bluuebunny/crossref_metadata_2025 huggingface dataset:
Polypedilum (Cerobregma) paracyclus sp. n., a new species from Oriental China (Diptera: Chironomidae)
Authors: QI XIN , SONG CHAO , GE KAIXUAN , WANG XINHUA
Published: November 2020

Polypedilum (Cerobregma) paracyclus sp. n. Qi & Song is described based on male imagines collected by light trap in Oriental China. The description is supported by both morphological and DNA barcode evidences. The new species is distinguished from its related congeners in having some atypical morphological characters: tibia and femur dark brown, knees yellow; abdominal segment VII distinctly triangular and tapered towards base; tergite IX broadly sub-trapezoidal, tapering posteriorly, anal tergite bands ending with a characteristic sub-oval area; superior volsella sickle-like shaped with pointed apex; inferior volsella with orally directed dorsal setae; distal inner margin of gonostylus without shortly branched setae.
A new species of the genus Tshurtshurnella Kusnezov, 1927 (Hemiptera: Fulgoromorpha: Issidae) from Turkey
Authors: TANYERİ RUKİYE , ZEYBEKOĞLU ÜNAL
Published: November 2020

Tshurtshurnella sinopei sp. nov. is described after the specimens collected in Sinop, Western Black Sea Region of Turkey, in August 2017. External morphology including male and female genital structures of the new species are described and illustrated.
Ukamenia Oku, 1981 (Lepidoptera: Tortricidae: Olethreutinae), new record for Thailand with descriptions of a new species
Authors: MUADSUB SOPITA , PINKAEW NANTASAK
Published: November 2020

The genus Ukamenia Oku, 1981 is recorded the first time for Thailand and a new species, Ukamenia thailandica n. sp., is described. Photograph of living specimens of U. thailandica n. sp. in natural resting posture is present. The one new taxon increases the number of described Ukamenia species to 4.
Revision of parasitoids of Massicus raddei (Blessig & Solsky) (Coleoptera, Cerambycidae) in China, with one new species and genus
Authors: CAO LIANG-MING , ACHTERBERG CORNELIS VAN , TANG YAN-LONG , WANG XIAO-YI , YANG ZHONG-QI
Published: November 2020

Fifteen parasitoids of Massicus raddei (Blessig & Solsky) (Coleoptera, Cerambycidae) are revised. The host is a serious pest of Quercus liaotungensis Koidz. and Q. mongolica Fisch. ex Ledeb. in NE China. All the parasitoids were reared from larvae of M. raddei. Pseudocyanopterus gen. nov. raddeivorus sp. nov., a new braconid wasp is described, and Cyanopterus tricolor (Ivanov) and Eubazus (E.) pallipes are new records for the Chinese fauna. An identification key to the parasitoids of M. raddei in China is provided. Detailed photographs of the parasitoids are provided.
Additions to the knowledge on the genus Carinostigmus Tsuneki (Hymenoptera: Crabronidae: Pemphredoninae) from the Indian subcontinent with the description of two new species
Authors: RAJAN TESSY , SURESHAN P. M. , KUMAR P. GIRISH
Published: November 2020

The genus Carinostigmus Tsuneki, 1954 is reviewed from the Indian subcontinent. Two new species, viz. C. parliensis Tessy, Sureshan & Girish Kumar, sp. nov. and C. nepalensis Tessy, Sureshan & Girish Kumar, sp. nov. are described from India (Maharashtra and Uttarakhand) and Nepal (Bagmati Pradesh), respectively and differences from similar species are also given. A modified key to species of Carinostigmus from the Indian subcontinent is provided. Records for the other six species in the genus known from the Indian subcontinent are also provided.
Two species of the genus Theristus Bastian, 1865 (Nematoda: Xyalidae) from the hypersaline water bodies of the Crimea (Azov-Black Sea basin)
Authors: REVKOVA TATIANA N.
Published: November 2020

Morphological descriptions of two species of the genus Theristus Bastian, 1865 belonging to group flevensis, found in the hypersaline water bodies of the Crimean Peninsula, are presented. Theristus siwaschensis sp. n. is morphologically closest to T. flevensis Schuurmans Stekhoven, 1935, T. parambronensis Timm, 1952, T. macroflevensis Gerlach, 1954, T. metaflevensis Gerlach, 1955, but differs from them by the structure of the reproductive system in females, number of cephalic setae and size of spicules. Specimens of T. flevensis found in the Lake Chersonesskoye are similar to the re-description of a large forms of T. flevensis from Chile by Murhy (1966) and Caspian Sea by Chesunov (1981). However, it differs from the Caspian Sea species by having larger amphids, longer cephalic setae and spicules. T. pratti Murph & Canaris, 1964 and T. ambronensis Schulz, 1937 are synonymized with T. flevensis.
Study of the genus Meleonoma Meyrick, 1914 (Lepidoptera: Autostichidae) from China, with descriptions of twenty-one new species (II)
Authors: WANG SHUXIA , ZHU XIAOJU
Published: November 2020

Twenty-one new species of the genus Meleonoma Meyrick are described: M. acutata sp. nov., M. annulignatha sp. nov., M. artivalva sp. nov., M. basiprocessa sp. nov., M. bicornea sp. nov., M. bidigitata sp. nov., M. circinans sp. nov., M. compacta sp. nov., M. cuneata sp. nov., M. forcipata sp. nov., M. ledongensis sp. nov., M. longihamata sp. nov., M. mecobursoides sp. nov., M. microdonta sp. nov., M. papillisetosa sp. nov., M. parallela sp. nov., M. recticostata sp. nov., M. segregnatha sp. nov., M. sinuicosta sp. nov., M. taiwanensis sp. nov. and M. taeniophylla sp. nov. The male of M. flavilineata Kitajima et Sakamaki, 2019 is described for the first time. Images of both adults and genitalia are provided. All species are divided into two species-groups, and a key to each group as well as a map showing the distribution of each group in China are given.
Species survey of the subfamily Cerambycinae (Coleoptera: Cerambycidae) in the Rio Doce State Park, Minas Gerais, Brazil
Authors: CORRÊA CARLOS A. , MIGLIORE LETIZIA J. , GARBELINI LUAN , ZANUNCIO JOSÉ C. , RIBEIRO SÉRVIO P.
Published: November 2020

The Rio Doce State Park (“PERD”) is the largest Atlantic Forest remnant in Minas Gerais State, Brazil, with predominantly semi-deciduous forests. The longhorned beetles of the Cerambycinae subfamily (Coleoptera: Cerambycidae) are distributed worldwide, developing on healthy, stressed or recently dead trees. Faunistic surveys are necessary to understand about the Minas Gerais’ cerambycid fauna due to a lack of research, especially in the eastern region of the state. A list of species of the subfamily Cerambycinae (Coleoptera: Cerambycidae), collected in the PERD during the rainy season (September 2013- February 2014), is presented. The beetles were collected using a light trap and through their emergence from Anadenanthera colubrina (Vell.) Brenan (Fabaceae) logs. A total of 663 individuals of 33 species, 30 genera, and 15 tribes of the Cerambycinae subfamily were collected. The species Malacopterus tenellus (Fabricius, 1801) was registered for the first time in Minas Gerais State, while A. colubrina is a new host plant for 14 Cerambycinae species. The geographical distribution, number of host plants and materials examined are presented for each species collected. This is the first list of Cerambycidae species from the Rio Doce State Park.
An Efficient and Accurate Algorithm for Computing Grid-Averaged Solar Fluxes for Horizontally Inhomogeneous Clouds
Authors: Jin Zhonghai , Lacis Andrew
Published: November 2020

A computationally efficient method is presented to account for the horizontal cloud inhomogeneity by using a radiatively equivalent plane-parallel homogeneous (PPH) cloud. The algorithm can accurately match the calculations of the reference (rPPH) independent column approximation (ICA) results but uses only the same computational time required for a single plane-parallel computation. The effective optical depth of this synthetic sPPH cloud is derived by exactly matching the direct transmission to that of the inhomogeneous ICA cloud. The effective scattering asymmetry factor is found from a precalculated albedo inverse lookup table that is allowed to vary over the range from −1.0 to 1.0. In the special cases of conservative scattering and total absorption, the synthetic method is exactly equivalent to the ICA, with only a small bias (about 0.2% in flux) relative to ICA resulting from imperfect interpolation in using the lookup tables. In principle, the ICA albedo can be approximated accurately regardless of cloud inhomogeneity. For a more complete comparison, the broadband shortwave albedo and transmission calculated from the synthetic sPPH cloud and averaged over all incident directions have RMS biases of 0.26% and 0.76%, respectively, for inhomogeneous clouds over a wide variation of particle size. The advantages of the synthetic PPH method are that 1) it is not required that all the cloud subcolumns have uniform microphysical characteristic, 2) it is applicable to any 1D radiative transfer scheme, and 3) it can handle arbitrary cloud optical depth distributions and an arbitrary number of cloud subcolumns with uniform computational efficiency.
Walls of Anxiety: The Iconography of Anti-NATO protests in Spain, 1981–6
Authors: Quaggio Giulia
Published: November 2020

This article addresses the protest culture of the Spanish anti-NATO movement during the first half of the 1980s. Adopting a multidisciplinary approach, it focuses on the collective practice of painting murals and graffiti ( pintadas) on walls in the outskirts of Spanish cities. This was done by neighbourhood associations, together with local artists, in order to display and disseminate the widespread angst regarding entering and remaining in NATO. Murals constituted a grassroots multi-layered phenomenon that emerged through the interaction of different communicative actors, social processes and semiotic forms. The article explores three themes. Firstly, the political iconography of anti-NATO murals in Spain whilst comparing it with the aesthetics of other European peace movements. Secondly, the domestic reframing of anti-war and antinuclear icons as well as anti-American clichés, violence and the army, gender relations, Spanish national sovereignty and, more generally, the process of modernisation and westernisation that was rapidly affecting post-Francoist society. Finally, the analysis of these visual expressions offers a bottom-up picture of the final stage of the Cold War and a better understanding of the role of Spanish civil society during the period of democratic consolidation.
Identifying cardiomegaly in chest X-rays: a cross-sectional study of evaluation and comparison between different transfer learning methods
Authors: Bougias Haralabos , Georgiadou Eleni , Malamateniou Christina , Stogiannos Nikolaos
Published: November 2020

Background

Cardiomegaly is a relatively common incidental finding on chest X-rays; if left untreated, it can result in significant complications. Using Artificial Intelligence for diagnosing cardiomegaly could be beneficial, as this pathology may be underreported, or overlooked, especially in busy or under-staffed settings.

Purpose

To explore the feasibility of applying four different transfer learning methods to identify the presence of cardiomegaly in chest X-rays and to compare their diagnostic performance using the radiologists’ report as the gold standard.

Material and Methods

Two thousand chest X-rays were utilized in the current study: 1000 were normal and 1000 had confirmed cardiomegaly. Of these exams, 80% were used for training and 20% as a holdout test dataset. A total of 2048 deep features were extracted using Google’s Inception V3, VGG16, VGG19, and SqueezeNet networks. A logistic regression algorithm optimized in regularization terms was used to classify chest X-rays into those with presence or absence of cardiomegaly.

Results

Diagnostic accuracy is reported by means of sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), with the VGG19 network providing the best values of sensitivity (84%), specificity (83%), PPV (83%), NPV (84%), and overall accuracy (84,5%). The other networks presented sensitivity at 64.1%–82%, specificity at 77.1%–81.1%, PPV at 74%–81.4%, NPV at 68%–82%, and overall accuracy at 71%–81.3%.

Conclusion

Deep learning using transfer learning methods based on VGG19 network can be used for the automatic detection of cardiomegaly on chest X-ray images. However, further validation and training of each method is required before application to clinical cases.
BRAFV595E Mutation Associates CCL17 Expression and Regulatory T Cell Recruitment in Urothelial Carcinoma of Dogs
Authors: Maeda Shingo , Yoshitake Ryohei , Chambers James K. , Uchida Kazuyuki , Eto Shotaro , Ikeda Namiko , Nakagawa Takayuki , Nishimura Ryohei , Goto-Koshino Yuko , Yonezawa Tomohiro , Momoi Yasuyuki
Published: November 2020

Regulatory T cells may serve as targets in cancer immunotherapy. A previous study showed that the chemokine CCL17 and the receptor CCR4 play roles in regulatory T cell recruitment in canine urothelial carcinoma. In this article, we show that the BRAFV595E mutation is associated with tumor-produced CCL17 and regulatory T cell infiltration in dogs with urothelial carcinoma. In comparison with healthy dogs, dogs with urothelial carcinoma showed increased CCL17 mRNA expression in the bladder and elevated CCL17 protein concentration in urine. Immunohistochemistry showed increased levels of Foxp3+ regulatory T cells in the tumor tissues of urothelial carcinoma. The density of Foxp3+ regulatory T cells was positively correlated with CCL17 concentration in urine, indicating that CCL17 is involved in regulatory T cell recruitment. Moreover, tumor-infiltrating regulatory T cells and urine CCL17 concentration were associated with poor prognosis in dogs with urothelial carcinoma. The number of tumor-infiltrating regulatory T cells, CCL17 mRNA expression, and urine CCL17 concentration in cases with BRAFV595E mutation were higher than those in cases with wild-type BRAF. In vitro, high CCL17 production was detected in a canine urothelial carcinoma cell line with BRAFV595E mutation but not in an urothelial carcinoma cell line with wild-type BRAF. Dabrafenib, a BRAF inhibitor, decreased CCL17 production in the cell line with BRAFV595E mutation. These results suggest that BRAFV595E mutation induced CCL17 production and contributed to regulatory T cell recruitment in canine urothelial carcinoma.
Still a New Kid on the Block? Computational Thinking as Problem Solving in Code.org
Authors: Kale Ugur , Yuan Jiangmei
Published: November 2020

Computational thinking is a means to understand and solve complex problems through using computer science concepts and techniques. While there is an increase in the number of initiatives focusing on coding, whether they (a) address computational thinking and problem-solving skills and (b) use methods of teaching problem solving is yet to be explored. As a preliminary step, this study focuses on examining 3rd grade lesson plans at Code.org. The analysis identified various components of computational thinking and problem solving as well as specific problem-solving teaching methods used to address these skills. Besides such cognitive outcomes, the findings also revealed affective, reflective, and social aspects of learning supported in the lessons.
On the Biopsychosocial Costs of Alienated Labor
Authors: Seeman Melvin , Merkin Sharon Stein , Karlamangla Arun , Koretz Brandon , Grzywacz Joseph G , Lachman Margie , Seeman Teresa
Published: November 2020

Data from the national, longitudinal Mid-Life in the US (MIDUS) study were used to examine work alienation and its relationship to biological health as well as psychological and social functioning. The alienation measure focuses on the autonomy and creativity the work provides. We hypothesized that alienated work would have negative associations with each of the three domains: in biology, higher ‘allostatic load’ (biological dysregulation); in psychology, poorer cognitive performance; and socially, negative impacts on family life. The outcomes are generally as predicted, though there are notable differences for men and women.
Development of a novel mobile robotic system for large-scale manufacturing
Authors: Ding Yabin , Zhang Zeyang , Liu Xianping , Fu Jinsheng , Huang Tian
Published: November 2020

The high demand of efficient large-scale machining operations by concurrently decreasing operating time and costs has led to an increasing usage of mobile robotic systems. This paper introduces a mobile robotic system which is consisted of a hybrid robot named TriMule on an automated guided vehicle, and a fringe-projection-based measurement system. TriMule exhibits desirable performance in terms of rigidity, accuracy, work envelop and reconfigurability. It is therefore suitable to be built on an autonomous platform for multi-station manufacturing in situ. In order to increase the absolute accuracy of the mobile robotic system, the fringe-projection-based measurement system obtains high accuracy and high density cloud to measure the position and orientation of the robot and workpiece in relation to each other. This system is suitable for large-scale manufacturing in situ, drilling, riveting and high-speed milling for example.
Safety Assessment of Trimellitic Anhydride Copolymers as Used in Cosmetics
Authors: Fiume Monice M. , Bergfeld Wilma F. , Belsito Donald V. , Hill Ronald A. , Klaassen Curtis D. , Liebler Daniel C. , Marks James G. , Shank Ronald C. , Slaga Thomas J. , Snyder Paul W. , Gill Lillian J. , Heldreth Bart
Published: November 2020

The Expert Panel for Cosmetic Ingredient Safety (Panel) assessed the safety of 6 trimellitic anhydride copolymers as used in cosmetics. These ingredients are related as copolymers in that they all share trimellitic anhydride (ie, 1,2,4-benzenetricarboxylic acid anhydride) as a monomer, are reported to function as film formers in cosmetics, and are reported to be primarily used in nail products. Very limited safety data were available or submitted. The Panel concluded that Adipic Acid/Neopentyl Glycol/Trimellitic Anhydride Copolymer and Phthalic Anhydride/Trimellitic Anhydride/Glycols Copolymer are safe in nail product formulations in the present practices of use and concentration, but the data are insufficient to make a determination of safety on the use of these 2 ingredients in all other types of cosmetic formulations. The Panel also concluded that the available data are insufficient to make a determination that the remaining trimellitic anhydride copolymers are safe for use in cosmetic formulations.
Safety Assessment of Monoglyceryl Monoesters as Used in Cosmetics
Authors: Fiume Monice M. , Bergfeld Wilma F. , Belsito Donald V. , Hill Ronald A. , Klaassen Curtis D. , Liebler Daniel C. , Marks James G. , Shank Ronald C. , Slaga Thomas J. , Snyder Paul W. , Gill Lillian J. , Heldreth Bart
Published: November 2020

The Expert Panel for Cosmetic Ingredient Safety (Panel) assessed the safety of 44 monoglyceryl monoesters that are structurally constituted as the esterification products of glycerin and carboxylic acids (the majority of which are fatty acids); 36 of these monoesters were previously reviewed by the Panel, and 8 are reviewed herein for the first time. Most of the monoglyceryl monoesters have several reported functions in cosmetics, but the most common function among the ingredients is skin conditioning agent; a few are reported to function only as surfactant–emulsifying agents. The Panel reviewed relevant new data, including frequency and concentration of use and considered the data from previous Cosmetic Ingredient Review reports. The Panel concluded that these ingredients are safe in cosmetics in the present practices of use and concentration described in this safety assessment.
The relationships between the 3 × 2 achievement goal model and test anxiety in Physical Education
Authors: Danthony Sarah , Mascret Nicolas , Cury François
Published: November 2020

The aim of the present study was to investigate the predictive role of the 3 × 2 achievement goal model on test anxiety in the specific context of Physical Education (PE). Four hundred and eighty-six French students (mean age = 15.83, standard deviation = 1.20) voluntarily and anonymously filled out the Revised Test Anxiety and Regulatory Dimension of Anxiety in Physical Education scale (RTAR-PE) assessing test anxiety in PE and the Achievement Goal Questionnaire for Sport (AGQ-S) assessing the six achievement goals. The results showed that task-avoidance and self-avoidance goals positively predicted the four negative factors of test anxiety (worry, self-focus, bodily symptoms, somatic tension), while task-approach and self-approach goals negatively predicted them. It was the opposite for perceived control, which is the positive factor of test anxiety. Contrary to academic general test anxiety, other-avoidance goals did not positively predict the negative factors of test anxiety in the PE context, but they negatively predicted perceived control. The previous pattern of results was reversed for task-approach, self-approach, and other-approach goals. Finally, a significant interaction was found between other-avoidance goals and gender in predicting bodily symptoms, but simple slope analyses did not reveal significant findings. Taking students’ psychological characteristics into account, such as achievement goals, may contribute to a better understanding of test anxiety in PE.
Promoting Prospective Teacher Competencies for Designing, Implementing, Evaluating, and Adapting Interactive Formative Feedback Strategies
Authors: Narciss Susanne , Hammer Elsa , Damnik Gregor , Kisielski Kerstin , Körndle Hermann
Published: November 2020

Formative assessment and feedback strategies play a core role in effective learning and instruction. Thus, teachers should be able to effectively apply the theoretical and empirical insights on formative assessment and feedback strategies in their classrooms. However, designing and implementing formative feedback strategies are complex tasks. Based on the Interactive Tutoring Feedback Model we developed a seminar concept combining case-based reflections of empirically based principles for the design of formative feedback strategies; planning and designing formative feedback strategies for a typical oral or written student assignment; and implementing, evaluating, and iteratively adapting this feedback strategy using on-campus micro-teaching sessions. The benefits and constraints of this seminar concept were explored in an evaluation study with teacher students ( N = 87). Students participating in the treatment seminars had higher gains in knowledge and competencies compared to students of control groups that had either a short theoretical input or no input on feedback. Furthermore, they appreciated the mix of instructional and micro-teaching components, and rated the transferability of the knowledge and competencies they had acquired as high.
All-cause and cancer-specific overall survival in kidney transplant recipients with pre-transplant malignancies in a German cohort
Authors: Jacoby Fabian , Tim Holland-Letz , Zeier Martin , Delecluse Susanne
Published: November 2020

Kidney insufficiency and immunosuppression are well established contributors of tumor development, both before and after kidney transplantation. Patients with pre-transplant malignancies (PTM) are at risk of tumor recurrence and of the development of an unrelated tumor after transplantation. In this retrospective study of a German patient cohort, we analyzed 1089 patients that underwent kidney transplantation to determine the frequency, recurrence rate and overall survival of patients with pre-existing tumors across a 10-year period. PTM were found in 5.79% of the patients and appeared at a mean time of 7.39 (SD 6.8) years before transplantation. The tumors were most frequently of urologic (41.43%) origin, followed by malignancies of the skin (25.71%) and gynecologic tumors (10%). Tumor recurrence was observed in one case (1.6%) where the patient died of metastatic spinocellular carcinoma. Patients with pre-existing malignancies had a statistically significantly worse overall survival compared to transplant recipients without tumors (HR = 2.71, 95% CI 1.49–4.969). However, these differences could be entirely ascribed to the age (HR = 1.06, 95% CI 1.04–1.08) and gender (HR = 1.67, 95% CI 1.11–2.52) of the patients. We found that there was no difference in cancer-specific mortality or posttransplant cancer rate between patients with and without pre-existing malignancies (HR = 0.94, 95% CI 0.21–4.26).
A Rare Case of Type 1 Neurofibromatosis-Associated Unilateral Gigantomastia: A Case Report and Literature Review
Authors: Phan Kim , Vignarajah Muralie , Huq Nasimul
Published: November 2020

Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder characterized by the formation of benign nerve sheath tumours known as neurofibromas. A 28-year-old female presented with a large neurofibroma extending from the elbow of the right arm into the axilla and across the right breast. A mastectomy was performed to excise 4 kg of tissue with an immediate flap reconstruction. Post-operatively, the patient’s hemoglobin levels dropped significantly due to excessive blood loss, but the patient was discharged by post-operative day 5 with no additional complications. This study raises awareness for NF1, describes possible complications that may arise following excision of highly vascularized neurofibromas, and outlines possible techniques for breast reconstruction.
Identification of early mild cognitive impairment using multi-modal data and graph convolutional networks
Authors: Liu Jin , Tan Guanxin , Lan Wei , Wang Jianxin
Published: November 2020

Background

The identification of early mild cognitive impairment (EMCI), which is an early stage of Alzheimer’s disease (AD) and is associated with brain structural and functional changes, is still a challenging task. Recent studies show great promises for improving the performance of EMCI identification by combining multiple structural and functional features, such as grey matter volume and shortest path length. However, extracting which features and how to combine multiple features to improve the performance of EMCI identification have always been a challenging problem. To address this problem, in this study we propose a new EMCI identification framework using multi-modal data and graph convolutional networks (GCNs). Firstly, we extract grey matter volume and shortest path length of each brain region based on automated anatomical labeling (AAL) atlas as feature representation from T1w MRI and rs-fMRI data of each subject, respectively. Then, in order to obtain features that are more helpful in identifying EMCI, a common multi-task feature selection method is applied. Afterwards, we construct a non-fully labelled subject graph using imaging and non-imaging phenotypic measures of each subject. Finally, a GCN model is adopted to perform the EMCI identification task.

Results

Our proposed EMCI identification method is evaluated on 210 subjects, including 105 subjects with EMCI and 105 normal controls (NCs), with both T1w MRI and rs-fMRI data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. Experimental results show that our proposed framework achieves an accuracy of 84.1% and an area under the receiver operating characteristic (ROC) curve (AUC) of 0.856 for EMCI/NC classification. In addition, by comparison, the accuracy and AUC values of our proposed framework are better than those of some existing methods in EMCI identification.

Conclusion

Our proposed EMCI identification framework is effective and promising for automatic diagnosis of EMCI in clinical practice.
AligNet: alignment of protein-protein interaction networks
Authors: Alcalá Adrià , Alberich Ricardo , Llabrés Mercè , Rosselló Francesc , Valiente Gabriel
Published: November 2020

Background

All molecular functions and biological processes are carried out by groups of proteins that interact with each other. Metaproteomic data continuously generates new proteins whose molecular functions and relations must be discovered. A widely accepted structure to model functional relations between proteins are protein-protein interaction networks (PPIN), and their analysis and alignment has become a key ingredient in the study and prediction of protein-protein interactions, protein function, and evolutionary conserved assembly pathways of protein complexes. Several PPIN aligners have been proposed, but attaining the right balance between network topology and biological information is one of the most difficult and key points in the design of any PPIN alignment algorithm.

Results

Motivated by the challenge of well-balanced and efficient algorithms, we have designed and implemented AligNet, a parameter-free pairwise PPIN alignment algorithm aimed at bridging the gap between topologically efficient and biologically meaningful matchings. A comparison of the results obtained with AligNet and with the best aligners shows that AligNet achieves indeed a good balance between topological and biological matching.

Conclusion

In this paper we present AligNet, a new pairwise global PPIN aligner that produces biologically meaningful alignments, by achieving a good balance between structural matching and protein function conservation, and more efficient computations than state-of-the-art tools.
DeepFrag-k: a fragment-based deep learning approach for protein fold recognition
Authors: Elhefnawy Wessam , Li Min , Wang Jianxin , Li Yaohang
Published: November 2020

Background

One of the most essential problems in structural bioinformatics is protein fold recognition. In this paper, we design a novel deep learning architecture, so-called DeepFrag-k, which identifies fold discriminative features at fragment level to improve the accuracy of protein fold recognition. DeepFrag-k is composed of two stages: the first stage employs a multi-modal Deep Belief Network (DBN) to predict the potential structural fragments given a sequence, represented as a fragment vector, and then the second stage uses a deep convolutional neural network (CNN) to classify the fragment vector into the corresponding fold.

Results

Our results show that DeepFrag-k yields 92.98% accuracy in predicting the top-100 most popular fragments, which can be used to generate discriminative fragment feature vectors to improve protein fold recognition.

Conclusions

There is a set of fragments that can serve as structural “keywords” distinguishing between major protein folds. The deep learning architecture in DeepFrag-k is able to accurately identify these fragments as structure features to improve protein fold recognition.
Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients
Authors: Wu Xueting , Li Xuetong , Wang Wei , Shan Yuanhong , Wang Cuiting , Zhu Mulan , La Qiong , Zhong Yang , Xu Ye , Nan Peng , Li Xuan
Published: November 2020

Background

Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiaois one of the most common herbs widely used in South and East Asia, to enhance people’s health and reinforce vital energy. Despite its prevalence, however, the knowledge about phytochemical compositions and metabolite biosynthesis inAstragalus membranaceus Bge. var. mongolicus (Bge.) Hsiaois very limited.

Results

An integrated metabolomics and transcriptomics analysis using state-of-the-art UPLC-Q-Orbitrap mass spectrometer and advanced bioinformatics pipeline were conducted to study global metabolic profiles and phytochemical ingredients/biosynthesis inAstragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. A total of 5435 metabolites were detected, from which 2190 were annotated, representing an order of magnitude increase over previously known. Metabolic profiling ofAstragalus membranaceus Bge. var. mongolicus (Bge.) Hsiaotissues found contents and synthetic enzymes for phytochemicals were significantly higher in leaf and stem in general, whereas the contents of the main bioactive ingredients were significantly enriched in root, underlying the value of root in herbal remedies. Using integrated metabolomics and transcriptomics data, we illustrated the complete pathways of phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis, in which some were first reported in the herb. More importantly, we discovered novel flavonoid derivatives using informatics method for neutral loss scan, in addition to inferring their likely synthesis pathways inAstragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao.

Conclusions

The current study represents the most comprehensive metabolomics and transcriptomics analysis on traditional herbAstragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. We demonstrated our integrated metabolomics and transcriptomics approach offers great potentials in discovering novel metabolite structure and associated synthesis pathways. This study provides novel insights into the phytochemical ingredients, metabolite biosynthesis, and complex metabolic network in herbs, highlighting the rich natural resource and nutritional value of traditional herbal plants.
A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model
Authors: Liu Jiaqi , Wang Jiayin , Xiao Xiao , Lai Xin , Dai Daocheng , Zhang Xuanping , Zhu Xiaoyan , Zhao Zhongmeng , Wang Juan , Li Zhimin
Published: November 2020

Background

The emergence of the third generation sequencing technology, featuring longer read lengths, has demonstrated great advancement compared to the next generation sequencing technology and greatly promoted the biological research. However, the third generation sequencing data has a high level of the sequencing error rates, which inevitably affects the downstream analysis. Although the issue of sequencing error has been improving these years, large amounts of data were produced at high sequencing errors, and huge waste will be caused if they are discarded. Thus, the error correction for the third generation sequencing data is especially important. The existing error correction methods have poor performances at heterozygous sites, which are ubiquitous in diploid and polyploidy organisms. Therefore, it is a lack of error correction algorithms for the heterozygous loci, especially at low coverages.

Results

In this article, we propose a error correction method, named QIHC. QIHC is a hybrid correction method, which needs both the next generation and third generation sequencing data. QIHC greatly enhances the sensitivity of identifying the heterozygous sites from sequencing errors, which leads to a high accuracy on error correction. To achieve this, QIHC established a set of probabilistic models based on Bayesian classifier, to estimate the heterozygosity of a site and makes a judgment by calculating the posterior probabilities. The proposed method is consisted of three modules, which respectively generates a pseudo reference sequence, obtains the read alignments, estimates the heterozygosity the sites and corrects the read harboring them. The last module is the core module of QIHC, which is designed to fit for the calculations of multiple cases at a heterozygous site. The other two modules enable the reads mapping to the pseudo reference sequence which somehow overcomes the inefficiency of multiple mappings that adopt by the existing error correction methods.

Conclusions

To verify the performance of our method, we selected Canu and Jabba to compare with QIHC in several aspects. As a hybrid correction method, we first conducted a groups of experiments under different coverages of the next-generation sequencing data. QIHC is far ahead of Jabba on accuracy. Meanwhile, we varied the coverages of the third generation sequencing data and compared performances again among Canu, Jabba and QIHC. QIHC outperforms the other two methods on accuracy of both correcting the sequencing errors and identifying the heterozygous sites, especially at low coverage. We carried out a comparison analysis between Canu and QIHC on the different error rates of the third generation sequencing data. QIHC still performs better. Therefore, QIHC is superior to the existing error correction methods when heterozygous sites exist.
The role of CXCR3 and its ligands expression in Brucellar spondylitis
Authors: Hu Xin , Shang Xiaoqian , Wang Liang , Fan Jiahui , Wang Yue , Lv Jie , Nazierhan Shaxika , Wang Hao , Wang Jing , Ma Xiumin
Published: November 2020

Aim

Brucellar spondylitis (BS) is one of the most serious complications of brucellosis. CXCR3 is closely related to the severity of disease infection. This research aimed to study the degree of BS inflammatory damage through analyzing the expression levels of CXCR3 and its ligands (CXCL9 and CXCL10) in patients with BS.

Methods

A total of 29 BS patients and 15 healthy controls were enrolled. Real-Time PCR was used to detect the mRNA expression levels of IFN-γ, CXCR3, CXCL9 and CXCL10 in peripheral blood mononuclear cells (PBMCs) of BS patients and healthy controls. Hematoxylin-Eosin staining was used to show the pathological changes in BS lesion tissues. Immunohistochemistry staining was used to show the protein expression levels of Brucella-Ab, IFN-γ, CXCR3, CXCL9 and CXCL10 in BS lesion tissues. At the same time, ELISA was used to detect the serum levels of IFN-γ, CXCL9 CXCL10 and autoantibodies against CXCR3 in patients with BS.

Results

In lesion tissue of BS patients, it showed necrosis of cartilage, acute or chronic inflammatory infiltration. Brucella-Ab protein was abundantly expressed in close lesion tissue. And the protein expression levels of IFN-γ, CXCR3 and CXCL10 were highly expressed in close lesion tissue and serum of BS patients. At the same time, the mRNA expression levels of IFN-γ, CXCR3 and CXCL10 in PBMCs of BS patients were significantly higher than those in controls.

Conclusion

In our research, the expression levels of IFN-γ, CXCR3 and its ligands were significantly higher than those in controls. It suggested that high expression levels of IFN-γ, CXCR3 and its ligands indicated a serious inflammatory damage in patients with BS.
Effect of magnesium supplementation on emergence delirium and postoperative pain in children undergoing strabismus surgery: a prospective randomised controlled study
Authors: Lee Ji-Hyun , Choi Seungeun , Lee Minkyoo , Jang Young-Eun , Kim Eun-Hee , Kim Jin-Tae , Kim Hee-Soo
Published: November 2020

Background

The benefits of intraoperative magnesium supplementation have been reported. In this prospective, randomized study, the effects of magnesium supplementation during general anaesthesia on emergence delirium and postoperative pain in children were evaluated.

Methods

A total of 66 children aged 2 to 5 years who underwent strabismus surgery were assigned to the magnesium or to the control group. Preoperative anxiety was assessed using the modified Yale Preoperative Anxiety Scale. After anaesthesia induction, the magnesium group received an initial loading dose of 30 mg/kg magnesium sulphate over 10 min and, then, continuous infusion of 10 mg/kg per h until 10 min before the end of the surgery. The control group received an equal volume of normal saline via the same regimen. The Paediatric Anaesthesia Emergence Delirium (PAED) score, pain score, and respiratory events were assessed at the postanaesthetic care unit.

Results

Data obtained from 65 children were analyzed. The PAED and pain scores of the two groups did not differ significantly. There were 26 of 33 (78.8%) and 27 of 32 (84.4%) children with emergence delirium in the control and the magnesium groups, respectively (odds ratio 0.69, 95% CI 0.19–2.44;p = 0.561). The preoperative anxiety score was not significantly correlated with the PAED score. The incidence of respiratory events during the emergence period did not differ significantly between the two groups.

Conclusions

Magnesium supplementation during anaesthesia had no significant effects on the incidence of emergence delirium or postoperative pain in children undergoing strabismus surgery.

Trial registration

ClinicalTrials.gov (NCT03132701). Prospectively registered May 8, 2017.
Addition of routine blood biomarkers to TIMI risk score improves predictive performance of 1-year mortality in patients with ST-segment elevation myocardial infarction
Authors: Oh Pyung Chun , Eom Young Sil , Moon Jeonggeun , Jang Ho-Jun , Kim Tae-Hoon , Suh Jon , Kong Min Gyu , Park Sang-Don , Kwon Sung Woo , Suh Soon Yong , Lee Kyounghoon , Han Seung Hwan , Ahn Taehoon , Kang Woong Chol
Published: November 2020

Background

Several biomarkers have been proposed as independent predictors of poor outcomes in ST-segment elevation myocardial infarction (STEMI). We investigated whether adding information obtained from routine blood tests including hypoxic liver injury (HLI), dysglycemia, anemia, and high neutrophil to lymphocyte ratio (NLR) could improve the prognostic performance of the TIMI risk score for the prediction of 1-year mortality.

Methods

A total of 1057 patients with STEMI undergoing primary percutaneous coronary intervention (PCI) between 2007 and 2014 were retrospectively enrolled from 4-regional hospitals. HLI and dysglycemia were defined as serum transaminase > twice the normal upper limit and glucose < 90 or > 250 mg/dL, respectively. The effect of adding biomarkers to the TIMI risk score on its discriminative ability was assessed using c-statistic, net reclassification improvement (NRI), and integrated discrimination improvement (IDI).

Results

The 1-year mortality rate was 7.1%. The best cutoff value of NLR for the prediction of 1-year mortality was 4.3 (sensitivity, 67%; specificity, 65%). HLI (HR 2.019; 95% CI 1.104–3.695), dysglycemia (HR 2.535; 95% CI 1.324–3.923), anemia (HR 2.071; 95% CI 1.093–3.923), and high NLR (HR 3.651; 95% CI 1.927–6.918) were independent predictors of 1-year mortality. When these 4 parameters were added to the TIMI risk score, the c-statistic significantly improved from 0.841 to 0.876 (p < 0.001), and the NRI and IDI were estimated at 0.203 (95% CI 0.130–0.275; p < 0.001) and 0.089 (95% CI 0.060–0.119; p < 0.001), respectively.

Conclusions

The addition of HLI, dysglycemia, anemia, and high NLR to the TIMI risk score may be useful for very early risk stratification in patients with STEMI receiving primary PCI.
Validation of age-specific survival prediction in pediatric patients with blunt trauma using trauma and injury severity score methodology: a ten-year Nationwide observational study
Authors: Toida Chiaki , Muguruma Takashi , Gakumazawa Masayasu , Shinohara Mafumi , Abe Takeru , Takeuchi Ichiro , Morimura Naoto
Published: November 2020

Background

In-hospital mortality in trauma patients has decreased recently owing to improved trauma injury prevention systems. However, no study has evaluated the validity of the Trauma and Injury Severity Score (TRISS) in pediatric patients by a detailed classification of patients’ age and injury severity in Japan. This retrospective nationwide study evaluated the validity of TRISS in predicting survival in Japanese pediatric patients with blunt trauma by age and injury severity.

Methods

Data were obtained from the Japan Trauma Data Bank during 2009–2018. The outcomes were as follows: (1) patients’ characteristics and mortality by age groups (neonates/infants aged 0 years, preschool children aged 1–5 years, schoolchildren aged 6–11 years, and adolescents aged 12–18 years), (2) validity of survival probability (Ps) assessed using the TRISS methodology by the four age groups and six Ps-interval groups (0.00–0.25, 0.26–0.50, 0.51–0.75, 0.76–0.90, 0.91–0.95, and 0.96–1.00), and (3) the observed/expected survivor ratio by age- and Ps-interval groups. The validity of TRISS was evaluated by the predictive ability of the TRISS method using the receiver operating characteristic (ROC) curves that present the sensitivity, specificity, positive predictive value, negative predictive value, accuracy, area under the receiver operator characteristic curve (AUC) of TRISS.

Results

In all the age categories considered, the AUC for TRISS demonstrated high performance (0.935, 0.981, 0.979, and 0.977). The AUC for TRISS was 0.865, 0.585, 0.614, 0.585, 0.591, and 0.600 in Ps-interval groups (0.96–1.00), (0.91–0.95), (0.76. − 0.90), (0.51–0.75), (0.26–0.50), and (0.00–0.25), respectively. In all the age categories considered, the observed survivors among patients with Ps interval (0.00–0.25) were 1.5 times or more than the expected survivors calculated using the TRISS method.

Conclusions

The TRISS methodology appears to predict survival accurately in Japanese pediatric patients with blunt trauma; however, there were several problems in adopting the TRISS methodology for younger blunt trauma patients with higher injury severity. In the next step, it may be necessary to develop a simple, high-quality prediction model that is more suitable for pediatric trauma patients than the current TRISS model.
Are general practitioners referring patients with low back pain for CTs appropriately according to the guidelines: a retrospective review of 3609 medical records in Newfoundland using routinely collected data
Authors: Logan Gabrielle S. , Dawe Russell Eric , Aubrey-Bassler Kris , Coombs Danielle , Parfrey Patrick , Maher Chris , Etchegary Holly , Hall Amanda
Published: November 2020

Background

CT Imaging is often requested for patients with low back pain (LBP) by their general practitioners. It is currently unknown what reasons are common for these referrals and if CT images are ordered according to guidelines in one province in Canada, which has high rates of CT imaging. The objective of this study is to categorise lumbar spine CT referrals into serious spinal pathology, radicular syndrome, and non-specific LBP and evaluate the appropriateness of CT imaging referrals from general practitioners for patients with LBP.

Methods

A retrospective medical record review of electronic health records was performed in one health region in Newfoundland and Labrador, Canada. Inclusion criteria were lumbar spine CT referrals ordered by general practitioners for adults ≥18 years, and performed between January 1st-December 31st, 2016. Each CT referral was identified from linked databases (Meditech and PACS). To the study authors’ knowledge, guidelines regarding when to refer patients with low back pain for CT imaging had not been actively disseminated to general practitioners or implemented at clinics/hospitals during this time period. Data were manually extracted and categorised into three groups: red flag conditions (judged to be an appropriate referral), radicular syndrome (judged be unclear appropriateness), or nonspecific LBP (determined to be inappropriate).

Results

Three thousand six hundred nine lumbar spine CTs were included from 2016. The mean age of participants was 54.7 (SD 14 years), with females comprising 54.6% of referrals. 1.9% of lumbar CT referrals were missing/unclear, 6.5% of CTs were ordered on a red-flag suspicion, 75.6% for radicular syndromes, and 16.0% for non-specific LBP; only 6.5% of referrals were clearly appropriate. Key information including patient history and clinical exams performed at appointment were often missing from referrals.

Conclusion

This audit found high proportions of inappropriate or questionable referrals for lumbar spine CT and many were missing information needed to categorise. Further research to understand the drivers of inappropriate imaging and cost to the healthcare system would be beneficial.