bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tumour-specific Causal Inference Discovers Distinct Disease Mechanisms Underlying Cancer Subtypes
Authors: Xue Yifan , Cooper Gregory , Cai Chunhui , Lu Songjian , Hu Baoli , Ma Xiaojun , Lu Xinghua 
Published: September 2019

AbstractCancer is a disease mainly caused by somatic genome alterations (SGAs) that perturb cellular signalling systems. Furthermore, the combination of pathway aberrations in a tumour defines its disease mechanism, and distinct disease mechanisms underlie the inter-tumour heterogeneity in terms of disease progression and responses to therapies. Discovering common disease mechanisms shared by tumours would provide guidance for precision oncology but remains a challenge. Here, we present a novel computational framework for revealing distinct combinations of aberrant signalling pathways in tumours. Specifically, we applied the tumour-specific causal inference algorithm (TCI) to identify causal relationships between SGAs and differentially expressed genes (DEGs) within tumours from the Cancer Genome Atlas (TCGA) study. Based on these causal inferences, we adopted a network-based method to identify modules of DEGs, such that the member DEGs within a module tend to be co-regulated by a common pathway. Using the expression status of genes in a module as a surrogate measure of the activation status of the corresponding pathways, we divided breast cancers (BRCAs) into five subgroups and glioblastoma multiformes (GBMs) into six subgroups with distinct combinations of pathway aberrations. The patient groups exhibited significantly different survival patterns, indicating that our approach can identify clinically relevant disease subtypes.
Controlling spin supercurrents via nonequilibrium spin injection
Authors: Ouassou Jabir Ali , Robinson Jason W. A. , Linder Jacob 
Published: September 2019

AbstractWe propose a mechanism whereby spin supercurrents can be manipulated in superconductor/ferromagnet proximity systems via nonequilibrium spin injection. We find that if a spin supercurrent exists in equilibrium, a nonequilibrium spin accumulation will exert a torque on the spins transported by this current. This interaction causes a new spin supercurrent contribution to manifest out of equilibrium, which is proportional to and polarized perpendicularly to both the injected spins and the equilibrium spin current. This is interesting for several reasons: as a fundamental physical effect; due to possible applications as a way to control spin supercurrents; and timeliness in light of recent experiments on spin injection in proximitized superconductors.
Generation of c-MycERTAM-transduced human late-adherent olfactory mucosa cells for potential regenerative applications
Authors: Santiago-Toledo Gerardo , Georgiou Melanie , dos Reis Joana , Roberton Victoria H. , Valinhas Ana , Wood Rachael C. , Phillips James B. , Mason Chris , Li Daqing , Li Ying , Sinden John D. , Choi David , Jat Parmjit S. , Wall Ivan B. 
Published: September 2019

AbstractHuman olfactory mucosa cells (hOMCs) have been transplanted to the damaged spinal cord both pre-clinically and clinically. To date mainly autologous cells have been tested. However, inter-patient variability in cell recovery and quality, and the fact that the neuroprotective olfactory ensheathing cell (OEC) subset is difficult to isolate, means an allogeneic hOMC therapy would be an attractive “off-the-shelf” alternative. The aim of this study was to generate a candidate cell line from late-adherent hOMCs, thought to contain the OEC subset. Primary late-adherent hOMCs were transduced with a c-MycERTAMgene that enables cell proliferation in the presence of 4-hydroxytamoxifen (4-OHT). Two c-MycERTAM-derived polyclonal populations, PA5 and PA7, were generated and expanded. PA5 cells had a normal human karyotype (46, XY) and exhibited faster growth kinetics than PA7, and were therefore selected for further characterisation. PA5 hOMCs express glial markers (p75NTR, S100ß, GFAP and oligodendrocyte marker O4), neuronal markers (nestin and ß-III-tubulin) and fibroblast-associated markers (CD90/Thy1 and fibronectin). Co-culture of PA5 cells with a neuronal cell line (NG108-15) and with primary dorsal root ganglion (DRG) neurons resulted in significant neurite outgrowth after 5 days. Therefore, c-MycERTAM-derived PA5 hOMCs have potential as a regenerative therapy for neural cells.
Evaluation of the postoperative stability of a counter-clockwise rotation technique for skeletal class II patients by using a novel three- dimensional position-posture method
Authors: Wan Zhuqing , Shen Steve Guofang , Gui Haijun , Zhang Peng , Shen Shunyao 
Published: September 2019

AbstractThe aim of this study is to evaluate the postsurgical stability of skeletal class II patients after performing a counter-clockwise rotational (CCWR) procedure for the maxilla-mandibular complex (MMC) by using a novel Three-dimensional (3D) Position-Posture(P-P) measuring method. Twenty-five patients (5 males and 20 females) were included in this study. The postoperative CT scans of the skull were taken before surgery(T0), 3–7 days (T1), 3 months (T2), and 6 months (T3) after surgery. Specific anatomic landmarks were chosen to determine the position of the segments, while three equally perpendicular planes were created to describe their posture. The results show that the linear relapse of maxillary landmarks during the follow-up were acceptable (≤0.5 mm). The relapse of maxillary pitch plane at 6-months follow-up is 1.52°, which is acceptable. There was a significant pitch plane relapse of the mandibular-body segment with an average of 1.86° between T1 and T2 models, 3.28° between T1 and T3 models. There was no significant difference between roll and yaw planes during the follow-up. We therefore conclude that the P-P method could be used to accurately analyze the postsurgical stability of skeletal class II orthognathic surgery cases. For CCWR procedures, it was also shown that the there is a tendency for recurrence most specially on the body of the mandible.
A small gene sequencing panel realises a high diagnostic rate in patients with congenital nystagmus following basic phenotyping
Authors: O’Gorman Luke , Norman Chelsea S. , Michaels Luke , Newall Tutte , Crosby Andrew H. , Mattocks Christopher , Cree Angela J. , Lotery Andrew J. , Baple Emma L. , Ratnayaka J. Arjuna , Baralle Diana , Lee Helena , Osborne Daniel , Shawkat Fatima , Gibson Jane , Ennis Sarah , Self Jay E. 
Published: September 2019

AbstractNystagmus is a disorder of uncontrolled eye movement and can occur as an isolated trait (idiopathic INS, IINS) or as part of multisystem disorders such as albinism, significant visual disorders or neurological disease. Eighty-one unrelated patients with nystagmus underwent routine ocular phenotyping using commonly available phenotyping methods and were grouped into four sub-cohorts according to the level of phenotyping information gained and their findings. DNA was extracted and sequenced using a broad utility next generation sequencing (NGS) gene panel. A clinical subpanel of genes for nystagmus/albinism was utilised and likely causal variants were prioritised according to methods currently employed by clinical diagnostic laboratories. We determine the likely underlying genetic cause for 43.2% of participants with similar yields regardless of prior phenotyping. This study demonstrates that a diagnostic workflow combining basic ocular phenotyping and a clinically available targeted NGS panel, can provide a high diagnostic yield for patients with infantile nystagmus, enabling access to disease specific management at a young age and reducing the need for multiple costly, often invasive tests. By describing diagnostic yield for groups of patients with incomplete phenotyping data, it also permits the subsequent design of ‘real-world’ diagnostic workflows and illustrates the changing role of genetic testing in modern diagnostic workflows for heterogeneous ophthalmic disorders.
A mantidfly in Cretaceous Spanish amber provides insights into the evolution of integumentary specialisations on the raptorial foreleg
Authors: Pérez-de la Fuente Ricardo , Peñalver Enrique 
Published: September 2019

AbstractMultiple predatory insect lineages have developed a raptorial lifestyle by which they strike and hold prey using modified forelegs armed with spine-like structures and other integumentary specialisations. However, how structures enabling the raptorial function evolved in insects remains largely hypothetical or inferred through phylogeny due to the rarity of meaningful fossils. This is particularly true for mantidflies (Neuroptera: Mantispidae), which have a scarce fossil record mostly based on rock compressions, namely isolated wings. Here,Aragomantispa laceratagen. et sp. nov. is described from ca. 105-million-year-old San Just amber (Spain), representing the oldest and one of the few mantidflies hitherto described from amber. The fossil shows exquisitely preserved forefemoral spine-like structures composed of integumentary processes each bearing a modified seta, and prostrate setae on foretibiae and foretarsi. The fine morphology of these structures was unknown in fossil mantidflies. An assessment of integumentary specialisations from raptorial forelegs across mantispoid lacewings is provided. The present finding reveals how the specialised foreleg armature associated to the raptorial lifestyle in extant mantidflies was present yet not fully established by the Early Cretaceous, at least in some lineages, and provides palaeontological evidence supporting certain evolutionary patterns of acquisition of integumentary specialisations related to the raptorial function in the group.
Technical considerations of multi-parametric tissue outcome prediction methods in acute ischemic stroke patients
Authors: Winder Anthony J. , Siemonsen Susanne , Flottmann Fabian , Thomalla Götz , Fiehler Jens , Forkert Nils D. 
Published: September 2019

AbstractDecisions regarding acute stroke treatment rely heavily on imaging, but interpretation can be difficult for physicians. Machine learning methods can assist clinicians by providing tissue outcome predictions for different treatment approaches based on acute multi-parametric imaging. To produce such clinically viable machine learning models, factors such as classifier choice, data normalization, and data balancing must be considered. This study gives comprehensive consideration to these factors by comparing the agreement of voxel-based tissue outcome predictions using acute imaging and clinical parameters with manual lesion segmentations derived from follow-up imaging. This study considers random decision forest, generalized linear model, and k-nearest-neighbor machine learning classifiers in conjunction with three data normalization approaches (non-normalized, relative to contralateral hemisphere, and relative to contralateral VOI), and two data balancing strategies (full dataset and stratified subsampling). These classifier settings were evaluated based on 90 MRI datasets from acute ischemic stroke patients. Distinction was made between patients recanalized using intraarterial and intravenous methods, as well as those without successful recanalization. For primary quantitative comparison, the Dice metric was computed for each voxel-based tissue outcome prediction and its corresponding follow-up lesion segmentation. It was found that the random forest classifier outperformed the generalized linear model and the k-nearest-neighbor classifier, that normalization did not improve the Dice score of the lesion outcome predictions, and that the models generated lesion outcome predictions with higher Dice scores when trained with balanced datasets. No significant difference was found between the treatment groups (intraarterial vs intravenous) regarding the Dice score of the tissue outcome predictions.
Silk physico-chemical variability and mechanical robustness facilitates intercontinental invasibility of a spider
Authors: Viera Carmen , Garcia Luis F. , Lacava Mariángeles , Fang Jian , Wang Xungai , Kasumovic Michael M. , Blamires Sean J. 
Published: September 2019

AbstractThere are substantive problems associated with invasive species, including threats to endemic organisms and biodiversity. Understanding the mechanisms driving invasions is thus critical. Variable extended phenotypes may enable animals to invade into novel environments. We explored here the proposition that silk variability is a facilitator of invasive success for the highly invasive Australian house spider,Badumna longinqua. We compared the physico-chemical and mechanical properties and underlying gene expressions of its major ampullate (MA) silk between a native Sydney population and an invasive counterpart from Montevideo, Uruguay. We found that while differential gene expressions might explain the differences in silk amino acid compositions and protein nanostructures, we did not find any significant differences in silk mechanical properties across the populations. Our results accordingly suggest thatB.longinqua’s silk remains functionally robust despite underlying physico-chemical and genetic variability as the spider expands its range across continents. They also imply that a combination of silk physico-chemical plasticity combined with mechanical robustness might contribute more broadly to spider invasibilities.
Hand size underestimation grows during childhood
Authors: Cardinali Lucilla , Serino Andrea , Gori Monica 
Published: September 2019

AbstractCortical body size representations are distorted in the adult, from low-level motor and sensory maps to higher levels multisensory and cognitive representations. Little is known about how such representations are built and evolve during infancy and childhood. Here we investigated how hand size is represented in typically developing children aged 6 to 10. Participants were asked to estimate their hand size using two different sensory modalities (visual or haptic). We found a distortion (underestimation) already present in the youngest children. Crucially, such distortion increases with age and regardless of the sensory modality used to access the representation. Finally, underestimation is specific for the body as no bias was found for object estimation. This study suggests that the brain does not keep up with the natural body growth. However, since motor behavior nor perception were impaired, the distortion seems functional and/or compensated for, for proper interaction with the external environment.
Nanomotor tracking experiments at the edge of reproducibility
Authors: Novotný Filip , Pumera Martin 
Published: September 2019

AbstractThe emerging field of self-propelling micro/nanorobots is teeming with a wide variety of novel micro/nanostructures, which are tested here for self-propulsion in a liquid environment. As the size of these microscopic movers diminishes into the fully nanosized region, the ballistic paths of an active micromotor become a random walk of colloidal particles. To test such colloidal samples for self-propulsion, the commonly adopted “golden rule” is to refer to the mean squared displacement (MSD) function of the measured particle tracks. The practical significance of the result strongly depends on the amount of collected particle data and the sampling rate of the particle track. Because micro/nanomotor preparation methods are mostly low-yield, the amount of used experimental data in published results is often on the edge of reproducibility. To address the situation, we perform MSD analysis on an experimental as well as simulated dataset. These data are used to explore the effects of MSD analysis on limited data and several situations where the lack of data can lead to insignificant results.
Bayesian Random Effect Modeling for analyzing spatial clustering of differential time trends of diarrhea incidences
Authors: Osei Frank Badu , Stein Alfred 
Published: September 2019

AbstractIn 2012, nearly 644,000 people died from diarrhea in sub-Saharan Africa. This is a significant obstacle towards the achievement of the Sustainable Development Goal 3 of ensuring a healthy life and promoting the wellbeing at all ages. To enhance evidence-based site-specific intervention and mitigation strategies, especially in resource-poor countries, we focused on developing differential time trend models for diarrhea. We modeled the logarithm of the unknown risk for each district as a linear function of time with spatially varying effects. We induced correlation between the random intercepts and slopes either by linear functions or bivariate conditional autoregressive (BiCAR) priors. In comparison, models which included correlation between the varying intercepts and slopes outperformed those without. The convolution model with the BiCAR correlation prior was more competitive than the others. The inclusion of correlation between the intercepts and slopes provided an epidemiological value regarding the response of diarrhea infection dynamics to environmental factors in the past and present. We found diarrhea risk to increase by 23% yearly, a rate far exceeding Ghana’s population growth rate of 2.3%. The varying time trends widely varied and clustered, with the majority of districts with at least 80% chance of their rates exceeding the previous years. These findings can be useful for active site-specific evidence-based planning and interventions for diarrhea.
ALKBH overexpression in head and neck cancer: potential target for novel anticancer therapy
Authors: Pilžys Tomaš , Marcinkowski Michał , Kukwa Wojciech , Garbicz Damian , Dylewska Małgorzata , Ferenc Karolina , Mieczkowski Adam , Kukwa Andrzej , Migacz Ewa , Wołosz Dominika , Mielecki Damian , Klungland Arne , Piwowarski Jan , Poznański Jarosław , Grzesiuk Elżbieta 
Published: September 2019

AbstractThe nine identified human homologues of E. coli AlkB 2-oxoglutarate (2OG) and Fe(II)-dependent dioxygenase, ALKBH1-8 and FTO, display different substrate specificities and diverse biological functions. Here we discovered the combined overexpression of members of the ALKBH family in head and neck squamous cell carcinomas (HNSCC). We found direct correlation of ALKBH3 and FTO expression with primary HNSCC tumor size. We observed unidentified thus far cytoplasmic localization of ALKBH2 and 5 in HNSCC, suggesting abnormal role(s) of ALKBH proteins in cancer. Further, high expression of ALKBHs was observed not only in HNSCC, but also in several cancerous cell lines and silencing ALKBH expression in HeLa cancer cells resulted in dramatically decreased survival. Considering the discovered impact of high expression of ALKBH proteins on HNSCC development, we screened for ALKBH blockers among newly synthetized anthraquinone derivatives and demonstrated their potential to support standard anticancer therapy.
Strain-induced switching of heat current direction generated by magneto-thermoelectric effects
Authors: Ota Shinya , Uchida Ken-ichi , Iguchi Ryo , Thach Pham Van , Awano Hiroyuki , Chiba Daichi 
Published: September 2019

AbstractSince the charge current plays a major role in information processing and Joule heating is inevitable in electronic devices, thermal management, i.e., designing heat flows, is required. Here, we report that strain application can change a direction of a heat current generated by magneto-thermoelectric effects. For demonstration, we used metallic magnets in a thin-film form, wherein the anomalous Ettingshausen effect mainly determines the direction of the heat flow. Strain application can alter the magnetization direction owing to the magnetoelastic effect. As a result, the heat current, which is in the direction of the cross product of the charge current and the magnetization vector, can be switched or rotated simply by applying a tensile strain to the metallic magnets. We demonstrate 180° switching and 90° rotation of the heat currents in an in-plane magnetized Ni sample on a rigid sapphire substrate and a perpendicularly magnetized TbFeCo film on a flexible substrate, respectively. An active thermography technique was used to capture the strain-induced change in the heat current direction. The method presented here provides a novel method for controlling thermal energy in electronic devices.
Wide-band Beam-scanning by Surface Wave Confinement on Leaky Wave Holograms
Authors: Moeini Mohammad Moein , Oraizi Homayoon , Amini Amrollah , Nayyeri Vahid 
Published: September 2019

AbstractA two-dimensional (2-D) metasurface design for backward leaky wave suppression in microwave regime is proposed based on the theory of holography. The so-called Rabbit’s ears phenomenon describes that the backward mode in the reference wave plays the destructive role and makes the holography principle to behave properly mainly in an only narrow frequency interval. Here, we explore the utilization of the surface wave reflectors to suppress the backward mode to achieve wide-band holograms. Therefore, the reference wave form is manipulated by the choice of various reflector shapes and some providing forward mode dominant reference wave are analyzed and simulated. The less backward mode participates in the reference wave; the wider operation frequency range is obtained. With the canceled Rabbit’s ears phenomenon, variations in the reference wave frequency cause elevation angle scan. The results provide general insights into relation of the Rabbit’s ears phenomenon and the object wave accuracy in frequencies except the design frequency. The idea is also applied to multiple object wave holograms. The concept is verified using both electromagnetic full-wave simulations and experimental measurements.
Fatty acid transport protein 4 is required for incorporation of saturated ultralong-chain fatty acids into epidermal ceramides and monoacylglycerols
Authors: Lin Meei-Hua , Hsu Fong-Fu , Crumrine Debra , Meyer Jason , Elias Peter M. , Miner Jeffrey H. 
Published: September 2019

AbstractFatty acid transport protein 4 (FATP4) is an acyl-CoA synthetase that is required for normal permeability barrier in mammalian skin. FATP4 (SLC27A4) mutations cause ichthyosis prematurity syndrome, a nonlethal disorder. In contrast, Fatp4−/− mice die neonatally from a defective barrier. Here we used electron microscopy and lipidomics to characterize defects in Fatp4−/− mice. Mutants showed lamellar body, corneocyte lipid envelope, and cornified envelope abnormalities. Lipidomics identified two lipids previously speculated to be present in mouse epidermis, sphingosine β-hydroxyceramide and monoacylglycerol; mutants displayed decreased proportions of these and the two ceramide classes that carry ultralong-chain, amide-linked fatty acids (FAs) thought to be critical for barrier function, unbound ω-O-acylceramide and bound ω-hydroxyceramide, the latter constituting the major component of the corneocyte lipid envelope. Other abnormalities included elevated amounts of sphingosine α-hydroxyceramide, phytosphingosine non-hydroxyceramide, and 1-O-acylceramide. Acyl chain length alterations in ceramides also suggested roles for FATP4 in esterifying saturated non-hydroxy and β-hydroxy FAs with at least 25 carbons and saturated or unsaturated ω-hydroxy FAs with at least 30 carbons to CoA. Our lipidomic analysis is the most thorough such study of the Fatp4−/− mouse skin barrier to date, providing information about how FATP4 can contribute to barrier function by regulating fatty acyl moieties in various barrier lipids.