bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses
Authors: Barbour Alan G. , Shao Hanjuan , Cook Vanessa J. , Baldwin-Brown James , Tsao Jean I. , Long Anthony D. 
Published: November 2019

AbstractThe cricetine rodents Peromyscus leucopus and P. maniculatus are key reservoirs for several zoonotic diseases in North America. We determined the complete circular mitochondrial genome sequences of representatives of 3 different stock colonies of P. leucopus, one stock colony of P. maniculatus and two wild populations of P. leucopus. The genomes were syntenic with that of the murids Mus musculus and Rattus norvegicus. Phylogenetic analysis confirmed that these two Peromyscus species are sister taxa in a clade with P. polionotus and also uncovered a distinction between P. leucopus populations in the eastern and the central United States. In one P. leucopus lineage four extended regions of mitochondrial pseudogenes were identified in the nuclear genome. RNA-seq analysis revealed transcription of the entire genome and differences from controls in the expression profiles of mitochondrial genes in the blood, but not in liver or brain, of animals infected with the zoonotic pathogen Borrelia hermsii. PCR and sequencing of the D-loop of the mitochondrion identified 32 different haplotypes among 118 wild P. leucopus at a Connecticut field site. These findings help to further establish P. leucopus as a model organism for studies of emerging infectious diseases, ecology, and in other disciplines.
Molecular signature of an ancient organizer regulated by Wnt/β-catenin signalling during primary body axis patterning in Hydra
Authors: Reddy Puli Chandramouli , Gungi Akhila , Ubhe Suyog , Pradhan Saurabh J. , Kolte Amol , Galande Sanjeev 
Published: November 2019

AbstractWnt/β-catenin signalling has been shown to play a critical role during head organizer formation inHydra. Here, we characterized the Wnt signalling regulatory network involved in formation of the head organizer. We found that Wnt signalling regulates genes that are important in tissue morphogenesis. We identified that majority of transcription factors (TFs) regulated by Wnt/β-catenin signalling belong to the homeodomain and forkhead families. Silencing ofMargin, one of the Wnt regulated homeodomain TFs, results in loss of the ectopic tentacle phenotype typically seen upon activation of Wnt signalling. Furthermore, we show that theMarginpromoter is directly bound and regulated by β-catenin. Ectopic expression ofMarginin zebrafish embryos results in body axis abnormalities suggesting thatMarginplays a role in axis patterning. Our findings suggest that homeobox TFs came under the regulatory umbrella of Wnt/β-catenin signalling presumably resulting in the evolution of primary body axis in animal phyla.
Origin of conformational dynamics in a globular protein
Authors: Damry Adam M. , Mayer Marc M. , Broom Aron , Goto Natalie K. , Chica Roberto A. 
Published: November 2019

AbstractProtein structures are dynamic, undergoing motions that can play a vital role in function. However, the link between primary sequence and conformational dynamics remains poorly understood. Here, we studied how conformational dynamics can arise in a globular protein by evaluating the impact of individual core-residue substitutions in DANCER-3, a streptococcal protein G domain β1 variant that we previously designed to undergo a specific mode of conformational exchange that has never been observed in the wild-type protein. Using a combination of solution NMR experiments and molecular dynamics simulations, we demonstrate that only two mutations are necessary to create this conformational exchange, and that these mutations work synergistically, with one destabilizing the native structure and the other allowing two new conformational states to be accessed on the energy landscape. Overall, our results show how dynamics can appear in a stable globular fold, a critical step in the molecular evolution of dynamics-linked functions.
Tailoring of an unusual oxidation state in a lanthanum tantalum(IV) oxynitride via precursor microstructure design
Authors: Bubeck Cora , Widenmeyer Marc , Richter Gunther , Coduri Mauro , Goering Eberhard , Yoon Songhak , Weidenkaff Anke 
Published: November 2019

AbstractPerovskite-type oxynitrides hold great potential for optical applications due to their excellent visible light absorption properties. However, only a limited number of such oxynitrides with modulated physical properties are available to date and therefore alternative fabrication strategies are needed to be developed. Here, we introduce such an alternative strategy involving a precursor microstructure controlled ammonolysis. This leads to the perovskite family member LaTa(IV)O2N containing unusual Ta4+ cations. The adjusted precursor microstructures as well as the ammonia concentration are the key parameters to precisely control the oxidation state and O:N ratio in LaTa(O,N)3. LaTa(IV)O2N has a bright red colour, an optical bandgap of 1.9 eV and a low (optically active) defect concentration. These unique characteristics make this material suitable for visible light-driven applications and the identified key parameters will set the terms for the targeted development of further promising perovskite family members.
Platform of chiral Majorana edge modes and its quantum transport phenomena
Authors: He James Jun , Liang Tian , Tanaka Yukio , Nagaosa Naoto 
Published: November 2019

AbstractMajorana fermions, as electronic quasi-particle modes in solid states, have been under the focus of research due to their exotic physical properties. While the evidence of Majorana fermions as zero-dimensional bound states has been well established, the existence of one-dimensional Majorana modes is still under debate. The main reason is that the current theoretical proposals of platforms supporting such states are very challenging experimentally. Here, we propose a method to create two-dimensional topological superconductors with a heterostructure of ferromagnet, topological insulator thin film and superconductor. We show that such a system supports one-dimensional chiral Majorana edge modes in a wide range of parameters which is readily achievable in experiments. We further propose a new transport measurement to detect these modes.
Pose detection of parallel robot based on improved Hough‐K‐means and SURF algorithms
Authors: Zhang Qian , Gao Guoqin , Liu Mengru 
Published: November 2019

It is difficult to detect end pose of auto electrocoating conveying parallel robot based on binocular vision because of less features, noise and blurred edges in image. So a pose detection method is presented. Firstly, according to distance and similarity between image points, the bilateral filtering is adopted to reduce noise. Secondly, for extracting straight lines on blurred edges and feature points in lines accurately, a Hough‐K‐means algorithm using K‐means clustering analysis in parameter space after Hough transform is proposed. Thirdly, the discrete Gaussian–Hermite moment is used as feature descriptor to solve the low accuracy problem of principal directions of feature points described by speeded‐up robust features (SURF) descriptor. The extracted feature points are selected according to the similarity metric between constructed feature vectors. Finally, the vision model is developed to calculate the three‐dimensional pose parameters of parallel robot based on obtained point pairs. The experiment results show that, compared with the SURF algorithm, the average matching time decreases by 21.58%, the average deviations of detected poses in x, z and β decrease by 1.149 mm, 0.646 mm and 1.164° respectively by using the proposed method. The speed and accuracy of pose detection of parallel robot can be improved.
Method of automatic steering system design and parameter optimisation for small tractors
Authors: Tian Guangzhao , Gu Baoxing , Chen Kai , Liu Yufeng , Wei Jiansheng 
Published: November 2019

In order to improve the operational efficiency and quality of small tractors, the original manual steering system needs to be renovated to include automatic steering functionality, which is the basis of autonomous navigation. Here, a modification method based on the steering circuit of a Dongfanghong SG250 tractor and a method to calculate the virtual steering angle is proposed. A small tractor steering model is established from the step response data of the system, and a PD controller for this model is also designed. The PD controller can also adapt to varying tractor speeds for optimal functionality in changing operational conditions, and a parameter optimisation approach for the speed‐adaptive PD controller is proposed. Test results show that at a speed of 0.5 m s−1, the steady‐state error in the step response is 0.32°, the percentage error is 2.3%, the overshoot is 1.86°, and the percentage overshoot is 13.7%. For a ramp response, the average signal latency is 0.82 s and the steady‐state error is 0.25°. The ability of the PD to adapt to changing speeds is also tested at different speeds. The results show that the steering system performs well.
Time-resolved photometry of the young dipper RX J1604.3-2130A
Authors: Sicilia-Aguilar A. , Manara C. F. , de Boer J. , Benisty M. , Pinilla P. , Bouvier J. 
Published: November 2019

Context. RX J1604.3-2130A is a young, dipper-type, variable star in the Upper Scorpius association, suspected to have an inclined inner disk, with respect to its face-on outer disk.
Aims. We aim to study the eclipses to constrain the inner disk properties.
Methods. We used time-resolved photometry from the Rapid Eye Mount telescope and Kepler 2 data to study the multi-wavelength variability, and archival optical and infrared data to track accretion, rotation, and changes in disk structure.
Results. The observations reveal details of the structure and matter transport through the inner disk. The eclipses show 5 d quasi-periodicity, with the phase drifting in time and some periods showing increased/decreased eclipse depth and frequency. Dips are consistent with extinction by slightly processed dust grains in an inclined, irregularly-shaped inner disk locked to the star through two relatively stable accretion structures. The grains are located near the dust sublimation radius (~0.06 au) at the corotation radius, and can explain the shadows observed in the outer disk. The total mass (gas and dust) required to produce the eclipses and shadows is a few % of a Ceres mass. Such an amount of mass is accreted/replenished by accretion in days to weeks, which explains the variability from period to period. Spitzer and WISE infrared variability reveal variations in the dust content in the innermost disk on a timescale of a few years, which is consistent with small imbalances (compared to the stellar accretion rate) in the matter transport from the outer to the inner disk. A decrease in the accretion rate is observed at the times of less eclipsing variability and low mid-IR fluxes, confirming this picture. The v sin i = 16 km s−1 confirms that the star cannot be aligned with the outer disk, but is likely close to equator-on and to be aligned with the inner disk. This anomalous orientation is a challenge for standard theories of protoplanetary disk formation.
Dayside nitrogen and carbon escape on Titan: the role of exothermic chemistry
Authors: Gu H. , Cui J. , Lavvas P. P. , Niu D.-D. , Wu X.-S. , Guo J.-H. , He F. , Wei Y. 
Published: November 2019

Context. Atmospheric escape has an appreciable impact on the long-term climate evolution on terrestrial planets. Exothermic chemistry serves as an important mechanism driving atmospheric escape and the role of such a mechanism is of great interest for Titan due to its extremely complicated atmospheric and ionospheric composition.
Aims. This study is devoted to a detailed investigation of neutral N and C escape on the dayside of Titan, which is driven by exothermic neutral–neutral, ion–neutral, and dissociative recombination (DR) reactions. It was carried out based on the extensive measurements of Titan’s upper atmospheric structure by a number of instruments on board Cassini, along with an improved understanding of the chemical network involved.
Methods. A total number of 14 C- and N-containing species are investigated based on 146 exothermic chemical reactions that release hot neutrals with nascent energies above their respective local escape energies. For each species and each chemical channel, the hot neutral production rate profile is calculated, which provides an estimate of the corresponding escape rate when combined with the appropriate escape probability profile obtained from a test particle Monte Carlo model.
Results. Our calculations suggest a total N escape rate of 9.0 × 1023 s−1 and a total C escape rate of 4.2 × 1023 s−1, driven by exothermic chemistry and appropriate for the dayside of Titan. The former is primarily contributed by neutral-neutral reactions, whereas the latter is dominated by ion–neutral reactions; however, contributions from neutral–neutral and DR reactions to the latter cannot be ignored either. Our calculations further reveal that the bulk of N escape is driven by hot N(4S) production from the collisional quenching of N(2D) by ambient N2, while C escape is mainly driven by hot CH3 and CH4 production via a number of important ion–neutral and neutral–neutral reactions.
Conclusions. Considered in the context of prior investigations of other known escape mechanisms, we suggest that exothermic chemistry is likely to contribute appreciably to non-thermal C escape on the dayside of Titan, although it plays an insignificant role in N escape.
Orthopaedic research in low-income countries: A bibliometric analysis of the current literature
Authors: Graham Simon Matthew , Brennan Ciaran , Laubscher Maritz , Maqungo Sithombo , Lalloo David G. , Perry Daniel C. , Mkandawire Nyengo , Harrison William J. 
Published: November 2019

Background: To perform a bibliometric analysis and quantify the amount of orthopaedic and trauma literature published from low-income countries (LICs).Methods and methods: The Web of Science database was utilised to identify all indexed orthopaedic journals. All articles published in the 76 orthopaedics journals over the last 10 years were reviewed, to determine their geographic origin.Results: A total of 131 454 articles were published across 76 orthopaedic journals over the last 10 years. Of these, 132 (0.1%) were published from LICs and 3515 (2.7%) were published from lower middle-income countries (LMICs); 85.7% (n = 112 716) of published orthopaedic research was undertaken in a high-income setting. The majority of the studies (n = 90, 74.4%) presented level IV evidence. Only 7.4% (n = 9) were high-quality evidence (level I or II). Additionally, the majority of research (74 articles, 56%) was published in partnership with high-income countries (HICs).Conclusions: There is a stark mismatch between the publication of scientific reports on orthopaedic research and the geographical areas of greatest clinical need. We believe there is an urgent need for orthopaedic research to be carried out in low-income settings to guide treatment and improve outcomes, rather than assuming that evidence from high-income settings will translate into this environment.Level of evidence: IV
Vitamin D Status and Thyroid Autoantibodies in Autoimmune Thyroiditis
Authors: Koehler Viktoria F. , Filmann Natalie , Mann W. Alexander 
Published: November 2019

AbstractA lack of vitamin D seems to be related to autoimmune diseases including autoimmune thyroiditis (AIT). This study intends to determine the correlation between improvement of 25-hydroxyvitamin D [25(OH)D] levels and AIT in patients from an outpatient endocrine clinic in Frankfurt, Germany. This study included 933 patients with thyroid peroxidase antibodies (anti-TPO-Ab) ≥34 kIU/l, including most patients with clear AIT due to a concurrent sonographic evidence of reduced echogenicity. We performed clinical evaluation and laboratory analysis at five points in time within two years retrospectively. Due to a high dropout rate within the observation period, we excluded the last two time points from analysis. Data from 933 AIT patients revealed 89% having vitamin D deficiency or insufficiency [25(OH)D <75 nmol/l] with a median 25(OH)D level of 39.7 nmol/l. At baseline, a weak inverse correlation between 25(OH)D and anti-TPO-Ab was observed during winter (rs=–0.09, p=0.048*), but not during summer time (p>0.2). We discovered 58 patients having initially a 25(OH)D level < 75 nmol/l (median: 40.2 nmol/l), which improved over time to a 25(OH)D level ≥ 75 nmol/l (median: 83.2 nmol/l, p<0.0005***). Simultaneously, the median anti-TPO-Ab level showed a significant decrease of 25% from 245.8 to 181.3 kIU/l (p=0.036*). A significant reduction of the median anti-TPO-Ab level of 9% was also observed in the control group, which consisted of patients having constantly a 25(OH)D level <75 nmol/l. The result may suggest that in particular patients with 25(OH)D levels < 75 nmol/l benefit from an increase of 25(OH)D levels ≥ 75 nmol/l. Further prospective randomized controlled clinical trials are needed to finally evaluate if vitamin D has immunmodulatory effects in AIT.
Endolichenic fungal diversity associated with some lichens of the Western Ghats
Authors: Rajulu Meenavalli Babu Govinda , Thirunavukkarasu Nagamani , Kumar Subramanya Shravan , Kaur Tanveer , Reddy Mondem Sudhakara , Suryanarayanan Trichur Subramanian 
Published: November 2019

AbstractA total of 389 strains of fungi belonging to 38 species were isolated from 10 lichen species of the Western Ghats, southern India. All the lichens screened, irrespective of their growth forms or location, harboured endolichenic fungi. Most of the fungi belonged to the Ascomycotina. Chaetomium sp. 1, Hypoxylon investiens, Nemania bipapillata, Nodulisporium sp., Paecilomyces sp., and Sporormiella intermedia were the most common ones and were present in 5 or more lichen species. Of the 28 sporulating fungi, 7 belonged to Xylariales, and their total colonization frequency in all the lichens was also high. This observation further substantiates the high ecological amplitude of Xylariales, possibly due to overlapping ecological niches and their ability to inhibit co-occurring endolichenic fungi.
Marginal Discrepancy of Single Implant-Supported Metal Copings Fabricated by Various CAD/CAM and Conventional Techniques Using Different Materials
Authors: Ghodsi Safoura , Alikhasi Marzieh , Soltani Nika 
Published: November 2019

Abstract
Objective Framework patterns can be formed using various materials such as wax, acrylic resin, or composite. Frameworks can be fabricated using either conventional or computerized techniques, using additive or subtractive method. This study aimed to compare the marginal adaptation of metal copings fabricated by two computerized technologies (milling and rapid prototyping) and additive conventional methods using different materials.
Materials and Methods Seventy-two fixture analogs were mounted vertically in acrylic resin. One-piece abutments with 5.5 mm in length and 6 degrees of convergence were secured into the analogs. The experimental frameworks were fabricated using either subtractive CAD/CAM milling (by wax, soft or hard metal), additive rapid prototyping (by wax), or conventional pattern fabrication (by wax [control] or acrylic resin). Wax and acrylic resin patterns were casted in Ni-Cr alloy. Marginal discrepancy was measured in 12 points by video measuring machine.
Statistical Analysis One-way ANOVA and posthoc tests were used to detect any significant difference among the groups at α= 0.05.
Results There was a statistically significant difference among the marginal discrepancy of six groups (p = 0.018). The Tukey test indicated a significant difference between CAD/milling of soft metal and conventional wax pattern groups (p = 0.011); a significant difference was also reported between CAD/milling of wax patterns and control group (p = 0.046).
Conclusions Frameworks fabricated by conventional wax-up showed the largest marginal gaps, while the marginal gap created by frameworks made of soft metal CAD/milling were the smallest. In addition, frameworks fabricated by rapid prototyping showed clinically acceptable adaptations.
Computed Tomography Evaluation of Brain in Chronic Alcoholics
Authors: Sandhu Gurpreet S. , Nagrale Hiresh R. 
Published: November 2019

Abstract

Background Chronic alcoholism causes brain damage. Published data from rural India is scant. Our aim is to determine computed tomography (CT) changes in the brain of rural chronic alcoholics.

Methods This prospective cross-sectional study was done in our tertiary care hospital on chronic alcoholic patients referred from deaddiction center over a period of 2 years. Age- and sex-matched nonalcoholic controls were included and Student’s t-test and chi-square test comparison was done. Correlation coefficient was obtained by Pearson’s correlation coefficient. Patients and the controls were studied in two age groups: 30 to 45 and 46 to 60 years. Noncontrast CT scan of head was done in each case and CT indices of brain damage were measured.

Results The study included 106 alcoholics out of which 55 were in the younger age group (30–45 years) and 51 in the older age group (46–60 years). Seven hundred age-matched, nonalcoholic controls were included. Mean values of ethanol were higher in the older age group than in the younger age group. As compared with controls, various CT scan indices of ventricular changes, cortical changes, and subcortical changes were significantly higher in both age groups. In both age groups, there was a significant decrease in the mean values of hemoglobin and a significant increase in the mean values of indices of brain damage with increase in the grade of alcoholism.

Conclusion The results of this prospective epidemiological study showed marked alterations in all CT indices of brain atrophy and were correlated to the duration and amount of ethanol consumption. This study highlights that chronic alcoholism is a significant risk factor for brain atrophy.
Correction to: Comparing engagement by migrants in domestic and in country-of-origin political activities across European cities
Authors: Pilati Katia , Herman Barbara 
Published: November 2019

The article Comparing engagement by migrants in domestic and in country-of-origin political activities across European cities, written by Katia Pilati and Barbara Herman, was originally published electronically on the publisher’s internet portal on 16 July 2018 without open access. With the author(s)’ decision to opt for Open Choice the copyright of the article changed on 21 November 2019 to © The Author(s) 2018 and the article is forthwith distributed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The original article has been corrected.