bluuebunny/crossref_metadata_2025 huggingface dataset:
About this title - Application of Analytical Techniques to Petroleum Systems
Authors: Dowey Patrick J. , Osborne Mark , Volk Herbert
Published: October 2020

Cutting-edge techniques have always been utilized in petroleum exploration and production to reduce costs and improve efficiencies. The demand for petroleum in the form of oil and gas is expected to increase for electricity production, transport and chemical production, largely driven by an increase in energy consumption in the developing world. Innovations in analytical methods will continue to play a key role in the industry moving forwards as society shifts towards lower carbon energy systems and more advantaged oil and gas resources are targeted. This volume brings together new analytical approaches and describes how they can be applied to the study of petroleum systems. The papers within this volume cover a wide range of topics and case studies, in the fields of fluid and isotope geochemistry, organic geochemistry, imaging and sediment provenance. The work illustrates how the current, state-of-the-art technology can be effectively utilised to address ongoing challenges in petroleum geoscience.
Metadata Harvesting and Quality Assurance within Open Urban Platforms
Authors: Lämmel Philipp , Dittwald Benjamin , Bruns Lina , Tcholtchev Nikolay , Glikman Yuri , Cuno Silke , Flügge Mathias , Schieferdecker Ina
Published: October 2020

During the past years, various activities and concepts have shaped and prepared the path for the development of urban environments toward smart cities across the world. One of the initial activities was relating to the opening of vast amounts of data from various public administrations and utility companies within a city in order to create a viable eco-system of urban services and applications. Thereby, the harvested metadata needed to be verified in terms of correctness and a corresponding level of quality had to be assured. In addition, the concept of an Open Urban Platform emerged as an overall solution for smart cities Information Communication Technology (ICT) in the sense that an abstract reference model was established and standardized, providing an overall picture of the ICT structures within a city. Within this article, we use the Open Urban Platform concept as the basics to describe and map our activities within the Open Data domain, focusing mainly on the Open Data prototype for German Open Governmental Data—namely GovData.DE. Thereby, we describe our metadata harvesting and metadata quality assurance approach and discuss on lessons learned, which flow into the definition of metadata quality metrics and have the potential to lead to a corresponding standard within the Deutsches Institut für Normung e.V. (DIN) German national standardization.
Core Placement Optimization for Multi-chip Many-core Neural Network Systems with Reinforcement Learning
Authors: Wu Nan , Deng Lei , Li Guoqi , Xie Yuan
Published: October 2020

Multi-chip many-core neural network systems are capable of providing high parallelism benefited from decentralized execution, and they can be scaled to very large systems with reasonable fabrication costs. As multi-chip many-core systems scale up, communication latency related effects will take a more important portion in the system performance. While previous work mainly focuses on the core placement within a single chip, there are two principal issues still unresolved: the communication-related problems caused by the non-uniform, hierarchical on/off-chip communication capability in multi-chip systems, and the scalability of these heuristic-based approaches in a factorially growing search space. To this end, we propose a reinforcement-learning-based method to automatically optimize core placement through deep deterministic policy gradient, taking into account information of the environment by performing a series of trials (i.e., placements) and using convolutional neural networks to extract spatial features of different placements. Experimental results indicate that compared with a naive sequential placement, the proposed method achieves 1.99× increase in throughput and 50.5% reduction in latency; compared with the simulated annealing, an effective technique to approximate the global optima in an extremely large search space, our method improves the throughput by 1.22× and reduces the latency by 18.6%. We further demonstrate that our proposed method is capable to find optimal placements taking advantages of different communication properties caused by different system configurations, and work in a topology-agnostic manner.
The Past and Future of ITiCSE
Authors: Settle Amber , Giannakos Michail , Zarb Mark
Published: October 2020

The Annual Conference on Innovation and Technology in Computer Science Education (ITiCSE) is the second oldest SIGCSE conference, celebrating its 25th anniversary in 2020. The conference has had impact beyond its immediate audience, as its organizers have pioneered conference activities that have been adopted by other SIGCSE conferences including working groups and conference-sponsored excursions.
CSEdGrad
Authors: Smith Julie
Published: October 2020

CSEdGrad, an NSF-funded collaboration between Purdue University, Michigan State University, and SageFox Consulting Group, is focused on exploring and developing the pathways for computer science education graduate students.
Renal Denervation to Treat Heart Failure
Authors: Sharp Thomas E. , Lefer David J.
Published: October 2020

Heart failure (HF) is a global pandemic with a poor prognosis after hospitalization. Despite HF syndrome complexities, evidence of significant sympathetic overactivity in the manifestation and progression of HF is universally accepted. Confirmation of this dogma is observed in guideline-directed use of neurohormonal pharmacotherapies as a standard of care in HF. Despite reductions in morbidity and mortality, a growing patient population is resistant to these medications, while off-target side effects lead to dismal patient adherence to lifelong drug regimens. Novel therapeutic strategies, devoid of these limitations, are necessary to attenuate the progression of HF pathophysiology while continuing to reduce morbidity and mortality. Renal denervation is an endovascular procedure, whereby the ablation of renal nerves results in reduced renal afferent and efferent sympathetic nerve activity in the kidney and globally. In this review, we discuss the current state of preclinical and clinical research related to renal sympathetic denervation to treat HF.
Characteristics and Real-Life Outcomes of Dementia and Cognitive Impairment at a Geriatric Clinic
Authors: Chulakadabba Kritapas , Muangpaisan Weerasak , Siritipakorn Pitiporn , Wongviriyawong Titima , Suraarunsumrit Patumporn , Chalermsri Chalobol , Intalapaporn Somboon , Chatthanawaree Wichai , Srinonprasert Varalak , Assantachai Prasert
Published: October 2020

Background: Various patterns of dementia care have been developed in different settings, depending on the availability of healthcare resources and facilities. The purpose of this study was to examine the epidemiology and characteristics of dementia care at a geriatric clinic, a field that has been subject to little prior evaluation. Methods: A retrospective chart review was undertaken of cohort patients with cognitive impairment who had received a diagnosis and were still on active follow-up at a geriatric clinic. A total of 892 patients were included. In addition, 203 geriatric patients with no cognitive impairment who attended the clinic during the study period were sampled as a control. Results: The main diagnoses of dementia were Alzheimer’s disease (AD) (40.1%), vascular dementia (16.9%), unspecified dementia (16.3%), mixed dementia (9.0%), AD with cerebrovascular disease (8.7%), and Parkinson’s disease dementia (6.1%). Atypical dementia was presented in 3.0% of cases. There were 178 patients with mild cognitive impairment, 20 with vascular cognitive impairment, and 18 with subjective cognitive decline. Other comorbidities were found in 97% of the subjects. Patients with cognitive impairment had a higher total number of other geriatric syndromes and higher percentages for delirium, falls, immobility, loss of appetite, and incontinence. Potentially reversible causes of dementia were found in 11.3% of the cases. Acetylcholinesterase inhibitors were administered to 61%, whereas 23.5% received an NMDA receptor antagonist. The need for a change in the antidementia medication was identified for 10.7% of the subjects; the major cause was adverse drug side effects. Nonpharmacological therapy only was administered to 52.4% of the people with dementia who had behavioral and psychological symptoms. Conclusions: Mixed brain pathologies, comorbidities, and the coexistence of other geriatric syndromes are common at geriatric clinics. Holistic, integrated, and continuous care are needed to improve the outcomes of patients with more complicated comorbidities.
Antitumoral Effects of Curcumin (Curcuma longa L.) and Thymoquinone (Nigella sativa L.) on Neuroblastoma Cell Lines
Authors: Korff Johanna Maria , Menke Katrin , Schwermer Melanie , Falke Katharina , Schramm Alexander , Längler Alfred , Zuzak Tycho Jan
Published: October 2020

Introduction: Overall survival of high-risk neuroblastoma patients is still poor, emphasizing the need for novel therapeutic options. There is evidence for anti-cancer properties of the herbal substances thymoquinone and curcumin. These substances are isolated from Nigella sativa L. and Curcuma longa L., respectively, which are used in traditional medicine. Objective: We investigated cytotoxic effects of thymoquinone and curcumin on neuroblastoma cell lines NLF, NB69, and SK-N-BE(2), in vitro. Methods: Cytotoxicity of compounds was investigated by MTT cell viability assays. For analyzing effects on cell proliferation BrdU assays were employed and induction of apoptosis was detected by Cell Death ELISA assays. Results: Both substances showed cytotoxic effects in all three neuroblastoma cell lines, whereby primary human fibroblast cells reacted less sensitively. Overall, lower IC50 values could be calculated for curcumin (3.75–7.42 µM) than for thymoquinone (5.16–16.3 µM). Decreased proliferation and increased apoptosis rates were observed under treatment. Conclusions: Both substances showed anti-tumoral properties on neuroblastoma cell lines and should be further investigated as therapeutic agents.
National Stroke Registry Programme in India for Surveillance and Research: Design and Methodology
Authors: Mathur Prashant , Rangamani Sukanya , Kulothungan Vaitheeswaran , Huliyappa Deepadarshan , Bhalla Bhoomika Bajaj , Urs Vinay
Published: October 2020

The burden of stroke is increasing, and India lacks comparable long-term data on stroke incidence and mortality. Disease surveillance using a registry model can provide long-term data on stroke for linking with public health interventions in stroke prevention, treatment, and rehabilitation. The objectives of the National Stroke Registry Programme (NSRP), India, are to generate reliable data on the incidence of first-ever stroke events in defined populations through a population-based stroke registry (PBSR) and to describe the patterns of care and outcomes of patients with stroke in different treatment settings through a hospital-based stroke registry (HBSR). Continuous systematic collection on a standardized format of diagnostic, treatment, and outcome information on stroke events in persons of defined population (PBSR) and those who attend hospitals (HBSR) is conducted through active data abstraction from review of records from all health facilities and imaging centres that cater to stroke patients. Data are ICD coded, verified, and completed by obtaining survival status of registered patients. IT tools are used for data collection,management and analysis. The NSRP shall establish a standardized stroke surveillance system that would reliably measure stroke incidence, subtypes, treatment patterns, complications, disability, case fatality, and survival. This evidence shall inform health planning of stroke interventions and control activities. It would facilitate improvement in stroke services to improve quality of care and outcomes of stroke. A thrust for research on stroke would be encouraged based on evidence-based hypothesis generation.
The Acute Effect of Meal Timing on the Gut Microbiome and the Cardiometabolic Health of the Host: A Crossover Randomized Control Trial
Authors: Papadopoulou Rodanthi Thalia , Theodorou Maria Rafailia , Ieong Chi San , Ballantyne Katrina , Marshall Danae , Verney Anais , Roig Marine , Nichols Ben , Gerasimidis Konstantinos
Published: October 2020

Purpose: The interaction of diet with gut microbiome has been implicated in the onset of cardiovascular disease. The gut microbiome displays diurnal rhythms, which may be influenced by meal timing. Objective: This study aimed to investigate the effect of the timing of main meal consumption on the microbiome and cardiometabolic biomarkers of the host. Methods: Seventeen healthy adults randomly consumed an isocaloric diet for 7 days, twice, by alternating lunch with dinner meals, and with a 2-week washout in-between. Sixty percent of the participants’ daily energy requirements was consumed either as lunch or dinner, respectively. Meals were provided free to the participants. All fecal samples produced the last 3 days of each intervention were collected and analyzed for microbial profiling (16S rRNA gene amplicon sequencing), quantitative estimation of representative bacterial groups (qPCR) of the gut microbiome, and the output of short-chain fatty acids (SCFA) in feces. Fasted blood samples were analyzed for low-grade inflammatory biomarkers, blood lipids, insulin, and glucose levels. Cumulative energy loss in feces was measured over the collection period using bomb calorimetry. Results: Meal timing had no significant effects on fecal SCFA output, energy loss in feces, microbial community profiling, and bacterial species relative abundance. The absolute concentration of Escherichia coli was significantly higher after the large lunch intervention (p = 0.02). No effects on blood biomarkers of cardiometabolic health were observed. Conclusions: In a well-controlled study, main meal timing displayed minimal acute effects on the gut microbiome composition, its diet-related function, and blood biomarkers of cardiometabolic health.
Efficacy of a Novel Second-Generation Somatostatin-Dopamine Chimera (TBR-065) in Human Medullary Thyroid Cancer: A Preclinical Study
Authors: Dicitore Alessandra , Cantone Maria Celeste , Gaudenzi Germano , Saronni Davide , Carra Silvia , Borghi Maria Orietta , Albertelli Manuela , Ferone Diego , Hofland Leo J. , Persani Luca , Vitale Giovanni
Published: October 2020

Introduction: Somatostatin and dopamine (DA) receptors have a pivotal role in controlling hormone secretion and cell proliferation in different neuroendocrine neoplasms, including medullary thyroid cancer (MTC). In the present preclinical study, we evaluated the anti-tumor activity of TBR-065 (formerly BIM-23B065), a second-generation somatostatin-DA chimera, in 2 human MTC cell lines. Methods: The effects of lanreotide (LAN) and TBR-065 on cell growth and proliferation, calcitonin (CT) secretion, cell cycle, apoptosis, cell migration, and tumor-induced angiogenesis have been evaluated through 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, DNA flow cytometry with propidium iodide (PI), Annexin V-FITC/PI staining, electrochemiluminescence immuno assay, wound-healing assay, and zebrafish platform, respectively. Results: TBR-065 exerted a more prominent anti-tumor activity than LAN in both MTC cell lines, as shown by inhibition of cell proliferation (maximal inhibition in TT: −50.3 and −37.6%, respectively; in MZ-CRC-1: −58.8 and −27%, respectively) and migration (in TT: −42.7 and −22.9%, respectively; in MZ-CRC-1: −75.5 and −58.2%, respectively). Only the new chimera decreased significantly the fraction of cells in S phase (TT: −33.8%; MZ-CRC-1: −18.8%) and increased cells in G2/M phase (TT: +13%; MZ-CRC-1: +30.5%). In addition, TBR-065 exerted a more prominent pro-apoptotic effect than LAN in TT cells. A concomitant decrease in CT secretion was observed after 2 days of incubation with both drugs, with a more relevant effect of TBR-065. However, neither LAN nor TBR-065 showed any effect on tumor-induced angiogenesis, as evaluated using a zebrafish/tumor xenograft model. Discussion/Conclusion: In MTC cell lines, a second-generation somatostatin-DA analog, TBR-065, exerts a more relevant anti-tumor activity than LAN, through modulation of cell cycle, induction of apoptosis, and reduction in migration. Further studies are required to establish whether TBR-065 has comparable potent inhibitory effects on tumor growth in vivo.
Duas metáforas históricas sobre o problema do sentido da ação
Authors: Mora Ernesto
Published: October 2020

O presente artigo descreve duas grandes tendências de abordagem do problema sociológico do sentido da ação. Elas podem ser melhor compreendidas fazendo uso de duas metáforas intuitivas. Trata a primeira da “mente como um computador”, e a segunda do “mundo como um texto”. Descrevem-se de modo geral os supostos filosóficos de cada tendência e os seus principais déficits ontológicos, epistemológicos e metodológicos. Em seguida, são apresentadas as suas convergências implícitas, ilustradas em três déficits teóricos: o dualismo, o atomismo e o holismo. O artigo ressalta a importância da pesquisa interdisciplinar, incluindo nela as chamadas ciências biossociais para a superação desses déficits.
Roberto Carlos como mediador cultural
Authors: Garson Marcelo
Published: October 2020

Os anos 1960 experimentaram profundas modificações nas hierarquias de poder da música popular brasileira. Entre as causas para esse fenômeno, duas nos interessam em particular: a perda de centralidade do rádio, que cede terreno à televisão, além da construção de um nicho de música jovem, decorrente do fenômeno da Jovem Guarda. Este artigo tem por objetivo estudar a trajetória de Roberto Carlos nesse período, tomando-o como um mediador cultural, agente de trânsito e intersecção que conformou e adaptou os signos do rádio à televisão e, ao mesmo tempo, conseguiu se afirmar como ídolo das massas, mas também da juventude.
“Sou brasileiro, democrata e editor”
Authors: Czajka Rodrigo
Published: October 2020

O artigo discute o problema da censura a livros durante a primeira fase do regime militar no Brasil e de que forma editores e empresários do ramo editorial criaram estratégias comerciais para a comercialização de obras classificadas como subversivas pelos órgãos de controle da ditadura. Para tanto, a Editora Civilização Brasileira assim como seu proprietário, Ênio Silveira, tornam-se aqui objetos centrais da análise para que possamos compreender as dinâmicas que se operaram no campo das esquerdas intelectualizadas, formado a partir da associação ambivalente entre engajamento e mercado.
Contemporary Diagnosis and Management of Rheumatic Heart Disease: Implications for Closing the Gap: A Scientific Statement From the American Heart Association
Authors: Kumar Raman Krishna , Antunes Manuel J. , Beaton Andrea , Mirabel Mariana , Nkomo Vuyisile T. , Okello Emmy , Regmi Prakash Raj , Reményi Boglarka , Sliwa-Hähnle Karen , Zühlke Liesl Joanna , Sable Craig ,   On behalf of the American Heart Association Council on Lifelong Congenital Heart Disease and Heart Health in the Young; Council on Cardiovascular and Stroke Nursing; and Council on Clinical Cardiology
Published: October 2020

The global burden of rheumatic heart disease continues to be significant although it is largely limited to poor and marginalized populations. In most endemic regions, affected patients present with heart failure. This statement will seek to examine the current state-of-the-art recommendations and to identify gaps in diagnosis and treatment globally that can inform strategies for reducing disease burden. Echocardiography screening based on World Heart Federation echocardiographic criteria holds promise to identify patients earlier, when prophylaxis is more likely to be effective; however, several important questions need to be answered before this can translate into public policy. Population-based registries effectively enable optimal care and secondary penicillin prophylaxis within available resources. Benzathine penicillin injections remain the cornerstone of secondary prevention. Challenges with penicillin procurement and concern with adverse reactions in patients with advanced disease remain important issues. Heart failure management, prevention, early diagnosis and treatment of endocarditis, oral anticoagulation for atrial fibrillation, and prosthetic valves are vital therapeutic adjuncts. Management of health of women with unoperated and operated rheumatic heart disease before, during, and after pregnancy is a significant challenge that requires a multidisciplinary team effort. Patients with isolated mitral stenosis often benefit from percutaneous balloon mitral valvuloplasty. Timely heart valve surgery can mitigate the progression to heart failure, disability, and death. Valve repair is preferable over replacement for rheumatic mitral regurgitation but is not available to the vast majority of patients in endemic regions. This body of work forms a foundation on which a companion document on advocacy for rheumatic heart disease has been developed. Ultimately, the combination of expanded treatment options, research, and advocacy built on existing knowledge and science provides the best opportunity to address the burden of rheumatic heart disease.
Effect of Dietary Sodium Modulation on Pig Adrenal Steroidogenesis and Transcriptome Profiles
Authors: Vohra Twinkle , Kemter Elisabeth , Sun Na , Dobenecker Britta , Hinrichs Arne , Burrello Jacopo , Gomez-Sanchez Elise P. , Gomez-Sanchez Celso E. , Wang Jun , Kinker Isabella-Sabrina , Teupser Daniel , Fischer Konrad , Schnieke Angelika , Peitzsch Mirko , Eisenhofer Graeme , Walch Axel , Reincke Martin , Wolf Eckhard , Williams Tracy Ann
Published: October 2020

Primary aldosteronism is a frequent form of endocrine hypertension caused by aldosterone overproduction from the adrenal cortex. Regulation of aldosterone biosynthesis has been studied in rodents despite differences in adrenal physiology with humans. We, therefore, investigated pig adrenal steroidogenesis, morphology, and transcriptome profiles of the zona glomerulosa (zG) and zona fasciculata in response to activation of the renin-angiotensin-aldosterone system by dietary sodium restriction. Six-week-old pigs were fed a low- or high-sodium diet for 14 days (3 pigs per group, 0.4 g sodium/kg feed versus 6.8 g sodium/kg). Plasma aldosterone concentrations displayed a 43-fold increase (
P
=0.011) after 14 days of sodium restriction (day 14 versus day 0). Low dietary sodium caused a 2-fold increase in thickness of the zG (
P
<0.001) and an almost 3-fold upregulation of
CYP11B
(
P
<0.05) compared with high dietary sodium. Strong immunostaining of the KCNJ5 (G protein-activated inward rectifier potassium channel 4), which is frequently mutated in primary aldosteronism, was demonstrated in the zG. mRNA sequencing transcriptome analysis identified significantly altered expression of genes modulated by the renin-angiotensin-aldosterone system in the zG (n=1172) and zona fasciculata (n=280). These genes included many with a known role in the regulation of aldosterone synthesis and adrenal function. The most highly enriched biological pathways in the zG were related to cholesterol biosynthesis, steroid metabolism, cell cycle, and potassium channels. This study provides mechanistic insights into the physiology and pathophysiology of aldosterone production in a species closely related to humans and shows the suitability of pigs as a translational animal model for human adrenal steroidogenesis.
In Vivo Magnetic Resonance Imaging‐Based Detection of Heterogeneous Endothelial Response in Thoracic and Abdominal Aorta to Short‐Term High‐Fat Diet Ascribed to Differences in Perivascular Adipose Tissue in Mice
Authors: Bar Anna , Kieronska‐Rudek Anna , Proniewski Bartosz , Suraj‐Prażmowska Joanna , Czamara Krzysztof , Marczyk Brygida , Matyjaszczyk‐Gwarda Karolina , Jasztal Agnieszka , Kuś Edyta , Majka Zuzanna , Kaczor Agnieszka , Kurpińska Anna , Walczak Maria , Pieterman Elsbet J. , Princen Hans M. G. , Chlopicki Stefan
Published: October 2020

Background

Long‐term feeding with a high‐fat diet (HFD) induces endothelial dysfunction in mice, but early HFD‐induced effects on endothelium have not been well characterized.

Methods and Results

Using an magnetic resonance imaging‐based methodology that allows characterization of endothelial function in vivo, we demonstrated that short‐term (2 weeks) feeding with a HFD to
C57BL/6
mice or to
E3L.CETP
mice resulted in the impairment of acetylcholine‐induced response in the abdominal aorta (AA), whereas, in the thoracic aorta (TA), the acetylcholine‐induced response was largely preserved. Similarly, HFD resulted in arterial stiffness in the AA, but not in the TA. The difference in HFD‐induced response was ascribed to distinct characteristics of perivascular adipose tissue in the TA and AA, related to brown‐ and white‐like adipose tissue, respectively, as assessed by histology, immunohistochemistry, and Raman spectroscopy. In contrast, short‐term HFD‐induced endothelial dysfunction could not be linked to systemic insulin resistance, changes in plasma concentration of nitrite, or concentration of biomarkers of glycocalyx disruption (syndecan‐1 and endocan), endothelial inflammation (soluble form of vascular cell adhesion molecule 1, soluble form of intercellular adhesion molecule 1 and soluble form of E‐selectin), endothelial permeability (soluble form of fms‐like tyrosine kinase 1 and angiopoietin 2), and hemostasis (tissue plasminogen activator and plasminogen activator inhibitor 1).

Conclusions

Short‐term feeding with a HFD induces endothelial dysfunction in the AA but not in the TA, which could be ascribed to a differential response of perivascular adipose tissue to a HFD in the AA versus TA. Importantly, early endothelial dysfunction in the AA is not linked to elevation of classical systemic biomarkers of endothelial dysfunction.
Citations driven by social connections? A multi-layer representation of coauthorship networks
Authors: Zingg Christian , Nanumyan Vahan , Schweitzer Frank
Published: October 2020

To what extent is the citation rate of new papers influenced by the past social relations of their authors? To answer this question, we present a data-driven analysis of nine different physics journals. Our analysis is based on a two-layer network representation constructed from two large-scale data sets, INSPIREHEP and APS. The social layer contains authors as nodes and coauthorship relations as links. This allows us to quantify the social relations of each author, prior to the publication of a new paper. The publication layer contains papers as nodes and citations between papers as links. This layer allows us to quantify scientific attention as measured by the change of the citation rate over time. We particularly study how this change correlates with the social relations of their authors, prior to publication. We find that on average the maximum value of the citation rate is reached sooner for authors who have either published more papers or who have had more coauthors in previous papers. We also find that for these authors the decay in the citation rate is faster, meaning that their papers are forgotten sooner.
A new synonym of Bulbophyllum ovalifolium (Orchidaceae: Epidendroideae)

Authors: METUSALA DESTARIO , WIBOWO ANINDA RETNO UTAMI , MAMBRASAR YASPER MICHAEL , HENDRIAN HENDRIAN
Published: October 2020

Bulbophyllum trinervosum (Orchidaceae) was described in mid 2020 as a new species from West Java, Indonesia. After careful examination and morphological comparisons, it has been concluded that the characters of B. trinervosum fall within the variation of widespread species, B. ovalifolium. Thus, B. trinervosum is proposed here as a synonym of B. ovalifolium. Detailed comparisons, including a series of photos of B. ovalifolium are provided.
New species and stages description of Traverella Edmunds, 1948 (Ephemeroptera: Leptophlebiidae) from Northeast Brazil
Authors: NASCIMENTO STÊNIO R. S. , LIMA LUCAS R. C. , MARIANO RODOLFO , AZEVÊDO CARLOS A. S.
Published: October 2020

The genus Traverella Edmunds, 1948 (Ephemeroptera: Leptophlebiidae) has 15 described species, three of them recorded from Brazil: Traverella bradleyi (Needham & Murphy, 1924), T. insolita Nascimento & Salles, 2013 and T. maranhensis Nascimento, Lima & Azevedo, 2019. In the present work, we provide the description of a new species to the genus based on nymphs and male imagos and provide description of the nymphal stage of T. maranhensis, based on collections from Maranhão State. Additionally, an updated key of male imagos is provided.
A new species of Horniolus Weise with remarks on the systematic position of the genus (Coleoptera: Coccinellidae)
Authors: SZAWARYN KAROL , VĚTROVEC JAROSLAV
Published: October 2020

Horniolus Weise is an Asian genus of ladybird beetles up to now comprising 15 species with the greatest diversity in China. A new species, H. minutus sp. nov., is described and illustrated. The position of the genus within the modern classification of Coccinellidae is discussed, and its transfer from the tribe Scymnini to Platynaspini is proposed.
A new species of the genus Celebesia Bolívar, 1917 (Orthoptera: Acrididae, Catantopinae) from Sulawesi Island with notes on composition of the tribe Mesambriini
Authors: STOROZHENKO SERGEY YU.
Published: October 2020

The genus Celebesia Bolívar, 1917 consists of four species endemic to Sulawesi Island, namely C. acuticerca C. Bolívar, 1917, C. ferruginata (Brunner von Wattenwyl, 1898), C. heinrichi Ramme, 1941, and C. linduensis Storozhenko, sp. nov. Distribution of species is clarified and an updated key to the species of Celebesia is given. Male genitalia of this genus is described and illustrated for the first time. The genus Pyrgophistes Key, 1992 is transferred from the tribe Catantopini to Mesambriini and a new synonymy is proposed: Mesambriini Brunner von Wattenwyl, 1893 = Pyrgophistina Key, 1993, syn. nov.
Exploring North Atlantic and North Pacific Decadal Climate Prediction Using Self-Organizing Maps
Authors: Gu Qinxue , Gervais Melissa
Published: October 2020

Decadal climate prediction can provide invaluable information for decisions made by government agencies and industry. Modes of internal variability of the ocean play an important role in determining the climate on decadal time scales. This study explores the possibility of using self-organizing maps (SOMs) to identify decadal climate variability, measure theoretical decadal predictability, and conduct decadal predictions of internal climate variability within a long control simulation. SOM is applied to an 11-yr running-mean winter sea surface temperature (SST) in the North Pacific and North Atlantic Oceans within the Community Earth System Model 1850 preindustrial simulation to identify patterns of internal variability in SSTs. Transition probability tables are calculated to identify preferred paths through the SOM with time. Results show both persistence and preferred evolutions of SST depending on the initial SST pattern. This method also provides a measure of the predictability of these SST patterns, with the North Atlantic being predictable at longer lead times than the North Pacific. In addition, decadal SST predictions using persistence, a first-order Markov chain, and lagged transition probabilities are conducted. The lagged transition probability predictions have a reemergence of prediction skill around lag 15 for both domains. Although the prediction skill is very low, it does imply that the SOM has the ability to predict some aspects of the internal variability of the system beyond 10 years.
Multi-Frequency Analysis of Simulated versus Observed Variability in Tropospheric Temperature
Authors: Pallotta Giuliana , Santer Benjamin D.
Published: October 2020

Studies seeking to identify a human-caused global warming signal generally rely on climate model estimates of the “noise” of intrinsic natural variability. Assessing the reliability of these noise estimates is of critical importance. We evaluate here the statistical significance of differences between climate model and observational natural variability spectra for global-mean mid- to upper-tropospheric temperature (TMT). We use TMT information from satellites and large multimodel ensembles of forced and unforced simulations. Our main goal is to explore the sensitivity of model-versus-data spectral comparisons to a wide range of subjective decisions. These include the choice of satellite and climate model TMT datasets, the method for separating signal and noise, the frequency range considered, and the statistical model used to represent observed natural variability. Of particular interest is the amplitude of the interdecadal noise against which an anthropogenic tropospheric warming signal must be detected. We find that on time scales of 5–20 years, observed TMT variability is (on average) overestimated by the last two generations of climate models participating in the Coupled Model Intercomparison Project. This result is relatively insensitive to different plausible analyst choices, enhancing confidence in previous claims of detectable anthropogenic warming of the troposphere and indicating that these claims may be conservative. A further key finding is that two commonly used statistical models of short-term and long-term memory have deficiencies in their ability to capture the complex shape of observed TMT spectra.
Disintegration of the K1 Internal Tide in the South China Sea due to Parametric Subharmonic Instability
Authors: Liu Kun , Zhao Zhongxiang
Published: October 2020

The disintegration of the equatorward-propagating K1 internal tide in the South China Sea (SCS) by parametric subharmonic instability (PSI) at its critical latitude of 14.52°N is investigated numerically. The multiple-source generation and long-range propagation of K1 internal tides are successfully reproduced. Using equilibrium analysis, the internal wave field near the critical latitude is found to experience two quasi-steady states, between which the subharmonic waves develop constantly. The simulated subharmonic waves agree well with classic PSI theoretical prediction. The PSI-induced near-inertial waves are of half the K1 frequency and dominantly high modes, the vertical scales ranging from 50 to 180 m in the upper ocean. From an energy perspective, PSI mainly occurs in the critical latitudinal zone from 13° to 15°N. In this zone, the incident internal tide loses ~14% energy in the mature state of PSI. PSI triggers a mixing elevation of O(10−5–10−4) m2 s−1 in the upper ocean at the critical latitude, which is several times larger than the background value. The contribution of PSI to the internal tide energy loss and associated enhanced mixing may differ regionally and is closely dependent on the intensity and duration of background internal tide. The results elucidate the far-field dissipation mechanism by PSI in connecting interior mixing with remotely generated K1 internal tides in the Luzon Strait.
A Hybrid Differential-Ensemble Linear Forecast Model for 4D-Var
Authors: Payne T. J.
Published: October 2020

A key component of the 4D-Var data assimilation method used widely for numerical weather prediction is the linear forecast model, which is approximately tangent linear to the forecast model. Traditionally this has been based on differentiating the forecast model, though recently some authors have experimented with an ensemble regression technique, the localized ensemble tangent linear model (LETLM). We propose a hybrid of the two, in which a simplified conventional tangent-linear model (e.g., just the dynamical core) is used together with an LETLM-like adjustment every time step to account for the remaining processes (in this example, the parameterized physics). This is much cheaper than the LETLM, and in tests using the Met Office’s linear model performs considerably better than either a pure LETLM (with a very large ensemble) or the existing linear model.
Overcoming T-cell exhaustion in LCH: PD-1 blockade and targeted MAPK inhibition are synergistic in a mouse model of LCH
Authors: Sengal Amel , Velazquez Jessica , Hahne Meryl , Burke Thomas M. , Abhyankar Harshal , Reyes Robert , Olea Walter , Scull Brooks , Eckstein Olive S. , Bigenwald Camille , Bollard Catherine M. , Yu Wendong , Merad Miriam , McClain Kenneth L. , Allen Carl E. , Chakraborty Rikhia
Published: October 2020

Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia characterized by granulomatous lesions containing pathological CD207+ dendritic cells (DCs) with persistent MAPK pathway activation. Standard-of-care chemotherapies are inadequate for most patients with multisystem disease, and optimal strategies for relapsed and refractory disease are not defined. The mechanisms underlying development of inflammation in LCH lesions, the role of inflammation in pathogenesis, and the potential for immunotherapy are unknown. Analysis of the immune infiltrate in LCH lesions identified the most prominent immune cells as T lymphocytes. Both CD8+ and CD4+ T cells exhibited “exhausted” phenotypes with high expression of the immune checkpoint receptors. LCH DCs showed robust expression of ligands to checkpoint receptors. Intralesional CD8+ T cells showed blunted expression of Tc1/Tc2 cytokines and impaired effector function. In contrast, intralesional regulatory T cells demonstrated intact suppressive activity. Treatment of BRAFV600ECD11c LCH mice with anti-PD-1 or MAPK inhibitor reduced lesion size, but with distinct responses. Whereas MAPK inhibitor treatment resulted in reduction of the myeloid compartment, anti-PD-1 treatment was associated with reduction in the lymphoid compartment. Notably, combined treatment with MAPK inhibitor and anti-PD-1 significantly decreased both CD8+ T cells and myeloid LCH cells in a synergistic fashion. These results are consistent with a model that MAPK hyperactivation in myeloid LCH cells drives recruitment of functionally exhausted T cells within the LCH microenvironment, and they highlight combined MAPK and checkpoint inhibition as a potential therapeutic strategy.
Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks
Authors: Ceol Arnaud , Montanari Piero , Bartolini Ilaria , Ceri Stefano , Ciaccia Paolo , Patella Marco , Masseroli Marco
Published: October 2020

Background

Genome browsers are widely used for locating interesting genomic regions, but their interactive use is obviously limited to inspecting short genomic portions. An ideal interaction is to provide patterns of regions on the browser, and then extract other genomic regions over the whole genome where such patterns occur, ranked by similarity.

Results

We developed SimSearch, an optimized pattern-search method and an open source plugin for the Integrated Genome Browser (IGB), to find genomic region sets that are similar to a given region pattern. It provides efficient visual genome-wide analytics computation in large datasets; the plugin supports intuitive user interactions for selecting an interesting pattern on IGB tracks and visualizing the computed occurrences of similar patterns along the entire genome. SimSearch also includes functions for the annotation and enrichment of results, and is enhanced with a Quickload repository including numerous epigenomic feature datasets from ENCODE and Roadmap Epigenomics. The paper also includes some use cases to show multiple genome-wide analyses of biological interest, which can be easily performed by taking advantage of the presented approach.

Conclusions

The novel SimSearch method provides innovative support for effective genome-wide pattern search and visualization; its relevance and practical usefulness is demonstrated through a number of significant use cases of biological interest. The SimSearch IGB plugin, documentation, and code are freely available at https://deib-geco.github.io/simsearch-app/ and https://github.com/DEIB-GECO/simsearch-app/.
Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study
Authors: Sinha Swati , Lynn Andrew M. , Desai Dhwani K.
Published: October 2020

Background

Homology based methods are one of the most important and widely used approaches for functional annotation of high-throughput microbial genome data. A major limitation of these methods is the absence of well-characterized sequences for certain functions. The non-homology methods based on the context and the interactions of a protein are very useful for identifying missing metabolic activities and functional annotation in the absence of significant sequence similarity. In the current work, we employ both homology and context-based methods, incrementally, to identify local holes and chokepoints, whose presence in the Mycobacterium tuberculosis genome is indicated based on its interaction with known proteins in a metabolic network context, but have not been annotated. We have developed two computational procedures using network theory to identify orphan enzymes (‘Hole finding protocol’) coupled with the identification of candidate proteins for the predicted orphan enzyme (‘Hole filling protocol’). We propose an integrated interaction score based on scores from the STRING database to identify candidate protein sequences for the orphan enzymes from M. tuberculosis, as a case study, which are most likely to perform the missing function.

Results

The application of an automated homology-based enzyme identification protocol, ModEnzA, on M. tuberculosis genome yielded 56 novel enzyme predictions. We further predicted 74 putative local holes, 6 choke points, and 3 high confidence local holes in the genome using ‘Hole finding protocol’. The ‘Hole-filling protocol’ was validated on the E. coli genome using artificial in-silico enzyme knockouts where our method showed 25% increased accuracy, compared to other methods, in assigning the correct sequence for the knocked-out enzyme amongst the top 10 ranks. The method was further validated on 8 additional genomes.

Conclusions

We have developed methods that can be generalized to augment homology-based annotation to identify missing enzyme coding genes and to predict a candidate protein for them. For pathogens such as M. tuberculosis, this work holds significance in terms of increasing the protein repertoire and thereby, the potential for identifying novel drug targets.
oposSOM-Browser: an interactive tool to explore omics data landscapes in health science
Authors: Loeffler-Wirth Henry , Reikowski Jasmin , Hakobyan Siras , Wagner Jonas , Binder Hans
Published: October 2020

Background

oposSOM is a comprehensive, machine learning based open-source data analysis software combining functionalities such as diversity analyses, biomarker selection, function mining, and visualization.

Results

These functionalities are now available as interactive web-browser application for a broader user audience interested in extracting detailed information from high-throughput omics data sets pre-processed by oposSOM. It enables interactive browsing of single-gene and gene set profiles, of molecular ‘portrait landscapes’, of associated phenotype diversity, and signalling pathway activation patterns.

Conclusion

The oposSOM-Browser makes available interactive data browsing for five transcriptome data sets of cancer (melanomas, B-cell lymphomas, gliomas) and of peripheral blood (sepsis and healthy individuals) at www.izbi.uni-leipzig.de/opossom-browser.
Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae)
Authors: Qu Zhe , Nong Wenyan , Yu Yifei , Baril Tobias , Yip Ho Yin , Hayward Alexander , Hui Jerome H. L.
Published: October 2020

Background

Teleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries and aquaculture. Additionally, the four-finger threadfin Eleutheronema tetradactylum is of conservation relevance since its populations are considered to be in rapid decline and it is classified as endangered. However, no genomic resources are currently available for the threadfin family Polynemidae.

Results

We sequenced and assembled the first threadfin fish genome, the four-finger threadfin E. tetradactylum. We provide a genome assembly for E. tetradactylum with high contiguity (scaffold N50 = 56.3 kb) and high BUSCO completeness at 96.5%. The assembled genome size of E. tetradactylum is just 610.5 Mb, making it the second smallest perciform genome assembled to date. Just 9.07–10.91% of the genome sequence was found to consist of repetitive elements (standard RepeatMasker analysis vs custom analysis), making this the lowest repeat content identified to date for any perciform fish. A total of 37,683 protein-coding genes were annotated, and we include analyses of developmental transcription factors, including the Hox, ParaHox, and Sox families. MicroRNA genes were also annotated and compared with other chordate lineages, elucidating the gains and losses of chordate microRNAs.

Conclusions

The four-finger threadfin E. tetradactylum genome presented here represents the first available genome sequence for the ecologically, biologically, and commercially important clade of threadfin fish. Our findings provide a useful genomic resource for future research into the interesting biology and evolution of this valuable group of food fish.
Comparative efficacy of glucocorticoid receptor agonists on Th2 cell function and attenuation by progesterone
Authors: Luchak Alexander , Solomon Lauren A. , Kanagalingam Tharsan , Vijeyakumaran Meerah , Rowe Brian H. , Cameron Lisa
Published: October 2020

Background

Corticosteroids (CS)s suppress cytokine production and induce apoptosis of inflammatory cells. Prednisone and dexamethasone are oral CSs prescribed for treating asthma exacerbations. While prednisone is more commonly prescribed, dexamethasone is long acting and a more potent glucocorticoid receptor (GR) agonist. It can be administered as a one or two dose regime, unlike the five to seven days required for prednisone, a feature that increases compliance. We compared the relative ability of these two oral CSs to suppress type 2 inflammation. Since progesterone has affinity for the GR and women are more likely to relapse following an asthma exacerbation, we assessed its influence on CS action.

Results

Dexamethasone suppressed the level of IL-5 and IL-13 mRNA within Th2 cells with ~ 10-fold higher potency than prednisolone (the active form of prednisone). Dexamethasone induced a higher proportion of apoptotic and dying cells than prednisolone, at all concentrations examined. Addition of progesterone reduced the capacity of both CS to drive cell death, though dexamethasone maintained significantly more killing activity. Progesterone blunted dexamethasone-induction of FKBP5 mRNA, indicating that the mechanism of action was by interference of the CS:GR complex.

Conclusions

Dexamethasone is both more potent and effective than prednisolone in suppressing type 2 cytokine levels and mediating apoptosis. Progesterone attenuated these anti-inflammatory effects, indicating its potential influence on CS responses in vivo. Collectively, our data suggest that when oral CS is required, dexamethasone may be better able to control type 2 inflammation, eliminate Th2 cells and ultimately lead to improved long-term outcomes. Further research in asthmatics is needed.