bluuebunny/crossref_metadata_2025 huggingface dataset:
D3h [A-CE3-A]− (E = Al and Ga, A = Si, Ge, Sn, and Pb): A new class of hexatomic mono-anionic species with trigonal bipyramidal carbon
Authors: Wu Yan-Bo , Li Yan-Qin , Bai Hui , Lu Hai-Gang , Li Si-Dian , Zhai Hua-Jin , Wang Zhi-Xiang
Published: March 2014

The non-classical trigonal bipyramidal carbon (TBPC) arrangement generally exists as transition states (TSs) in nucleophilic bimolecular substitution (SN2) reactions. Nevertheless, chemists have been curious about whether such a carbon bonding could be stable in equilibrium structures for decades. As the TBPC arrangement was normally realized as cationic species theoretically and experimentally, only one anionic example ([At-C(CN)3-At]−) was computationally devised. Herein, we report the design of a new class of anionic TBPC species by using the strategy similar to that for stabilizing the non-classical planar hypercoordinate carbon. When electron deficient Al and Ga were used as the equatorial ligands, eight D3h [A-CE3-A]− (E = Al and Ga, A = Si, Ge, Sn, and Pb) TBPC structures were found to be the energy minima rather than TSs at both the B3LYP and MP2 levels. Remarkably, the energetic results at the CCSD(T) optimization level further identify [Ge-CAl3-Ge]− and [Sn-CGa3-Sn]− even to be the global minima and [Si-CAl3-Si]− and [Ge-CGa3-Ge]− to be the local minima, only slightly higher than their global minima. The electronic structure analyses reveal that the substantial ionic C–E bonding, the peripheral E–A covalent bonding, and the axial mc-2e (multi center-two electrons) bonding play roles in stabilizing these TBPC structures. The structural simplicity and the high thermodynamic stability suggest that some of these species may be generated and captured in the gas phase. Furthermore, as mono-anionic species, their first vertical detachment energies are differentiable from those of their nearest isomers, which would facilitate their characterization via experiments such as the negative ion photoelectron spectroscopy.
Encapsulated formulation of the selective frequency damping method
Authors: Jordi Bastien E. , Cotter Colin J. , Sherwin Spencer J.
Published: March 2014

We present an alternative “encapsulated” formulation of the selective frequency damping method for finding unstable equilibria of dynamical systems, which is particularly useful when analysing the stability of fluid flows. The formulation makes use of splitting methods, which means that it can be wrapped around an existing time-stepping code as a “black box.” The method is first applied to a scalar problem in order to analyse its stability and highlight the roles of the control coefficient χ and the filter width Δ in the convergence (or not) towards the steady-state. Then the steady-state of the incompressible flow past a two-dimensional cylinder at Re = 100, obtained with a code which implements the spectral/hp element method, is presented.
Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. III. Impact of combining rules on mixtures properties
Authors: Desgranges Caroline , Delhommelle Jerome
Published: March 2014

Combining rules, such as the Lorentz-Berthelot rules, are routinely used to calculate the thermodynamic properties of mixtures using molecular simulations. Here we extend the expanded Wang-Landau simulation approach to determine the impact of the combining rules on the value of the partition function of binary systems, and, in turn, on the phase coexistence and thermodynamics of these mixtures. We study various types of mixtures, ranging from systems of rare gases to biologically and technologically relevant mixtures, such as water-urea and water-carbon dioxide. Comparing the simulation results to the experimental data on mixtures of rare gases allows us to rank the performance of combining rules. We find that the widely used Lorentz-Berthelot rules exhibit the largest deviations from the experimental data, both for the bulk and at coexistence, while the Kong and Waldman-Hagler provide much better alternatives. In particular, in the case of aqueous solutions of urea, we show that the use of the Lorentz-Berthelot rules has a strong impact on the Gibbs free energy of the solute, overshooting the value predicted by the Waldman-Hagler rules by 7%. This result emphasizes the importance of the combining rule for the determination of hydration free energies using molecular simulations.
Cavity morphology in a Ni based superalloy under heavy ion irradiation with cold pre-injected helium. I
Authors: Zhang He , Yao Zhongwen , Daymond Mark R. , Kirk Marquis A.
Published: March 2014

In order to understand radiation damage in the nickel based superalloy Inconel X-750 in thermal reactors, where (n, α) transmutation reaction also occurred in addition to fast neutron induced atomic displacement, heavy ion (1 MeV Kr2+) irradiation with pre-injected helium was performed under in-situ observations of an intermediate voltage electron microscope at Argonne National Laboratory. By comparing to our previous studies using 1 MeV Kr2+ irradiation solely, the pre-injected helium was found to be essential in cavity nucleation. Cavities started to be visible after Kr2+ irradiation to 2.7 dpa at ≥200 °C in samples containing 200 appm, 1000 appm, and 5000 appm helium, respectively, but not at lower temperatures. The cavity growth was observed during the continuous irradiation. Cavity formation appeared along with a reduced number density of stacking fault tetrahedra, vacancy type defects. With higher pre-injected helium amount, a higher density of smaller cavities was observed. This is considered to be the result of local trapping effect of helium which disperses vacancies. The average cavity size increases with increasing irradiation temperatures; the density reduced; and the distribution of cavities became heterogeneous at elevated temperatures. In contrast to previous characterization of in-reactor neutron irradiated Inconel X-750, no obvious cavity sink to grain boundaries and phase boundaries was found even at high doses and elevated temperatures. MC-type carbides were observed as strong sources for agglomeration of cavities due to their enhanced trapping strength of helium and vacancies.
Cavity morphology in a Ni based superalloy under heavy ion irradiation with hot pre-injected helium. II
Authors: Zhang He , Yao Zhongwen , Daymond Mark R. , Kirk Marquis A.
Published: March 2014

In the current investigation, TEM in-situ heavy ion (1 MeV Kr2+) irradiation with helium pre-injected at elevated temperature (400 °C) was conducted to simulate in-reactor neutron irradiation induced damage in CANDU spacer material Inconel X-750, in an effort to understand the effects of helium on irradiation induced cavity microstructures. Three different quantities of helium, 400 appm, 1000 appm, and 5000 appm, were pre-injected directly into TEM foils at 400 °C. The samples containing helium were then irradiated in-situ with 1 MeV Kr2+ at 400 °C to a final dose of 5.4 dpa (displacement per atom). Cavities were formed from the helium injection solely and the cavity density and size increased with increasing helium dosage. In contrast to previous heavy ion irradiations with cold pre-injected helium, heterogeneous nucleation of cavities was observed. During the ensuing heavy ion irradiation, dynamical observation showed noticeable size increase in cavities which nucleated close to the grain boundaries. A “bubble-void” transformation was observed after Kr2+ irradiation to high dose (5.4 dpa) in samples containing 1000 appm and 5000 appm helium. Cavity distribution was found to be consistent with in-reactor neutron irradiation induced cavity microstructures. This implies that the distribution of helium is greatly dependent on the injection temperature, and helium pre-injection at high temperature is preferred for simulating the migration of the transmutation produced helium.
Influencing dielectric properties of relaxor polymer system by blending vinylidene fluoride–trifluoroethylene-based terpolymer with a ferroelectric copolymer
Authors: Casar G. , Li X. , Zhang Q. M. , Bobnar V.
Published: March 2014

We report the influence of blending the poly(vinylidene fluoride–trifluoroethylene–chlorofluoroethylene) terpolymer [P(VDF–TrFE–CFE), a member of the relaxor polymer family that exhibits fast response speeds, giant electrostriction, high electric energy density, and large electrocaloric effect] with the ferroelectric poly(vinylidene fluoride–trifluoroethylene) copolymer [P(VDF–TrFE)] on its dielectric response. Although both components form separate crystalline phases, at low copolymer content, the P(VDF–TrFE–CFE)/P(VDF–TrFE) blends entirely exhibit a relaxorlike linear dielectric response, since the interfacial couplings to the bulky defects in the terpolymer convert the normal ferroelectric copolymer into a relaxor. On the other hand, the linear and particularly nonlinear dielectric experiments, i.e., temperature dependences of the second and the third harmonic dielectric response, clearly evidence that in blends with 20–50 wt. % of P(VDF–TrFE), the ferroelectric and relaxor states coexist. The nonlinear dielectric response further reveals the onset of ferroelectric behavior also in blends with low copolymer amount, due to a high VDF content in the terpolymer, which increases the ferroelectric interactions: While in relaxor polymers with lower VDF content, the third order nonlinear dielectric constant, in accordance with the theoretical predictions, exhibits solely positive values, here it changes sign even in the pure P(VDF–TrFE–CFE).
Single-friction-surface triboelectric generator with human body conduit
Authors: Meng Bo , Cheng Xiaoliang , Zhang Xiaosheng , Han Mengdi , Liu Wen , Zhang Haixia
Published: March 2014

We present a transparent single-friction-surface triboelectric generator (STEG) employing human body as the conduit, making the applications of STEG in portable electronics much more practical and leading to a significant output improvement. The STEG with micro-patterned polydimethylsiloxane surface achieved an output voltage of over 200 V with a current density of 4.7 μA/cm2. With human body conduit, the output current increased by 39% and the amount of charge that transferred increased by 34% compared to the results with grounded electrode. A larger increment of 210% and 81% was obtained in the case of STEG with a large-size flat polyethylene terephthalate surface.
Cathodoluminescence of stacking fault bound excitons for local probing of the exciton diffusion length in single GaN nanowires
Authors: Nogues Gilles , Auzelle Thomas , Den Hertog Martien , Gayral Bruno , Daudin Bruno
Published: March 2014

We perform correlated studies of individual GaN nanowires in scanning electron microscopy combined to low temperature cathodoluminescence, microphotoluminescence, and scanning transmission electron microscopy. We show that some nanowires exhibit well localized regions emitting light at the energy of a stacking fault bound exciton (3.42 eV) and are able to observe the presence of a single stacking fault in these regions. Precise measurements of the cathodoluminescence signal in the vicinity of the stacking fault give access to the exciton diffusion length near this location.
Periodic striations on beryllium and tungsten surfaces by indirect femtosecond laser irradiation
Authors: Lungu C. P. , Ticoş C. M. , Poroşnicu C. , Jepu I. , Lungu M. , Marcu A. , Luculescu C. , Cojocaru G. , Ursescu D. , Bănici R. , Ungureanu G. R.
Published: March 2014

Femtosecond laser pulses with λ = 800 nm were focused in air at one atmosphere and in deuterium (D) at low pressure. Submicron periodic structures were observed on surfaces made of Be, W and a mixture of Be-W immersed in these gases and placed nearly parallel with the laser beam, at 300 μm from the focal spot. In air, no structures were observed on Be. For the Be-W mixture, the periodic structures were uniform and parallel when formed in D but irregular in air. In this last case the striations were organized into small patches of 1 to 2 μm in size.
A microfluidic model for organ-specific extravasation of circulating tumor cells
Authors: Riahi R. , Yang Y. L. , Kim H. , Jiang L. , Wong P. K. , Zohar Y.
Published: March 2014

Circulating tumor cells (CTCs) are the principal vehicle for the spread of non-hematologic cancer disease from a primary tumor, involving extravasation of CTCs across blood vessel walls, to form secondary tumors in remote organs. Herein, a polydimethylsiloxane-based microfluidic system is developed and characterized for in vitro systematic studies of organ-specific extravasation of CTCs. The system recapitulates the two major aspects of the in vivo extravasation microenvironment: local signaling chemokine gradients in a vessel with an endothelial monolayer. The parameters controlling the locally stable chemokine gradients, flow rate, and initial chemokine concentration are investigated experimentally and numerically. The microchannel surface treatment effect on the confluency and adhesion of the endothelial monolayer under applied shear flow has also been characterized experimentally. Further, the conditions for driving a suspension of CTCs through the microfluidic system are discussed while simultaneously maintaining both the local chemokine gradients and the confluent endothelial monolayer. Finally, the microfluidic system is utilized to demonstrate extravasation of MDA-MB-231 cancer cells in the presence of CXCL12 chemokine gradients. Consistent with the hypothesis of organ-specific extravasation, control experiments are presented to substantiate the observation that the MDA-MB-231 cell migration is attributed to chemotaxis rather than a random process.
Connective management and governance network performance: the mediating role of throughput legitimacy. Findings from survey research on complex water projects in the Netherlands
Authors: van Meerkerk Ingmar , Edelenbos Jurian , Klijn Erik-Hans
Published: March 2014

In this paper we empirically examine the relationship between connective management, democratic legitimacy, and network performance in governance networks around complex water projects in the Netherlands. Realizing effective and legitimate solutions in such a context is highly challenging, as a variety of interests are at stake, and actors often disagree about goals of the water issue at stake. Although previous research has indicated the importance of network management for the performance of governance networks, the issue of democratic legitimacy is not much addressed in this relationship. Building on the literature, we expect to find that throughput legitimacy has a partly mediating role in the relationship between connective management and network performance. The results, based on survey research, indicate that governance networks have indeed democratic potential but, in order to make this potential manifest, network managers can play a key ‘connective’ role. Furthermore, the results confirm our hypotheses that throughput legitimacy positively affects network performance and that it has a mediating effect on the relationship between connective management and network performance. Network managers can create important conditions for the evolution of a democratic governance process, but are dependent on the way stakeholders interact with one another and the democratic quality of that interaction.
Influence of high pre-rigor temperature and fast pH fall on muscle proteins and meat quality: a review
Authors: Kim Yuan H. Brad , Warner Robyn D. , Rosenvold Katja
Published: March 2014

The impacts of accelerated pH decline combined with high muscle temperature on post-mortem muscle metabolism and subsequent meat quality attributes have been extensively studied. Traditionally, this phenomenon has been observed in pork muscles, primarily due to the relatively fast post-mortem glycolysis rate and its relationships to stress susceptibility of pigs before slaughter. However, the protein-denaturing condition of high temperature/rapid pH fall and subsequent PSE (pale, soft and exudative)-like abnormal meat quality characteristics have been observed in muscles from other species such as beef, lamb, venison and even poultry. Various pre-rigor conditions including the application of electrical stimulation, hot-boning, and/or pre-rigor carcass chilling temperatures in various muscles, in conjunction with carcass stretching/hanging methods, can also contribute to muscle-protein denaturation pre-rigor. This review considers the influence of a faster than normal pH fall at a higher than normal pre-rigor temperature on glycolysis, post-mortem muscle proteins and subsequently meat quality attributes. Gaps in current knowledge are identified and recommendations made for additional research.
Gender norms and sexual behaviours among men in western Jamaica
Authors: Walcott Melonie M. , Funkhouser Ellen , Aung Maung , Kempf Mirjam C. , Ehiri John , Zhang Kui , Bakhoya Marion , Hickman Deborah , Jolly Pauline E.
Published: March 2014

Objectives Gender norms, especially among men, can reduce the effectiveness of HIV prevention programs. We sought to assess the association between attitudes towards gender norms and risky sexual behaviours, and identify sociodemographic factors that predict gender-inequitable and masculinity norms among men in western Jamaica. Methods: A cross-sectional, survey of 549 men aged 19–54 years was conducted. Attitudes towards gender norms were measured using the Gender Equitable Men and Macho scales. Logistic regression and general linear models were used to assess associations between gender norms and multiple sexual partners, and to identify the associated sociodemographic factors. Adjusted odds ratios (AORs) and 95% confidence intervals (CIs) are presented. Results: Fifty-four percent of the participants (mean age = 32.4 years) reported multiple sex partners and 22% reported unprotected sex with non-regular partner in the past 12 months. Men with moderate (AOR = 2.2; 95% CI = 1.4–3.3) and high (AOR = 4.2; 95% CI = 2.0–8.5) support for inequitable gender norms, and moderate (AOR = 1.7; 95% CI = 1.1–2.7) and high (AOR = 2.5; 95% CI = 1.5–4.3) support for masculinity norms were more likely to report multiple sex partners. Similarly, men with moderate (AOR = 2.4; 95% CI = 1.3–4.3) and high (AOR = 2.5; 95% CI = 1.2–5.2) support for inequitable gender norms were more likely to report unprotected sex with a nonregular partner. Conclusion: A high proportion of Jamaican men engage in risky sexual behaviours. These results highlight the need for behaviour change interventions addressing gender norms targeting Jamaican men.
Uptake, yield and resource requirements of screening for asymptomatic sexually transmissible infections among HIV-positive people attending a hospital outpatient clinic
Authors: Ritchie Stephen , Henley Rebecca , Hilton Jackie , Handy Rupert , Ingram Joan , Mundt Susan , Nisbet Mitzi , Thomas Mark , Briggs Simon
Published: March 2014

Background
We performed a prospective audit of screening for asymptomatic sexually transmissible infections (STIs), during an intensive effort to screen all patients at our hospital-based HIV clinic. We aimed to measure the effectiveness and resource implications of our screening program. Methods: All outpatients who attended during an 8-month period were invited to take part in opt-out screening for chlamydia (Chlamydia trachomatis), gonorrhoea (Neisseria gonorrhoeae) and syphilis. Participants completed a brief questionnaire, were asked about current symptoms of STIs and self-collected specimens for laboratory testing. Results: The majority (535 out of 673, 80%) of the patients who were asked to participate provided specimens for screening. No chlamydia, gonorrhoea or syphilis infections were identified in women (n = 91) or in heterosexual men (n = 76). In contrast, 34 out of 368 (10%) of men who have sex with men tested positive (chlamydia, 25; gonorrhoea, 2; chlamydia and gonorrhoea, 2; syphilis, 5). The laboratory cost of diagnosing each case of rectal chlamydia or gonorrhoea (NZ$664) was substantially lower than the cost of diagnosing each case of urethral infection (NZ$5309). Conclusions: There was high uptake of screening among our clinic population, who preferred screening to be performed at the hospital clinic. The yield of screening men who have sex with men warrants continued annual screening for rectal gonorrhoea and chlamydia and for syphilis.
Management rates of sexually transmissible infections by Australian general practitioners, 2000–2012
Authors: Santella Anthony J. , Pollack Allan , Harrison Christopher , Sawleshwarkar Shailendra N. , Britt Helena C. , Hillman Richard J.
Published: March 2014

Background In Australia, general practitioners (GPs) manage the majority of sexually transmissible infections (STIs). Most STIs are diagnosed and treated by GPs as a result of symptom recognition or risk identification. We aimed to determine how frequently six common STIs were managed by GPs, the characteristics of the GPs and patients, and any changes over time. Methods: Data from the Bettering the Evaluation and Care of Health (BEACH) program for April 2000–March 2012 were analysed. BEACH is a national study of GP activity. The overall management rates of genital herpes (herpes simplex virus, HSV), genital warts, HIV, chlamydia (Chlamydia trachomatis), gonorrhoea (Neisseria gonorrhoeae) and syphilis were calculated. Results: In total, 11 784 GPs recorded details of 1 178 400 patient encounters. These included: 115 cases of genital HSV per 100 000 encounters, 92 of genital warts, 67 of HIV, 39 of chlamydia, 6 of gonorrhoea and 7 of syphilis. Higher management rates occurred among patients who were male, 15–24 years old, more socially advantaged, Aboriginal or Torres Strait Islander, resident in a major city or of English-speaking background. GPs who were female and those aged under 60 years had higher STI management rates than their counterparts. Conclusions: HSV and warts were the most common STIs managed. Lower management rates for the other STIs may reflect lower incidence or lower testing rates, because these other STIs are frequently asymptomatic. It is important to determine whether existing approaches effectively target the most at-risk communities and what barriers to presentation exist.
High prevalence and incidence of HIV, sexually transmissible infections and penile foreskin cutting among sexual health clinic attendees in Papua New Guinea
Authors: Vallely Andrew , Ryan Claire E. , Allen Joyce , Sauk Joyce C. , Simbiken Cassey S. , Wapling Johanna , Kaima Petronia , Kombati Zure , Law Greg , Fehler Glenda , Murray John M. , Siba Peter , Kaldor John M.
Published: March 2014

Background Papua New Guinea (PNG) has one of the highest prevalences of HIV and sexually transmissible infections (STIs) in the Asia-Pacific region, and one of the highest burdens of maternal syphilis and cervical cancer globally. Despite this disease burden, only limited clinical research in sexual and reproductive health has been conducted in PNG. Methods: A longitudinal clinical cohort study was conducted at two sexual health clinics. Participants completed a behavioural interview, clinical assessment and genital examination at baseline, and at 12, 24 and 50 weeks, including specimen collection for STI diagnostics. Results: In total, 154 people attended a screening visit. Reattendance at 12, 24 and 50-weeks was 87%, 78% and 80% respectively. At baseline, HIV prevalence was 3.3%; chlamydia (Chlamydia trachomatis), 29.2%; gonorrhoea (Neisseria gonorrhoeae), 22.1%; Trichomonas vaginalis 15.6%; herpes simplex type-2 (HSV-2), 46.1%; active syphilis, 11.7%. Multiple infections were common particularly among women. The incidence of chlamydia was 27 per 100 person-years (PY); gonorrhoea, 15 out of 100 PY; T. vaginalis, 29 out of 100 PY; HSV-2, 12 out of 100 PY; syphilis, 8 out of 100 PY. No incident HIV cases were recorded. At baseline, 39% of men in Mt Hagen and 65% in Port Moresby had a penile foreskin cut, with a dorsal slit being the most common. Two men underwent penile cutting during the follow-up period. Conclusions: The prevalence and incidence of STIs, HIV and penile cutting were high among sexual health clinic attendees. High retention figures suggest that this population may be suitable for future interventions research and clinical trials.
Turtle: Identifying frequent
k
-mers with cache-efficient algorithms
Authors: Roy Rajat Shuvro , Bhattacharya Debashish , Schliep Alexander
Published: March 2014

Motivation: Counting the frequencies of k -mers in read libraries is often a first step in the analysis of high-throughput sequencing data. Infrequent k -mers are assumed to be a result of sequencing errors. The frequent k -mers constitute a reduced but error-free representation of the experiment, which can inform read error correction or serve as the input to de novo assembly methods. Ideally, the memory requirement for counting should be linear in the number of frequent k -mers and not in the, typically much larger, total number of k -mers in the read library.

Results: We present a novel method that balances time, space and accuracy requirements to efficiently extract frequent k -mers even for high-coverage libraries and large genomes such as human. Our method is designed to minimize cache misses in a cache-efficient manner by using a pattern-blocked Bloom filter to remove infrequent k -mers from consideration in combination with a novel sort-and-compact scheme, instead of a hash, for the actual counting. Although this increases theoretical complexity, the savings in cache misses reduce the empirical running times. A variant of method can resort to a counting Bloom filter for even larger savings in memory at the expense of false-negative rates in addition to the false-positive rates common to all Bloom filter-based approaches. A comparison with the state-of-the-art shows reduced memory requirements and running times.

Availability and implementation: The tools are freely available for download at http://bioinformatics.rutgers.edu/Software/Turtle and http://figshare.com/articles/Turtle/791582 .

Contact:  rajatroy@cs.rutgers.edu or schliep@cs.rutgers.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation
Authors: Kocher Jean-Pierre A. , Quest Daniel J. , Duffy Patrick , Meiners Michael A. , Moore Raymond M. , Rider David , Hossain Asif , Hart Steven N. , Dinu Valentin
Published: March 2014

Motivation:  The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines.

Availability and implementation: The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu .

Contact:  Kocher.JeanPierre@mayo.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A gradient-boosting approach for filtering
de novo
mutations in parent–offspring trios
Authors: Liu Yongzhuang , Li Bingshan , Tan Renjie , Zhu Xiaolin , Wang Yadong
Published: March 2014

Motivation: Whole-genome and -exome sequencing on parent–offspring trios is a powerful approach to identifying disease-associated genes by detecting de novo mutations in patients. Accurate detection of de novo mutations from sequencing data is a critical step in trio-based genetic studies. Existing bioinformatic approaches usually yield high error rates due to sequencing artifacts and alignment issues, which may either miss true de novo mutations or call too many false ones, making downstream validation and analysis difficult. In particular, current approaches have much worse specificity than sensitivity, and developing effective filters to discriminate genuine from spurious de novo mutations remains an unsolved challenge.

Results: In this article, we curated 59 sequence features in whole genome and exome alignment context which are considered to be relevant to discriminating true de novo mutations from artifacts, and then employed a machine-learning approach to classify candidates as true or false de novo mutations. Specifically, we built a classifier, named De Novo Mutation Filter (DNMFilter), using gradient boosting as the classification algorithm. We built the training set using experimentally validated true and false de novo mutations as well as collected false de novo mutations from an in-house large-scale exome-sequencing project. We evaluated DNMFilter’s theoretical performance and investigated relative importance of different sequence features on the classification accuracy. Finally, we applied DNMFilter on our in-house whole exome trios and one CEU trio from the 1000 Genomes Project and found that DNMFilter could be coupled with commonly used de novo mutation detection approaches as an effective filtering approach to significantly reduce false discovery rate without sacrificing sensitivity.

Availability: The software DNMFilter implemented using a combination of Java and R is freely available from the website at http://humangenome.duke.edu/software .

Contact:  ydwang@hit.edu.cn
Use of biomimetic hexagonal surface texture in friction against lubricated skin
Authors: Tsipenyuk Alexey , Varenberg Michael
Published: March 2014

Smooth contact pads that evolved in insects, amphibians and mammals to enhance the attachment abilities of the animals' feet are often dressed with surface micropatterns of different shapes that act in the presence of a fluid secretion. One of the most striking surface patterns observed in contact pads of these animals is based on a hexagonal texture, which is recognized as a friction-oriented feature capable of suppressing both stick–slip and hydroplaning while enabling friction tuning. Here, we compare this design of natural friction surfaces to textures developed for working in similar conditions in disposable safety razors. When slid against lubricated human skin, the hexagonal surface texture is capable of generating about twice the friction of its technical competitors, which is related to it being much more effective at channelling of the lubricant fluid out of the contact zone. The draining channel shape and contact area fraction are found to be the most important geometrical parameters governing the fluid drainage rate.
Non-steady-state heat conduction in composite walls
Authors: Deconinck Bernard , Pelloni Beatrice , Sheils Natalie E.
Published: March 2014

The problem of heat conduction in one-dimensional piecewise homogeneous composite materials is examined by providing an explicit solution of the one-dimensional heat equation in each domain. The location of the interfaces is known, but neither temperature nor heat flux is prescribed there. Instead, the physical assumptions of their continuity at the interfaces are the only conditions imposed. The problem of two semi-infinite domains and that of two finite-sized domains are examined in detail. We indicate also how to extend the solution method to the setting of one finite-sized domain surrounded on both sides by semi-infinite domains, and on that of three finite-sized domains.
Gradual adaptation of bone structure to aquatic lifestyle in extinct sloths from Peru
Authors: Amson Eli , de Muizon Christian , Laurin Michel , Argot Christine , de Buffrénil Vivian
Published: March 2014

Non-pathological densification (osteosclerosis) and swelling (pachyostosis) of bones are the main modifications affecting the skeleton of land vertebrates (tetrapods) that returned to water. However, a precise temporal calibration of the acquisition of such adaptations is still wanting. Here, we assess the timing of such acquisition using the aquatic sloth
Thalassocnus
, from the Neogene of the Pisco Formation, Peru. This genus is represented by five species occurring in successive vertebrate-bearing horizons of distinct ages. It yields the most detailed data about the gradual acquisition of aquatic adaptations among tetrapods, in displaying increasing osteosclerosis and pachyostosis through time. Such modifications, reflecting a shift in the habitat from terrestrial to aquatic, occurred over a short geological time span (
ca
4 Myr). Otherwise, the bones of terrestrial pilosans (sloths and anteaters) are much more compact than the mean mammalian condition, which suggests that the osteosclerosis of
Thalassocnus
may represent an exaptation.
Natronoarchaeum rubrum sp. nov., isolated from a marine solar saltern, and emended description of the genus Natronoarchaeum
Authors: Qiu Xing-Xing , Zhao Mei-Lin , Cui Heng-Lin
Published: March 2014

A halophilic archaeal strain, GX48T, was isolated from the Gangxi marine solar saltern near Weihai city in Shandong Province, China. Cells of the strain were rod-shaped, stained Gram-negative and formed red-pigmented colonies. Strain GX48T was able to grow at 25–50 °C (optimum 37 °C), in the presence of 1.4–4.8 M NaCl (optimum 2.6 M NaCl), with 0–1.0 M MgCl2 (optimum 0.05 M MgCl2) and at pH 5.5–9.5 (optimum pH 7.0). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). The major polar lipids of the strain were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and two major glycolipids chromatographically identical to those of

Natronoarchaeum mannanilyticum

YSM-123T and

Natronoarchaeum philippinense

294-194-5T. 16S rRNA gene analysis revealed that strain GX48T had two dissimilar 16S rRNA genes and both of them were phylogenetically related to those of the two current members of the genus

Natronoarchaeum

(96.2–98.3 % similarities). The rpoB′ gene sequence similarities between strain GX48T and

Natronoarchaeum mannanilyticum

YSM-123T and

Natronoarchaeum philippinense

294-194-5T were 96.0 % and 94.7 %, respectively. The DNA G+C content of strain GX48T was 66.2 mol%. Strain GX48T showed low DNA–DNA relatedness with the two members of the genus

Natronoarchaeum

. It was concluded that strain GX48T ( = CGMCC 1.10388T = JCM 17119T) represents a novel species of the genus

Natronoarchaeum

, for which the name Natronoarchaeum rubrum sp. nov. is proposed. An emended description of the genus

Natronoarchaeum

is also presented.
Notification that new names of prokaryotes, new combinations and new taxonomic opinions have appeared in volume 63, part 12, of the IJSEM
Authors: Oren Aharon , Garrity George M.
Published: March 2014

This listing of names of prokaryotes published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol
41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).
List of new names and new combinations previously effectively, but not validly, published
Authors: Oren Aharon , Garrity George M.
Published: March 2014

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological
Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send a covering letter, a copy of, or a link to the published paper and electronic copies of certificates of deposit from at least two culture collections in different countries to the IJSEM Editorial Office (ijsem@sgm.ac.uk) for confirmation that all of the other requirements for valid publication have been met. It
is
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IJSEM
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the
ICSP
that
authors
of
new
species, new
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and
new
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evidence
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types
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deposited
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collections
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countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
Correction method for the self-absorption effects in fluorescence extended X-ray absorption fine structure on multilayer samples
Authors: Li Wen-Bin , Yang Xiao-Yue , Zhu Jing-Tao , Tu Yu-Chun , Mu Bao-Zhong , Yu Hai-Sheng , Wei Xiang-Jun , Huang Yu-Ying , Wang Zhan-Shan
Published: March 2014

A novel correction method for self-absorption effects is proposed for extended X-ray absorption fine structure (EXAFS) detected in the fluorescence mode on multilayer samples. The effects of refraction and multiple reflection at the interfaces are fully considered in this correction method. The correction is performed ink-space before any further data analysis, and it can be applied to single-layer or multilayer samples with flat surfaces and without thickness limit when the model parameters for the samples are known. The validity of this method is verified by the fluorescence EXAFS data collected for a Cr/C multilayer sample measured at different experimental geometries.
Case of tumor thrombus inside femoral vein, formed by melanoma metastasized to inguinal lymph node
Authors: Takai Toshihiro , Murata Yozo
Published: March 2014

Inguinal lymph nodes are often excised in dermatological surgery, because they are the most common of the lymphatic basin involved in metastasis of malignant skin tumor on the lower extremities or genital region. Herein, we describe a case of cutaneous malignant melanoma on the buttock of a 78‐year‐old woman. Under the huge metastasized inguinal lymph node, there was tumor invasion into the femoral vein with intraluminal tumor thrombus formation. Careful preoperative radiological assessment enabled successful resection on surgery. A review of the published work revealed that tumor thrombus due to direct invasion of melanoma may be rare. The possibility of intravenous tumor thrombus should be considered in the settings of surgery of inguinal metastasis of melanoma, especially when a large‐sized node is located near the great veins.
Workplace Flexibility Practices and Corporate Performance: Evidence from the British Private Sector
Authors: Whyman Philip B. , Baimbridge Mark J. , Buraimo Babatunde A. , Petrescu Alina I.
Published: March 2014

This paper investigates the relationship between workplace flexibility practices (WFPs) and corporate performance using data from the British Workplace Employment Relations Survey 2004. Disaggregating WFPs into numerical, functional and cost aspects enables the analysis of their relationships to an objective measure of corporate performance, namely workplace financial turnover. Furthermore separate analyses are presented for different types of workplace: differentiated by workforce size; ownership; age; wage level; and unionization. Results show that different types of workplaces need to pay attention to the mix of WFPs they adopt. We find that certain cost WFPs (profit‐related pay, merit pay and payment‐by‐results) have strong positive relationships with corporate performance. However, training delivers mixed corporate performance results, while the extent of job autonomy and the proportion of part‐time employees in a workplace have an inverse association with corporate performance. Given the limited existing research examining disaggregated measures of WFPs and objectively measured corporate performance, this paper offers useful insights for firms, policy makers and the overall economy.
The impact of obesity on outcomes of midwife‐led pregnancy and childbirth in a primary care population: a prospective cohort study
Authors: Daemers DOA , Wijnen HAA , van Limbeek EBM , Budé LM , Nieuwenhuijze MJ , Spaanderman MEA , de Vries RG
Published: March 2014

Objective

To assess the impact of obesity on the likelihood of remaining in midwife‐led care throughout pregnancy and childbirth.

Design

Secondary analysis of data from a prospective cohort study.

Setting

Dutch midwife‐led practices.

Population

A cohort of 1369 women eligible for midwife‐led care after their first antenatal visit.

Methods

First‐trimester body mass index (BMI) was calculated as weight measured at booking divided by height squared. Obstetric data were retrieved from medical records. Multiple logistic regressions were performed to examine the effects of BMI classification on midwife‐led pregnancies and childbirths.

Main outcome measures

Percentages of women remaining in midwife‐led care throughout pregnancy and throughout childbirth.

Results

Of women in obesity classes II and III, 55% remained in midwife‐led care throughout pregnancy and 30% remained in midwife‐led care throughout birth. Compared with women of normal weight, women in obesity classes II and III had fewer midwife‐led pregnancies (OR 0.38, 95% CI 0.21–0.69), and women who were overweight or in obesity class I had fewer midwife‐led childbirths (OR 0.63, 95% CI 0.44–0.90; OR 0.49, 95% CI 0.29–0.84, respectively). Compared with women of normal weight, women who were obese had higher referral rates for hypertensive disorders (4 versus 14%), prolonged labour (4.6 versus 10.4%), and intrapartum pain relief (4 versus 10.4%). The women who were eligible for midwife‐led birth and who were overweight or obese, had no more urgent referrals than women of normal weight. Women who were obese and who completed a midwife‐led birth had no more adverse outcomes than women of normal weight, with the exception of higher rates of large for gestational age (LGA) babies (>97.7 centile; 12.1%, versus 1.9% in normal weight and versus 3.3% in overweight women).

Conclusions

Although fewer women who were obese remain in midwife‐led care during pregnancy and childbirth, there was no increased risk of unfavourable birth outcomes for women who were obese and eligible for a midwife‐led birth when compared with women of normal weight. This indicates that when primary care midwives use a risk assessment tool throughout pregnancy and childbirth they are able to safely assign women who are obese to either midwife‐led or obstetrician‐led care.
Effects of concentration, distance, and application methods of Altriset (Chlorantraniliprole) on eastern subterranean termite (Isoptera: Rhinotermitidae)
Authors: Barwary Znar , Gorzlancyk Austin , Hu Xing Ping
Published: March 2014

The effects of various concentrations, distance, and application methods of Altriset (Chlorantraniliprole) were investigated against one of the most destructive termites, the eastern subterranean termite, Reticulitermes flavipes Kollar. Three laboratory experiments were conducted. First, we examined the concentration effect of treating the soil contiguously to established foraging tunnels at a fixed 1 m distance. The results demonstrated 100% termite control in 19 d posttreatment at 100 and 50 μg/g and 27% termite mortality at 25 μg/g. Second, we tested the distance effect of the soil treatment (2 and 4 m) on the efficacy of Altriset to the satellite termite populations at a fixed 50 μg/g concentration. This resulted in 100% termite control in 22 d posttreatment at both 2 and 4 m. Third, we examined the effect of differing application methods using 12.5 and 25 μg/g prior to the establishment of foraging tunnels at a fixed 1m distance. This illustrated 100% termite control in 9 d posttreatment at 25 μg/g and 12 d posttreatment at 12.5 μg/g. The third experiment demonstrated soil treatments that were applied prior to termite tunnel establishment had greater efficacy than applications made post tunnel construction. Our results provide a comprehensive understanding about the efficacy of Altriset treatments on eastern subterranean termites.
Improving workplace mental health: a training needs analysis to inform beyondblue's online resource for leaders
Authors: Shann Clare , Martin Angela , Chester Andrea
Published: March 2014

The management of employees with mental health problems in the workplace is an emerging organisational challenge for leaders and HR managers. Training programs on this topic are increasingly being implemented in organisations. However, this training is rarely built into leadership programs, and relevant skills and attitudes can fail to be sustainably integrated into organisational cultures. The aim of this study was to investigate the training needs of leaders. A survey of 379 leaders and 364 HR and learning and development professionals was undertaken. The majority of leaders surveyed had experienced a situation requiring management of mental health in the workplace and recognised the importance of workplace strategies. However, very few had participated in mental health training. Discrepancies between rated levels of importance and confidence on a range of relevant skills and knowledge areas were identified. These findings highlight for HR professionals the priorities for the design of leader‐focused workplace mental health training. Such content prioritisations are critical to ensure engagement of time‐poor leaders is maximised.
Identifying leadership potential in an Australian context
Authors: Troth Ashlea C , Gyetvey Christopher
Published: March 2014

There is increasing recognition that identifying leadership potential is vital for long‐term organizational survival. Using a sample of 166 Australian public service employees, and their 149 managers, this article empirically examines the role of general mental ability, problem‐solving skill, emotional intelligence, employee engagement and career aspiration in identifying leadership potential. Both manager and employee self‐ratings of leadership potential perceptions are considered as well as the presence of rater effects. Manager perceptions about problem‐solving ability, engagement and aspiration predicted their ratings of employee future leadership potential. Employee self‐ratings, apart from aspiration, did not. Rater effects were found. We discuss the implications of these results and suggest some strategies to more closely align managerial and employee views of leadership potential.