bluuebunny/crossref_metadata_2025 huggingface dataset:
Rehabilitation Following Hand Transplantation
Authors: Bueno Ericka , Benjamin Marie-Jose , Sisk Geoffroy , Sampson Christian E. , Carty Matthew , Pribaz Julian J. , Pomahac Bohdan , Talbot Simon G.
Published: October 2013

Background

Hand allotransplantation can restore motor, sensory and cosmetic functions to upper extremity amputees. Over 70 hand transplant operations have been performed worldwide, but there is little published regarding post-hand transplant rehabilitation.

Methods

The Brigham and Women's Hospital (BWH) Hand Transplantation Team's post-hand transplant rehabilitation protocol is presented here. The protocol must be modified to address each transplant recipient's unique needs. It builds on universally used modalities of hand rehabilitation such as splinting, edema and scar management, range of motion exercises, activities of daily living training, electrical stimulation, cognitive training and strengthening.

Results

The BWH hand transplant rehabilitation protocol consists of four phases with distinct goals, frequency, and modalities. (1) Pre-operative: functional assessments are completed and goals and expectations of transplantation are established. (2) Initial post-operative (post-operative weeks 1–2): hand protection, minimization of swelling, education, and discharge. (3) Intermediate (post-operative weeks 2–8): therapy aims to prevent and/or decrease scar adhesion, increase tensile strength, flexibility and function, and prevent joint contractures. (4) Late (from 8 weeks forward): maximization of function and strength, and transition to routine activities. The frequency of rehabilitation therapy decreases gradually from the initial to late phases.

Conclusions

Rehabilitation therapy after hand transplantation follows a progressive increase in activity in parallel with wound healing and nerve regeneration. Careful documentation of progress and outcomes is essential to demonstrate the utility of interventions and to optimize therapy protocols.
Representing the ‘Butterfly’ Projection in FITS—Projection Code XPH
Authors: Calabretta Mark R. , Lowe Stuart R.
Published: October 2013

The ‘butterfly’ projection is constructed as the polar layout of the HEALPix projection with (H, K) = (4, 3). This short article formalises its representation in FITS.
Detection of hepatitis B virus in the cerumen of patients with chronic hepatitis B infection
Authors: Eftekharian A , Moghaddasi H , Gachkar L , Amlashi S S A
Published: October 2013

Objective:

To investigate hepatitis B virus DNA in the cerumen of hepatitis B virus infected patients.

Methods:

This study comprised 30 confirmed cases of chronic hepatitis B. Patients' serum samples were examined for hepatitis B surface antigen and antibodies using enzyme immunoassay systems. The presence of hepatitis B virus DNA in cerumen was investigated using a polymerase chain reaction test.

Results:

All of the samples were positive for hepatitis B surface antigen and negative for hepatitis B surface antibodies. Hepatitis virus DNA was detected in two cerumen samples (6.6 per cent of patients).

Conclusion:

Cerumen can be a potential source of transmission of hepatitis B virus.
MTHFR677TT genotype and disease risk: is there a modulating role for B-vitamins?
Authors: Reilly R. , McNulty H. , Pentieva K. , Strain J. J. , Ward M.
Published: October 2013

Methylenetetrahydrofolate reductase (MTHFR) is a critical folate-metabolising enzyme which requires riboflavin as its co-factor. A common polymorphism (677C→T) in theMTHFRgene results in reduced MTHFR activityin vivowhich in turn leads to impaired folate metabolism and elevated homocysteine concentrations. Homozygosity for this polymorphism (TT genotype) is associated with an increased risk of a number of conditions including heart disease and stroke, but there is considerable variability in the extent of excess risk in various reports. The present review will explore the evidence which supports a role for this polymorphism as a risk factor for a number of adverse health outcomes, and the potential modulating roles for B-vitamins in alleviating disease risk. The evidence is convincing in the case which links this polymorphism with hypertension and hypertensive disorders of pregnancy, particularly preeclampsia. Furthermore, elevated blood pressure was found to be highly responsive to riboflavin intervention specifically in individuals with theMTHFR677TT genotype. Future intervention studies targeted at these genetically predisposed individuals are required to further investigate this novel gene–nutrient interaction. This polymorphism has also been associated with an increased risk of neural tube defects (NTD) and other adverse pregnancy outcomes; however, the evidence in this area has been inconsistent. Preliminary evidence has suggested that there may be a much greater need for women with theMTHFR677TT genotype to adhere to the specific recommendation of commencing folic acid prior to conception for the prevention of NTD, but this requires further investigation.
Habitat of the Vulnerable Formosan sambar deerRusa unicolor swinhoiiin Taiwan
Authors: Yen Shih-Ching , Wang Ying , Ou Heng-You
Published: October 2013

The sambar deerRusa unicoloris categorized as Vulnerable on the IUCN Red List because of continuous population decline across its native range. In Taiwan the Formosan sambar deerR. unicolor swinhoiiis listed as a protected species under the Wildlife Conservation Act because of human overexploitation. However, its population status remains unclear. We used presence and absence data from line transect and camera-trap surveys to identify key habitat variables and to map potential habitats available to this subspecies in Taiwan. We applied five habitat-suitability models: logistic regression, discriminant analysis, ecological-niche factor analysis, genetic algorithm for rule-set production, and maximum entropy. We then combined the results of all five models into an ensemble-forecasting model to facilitate a more robust prediction. This model indicated the existence of 7,865 km2of suitable habitat for the sambar deer. Distance from roads and elevation were identified as the most important environmental variables for habitat suitability, and deer preferred areas far from roads and > 1,500 m altitude. The results predicted that suitable deer habitat is mainly located in Taiwan's Central Mountain Range and Xue Mountain Range, with c. 70% of this suitable habitat in protected areas. However, the habitat predicted to be suitable is in five areas separated by mountain highways. We recommend that deer habitats close to the highways should be monitored for the future establishment of corridors between Formosan sambar deer sub-populations.
Effects of different sampling scales and selection criteria on modelling net primary productivity of Indonesian tropical forests
Authors: GMUR STEPHAN J. , VOGT DANIEL J. , VOGT KRISTIINA A. , SUNTANA ASEP S.
Published: October 2013

The availability of spatial data sourced from either field-derived or satellite-based systems has created new opportunities to estimate and/or monitor changes in carbon sequestration rates, climate change impacts or the potential habitat alterations occurring across large landscapes. However, an effort to create models is not standardized, in part, due to different needs and data sources available for the models. For example, data may have different spatial resolutions with varying degrees of complexity in regards to inputs and statistical methods. This study determines effects of 20, 15, 10, five and one km sampling resolutions on detection of changes in net primary productivity (NPP), occupancy selection criteria for areas to be included in the sample and identification of significant variables impacting NPP in Indonesia forests. Production forest designated for selective harvest was used to define the sampling areas. Variances explained by predictive models were similar across cell sizes although relative importance of variables was different. Partial dependence plots were used to search for potential thresholds or tipping points of NPP change as affected by an independent variable such as minimum daytime temperature. Applying different cell occupancy selection rules significantly changed the overall distribution of NPP values. The magnitude of those changes within a cell size varied with changes in cell size. The mean estimated NPP for production forests across Indonesia differed significantly at every sampling resolution and occupancy selection criteria. Lows ranged from 1.107 to 1.121 kg C m−2yr−1for the 1-km cell size for the three occupancy selection criteria with highs ranging from 1.245 to 1.189 kg C m−2yr−1for the 20-km cell size. The difference in NPP values between these two cell sizes for the three occupancy selection criteria extrapolates to a range in annual biomass of 132 × 106to 66 × 106t for the total area of production forests in Indonesia.
Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters
Authors: Taylor Joe D , Cottingham Samuel D , Billinge Jack , Cunliffe Michael
Published: October 2013

Phytoplankton produce large amounts of polysaccharide gel material known as transparent exopolymer particles (TEP). We investigated the potential links between phytoplankton-derived TEP and microbial community structure in the sea surface microlayer and underlying water at the English Channel time-series station L4 during a spring diatom bloom, and in two adjacent estuaries. Major changes in bacterioneuston and bacterioplankton community structure occurred after the peak of the spring bloom at L4, and coincided with the significant decline of microlayer and water column TEP. Increased abundance of Flavobacteriales and Rhodobacterales in bacterioneuston and bacterioplankton communities at L4 was significantly related to the TEP decline, indicating that both taxa could be responsible. The results suggest that TEP is an important factor in determining microbial diversity in coastal waters, and that TEP utilisation could be a niche occupied by Flavobacteriales and Rhodobacterales.
Back-scatter based whispering gallery mode sensing
Authors: Knittel Joachim , Swaim Jon D. , McAuslan David L. , Brawley George A. , Bowen Warwick P.
Published: October 2013

Whispering gallery mode biosensors allow selective unlabelled detection of single proteins and, combined with quantum limited sensitivity, the possibility for noninvasive real-time observation of motor molecule motion. However, to date technical noise sources, most particularly low frequency laser noise, have constrained such applications. Here we introduce a new technique for whispering gallery mode sensing based on direct detection of back-scattered light. This experimentally straightforward technique is immune to frequency noise in principle and further, acts to suppress thermorefractive noise. We demonstrate 27 dB of frequency noise suppression, eliminating frequency noise as a source of sensitivity degradation and allowing an absolute frequency shift sensitivity of 76 kHz. Our results open a new pathway towards single molecule biophysics experiments and ultrasensitive biosensors.
Identification and quantitation of diethylstilbestrol in aquatic products using gas chromatography coupled with triple quadrupole tandem mass spectrometry
Authors: Ke Chang-liang , Wang Zeng-huan , Gan Ju-li , Gu Yang-guang , Huang Ke , Li Liu-dong , Lin Qin
Published: October 2013

GC-MS-MS was utilized to identify the cis-DES derivative in fish meat with the help of the NIST spectra library.
High spatial resolution Raman thermometry analysis of TiO2 microparticles
Authors: Lundt Nils , Kelly Stephen T. , Rödel Tobias , Remez Benjamin , Schwartzberg Adam M. , Ceballos Alejandro , Baldasseroni Chloé , Anastasi Peter A. F. , Cox Malcolm , Hellman Frances , Leone Stephen R. , Gilles Mary K.
Published: October 2013

A new technique of high-resolution micro-Raman thermometry using anatase TiO2 microparticles (0.5–3 μm) is presented. These very high spatial resolution measurements (280 nm) reveal temperature gradients even within individual microparticles. Potential applications of this technique are demonstrated by probing the temperature distribution of a micro-fabricated heater consisting of a thin silicon nitride (Si-N) membrane with a gold coil on top of the membrane. Using TiO2 microparticle micro-Raman thermometry, the temperature from the outer edge of the coil to the inner portion was measured to increase by ∼40 °C. These high spatial resolution microscopic measurements were also used to measure the temperature gradient within the 20 μm wide Si-N between the gold heating coils. 2D numerical simulations of the micro heater temperature distribution are in excellent agreement with the experimental measurements of the temperatures. These measurements illustrate the potential to extend applications of micro-Raman thermometry to obtain temperature details on a sub-micrometer spatial resolution by employing microparticles.
An ab initio study of the electronic structure of boron arsenide, BAs
Authors: Magoulas Ilias , Kalemos Apostolos
Published: October 2013

The completely unexplored BAs diatomic has been thoroughly studied by high level multireference variational ab initio methods. Potential energy curves for 42 molecular states dissociating to the first four asymptotic channels and covering an energy range of 5.8 eV have been constructed revealing an interesting morphology and a rich spectroscopy. The ground state is of 3Π symmetry while its first excited 1Σ+ state lies ∼8 kcal/mol higher. A general feature of the potential curves is the presence of avoided crossings that challenge the validity of the Born Oppenheimer approximation.
High current proton beams production at Simple Mirror Ion Source 37
Authors: Skalyga V. , Izotov I. , Razin S. , Sidorov A. , Golubev S. , Kalvas T. , Koivisto H. , Tarvainen O.
Published: October 2013

This paper presents the latest results of high current proton beam production at Simple Mirror Ion Source (SMIS) 37 facility at the Institute of Applied Physics (IAP RAS). In this experimental setup, the plasma is created and the electrons are heated by 37.5 GHz gyrotron radiation with power up to 100 kW in a simple mirror trap fulfilling the ECR condition. Latest experiments at SMIS 37 were performed using a single-aperture two-electrode extraction system. Proton beams with currents up to 450 mA at high voltages below 45 kV were obtained. The maximum beam current density was measured to be 600 mA/cm2. A possibility of further improvement through the development of an advanced extraction system is discussed.
Stability analysis and synchronization in discrete-time complex networks with delayed coupling
Authors: Cheng Ranran , Peng Mingshu , Yu Weibin , Sun Bo , Yu Jinchen
Published: October 2013

A new network of coupled maps is proposed in which the connections between units involve no delays but the intra-neural communication does, whereas in the work of Atay et al. [Phys. Rev. Lett. 92, 144101 (2004)], the focus is on information processing delayed by the inter-neural communication. We show that the synchronization of the network depends on not only the intrinsic dynamical features and inter-connection topology (characterized by the spectrum of the graph Laplacian) but also the delays and the coupling strength. There are two main findings: (i) the more neighbours, the easier to be synchronized; (ii) odd delays are easier to be synchronized than even ones. In addition, compared with those discussed by Atay et al. [Phys. Rev. Lett. 92, 144101 (2004)], our model has a better synchronizability for regular networks and small-world variants.
Note: High resolution alternating current/direct current Harman technique
Authors: Chavez R. , Becker A. , Bartel M. , Kessler V. , Schierning G. , Schmechel R.
Published: October 2013

This note describes the construction and engineering of a high precision Harman set-up for metrology of the thermoelectric figure of merit (ZT) of modules and materials based on steady state AC and DC measurements. The Harman technique presented in this article has a resolution of milli-ZT and it does not employ lock-in amplifiers or AC bridges; rather, the technique is developed to avoid typical complications experienced in AC Harman systems. By one-time reference measurements the best operation point for the system is chosen, minimizing the effects of capacitive loads due to AC signals.
Self-assembly of a new type of periodic surface structure in a copolymer by excimer laser irradiation above the ablation threshold
Authors: Dorronsoro Carlos , Bonse Jörn , Siegel Jan
Published: October 2013

We report self-assembly of periodic surface structures in a commercial block copolymer (BCP) (Filofocon A) upon irradiation with a few tens of excimer laser pulses (20 ns, 193 nm) at fluences above the ablation threshold. This new type of structures is characterized by much larger periods than those characteristic for Laser-Induced Periodic Surface Structures (LIPSS) and features nanochains instead of ripples. We find a period of 790 nm at 400 mJ/cm2, scaling linearly with laser fluence up to a maximum of 1.0 μm. While an entangled random network of nanochains is produced for normal-incidence and non-polarized light, nanochain alignment can be achieved either by irradiation at an angle or by using linearly polarized light, forming a lamella-like structure. In both cases, the nanochains are aligned parallel to the penetrating polarization orientation and their period does not show a dependence on the angle of incidence, as opposed to the general behavior of standard LIPSS. Also, our results show that the chains are not formed by frozen capillary waves. In contrast, we show analogies of the nanochains produced to lamellar structures fabricated on a smaller scale in other BCP. We discuss the origin of the self-assembly process in terms of a combination of chemical (BCP), optical (surface scattering), and thermal (melting, coarsening, and ablation) effects.
High quality relaxed germanium layers grown on (110) and (111) silicon substrates with reduced stacking fault formation
Authors: Huy Nguyen Van , Dobbie A. , Myronov M. , Leadley D. R.
Published: October 2013

Epitaxial growth of Ge on Si has been investigated in order to produce high quality Ge layers on (110)- and (111)-orientated Si substrates, which are of considerable interest for their predicted superior electronic properties compared to (100) orientation. Using the low temperature/high temperature growth technique in reduced pressure chemical vapour deposition, high quality (111) Ge layers have been demonstrated almost entirely suppressing the formation of stacking faults (< 107 cm−2) with a very low rms roughness of less than 2 nm and a reduction in threading dislocation density (TDD) (∼ 3 × 108 cm−2). The leading factor in improving the buffer quality was use of a thin, partially relaxed Ge seed layer, where the residual compressive strain promotes an intermediate islanding step between the low temperature and high temperature growth phases. (110)-oriented layers were also examined and found to have similar low rms roughness (1.6 nm) and TDD below 108 cm−2, although use of a thin seed layer did not offer the same relative improvement seen for (111).
Density functional theory study on the impact of heavy doping on Si intrinsic point defect properties and implications for single crystal growth from a melt
Authors: Sueoka Koji , Kamiyama Eiji , Vanhellemont Jan
Published: October 2013

Density functional theory (DFT) calculations are performed to obtain the formation energies of the vacancy V and the self-interstitial I at all sites within a sphere around the dopant atom with 6 Å radius for V and 5 Å radius for I in Si crystals. Substitutional p-type (B and Ga), neutral (C, Ge, and Sn), and n-type (P, As, Sb, and Bi) dopants were considered. The results show that the formation energies of V and I around dopant atoms change depending on the types and sizes of the dopants, i.e., depending on the electrical state and the local strain around the dopants. The dependence of the total thermal equilibrium concentrations of point defects (sum of free V or I and V or I around the dopants) at melting temperature on the type and concentration of each dopant is obtained. Further DFT calculations reveal that most of the total incorporated point defects from the melt contribute to pair recombination. An appropriate model of point defect behavior in heavily doped single crystal Si growing from a melt is proposed on the basis of DFT calculations. (1) The incorporated total V and I concentrations at melting point depend on the types and concentrations of dopants. (2) Most of the total V and I concentrations during Si crystal growth contribute to the pair recombination at temperatures much higher than those to form grown-in defects. The Voronkov model successfully explains all reported experimental results on intrinsic point defect behavior dependence on dopant type and concentration for heavily doped Si while taking the present model into consideration.
Epitaxy and stress of MgO/GaAs(001) heterostructures
Authors: Wang Shibo , Sarkar Anirban , Gruber Markus , Koch Reinhold
Published: October 2013

We report on the preparation of epitaxial MgO film on GaAs(001) substrates by molecular beam epitaxy at growth temperature of 20–200 °C. Reflection high energy electron diffraction, x-ray diffraction, and high resolution transmission electron microscopy reveal the growth of ordered crystalline cubic MgO(001) film at ∼200 °C with MgO(001)[100] || GaAs(001)[100] and a 4 : 3 lattice registry. The surface of the MgO films, characterized by atomic force microscopy, exhibits a root mean square roughness of only 0.5 nm. In situ stress measurements reveal tensile stress as low as 1.7 GPa for a growth temperature of 200 °C in good agreement with the calculated residual misfit strain.
Plasmon resonance of gold nanorods for all-optical drawing of liquid droplets
Authors: de Angelis M. , Matteini P. , Ratto F. , Pini R. , Coppola S. , Grilli S. , Vespini V. , Ferraro P.
Published: October 2013

We present a laser-assisted system for dispensing liquid micro-droplets by near infrared illumination of a pyroelectric crystal functionalized with gold nanorods embedded into polyvinyl alcohol. The non-invasive near infrared source resonates with the plasmon oscillations of the gold nanorods, providing a controlled thermal stimulus able to generate the pyroelectric effect. The resulting electric field interacts electro-hydrodynamically with a liquid reservoir leading to precise drawing of micro-litre droplets. This laser-assisted electro-hydrodynamic technique may open the way to the development of more compact and non-invasive nano-dispensing devices.
Charge distribution and chemical bonding in B-O complexes in Cz-Si solar cells
Authors: Mao Yuliang , Caliste Damien , Pochet Pascal
Published: October 2013

Density functional calculations based on wavelet basis set are performed to investigate charge distribution and chemical bonding in possible BiOi (interstitial boron and interstitial oxygen), BsO2i (substitutional boron and interstitial oxygen dimer), and BiO2i (interstitial boron and interstitial oxygen dimer) complexes in Cz-Si solar cells. It is confirmed that the BsO2ist complex composed by Bs and staggered oxygen dimer (O2ist) at second nearest site to boron has the lowest formation energy, resulting in better agreement with experiment. This is resulted by Coulomb attraction between Si−Oi and Si−Bs and consequently a decreased Coulomb repulsion between Bs−Oi in BsO2ist complex. A more physical description of the localized nature on bonding has been analyzed by maximally localized Wannier functions. It is found through the predicted Wannier centers that a doubly negative charge state of interstitial oxygen exists, which is consistent with our Bader charge analysis.
Nanograting formation through surface plasmon fields induced by femtosecond laser pulses
Authors: Miyazaki Kenzo , Miyaji Godai
Published: October 2013

Ablation of solid surfaces irradiated with superimposed multiple shots of low fluence femtosecond (fs) laser pulses often results in the formation of periodic nanostructures on the target surface. We demonstrate that the self-organization process of nanostructuring can be regulated to fabricate a homogeneous nanograting on the target surface in air. A simple two-step ablation process was used to control the nanoscale energy deposition that should be developed through the excitation of surface plasmon polaritons (SPPs) during the fs laser-surface interaction. The results obtained for crystalline gallium nitride represent exactly the nature of a single spatial standing wave mode of SPPs of which periodically enhanced near-fields ablate the target surface to form the nanograting with a period of ∼200 nm. The calculated results for a model target reproduce well the observed nanograting period and explain the origin of its characteristic properties.
Giant junction magnetoresistance effect in ferromagnet/semiconductor heterostructures
Authors: Sarkar Anirban , Adhikari Rajdeep , Das Amal Kumar
Published: October 2013

The effect of magnetic field on the electrical transport across the ferromagnet/semiconductor heterostructures has been investigated. The heterostructures were fabricated by growing ferromagnetic layer of cobalt on silicon and germanium substrates. Studies were made for both etched and oxide (alumina) coated surfaces. Some of the heterostructures show very good rectifying property at all temperatures and spin-valve like characteristics at low temperatures. Positive giant junction magnetoresistance is observed in the heterostructures below a critical temperature. This resulted to a drastic reduction of the forward current in the devices on application of a small magnetic field. The observed giant magnetoresistance is unique, and the interface of the heterostructures is inferred to be strongly influencing the transport characteristics of the device.
Gaze Cueing by Pareidolia Faces
Authors: Takahashi Kohske , Watanabe Katsumi
Published: October 2013

Visual images that are not faces are sometimes perceived as faces (the pareidolia phenomenon). While the pareidolia phenomenon provides people with a strong impression that a face is present, it is unclear how deeply pareidolia faces are processed as faces. In the present study, we examined whether a shift in spatial attention would be produced by gaze cueing of face-like objects. A robust cueing effect was observed when the face-like objects were perceived as faces. The magnitude of the cueing effect was comparable between the face-like objects and a cartoon face. However, the cueing effect was eliminated when the observer did not perceive the objects as faces. These results demonstrated that pareidolia faces do more than give the impression of the presence of faces; indeed, they trigger an additional face-specific attentional process.
Self-management of chronic conditions in a rural and remote context
Authors: Sav Adem , King Michelle A. , Kelly Fiona , McMillan Sara S. , Kendall Elizabeth , Whitty Jennifer A. , Wheeler Amanda J.
Published: October 2013

Living in a rural or remote environment presents unique challenges for people with chronic conditions, mainly those created by limited health-care services and the physical and emotional isolation. Yet, research on how people self-manage their chronic conditions in such locations is limited. This study aims to contribute to research and clinical practice by describing the ways in which a diverse group of rural and remote people with a range of chronic conditions, and their unpaid carers, self-manage their conditions. Using semi-structured in-depth interviews, data was collected from a sample of 32 participants, residing in one of two regions of Australia: Mount Isa/North West region of Queensland and the Northern Rivers area of New South Wales. Our findings suggest that although self-managing in a rural and remote context requires many of the lifestyle changes necessary in urban areas, the uniqueness of the rural lifestyle and the limited availability of health care results in, at times, creative forms of self-management. Health-care professionals and policy makers need to be cognisant of the ways in which rural and remote residents modify self-management strategies to suit their needs, and help them develop self-management plans tailored to the realities of their rural environment.
Factors associated with virological failure in a cohort of combination antiretroviral therapy-treated patients managed at a tertiary referral centre
Authors: Fong Raymond , Cheng Allen C. , Vujovic Olga , Hoy Jennifer F.
Published: October 2013

Background
Recent antiretroviral regimens are potent and better tolerated, resulting in a low prevalence of treatment failure. It is important to identify the drivers of virological failure, so that patients at risk can be identified early and prevention strategies implemented. Methods: We performed a retrospective case–control study of HIV-positive patients on antiretroviral therapy and managed at The Alfred Hospital during 2010 to evaluate the predictors of virological failure. Controls were matched 3 : 1 to cases by gender, and by clinical review in the same week as the diagnosis of virological failure in the case. Predictors of virological failure were identified by multivariate conditional logistic regression. Results: Thirty-nine patients were identified with treatment failure. In the multivariate model, characteristics associated with virological failure were missed clinic appointments in 1 year before virological failure (odds ratio (OR) = 13.1, 95% confidence interval (CI): 2.8–61.1), multiple previous combined antiretroviral therapy regimens (OR = 4.2, 95% CI:1.2–15.3), current hepatitis C infection (OR = 8.6, 95% CI: 1.9–38.7), older age at HIV diagnosis (OR = 1.1, 95% CI: 1.0–1.2), younger age at time of virological failure (OR = 0.9, 95% CI: 0.8 to 1.0), and CD4 cell count at virological failure (OR = 0.7, 95% CI: 0.5 to 0.9). Conclusions: Targeted and appropriate adherence support should be provided to treatment-experienced patients, particularly those who have missed clinical appointments and those with hepatitis C coinfection. Further elucidation of the barriers to clinic attendance may optimise linkage and retention in care.
Childhood abuse and depressive vulnerability in clients with gender dysphoria
Authors: Firth Malcolm T.
Published: October 2013

Background: Childhood abuse in the early lives of gender variant people has been under‐reported, although higher psychiatric morbidity, particularly depression and suicidality, than in the general population is more widely recognised. There are increasing numbers of people seeking advice and treatment for gender dysphoria (GD) some of whose experiences of depression and childhood abuse may be additional treatment considerations. Aim: To illuminate the issues relating to childhood abuse, depression and GD via case examples underpinned by a summary review of the relevant literature, for their combined relevance to therapeutic practice and service provision. Methods: A review of relevant online literature was conducted and two case examples were developed subsequently to capture the core review themes from a practice perspective. Results: Nine studies met the inclusion criteria. Gender variant children and adolescents may experience abuse by peers and teachers, as well as parents and caregivers. Emotional abuse and neglect may have more adverse consequences than more active forms of abuse. Conclusions: This is an under‐researched area, and inconsistencies of design, definition, measurement and controls were evident in the literature. While no clear association between depressive vulnerability and childhood abuse could be found, prevalence of such abuse was high. A case is made for clients with GD to have the opportunity to explore the influence and meaning of their adverse childhood experiences on their social and psychological development, and for additional training and education for practitioners.
Finite element differential forms on cubical meshes
Authors: Arnold Douglas , Awanou Gerard
Published: October 2013

We develop a family of finite element spaces of differential forms defined on cubical meshes in any number of dimensions. The family contains elements of all polynomial degrees and all form degrees. In two dimensions, these include the serendipity finite elements and the rectangular BDM elements. In three dimensions they include a recent generalization of the serendipity spaces, and new

H
(

c
u
r
l

)

H(\mathrm {curl})

and

H
(

d
i
v

)

H(\mathrm {div})

finite element spaces. Spaces in the family can be combined to give finite element subcomplexes of the de Rham complex which satisfy the basic hypotheses of the finite element exterior calculus, and hence can be used for stable discretization of a variety of problems. The construction and properties of the spaces are established in a uniform manner using finite element exterior calculus.
MFCompress: a compression tool for FASTA and multi-FASTA data
Authors: Pinho Armando J. , Pratas Diogo
Published: October 2013

Motivation: The data deluge phenomenon is becoming a serious problem in most genomic centers. To alleviate it, general purpose tools, such as gzip, are used to compress the data. However, although pervasive and easy to use, these tools fall short when the intention is to reduce as much as possible the data, for example, for medium- and long-term storage. A number of algorithms have been proposed for the compression of genomics data, but unfortunately only a few of them have been made available as usable and reliable compression tools.

Results: In this article, we describe one such tool, MFCompress, specially designed for the compression of FASTA and multi-FASTA files. In comparison to gzip and applied to multi-FASTA files, MFCompress can provide additional average compression gains of almost 50%, i.e. it potentially doubles the available storage, although at the cost of some more computation time. On highly redundant datasets, and in comparison with gzip, 8-fold size reductions have been obtained.

Availability: Both source code and binaries for several operating systems are freely available for non-commercial use at http://bioinformatics.ua.pt/software/mfcompress/.

Contact:  ap@ua.pt

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Employment Effects of Credit Market Disruptions: Firm-level Evidence from the 2008–9 Financial Crisis
*
Authors: Chodorow-Reich Gabriel
Published: October 2013

This article investigates the effect of bank lending frictions on employment outcomes. I construct a new data set that combines information on banking relationships and employment at 2,000 nonfinancial firms during the 2008–9 crisis. The article first verifies empirically the importance of banking relationships, which imply a cost to borrowers who switch lenders. I then use the dispersion in lender health following the Lehman crisis as a source of exogenous variation in the availability of credit to borrowers. I find that credit matters. Firms that had precrisis relationships with less healthy lenders had a lower likelihood of obtaining a loan following the Lehman bankruptcy, paid a higher interest rate if they did borrow, and reduced employment by more compared to precrisis clients of healthier lenders. Consistent with frictions deriving from asymmetric information, the effects vary by firm type. Lender health has an economically and statistically significant effect on employment at small and medium firms, but the data cannot reject the hypothesis of no effect at the largest or most transparent firms. Abstracting from general equilibrium effects, I find that the withdrawal of credit accounts for between one-third and one-half of the employment decline at small and medium firms in the sample in the year following the Lehman bankruptcy.
Insertional Mutagenesis and Cloning of the Gene Required for the Biosynthesis of the Non-Host-Specific Toxin in Cochliobolus lunatus that Causes Maize Leaf Spot
Authors: Gao Jin-Xin , Liu Tong , Chen Jie
Published: October 2013

The maize pathotype Cochliobolus lunatus causes Curvularia leaf spot by producing a non-host-specific toxin known as methyl 5-(hydroxymethyl) furan-2-carboxylate (M5HF2C). However, related research that explores the genes that control the production of this toxin is rare. In the current work, Agrobacterium tumefaciens-mediated transformation (ATMT) was employed to tag the gene required for the biosynthesis of the toxin. Of the 3,000 ATMT transformants recovered, 4 showed a significant decline in pathogenicity on maize leaves; 1 transformant, T806, produced no detectable M5HF2C. Genomic DNA that flanks the integrated plasmid was recovered from one of the mutants. A cosmid clone of the wild-type strain was isolated using the recovered DNA as a probe. The results of the structural and functional analyses of the region corresponding to the tagged site were then used as a basis to successfully clone one gene, called Clt-1. Bioinformatics analysis showed that the gene coded a BTB domain-containing protein that comprises 745 amino acids. Southern analysis revealed that the gene was localized in the genome as a single copy. The essential roles of Clt-1 in both toxin production and pathogenicity were confirmed by gene disruption experiments. In summary, the novel gene Clt-1 is closely associated with toxin production and pathogen virulence in leaves of susceptible varieties.
The M6-C Cervical Disk Prosthesis
Authors: Thomas Sam , Willems Karel , Van den Daelen Luc , Linden Patrick , Ciocci Maria-Cristina , Bocher Philippe
Published: October 2013

Study Design:

Retrospective study.

Objective:

To determine the short-term clinical succesrate of the M6-C cervical disk prosthesis in primary and secondary surgery.

Summary of Background Data:

Cervical disk arthroplasty (CDA) provides an alternative to anterior cervical decompression and fusion for the treatment of spondylotic radiculopathy or myelopathy. The prevention of adjacent segment disease (ASD), a possible complication of anterior cervical decompression and fusion, is its most cited—although unproven—benefit. Unlike older arthroplasty devices that rely on a ball-and-socket–type design, the M6-C cervical disk prosthesis represents a new generation of unconstrained implants, developed to achieve better restoration of natural segmental biomechanics. This device should therefore optimize clinical performance of CDA and reduce ASD.

Materials and Methods:

All patients had preoperative computed tomography or magnetic resonance imaging and postoperative x-rays. Clinical outcome was assessed using the Neck Disability Index, a Visual Analog Scale, and the SF-36 questionnaire. Patients were asked about overall satisfaction and whether they would have the surgery again.

Results:

Thirty-three patients were evaluated 17.1 months after surgery, on average. Nine patients had a history of cervical interventions. Results for Neck Disability Index, Visual Analog Scale, and SF-36 were significantly better among patients who had undergone primary surgery. In this group, 87.5% of patients reported a good or excellent result and 91.7% would have the procedure again. In contrast, all 4 device-related complications occurred in the small group of patients who had secondary surgery.

Conclusions:

The M6-C prosthesis appears to be a valuable addition to the CDA armatorium. It generates very good results in patients undergoing primary surgery, although its use in secondary surgery should be avoided. Longer follow-up is needed to determine to what measure this device can prevent ASD.
Pedicle Screw Fluid Sign
Authors: Kimura Hiroaki , Shikata Jitsuhiko , Odate Seiichi , Soeda Tsunemitsu
Published: October 2013

Study Design:

A single-center case-referent study.

Objective:

To assess whether the “pedicle screw (PS) fluid sign” on magnetic resonance imaging (MRI) can be used to diagnose deep surgical site infection (SSI) after posterior spinal instrumentation (PSI).

Summary of Background Data:

MRI is a useful tool for the early diagnosis of a deep SSI. However, the diagnosis is frequently difficult with feverish patients with clear wounds after PSI because of artifacts from the metallic implants. There are no reports on MRI findings that are specific to a deep SSI after PSI. We found that fluid collection outside the head of the PS on an axial MRI scan (PS fluid sign) strongly suggested the possibility of an abscess.

Methods:

The SSI group comprised 17 patients with a deep SSI after posterior lumbar spinal instrumentation who had undergone an MRI examination at the onset of the SSI. The non-SSI group comprised 64 patients who had undergone posterior lumbar spinal instrumentation who did not develop an SSI and had an MRI examination within 4 weeks after surgery. The frequency of a positive PS fluid sign was compared between both groups.

Results:

The PS fluid sign had a sensitivity of 88.2%, specificity of 89.1%, positive predictive value of 68.1%, and negative predictive value of 96.6%. The 2 patients with a false-negative PS fluid sign in the SSI group had an infection at the disk into which the interbody cage had been inserted. Three of the 7 patients with a false-positive PS fluid sign in the non-SSI group had a dural tear during surgery.

Conclusions:

The PS fluid sign is a valuable tool for the early diagnosis of a deep SSI. The PS fluid sign is especially useful for diagnosing a deep SSI in difficult cases, such as feverish patients without wound discharge.
Iron Requirements of Infants and Toddlers
Authors: Domellöf Magnus , Braegger Christian , Campoy Cristina , Colomb Virginie , Decsi Tamas , Fewtrell Mary , Hojsak Iva , Mihatsch Walter , Molgaard Christian , Shamir Raanan , Turck Dominique , van Goudoever Johannes
Published: October 2013

Iron deficiency (ID) is the most common micronutrient deficiency worldwide and young children are a special risk group because their rapid growth leads to high iron requirements. Risk factors associated with a higher prevalence of ID anemia (IDA) include low birth weight, high cow's‐milk intake, low intake of iron‐rich complementary foods, low socioeconomic status, and immigrant status. The aim of this position paper was to review the field and provide recommendations regarding iron requirements in infants and toddlers, including those of moderately or marginally low birth weight. There is no evidence that iron supplementation of pregnant women improves iron status in their offspring in a European setting. Delayed cord clamping reduces the risk of ID. There is insufficient evidence to support general iron supplementation of healthy European infants and toddlers of normal birth weight. Formula‐fed infants up to 6 months of age should receive iron‐fortified infant formula, with an iron content of 4 to 8 mg/L (0.6–1.2 mg · kg−1 · day−1). Marginally low‐birth‐weight infants (2000–2500 g) should receive iron supplements of 1–2 mg · kg−1 · day−1. Follow‐on formulas should be iron‐fortified; however, there is not enough evidence to determine the optimal iron concentration in follow‐on formula. From the age of 6 months, all infants and toddlers should receive iron‐rich (complementary) foods, including meat products and/or iron‐fortified foods. Unmodified cow's milk should not be fed as the main milk drink to infants before the age of 12 months and intake should be limited to <500 mL/day in toddlers. It is important to ensure that this dietary advice reaches high‐risk groups such as socioeconomically disadvantaged families and immigrant families.
Arthrobacter gyeryongensis sp. nov., isolated from soil of a Gynostemma pentaphyllum field
Authors: Hoang Van-An , Kim Yeon-Ju , Nguyen Ngoc-Lan , Yang Deok-Chun
Published: October 2013

A Gram-stain-positive, flagellate, rod-shaped, catalase- and oxidase-positive bacterium, designated DCY72T, was isolated from the soil of a Gynostemma pentaphyllum field. Growth occurred at 4–34 °C (optimum 30 °C), at pH 4–10 (optimum pH 7), and with 0–5 % NaCl (w/v). The major menaquinones of strain DCY72T were MK-9(H2) (81.0 %) and MK-10(H2) (12.2 %). The major amino acid present in the cell-wall peptidoglycan was l-lysine. The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 64.5 mol%. 16S rRNA gene sequence analysis revealed that strain DCY72T belonged to the family

Micrococcaceae

and was most closely related to

Arthrobacter ramosus

CCM 1646T (98.2 % similarity). The DNA–DNA relatedness between strain DCY72T and

A. ramosus

KACC 14391T (98.2 % 16S rRNA gene sequence similarity),

Arthrobacter nitroguajacolicus

KACC 14581T (97.6 %),

Arthrobacter nicotinovorans

KACC 20508T (97.3 %) and

Arthrobacter aurescens

KACC 20528T (97.3 %). was 12.9 %±0.3, 25.6 %±0.3, 26.6 %±0.5 and 23.2 %±0.9, respectively. On the basis of the phenotypic characteristics, genotypic analysis and physiological characteristics, strain DCY72T represents a novel species of the genus

Arthrobacter

, for which the name Arthrobacter gyeryo
ngensis sp. nov. is proposed. The type strain is DCY72T ( = KCTC 33072T = JCM 18514T).
Development of a multilocus sequence typing scheme for Streptococcus gallolyticus
Authors: Shibata Yusuke , Tien Le Hong Thuy , Nomoto Ryohei , Osawa Ro
Published: October 2013

Streptococcus gallolyticusis often found as a member of the normal gut microflora in various animals. However, it has been reported to cause mastitis in cattle, septicaemia in pigeons, and meningitis, septicaemia and endocarditis in humans. However, little is known about the epidemiology and crucial virulence factors ofS. gallolyticus. To help address these issues, we developed a multilocus sequence typing (MLST) scheme forS. gallolyticus. Seven housekeeping gene fragments were sequenced from each of 58S. gallolyticusisolates collected from diverse origins and sources. The MLST scheme had good discriminatory ability. The 63 strains, including the 5 whole genome sequenced strains examined, resolved into 57 sequence types (STs), with 52 STs represented by only a single strain. With respect to the identification ofS. gallolyticussubspecies (i.e.S. gallolyticussubsp.gallolyticus,S. gallolyticussubsp.pasteurianusandS. gallolyticussubsp.macedonicus), the results of biochemical tests and DNA–DNA hybridization were in high concordance with those of the MLST scheme. The MLST scheme developed in this study may be a useful tool capable of replacing the conventional methods used forS. gallolyticussubspecies identification. The results of this study suggest that the biology and virulence of two pathogenicS. gallolyticussubspecies (i.e.S. gallolyticussubsp.gallolyticusandS. gallolyticussubsp.pasteurianus) are very different. The MLST scheme offers researchers a valuable typing tool that will promote further investigation of the epidemiology ofS. gallolyticus.
A new equation proposed for evaluation of IR drop on buried pipelines
Authors: Naderi Esmaeel , Hadi Moayed Mohammad , Rahman Mohsen
Published: October 2013

Purpose

– In this investigation, attempts were made to distinguish critical coating faults in order of repair priority in DCVG+CIPS survey data by new proposed equation for calculating IR drop. The paper aims to discuss these issues.

Design/methodology/approach

– DCVG+CIPS, XRD, EDS.

Findings

– A new empirical equation was developed which is able to predict the importance more precisely. Besides, the studies proved the corrosion products were mainly hematite and goethite, and the presence of Cl anions was not noticed. As a result, the corrosion attack had a form of non-uniform localized corrosion.

Originality/value

– The values were gathered by DCVG+CIPS method of survey.