bluuebunny/crossref_metadata_2025 huggingface dataset:
Altered sub-seasonal predictability of Community Atmosphere Model 5 (CAM5) in CESM 1.2.1 by the choices of dynamical core
Authors: Kim Ha-Rim , Kim Baek-Min , Jun Sang-Yoon , Choi Yong-Sang
Published: April 2020

Abstract. This study investigates the prediction skill of sub-seasonal prediction models that vary based on the choice of two dynamical cores: the finite volume (FV) dynamical core on a latitude-longitude grid system and the spectral element (SE) dynamical core on a cubed-sphere grid system. Recent research showed that the SE dynamical core on a uniform grid system increases parallel scalability and removes the need for polar filters for mitigating uncertainty in climate prediction, particularly for the Arctic region. However, it still remains questionable whether the choice of dynamical cores can actually yield significant changes in prediction skill. To tackle this issue, we implemented a sub-seasonal prediction model based on the Community Atmospheric Model version 5 by incorporating the above two dynamical cores with virtually the same physics schemes. Sub-seasonal prediction skills of the SE dynamical core and FV dynamical core are verified with ERA-Interim reanalysis during the early winter (November–December) and the late winter (January–February) from 2001/2002 to 2017/2018. The prediction skills of two different dynamical cores were significantly different regardless of the similar physics scheme. In the ocean, the predictability of the SE dynamical core is similar to that of the FV dynamical core, mostly because our simulation configuration imposes the same boundary and initial conditions at the surface. Notable differences in the one-month predictability between the two cores are observed for the wintertime Arctic and mid-latitudes, particularly over North America and Eurasia continents. With a one-month lead, the SE dynamical core exhibited higher predictability over North America in late winter (r ≈ 0.45 in SE, r ≈ 0.10 in FV) whereas the FV dynamical core showed relatively higher predictability in East Asia and Eurasia in early winter (r ≈ 0.15 in SE, r ≈ 0.43 in FV). Therefore, we conclude that caution is needed when selecting the dynamical cores of sub-seasonal prediction models. Partially, these differences can be ascribed to the different manifestations of Arctic-mid-latitude linkage in the two dynamical cores; the SE dynamical core captures warmer Arctic and colder mid-latitudes relatively better than the FV dynamical core.
Influence of multidecadal variability on high and low flows: the case of the Seine basin
Authors: Bonnet Rémy , Boé Julien , Habets Florence
Published: April 2020

Abstract. The multidecadal hydroclimate variations of the Seine basin since the 1850s are investigated. Given the scarcity of long-term hydrological
observations, a hydrometeorological reconstruction is developed based on hydrological modeling and a method that combines the results of
a downscaled long-term atmospheric reanalysis and local observations of precipitation and temperature. This method improves previous attempts and
provides a realistic representation of daily and monthly river flows. This new hydrometeorological reconstruction, available over more than
150 years while maintaining fine spatial and temporal resolutions, provides a tool to improve our understanding of the multidecadal hydrological
variability in the Seine basin, as well as its influence on high and low flows. This long-term reconstruction allows analysis of the strong
multidecadal variations of the Seine river flows. The main hydrological mechanisms at the origin of these variations are highlighted. Spring
precipitation plays a central role by directly influencing not only the multidecadal variability in spring flows but also soil moisture and groundwater
recharge, which then regulate summer river flows. These multidecadal hydroclimate variations in the Seine basin are driven by anomalies in large-scale atmospheric circulation, which themselves appear to be influenced by sea surface temperature anomalies over the North Atlantic and the
North Pacific. The multidecadal hydroclimate variations also influence high and low flows over the last 150 years. The analysis of two
particularly severe historical droughts, the 1921 and the 1949 events, illustrates how long-term hydroclimate variations may impact short-term
drought events, particularly through groundwater–river exchanges. The multidecadal hydroclimate variations described in this study, probably of
internal origin, could play an important role in the evolution of water resources in the Seine basin in the coming decades. It is therefore
essential to take the associated uncertainties into account in future projections.
Basin inversion and structural architecture as constraints on fluid flow and Pb-Zn mineralisation in the Paleo-Mesoproterozoic sedimentary sequences of northern Australia
Authors: Gibson George M. , Edwards Sally
Published: April 2020

Abstract. As host to several world-class sediment-hosted Pb-Zn deposits and unknown quantities of conventional and unconventional gas, the variably inverted 1730–1640 Ma Calvert and 1640–1580 Ma Isa superbasins of northern Australia have been the subject of numerous seismic reflection studies with a view to better understanding basin architecture and fluid migration pathways. Strikingly similar structural architecture has been reported from much younger inverted sedimentary basins considered prospective for oil and gas elsewhere in the world. Such similarities suggest that the mineral and petroleum systems in Paleo-Mesoproterozoic northern Australia may have spatially and temporally overlapped consistent with the observation that basinal sequences hosting Pb-Zn mineralisation in northern Australia are bituminous or abnormally enriched in hydrocarbons. This points to the possibility of a common tectonic driver and shared fluid pathways. Sediment-hosted Pb-Zn mineralisation coeval with basin inversion first occurred during the 1650–1640 Ma Riversleigh Tectonic Event towards the close of the Calvert Superbasin with further pulses accompanying the 1620–1580 Ma Isa Orogeny which brought about closure of the Isa Superbasin. Mineralisation in all cases is hosted by the syn-inversion fraction of basin fill, contrary to most existing interpretations of Pb-Zn ore genesis where the ore-forming fluids are introduced during the rifting or syn-extensional phase of basin development. Syn-extensional normal faults of Calvert and Isa age are mutually orthogonal, giving rise to a complex compartmentalisation of sub-basins with predominantly NNW and ENE strikes. Basin inversion subsequent to 1640 Ma occurred overall in a transpressive tectonic regime linked to continent-continent collision accompanied by orogen-parallel extensional collapse and right-stepping strike-slip faulting.
Mitigating impact of spatial variance of turbulence in wind energy applications
Authors: Kazda Jonas , Mann Jakob
Published: April 2020

Abstract. For the first time an analytical solution for the quantification of the spatial variance of the second-order moment of correlated wind speeds was
developed in this work. The spatial variance is defined as random differences in the sample variance of wind speed between different points in
space. The approach is successfully verified using simulation and field data. The impact of the spatial variance on three selected applications
relevant to the wind energy sector is then investigated including mitigation measures. First, the difference of the second-order moment between
front-row wind turbines of Lillgrund wind farm is investigated. The variance of the difference ranges between 25 % and 48 % for turbulence
intensities ranging from 7 % to 10 % and a sampling period of 10 min. It is thus suggested to use the second-order moment measured at each
individual turbine as input to flow models of wind farm controllers in order to mitigate random error. Second, the impact of the spatial variance of
the measured second-order moment on the verification of wind turbine performance is investigated. Misalignment between the mean wind direction and
the line connecting the meteorological mast and wind turbine is observed to result in an additional random error in the observed second-order moment
of wind speed. In the investigated conditions the random error was up to 34 %. Such a random error adds uncertainty to the turbulence
intensity-based classification of the fatigue loads and power output of a wind turbine. To mitigate the random error, it is suggested to either
filter the measured data for low angles of misalignment or quantify wind turbine performance using the ensemble-averaged measurements of the
same wind conditions. Third, the verification of sensors in wind farms was investigated with respect to the impact of distant reference
measurements. In the case of a misalignment between the wind direction and the line connecting sensor and reference, an increased random error will
hamper the comparison of the measured second-order moments. The suggested mitigation measures are equivalent to those for the verification of
turbine performance.
Approaching EdD Program Redesign as a Problem of Practice
Authors: Leach Lesley F , Reyes Juanita M , Baker Credence , Glaman Ryan , Barkley Jordan M , Beach Don M , Higham J Russell , Rynearson Kimberly , Weber Mark , Farmer Tod Allen , Bowden Randall , Brock Jesse , Bunch Phillis
Published: April 2020

As members of the Carnegie Project on the Education Doctorate (CPED), universities across the United States are restructuring EdD programs to better prepare professional practitioners with the practical skills and theoretical knowledge needed to improve the educational environments that they serve. The hallmark of these programs is often the dissertation in practice, a scholarly investigation within which students define a problem of practice and then systematically test solutions to that problem. In this study, we investigate the experiences of university faculty participating in the redesign of an Educational Leadership EdD program who approach the redesign as a problem of practice. Root causes of identified program issues are presented in addition to the changes implemented in the redesigned program to improve upon the problem of practice.
Real-Time Block Rate Targeting
Authors: Harding Thomas M
Published: April 2020

A proof-of-work blockchain uses a retargeting algorithm, also termed a difficulty adjustment algorithm, to manage the rate of block production in the presence of changing hashrate. To derive the parameters that guide the search for the next block, nearly all such algorithms rely on averages of past inter-block time observations, as measured by on-chain timestamps. We are motivated to seek better responsiveness to changing hashrate, while improving stability of the block production rate and retaining the progress-free property of mining. We describe a class of retargeting algorithms for which the sole inter-block time input is that of the block being searched for, and whose response is nonlinear in that time. We discuss how these algorithms allow the other consensus rules that govern allowable timestamps to be tightened, which may improve the blockchain’s effectiveness as a time-stamping machine.
Global Prevalence and Device Related Causes of Needle Stick Injuries among Health Care Workers: A Systematic Review and Meta-Analysis
Authors: Bouya Salehoddin , Balouchi Abbas , Rafiemanesh Hosien , Amirshahi Mehrbanoo , Dastres Majid , Moghadam Mahdieh Poodineh , Behnamfar Niaz , Shyeback Mahmood , Badakhsh Mahin , Allahyari Jasem , Al Mawali Adhra , Ebadi Abbas , Dezhkam Asiyeh , Daley Karen A.
Published: April 2020

Background: Healthcare workers (HCWs) suffer more than 2 million occupational needle-stick injuries (NSIs) annually.Goal: To determine the global prevalence and causes of NSIs among HCWs.Methods: In this systematic review and meta-analysis, three databases (PubMed, Web of science, and Scopus) were searched for reports from January 1, 2000 to December 31, 2018. The random effects model was used to determine the prevalence of NSIs among HCWs. Hoy et al.’s instrument was employed to evaluate the quality of the included studies.Findings: A total of 87 studies performed on 50,916 HCWs in 31 countries worldwide were included in the study. The one-year global pooled prevalence of NSIs among HCWs was 44.5% (95% CI: 35.7, 53.2). Highest prevalence of NSIs occurred in the South East Asia region at 58.2% (95%, CI: 36.7, 79.8). By job category, prevalence of NSIs was highest among dentists at 59.1% (95% CI: 38.8, 79.4), Hypodermic needles were the most common cause of NSIs at 55.1% (95% CI: 41.4, 68.9).Conclusion: The current high prevalence of NSIs among HCWs suggests need to improve occupational health services and needle-stick education programs globally.
CURRENT VIEWS ON NEUROPLASTICITY: WHAT IS NEW AND WHAT IS OLD?
Authors: Kaczmarek Bożydar L.J.
Published: April 2020

The main aim of the paper is to show that many previously forgotten discoveries within the field of neuroscience own their rediscovery and renaissance to the refinement of tools provided by the technological advances. Most spectacular is the advancement of brain imaging techniques, which provide hard data that support for evidence for previously neglected presumptions and ideas. Neuroplasticity is an example of such a long ignored historical discovery. One reason for that neglect is that it stood in contradiction to beliefs and theories prevailing at the first half of the twenties century. The idea of neuronal plasticity is not disputed any longer since it has found confirmation not only in a dramatic development of neuroimaging but also in the advancement of neurobiology. Most authors concentrate upon neuronal plasticity, recent studies, however, have produced a wealth of information regarding neurogenesis, in which astrocytes have proved to play a significant role. The significance of adult neurogenesis for learning and memory and for treatment of depression is outlined. Moreover, it was observed that neuroplasticity benefits patients suffering from obsessive-compulsive disorder (OCD) who undergo effective, evidence-based treatment. Convincing examples of brain plasticity brings also clinical practice, which often unveils the appearance of hitherto hidden artistic abilities in people who have suffered from brain damage. In addition, the possibilities of altering the brain functions by mental force alone are discussed. Thus, the paper reveals that many “controversial” ideas were confirmed by contemporary studies forcing changes in a traditional view on brain works.
PRAXIS AND LANGUAGE ORGANIZATION IN LEFT-HANDERS
Authors: Króliczak Grzegorz , Piper Brian J. , Potok Weronika , Buchwald Mikołaj , Kleka Paweł , Przybylski Łukasz , Styrkowiec Piotr P.
Published: April 2020

The performance of learned manual gestures (praxis) and the production of speech are thought to depend on related neural processes. If this relationship is not invoked by an unknown, third variable then shifts in their laterality, including dissociations of these two functions, would be unlikely unless the sharing of some neural resources with other functions is advantageous. This could be the case in lefthanders, in whom actions requiring manual precision are controlled by their right hemispheres, and whose representations could attract the control of skilled gesture.

Functional neuroimaging (fMRI) was used to study praxis and language functions. Their lateralization indices were measured in 56 consecutively tested lefthanders (28 females), with the mean age of 23.3±4.9 years (range 18.4 – 47 years), and an Edinburgh Handedness Inventory quotient between –100 and –55.6 (with the mean of –83.8±14.2).

We show that atypical, bilateral organization or right-lateralization of praxis is more common than atypical organization/lateralization of language, observed, respectively, in 23 (41%) vs. 15 (26.8%) of cases. Specifically, we found: (a) seven cases (12.5%) of clear, and an additional three cases (5.4%) of less pronounced dissociations of atypically represented praxis from typically represented language; (b) 13 cases (23.2%) with atypically organized praxis also associated with atypically organized language, and (c) only two cases (3.6%) of rather strongly atypical lateralization of language, yet with quite typical lateralization of praxis.

These outcomes are consistent with an idea that, in some lefthanders, the guidance of skilled manual actions can profit from tighter links with the right hemisphere, whose motor specialization is linked in this particular population to manual precision, but in general to attentional resources, visuo-spatial processing and even bimanual coordination. Because of the presumed links of praxis with productive language, such transfers are often, and unsurprisingly accompanied by the reorganization of the latter. Yet, the very rare cases of reversed language functions, without any pronounced shifts in representations of praxis, indicate that such a pattern of segregation – or inverse dissociation – of these two functions could be maladaptive.
CAGP-CCSMH Annual Scientific Meeting Book Of Abstracts Building Resilience In Seniors’ Mental Health In Canada October 25-26, 2019, Banff Alberta
Authors: Authors Various
Published: April 2020

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Canadian Guidelines on Cannabis Use Disorder Among Older Adults
Authors: Bertram Jonathan R. , Porath Amy , Seitz Dallas , Kalant Harold , Krishnamoorthy Ashok , Smith Andra , Teed Rand
Published: April 2020

BackgroundCannabis Use Disorder (CUD) is an emerging and diverse challenge among older adults.MethodsThe Canadian Coalition for Seniors’ Mental Health, with financial support from Health Canada, has produced evidencebased guidelines on the prevention, identification, assessment, and treatment of this form of substance use disorder.ConclusionsOlder adults may develop CUD in the setting of recreational and even medical use. Clinicians should remain vigilant for the detection of CUD, and they should be aware of strategies for prevention and managing its emergence and consequences The full version of these guidelines can be accessed at www.ccsmh.ca.
Wave Drag Modification in the Presence of Discharges
Authors: Markhotok Anna
Published: April 2020

A phenomenological model of wave drag modification following the thermal energy deposition in a hypersonic flow is presented. While most of the previous research was concentrated on finding optimal gas parameter values and the amount of energy, this work points at closer attention to the effect of the parameter distribution and the geometry of experimental arrangements. The approach discussed here is to fill the gap in the understanding of the complex mechanism of the flow transformation leading to the wave drag reduction. Analytical expressions used in the model identify a number of adjustment parameters that can be used to optimize thermal energy input and thus achieve fundamentally lower drag values than that of conventional approaches.
Group sequential designs applied in psychological research
Authors: Weigl Klemens , Ponocny Ivo
Published: April 2020

Psychological research is confronted with ever-increasing demands to save resources such as time and money while assuring high ethical standards. In medical and pharmaceutical research, group sequential designs have fundamentally changed traditional statistical testing approaches featuring only one analysis at the end of a single-stage study. They enable early stopping at an interim stage, after a group of observations, for efficacy or futility in case of an overwhelmingly large or small effect, respectively. Otherwise, the trial is continued to the next stage. On average over many studies time and money are saved and more ethical trials are facilitated by diminishing the risk of patients' exposure to inferior treatments. We provide an easy-to-use tutorial for psychological research replete with easily understandable figures highlighting the core idea of different group sequential designs, a workflow chart, an empirical real-world data set, and the annotated R code. Finally, we demonstrate the application of early stopping for efficacy.
COUPLING EFFECT ANALYSIS OF TENSION AND REVERSE TORQUE DURING AXIAL TENSILE TEST OF ANCHOR CABLE
Authors: WANG SHUREN , WANG ZELIANG , GONG JIAN , WANG YUHAO , HUANG QINGXIANG
Published: April 2020

In view of lack of the coupling effect analysis of tension and reverse torque of the anchor cable, the self-developed equipment was used to perform a tensile test on the anchor cables with three different diameters (9.5 mm, 12.7 mm, 15.2 mm) under free rotation and without rotation conditions. Then the three-dimension numerical model of the anchor cable was built, the process of the axial tension test was simulated and the computational results were consistent with experimental results. Based on the work and energy principle, a formula for the tensile force is proposed for the decoupling tensile and reverse torque of the anchor cable. Results show that the peak tension and peak torque both increase with the diameter of the anchor cable, and the effect of the locking length on the peak tension and torque is not obvious. The anchor cable will generate reverse torque when it is pulled without rotation, the torque change process is divided into the elastic and plastic phases, the torque in the elastic phase increases linearly with the increase of the tensile force, while the torque in the plastic phase remains stable and the tensile force increases slightly. Under the condition of free rotation, the elastic modulus of the anchor cable will decrease, the percentage of the pulling force used for untwisting of three different diameter cables (9.5 mm, 12.7 mm, 15.2 mm) were 11%, 12%, and 10%, respectively. The conclusions obtained in the study can provide a reference to direct the similar engineering practice.

Keywords: Anchor cable, Tensile test, Tension-torsion coupling, Mechanical properties, Numerical simulation
IDENTIFICATION OF FOOD SAFETY RISK FACTORS BASED ON INTELLIGENCE FLOW AND DEMATEL-ISM
(DECISION MAKING TRIAL AND EVALUATION LABORATORY-INTERPRETIVE STRUCTURAL MODELING)
Authors: ZHANG YU , SONG YINGHUA
Published: April 2020

In recent years, increasing number of countries have focused on potential food safety risk factors with the frequent exposures of food safety incidents, including “bovine spongiform encephalopathy,” “illegal cooking oil,” and “hygiene of take-out.” Food safety risks are frequently carried by multiple subjects in most cases, and intelligence flow among these subjects is easily ignored. To identify food safety risk factors from the perspective of intelligence flow, the internal relationship between intelligence flow and food safety risks was analyzed, and an index system of food safety risk factors was established. Furthermore, a food safety risk recognition model was constructed with the Decision-Making Trial and Evaluation Laboratory and Interpretative Structural Modeling (DEMATEL–ISM). Results demonstrate that poor supervision, activity degree of public opinion information, and personal safety risk awareness are the key factors influencing food safety risks. In addition, unhygienic processing environment and inappropriate processing and eating are the superficial causes of food safety risks or food safety incidents. The conclusions serve as reference to strengthen accurate recognition and notification of food safety risk factors from the perspective of intelligence flow.

Keywords: food safety risk, intelligence flow, DEMATEL–ISM, risk factor
Perspektywy rozwoju innowacyjnych funkcji pomorskich wsi = Perspectives for the development of innovative functions of Pomeranian villages
Authors: Czapiewska Gabriela
Published: April 2020

Contemporary villages are becoming increasingly differentiated, both in the regional and socio-economic sense. Transformation of these areas is an ongoing process, resulting in changing their functions. Growing diversity of agriculture gives way to increasing multi-functionality of rural areas. Along with the progressive development processes in rural areas, significance of various functions – not yet accentuated – is being revealed and amplified. The study presents functional transformation of rural areas on the example of Pomerania region. These areas have enhanced their socio-economic, environmental, cultural and spatial functions. The aim of this study is to define changes taking place in individual functions of rural areas and their mutual relations. Agriculture and forestry play an important role in rural areas, acting as a basis for natural resource management and development of the rural landscape. The article illustrates classifications of village and agriculture functions based on various criteria. Significant role of emerging new functions in the villages of the studied area, often innovative and prospective, influencing further development of Pomeranian rural areas was emphasized. Fundamental condition for the development of the researched villages is to increase their diversity, in particular by enriching the socio-economic functions. Rural areas are currently facing numerous challenges and the driving force for their development lies within activity of their residents.
Partycypacja społeczna w rozwoju lokalnym na przykładzie gmin w Specjalnej Strefie Włączenia województwa zachodniopomorskiego = Social participation in local development on the example of municipalities in the Special Inclusion Zone of Zachodniopomorskie Voivodeship
Authors: Mazurek Damian
Published: April 2020

The importance of society in shaping spatial order is increasingly emphasized in research as well as in the creation of local politics. Social potential and its importance in development is the subject of research of both sociologists and geographers. The article addresses issues related to the relationship between the level of social potential and the degree of involvement of local communities in development. An analysis of ventures indicated by local communities to solve the diagnosed problems was also conducted. Data was used for municipalities indicated as problem areas and qualified for the so-called Special Inclusion Zone of Zachodniopomorskie Voivodeship from revitalization programs. The analysis also used statistical data from the Central Statistical Office to calculate the synthetic indicator of social potential. The results show that in areas with low social potential, residents show more revitalization initiatives, but are limited to infrastructural needs.
A survey on exponential random graph models: an application perspective
Authors: Ghafouri Saeid , Khasteh Seyed Hossein
Published: April 2020

The uncertainty underlying real-world phenomena has attracted attention toward statistical analysis approaches. In this regard, many problems can be modeled as networks. Thus, the statistical analysis of networked problems has received special attention from many researchers in recent years. Exponential Random Graph Models, known as ERGMs, are one of the popular statistical methods for analyzing the graphs of networked data. ERGM is a generative statistical network model whose ultimate goal is to present a subset of networks with particular characteristics as a statistical distribution. In the context of ERGMs, these graph’s characteristics are called statistics or configurations. Most of the time they are the number of repeated subgraphs across the graphs. Some examples include the number of triangles or the number of cycle of an arbitrary length. Also, any other census of the graph, as with the edge density, can be considered as one of the graph’s statistics. In this review paper, after explaining the building blocks and classic methods of ERGMs, we have reviewed their newly presented approaches and research papers. Further, we have conducted a comprehensive study on the applications of ERGMs in many research areas which to the best of our knowledge has not been done before. This review paper can be used as an introduction for scientists from various disciplines whose aim is to use ERGMs in some networked data in their field of expertise.
Living (stained) foraminifera in the Lesser Syrtis (Tunisia): influence of pollution and substratum
Authors: El Kateb Akram , Beccari Valentina , Stainbank Stephanie , Spezzaferri Silvia , Coletti Giovanni
Published: April 2020

Foraminifera are protozoans with biomineralized tests that can be successfully used as a low cost monitoring tool to assess the health status of marine environments. Living benthic foraminiferal assemblages can provide essential information on natural and/or anthropogenic stresses and provide baseline conditions for studies on fossil material. Several studies have highlighted the negative impact of phosphate treatment industries along the Gulf of Gabes (Lesser Syrtis, Tunisia) on the marine environment. However, only a few studies, based on living (stained) benthic foraminifera, are presently available to assess environmental and/or ecological conditions in this Gulf. Thirty-eight surface sediment samples were quantitatively investigated to identify the dominant living benthic foraminiferal species and potential pollution-sensitive and stress-tolerant species. One-hundred and sixty-one species were identified, and grouped into seven clusters representing different environments within the Gulf. These groups represent polluted settings (Cluster A and B), polluted environments characterized by physicochemical variability (Cluster C), seagrass meadows and “pristine” sites (Cluster D and E) and the region subjected to major industrial impact (Cluster F). The final outlier Cluster, identified the foraminifera barren and all shallow coastal stations. A SIMPER analysis helped identify species with clear and fast responses to environmental perturbations (Ammonia tepida,Amphistegina lessonii,Brizalina striatula,Bulimina marginata,Buliminella elegantissima,Eggereloides scaber,Peneroplis perutusus,Rosalina macropora,Rosalina villardeboana,Trochammina inflata). A comparison with the measured geochemical parameters (TOC, phosphorus in the sediments and heavy metal concentrations in the seawater) has shown that the benthic foraminiferal assemblages are mainly linked to phosphorus, TOC, As and Cd pollution. We also provide here the first compilation of the identified living species in the Lesser Syrtis, their synonyms and digital images of important species.
DeepBindPoc: a deep learning method to rank ligand binding pockets using molecular vector representation
Authors: Zhang Haiping , Saravanan Konda Mani , Lin Jinzhi , Liao Linbu , Ng Justin Tze-Yang , Zhou Jiaxiu , Wei Yanjie
Published: April 2020

Accurate identification of ligand-binding pockets in a protein is important for structure-based drug design. In recent years, several deep learning models were developed to learn important physical–chemical and spatial information to predict ligand-binding pockets in a protein. However, ranking the native ligand binding pockets from a pool of predicted pockets is still a hard task for computational molecular biologists using a single web-based tool. Hence, we believe, by using closer to real application data set as training and by providing ligand information, an enhanced model to identify accurate pockets can be obtained. In this article, we propose a new deep learning method called DeepBindPoc for identifying and ranking ligand-binding pockets in proteins. The model is built by using information about the binding pocket and associated ligand. We take advantage of the mol2vec tool to represent both the given ligand and pocket as vectors to construct a densely fully connected layer model. During the training, important features for pocket-ligand binding are automatically extracted and high-level information is preserved appropriately. DeepBindPoc demonstrated a strong complementary advantage for the detection of native-like pockets when combined with traditional popular methods, such as fpocket and P2Rank. The proposed method is extensively tested and validated with standard procedures on multiple datasets, including a dataset with G-protein Coupled receptors. The systematic testing and validation of our method suggest that DeepBindPoc is a valuable tool to rank near-native pockets for theoretically modeled protein with unknown experimental active site but have known ligand. The DeepBindPoc model described in this article is available at GitHub (https://github.com/haiping1010/DeepBindPoc) and the webserver is available at (http://cbblab.siat.ac.cn/DeepBindPoc/index.php).
Genetic editing of the virulence gene of Escherichia coli using the CRISPR system
Authors: Hou Meijia , Sun Simeng , Feng Qizheng , Dong Xiumei , Zhang Ping , Shi Bo , Liu Jiali , Shi Dongfang
Published: April 2020

Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 is an emerging gene-editing technology that is widely used in prokaryotes and eukaryotes. It can realize the specific manipulation of the genome efficiently and accurately. CRISPR/Cas9 coupled λ-Red recombination technology was used to perform genome editing in different genes. For finding an efficient method to edit the virulence genes of enterotoxigenic E. coli (ETEC), the two-plasmid system was used. The coding sequence (CDS) region of the estA, eltI, estB, eltIIc1, and faeG locus were deleted. The coding region of estB was substituted with estA. Gene recombination efficiency ranged from 0 to 77.78% when the length of the homology arm was from 50 to 300 bp. Within this range, the longer the homology arm, the higher the efficiency of genetic recombination. The results showed that this system can target virulence genes located in plasmids and on chromosomes of ETEC strains. A single base mutation was performed by two-step gene fragment replacement. This study lays the foundation for research on virulence factors and genetic engineering of vaccines for ETEC.
ELMO2 association with Gαi2 regulates pancreatic cancer cell chemotaxis and metastasis
Authors: Wang Yecheng , Li Hongyan , Li Fei
Published: April 2020

Background

Pancreatic cancer is a highly lethal disease. Nearly half of the patients have distant metastasis and remain asymptomatic. Emerging evidence suggests that the chemokine, CXCL12, has a role in cancer metastasis. The interaction between CXCL12 and CXCR4 activates heterotrimeric G proteins, which regulates actin polymerization and cancer cell migration. However, the molecular mechanisms underlying pancreatic cancer cell migration are still largely obscure. Here, we addressed the role of ELMO2 in chemotaxis and metastasis of pancreatic cancer cells.

Methods

Pancreatic cancer cell lines PANC-1 and AsPC-1 and siRNA-mediated knockdown of ELMO2 were used to determine the effects of ELMO2 on cancer cell chemotaxis, invasion, migration. Co-immunoprecipitation assays were carried out to identify interacting partners of ELMO2.

Results

ELMO2 knockdown inhibited pancreatic cancer cell chemotaxis, migration, invasion, and F-actin polymerization. Co-immunoprecipitation assays revealed that ELMO2 interacted with Gαi2 and that CXCL12 triggered Gα i2-dependent membrane translocation of ELMO2. Thus, ELMO2 is a potential therapeutic target for pancreatic cancer.
First de novo whole genome sequencing and assembly of the bar-headed goose
Authors: Wang Wen , Wang Fang , Hao Rongkai , Wang Aizhen , Sharshov Kirill , Druzyaka Alexey , Lancuo Zhuoma , Shi Yuetong , Feng Shuo
Published: April 2020

Background

The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese.

Methods

In this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation.

Results

10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau.

Conclusion

We reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.
OFICINA E INTERAÇÃO SOBRE ENERGIAS RENOVÁVEIS E SISTEMAS FOTOVOLTAICOS COM ENFOQUE CTSA: UMA PROPOSTA PARA A FORMAÇÃO DE PROFESSORES NA UNIVERSIDADE DO ESTADO DO PARÁ / CAMPUS XX / WORKSHOP AND INTERACTION ON RENEWABLE ENERGIES AND PHOTOVOLTAIC SYSTEMS WITH STS APPROACH: A PROPOSAL FOR THE TRAINING OF TEACHERS OF THE UNIVERSITY OF THE STATE OF PARÁ / CAMPUS XX
Authors: Leal José Fernando Pereira , Ribeiro Erick Elisson Hosana , Santos Janaina Laura Barboza
Published: April 2020

O avanço tecnológico e o aumento populacional global vêm estimulando a sociedade a explorar cada vez mais novas matrizes energéticas que garantam a sustentabilidade e estejam amparadas por legislações de preservação ambiental. Portanto, há interessantes possibilidades didáticas tanto para o ensino de ciências como para a formação de professores, possibilitando discussões mais significativas e abrangentes. Assim, o objetivo é analisar as contribuições de uma oficina temática sobre energias renováveis para a formação de licenciandos de um curso da Universidade do Estado do Pará, no município de Castanhal, envolvendo a construção e a análise da eficiência energética de corrente elétrica gerada por dois tipos de sistemas fotovoltaicos, placas de diodo emissor de luz e comercial, com enfoque em Ciência, Tecnologia, Sociedade e Ambiente. Destarte, esta abordagem pedagógica possibilitou a compreensão da temática proposta e os benefícios oferecidos ao meio ambiente e sociedade, colaborando para a formação acadêmica e cidadã.
PRODUÇÃO DE VÍDEOS COMO OBJETOS DIGITAIS DE ENSINO E DE APRENDIZAGEM POTENCIALMENTE SIGNIFICATIVOS PARA UM CANAL DO YOUTUBE ORGANIZADO POR ESTUDANTES DO ENSINO SUPERIOR / PRODUCTION OF VIDEOS AS DIGITAL OBJECTS OF TEACHING AND LEARNING POTENTIALLY SIGNIFICANT
Authors: Neuenfeldt Adriano Edo , Schuck Rogério José , Miorando Tânia Micheline
Published: April 2020

Este trabalho é parte de uma pesquisa para fins de doutoramento que iniciou em meados de 2016, tendo como meta a produção de vídeos como Objetos Digitais de Ensino e de Aprendizagem Potencialmente Significativos (ODEAPSs). No presente artigo busca-se analisar e compreender pela análise textual discursiva os impactos a respeito do processo de produção desses objetos para um canal do YouTube e suas contribuições para o Ensino e a Aprendizagem a partir das percepções dos estudantes de graduação. Trata-se de um estudo de caso, que envolveu 32 estudantes que integram os cursos de diversas Engenharias de uma Instituição de Ensino Superior Comunitária do sul do Brasil, vinculados à disciplina de Cálculo III. Resultados preliminares permitem auferir, até o momento, a produção de 22 ODEAPSs apontando para uma aprendizagem significativa estabelecida pela mediação pedagógica que permeia as relações entre estudantes, professor e as tecnologias digitais.
Physico-chemical Properties of Starches from Two Varieties of Sweet Potato and Yam Tubers Available in Nigeria
Authors: Donaldben N. S. , Tanko O. O. , Hussaina T. O.
Published: April 2020

The research sought to investigate the functional properties of starches obtained from four Nigerian root and tubers, yam and sweet potato varieties, in order to facilitate their exploitation as substitute raw material for the local food and pharmaceutical manufacturing industry. The varieties, namely: white yam (Dioscorea rotundata), water yam (Dioscorea alorta), orange flesh sweet potato (Ipomoea batatas) and cream flesh sweet potato (Ipomoea batatas), their respective starches were obtained by wet separation techniques and were analyzed for their pasting properties, physic-chemical properties, starch yield on dry and wet basis, functional, starch purity, amylase and amylo-pectin were undertaken in order to determine their suitability for food and other uses. The peak time, pasting temperature, peak viscosity, holding strength, breakdown, set from peak and set back from through ranged from 7.3 – 8.3 mins, 65.4 – 71.3°C, 511.5 – 1001.2 BU, 860.8 – 871.3 BU, 300.1 – 306.9 BU, 240.8 – 248.1 BU and 400.4 – 510.9 BU respectively. There were significant differences (p<0.05) in the pasting properties. The crude protein, crude fat, crude fibre, ash, moisture and carbohydrate ranged from 1.55 – 1.85%, 0.09 – 0.12%, 0.12 – 0.22%, 1.32 – 2.05%, 10.72 – 11.09% and 85.59 – 86.20% respectively. There were significant differences (p<0.05) in the proximate composition of the starches. The starch yield on dry weight basis, starch weight on fresh weight basis, starch yield from tubers and percentage dry matter ranged from 56.84 – 85.88%, 22.75 – 36.07%, 18.02 – 26.00% and 40.02 – 44.01% respectively. There were significant differences (p<0.05) in the all the parameters. The bulk density, water absorption capacity, oil absorption capacity, gelatinization temperature, starch purity, amylase, amylo-pectin and pH ranged from 0.56 – 0.61g/cm3, 86.8 – 99.4%, 103.2 – 125.4%, 59.78 – 60.42°C, 95.28 – 96.55%, 27.25 – 29.37%, 70.63 – 72.63% and 6.82 – 6.91 respectively. There were significant differences (p<0.05) in all the parameters but no significant difference (p>0.05) in the pH. The starches from yam and sweet potato varieties starches can be exploited for diverse uses based on their different characteristics.
Socio-demographic and Economic Dynamics of Climate Change and Adaptation: A Study on Rural Farmers in Oyo State, Nigeria
Authors: Sedegah Daniella Delali , Ajayi Adesola , Adu-Okoree Benzies
Published: April 2020

The study explored the relationship between key socio-demographic and economic variables on climate change adaptation strategies of rural farmers in Oyo State, Nigeria. Three hundred (300) rural farmers were randomly selected from six (6) farming communities for the study. Multiple regression analysis was utilized to enrich understanding of relationships between socio-demographic variables and climate change. These variables: age, sex and marital status, size of households, religion, educational level, income source and social group belongingness were examined independently against the 16 adaptation strategies. The results showed high significance between some socio-economic variables and the adaptation strategy among farmers. The study revealed that age, gender, religious affiliation and social group belongingness showed significant relationships with coping strategies of the farmers. The study therefore recommends governmental and non-governmental activities directed towards enhancing capacities of agricultural extension services to address climate change susceptibility of rural farmers.
Predictors of Job and Workplace Satisfaction among Community Pharmacists
Authors: Iqbal Muhammad Shahid , Al-Saikhan Fahad I. , Ahmed Nehad J. , Iqbal Muhammad Zahid
Published: April 2020

Aims: This study aimed to assess the current levels of job and workplace satisfaction among community pharmacists (CPs) and to explore the factors that can affect their job and workplace satisfaction.

Methods: A self-administered research tool (questionnaire) was developed based on previously published literature. After its reliability and validity measurements, the questionnaire was distributed to the target population and data was collected. Data were entered into Statistical Package for Social Science (SPSS) ver. 22.0 and analyzed using descriptive statistics, chi-square, and multiple regression analysis. The level of significance (α) was set at 0.05.

Results: CPs reported high satisfaction (76.7%) concerning their jobs. Only 23.3% of them were not satisfied with their current job. Univariate analysis showed that job and workplace satisfaction among CPs was not significantly associated with gender, age, length of service, position and salary. However, the univariate analysis demonstrated a significant difference between practice settings and job and workplace satisfaction with p = 0.013. Among the respondents, those who worked in the chain pharmacies (83.7%) expressed greater job and workplace satisfaction, which is 16% higher than those working in independent pharmacies (67.6%). Therefore, practice setting was shown as the predictor of job and workplace satisfaction among CPs by using multiple regression analysis.

Conclusion: Overall, CPswere relatively satisfied with their current job. Our results had reinforced previous studies that reported that practice settings can affect pharmacists’ job and workplace satisfaction.
The generation of hydroxyl radicals following superoxide production by neutrophil NADPH oxidase
Authors: Bannister J.V. , Bellavite P. , Davoli A. , Thornalley P.J. , Rossi F.
Published: July 2002

Stimulated neutrophils generate superoxide and hydroxyl radicals. A membrane‐bound NADPH oxidase, inactive in the resting state, is responsible for superoxide production. The production of hydroxyl radicals is through a secondary reaction. A Fenton‐catalysed Haber—Weiss reaction is proposed. Transferrin was used as the catalyst in this investigation.
Control of redox properties of cytochrome c by special electrostatic interactions
Authors: Moore Geoffrey R.
Published: July 2002

An assessment is made of the proposal: electrostatic interactions between the ferric ion of oxidised cytochrome c and its haem propionate sidechains assits in determining the value of the redox potential and plays an important role in the redox state conformation change. Differences between the properties of homologous cytochromes are proposed to be due to differences associated with the charge on their haem propionates.
Ferulic acid 5‐hydroxylase: a new cytochrome P‐450‐dependent enzyme from higher plant microsomes involved in lignin synthesis
Authors: Grand Claude
Published: July 2002

Ferulic acid 5‐hydroxylase, involved in the synthesis of sinapic acid (a precursor of lignin monomers), has been characterized for the first time in plants. This enzyme is localized in the microsomal fraction of the poplar stem and was identified as a cytochrome P‐450‐dependent mixed‐function monooxygenase. Comparison of the regulating properties and tissue distribution of ferulic acid 5‐hydroxylase and cinnamic acid 4‐hydroxylase suggests that these hydroxylase activities depend on two distinct cytochrome P‐450 systems. A correlation was established between the monomeric composition of lignins isolated from xylem and sclerenchyma and the tissue distribution of ferulic acid 5‐hydroxylase. The results obtained indicate that this enzyme could be involved, at least partly, in the qualitative control of lignification.