bluuebunny/crossref_metadata_2025 huggingface dataset:
Disruption and restoration of nucleolar FC and DFC during S phase in HeLa cells
Authors: Guan Xin , Jiao Yang , Chen Lingling , Li Xiliang , Shang Guangbin , Wang Fengcai , Feng Yunpeng , Jiao Mingda
Published: December 2016

In the higher eukaryotic nucleolus, fibrillar centers (FCs), the dense fibrillar components (DFCs), and the granular components (GCs) are functional domains structurally relatively well‐defined by electron microscopy (EM). However, ultrastructural alterations in FC, DFC, and GC during the cell cycle and their associated cellular functions are still largely unclear. Based on synchronized HeLa cells, we followed the structural dynamics of nucleolus during cell cycle by EM. We found that nucleolus structure shifted from tripartite to bipartite organization and FC/DFCs were reorganized in S phase with three distinct stages: (1) In early‐S phase, FC/DFC structures were disassembled. (2) In mid‐S phase, a transition from FC/DFC disruption to restoration occurred. As FC/DFC structures were completely disassembled, nucleoli became structurally homogenous. (3) In late‐S phase, the number of small FC/DFCs increased and subsequently large FC/DFCs were constructed. Our data demonstrated that nucleolar FC/DFCs in interphase are presented in two different forms or states due to disassembly and reassembly. FC/DFCs in G1 are nucleolar structures constructed concomitantly with the establishment of nucleoli derived from the nucleolar organizer region (NOR). FC/DFCs in G2 are nucleolar components reconstituted after the global reassembly in mid‐S phase. Dynamic nucleolus structures revealed in this study may serve as ultrastructural characteristics to reflect distinct stages of the cell cycle. By providing evidence for the temporal and spatial regulation of nucleolus, our findings contribute to the coupling of nucleolus structures to cell cycle dependent functions.
DNA base excision repair and nucleotide excision repair synergistically contribute to survival of stationary‐phase cells of the fission yeast Schizosaccharomyces pombe
Authors: Senoo Takanori , Kawano Shinji , Ikeda Shogo
Published: December 2016

Defects of genome maintenance may causally contribute to aging. In general, base excision repair (BER) is involved in the repair of subtle base lesions and AP sites, and bulky helix‐distorting lesions are restored by nucleotide excision repair (NER). Here, we measured the chronological lifespan (CLS) of BER‐ and NER‐deficient mutants of the fission yeast Schizosaccharomyces pombe, and observed the aging process of cells. The CLS of the nth1 (gene for DNA glycosylase/AP lyase) mutant and the rad16 (a homolog of human XPF) mutant were slightly shorter than that of the wild‐type (WT) strain. However, survival of the nth1Δ rad16Δ double mutant was significantly reduced after entry into the stationary phase. Deletion of rad16 in an AP endonuclease mutant apn2Δ also accelerated chronological aging. These results indicate that BER and NER synergistically contribute to genome maintenance in non‐dividing cells. Reactive oxygen species (ROS) accumulated in cells during the stationary phase, and nth1Δ rad16Δ cells produced more ROS than WT cells. High mutation frequencies and nuclear DNA fragmentation were observed in nth1Δ rad16Δ stationary‐phase cells concurrent with apoptotic‐like cell death. Calorie restriction significantly reduced the level of ROS in the stationary phase and extended the CLS of nth1Δ rad16Δ cells. Therefore, ROS production critically affects the survival of the DNA repair mutant during chronological aging.
Copper deficiency‐related bone marrow changes secondary to long‐term total parenteral nutrition
Authors: Oo Thein Hlaing , Hu Shimin
Published: December 2016

Key Clinical Message

Total parenteral nutrition can be complicated by the marrow sea‐blue histiocytes as well as copper deficiency‐related bone marrow changes. Cytoplasmic vacuoles in the erythroid and myeloid precursors raise the possibility of copper deficiency anemia. If the diagnosis is delayed, the clinical course can be complicated by neurologic deficits.
A new method for robust mixture regression
Authors: Yu Chun , Yao Weixin , Chen Kun
Published: December 2016

Finite mixture regression models have been widely used for modelling mixed regression relationships arising from a clustered and thus heterogenous population. The classical normal mixture model, despite its simplicity and wide applicability, may fail in the presence of severe outliers. Using a sparse, case‐specific, and scale‐dependent mean‐shift mixture model parameterization, we propose a robust mixture regression approach for simultaneously conducting outlier detection and robust parameter estimation. A penalized likelihood approach is adopted to induce sparsity among the mean‐shift parameters so that the outliers are distinguished from the remainder of the data, and a generalized Expectation–Maximization (EM) algorithm is developed to perform stable and efficient computation. The proposed approach is shown to have strong connections with other robust methods including the trimmed likelihood method and M‐estimation approaches. In contrast to several existing methods, the proposed methods show outstanding performance in our simulation studies.The Canadian Journal of Statistics45: 77–94; 2017 © 2016 Statistical Society of Canada
Safety, Tolerability, and Antihypertensive Effect of SER100, an Opiate Receptor‐Like 1 (ORL‐1) Partial Agonist, in Patients With Isolated Systolic Hypertension
Authors: Kantola Ilkka , Scheinin Mika , Gulbrandsen Trygve , Meland Nils , Smerud Knut T.
Published: December 2016

The purpose of the present trial was to evaluate safety, tolerability, and effect on systolic blood pressure (SBP) of SER100 in a small group of patients with isolated systolic hypertension (ISH) in treatment with at least 1 antihypertensive drug. Eligible patients were randomized to either SER100 (10 mg) or placebo in a crossover design, and 2 doses were given subcutaneously (SC), 8 hours apart, on 2 consecutive days. On all treatment days patients were monitored with an ambulatory blood pressure measurement device for 12 daytime hours. Seventeen patients completed treatment. There were no serious or severe adverse events. Relative to placebo SER100 induced an average reduction of SBP during the 2 treatment days of 7.0 mm Hg (P = 0.0032), whereas the average reduction of diastolic blood pressure (DBP) over the same period was 3.8 mm Hg (P = 0.0011). For patients with ISH, this short‐term cross‐over study of SC SER100 demonstrated an acceptable safety profile and consistent, significant lowering of SBP and DBP. As initial clinical proof of concept for a new class of drugs, a nociceptin agonist peptide, the results were encouraging and warrant further research.
A resource allocation game with restriction mechanism in VANET cloud
Authors: Tao Jun , Xu Yifan , Zhang Ziyi , Feng Fuqin , Tong Fei , Dong Fang
Published: December 2016

In Vehicular Ad hoc Networks (VANETs), because of the selfishness of the vehicles, the resource allocation in VANET has become one of the primary tasks. Exploiting the Road Side Units (RSUs), which constructs the Cloud Computing environment, provides more data access opportunities and stable communication time for the vehicles. We investigated the cloud resource allocation for data access with noncooperative game based on a Gauss–Seidel iteration method. We further proposed a repeated game scheme, which can approximately achieve the near Pareto‐optimal flow allocation among the vehicles. Considering the vehicles' irrational behavior, a punishment strategy was designed to prevent the vehicles from behavior deviation. The analysis based on these models lays a theoretical method foundation on cloud resource allocation process. The validity of the modeling and the accuracy of the analysis were verified through the extensive simulations, which also guide the future design of more sophisticated cloud resource allocation schemes. Copyright © 2016 John Wiley & Sons, Ltd.
Research and implementation of a high performance parallel computing digital down converter on graphics processing unit
Authors: Shao Guo‐lin , Chen Xing‐shu , Yang Lu
Published: December 2016

Digital down converter (DDC) is a time‐intensive and data‐intensive computing task and considered as the key technology in software defined radio. This paper proposes a high‐performance implementation of DDC on a graphics processing unit (GPU) using CUDA, which is composed of a numerically controlled oscillator stage, a cascaded integrator‐comb (CIC) decimation filter stage, and a finite impulse response (FIR) filter stage. The GPU implementation and optimizing of all the stages are studied in detail. Additionally, for handling a long‐duration signal, the signal data sequence is truncated into segments; the overlap‐save and overlap‐add mechanisms were applied in CIC stage and FIR stage, respectively. Finally, experiments were conducted to evaluate the performance of GPU‐based DDC with respect to a sequential version CPU implementation and an OpenMP implementation (16 threads). Experimental results demonstrate that the DDC achieves significant improvements on the GPU; the maximum speed ups in numerically controlled oscillator stage, CIC stage, and FIR stage can achieve more than 1242, 527, and 179 times, including data‐transfer, kernel execution, and other processing operations; the overall speed up of DDC can achieve more than 180. In the meantime, the speed ups of GPU implementation are far above the OpenMP implementation (about 2.5‐6.4 times).
A New Method for Evaluating Stallion Sperm Viability and Mitochondrial Membrane Potential in Fixed Semen Samples
Authors: Peña F.J. , Ball B. A. , Squires E. L.
Published: December 2016

Multiparametric assessment of stallion sperm quality using flow cytometry can be a useful adjunct in semen evaluation; however, the availability of flow cytometers in veterinary practice is limited. The ability to preserve and transport sperm samples for later flow cytometric analysis using fixable probes would potentially facilitate this process. In the current study, we validated the combination of live/dead Zombie Green® (a fixable dye used to assess live and dead sperm) and MitoTracker Deep Red® (used to assess mitochondrial membrane potential). The assay was validated against classic, non‐fixable, membrane assays (SYBR‐14/PI). Our results demonstrated the feasibility of the assay. In conclusion, stained and fixed semen samples stored for 72 h obtained equivalent results to the exam on the same day; this new protocol shall facilitate the wider use of flow cytometry in stallion andrology in the future. © 2017 International Clinical Cytometry Society
SNARE proteins play a role in motor axon guidance in vertebrates and invertebrates
Authors: Barrecheguren Pablo José , Ros Oriol , Cotrufo Tiziana , Kunz Beat , Soriano Eduardo , Ulloa Fausto , Stoeckli Esther T. , Araújo Sofia J.
Published: December 2016

Axonal growth and guidance rely on correct growth cone responses to guidance cues, both in the central nervous system (CNS) and in the periphery. Unlike the signaling cascades that link axonal growth to cytoskeletal dynamics, little is known about the cross‐talk mechanisms between guidance and membrane dynamics and turnover in the axon. Our studies have shown that Netrin‐1/deleted in colorectal cancer signaling triggers exocytosis through the SNARE Syntaxin‐1 (STX‐1) during the formation of commissural pathways. However, limited in vivo evidence is available about the role of SNARE proteins in motor axonal guidance. Here we show that loss‐of‐function of SNARE complex members results in motor axon guidance defects in fly and chick embryos. Knock‐down of Syntaxin‐1, VAMP‐2, and SNAP‐25 leads to abnormalities in the motor axon routes out of the CNS. Our data point to an evolutionarily conserved role of the SNARE complex proteins in motor axon guidance, thereby pinpointing an important function of SNARE proteins in axonal navigation in vivo. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 963–974, 2017
Topographic and fire weather controls of fire refugia in forested ecosystems of northwestern North America
Authors: Krawchuk Meg A. , Haire Sandra L. , Coop Jonathan , Parisien Marc‐André , Whitman Ellen , Chong Geneva , Miller Carol
Published: December 2016

Fire refugia, sometimes referred to as fire islands, shadows, skips, residuals, or fire remnants, are an important element of the burn mosaic, but we lack a quantitative framework that links observations of fire refugia from different environmental contexts. Here, we develop and test a conceptual model for how predictability of fire refugia varies according to topographic complexity and fire weather conditions. Refugia were quantified as areas unburned or burned at comparatively low severity based on remotely sensed burn severity data. We assessed the relationship between refugia and a suite of terrain‐related explanatory metrics by fitting a collection of boosted regression tree models. The models were developed for seven study fires that burned in conifer‐dominated forested landscapes of the Western Cordillera of Canada between 2001 and 2014. We fit nine models, each for distinct levels of fire weather and terrain ruggedness. Our framework revealed that the predictability and abundance of fire refugia varied among these environmental settings. We observed highest predictability under moderate fire weather conditions and moderate terrain ruggedness (ROC‐AUC = 0.77), and lowest predictability in flatter landscapes and under high fire weather conditions (ROC‐AUC = 0.63–0.68). Catchment slope, local aspect, relative position, topographic wetness, topographic convergence, and local slope all contributed to discriminating where refugia occur but the relative importance of these topographic controls differed among environments. Our framework allows us to characterize the predictability of contemporary fire refugia across multiple environmental settings and provides important insights for ecosystem resilience, wildfire management, conservation planning, and climate change adaptation.
Highly Sensitive Hydrazine Sensor Based on Co(OH)2 Nanoflakes Electrochemically Deposited on MWCNTs
Authors: Kohila rani Karuppasamy , Devasenathipathy Rajkumar , Wang Sea‐Fue , Subramanian K. Sundara
Published: December 2016

We delineate the electrochemical preparation of cobalt hydroxide nanoflakes Co(OH)2 NFs on multi‐walled carbon nanotubes (MWCNTs) by potentiostatic methods. The preparation was done on the surface of glassy carbon electrode (GCE). The prepared nanocomposite was characterized by field emission scanning electron microscopy (FESEM), X‐ray diffraction spectroscopy (XRD) and X‐ray photo electron spectroscopy (XPS). The resulting f‐MWCNTs/Co(OH)2 NFs modified GCE exhibits a good electrocatalytic activity for the oxidation of hydrazine in terms of decreasing over potential and increasing peak current. The modified electrode holds good in the linear range from 0.5 to 15.5 μM with limit of detection as 87.5 nM. The sensitivity of our modified electrode is calculated to be 5733 μA/mM cm‐2. Remarkably, the obtained LOD value of our sensor is very lower compared to the recommended concentration of hydrazine in water by World health organization (WHO) and Environmental protective agency (EPA). The modified electrode detects hydrazine selectively even in the presence of common interferants. Various water samples were chosen to study the practical feasibility of our sensor. The sensor also exhibited an appreciable stability, repeatability and reproducibility.
Hydrothermal Synthesis of Three Dimensional Graphene‐Multiwalled Carbon Nanotube Nanocomposite for Enhanced Electro Catalytic Oxidation of Caffeic Acid
Authors: Sakthinathan Subramanian , Kubendhiran Subbiramaniyan , Chen Shen‐Ming
Published: December 2016

Three dimensional graphene‐multiwalled carbon nanotube nano composite (3DG/MWCNTs−Nc) was synthesized by simple hydrothermal method for the amperometric determination of caffeic acid (CA). The prepared nanocomposite was characterized by scanning electron microscopic technique (SEM), ultraviolet‐visible spectroscopy (UV), Raman spectroscopy and infrared spectroscopy (IR). Moreover, the interfacial electron transfer properties of the modified electrode were carried out by the electro chemical impedance spectroscopy (EIS). Besides, the electro chemical performance of the modified electrode was carried out by the cyclic voltammetry (CV) and amperometric (i‐t) technique. The proposed electrode was exhibited an enhanced electrocatalytic activity towards the detection of CA. Under the optimal condition, the 3DG/MWCNTs−Nc modified electrode displayed a linear range from 0.2 to 174 μM, detection limit (LOD) 17.8 nM and sensitivity of 5.8308 μA μM−1 cm−2 and on applied potential + 0.2 V. These result showed, 3DG/MWCNTs−Nc modified electrodes showed good repeatability, reproducibility, and higher stability. In addition, the fabricated electrode was then successfully used to determine the CA in real samples with satisfactory recoveries. Which suggests that the 3DG/MWCNTs−Nc as a robust sensing materials for the electrochemical detection of CA.
Characterisation of the genomic landscape of CRLF2‐rearranged acute lymphoblastic leukemia
Authors: Russell Lisa J. , Jones Lisa , Enshaei Amir , Tonin Stefano , Ryan Sarra L. , Eswaran Jeyanthy , Nakjang Sirintra , Papaemmanuil Elli , Tubio Jose M. C. , Fielding Adele K. , Vora Ajay , Campbell Peter J. , Moorman Anthony V. , Harrison Christine J.
Published: December 2016

Deregulated expression of the type I cytokine receptor, CRLF2, is observed in 5–15% of precursor B‐cell acute lymphoblastic leukaemia (B‐ALL). We aimed to determine the clinical and genetic landscape of those with IGH‐CRLF2 or P2RY8‐CRLF2 (CRLF2‐r) using multiple genomic approaches. Clinical and demographic features of CRLF2‐r patients were characteristic of B‐ALL. Patients with IGH‐CRLF2 were older (14 y vs. 4 y, P < .001), while the incidence of CRLF2‐r among Down syndrome patients was high (50/161, 31%). CRLF2‐r co‐occurred with primary chromosomal rearrangements but the majority (111/161, 69%) had B‐other ALL. Copy number alteration (CNA) profiles were similar to B‐other ALL, although CRLF2‐r patients harbored higher frequencies of IKZF1 (60/138, 43% vs. 77/1351, 24%) and BTG1 deletions (20/138, 15% vs. 3/1351, 1%). There were significant differences in CNA profiles between IGH‐CRLF2 and P2RY8‐CRLF2 patients: IKZF1 (25/35, 71% vs. 36/108, 33%, P < .001), BTG1 (11/35, 31% vs. 10/108, 9%, P =.004), and ADD3 deletions (9/19, 47% vs. 5/38, 13%, P =.008). A novel gene fusion, USP9X‐DDX3X, was discovered in 10/54 (19%) of patients. Pathway analysis of the mutational profile revealed novel involvement for focal adhesion. Although the functional relevance of many of these abnormalities are unknown, they likely activate additional pathways, which may represent novel therapeutic targets.
Modular‐level alterations of structure–function coupling in schizophrenia connectome
Authors: Sun Yu , Dai Zhongxiang , Li Junhua , Collinson Simon L. , Sim Kang
Published: December 2016

Convergent evidences have revealed that schizophrenia is associated with brain dysconnectivity, which leads to abnormal network organization. However, discrepancies were apparent between the structural connectivity (SC) and functional connectivity (FC) studies, and the relationship between structural and functional deficits in schizophrenia remains largely unknown. In this study, resting‐state functional magnetic resonance imaging and structural diffusion tensor imaging were performed in 20 patients with schizophrenia and 20 matched healthy volunteers (patients/controls = 19/17 after head motion rejection). Functional and structural brain networks were obtained for each participant. Graph theoretical approaches were employed to parcellate the FC networks into functional modules. The relationships between the entries of SC and FC were estimated within each module to identify group differences and their correlations with clinical symptoms. Although five common functional modules (including the default mode, occipital, subcortical, frontoparietal, and central modules) were identified in both groups, the patients showed a significantly reduced modularity in comparison with healthy participants. Furthermore, we found that schizophrenia‐related aberrations of SC–FC coupling exhibited complex patterns among modules. Compared with controls, patients showed an increased SC–FC coupling in the default mode and the central modules. Moreover, significant SC–FC decoupling was demonstrated in the occipital and the subcortical modules, which was associated with longer duration of illness and more severe clinical manifestations of schizophrenia. Taken together, these findings demonstrated that altered module‐dependent SC–FC coupling may underlie abnormal brain function and clinical symptoms observed in schizophrenia and highlighted the potential for using new multimodal neuroimaging biomarkers for diagnosis and severity evaluation of schizophrenia. Hum Brain Mapp 38:2008–2025, 2017. © 2017 Wiley Periodicals, Inc.
Hippocampal damage and memory impairment in congenital cyanotic heart disease
Authors: Muñoz‐López Mónica , Hoskote Aparna , Chadwick Martin J. , Dzieciol Anna M. , Gadian David G. , Chong Kling , Banks Tina , de Haan Michelle , Baldeweg Torsten , Mishkin Mortimer , Vargha‐Khadem Faraneh
Published: December 2016

Neonatal hypoxia can lead to hippocampal atrophy, which can lead, in turn, to memory impairment. To test the generalizability of this causal sequence, we examined a cohort of 41 children aged 8‐16, who, having received the arterial switch operation to correct for transposition of the great arteries, had sustained significant neonatal cyanosis but were otherwise neurodevelopmentally normal. As predicted, the cohort had significant bilateral reduction of hippocampal volumes relative to the volumes of 64 normal controls. They also had significant, yet selective, impairment of episodic memory as measured by standard tests of memory, despite relatively normal levels of intelligence, academic attainment, and verbal fluency. Across the cohort, degree of memory impairment was correlated with degree of hippocampal atrophy suggesting that even as early as neonatal life no other structure can fully compensate for hippocampal injury and its special role in serving episodic long term memory. © 2017 Wiley Periodicals, Inc.
Further analysis of subtypes of automatically reinforced SIB: A replication and quantitative analysis of published datasets
Authors: Hagopian Louis P. , Rooker Griffin W. , Zarcone Jennifer R. , Bonner Andrew C. , Arevalo Alexander R.
Published: December 2016

Hagopian, Rooker, and Zarcone (2015) evaluated a model for subtyping automatically reinforced self‐injurious behavior (SIB) based on its sensitivity to changes in functional analysis conditions and the presence of self‐restraint. The current study tested the generality of the model by applying it to all datasets of automatically reinforced SIB published from 1982 to 2015. We identified 49 datasets that included sufficient data to permit subtyping. Similar to the original study, Subtype‐1 SIB was generally amenable to treatment using reinforcement alone, whereas Subtype‐2 SIB was not. Conclusions could not be drawn about Subtype‐3 SIB due to the small number of datasets. Nevertheless, the findings support the generality of the model and suggest that sensitivity of SIB to disruption by alternative reinforcement is an important dimension of automatically reinforced SIB. Findings also suggest that automatically reinforced SIB should no longer be considered a single category and that additional research is needed to better understand and treat Subtype‐2 SIB.
Stand‐Alone Sustainability Reporting Practices in an Emerging Market: A Longitudinal Investigation
Authors: Uyar Ali
Published: December 2016

This study investigates sustainability reporting practices in the emerging market of Turkey for a 10‐year period between 2004 and 2013. While there are several Turkish firms preparing sustainability reports consistently during the sample period, there is also a long road to be traveled with regard to consistent and complete reporting on sustainability. The most widespread framework used in sustainability reporting is the Global Reporting Initiative (GRI) framework. One of the main features of the GRI framework is that it provides grades, known as application levels, for the extent of a company's sustainability initiatives and reporting. The number of reports containing GRI‐verified application levels and the levels of sustainability are both on the rise. Moreover, there is a slow increase in the number of externally prepared assurance reports on sustainability numbers. The majority of these reports were prepared by Big Four accounting firms. Finally, the outsourcing of sustainability reporting has become more prevalent during the sample period. © 2017 Wiley Periodicals, Inc.
The Inspector General Function and Outsourcing: An Introduction
Authors: Shapiro David M.
Published: December 2016

In light of the apparent lack of success of one‐size‐fits‐all approaches to process improvement generally and the importance of localized conditions to problem solving, the inspector general (IG) function may conceivably be performed, entirely or in part, by the private sector without any clearly obvious detriments in fact; that is, particular circumstances may support the IG as a private‐sector outsourced inspection and oversight unit. As public‐sector budgets become strained and the significance of the independent (not‐for‐profit) sector gains in prominence and influence, the role of the IG may be redesigned and reimplemented as a function within the independent/private sector, separate and apart from the agency under its inspection and oversight responsibilities. Thus, it would be directly subject to the demands and constraints commonly applied to the private sector, including performance measures such as profitability, maintenance of adequate capital reserves, and so on. The relationships among the public, private, and independent sectors, including analysis of the effectiveness of financial and performance standards, as well as potential effects on the IG unit of obligations to stakeholders distinct from the current mix of stakeholders in the provision of public‐sector service such as private shareholders, will form part of this discussion. © 2017 Wiley Periodicals, Inc.
Alternative Earnings Management Techniques: What Audit Committees and Internal Auditors Should Know
Authors: Braswell Mike , Daniels Roger B.
Published: December 2016

The desire to meet analysts' earnings expectations has driven companies to abandon credible financial reporting by stretching the boundaries of generally accepted accounting principles (GAAP), and even making operational and investment decisions that compromise future financial performance. Although external auditors have made strides in curtailing GAAP‐based earnings management, real earnings management (REM) has been adopted by management who hope to improve reported earnings. Such behavior should be of concern to audit committees (ACs) whose responsibilities extend beyond simple compliance with GAAP, to include ensuring that financial information is credible enough to facilitate risk assessments and to maintain effective internal control systems to monitor the effective use of resources by management to maximize long‐term shareholder wealth.

The purpose of this article is to increase awareness about the nature, extent, and consequences of management's use of REM to meet Wall Street expectations. We also discuss company and governance attributes that are associated with REM so that ACs and internal auditors (IAs) are able to identify circumstances in which REM is employed to generate earnings that satisfy Wall Street. Specific techniques to detect REM are provided, as well as disclosure alternatives that the AC may use to assist financial statement users in assessing current‐ and future‐period financial performance. © 2017 Wiley Periodicals, Inc.
pyMolDyn: Identification, structure, and properties of cavities/vacancies in condensed matter and molecules
Authors: Heimbach Ingo , Rhiem Florian , Beule Fabian , Knodt David , Heinen Josef , Jones Robert O.
Published: December 2016

pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos. © 2016 Wiley Periodicals, Inc.
Optimal Two‐Dimensional Optical Orthogonal Codes with the Best Cross‐Correlation Constraint
Authors: Feng Tao , Wang Lidong , Wang Xiaomiao , Zhao Yancai
Published: December 2016

The study of optical orthogonal codes has been motivated by an application in an optical code‐division multiple access system. From a practical point of view, compared to one‐dimensional optical orthogonal codes, two‐dimensional optical orthogonal codes tend to require smaller code length. On the other hand, in some circumstances only with good cross‐correlation one can deal with both synchronization and user identification. These motivate the study of two‐dimensional optical orthogonal codes with better cross‐correlation than auto‐correlation. This paper focuses on optimal two‐dimensional optical orthogonal codes with the auto‐correlationand the best cross‐correlation 1. By examining the structures ofw‐cyclic group divisible designs and semi‐cyclic incomplete holey group divisible designs, we present new combinatorial constructions for two‐dimensional‐optical orthogonal codes. Whenand, the exact number of codewords of an optimal two‐dimensional‐optical orthogonal code is determined for any positive integersnand.
Ecophysiological Indicators to Assess Drought Responses of Arid Zone Native Seedlings in Reconstructed Soils
Authors: Bateman Amber , Lewandrowski Wolfgang , Stevens Jason C. , Muñoz‐Rojas Miriam
Published: December 2016

Restoration of degraded arid and semi‐arid land faces the challenge of reinstating vegetation communities exposed to limited and variable rainfall events that in combination with a deficit of original topsoil may exceed thresholds for seedling development. In a series of glasshouse experiments, we evaluated variation in drought responses of (i) 21 arid zone plant species from the mining intensive Pilbara region of Western Australia in an original topsoil substrate and (ii) four selected species (Acacia inaequilatera,Acacia spondylophylla,Eucalyptus leucophloiaandTriodia epactia) in three different soil substrates (topsoil, overburden material and a blend of both soil materials) that may be considered as an alternative substrate for restoration. Seedling drought responses were tested using ecophysiological indicators (e.g. stomatal conductance and leaf water potential (Ψleaf) at the time of stomatal closure, among others) during soil drying. Our results showed that plant life form and morphological traits interact with ecophysiological indicators to show that trees are significantly less tolerant to drought‐related stress than shrubs and herbs (p ≤ 0·05). When grown in overburden material seedlings experienced a decline in overall plant growth (87% inT. epactiaand 62% inE. leucophloia) and ecophysiological drought tolerance. These responses are evidence of the low quality of the overburden substrate, which has a depleted nutrient content and low water retention capacity. Overall, this study highlights the sensitivity of early seedling development and the importance of facilitating seedling recruitment and survival to secure successful arid zone restoration. Copyright © 2016 John Wiley & Sons, Ltd.
On quality of radar rainfall with respect to temporal and spatial resolution for application to urban areas
Authors: Yoon Jungsoo , Joo Jingul , Yoo Chulsang , Hwang Seokhwan , Lim Sanghun
Published: December 2016

In this study the quality of radar rainfall with respect to temporal and spatial resolution was examined. Gwangdeoksan Radar and the Korea Institute of Civil Engineering and Building Technology (KICT) Radar were used for this purpose, along with the automatic weather systems data within Seoul. In addition, several quantitative quality measures were applied to examine the resolution. A negative bias of more than 40% in the radar rainfall of Gwangdeoksan Radar occurred with changes in the temporal and spatial resolution. However, the negative bias in the radar rainfall of KICT Radar was less than 10%. The mean square error in the radar rainfall of Gwangdeoksan Radar ranged from 5.5 to 0.4 mm2 h−2 and the mean square error in the radar rainfall of KICT Radar ranged from 30.2 to 1.5 mm2 h−2. The correlation co‐efficient of the accumulated time of 30 min was more than 0.7, which increased by 30% from the correlation co‐efficient of the accumulated time of 10 min. The bias in the radar rainfall of Gwangdeoksan Radar was still large with changes in the temporal and spatial resolution. However, the radar rainfall of KICT Radar was quantitatively similar to the gauge rainfall, and so the radar rainfall did not need any further quantitative correction.
Analysis of components of variance determining probability of setup errors in CBCT‐guided stereotactic radiotherapy of lung tumors
Authors: Cuijpers Johan P. , Dahele Max , Jonker Marianne , Kraan Bianca , Senan Suresh , Slotman Ben , Verbakel Wilko FAR
Published: December 2016

Purpose

Online tumor matching for SABR lung setup requires margins for inaccuracies due to intra‐fraction variability of breathing‐averaged tumor position (BATP) and CBCT image guidance. We studied intra‐fraction variability during SABR delivery using VMAT, corrected these for measurement inaccuracies, and quantified the CBCT image‐guidance uncertainties.

Materials and methods

For 193 fractions in 38 patients positioned without immobilization devices, CBCT scans were acquired before and after 2 arcs of a RapidArc treatment. A hidden marker test was performed to determine the accuracy of the CBCT system and an inter‐observer test was performed to measure registration accuracy. Intra‐fraction variability was calculated after correction for these components of variance, and the prediction interval for setup inaccuracies was determined.

Results

Correction for measurement inaccuracies reduced the intra‐fraction variability of the BATP from 1.9 to 1.6 mm in AP, from 1.7 to 1.4 mm in SI and from 1.5 to 1.1 mm in LR direction (1 SD). Intra‐fraction variability in bony anatomy after correction was ≤ 1 mm (1 SD). The 95% prediction interval to account for CBCT image‐guidance uncertainties and intra‐fraction variability was determined, and was found to be within our institutional PTV margins of 5 mm.

Conclusions

Our findings show that it is essential to account for measurement and system inaccuracies when obtaining data for validating PTV margins from online CBCT image guidance.
Evaluating psychological distress data
Authors: McIntosh James
Published: December 2016

Kessler k6 psychological distress scores are analyzed using a count model and item response theory (IRT) models are applied to the items which produce the k6 score and generate an alternative distress score, θ*. Other ways of utilizing the constituent items are also examined. The data used in the analysis comes from the 2014 National Survey of Drug Use and Health. Three important results emerge. First, θ* and k6 are not highly correlated and their distributions are quite different. The k6 score gives a much more favourable picture of mental health than θ*. Second, k6 does a much better job in explaining participation in treatment programs than θ* suggesting a very limited role for IRT methods in the analysis of psychological distress data. As a diagnostic tool k6 is an effective and simple way of summarizing the item data. Third, for researchers interested in which individual characteristics determine psychological distress better results are obtained by analyzing the six constituent items which are used to generate the k6 score using ordered probability models rather than k6 itself.
The varied ways of being male and female
Authors: Schärer Lukas
Published: December 2016

Our understanding of sexual reproduction is mainly informed by research on gonochorists (i.e., species with separate sexes), including insects, birds, and mammals. But the male and female sexes are not two types of individuals; they actually represent two different reproductive strategies, and in many organisms, these two strategies are distributed among individuals in a population in a variety of ways. For example, sequential hermaphrodites (or sex‐changers) exhibit one strategy early in life and later switch to the other, while simultaneous hermaphrodites exhibit both strategies at the same time. There are also many intermediate sexual systems that mix gonochorists and hermaphrodites in the same species and within many organismal groups, shifts occur between these sexual systems. A fascinating collection of six articles in this special issue on Hermaphroditism & Sex Determination impressively documents some important challenges to our understanding of sex determination, and the specification of male and female reproductive function when these need to occur within the same individual rather than in two separate individuals. Moreover, hermaphroditism changes how we need to think about reproductive allocation to sexual functions, how such allocation can be specified, as well as how the sexual system affects sexual conflict and the resulting antagonistic coevolution. Our understanding of sexual reproduction will profit greatly from exploring the varied ways of being male and female. Mol. Reprod. Dev. 84: 94–104, 2017. © 2017 Wiley Periodicals, Inc.
A narrative review of musculoskeletal problems of the lower extremity and back associated with the interface between occupational tasks, feet, footwear and flooring
Authors: Anderson Jennifer , Williams Anita E , Nester Christopher J
Published: December 2016

At least 50% of workers are exposed to the risk of musculoskeletal disorders (MSD) due to spending prolonged hours standing at work. There is a lack of information regarding issues with the feet, solutions to the problem, and links between MSD, feet, footwear and flooring. The present article provides a narrative review of the research in this area, based on 31 papers. Workers who stand for large proportions of the working day had a level of MSD considerably greater than a normal population. Muscle co‐activation, blood pooling, muscle fatigue and individual characteristics are all associated with MSD. Altering flooring provided mixed results, while footwear appeared to have the potential to affect MSD, although the dearth of literature limited the conclusions that could be drawn. Despite their inextricable link, literature regarding the relationship between occupational tasks, MSD, footwear and flooring remains limited and future studies will benefit from rigorously designed protocols.
Cognitive fatigue in patients with myasthenia gravis
Authors: Jordan Berit , Schweden Tabea L.K. , Mehl Theresa , Menge Uwe , Zierz Stephan
Published: December 2016

Introduction: Cognitive fatigue has frequently been reported in myasthenia gravis (MG). However, objective assessment of cognitive fatigability has never been evaluated. Methods: Thirty‐three MG patients with stable generalized disease and 17 healthy controls underwent a test battery including repeated testing of attention and concentration (d2‐R) and Paced Auditory Serial Addition Test. Fatigability was based on calculation of linear trend (LT) reflecting dynamic performance within subsequent constant time intervals. Additionally, fatigue questionnaires were used. Results: MG patients showed a negative LT in second d2‐R testing, indicating cognitive fatigability. This finding significantly differed from stable cognitive performance in controls (P < 0.05). Results of Paced Auditory Serial Addition Test testing did not differ between groups. Self‐assessed fatigue was significantly higher in MG patients compared with controls (P < 0.001), but did not correlate with LT. Conclusions: LT quantifies cognitive fatigability as an objective measurement of performance decline in MG patients. Self‐assessed cognitive fatigue is not correlated with objective findings. Muscle Nerve 56: 449–457, 2017
Proton and phosphorus magnetic resonance spectroscopy of the healthy human breast at 7 T
Authors: van der Kemp Wybe J.M. , Stehouwer Bertine L. , Boer Vincent O. , Luijten Peter R. , Klomp Dennis W.J. , Wijnen Jannie P.
Published: December 2016

In vivo water‐ and fat‐suppressed 1H magnetic resonance spectroscopy (MRS) and 31P magnetic resonance adiabatic multi‐echo spectroscopic imaging were performed at 7 T in duplicate in healthy fibroglandular breast tissue of a group of eight volunteers. The transverse relaxation times of 31P metabolites were determined, and the reproducibility of 1H and 31P MRS was investigated. The transverse relaxation times for phosphoethanolamine (PE) and phosphocholine (PC) were fitted bi‐exponentially, with an added short T2 component of 20 ms for adenosine monophosphate, resulting in values of 199 ± 8 and 239 ± 14 ms, respectively. The transverse relaxation time for glycerophosphocholine (GPC) was also fitted bi‐exponentially, with an added short T2 component of 20 ms for glycerophosphatidylethanolamine, which resonates at a similar frequency, resulting in a value of 177 ± 6 ms. Transverse relaxation times for inorganic phosphate, γ‐ATP and glycerophosphatidylcholine mobile phospholipid were fitted mono‐exponentially, resulting in values of 180 ± 4, 19 ± 3 and 20 ± 4 ms, respectively. Coefficients of variation for the duplicate determinations of 1H total choline (tChol) and the 31P metabolites were calculated for the group of volunteers. The reproducibility of inorganic phosphate, the sum of phosphomonoesters and the sum of phosphodiesters with 31P MRS imaging was superior to the reproducibility of 1H MRS for tChol. 1H and 31P data were combined to calculate estimates of the absolute concentrations of PC, GPC and PE in healthy fibroglandular tissue, resulting in upper limits of 0.1, 0.1 and 0.2 mmol/kg of tissue, respectively.
Conflict processing among multiple frames of reference
Authors: Nan Weizhi , Li Qi , Sun Yanlong , Wang Hongbin , Liu Xun
Published: December 2016

People rely on multiple frames of reference (FORs) to represent and update spatial relationships of different objects in a complex environment. According to the “Frame of Reference‐based Map of Salience” theory (FORMS), FORs with high salience are processed in priority, and human performance is determined by the interaction of all relevant FOR‐based representations. We conducted a modified two‐cannon task manipulating conflicts among FORs (e.g., egocentric [FOR‐EFOR], intrinsic [FOR‐IFOR]) in order to explore how FORs interact with each other. We found that participants responded slower when two IFORs were incongruent than when they were congruent. There was also an interaction between these two conflicts. Moreover, the effect size of conflict between two IFORs was much larger than that between an IFOR and an EFOR. These results suggest that although the IFOR and EFOR may be coded by different spatial representations, they rely on a common processing mechanism and compete with each other. The findings from the current study provide support for the FORMS theory.
Population Pharmacokinetics Modeling of Unbound Efavirenz, Atazanavir, and Ritonavir in HIV‐Infected Subjects With Aging Biomarkers
Authors: Dumond JB , Chen J , Cottrell M , Trezza CR , Prince HMA , Sykes C , Torrice C , White N , Malone S , Wang R , Patterson KB , Sharpless NE , Forrest A
Published: December 2016

Unbound drug is the pharmacodynamically relevant concentration. This study aimed to determine if chronologic age or markers of biologic aging, such as the frailty phenotype and p16INK4a gene expression, altered unbound pharmacokinetics (PKs) of efavirenz (EFV) and atazanavir/ritonavir (ATV/RTV). Sixty human immunodeficiency virus (HIV)‐infected participants receiving EFV and 31 receiving ATV/RTV provided 1 to 11 samples to quantify total and unbound plasma concentrations. Population PK models with total and unbound concentrations simultaneously described are developed for each drug. The unbound fractions for EFV, ATV, and RTV are 0.65%, 5.67%, and 0.63%, respectively. Covariate analysis suggests RTV unbound PK is sensitive to body size; unbound fraction of RTV is 34% lower with body mass index (BMI) above 30 kg/m2. No alterations in drug clearance or unbound fraction with age, frailty, or p16INK4a expression were observed. Assessing functional and physiologic aging markers to inform potential PK changes is necessary to determine if drug/dosing changes are warranted in the aging population.
Beneficiation of High‐Phosphorus Siderite Ore by Acid Leaching and Alkaline Oxide Reinforced Carbothermic Reduction‐Magnetic Separation Process
Authors: Lv Chao , Wen Shuming , Yang Kun , Bai Shaojun
Published: December 2016

In this study, the beneficiation of high‐phosphorus siderite ore by acid leaching dephosphorization, alkaline oxide reinforced carbothermic reduction and magnetic separation is investigated. X‐ray diffraction (XRD), scanning electron microscopy (SEM), and energy‐dispersive analysis (EDS) are employed to characterize the samples. The results indicate that the phosphorous mainly exists as fluorapatite and can be removed effectively by sulfuric acid leaching. The dephosphorization rate is 90.41% under proper conditions. Iron grain size in reductive ore without alkaline oxide additive (performed at 1000 °C for 150 min with 20% dosage of reductant coal) is tiny, and the fayalite is abundant. Moreover, the iron grain is closely associated with slag. With 12% dosage of alkaline oxide additive (Na2CO3:CaO = 1:1), the reduction of siderite is reinforced. The iron particle size in reduced ore is coarse and the diffraction intensity of metallic iron increases obviously. The reinforcing affect is mainly caused by an increase of the reducing reaction activity of FeO. After the grinding and magnetic separation process, an iron concentrate with 70.83% Fe and 0.05% P is obtained, which can be served as raw material for ironmaking.