuously while sitting using the bioelectrical impedance method. Fluid accumulation in the leg was reduced by more than 40% using active ES, compared to sham ES (∆ = 51.9 ± 8.8 ml vs. ∆ = 91.5 ± 8.9 ml, P < 0.001). In summary, calf muscle ES is an effective method for reducing accumulation of fluid during long sedentary periods and has potential use as a device for preventing leg edema to treat associated health consequences in at-risk groups and settings.
An easy gene assembling strategy for light-promoted transfection by combining host-guest interaction of cucurbit[7]uril and gold nanoparticles
Authors: Du Jianwei , Zhang Peng , Zhao Xiao , Wang Youxiang
Published: July 2017

Cucurbit[7]uril (CB[7]), a representative member of the host family cucurbit[n]uril, can host-guest interact with many guest molecules such as adamantane, viologen and naphthalene derivatives. This host-guest interaction provides an easy strategy in gene vector assembling. Furthermore, CB[7] can self-assemble on gold nanospheres (AuNSs). Herein, the combination of CB[7] and AuNSs provides both advantages of host-guest interaction and photo-thermal effect of AuNSs. In this study, polyethyleneimine (PEI) and polyethylene glycol (PEG) were separately interacted with CB[7] via host-guest interaction. Then by assembling on AuNSs, PEI and PEG were combined together to condense DNA into polyplexes as well as enhance circulation stability of the polyplexes. These gene vectors were found to have high cellular uptake efficiency and low cytotoxicity. Furthermore, the well distributed AuNSs in the polyplexes could transform light into heat under light exposure because of the photo-thermal effect. This was found to effectively promote the entry of gene into cytoplasm and highly enhanced gene transfection efficiency.
New insights into the karyotype evolution of the free-living flatworm Macrostomum lignano (Platyhelminthes, Turbellaria)
Authors: Zadesenets Kira S. , Schärer Lukas , Rubtsov Nikolay B.
Published: July 2017

The free-living flatworm Macrostomum lignano is a model organism for evolutionary and developmental biology studies. Recently, an unusual karyotypic diversity was revealed in this species. Specifically, worms are either ‘normal’ 2n = 8, or they are aneuploid with one or two additional large chromosome(s) (i.e. 2n = 9 or 2n = 10, respectively). Aneuploid worms did not show visible behavioral or morphological abnormalities and were successful in reproduction. In this study, we generated microdissected DNA probes from chromosome 1 (further called MLI1), chromosome 2 (MLI2), and a pair of similar-sized smaller chromosomes (MLI3, MLI4). FISH using these probes revealed that MLI1 consists of contiguous regions homologous to MLI2-MLI4, suggesting that MLI1 arose due to the whole genome duplication and subsequent fusion of one full chromosome set into one large metacentric chromosome. Therefore, one presumably full haploid genome was packed into MLI1, leading to hidden tetraploidy in the M. lignano genome. The study of Macrostomum sp. 8 — a sibling species of M. lignano — revealed that it usually has one additional pair of large chromosomes (2n = 10) showing a high homology to MLI1, thus suggesting hidden hexaploidy in its genome. Possible evolutionary scenarios for the emergence of the M. lignano and Macrostomum sp. 8 genomes are discussed.
Research on a beef tenderness detection method using a bionic mastication system based on a pressure sensor
Authors: Wang Xiaodan , Wang Hongmei , Cai Yingming , Jin Jiahui , Zhu Lingtao , Xu Liping
Published: July 2017

A novel method using bionic mastication system based on a pressure sensor was developed to predict beef tenderness with convenience, stability and high accuracy. What's more, this method can be applied to detect other meat tenderness such as those of chicken and pork as well, which indicates a universality of this method.
The controlled catalytic oxidation of furfural to furoic acid using AuPd/Mg(OH)2
Authors: Douthwaite Mark , Huang Xiaoyang , Iqbal Sarwat , Miedziak Peter J. , Brett Gemma L. , Kondrat Simon A. , Edwards Jennifer K. , Sankar Meenakshisundaram , Knight David W. , Bethell Donald , Hutchings Graham J.
Published: July 2017

The selective oxidation of furfural to furoic acid is achieved at mild reaction conditions over an AuPd/Mg(OH)2 heterogeneous catalyst.
Structures of defects on anatase TiO2(001) surfaces
Authors: Shi Yongliang , Sun Huijuan , Nguyen Manh Cuong , Wang Caizhuang , Ho Kaiming , Saidi Wissam A. , Zhao Jin
Published: July 2017

Defects on oxide surfaces play a crucial role in surface reactivity and thus it is crucial to understand their atomic and electronic structures.
Unconventional magnetic anisotropy in one-dimensional Rashba system realized by adsorbing Gd atom on zigzag graphene nanoribbons
Authors: Qin Zhenzhen , Qin Guangzhao , Shao Bin , Zuo Xu
Published: July 2017

The Rashba effect, a spin splitting in electronic band structure, can be induced to the graphene nanoribbon by the transverse electronic field due to the asymmetric adsorption of Gd atom, which would impact the magnetic anisotropy distribution in k-space.
Borazine-based inorganic–organic hybrid cyclomatrix microspheres by silicon/boron exchange precipitation polycondensation
Authors: Riensch Nicolas A. , Deniz Ayse , Kühl Sebastian , Müller Lars , Adams Alina , Pich Andrij , Helten Holger
Published: July 2017

Borazine-based inorganic–organic hybrid cyclomatrix microspheres with a mean diameter of about 900 nm have been obtained via a novel silicon/boron exchange precipitation polycondensation approach.
Origin of nanostructural inhomogeneity in polymer-network gels
Authors: Seiffert Sebastian
Published: July 2017

Polymer-network gels often display nano- to microstructural inhomogeneity; this article reviews multiple types of origin of this structural feature.
Molecular dynamics simulation of low-energy recoil events in titanate pyrochlores
Authors: Dong Liyuan , Setyawan Wahyu , Li Yuhong , Devanathan Ram , Gao Fei
Published: July 2017

Molecular dynamics simulations of low-energy displacements in titanate pyrochlores have been carried out along three main directions, to determine Ed for A, Ti and O, corresponding defect configurations, and defect formation dynamics.
Alkaloids from the stems of Clausena lansium and their neuroprotective activity
Authors: Liu Jie , Du Yi-Qian , Li Chuang-Jun , Li Li , Chen Fang-You , Yang Jing-Zhi , Chen Nai-Hong , Zhang Dong-Ming
Published: July 2017

Eight new alkaloid derivatives (1–5), including three pairs of enantiomers, were obtained from Clausena lansium, and showed moderate neuroprotective effects.
From imine to amine: an unexpected left turn. Cis-β iron(ii) PNNP′ precatalysts for the asymmetric transfer hydrogenation of acetophenone
Authors: Demmans Karl Z. , Seo Chris S. G. , Lough Alan J. , Morris Robert H.
Published: July 2017

A slight change in the iron catalyst structure (amine arm with PEt2 to imine arm with PPh2) results in a complete reversal of the enantioselectivity toward ketone reduction.
Mg–Ti co-doping behavior of porous LiFePO4 microspheres for high-rate lithium-ion batteries
Authors: Tu Jiguo , Wu Kai , Tang Hui , Zhou Henghui , Jiao Shuqiang
Published: July 2017

Porous Mg–Ti co-doped LiFePO4 microspheres are successfully synthesized through the feasible carbothermic reduction reaction combined with the spray drying process, showing excellent high-rate cycling stability.
Surface enhancement of a molecularly imprinted polymer film using sacrificial silica beads for increasingl-arabitol chemosensor sensitivity and detectability
Authors: Dabrowski Marcin , Cieplak Maciej , Noworyta Krzysztof , Heim Matthias , Adamkiewicz Witold , Kuhn Alexander , Sharma Piyush Sindhu , Kutner Wlodzimierz
Published: July 2017

Sacrificial silica beads, used for increasing the specific surface area of a molecularly imprinted polymer film, improve the performance of the chemosensor.
Graphene quantum dots supported by graphene oxide as a sensitive fluorescence nanosensor for cytochrome c detection and intracellular imaging
Authors: Cao Lin , Li Xiangqing , Qin Lixia , Kang Shi-Zhao , Li Guodong
Published: July 2017

A new class of Cyt c detection fluorescence sensor based on graphene quantum dots supported by graphene oxide has been facilely developed. The sensor shows a high sensitivity and selectivity for Cyt c detection, and further exhibits favorable intracellular imaging in A549 cells.
n-Doping-induced efficient electron-injection for high efficiency inverted organic light-emitting diodes based on thermally activated delayed fluorescence emitter
Authors: Chen Yongzhen , Wei Xiaofang , Li Zhiyi , Liu Yanwei , Liu Jianjun , Wang Ruifang , Wang Pengfei , Yamada-Takamura Yukiko , Wang Ying
Published: July 2017

Inverted organic light-emitting diodes (OLEDs) based on thermally activated delayed fluorescence (TADF) emitters achieved a maximum external quantum efficiency of 16.4%.
How tetraspanins shape endothelial and leukocyte nano-architecture during inflammation
Authors: Franz Jonas , Tarantola Marco , Riethmüller Christoph
Published: July 2017

Tetraspanins are ubiquitous membrane proteins that induce local membrane curvature and hence co-ordinate cell-to-cell contacts. This review highlights their role in inflammation, which requires control of the nano-architecture of attachment sites between endothelial cells and leukocytes. The active role of endothelial cells in preparing for transmigration of leukocytes and determining the severity of an inflammation is often underscored. A clear hint to endothelial pre-activation is their ability to protrude clustered adhesion proteins upward prior to leukocyte contact. The elevation of molecular adhesive platforms toward the blood stream is crucially dependent on tetraspanins. In addition, leukocytes require tetraspanins for their activation. The example of the B-cell receptor is referenced in some detail here, since it provides deeper insights into the receptor–coreceptor interplay. To lift the role of tetraspanins from an abstract model of inflammation toward a player of clinical significance, two pathologies are analyzed for the known contributions of tetraspanins. The recent publication of the first crystal structure of a full-length tetraspanin revealed a cholesterol-binding site, which provides a strong link to the pathophysiological condition of atherosclerosis. Dysregulation of the inflammatory cascade in autoimmune diseases by endothelial cells is exemplified by the involvement of tetraspanins in multiple sclerosis.
Perceptual medical image fusion with internal generative mechanism
Authors: Qian Jiansheng , Bao Rong , Shen Wei , Hu Junfeng , Tang Lu , Xia Zhifang
Published: July 2017

Medical image fusion is the process of integrating two medical images with a visual enhanced single fused image, to attain a resultant image richer in information to aid medical practitioners in better diagnosis. A perceptual medical image fusion method is proposed by employing Internal Generative Mechanism. First, source images are divided into a predicted layer and a detail layer with a Bayesian prediction model. Then, the detail layer is merged with the energy of Tchebichef moments for blocks while the predicted layer is fused using the averaging strategy as activity level measurement. The fused image is finally obtained by merging coefficients in both fused layers. Experimental results prove that the proposed fusion algorithm is superior to the previously developed methods.
Parameters identification of a brushless doubly fed induction machine using pseudo‐random binary signal excitation signal for recursive least squares method
Authors: Djadi Hammou , Yazid Krim , Menaa Mohamed
Published: July 2017

Accurate brushless doubly fed induction machine (BDFIM) control is considered as a good alternative to traditional generators. Therefore, the knowledge of the parameters accuracy is necessary to design high‐performance drives. In this study, an offline identification method to identify the BDFIM parameters is presented. This study investigates the input signal effects on the accuracy of the identified parameters. The similarity between BDFIM frequency model and the standard induction machine frequency model has been verified by comparing the step responses of the corresponding transfer functions. The obtained results would be a motivation for online identification techniques and BDFIM field‐oriented control strategies. The proposed identification method has been validated by performing experimental results.
An islanding detection methodology combining decision trees and Sandia frequency shift for inverter‐based distributed generations
Authors: Azim Riyasat , Li Fangxing , Xue Yaosuo , Starke Michael , Wang Honggang
Published: July 2017

Distributed generations (DGs) for grid‐connected applications require an accurate and reliable islanding detection methodology (IDM) for secure system operation. This study presents an IDM for grid‐connected inverter‐based DGs. The proposed method is a combination of passive and active islanding detection techniques for aggregation of their advantages and elimination/minimisation of the drawbacks. In the proposed IDM, the passive method utilises critical system attributes extracted from local voltage measurements at target DG locations as well as employs decision tree‐based classifiers for characterisation and detection of islanding events. The active method is based on Sandia frequency shift technique and is initiated only when the passive method is unable to differentiate islanding events from other system events. Thus, the power quality degradation introduced into the system by active islanding detection techniques can be minimised. Furthermore, a combination of active and passive techniques allows detection of islanding events under low power mismatch scenarios eliminating the disadvantage associated with the use of passive techniques alone. Detailed case study results demonstrate the effectiveness of the proposed method in detection of islanding events under various power mismatch scenarios, load quality factors and in the presence of single or multiple grid‐connected inverter‐based DG units.
General topology for asymmetrical multilevel inverter with reduced number of switches
Authors: Boora Kamaldeep , Kumar Jagdish
Published: July 2017

The new emerging topologies in multilevel inverter field with reduced dc voltage sources and device counts, offer high power capability with less commutation losses and less harmonics in output voltage. However, these topologies have some disadvantages such as voltage balancing problem, increased number of electronic components, larger in size and complex control techniques. This study proposes a new asymmetrical multilevel inverter topology which requires less number of switching devices and driver circuits as compared to conventional multilevel inverter topologies. In the proposed topology, eight switches are required for generation of 15‐level single phase output voltage. The proposed topology is simple and can be extended easily to get more number of levels in the output voltage. Therefore, there is a significant reduction in size, cost and complexity for higher number of levels in output voltage. All positive and negative levels as well as performance parameter in term of Total Harmonic Distortion in the output voltage generated by proposed MLI have been evaluated using simulation in MATLAB environment. Various simulation and experimental results are presented to verify the operational accuracy of the proposed topology for a single phase 15‐level inverter.
Cognitive FDA‐MIMO radar for LPI transmit beamforming
Authors: Xiong Jie , Wang Wen‐Qin , Cui Can , Gao Kuandong
Published: July 2017

Active radar is vulnerable to illegal eavesdroppers due to its high‐gain beam‐scanning signals. To reduce active radar visibility and enhance its low probability of intercept (LPI) capability, this study proposes a cognitive LPI transmit beamforming scheme using frequency diverse array (FDA) and multiple‐input multiple‐output (MIMO) hybrid array antenna. The achievement of LPI is due to the unique range‐angle‐dependent transmitting beampattern of FDA‐MIMO radar, which minimises the beam power at the target location to reduce its visibility and simultaneously maximise the power at the radar receiver without degrading the radar detection performance. Furthermore, the FDA‐MIMO radar operates in a cognitive way: the receiver estimates the target range and the direction of arrival with a two‐dimensional multiple signal classification algorithm, and feedbacks their estimates to the transmitter to update the FDA‐MIMO transmit beamforming. As the transmit beamforming optimisation is non‐convex problem, the authors propose three methods, namely linear combination, non‐linear combination and closed form solution. All the proposed methods are verified by simulation results.
Detoxifikation
Authors: Bieger Wilfried P.
Published: July 2017

In Phase I der Entgiftung werden Endo- und Exotoxine aktiviert, in Phase II mit verschiedenen Verbindungen konjugiert und anschließend mit Urin oder Galle ausgeschieden. Wichtige Bestandteile der Detoxifikation sind zudem der Transport von Konjugaten über Membranen durch Antiportersysteme sowie die luminale Entgiftung. Unzureichende Detoxifikation wird mit zahlreichen Erkrankungen in Verbindung gebracht. Ein Beitrag von Polymorphismen der Entgiftungsenzyme zur Krebsentstehung wird diskutiert.
Comparisons of meat quality and muscle fibre characteristics on multiple pig breeds and sexes using principal component analysis
Authors: Kim Jun-Mo , Lee Sang-Hoon , Ryu Youn-Chul
Published: July 2017

Comprehensive understanding of the effect of pig breed and sex on meat quality and post-mortem muscle conditions will be necessary to estimate meat quality post mortem. In this study, we applied multiple regression and principal component analysis (PCA) using conventional meat quality traits and muscle fibre characteristics on six pig breeds and different sexes. A total of 1374 pigs from six breeds [Berkshire, Duroc, Landrace, Meishan, Yorkshire, and LYD (Landrace × Yorkshire sows with Duroc as terminal sires) crossbreed] belonging to three sexes (male, castrated male and female) were used in this study. Most of the muscle fibre characteristics showed moderate to high significant correlations with conventional meat quality traits. In particularly, the cross-sectional area (CSAF) of muscle fibres was strongly correlated with muscle pH values, water-holding capacity values and lightness (0.10 < |r| <0.26 and P < 0.01). Multiple regression analysis by general linear model revealed that the effects of breed were significant on muscle pH24h, lightness, drip loss, and marbling score (P < 0.01), whereas sex had no significant effect on meat quality. In the muscle fibre characteristics, the effects of breed and sex were significant on composition of area and density of muscle fibres (P < 0.05). We observed that the Meishan breed was clearly inferior to other breeds, whereas the LYD or Berkshire breeds showed better meat quality and muscle fibre properties. Moreover, we observed clear separations between pig breeds based on the PCA, whereas the sexes in each breed presented a continuum cluster. In summary, we suggest that muscle pH24h, lightness, and drip loss are conventional meat quality traits that can be considered as quantitative factors important in estimating ultimate meat quality of pigs along with the CSAF of muscle fibres; we conclude that Meishan pigs have low meat quality, whereas Berkshire and LYD crossbred pigs have higher quality of pork.
Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM
Authors: Roh Soung-Hun , Hryc Corey F. , Jeong Hyun-Hwan , Fei Xue , Jakana Joanita , Lorimer George H. , Chiu Wah
Published: July 2017

Significance

Using cryo-EM and expanding on focused classification allowed for the bacterial chaperone, GroEL, to be structurally resolved at atomic detail one particle at a time. This approach differs from generating the traditional structural ensemble average of presumably identical particle images. Three dominant subunit conformations were identified, and their spatial distributions were found to be different in each individual GroEL oligomer. This strategy demonstrates the application of cryo-EM to characterize the biophysical properties of structural dynamics of individual molecular machines one at a time.
SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces
Authors: Kochańczyk Marek , Hlavacek William S , Lipniacki Tomasz
Published: July 2017

Rule-based modeling is a powerful approach for studying biomolecular site dynamics. Here, we present SPATKIN, a general-purpose simulator for rule-based modeling in two spatial dimensions. The simulation algorithm is a lattice-based method that tracks Brownian motion of individual molecules and the stochastic firing of rule-defined reaction events. Because rules are used as event generators, the algorithm is network-free, meaning that it does not require to generate the complete reaction network implied by rules prior to simulation. In a simulation, each molecule (or complex of molecules) is taken to occupy a single lattice site that cannot be shared with another molecule (or complex). SPATKIN is capable of simulating a wide array of membrane-associated processes, including adsorption, desorption and crowding. Models are specified using an extension of the BioNetGen language, which allows to account for spatial features of the simulated process.

Availability and implementation

The C ++ source code for SPATKIN is distributed freely under the terms of the GNU GPLv3 license. The source code can be compiled for execution on popular platforms (Windows, Mac and Linux). An installer for 64-bit Windows and a macOS app are available. The source code and precompiled binaries are available at the SPATKIN Web site (http://pmbm.ippt.pan.pl/software/spatkin).

Supplementary information

Supplementary data are available at Bioinformatics online.
Assessment of Optimal Imaging Protocol Sequences After Laser-Induced Thermal Therapy for Intracranial Tumors
Authors: Parisi Anthony J , Sundararajan Sri Hari , Garg Rahul , Hargreaves Eric L , Patel Nitesh V , Danish Shabbar F
Published: July 2017

BACKGROUND

Magnetic resonance-guided laser-induced thermal therapy (MRgLITT) is a novel, minimally invasive method currently being used to treat a wide range of intracranial pathologies. No accepted guidelines exist on what the appropriate magnetic resonance imaging (MRI) sequences are for evaluating short-term postablation changes, especially when patients are not able to receive gadolinium.

OBJECTIVE

To evaluate which MRI sequences provide the greatest inter-rater reliability and least amount of variability in assessment of ablation volume after MRgLITT for intracranial neoplasms.

METHODS

Twenty patients who received MRgLITT were included. Three raters calculated volumetric measurements on postprocedural axial spoiled gradient recalled (SPGR), fluid-attenuated inversion recovery (FLAIR), diffusion-weighted imaging (DWI), and gradient echo (GRE) sequences. Measured volumes were analyzed using intraclass correlation to determine which protocol had the most concordance among the 3 raters.

RESULTS

Postcontrast SPGR sequences were most concordant in our study, with an intraclass correlation of 0.981. DWI was the next-most concordant imaging sequence with an intraclass correlation of 0.958. The least concordant were GRE (0.895) and FLAIR (0.866) images. SPGR was also the least variable and had the most consistent volume ratings compared to the other sequences.

CONCLUSION

This study is the first to evaluate the inter-rater reliability of different MRI sequence protocols in the context of post-MRgLITT volumetric evaluation. SPGR postcontrast images facilitate the greatest interobserver concordance when characterizing post-MRgLITT tumor appearance and volumetrics, with DWI ranked second. Based on our findings, SPGR sequences are likely to yield the highest degree of concordance in post-MRgLITT lesion evaluation. When gadolinium cannot be given, DWI should provide the next most reliable estimation.
Syndesmotic Ankle Fractures
Authors: Michelson James D. , Wright Michael , Blankstein Michael
Published: July 2017

Objectives:

The diagnosis and treatment of syndesmotic ankle fractures is controversial. This systematic review was performed to clarify the current understanding addressing several clinical questions that arise in the treatment of such injuries.

Data Sources:

The English language literature was searched using PubMed, EMBASE, and Web of Science. The search terms were “syndesmosis” or “syndesmotic” in combination with the terms “ankle fracture” or “fracture.” The included dates were between 1967 and July 2015.

Study Selection:

Inclusion criteria were number of patients >20, patient age ≥18 years, follow-up ≥1 year, ankle fracture classification was reported, criteria for surgery was reported, technique of surgery was reported, and a validated outcome measure was used. Studies limited to biomechanical or imaging investigations were excluded.

Data Extraction:

Information was abstracted using a standardized template, which encompassed the inclusion criteria together with the study type, postoperative regimen, and complications. Study quality was evaluated using the modified CONSORT statement and Coleman criteria. Study bias was assessed, and methodological quality was rated. Any difference in ratings was resolved by consensus.

Data Synthesis:

None.

Conclusions:

The overall quality of the studies was poor. The number or placement of syndesmotic screws or the breakage of trans-syndesmotic screws postoperatively had no adverse effect on outcomes (both with moderate strength of evidence). The use of alternative fixation devices (bioabsorbable and endobutton) had poor strength of evidence, as did the opinion that nondisplaced, unstable by stress test, syndesmotic injuries required fixation. There are insufficient data that link subtle rotational syndesmotic malreduction to clinical outcomes.

Level of Evidence:

Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Patulous Eustachian Tube and Otitis Media With Effusion as Complications After Trigeminal Nerve Injury
Authors: Ikeda Ryoukichi , Kobayashi Toshimitsu , Yoshida Masayuki , Yoshida Naohiro , Kikuchi Toshiaki , Oshima Takeshi , Kawase Tetsuaki , Katori Yukio
Published: July 2017

Objectives:

To describe three patients of patulous Eustachian tube (pET) after trigeminal nerve injury and to demonstrate for the first time their magnetic resonance imaging (MRI) findings to hypothesize the mechanism of the pET after trigeminal nerve injury.

Patients:

Three patients presented with autophony after trigeminal nerve injury caused by the removal of intracranial tumors.

Main Outcome Measures:

Clinical patient records, audiological data, and MRI.

Results:

Each patient initially developed transient otitis media with effusion (OME) within a few months after surgery and subsequently developed pET. The MRI of the three patients when they developed pET demonstrated atrophy and fat infiltration of the muscles innervated by the mandibular branch of the trigeminal nerve.

Conclusion:

All three patients transiently manifested OME before pET was diagnosed. Based on the MRI findings and anatomical considerations, this chronological transition from OME to pET was speculated as an initial motor paralysis of the tensor veli palatini muscle, followed by volume decrease of the muscles in the vicinity of the ET due to denervation atrophy and fat infiltration, which resulted in ET closing failure.
Effect of Increased Evaluation Objectivity on Grade Inflation
Authors: White Krista Alaine , Heitzler Ella Thomas
Published: July 2017

This retrospective, comparative study examined the effect of increasing objectivity of evaluation methods on grade inflation in a graduate nursing research course. Multiple-choice testing and increased precision in grading rubrics were added to the course. Outcome measures of student grade distributions for the course were measured pre/post course revision. Statistically significant reductions in grade distributions were observed after course evaluation method revisions were implemented (U = 4575.0, P < .001).
Process Matters
Authors: Raymond Christy , Profetto-McGrath Joanne , Myrick Florence , Strean William B.
Published: July 2017

Researchers who study nursing education encounter difficulty when trying to recruit and retain nurse educator participants. Researchers would benefit from knowing more about effective and ineffective sampling strategies and methods to increase the efficiency of the research process. This article outlines the struggles and successes encountered with a mixed methods study that examined nurse educators’ critical thinking. Specific examples are interwoven with current literature to uncover some important insights and future recommendations for researchers in nursing education.
Gender Differences in Outcomes of Antiretroviral Treatment Among HIV-Infected Patients in China: A Retrospective Cohort Study, 2010–2015
Authors: Chen Meiling , Dou Zhihui , Wang Liming , Wu Yasong , Zhao Decai , Gan Xiumin , Hu Ran , Ma Ye , Zhang Fujie
Published: July 2017

Backgroud:

Women now account for about half of all people living with HIV worldwide, but researchers lack clear information and large population-based study about gender differences in treatment outcomes.

Methods:

A nationwide retrospective observational cohort study with data from the China National Free Antiretroviral Treatment Program was performed. Antiretroviral-naive patients older than 18 years initiating standard antiretroviral therapy between January 1, 2010, and December 31, 2011, were included and followed up to December 31, 2015. We used modified Poisson regression models to estimate the impact of gender on virological suppression and retention in treatment, and Kaplan–Meier analysis and Cox proportional hazard models to evaluate gender difference in mortality.

Results:

Sixty-eight thousand six hundred forty-six patients [46,083 (67.1%) men and 22,563 (32.9%) women] with HIV met eligibility criteria. Women were significantly more likely to achieve virological suppression than men both at 12 months [adjusted relative risk (aRR) 1.02, 95% confidence interval (CI): 1.01 to 1.03, P < 0.001] and 48 months (aRR 1.01, 95% CI: 1.00 to 1.02, P = 0.005) after initiating antiretroviral treatment. Women were also more likely to remain in treatment at 12 months (aRR 1.02, 95% CI: 1.01 to 1.02, P < 0.001) and 48 months (aRR 1.04, 95% CI: 1.03 to 1.05, P < 0.001), although the difference became insignificant in alive patients. All-cause mortality was lower in women than in men (2.34 vs. 4.03 deaths/100PY, adjusted hazard ratio 0.72, 95% CI: 0.67 to 0.77, P < 0.001).

Conclusions:

In China, women are more likely to achieve virological suppression, remain in treatment, and have a significantly lower risk of death than men. Future studies could take both biological and sociobehavioral factors into analysis to clarify the influence factors.
Laparoscopic Appendectomy for Complicated Acute Appendicitis in the Elderly: A Single-center Experience
Authors: Yang Jiahua , Yu Kun , Li Wei , Si Xianke , Zhang Jixun , Wu Wentao , Cao Yijun
Published: July 2017

Background:

The use of laparoscopic appendectomy for complicated acute appendicitis remains controversial in the elderly. This study aimed to compare the postoperative outcomes of elderly patients who received either laparoscopic appendectomy or open appendectomy.

Patients and Methods:

A single-centre retrospective analysis of the clinical records of elderly patients (age, above 65 y) who underwent operations from January 2012 to November 2015 was performed. Demographic data, intraoperative variables, length of stay, and surgical complications were retrieved.

Results:

A total of 145 elderly patients were preoperatively diagnosed with acute appendicitis. There were 43 (29.66%) complicated and 102 (70.34%) uncomplicated appendicitis cases. A total of 65 (44.83%) procedures were performed using the open technique (OA group) and 80 (55.17%) using the laparoscopic technique (LA group). In the laparoscopic group, 19 (23.75%) patients had complicated acute appendicitis (CLA group), and 61 (76.25%) had uncomplicated acute appendicitis (UCLA group). In the complicated group, 19 (44.19%) patients underwent operation using the laparoscopic technique (CLA group) and 24 (55.81%) using the open technique (COA group). There were no significant differences between the LA and OA groups in terms of age, sex distribution, duration of symptoms, American Society of Anesthesiologists score, white blood cells, complicated appendicitis, operation time, drain apposition, days to resumption of liquids, and postoperative complications (P>0.05). Significant differences were found in days to start walking and days to resumption of solids in the LA group (P<0.05). The OA group had a longer length of hospital stay than the LA group (P<0.05). Postoperative complications were not significantly different between the groups (P>0.05). The CLA group had a significantly longer duration of symptoms, operation times, days to resumption of liquids, and days to resumption of solids than the UCLA group (P<0.05). The COA group had significantly longer days to walking and hospital stays than the CLA group (P<0.05).

Conclusions:

Our study demonstrated that using LA to treat complicated acute appendicitis in the elderly was not associated with additional surgical complications. Therefore, it seems feasible to use LA as a safe technique for complicated acute appendicitis in the elderly.
Color Pupillography in Dorsal Midbrain Syndrome
Authors: Kelbsch Carina B. , Maeda Fumiatsu , Strasser Torsten , Peters Tobias M. , Wilhelm Barbara J. C. , Wilhelm Helmut M.
Published: July 2017

Objective:

The purpose of this study was to evaluate the pupil response to chromatic stimuli in patients with lesions in the dorsal midbrain and possibly gain new insights into the afferent pupillary pathways.

Methods:

Color pupillography was performed in 5 patients with dorsal midbrain syndrome (DMS), and their results were compared with those of 20 healthy control subjects. We used full-field red stimuli (605 nm) that primarily address the rod/cone system and blue stimuli (420 nm) that preferentially activate intrinsically photosensitive retinal ganglion cells (ipRGCs) directly, with a duration of 4 seconds and a stimulus intensity of 28 lx corneal illumination under mesopic conditions. One eye was stimulated, and the consensual pupil response was recorded and analyzed.

Results:

The pupillary light reflex in patients with DMS was reduced, differed in shape, and showed a prolonged latency time compared to normal subjects. The blue response was less affected than the red response: the mean maximal relative amplitude (M) was 15.8% (SD = 7.8) in patients with DMS compared with 43.0% (SD = 5.5) in normal subjects for red stimulation, and M = 40.8%, SD = 8.4 (DMS) with M = 58.3%, SD = 4.8 (normals) for blue stimulation. The reduction was 63% for red stimulation but only 30% for blue stimulation in patients with DMS. Moreover, there was a preserved postillumination pupil response to blue stimulation in DMS patients.

Conclusions:

In DMS, the melanopsin-mediated ipRGC pathway appeared relatively preserved.
A mutation in theLMOD1actin-binding domain segregating with disease in a large British family with thoracic aortic aneurysms and dissections
Authors: Wan Y.B.A. , Simpson M.A. , Aragon-Martin J.A. , Osborn D.P.S. , Regalado E. , Guo D.C. , Boileau C. , Jondeau G. , Benarroch L. , Isekame Y. , Bharj J. , Sneddon J. , Fisher E. , Dean J. , Tome Esteban M.T. , Saggar A. , Milewicz D. , Jahangiri M. , Behr E. R. , Smith A. , Child A. H.
Published: July 2017

We describe a mutation inLMOD1, which predisposes individuals to thoracic aortic aneurysms and dissections in a large multi-generation British family. Exome variant profiles for the proband and two distantly related affected relatives were generated and a rare protein-altering, heterozygous variant was identified, present in all the exome-sequenced affected individuals. The allele c.1784T>C, p.(V595A) inLMOD1is located in a known actin-binding WH2 domain and is carried by all living affected individuals in the family.LMOD1was further assessed in a consecutive series of 98 UK TAAD patients and one further mutation was found, yielding an incidence of ∼2% in our study group. Assessment ofLMOD1in international TAAD cohorts discovered nine other missense variants of which three were classed as likely pathogenic.

Validation ofLMOD1was undertaken using a zebrafish animal model. Knock-down of bothlmod1aandlmod1bparalogs using morpholino oligonucleotides showed a reproducible abnormal phenotype involving the aortic arches under off-target controls. Injection of the humanLMOD1c.1784T>C, p.(V595A) mutation demonstrated a likely dominant negative effect and illustrated a loss of function cause.

Mutations found in the WH2 actin-binding domain ofLMOD1may delay actin polymerization and therefore compromise actin length, dynamics and interaction with myosin in the smooth muscle contraction pathway.
Distinct C4Sub-Types and C3Bundle Sheath Isolation In The Paniceae Grasses
Authors: Washburn Jacob D. , Strable Josh , Dickinson Patrick , Kothapalli Satya S. , Brose Julia M. , Covshoff Sarah , Conant Gavin C. , Hibberd Julian M. , Pires J. Chris
Published: July 2017

In C4plants, the enzymatic machinery underpinning photosynthesis can vary, with, for example, three distinct C4acid decarboxylases being used to release CO2in the vicinity of RuBisCO. For decades, these decarboxylases have been used to classify C4species into three biochemical sub-types. However, more recently the notion that C4species mix and match C4acid decarboxylases has increased in popularity and, as a consequence, the validity of specific biochemical sub-types has been questioned. Using five species from the grass tribe Paniceae, we show that, while in some species transcripts encoding multiple C4acid decarboxylases accumulate, in others, transcript abundance and enzyme activity is almost entirely from one decarboxylase. In addition, the development of a bundle sheath isolation procedure for a close C3species in the Paniceae enables the preliminary exploration of C4sub-type evolution.
Soluble Syntaxin 3 Functions as a Transcription Regulator
Authors: Giovannone Adrian J. , Winterstein Christine , Bhattaram Pallavi , Reales Elena , Low Seng Hui , Baggs Julie E. , Xu Mimi , Lalli Matthew A. , Hogenesch John B. , Weimbs Thomas
Published: July 2017

Syntaxins - a conserved family of SNARE proteins - contain C-terminal transmembrane anchors required for their membrane fusion activity. Here we show that syntaxin 3 (Stx3) unexpectedly also functions as a nuclear regulator of gene expression. Alternative splicing leads to a soluble isoform, termed Stx3S, lacking the transmembrane anchor. Soluble Stx3S binds to the nuclear import factor RanBP5, targets to the nucleus and interacts physically and functionally with several transcription factors, including ETV4 and ATF2. Stx3S is differentially expressed in normal human tissues, during epithelial cell polarization, and in breast cancer vs. normal breast tissue. Inhibition of endogenous Stx3S expression leads to changes in the expression of cancer-associated genes and promotes cell proliferation. Similar nuclear-targeted, soluble forms of other syntaxins were identified suggesting that nuclear signaling is a conserved, novel function common among these membrane trafficking proteins.
The path to re-evolve cooperation is constrained inPseudomonas aeruginosa
Authors: Granato Elisa T. , Kümmerli Rolf
Published: July 2017

Background

A common form of cooperation in bacteria is based on the secretion of beneficial metabolites, shareable as public good among cells at the group level. Because cooperation can be exploited by “cheat” mutants, which contribute less or nothing to the public good, there has been great interest in understanding the conditions required for cooperation to remain evolutionarily stable. In contrast, much less is known about whether cheats, once fixed in the population, are able to revert back to cooperation when conditions change. Here, we tackle this question by subjecting experimentally evolved cheats ofPseudomonas aeruginosa, partly deficient for the production of the iron-scavenging public good pyoverdine, to conditions previously shown to favor cooperation.

Results

Following approximately 200 generations of experimental evolution, we screened 720 evolved clones for changes in their pyoverdine production levels. We found no evidence for the re-evolution of full cooperation, even in environments with increased spatial structure, and reduced costs of cooperation – two conditions that have previously been shown to maintain cooperation. In contrast, we observed selection for complete abolishment of pyoverdine production. The patterns of complete trait degradation were likely driven by “cheating on cheats” in unstructured, iron-limited environments where pyoverdine is important for growth, and selection against a maladaptive trait in iron-rich environments where pyoverdine is superfluous.

Conclusions

Our study shows that the path to re-evolve cooperation seems constrained. One reason might be that the number of mutational targets potentially leading to reversion is limited. Alternatively, it could be that the selective conditions required for revertants to spread from rare are much more stringent than those needed to maintain cooperation.