bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomedical image augmentation using Augmentor
Authors: Bloice Marcus D , Roth Peter M , Holzinger Andreas 
Published: April 2019

Abstract

Motivation
Image augmentation is a frequently used technique in computer vision and has been seeing increased interest since the popularity of deep learning. Its usefulness is becoming more and more recognized due to deep neural networks requiring larger amounts of data to train, and because in certain fields, such as biomedical imaging, large amounts of labelled data are difficult to come by or expensive to produce. In biomedical imaging, features specific to this domain need to be addressed.

Results
Here we present the Augmentor software package for image augmentation. It provides a stochastic, pipeline-based approach to image augmentation with a number of features that are relevant to biomedical imaging, such as z-stack augmentation and randomized elastic distortions. The software has been designed to be highly extensible meaning an operation that might be specific to a highly specialized task can easily be added to the library, even at runtime. Although it has been designed as a general software library, it has features that are particularly relevant to biomedical imaging and the techniques required for this domain.

Availability and implementation
Augmentor is a Python package made available under the terms of the MIT licence. Source code can be found on GitHub under https://github.com/mdbloice/Augmentor and installation is via the pip package manager (A Julia version of the package, developed in parallel by Christof Stocker, is also available under https://github.com/Evizero/Augmentor.jl).
Genetic differentiation predicts body size divergence between island and mainland populations of common wall lizards (Podarcis muralis)
Authors: Uller Tobias , Laakkonen Hanna , Michaelides Sozos , While Geoffrey M , Coulon Aurélie , Aubret Fabien 
Published: April 2019

AbstractSmall-bodied vertebrates sometimes evolve gigantism on islands, but there is a lack of consistent association with ecological factors or island characteristics. One possible reason is that, even if the ecological conditions are right, body size might fail to diverge on islands that were isolated recently or if there is gene flow between islands and the mainland. We studied body size, ventral colour polymorphism and genetic structure across nine islands and adjacent mainland populations of common wall lizards (Podarcis muralis) off the western coast of France. Population genetic data suggested that island populations might have maintained gene flow after their geographical isolation from the mainland. Island lizards were larger and heavier than mainland lizards on average, but the extent of gigantism varied substantially between islands. Island size and distance from the mainland were poor predictors of body size, but lizards from populations that were highly genetically differentiated from the mainland were larger than lizards from less differentiated populations. Colour morphs that were rare on the mainland tended to be more common on islands. We propose that genetic isolation or bottlenecks promote body size evolution in island lizards, which makes it challenging to identify ecological causes of island gigantism without complementary genetic information.
Genomic pattern of intratumor heterogeneity predicts the risk of progression in early stage diffuse large B-cell lymphoma
Authors: Wang Yue , Feng Wanjing , Liu Peng 
Published: April 2019

Abstract
Intratumor heterogeneity (ITH) plays an important role in tumor development, metastases, recurrence and has impact on clinical diagnosis, therapeutic responses. In this study, we used mutant-allele tumor heterogeneity (MATH) through whole-exome sequencing data to evaluate ITH in early stage diffuse large B-cell lymphoma (DLBCL). A discovery set of 22 patients and a validation set of 35 patients with primary DLBCL which staged I or II were chosen from The Cancer Genome Atlas database and The Gene Index Project database, respectively. Then patients were divided into low and high MATH score groups according to the median expression level. As a result, higher MATH score displayed an increasing risk of progression compared with lower MATH score both in the discovery set (P = 0.045) and the validation set (P = 0.025). Further, the genomic pattern according to MATH demonstrated that mutation rates of immunoglobulin lambda locus, B-cell translocation gene and membrane-associated guanylate kinase were the sites with the highest mutation rate. Moreover, Gene enrichment analysis showed that immunoglobulin lambda constant 2 (IGLC2) which belongs to immunoglobulin lambda locus was only enriched in high MATH group. Besides, BTG2 and Caspase recruitment domain-containing protein 11 were cancer driver genes which listed on the top three high rate of mutation. Our study revealed the prognostic value of MATH and relevant genomic pattern in early stage DLBCL. Potential mechanisms on genetic level of how genomic aberration influence the ITH of DLBCL are provided. MATH based on whole genome sequencing may be feasible for deciding clinical treatment of DLBCL patients in the future researches.
Interspecific relationships between Palmaria palmata and three Fucus species at the Murman Coast
Authors: Malavenda Sergey S , Malavenda Svetlana V , Chovgan Olga 
Published: April 2019

Abstract
The mutual influence of the dominant macroalgae species inhabiting the intertidal zone of the Murman Coast was studied. Particularly, the proposed negative effect of Palmaria palmata on the growth of Fucus algae was tested. The interspecific interactions of the Fucus vesiculosus, F. distichus, F. serratus, and P. palmata were studied experimentally. The species were cultivated pairwise in the laboratory. A field experiment with species removal was performed in the intertidal zone of the Zelenetskaya Bay, the Barents Sea. The growth rate, algae biomass, and the content of chlorophyll pigments was measured. Fucus species affected positively the growth of P. palmata. No effect of the other species on F. vesiculosus was recorded under the experimental conditions. Palmaria palmata affected negatively the growth of F. serratus; its presence led to an increase in the pigment content in F. serratus and F. distichus.
On Sevostyanov’s Construction of Quantum Difference Toda Lattices
Authors: Gonin Roman , Tsymbaliuk Alexander 
Published: April 2019

Abstract
We propose a natural generalization of the construction of the quantum difference Toda lattice [6, 22] associated with a simple Lie algebra $\mathfrak{g}$. Our construction depends on two orientations of the Dynkin diagram of $\mathfrak{g}$ and some other data (which we refer to as a pair of Sevostyanov triples). In types $A$ and $C$, we provide an alternative construction via Lax matrix formalism, cf. [15]. We also show that the generating function of the pairing of Whittaker vectors in the Verma modules is an eigenfunction of the corresponding modified quantum difference Toda system and derive fermionic formulas for the former in spirit of [7]. We give a geometric interpretation of all Whittaker vectors in type $A$ via line bundles on the Laumon moduli spaces and obtain an edge-weight path model for them, generalizing the construction of [4].
Balloon Catheter Dilatation for Treatment of a Patient With Cricopharyngeal Dysfunction After Thermal Burn Injury
Authors: Joo So Young , Lee Seung Yeol , Cho Yoon Soo , Seo Cheong Hoon 
Published: April 2019

AbstractDeglutition disorder is a clinical symptom that has been associated with inhalation and cutaneous thermal burn injuries. Deglutition disorder is present in approximately 11% of patients with burn injury and is known to persist for weeks to months postinjury. Here, we report a case of deglutition disorder associated with cricopharyngeal dysfunction in a patient with thermal burn injury. Two patients presented with deglutition disorder lasting for several weeks after thermal injury. Clinically, it manifested as combined liquid and solid food dysphagia. The findings of videofluoroscopic swallow study (VFSS) were poor relaxation of the pharyngoesophageal sphincter (PES), decreased elevation of the laryngohyoid, and inadequate pharyngeal contraction. The PES was dilated with a 20-mm expansion balloon catheter multiple times. The symptoms of deglutition disorder were relieved immediately after the procedure. Balloon catheter dilatation was performed four times at 1- to 2-week intervals. Follow-up VFSS showed that poor relaxation of the PES was improved. The VFSS showed no recurrence at the 3-month follow-up. We found that balloon catheter dilatation for treatment of a patient with cricopharyngeal dysfunction after thermal burn injury was effective, ease of use, and safe.
A new species of Sunamphitoe (Amphipoda: Ampithoidae) that bores into the primary fronds of kelps in South Africa
Authors: Griffiths Charles L 
Published: April 2019

Abstract
The herbivorous amphipod Sunamphitoe robertan. sp. is described from the canopy of kelp beds in False Bay, South Africa. The new species has unusual habits, small family groups burrowing directly into the margins of the swollen primary fronds of the kelp Ecklonia maxima (Osbeck) Papenfuss, 1940. Morphologically, the new species is best distinguished from other species of Sunamphitoe by strong rows of dorsal spines on the outer rami of uropods 1 and 2. These spine rows appear to be employed as ‘drill-bits’ to excavate kelp tissue and create the burrows. Damage to hosts does not appear to be fatal, but requires further investigation.
Blood DNA Methylation and Breast Cancer: A Prospective Case-Cohort Analysis in the Sister Study
Authors: Xu Zongli , Sandler Dale P , Taylor Jack A 
Published: April 2019

AbstractBackgroundPeripheral blood DNA methylation may be associated with breast cancer, but studies of candidate genes and global and genome-wide DNA methylation have been inconsistent.MethodsWe performed an epigenome-wide study using Infinium HumanMethylation450 BeadChips with prospectively collected blood DNA samples from the Sister Study (1552 cases, 1224 subcohort). Differentially methylated cytosine-phosphate-guanine sites (dmCpGs) were identified using case-cohort proportional hazard models and replicated using deposited data from European Prospective Investigation into Cancer and Nutrition in Italy (EPIC-Italy) (n = 329). The correlation between methylation and time to diagnosis was examined using robust linear regression. Causal or consequential relationships of methylation to breast cancer were examined by Mendelian randomization using OncoArray 500 K single-nucleotide polymorphism data. All statistical tests were two-sided.ResultsWe identified 9601 CpG markers associated with invasive breast cancer (false discovery rate = q &lt; 0.01), with 510 meeting a strict Bonferroni correction threshold (10–7). A total of 2095 of these CpGs replicated in the independent EPIC-Italy dataset, including 144 meeting the Bonferroni threshold. Sister Study women who developed ductal carcinoma in situ had methylation similar to noncases. Most (1501, 71.6%) dmCpGs showed lower methylation in invasive cases. In case-only analysis, methylation was statistically significantly associated (false discovery rate = q &lt; 0.05) with time to diagnosis for 892 (42.6%) of the dmCpGs. Analyses based on genetic association suggest that methylation differences are likely a consequence rather than a cause of breast cancer. Pathway analysis shows enrichment of breast cancer-related gene pathways, and dmCpGs are overrepresented in known breast cancer susceptibility genes.ConclusionsOur findings suggest that the DNA methylation profile of blood starts to change in response to invasive breast cancer years before the tumor is clinically detected.
A fast radio burst with frequency-dependent polarization detected during Breakthrough Listen observations
Authors: Price D C , Foster G , Geyer M , van Straten W , Gajjar V , Hellbourg G , Karastergiou A , Keane E F , Siemion A P V , Arcavi I , Bhat R , Caleb M , Chang S-W , Croft S , DeBoer D , de Pater I , Drew J , Enriquez J E , Farah W , Gizani N , Green J A , Isaacson H , Hickish J , Jameson A , Lebofsky M , MacMahon D H E , Möller A , Onken C A , Petroff E , Werthimer D , Wolf C , Worden S P , Zhang Y G 
Published: April 2019

ABSTRACT
Here, we report on the detection and verification of fast radio burst FRB 180301, which occurred on utc 2018 March 1 during the Breakthrough Listen observations with the Parkes telescope. Full-polarization voltage data of the detection were captured – a first for non-repeating FRBs – allowing for coherent de-dispersion and additional verification tests. The coherently de-dispersed dynamic spectrum of FRB 180301 shows complex, polarized frequency structure over a small fractional bandwidth. As FRB 180301 was detected close to the geosynchronous satellite band during a time of known 1–2 GHz satellite transmissions, we consider whether the burst was due to radio interference emitted or reflected from an orbiting object. Based on the pre-ponderance of our verification tests, we cannot conclusively determine FRB 180301 to be either astrophysical or anthropogenic in origin.
Formation of short-period planets by disc migration
Authors: Carrera Daniel , Ford Eric B , Izidoro Andre 
Published: April 2019

ABSTRACT
Protoplanetary discs are thought to be truncated at orbital periods of around 10 d. Therefore, the origin of rocky short-period planets with P &lt; 10 d is a puzzle. We propose that many of these planets may form through the Type-I migration of planets locked into a chain of mutual mean motion resonances. We ran N-body simulations of planetary embryos embedded in a protoplanetary disc. The embryos experienced gravitational scatterings, collisions, disc torques, and dampening of orbital eccentricity and inclination. We then modelled Kepler observations of these planets using a forward model of both the transit probability and the detection efficiency of the Kepler pipeline. We found that planets become locked into long chains of mean motion resonances that migrate in unison. When the chain reaches the edge of the disc, the inner planets are pushed past the edge due to the disc torques acting on the planets farther out in the chain. Our simulated systems successfully reproduce the observed period distribution of short-period Kepler planets between 1 and 2 R⊕. However, we obtain fewer closely packed short-period planets than in the Kepler sample. Our results provide valuable insight into the planet formation process, and suggests that resonance locks, migration, and dynamical instabilities play important roles in the formation and evolution of close-in small exoplanets.
Hunting for brown dwarfs in the globular cluster M4: second epoch HST NIR observations
Authors: Dieball A , Bedin L R , Knigge C , Geffert M , Rich R M , Dotter A , Richer H , Zurek D 
Published: April 2019

ABSTRACT
We present an analysis of the second epoch Hubble Space TelescopeWide Field Camera 3 F110W near-infrared (NIR) imaging data of the globular cluster M 4. The new data set suggests that one of the previously suggested four brown dwarf candidates in this cluster is indeed a high-probability cluster member. The position of this object in the NIR colour–magnitude diagrams (CMDs) is in the white dwarf/brown dwarf area. The source is too faint to be a low-mass main-sequence (MS) star, but, according to theoretical considerations, also most likely somewhat too bright to be a bona-fide brown dwarf. Since we know that the source is a cluster member, we determined a new optical magnitude estimate at the position the source should have in the optical image. This new estimate places the source closer to the white dwarf sequence in the optical–NIR CMD and suggests that it might be a very cool (Teff ≤ 4500 K) white dwarf at the bottom of the white dwarf cooling sequence in M 4, or a white dwarf/brown dwarf binary. We cannot entirely exclude the possibility that the source is a very massive, bright brown dwarf, or a very low-mass MS star, however, we conclude that we still have not convincingly detected a brown dwarf in a globular cluster, but we expect to be very close to the start of the brown dwarf cooling sequence in this cluster. We also note that the MS ends at F110W ≈ 22.5 mag in the proper-motion cleaned CMDs, where completeness is still high.
Jediism: Religion at Law?
Authors: Cheung Tommy 
Published: April 2019

Abstract
This article explores whether Jediism, one of the ‘fiction-based religions’ in contemporary times, meets the requirements of religion under the English charity law. This article argues that the reasons gave by the Charity Commission of the UK in rejecting the application of the Jediist religious group the Temple of The Jedi Order (TOTJO) as a Charitable Incorporation Organization in 2016 was not made under solid legal grounds but on a moral judgment that Jediism, in their opinion, is not serious. This article argues that the principles adopted by the Charity Commission is wrong and they could reach the same conclusion by using a correct legal approach.
Through a detailed study on the origin and the current situation of Jediism as a ‘fiction-based religious group’ and TOTJO, this article suggests that for Jediism to be considered as a bona fide religion, it needs to complete its belief system and bring back the concept of Dark Side from Star Wars. It was absent because of the Jediists’ deliberate effort to distance themselves from the Star Wars fandom. Finally, through looking at the history and evolvement of the English charity law, argues that there is room for the current English charity law to give a more liberal interpretation to allow a better balance between regulation of charity and the freedom of religion. It is necessary because of the public benefit brought by any bona fide religion.
Expression and characterization of functional domains of FK506-binding protein 35 from Plasmodium knowlesi
Authors: Goh Carlmond Kah Wun , Silvester Jovi , Wan Mahadi Wan Nur Shuhaida , Chin Lee Ping , Ying Lau Tiek , Leow Thean Chor , Kurahashi Ryo , Takano Kazufumi , Budiman Cahyo 
Published: April 2019

AbstractThe FK506-binding protein of Plasmodium knowlesi (Pk-FKBP35) is considerably a viable antimalarial drug target, which belongs to the peptidyl-prolyl cis-trans isomerase (PPIase) protein family member. Structurally, this protein consists of an N-terminal FK506-binding domain (FKBD) and a C-terminal tetratricopeptide repeat domain (TPRD). This study aims to decipher functional properties of these domains as a platform for development of novel antimalarial drugs. Accordingly, full-length Pk-FKBP35 as well as its isolated domains, Pk-FKBD and Pk-TPRD were overexpressed, purified, and characterized. The results showed that catalytic PPIase activity was confined to the full-length Pk-FKBP35 and Pk-FKBD, suggesting that the catalytic activity is structurally regulated by the FKBD. Meanwhile, oligomerization analysis revealed that Pk-TPRD is essential for dimerization. Asp55, Arg60, Trp77 and Phe117 in the Pk-FKBD were considerably important for catalysis as underlined by significant reduction of PPIase activity upon mutations at these residues. Further, inhibition activity of Pk-FKBP35 towards calcineurin phosphatase activity revealed that the presence of FKBD is essential for the inhibitory property, while TPRD may be important for efficient binding to calcineurin. We then discussed possible roles of FKBP35 in Plasmodium cells and proposed mechanisms by which the immunosuppressive drug, FK506, interacts with the protein.
The Rate of Return on Everything, 1870–2015*
Authors: Jordà Òscar , Knoll Katharina , Kuvshinov Dmitry , Schularick Moritz , Taylor Alan M 
Published: April 2019

Abstract
What is the aggregate real rate of return in the economy? Is it higher than the growth rate of the economy and, if so, by how much? Is there a tendency for returns to fall in the long run? Which particular assets have the highest long-run returns? We answer these questions on the basis of a new and comprehensive data set for all major asset classes, including housing. The annual data on total returns for equity, housing, bonds, and bills cover 16 advanced economies from 1870 to 2015, and our new evidence reveals many new findings and puzzles.
Inhibition of Autophagy Alleviates Cadmium-Induced Mouse Spleen and Human B Cells Apoptosis
Authors: Gu Jie , Wang Yanwei , Liu Yanmin , Shi Meilin , Yin Liangdong , Hou Yongzhong , Zhou Yang , Chu Wong Chris Kong , Chen Dongfeng , Guo Zhigang , Shi Haifeng 
Published: April 2019

Abstract
Cadmium (Cd) is a toxic heavy metal that can accumulate and cause severe damage to many organs, such as liver, kidney, lung, etc. Cd also significantly suppresses immunity, however, the underlying mechanism involved in Cd-induced immunnotoxicity is still unclear. The present study indicated that semichronic Cd exposure (7 days) induced apoptotic damage of mouse spleen. In human Ramos B cells, Cd exposure also induced apoptosis, which was dependent on Cd-induced vacuole membrane protein 1 (VMP1) expression and autophagy. Cd-induced autophagy and apoptosis were abated when VMP1 expression was knockdown. In addition, Cd-induced VMP1 expression, autophagy, and apoptosis were dependent on the elevation of Ca2+ and reactive oxygen species (ROS). More important, Cd exposure also induced VMP1 expression and autophagy in mouse spleen tissue, and the intraperitoneal injection of the autophagy inhibitor chloroquine (CQ) into mice effectively reduced Cd-induced spleen apoptotic damage. Taken together, these results indicate Cd-induced autophagy, promotes apoptosis in immune cells, and inhibition of autophagy can alleviate Cd-induced spleen and immune cell apoptosis. This study might provide the groundwork for future studies on Cd-induced immunomodulatory effects and immune diseases.
Effects of Hemodynamic Factors and Oxygenation on the Incidence of Pressure Ulcers in the ICU
Authors: Soodmand Mostafa , Moghadamnia Mohammad Taghi , Aghaei Iraj , Ghasemzadeh Golshan , Kazemnejad Lili Ehsan , Homaie Rad Enayatollah 
Published: April 2019

ABSTRACT

OBJECTIVE
To investigate the roles of hemodynamic factors and oxygenation on the incidence of pressure ulcers in patients in the ICU on mechanical ventilation.

METHODS
This prospective analytical cross-sectional study was performed in several ICUs for a period of 8 months in Iran. Researchers checked patients for pressure ulcers on a daily basis. They collected demographic, hemodynamic, and oxygenation data until a pressure ulcer occurred, the patient’s artificial airway was removed, the patient died, or the patient was discharged.

RESULTS
From August 2017 to February 2018, a total of 2,581 patients were admitted to the study ICUs; of these, 133 patients were eligible for the study. The results indicated that 41.4% (n = 55) of the patients ended up with pressure ulcers. Investigation of the variables using a Cox regression model showed that, among other variables considered in this study, age, mean arterial pressure, and positive end-expiratory pressure in the mechanical ventilator can contribute to the risk of pressure ulcers.

CONCLUSIONS
Providers should pay attention to changes in hemodynamic parameters, especially mean arterial pressure; carefully determine the most appropriate positive end-expiratory pressure for patients connected to mechanical ventilation; and take special care of susceptible groups such as older adults and hospitalized patients to decrease the incidence of pressure ulcers.