bluuebunny/crossref_metadata_2025_split huggingface dataset:
2D/3D reconstruction of the distal femur using statistical shape models addressing personalized surgical instruments in knee arthroplasty: A feasibility analysis
Authors: Cerveri Pietro , Sacco Costanza , Olgiati Gianluca , Manzotti Alfonso , Baroni Guido 
Published: April 2017

AbstractBackgroundPersonalized surgical instruments (PSI) have gained success in the domain of total knee replacement, demonstrating clinical outcomes similar or even superior to both traditional and navigated surgeries. The key requirement for prototyping PSI is the availability of the digital bony surface. In this paper, we aim at verifying whether the 2D/3D reconstruction of the distal femur, based on statistical shape models (SSM), grants sufficient accuracy, especially in the condylar regions, to support a PSI technique.MethodsComputed tomographic knee datasets acquired on 100 patients with severe cartilage damage were retrospectively considered in this work. All the patients underwent total knee replacement using the PSI‐based surgical technique. Eighty out of 100 reconstructed distal femur surfaces were used to build the statistical model. The remaining 20 surfaces were used for testing. The 2D/3D reconstruction process was based on digital reconstructed radiographies (DRRs) obtained with a simulated X‐ray projection process. An iterative optimization procedure, based on an evolutionary algorithm, systematically morphed the statistical model to decrease the difference between the DRR, obtained by the original CT dataset, and the DRR obtained from the morphed surface.ResultsOver the 80 variations, the first ten modes were found sufficient to reconstruct the distal femur surface with accuracy. Using three DRR, the maximum Hausdorff and RMS distance errors were lower than 1.50 and 0.75 mm, respectively. As expected, the reconstruction quality improved by increasing the number of DRRs. Statistical difference (P < 0.001) was found in the 2 vs 3, 2 vs 4 and 2 vs 5 DRR, thus proving that adding just a single displaced projection to the two traditional sagittal and coronal X‐ray images improved significantly the reconstruction quality. The effect of the PSI contact area errors on the distal cut direction featured a maximum median error lower than 2° and 0.5° on the sagittal and frontal plane, respectively. Statistical difference was found (P < 0.0001) in the reconstruction accuracy when comparing SSM built using pathologic with respect to non‐pathologic shapes (cadavers), meaning that, to improve the patient‐specific reconstruction, the morphologic anomalies, specific to the pathology, must be embedded into the SSM.ConclusionsWe showed that the X‐ray based reconstruction of the distal femur is reasonable also in presence of pathologic bony conditions, featuring accuracy results similar to earlier reports in the literature that reconstructed normal femurs. This finding discloses the chance of applying the proposed methodology to the reconstruction of bony surfaces used in the PSI surgical approach.
Mental rotation: an examination of assumptions
Authors: Searle Jordan A. , Hamm Jeff P. 
Published: April 2017

Since first presented by Shepard and Metzler, Science 1971, 171: 701–703, mental rotation has been described as a rotary transformation of a visual stimulus allowing it to be represented in a new orientation. For a given stimulus, the transformation is thought to occur at a constant speed, though speed may vary between stimuli; three‐dimensional abstract shapes made out of blocks tend to be rotated much more slowly than alphanumeric characters or line drawings of common objects. Rotation is also presumed to be performed through the shortest angle. These assumptions are based upon the fact that response times tend to increase with angle of rotation, peaking at 180° of separation for abstract block figures or from upright for common objects and alphanumeric stimuli. The symmetry about 180° provides evidence supporting rotation through the shortest angle. In order to determine the shortest direction, the current orientation of the stimulus is assumed to be known prior to mental rotation. Moreover, in order to determine the current orientation of a common object or alphanumeric stimulus, it is assumed the stimulus is identified prior to mental rotation because the current orientation is defined by what the object is. In mirror/normal discriminations or left/right facing discriminations of rotated stimuli response times are often examined by collapsing over response options as this variable is assumed to be uninteresting in terms of mental rotation. This article examines these assumptions, and suggests that many of them are not entirely safe. WIREs Cogn Sci 2017, 8:e1443. doi: 10.1002/wcs.1443This article is categorized under:

Psychology > Theory and Methods
Proximity‐dependent labeling methods for proteomic profiling in living cells
Authors: Chen Chiao‐Lin , Perrimon Norbert 
Published: April 2017

Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling‐based methods coupled with mass spectrometry (MS) offer a high‐throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins with biotin. The biotinylated endogenous proteins can then be isolated for further analysis by MS. To analyze protein–protein interactions or identify components that localize to discrete subcellular compartments, spatial expression is achieved by fusing the enzyme to specific proteins or signal peptides that target to particular subcellular regions. Although these technologies have only been introduced recently, they have already provided deep insights into a wide range of biological processes. Here, we describe and compare current methods of proximity labeling as well as their applications. As each method has its own unique features, the goal of this review is to describe how different proximity labeling methods can be used to answer different biological questions. WIREs Dev Biol 2017, 6:e272. doi: 10.1002/wdev.272This article is categorized under:

Technologies > Analysis of Proteins
Targeted nanoparticles for head and neck cancers: overview and perspectives
Authors: Zhao Yuying , Chen Haolin , Chen Xing , Hollett Geoffrey , Gu Zhipeng , Wu Jun , Liu Xiqiang 
Published: April 2017

Head and neck cancer (HNC) is common in several regions and is associated with high morbidity and mortality worldwide. This review summarizes the recent progress in the development of targeted nanoparticle systems for HNC therapy. WIREs Nanomed Nanobiotechnol 2017, 9:e1469. doi: 10.1002/wnan.1469This article is categorized under:

Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease
Novel basin modelling concept for simulating deformation from mechanical compaction using level sets
Authors: McGovern Sean , Kollet Stefan , Bürger Claudius M. , Schwede Ronnie L. , Podlaha Olaf G. 
Published: April 2017

Abstract
As sedimentation progresses in the formation and evolution of a depositional geologic basin, the rock strata are subject to various stresses. With increasing lithostatic pressure, compressional forces act to compact the porous rock matrix, leading to overpressure buildup, changes in the fluid pore pressure and fluid flow. In the context of petroleum systems modelling, the present study concerns the geometry changes that a compacting basin experiences subject to deposition. The purpose is to track the positions of the rock layer interfaces as compaction occurs. To handle the challenge of potentially large geometry deformations, a new modelling concept is proposed that couples the pore pressure equation with a level set method to determine the movement of lithostratigraphic interfaces. The level set method propagates an interface according to a prescribed speed. The coupling term for the pore pressure and level-set equations consists of this speed function, which is dependent on the compaction law. The two primary features of this approach are the simplicity of the grid and the flexibility of the speed function. A first evaluation of the model concept is presented based on an implementation for one spatial dimension accounting for vertical effective stress. Isothermal conditions with a constant fluid density and viscosity were assumed. The accuracy of the implemented numerical solution for the case of a single stratigraphic unit with a linear compaction law was compared to the available analytical solution [38]. The multi-layer setup and the nonlinear case were tested for plausibility.
Gender-gaps and glass ceilings: A survey of gender-specific publication trends in Psychiatry between 1994 and 2014
Authors: Süßenbacher S. , Amering M. , Gmeiner A. , Schrank B. 
Published: April 2017

AbstractBackground:Within academic psychiatry, women are underrepresented in the higher academic ranks. However, basic determinants of women's lack of academic advancement such as publication activity are poorly understood. The present study examines women's publication activity in high-impact psychiatry journals over two decades and reports developments in the numbers of male and female authorship over time and across cultural areas.Methods:We conducted a retrospective bibliometric review of all articles published in 2004 and 2014 in three high-ranking general psychiatry journals. Statistical comparisons were made between the two years and with results from a baseline assessment in 1994.Results:The overall percentage of female authors increased from 24.6% in 1994 to 33.2% in 2004 to 38.9% in 2014. Though increases in female authorship were statistically significant for both decades, there was less difference between 2004 and 2014, indicating a possible ceiling effect. Rates of female first authors increased between 1994 and 2014, though to a lesser degree between 2004 and 2014. Numbers of female corresponding authors plateaued between 2004 and 2014. Within Europe, Scandinavia displayed the most balanced gender-wise first author ratios. Western European and Central European countries increased their rates of female first authors substantially between 2004 and 2014.Conclusions:Despite gains in some areas, our study reveals considerable deficits in the diversity of the current academic psychiatric landscape. Ongoing efforts and interventions to enhance the participation of underrepresented groups on institutional, political and editorial levels are necessary to diversify psychiatric research.
Circulating Tumor DNA as Biomarkers for Cancer Detection
Authors: Han Xiao , Wang Junyun , Sun Yingli 
Published: April 2017

Abstract
Detection of circulating tumor DNAs (ctDNAs) in cancer patients is an important component of cancer precision medicine ctDNAs. Compared to the traditional physical and biochemical methods, blood-based ctDNA detection offers a non-invasive and easily accessible way for cancer diagnosis, prognostic determination, and guidance for treatment. While studies on this topic are currently underway, clinical translation of ctDNA detection in various types of cancers has been attracting much attention, due to the great potential of ctDNA as blood-based biomarkers for early diagnosis and treatment of cancers. ctDNAs are detected and tracked primarily based on tumor-related genetic and epigenetic alterations. In this article, we reviewed the available studies on ctDNA detection and described the representative methods. We also discussed the current understanding of ctDNAs in cancer patients and their availability as potential biomarkers for clinical purposes. Considering the progress made and challenges involved in accurate detection of specific cell-free nucleic acids, ctDNAs hold promise to serve as biomarkers for cancer patients, and further validation is needed prior to their broad clinical use.
Lirex: A Package for Identification of Long Inverted Repeats in Genomes
Authors: Wang Yong , Huang Jiao-Mei 
Published: April 2017

Abstract
Long inverted repeats (LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is highly complicated when mismatches and indels between the repeats are permitted. Long inverted repeat explorer (Lirex) was developed and introduced in this report. Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats. Recombinogenic LIRs can be selected on the basis of mismatch rate and internal spacer size from identified LIRs. Lirex, as a cross-platform tool to identify LIRs in a genome, may assist in designing following experiments to explore the function of LIRs. Our tool can identify more LIRs than other LIR searching tools. Lirex is publicly available at http://124.16.219.129/Lirex.
Prevalence of homeopathy use by the general population worldwide: a systematic review
Authors: Relton Clare , Cooper Katy , Viksveen Petter , Fibert Philippa , Thomas Kate 
Published: April 2017

Aim: To systematically review surveys of 12-month prevalence of homeopathy use by the general population worldwide.Methods: Studies were identified via database searches to October 2015. Study quality was assessed using a six-item tool. All estimates were in the context of a survey which also reported prevalence of any complementary and alternative medicine use.Results: A total of 36 surveys were included. Of these, 67% met four of six quality criteria.Twelve-month prevalence of treatment by a homeopath was reported in 24 surveys of adults (median 1.5%, range 0.2–8.2%). Estimates for children were similar to those for adults. Rates in the USA, UK, Australia and Canada all ranged from 0.2% to 2.9% and remained stable over the years surveyed (1986–2012).Twelve-month prevalence of all use of homeopathy (purchase of over-the-counter homeopathic medicines and treatment by a homeopath) was reported in 10 surveys of adults (median 3.9%, range 0.7–9.8%) while a further 11 surveys which did not define the type of homeopathy use reported similar data. Rates in the USA and Australia ranged from 1.7% to 4.4% and remained stable over the years surveyed. The highest use was reported by a survey in Switzerland where homeopathy is covered by mandatory health insurance.Conclusions: This review summarises 12-month prevalence of homeopathy use from surveys conducted in eleven countries (USA, UK, Australia, Israel, Canada, Switzerland, Norway, Germany, South Korea, Japan and Singapore). Each year a small but significant percentage of these general populations use homeopathy. This includes visits to homeopaths as well as purchase of over-the-counter homeopathic medicines.
Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota
Authors: Bonfante Paola , Desirò Alessandro 
Published: April 2017

Abstract
Bacterial interactions with plants and animals have been examined for many years; differently, only with the new millennium the study of bacterial–fungal interactions blossomed, becoming a new field of microbiology with relevance to microbial ecology, human health and biotechnology. Bacteria and fungi interact at different levels and bacterial endosymbionts, which dwell inside fungal cells, provide the most intimate example. Bacterial endosymbionts mostly occur in fungi of the phylum Mucoromycota and include Betaproteobacteria (Burkhoderia-related) and Mollicutes (Mycoplasma-related). Based on phylogenomics and estimations of divergence time, we hypothesized two different scenarios for the origin of these interactions (early vs late bacterial invasion). Sequencing of the genomes of fungal endobacteria revealed a significant reduction in genome size, particularly in endosymbionts of Glomeromycotina, as expected by their uncultivability and host dependency. Similar to endobacteria of insects, the endobacteria of fungi show a range of behaviours from mutualism to antagonism. Emerging results suggest that some benefits given by the endobacteria to their plant-associated fungal host may propagate to the interacting plant, giving rise to a three-level inter-domain interaction.
Class 1 integrons are low-cost structures in Escherichia coli
Authors: Lacotte Yohann , Ploy Marie-Cécile , Raherison Sophie 
Published: April 2017

Abstract
Resistance integrons are bacterial genetic platforms that can capture and express antibiotic resistance genes embedded within gene cassettes. The capture and shuffling of gene cassettes are mediated by the integrase IntI, the expression of which is regulated by the SOS response in Escherichia coli. Gene cassettes are expressed from a common Pc promoter. Despite the clinical and environmental relevance of integrons, the selective forces responsible for their evolution and maintenance are poorly understood. Here, we conducted pairwise competition experiments in order to assess the fitness cost of class 1 integrons in E. coli. We found that integrons are low-cost structures and that their cost is further reduced by their tight regulation. We show that the SOS response prevents the expression of costly integrases whose cost is activity dependent. Thus, when an integron is repressed, its cost depends mostly on the expression of its gene cassettes array and increases with Pc strength and the number of cassettes in the array. Furthermore, different cassettes have different costs. Lastly, we showed that subinhibitory antibiotic concentrations promoted the selection of integron-carrying bacteria, especially those with a strong Pc promoter. These results provide new insights into the evolutionary dynamics of integron-carrying bacterial populations.
Defective Gpsm2/Gαi3 signalling disrupts stereocilia development and growth cone actin dynamics in Chudley-McCullough syndrome
Authors: Mauriac Stephanie A. , Hien Yeri E. , Bird Jonathan E. , Carvalho Steve Dos-Santos , Peyroutou Ronan , Lee Sze Chim , Moreau Maite M. , Blanc Jean-Michel , Gezer Aysegul , Medina Chantal , Thoumine Olivier , Beer-Hammer Sandra , Friedman Thomas B. , Rüttiger Lukas , Forge Andrew , Nürnberg Bernd , Sans Nathalie , Montcouquiol Mireille 
Published: April 2017

AbstractMutations inGPSM2cause Chudley-McCullough syndrome (CMCS), an autosomal recessive neurological disorder characterized by early-onset sensorineural deafness and brain anomalies. Here, we show that mutation of the mouse orthologue ofGPSM2affects actin-rich stereocilia elongation in auditory and vestibular hair cells, causing deafness and balance defects. The G-protein subunit Gαi3, a well-documented partner of Gpsm2, participates in the elongation process, and its absence also causes hearing deficits. We show that Gpsm2 defines an ∼200 nm nanodomain at the tips of stereocilia and this localization requires the presence of Gαi3, myosin 15 and whirlin. Using single-molecule tracking, we report that loss ofGpsm2leads to decreased outgrowth and a disruption of actin dynamics in neuronal growth cones. Our results elucidate the aetiology of CMCS and highlight a new molecular role for Gpsm2/Gαi3in the regulation of actin dynamics in epithelial and neuronal tissues.
Electrical spin injection and detection in molybdenum disulfide multilayer channel
Authors: Liang Shiheng , Yang Huaiwen , Renucci Pierre , Tao Bingshan , Laczkowski Piotr , Mc-Murtry Stefan , Wang Gang , Marie Xavier , George Jean-Marie , Petit-Watelot Sébastien , Djeffal Abdelhak , Mangin Stéphane , Jaffrès Henri , Lu Yuan 
Published: April 2017

AbstractMolybdenum disulfide has recently emerged as a promising two-dimensional semiconducting material for nano-electronic, opto-electronic and spintronic applications. However, the demonstration of an electron spin transport through a semiconducting MoS2 channel remains challenging. Here we show the evidence of the electrical spin injection and detection in the conduction band of a multilayer MoS2 semiconducting channel using a two-terminal spin-valve configuration geometry. A magnetoresistance around 1% has been observed through a 450 nm long, 6 monolayer thick MoS2 channel with a Co/MgO tunnelling spin injector and detector. It is found that keeping a good balance between the interface resistance and channel resistance is mandatory for the observation of the two-terminal magnetoresistance. Moreover, the electron spin-relaxation is found to be greatly suppressed in the multilayer MoS2 channel with an in-plane spin polarization. The long spin diffusion length (approximately ∼235 nm) could open a new avenue for spintronic applications using multilayer transition metal dichalcogenides.
Easy access to nucleophilic boron through diborane to magnesium boryl metathesis
Authors: Pécharman Anne-Frédérique , Colebatch Annie L. , Hill Michael S. , McMullin Claire L. , Mahon Mary F. , Weetman Catherine 
Published: April 2017

AbstractOrganoboranes are some of the most synthetically valuable and widely used intermediates in organic and pharmaceutical chemistry. Their synthesis, however, is limited by the behaviour of common boron starting materials as archetypal Lewis acids such that common routes to organoboranes rely on the reactivity of boron as an electrophile. While the realization of convenient sources of nucleophilic boryl anions would open up a wealth of opportunity for the development of new routes to organoboranes, the synthesis of current candidates is generally limited by a need for highly reducing reaction conditions. Here, we report a simple synthesis of a magnesium boryl through the heterolytic activation of the B–B bond of bis(pinacolato)diboron, which is achieved by treatment of an easily generated magnesium diboranate complex with 4-dimethylaminopyridine. The magnesium boryl is shown to act as an unambiguous nucleophile through its reactions with iodomethane, benzophenone and N,N′-di-isopropyl carbodiimide and by density functional theory.
The epidemiology, radiology and biological characteristics of interval breast cancers in population mammography screening
Authors: Houssami Nehmat , Hunter Kylie 
Published: April 2017

AbstractAn interval breast cancer is a cancer that emerges following a negative mammographic screen. This overview describes the epidemiology, and the radiological and biological characteristics of interval breast cancers in population mammography screening. Notwithstanding possible differences in ascertainment of interval breast cancers, there was broad variability in reported interval breast cancer rates (range 7.0 to 49.3 per 10,000 screens) reflecting heterogeneity in underlying breast cancer rates, screening rounds (initial or repeat screens), and the length and phase of the inter-screening interval. The majority of studies (based on biennial screening) reported interval breast cancer rates in the range of 8.4 to 21.1 per 10,000 screens spanning the two-year interval with the larger proportion occurring in the second year. Despite methodological limitations inherent in radiological surveillance (retrospective mammographic review) of interval breast cancers, this form of surveillance consistently reveals that the majority of interval cancers represent either true interval or occult cancers that were not visible on the index mammographic screen; approximately 20–25% of interval breast cancers are classified as having been missed (false-negatives). The biological characteristics of interval breast cancers show that they have relatively worse tumour prognostic characteristics and biomarker profile, and also survival outcomes, than screen-detected breast cancers; however, they have similar characteristics and prognosis as breast cancers occurring in non-screened women. There was limited evidence on the effect on interval breast cancer frequency and outcomes following transition from film to digital mammography screening.