bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-performing loan in fishery sector, Indonesia
Authors: Oktavilia Shanty , Firmansyah  , Sugiyanto FX. , Prayogi Ryan , Aprilian Hidayat Hendy
Published: September 2020

The fisheries sector’s potential is quite large in Indonesia, and during the administration of President Joko Widodo, the demand for fisheries experienced a positive growth trend, which increased 48 percent from 2014 to 2018, from 6,400 thousand tons in 2014 to 9,480 thousand tons in 2018. On the demand side, in addition to domestic demand, the demand for fisheries exports has also increased. Even though there is great potential in output, the absorption of fisheries sector loans is very low, which is only 0.20 percent on average along 2014-2018, and the Non-Performing Loans (NPL) of bank loans in the fisheries sector are quite high. From the data of April 2019, the NPL of the fisheries sector was 6.9 percent of the total loans in the sector. This study aims to analyze the factors that affect the NPL in the fisheries sector in Indonesia by using the error correction model (ECM) on the 2010-2019 monthly data, for long and short-term of variables relationship. The empirical model developed to analyze the NPL value of the fisheries are affected by the interest rates, inflation, and output growth of the fisheries sector. This study finds that in the long run NPL is negatively affected by output growth of fisheries sector, and positively affected by inflation and the interest rate of fisheries sector. The cointegration test supports the long-term relationship of the dependent and independent variables of the model. The results of the short run model analysis indicate the suitability of the sign with the hypothesis and in line with the results on the long-term model. The results of the long and short-term analysis can be a policy consideration for financial authorities regarding the projection of NPL in the future.
Social and economic influences on CO2 emission from capture fisheries in West Java Province
Authors: Hamdiyah Sitti , Supriatna Jatna , Prihanto Yosef , Susetyo Adi Novi , Setiyo Pranowo Widodo
Published: September 2020

Low carbon development has become a trendsetter in this millennial era. The social and economic factors of the community are commonly used variables in assessing linear functions of the level of social welfare. The level of social welfare is then thought to be one of the main drivers of anthropogenic pressure on the environment. We examine the extent to which social and economic aspects of capture fisheries activities influence the dynamics of CO2 emissions generated from capture fisheries activities in all coastal areas in West Java Province during the 2007-2016 period. Based on the results of geographic information system and statistical analysis, we find that the increasing economic factor can reduce the ghg emission while the increasing of social factor on the contrary can increase the ghg emission. The GIS analysis also show that the level of CO2 emissions was found to be lower in districts that had relatively high levels of social index. It is estimated, the higher level of education and social welfare has a real positive correlation with increasing public awareness in conducting fishing activities that are environmentally friendly and carbon friendly.
The effects of exogeneous papain enzyme in the feed on growth and blood profiles of Sangkuriang catfish (Clarias sp.) cultivated in the pond
Authors: Rachmawati Diana , Samidjan Istiyanto , Hutabarat Johannes
Published: September 2020

The objectives of the study were to evaluate the effects of exogeneous papain enzyme supplemented feed on the growth and blood profiles of Sangkuriang catfish (Clarias sp). The intensive culture system of Sangkuriang catfish decreases water quality that hinders fish growth. The cultivation practices also develop diseases that further decreases the production, including through feeding that contain immunostimulant. The fish sample was Sangkuriang catfish with the average weight of 12.84 (±0.69) g per fish. The experiment used papain enzyme supplemented feed with 5 (five) treatments. Those treatments were A (0 g papain per kg feed), B (0.5 g papain per kg feed), C (1 g papain per kg feed), D (1.5 g papain per kg feed), E (2 g papain per kg feed). Parameters observed were diet usage efficiency (EFU), ratio of protein efficiency (PER), relative growth rate (RGR), survival rate (SR), blood profiles and water quality. The results show that papain enzyme supplementation in the feed significantly (P<0.01) affected on EFU, PER, and RGR; however, it did not significantly influence SR and blood profiles of Sangkuriang catfish. The optimal dose of the papain enzyme for EFU, PER and RGR were 1 g per kg feed. The water quality during study had been in feasible condition for Sangkuriang catfish cultivation.
Biodiversity of phytoplankton from polyculture milkfish and white shrimp vanname pond culture waters, Pekalongan region
Authors: Samidjan Istiyanto , Dody Safar , Rachmawati Diana
Published: September 2020

The objectives to study the effect of Biodiversity of Phytoplankton on the productivity in Polyculture Milkfish and White shrimp vanname Pond Culture waters, Kandang Panjang Pekalongan Region, Centre of Java. Methodology The sampling have tried station T1,T2,T3,T4 were in pond culture of polyculture waters to identify a phyto planton in polyculture pond Kandang Panjang waters. The sampling was carryout between Pebruary to Mei 2018. The result study showed that the value of the diversity indices in T1 treatment obtained the value of diversity indices (H’ = 1.093), T2 obtained diversity values (H’ = 1,072), T3 found (H’ = 1,804) and T4 showed (H’ = 1,907). The similliarity indexs are T1 (values, E = 0.765), values (E = 0.606), T3 ((E = 0.785) and T4 (E = 0.895).The dominance indices values phyto plankton showed T1 (value D = 0.725), T2 (D = 0.606,), T3(D = 00.595) and T4 (D = 00.578).The diversity indices showed higher vlues at T4 showed variety of diversity indices (H’ = 1,907).sampling site as compared to other three (T1,T2, and T3).During experiment showed the water quality of pond culture polyculture milkfish and white shrimp vanname was in viable condition.
Diversity of brittle star and sea urchin (Echinoderm: Ophiuroidea, Echinoidea) of Krakal and Watu Kodok beach, Gunung Kidul, Yogyakarta
Authors: Tarigan R S , Hartati R , Widowati I
Published: September 2020

Ophiuroidea and echinoidea are usually lived associated with coral reef and seaweed. Krakal and Watu Kodok Beach of Gunung Kidul Regency have characteristics of karst rocks, rubble and fast-current sea. They have large intertidal zone that allows ophiuroid and echinoid trapped among the basin during low tide. The research was aimed to identify and determine the diversity of Brittle Star and Sea Urchin in Krakal and Watu Kodok Beach. Survey was conducted on November-December 2018 at Krakal and Watu Kodok Beach. The samples were taken using quadrant transect method during low tide. The result of present work showed a total of 391 individuals belonging to Ophiocomidae Ophiuroid (2 species) and 279 individuals of 4 species echinoids belong to 2 families (Echinometridae and Diadematidae) lived in both beach. The highest abundance of Ophiocoma scolopendrina was found in Krakal beach (33.4 ind.m−2) while Echinometra oblonga was biggest in Watu Kodok beach (14.4 ind.m−2). In both location the diversity was low with medium to high similarity.
Co-existence between Scylla serrata and Scylla transquebarica in the lagoon of Segara Anakan, Cilacap, Indonesia
Authors: Redjeki Sri , Hartati Retno , Azizah Tri Nuraeni Ria , Riniatsih Ita , Endrawati Hadi , Widianingsih Widianingsih
Published: September 2020

In the Laguna Segara Anakan, there are two species of mangrove crab such as: Scylla serrate and Scylla transquebarica. Both of these species are always in the same water conditions in the Segara Anakan Lagoon, Cilacap. The purpose of this study was to examine the co-existence both species populations (S. serrate and S. transquebarica) in the Segara Anakan Lagoon. Sampling were carried out on April and June 2019 in three locations namely Klaces, Panikel and Sapuregel. Traps were used to collect crab samples. According to the research result that in the Klaces, the number of S. serrata (n=17) is greater than the number of S. transquebarica (n=4). Whereas in Panikel and Sapuregel, the number of S. transquebarica was more than the number of S. serrata. The presence of S. serrata and S. transquebarica in mangrove habitat is always side by side.
Retraction: Study of the principal component analysis in air quality databases (IOP Conf. Series: Materials Science and Engineering
872 012030)
Authors: Silva Jesús , Londoño Luz Adriana , Varela Noel , Pineda Lezama Omar Bonerge
Published: September 2020

Published 15 September 2020

This article, and others within this volume, has been retracted by IOP Publishing following clear evidence of plagiarism and citation manipulation.

This work was originally published in Spanish (1) and has been translated and published without permission or acknowledgement to the original authors. IOP Publishing Limited has discovered other papers within this volume that have been subjected to the same treatment. This is scientific misconduct.

Misconduct investigations are ongoing at the author’s institutions. IOP Publishing Limited will update this notice if required once those investigations have concluded.

IOP Publishing Limited request any citations to this article be redirected to the original work (1).

Anyone with any information regarding these papers is requested to contact conferenceseries@ioppublishing.org.
Retraction: Thermographic imaging for use in artificial intelligence and vision algorithms (IOP Conf. Series: Materials Science and Engineering
872 012035)
Authors: Silva Jesús , Echeverría Ana María , Varela Noel , Pineda Lezama Omar Bonerge
Published: September 2020

Published 15 September 2020

This article, and others within this volume, has been retracted by IOP Publishing following clear evidence of plagiarism and citation manipulation.

This work was originally published in Spanish (1) and has been translated and published without permission or acknowledgement to the original authors. IOP Publishing Limited has discovered other papers within this volume that have been subjected to the same treatment. This is scientific misconduct.

Misconduct investigations are ongoing at the author’s institutions. IOP Publishing Limited will update this notice if required once those investigations have concluded.

IOP Publishing Limited request any citations to this article be redirected to the original work (1).

Anyone with any information regarding these papers is requested to contact conferenceseries@ioppublishing.org.
Development of a parametric model for calculating cutting forces for external cylindrical turning of steel 20CrMNTi
Authors: Balabanov I P , Balabanova O N , Gilman V N
Published: September 2020

The paper presents a mathematical model for calculating the cutting force when processing 20crmnti steel with the Sandvik CNMG 120408 16P25T tool. The stand based on the 16d25 machine is presented. It allows measuring the actual values of the spindle speed, longitudinal feed, cutting depth, and cutting force. The results are transmitted to the computer via the LTR-EU-8 workstation with galvanically isolated LTE modules and a synchronization interface. According to the test results, the obtained theoretical model has a deviation from the actual measurements of no more than 0.12%. It is shown that the calculation results provided by the leading tool manufacturers are expected to be overstated. The difference in cutting forces can be more than 1.5 times.
Hardening of the working bodies of agricultural machines by electric spark and vibratory arc processing
Authors: Bayniyazova A T , Abzhaev M M , Sharifullin S N
Published: September 2020

The paper presents the results of studies of some physical and mechanical properties of metal samples made of 65G steel, hardened by electric spark and vibratory arc methods. Research is related to solving the problems of increasing the working resource of the working bodies of agricultural machines. The studied elemental composition, phase composition, and microstructure of the surface of the samples.
Features of robotization of agricultural processes
Authors: Kashapov N F , Nafikov M M , Nigmatzyanov A R , Sayfutdinov R F , Mingazov R A
Published: September 2020

The agro-industrial complex, as an industry, currently faces the problems of climate change, limited water resources, soil degradation and biodiversity conservation. It is necessary to significantly increase the production of agricultural products, while it should follow the trend of sustainable development. Resources must be used more efficiently. Intelligent solutions are needed to address conflicts of interest and meet the need for healthy and nutrient-rich foods and feeds. Therefore, it is necessary to assign an increasing role to the digitalization and robotization of agriculture in achieving these goals.
Estimation of precision parameters of milling machines
Authors: Khusainov R M , Ziangirova E R , Davletshina G K
Published: September 2020

The paper considers a mathematical model that allows to evaluate the performance parameters of milling machines during the functioning of the working bodies. An example of the task of selecting equipment is given. The mathematical model is based on the mathematical apparatus of coordinate transformation. Using the proposed methodology, it is possible to solve the direct problem - to evaluate the capabilities of an existing machine for manufacturing parts with a given accuracy, or the inverse problem - to choose a machine for manufacturing parts with a given accuracy.
Influence of nonlinear viscosity of waxy crude oils on the thermohydraulic characterization of their flow in helical channels: theory and experiment
Authors: Khusnutdinova E M , Konakhina I A
Published: September 2020

The authors looked into a matter of how the nonlinear viscosity of waxy crude oils has an effect on the thermohydraulic characterization of their flow in helical symmetry channels. The consideration was given to the energy equation in a helical coordinate system followed by theoretical and experimental values.
Improving the performance of cylinder liners by creating thin-layer coatings in the interface
Authors: Kulakov A T , Baryshnikova E P , Snarsky S V , Gafiatullin A A , Nazarov F L , Malachowski A F
Published: September 2020

The paper presents the technological process of brass plating of the cylinder bore. Application of the coating allows to increase the operational reliability of parts of the cylinder-piston group and the technical life of the entire engine
The use of mathematical models to improve the effective functioning of enterprises
Authors: Kuzmina I A
Published: September 2020

In the process of ensuring the innovative development of machine-building enterprises within the framework of the concept, it is necessary to use mathematical models that correspond to machine vision technologies, robotic technology, automated and intelligent production and control systems at enterprises. Mathematical models of robotic technology allow us to create new equipment, improve technological processes and production organization systems.
Development of cast dispersion-hardening ferrite-carbide steel
Authors: Mukhametzyanova G F , Kolesnikov M S , Astashchenko V I , Mukha-metzyanov I R
Published: September 2020

A method is proposed for producing cast dispersion-hardening ferrite-carbide steel for manufacture of cast molds of hot deformation, molds for die casting under pressure and forging dies for solid-liquid forming, providing production of steel with fine-grain structure and uniform distribution of carbides in a ferrite matrix without formation of casting cracks. In the process of steel production waste carbide ceramic-metal inserts of a cutting tool from alloys are used, they are of the following types: T5K6, T15K6, T5K10, T21K8, TT7K12, TT8K6, TT10K9, TT20K9 and T30K4 containing titanium carbides (TiC), tantalum carbides (TaC), tungsten carbides (WC).
Evaluation of the wear resistance and resource hardened by electrospark machining of the cutting surfaces of the fingers of the headers of combine harvesters
Authors: Velichko S A , Sharifullin S N , Kuznetsov I S , Kolomeichenko A V , Solovyev R Y , Kravchenko I N , Adigamov N R
Published: September 2020

The article presents the technology of hardening the fingers of the reapers of combine harvesters by electrospark processing. To strengthen the cutting surfaces of the fingers, it is recommended to use an amorphous alloy grade 84KXSR. The operational tests presented in the work showed that wear and dulling of both serial products and experimental parts with electric spark coatings is characterized by two stages: running-in and natural wear. The running-in occurs during the running time of the fingers in 1 ha. The results of operational tests showed that the application of a wear-resistant electrospark coating of amorphous alloy grade 84KXSR with a thickness of 30 μm and a track width of 2 mm on the cutting surfaces of the fingers of the headers of grain harvesters makes it possible to increase the resource from 1.4 to 2 times.
Quantum implementation of an artificial feed-forward neural network
Authors: Tacchino Francesco , Barkoutsos Panagiotis , Macchiavello Chiara , Tavernelli Ivano , Gerace Dario , Bajoni Daniele
Published: September 2020

Artificial intelligence algorithms largely build on multi-layered neural networks. Coping with their increasing complexity and memory requirements calls for a paradigmatic change in the way these powerful algorithms are run. Quantum computing promises to solve certain tasks much more efficiently than any classical computing machine, and actual quantum processors are now becoming available through cloud access to perform experiments and testing also outside of research labs. Here we show in practice an experimental realization of an artificial feed-forward neural network implemented on a state-of-art superconducting quantum processor using up to 7 active qubits. The network is made of quantum artificial neurons, which individually display a potential advantage in storage capacity with respect to their classical counterpart, and it is able to carry out an elementary classification task which would be impossible to achieve with a single node. We demonstrate that this network can be equivalently operated either via classical control or in a completely coherent fashion, thus opening the way to hybrid as well as fully quantum solutions for artificial intelligence to be run on near-term intermediate-scale quantum hardware.
Shaping of the flame geometry by non-conventional cold plasma arrangements
Authors: Bardos L , Baránková H
Published: September 2020

Experimental examination of possibility to affect the shapes of flames under combustion of the liquified petroleum gas (LPG) were performed by several non-conventional cold atmospheric plasma arrangements. The lateral fused hollow cathode, the microwave surface wave plasma jet and the combination of these systems confirmed possibility of an efficient control of the flame shapes, increasing stability of flames and broadening of their front parts.
Advances in mechanical characterization of 1D and 2D nanomaterials: progress and prospects
Authors: Pantano Maria F , Kuljanishvili Irma
Published: September 2020

Last several decades have sparked a tremendous interest in mechanical properties of low dimensional systems specifically 1D and 2D nanomaterials, in large, due to their remarkable behavior and potential to possess unique and customizable physical properties, which have encouraged the fabrication of new structures to be tuned and utilized for targeted applications. In this critical review we discuss examples that represent evolution of the mechanical characterization techniques developed for 1D and 2D nanomaterials, with special emphasis on specimen fabrication and manipulation, and the different strategies, tools and metrologies, employed for precise positioning and accurate measurements of materials’ strength, elastic modulus, fracture toughness as well as analysis of failure modes. We focus separately on techniques for the mechanical characterization of 1D and 2D nanomaterials and categorize those methods into top-down and bottom-up approaches. Finally, we discuss advantages and some drawbacks in most common methodologies used for 1D and 2D specimen testing and outline future possibilities and potential paths that could boost the development of more universal approaches for technologically viable solutions which would allow for more streamlined and standardized mechanical testing protocols to be developed and implemented.
Tuning the length/width aspect ratio of epitaxial unidirectional silicide nanowires on Si(110)-16 × 2 surfaces
Authors: Mahato J C , Das Debolina , Das P , Chini T K , Dev B N
Published: September 2020

The reactive deposition epitaxy growth of self-organized cobalt silicide nanowires (NWs) on clean Si(110) surfaces has been investigated by in situ scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) as well as by scanning electron microscopy (SEM). Half a monolayer of cobalt was deposited on the Si(110) surfaces at ∼600 °C substrate temperature. Following cobalt deposition, the substrates have been annealed for different durations. Cobalt forms aligned cobalt disilicide nanowires upon reaction with the silicon substrate, following the twofold substrate symmetry. With increasing duration of annealing, the NWs have been found to grow with larger aspect ratio (length/width), eventually producing narrower NWs. These self-organized unidirectional NWs of sub-hundred nanometer width and ∼4–7 nm height produce a Schottky barrier with the silicon substrate and are expected to find applications in nanoelectronic devices.
Spinoriality of orthogonal representations of reductive groups
Authors: Joshi Rohit , Spallone Steven
Published: September 2020

Let

G
G

be a connected reductive group over a field

F
F

of characteristic

0
0

, and

φ
:
G
→
SO
⁡
(
V
)

\varphi : G \to \operatorname {SO}(V)

an orthogonal representation over

F
F

. We give criteria to determine when

φ
\varphi

lifts to the double cover

Spin
⁡
(
V
)

\operatorname {Spin}(V)

.
Categorical joins
Authors: Kuznetsov Alexander , Perry Alexander
Published: September 2020

We introduce the notion of a categorical join, which can be thought of as a categorification of the classical join of two projective varieties. This notion is in the spirit of homological projective duality, which categorifies classical projective duality. Our main theorem says that the homological projective dual category of the categorical join is naturally equivalent to the categorical join of the homological projective dual categories. This categorifies the classical version of this assertion and has many applications, including a nonlinear version of the main theorem of homological projective duality.
Swan: a library for the analysis and visualization of long-read transcriptomes
Authors: Reese Fairlie , Mortazavi Ali
Published: September 2020

Motivation

Long-read RNA-sequencing technologies such as PacBio and Oxford Nanopore have discovered an explosion of new transcript isoforms that are difficult to visually analyze using currently available tools. We introduce the Swan Python library, which is designed to analyze and visualize transcript models.

Results

Swan finds 4909 differentially expressed transcripts between cell lines HepG2 and HFFc6, including 279 that are differentially expressed even though the parent gene is not. Additionally, Swan discovers 285 reproducible exon skipping and 47 intron retention events not recorded in the GENCODE v29 annotation.

Availability and implementation

The Swan library for Python 3 is available on PyPi at https://pypi.org/project/swan-vis/ and on GitHub at https://github.com/mortazavilab/swan_vis.
Geometricus represents protein structures as shape-mers derived from moment invariants
Authors: Durairaj Janani , Akdel Mehmet , de Ridder Dick , van Dijk Aalt D J
Published: September 2020

Motivation

As the number of experimentally solved protein structures rises, it becomes increasingly appealing to use structural information for predictive tasks involving proteins. Due to the large variation in protein sizes, folds and topologies, an attractive approach is to embed protein structures into fixed-length vectors, which can be used in machine learning algorithms aimed at predicting and understanding functional and physical properties. Many existing embedding approaches are alignment based, which is both time-consuming and ineffective for distantly related proteins. On the other hand, library- or model-based approaches depend on a small library of fragments or require the use of a trained model, both of which may not generalize well.

Results

We present Geometricus, a novel and universally applicable approach to embedding proteins in a fixed-dimensional space. The approach is fast, accurate, and interpretable. Geometricus uses a set of 3D moment invariants to discretize fragments of protein structures into shape-mers, which are then counted to describe the full structure as a vector of counts. We demonstrate the applicability of this approach in various tasks, ranging from fast structure similarity search, unsupervised clustering and structure classification across proteins from different superfamilies as well as within the same family.

Availability and implementation

Python code available at https://git.wur.nl/durai001/geometricus.
An assumption-free exact test for fixed-design linear models with exchangeable errors
Authors: Lei Lihua , Bickel Peter J
Published: September 2020

We propose the cyclic permutation test to test general linear hypotheses for linear models. The test is nonrandomized and valid in finite samples with exact Type I error $\alpha$ for an arbitrary fixed design matrix and arbitrary exchangeable errors, whenever $1 / \alpha$ is an integer and $n / p \geqslant 1 / \alpha - 1$, where $n$ is the sample size and $p$ is the number of parameters. The test involves applying the marginal rank test to $1 / \alpha$ linear statistics of the outcome vector, where the coefficient vectors are determined by solving a linear system such that the joint distribution of the linear statistics is invariant with respect to a nonstandard cyclic permutation group under the null hypothesis. The power can be further enhanced by solving a secondary nonlinear travelling salesman problem, for which the genetic algorithm can find a reasonably good solution. Extensive simulation studies show that the cyclic permutation test has comparable power to existing tests. When testing for a single contrast of coefficients, an exact confidence interval can be obtained by inverting the test.
Assessing cure status prediction from survival data using receiver operating characteristic curves
Authors: Amico M , Van Keilegom I , Han B
Published: September 2020

Survival analysis relies on the hypothesis that, if the follow-up is long enough, the event of interest will eventually be observed for all observations. This assumption, however, is often not realistic. The survival data then contain a cure fraction. A common approach to modelling and analysing this type of data consists in using cure models. Two types of information can therefore be obtained: the survival at a given time and the cure status, both possibly modelled as a function of the covariates. The cure status is often of interest to medical practitioners, and one is usually interested in predicting it based on markers. Receiver operating characteristic, Roc, curves are one way to evaluate the predicted performance; however, the classical Roc curve method is not appropriate since the cure status is partially unobserved due to the presence of censoring in survival data. We propose a Roc curve estimator that aims to evaluate the cured/noncured status classification performance from cure survival data. This estimator, which handles the presence of censoring, decomposes sensitivity and specificity by means of the definition of conditional probability, and estimates these two quantities by means of weighted empirical distribution functions. The mixture cure model is used to calculate the weights. Based on simulations, we demonstrate good performance of the proposed method, and compare it with the classical Roc curve nonparametric estimator that would be obtained if the cure status was fully observed. We also compare our proposed method with the Roc curves of Heagerty et al. (2000) for classical survival analysis. Finally, we illustrate the methodology on a breast cancer dataset.
Effects of dopamine on reinforcement learning in Parkinson’s disease depend on motor phenotype
Authors: van Nuland Annelies J , Helmich Rick C , Dirkx Michiel F , Zach Heidemarie , Toni Ivan , Cools Roshan , den Ouden Hanneke E M
Published: September 2020

Parkinson’s disease is clinically defined by bradykinesia, along with rigidity and tremor. However, the severity of these motor signs is greatly variable between individuals, particularly the presence or absence of tremor. This variability in tremor relates to variation in cognitive/motivational impairment, as well as the spatial distribution of neurodegeneration in the midbrain and dopamine depletion in the striatum. Here we ask whether interindividual heterogeneity in tremor symptoms could account for the puzzlingly large variability in the effects of dopaminergic medication on reinforcement learning, a fundamental cognitive function known to rely on dopamine. Given that tremor-dominant and non-tremor Parkinson’s disease patients have different dopaminergic phenotypes, we hypothesized that effects of dopaminergic medication on reinforcement learning differ between tremor-dominant and non-tremor patients. Forty-three tremor-dominant and 20 non-tremor patients with Parkinson’s disease were recruited to be tested both OFF and ON dopaminergic medication (200/50 mg levodopa-benserazide), while 22 age-matched control subjects were recruited to be tested twice OFF medication. Participants performed a reinforcement learning task designed to dissociate effects on learning rate from effects on motivational choice (i.e. the tendency to ‘Go/NoGo’ in the face of reward/threat of punishment). In non-tremor patients, dopaminergic medication improved reward-based choice, replicating previous studies. In contrast, in tremor-dominant patients, dopaminergic medication improved learning from punishment. Formal modelling showed divergent computational effects of dopaminergic medication as a function of Parkinson’s disease motor phenotype, with a modulation of motivational choice bias and learning rate in non-tremor and tremor patients, respectively. This finding establishes a novel cognitive/motivational difference between tremor and non-tremor Parkinson’s disease patients, and highlights the importance of considering motor phenotype in future work.
Warp Speed for Coronavirus Disease 2019 (COVID-19) Vaccines: Why Are Children Stuck in Neutral?
Authors: Anderson Evan J , Campbell James D , Creech C Buddy , Frenck Robert , Kamidani Satoshi , Munoz Flor M , Nachman Sharon , Spearman Paul
Published: September 2020

While adult clinical trials of coronavirus disease 2019 (COVID-19) vaccines have moved quickly into phase 3 clinical trials, clinical trials have not started in children in the United States. The direct COVID-19 impact upon children is greater than that observed for a number of other pathogens for which we now have effective pediatric vaccines. Additionally, the role of children in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission has clearly been underappreciated. Carefully conducted phase 2 clinical trials can adequately address potential COVID-19 vaccine safety concerns. Delaying phase 2 vaccine clinical trials in children will delay our recovery from COVID-19 and unnecessarily prolong its impact upon children’s education, health, and emotional well-being, and equitable access to opportunities for development and social success. Given the potential direct and indirect benefits of pediatric vaccination, implementation of phase 2 clinical trials for COVID-19 vaccines should begin now.
WGVD: an integrated web-database for wheat genome variation and selective signatures
Authors: Wang Jierong , Fu Weiwei , Wang Rui , Hu Dexiang , Cheng Hong , Zhao Jing , Jiang Yu , Kang Zhensheng
Published: September 2020

Bread wheat is one of the most important crops worldwide. With the release of the complete wheat reference genome and the development of next-generation sequencing technology, a mass of genomic data from bread wheat and its progenitors has been yield and has provided genomic resources for wheat genetics research. To conveniently and effectively access and use these data, we established Wheat Genome Variation Database, an integrated web-database including genomic variations from whole-genome resequencing and exome-capture data for bread wheat and its progenitors, as well as selective signatures during the process of wheat domestication and improvement. In this version, WGVD contains 7 346 814 single nucleotide polymorphisms (SNPs) and 1 044 400 indels focusing on genic regions and upstream or downstream regions. We provide allele frequency distribution patterns of these variations for 5 ploidy wheat groups or 17 worldwide bread wheat groups, the annotation of the variant types and the genotypes of all individuals for 2 versions of bread wheat reference genome (IWGSC RefSeq v1.0 and IWGSC RefSeq v2.0). Selective footprints for Aegilops tauschii, wild emmer, domesticated emmer, bread wheat landrace and bread wheat variety are evaluated with two statistical tests (FST and Pi) based on SNPs from whole-genome resequencing data. In addition, we provide the Genome Browser to visualize the genomic variations, the selective footprints, the genotype patterns and the read coverage depth, and the alignment tool Blast to search the homologous regions between sequences. All of these features of WGVD will promote wheat functional studies and wheat breeding.

Database URL

http://animal.nwsuaf.edu.cn/code/index.php/Wheat
A climate-sensitive transition matrix growth model for uneven-aged mixed-species oak forests in North China
Authors: Du Xue , Chen Xinyun , Zeng Weisheng , Meng Jinghui
Published: September 2020

Oak-dominated forests, economically and ecologically valuable ecosystems, are widely distributed in China. These oak-dominated forests are now generally degraded coppice forests, and are of relatively low quality. Climate change has been shown to affect forest growth, tree mortality, and recruitment, but available forest growth models are lacking to study climate effects. In this study, a climate-sensitive, transition-matrix growth model (CM) was developed for uneven-aged, mixed-species oak forests using data collected from 253 sample plots from the 8th (2010) and 9th (2015) Chinese National Forest Inventory in Shanxi Province, China. To investigate robustness of the model, we also produced a variable transition model that did not consider climate change (NCM), and fixed parameter transition matrix model (FM), using the same data. Short-term and long-term predictive performance of CM, NCM, and FM were compared. Results indicated that for short-term prediction (5 years), there was almost no significant difference among the three predictive models, though CM exhibited slightly better performance. In contrast, for long-term prediction (100 years), CM, under the three representative concentration pathways (RCPs), i.e. RCP2.6, RCP4.5 and RCP8.5, indicated rather different dynamics that were more reliable because climate factors were considered which could significantly influence forest dynamics, especially in long-term prediction intervals. The CM model provides a framework for the management of mixed-species oak forests in the context of climate change.
Engaging Māori with qualitative healthcare research using an animated comic
Authors: Kearns Ciléin , Baggott Christina , Harwood Matire , Reid Alice , Fingleton James , Levack William , Beasley Richard
Published: September 2020

This article reports an effective strategy for recruiting patients with asthma to a qualitative study using an animated comic advertised on social media. An ad spend of NZ$432 on Facebook resulted in 101 study enquiries, and 27 participants taking part in the focus groups, of which 16 (56%) were Māori, the Indigenous Peoples of New Zealand. Representation of Māori amongst participants was over five times higher than their proportion in the local population (9.7%), resulting in data fulfilling the principle of equal explanatory power, an approach to research which can help advance Māori health development and address inequity. The success of this campaign is of particular interest for health researchers in New Zealand where Māori continue to be disproportionately affected by poorer health outcomes compared with non-Māori, particularly those with asthma. Approaches that better engage and support participation of under-represented communities in clinical research are of wider global interest. We reflect on the recruitment strategy and outcomes within a Kaupapa Māori framework, explore how this can be applied more widely in healthcare, and suggest direction for future study and implementation.

Lay summary

We designed an animated comic to advertise a study for patients with asthma. This was shared locally with a Facebook ad. The approach was highly engaging with the public, and resulted in rapid recruitment. Interestingly, participation of Māori (the Indigenous People of New Zealand) was over five times higher than their proportion in the local population. Māori have poorer health outcomes and increased barriers to healthcare access compared with non-Māori, particularly those with asthma. Approaches which can engage and support under-represented communities to participate in clinical research are of wider global interest. In this article, we reflect on the recruitment strategy and outcomes, and suggest direction for future study and implementation.
The Evolutionary Continuum of Functional Homodonty to Heterodonty in the Dentition of Halichoeres Wrasses
Authors: Cohen Karly E , Weller Hannah I , Westneat Mark W , Summers Adam P
Published: September 2020

Synopsis

Vertebrate dentitions are often collapsed into a few discrete categories, obscuring both potentially important functional differences between them and insight into their evolution. The terms homodonty and heterodonty typically conflate tooth morphology with tooth function, and require context-dependent subcategories to take on any specific meaning. Qualifiers like incipient, transient, or phylogenetic homodonty attempt to provide a more rigorous definition but instead highlight the difficulties in categorizing dentitions. To address these issues, we recently proposed a method for quantifying the function of dental batteries based on the estimated stress of each tooth (inferred using surface area) standardized for jaw out-lever (inferred using tooth position). This method reveals a homodonty–heterodonty functional continuum where small and large teeth work together to transmit forces to a prey item. Morphological homodonty or heterodonty refers to morphology, whereas functional homodonty or heterodonty refers to transmission of stress. In this study, we use Halichoeres wrasses to explore how a functional continuum can be used in phylogenetic analyses by generating two continuous metrics from the functional homodonty–heterodonty continuum. Here we show that functionally heterodont teeth have evolved at least 3 times in Halichoeres wrasses. There are more functionally heterodont teeth on upper jaws than on lower jaws, but functionally heterodont teeth on the lower jaws bear significantly more stress. These nuances, which have functional consequences, would be missed by binning entire dentitions into discrete categories. This analysis points out areas worth taking a closer look at from a mechanical and developmental point of view with respect to the distribution and type of heterodonty seen in different jaws and different areas of jaws. These data, on a small group of wrasses, suggest continuous dental variables can be a rich source of insight into the evolution of fish feeding mechanisms across a wider variety of species.
Stock dynamics and predator–prey effects of Atlantic bonito and bluefish as top predators in the Black Sea
Authors: Daskalov Georgi M , Demirel Nazli , Ulman Aylin , Georgieva Yoana , Zengin Mustafa
Published: September 2020

This study uses surplus production model-based methods to assess data-poor stocks and estimate key reference points for Atlantic bonito (Sarda sarda) and bluefish (Pomatomus saltatrix) in the Black Sea. Our results demonstrate that the catch maximum sustainable yield (CMSY) method, using catch data only, yields similar results to the more accurate Bayesian Schaefer model (BSM) method, fitted with commercial catch-per-unit-of-effort data, and therefore is suitable in assessing data-poor stocks. We explore the ecological impacts of the two stocks on other commercial species and compare impacts of predation and fishing. Prior to 1995, the consumption of bonito and bluefish on anchovy, horse mackerel, and sprat exceeded the removal of those prey species by the fisheries. Later on, the trends reversed, with catches of prey species becoming more than three times higher than their predation by bonito and bluefish. Horse mackerel, the main prey of bluefish, has declined to critical levels since 1995, which is likely contributing to the general decline in bluefish, along with overfishing. Heavy fishing of bonito and bluefish has caused their current depleted states and combined with their significant impact on prey fish contributed to the ecosystem regime shift in the Black Sea. Due to the present steady positioning of low stock regimes, the recovery of the two stocks need decisive and possibly prolonged rebuilding measures, including a reduction in fishing pressure, efficient control of under-sized catch, and ensuring sufficient prey biomass availability.
Rose vs. Rho: a comparison of two approaches to address retrospective patterns in stock assessments
Authors: Legault Christopher M
Published: September 2020

Two approaches to address retrospective patterns in stock assessments are compared. The Rose approach is an ensemble of models that all remove the retrospective pattern through changes in data, parameter values, or model assumptions. It is time intensive and can result in a wide range of historical abundance trends. The Rho approach modifies the terminal year estimates of a single model that exhibits a retrospective pattern. It is fast and easy to apply but results in a discontinuous time series. Neither approach identifies the source of the retrospective pattern. The pros and cons of these two approaches are compared in terms of catch advice and stock status using four examples with varying strength and direction of retrospective patterns. The choice of which approach to use could be based on time and expertise available to conduct and maintain an assessment, with Rose preferred if a lot of both are available while Rho preferred otherwise. If the Rho approach is used, managers should consider adjusting their control rule or risk buffer to account for the difference between Rose and Rho results shown here.
Translational and Sliding Stability for Two-Dimensional Minimal Cones in Euclidean Spaces
Authors: Liang Xiangyu
Published: September 2020

In this article, we prove the translational stability for all two-dimensional Almgren minimal cones in ${\mathbb{R}}^n$ and the Almgren (resp. topological) sliding stability for the two-dimensional Almgren (resp. topological) minimal cones in ${\mathbb{R}}^3$. As proved in [ 19], when several two-dimensional Almgren (resp. topological) minimal cones are translational, Almgren (resp. topological) sliding stable, and Almgren (resp. topological) unique, their almost orthogonal union stays minimal. As a consequence, the results of this article, together with the uniqueness properties proved in [ 14], permit us to use all two-dimensional minimal cones in ${\mathbb{R}}^3$ to generate new families of minimal cones by taking their almost orthogonal unions.
The emerging role of clinical informatics fellows in service learning during the COVID-19 pandemic
Authors: Subash Meera , Sakumoto Matthew , Bass Jeremy , Hong Peter , Muniyappa Anoop , Pierce Logan , Purmal Colin , Ramaswamy Priya , Sono Reiri , Uptegraft Colby , Feinstein David , Khanna Raman
Published: September 2020

Objective

The study sought to describe the contributions of clinical informatics (CI) fellows to their institutions’ coronavirus disease 2019 (COVID-19) response.

Materials and Methods

We designed a survey to capture key domains of health informatics and perceptions regarding fellows’ application of their CI skills. We also conducted detailed interviews with select fellows and described their specific projects in a brief case series.

Results

Forty-one of the 99 CI fellows responded to our survey. Seventy-five percent agreed that they were “able to apply clinical informatics training and interest to the COVID-19 response.” The most common project types were telemedicine (63%), reporting and analytics (49%), and electronic health record builds and governance (32%). Telehealth projects included training providers on existing telehealth tools, building entirely new virtual clinics for video triage of COVID-19 patients, and pioneering workflows and implementation of brand-new emergency department and inpatient video visit types. Analytics projects included reports and dashboards for institutional leadership, as well as developing digital contact tracing tools. For electronic health record builds, fellows directly contributed to note templates with embedded screening and testing guidance, adding COVID-19 tests to order sets, and validating clinical triage workflows.

Discussion

Fellows were engaged in projects that span the breadth of the CI specialty and were able to make system-wide contributions in line with their educational milestones.

Conclusions

CI fellows contributed meaningfully and rapidly to their institutions’ response to the COVID-19 pandemic.