bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of the current positions of pea crop in the Russian market
Authors: Polukhin A A , Panarina V I
Published: March 2021

The paper considers the current situation in the Russian Federation of such a crop as peas. Data on the area of crop cultivation is presented not only in the world, but also in the context of Federal districts and regions. In the world, the main producers of peas are countries such as Canada, Russia, China and India. In the Russian Federation, the main areas under crop are located in the Volga, Siberian, Southern and Central Federal districts. They are also leaders in the gross harvest of pea grains. It also shows data on the yield of peas sown in the leading regions of Russia for several years, which allows assessing more accurately the value of this indicator. So the highest yield of peas is obtained in the Oryol and Kursk regions, as well as in the Krasnodar territory. The dynamics of inclusion of pea breeds in the State register of breeding achievements allowed for use is analyzed. As before, national breeds prevail over foreign ones in terms of the total number in the register, but producers prefer Western European varieties to a greater extent. Due to its self-sufficiency in peas, Russia is an exporter to countries such as Spain, India, Turkey, Italy, etc. The reasons for the low competitiveness of national breeds are indicated.
Research of innovative activity of business entities of the Russian Federation
Authors: Levushkina S V , Shutova O A
Published: March 2021

The article presents the results of research of innovative activity of organizations that develop, realize and implement technological, marketing and organizational innovations in Federal districts of the Russian Federation. The special role of branch science is defined, which provides the process of organizing and coordinating scientific research and innovative development, creates conditions for strengthening the innovative potential of business. The functions of public-private partnership, which is a mechanism that increases the effectiveness of the relationship between the state and the business sector in the innovation process, are identified. Recommendations were made to Russian organizations to develop digital strategies that help them realize their innovative potential in the modern digital economy.
Development of information technology to identify the imbalance between labor and educational services markets in the construction sector
Authors: Udovenko I V , Zaitseva T V , Putivzeva N P
Published: March 2021

The paper analyzes the current state of the labor market in Russia, shows the need to improve mathematical and software tools for managing the regional human resources potential and the imbalance between the labor markets (LM) and educational services market (ESM), and suggests an approach to building a model for identifying criteria that affect LM and ESM in the construction sector on the example of the Belgorod region. The features of the development of the construction sector in the Belgorod region are considered. Based on the analysis of the collected statistical data and expert judgments, groups of criteria and criteria in each group that affect the amount of imbalance are identified. A generalized model for determining the balance between LM and ESM is constructed in the form of a system of equations. The paper presents a model of interaction between markets in the form of criteria and their groups, which allows determining the imbalance between the labor and educational services markets in the Belgorod region. The developed software tools are presented for determining the most influential criteria and their groups, as well as for the initial calculation of the imbalance. The program sets the number of groups of criteria and the number of criteria in each group. The following matrices are filled in: probabilities of criteria influence, criteria significance, criteria signs. The values of influence and weights for groups of criteria, minimum and maximum values for groups, and the imbalance between LM and ESM are calculated.
Partnership between science, education and business to train young professionals in the conditions of digitalization
Authors: Klimova S P , Kondykov A V
Published: March 2021

This paper puts forward the problem that it is necessary to train personnel that meet the modern requirements of highly dynamic developing agriculture in the conditions of digitalization of the country in the post-pandemic period. The relevance of the research topic is explained by the fact that the agricultural labor market is experiencing a shortage of young highly qualified specialists with knowledge of IT technologies in digital agriculture. At present, a modern young professional must meet the conjuncture-forming selection criteria in the agricultural labor market and have a risk-oriented thinking. It is necessary to update the structure of the formation of an effective mechanism for training highly qualified personnel on the basis of industry universities in the region. The aim of the research is to analyze the challenges facing the agricultural university in training young professionals for agriculture as a branch of the digital economy of Russia. Objectives: to develop a model for developing partnerships and promoting the employment of young professionals in a post-pandemic economy to develop optimal options for covering the personnel deficit in the agricultural sector; to form practical recommendations for regulating the labor market for young professionals. The solution of these tasks will allow training highly qualified young specialists who have all the necessary competencies and are able to meet the requirements of the modern agricultural labor market.
Handwritten Character Recognition of Kannada Language Using Convolutional Neural Networks and Transfer Learning
Authors: Parikshith H , Naga Rajath S M , Shwetha D , Sindhu C M , Ravi P
Published: March 2021

Recognition of Kannada Handwritten Characters in recent times is one among the active research fields of study. It is one of the challenging topics in the pattern recognition field due vocabulary in large scale, complicated structural hierarchy and different people have different handwriting styles. In this study, we put forward a technique for recognition of characters in kannada which are handwritten based on convolutional neural networks and transfer learning. We have first pre-processed each character to remove noise, cropped each character image and resize the images. After the pre-processing the enhanced pixel values in the image helps in training of the neural network for an efficient classification of characters to their respective classes. We have considered vowels, consonants and numerals of Kannada language which are handwritten. Even though some of the characters in kannada language have similarities in structures our model is capable of classifying the character to their correct respective class. We have also used transfer learning to further improve the model so that any new style of handwritten character can be correctly predicted. Our method is efficient in neural network approach and it achieves competitive performance on the rest of the other traditional recognition methods in the literature.
A Blockchain-based framework for Agriculture subsidy disbursement
Authors: Bakare Savita , Shinde Suneel C , Hubballi Roopa , Hebbale Giridhar , Joshi Vinayak
Published: March 2021

Agriculture is the primary livelihood factor in the growth of India’s economy. One of the significant challenges faced by the Government of India in the agriculture sector is to increase the delivery of subsidies by re-engineering the existing process. One of the solutions initiated by the government of India on 1st January 2013 with the highest priority is called a Direct Cash transfer scheme under the Direct Benefit Transfer (DBT) scheme. It involves crediting subsidies (cash/payments) directly to the farmer’s account. However, the major problem associated with this scheme is that the government subsidies do not reach all the eligible farmers due to corruption, delay, intermediaries, and other reasons. The present direct cash transfers system’s major drawbacks such as (key loopholes are) lack of proper auditing, inability to track subsidy, and inadequate digital banking infrastructure especially in rural areas. In this regard, the disbursement of direct cash transfer scheme is addressed benefitting the farmers directly via Blockchain Smart Contracts technology thereby ensuring transparency, de-duplication, reduced delays, and reducing instances of fraud in the existing government subsidy delivery system. We aim to develop a blockchain-based smart contracts prototype model called a single-window approach for automating farmer’s subsidies and eliminating middlemen. The automated model will be fast, transparent, and immutable by reducing the complexities faced by Indian farmers.
Multi-Agents Based Coordinated Scheduling in Hospitals
Authors: Dhiviya Rose J. , Christalin Nelson S.
Published: March 2021

Patient Scheduling is the process of scheduling the patients by creating an optimal schedule for the patients in using the resources in hospitals. The real time scheduling with various constraints like emergency situations like accident case makes this problem complex. The manually scheduling algorithms and the traditional approaches needs more coordination, time and manpower to achieve its efficiency. Agents are a natural choice because they are known to represent a distributed environment well and they are capable of coordinating with each other in dynamic environment. The architectural components like Belief that maintains the internal state of the system, Desires that represents the motivational state of the agent and Intentions that helps to deliberate the state of the goal make this autonomous system adaptable and fault tolerant. In the proposed system each resources and patient is constructed to be software agents, which has the ability to coordinate among them. The optimal schedule is calculated in minimal time using the Genetic Algorithm (GA), an efficient search-based optimization technique. When a patient arrives, he/she is served by a common agent where the priority, resource requirement, processing time, and sequence are assigned to each patient. Hence in this highly dynamic domain optimal schedule generation with minimal time and hardware/software requirements will provide the customers satisfaction with their visit to the hospitals.
RETRACTED: A Hybrid Clustering Based Approach To Extract Drug Elements Which Causes Side Effects
Authors: Vijayan Alpha , Chandrasekar B.S
Published: March 2021

Prescription manifestations or drug reactions are an imperative and complex test. Medications are synthetic substances for treating illnesses, however, may actuate unfriendly responses or results. Medication revelation is tedious and works concentrated, and applicant drugs experience the ill effects of likely side. Heaps of affirmed drugs were removed from the market due to sudden results. Since drug results are an incredible worry of the general wellbeing, the recognizable proof of medication results assists with diminishing dangers in drug revelation. With the expansion of medication information, scientists gathered data about endorsed sedates, and recognize possible symptoms of new applicant drugs. Medication disappointments because of unexpected unfriendly impacts at clinical preliminaries present wellbeing hazards for the members and lead to generous monetary misfortunes. Side effect forecast calculations can possibly direct the medication configuration measure. Drug utilized in remedy relies upon the harmony between anticipated favourable circumstances and possible threats.
Extracting information for failure prediction from intermittent data
Authors: Kesavan Balakrishna S , Mahamuni Amol B
Published: March 2021

The edge devices used for edge analytics usually record data intermittently. So, it is hard to extract patterns of device failures, using common temporal approaches, like Long Short-Term Memory, or multivariate models, like boosted trees. Survival analysis can produce actionable insights in such scenarios.
Data analysis of a match using soccer-log
Authors: Srinath R , Devarakonda NagaSwetha , Biradar Arun , Biradar Shilpa
Published: March 2021

Applying Machine learning, data analytics etc have proven a greater improvement in decision making in all levels. A special attention has been made in the field of sports. As a whole, team improvement is a main concerned in all directions. The goal of any team would be to win every match they play. This can happen only if there is an excellent team efforts i.e. good coordination between players. We propose Sports Analysis an approach for better performance day by day. In this paper we talk about acquiring the details of a match and presenting team statistics.
RETRACTED: A Comparative Analysis of Pre-Processing Time in Summary of Hindi Language using Stanza and Spacy
Authors: Kumar Atul , Katiyar Vinodani , Kumar Pankaj
Published: March 2021

Text summarization is a method or say way for converting large texts into smaller ones by keeping all important points of the larger text as it is in the smaller ones and giving the output in the modified form called summary of original text document. This task is very difficult for humans as it required large amount of rigorous analysis of the document. In this proposed paper we are comparing pre-processing time for two tools of natural language processing one is STANZA and the other is SPACY both are based on modern technologies and are examine for HINDI language processing. In this paper we are preforming a comparative study of both the tools on the bases of their pre-processing time for processing HINDI language.

Now a days, a lot of text summarizer tools are present in the environment and we are keen to use them but here the point of this paper comes into light that how we know which Summarizer is fast enough to get us the same accuracy.
RETRACTED: Indoor human occupancy detection using Machine Learning classification algorithms & their comparison
Authors: Giri Disha , Shreya Sakshi , Kumari Pushpanjali , Yadav Richa
Published: March 2021

This paper presents a method to determine the occupancy in a room with the help of datasets whose data was collected from different sensors and using different ML algorithms. Features representing the occupancy level and the relative changes are taken from different sensors: Humidity sensors, light sensors,temperature sensors carbon dioxide (CO2) sensors. Different classification algorithms which are used for detection of occupancy are: Naive Bayes, classification via regression, random forest, simple logistic, multiclass classification, decision table. The result of the classifier can be classified in the class called - binary-class (which refers to the presence or absence of the person).
Effects of direct current bias on nucleation density of superhard boron-rich boron carbide films made by microwave plasma chemical vapor deposition
Authors: Ramkorun Bhavesh , Chakrabarty Kallol , Catledge Shane A
Published: March 2021

We report bias enhanced nucleation and growth of boron-rich deposits through systematic study of the effect of a negative direct current substrate bias during microwave plasma chemical vapor deposition. The current flowing through a silicon substrate with an applied bias of −250 V was investigated for a feedgas containing fixed hydrogen (H2) flow rate but with varying argon (Ar) flow rates for 1330, 2670, and 4000 Pa chamber pressure. For 1330 and 2670 Pa, the bias current goes through a maximum with increasing Ar flow rate. This maximum current also corresponds to a peak in substrate temperature. However, at 4000 Pa, no maximum in bias current or substrate temperature is observed for the range of argon flow rates tested. Using these results, substrate bias pre-treatment experiments were performed at 1330 Pa in an Ar/H2 plasma, yielding the maximum bias current. Nucleation density of boron deposits were measured after subsequent exposure to B2H6 in H2 plasma and found to be a factor of 200 times higher than when no bias and no Ar was used. Experiments were repeated at 2670 and 4000 Pa (fixed bias voltage and Ar flow rate) in order to test the effect of chamber pressure on the nucleation density. Compared to 4000 Pa, we find nearly 7 times higher boron nucleation densities for both 1330 and 2670 Pa when the substrate was negatively biased in the Ar/H2 plasma. Results are explained by incorporating measurements of plasma optical emission and by use of heterogeneous nucleation theory. The optimal conditions at 1330 Pa for nucleation were used to grow boron-rich amorphous films with measured hardness as high as 58 GPa, well above the 40 GPa threshold for superhardness.
Detection of atmospheric pressure plasma-induced removal of fingerprints via analysis of histograms obtained by imaging ellipsometry
Authors: Koulouris N A , Tasche D , Scheglov A , Mrotzek J , Gerhard C , Viöl W
Published: March 2021

In this publication we report on the suitability of imaging ellipsometry for the semi-quantitative investigation of a contactless removal of human fingerprints from surfaces by an atmospheric pressure plasma tretament. Special attention is paid to the impact of the applied plasma on the complex mixture of biological substances of a fingerprint. For this purpose, the cleaning effect of an argon plasma at two different electrical powers is investigated. By using imaging ellipsometry as a analysis method it could be shown that the cleaning efficiency increases with increasing electrical power and plasma treatment time. In addition, measurements were made by means of x-ray photoelectron spectroscopy (XPS) in order to characterize the chemical composition of surface-adherent contamination and its plasma-induced modifications. It was found that especially the amount of organic impurities is reduced in the course of plasma treatment.
Evidence of warm core structure maintenance over land: a case study analysis of cyclone Kelvin
Authors: Shepherd J M , Thomas A M , Santanello J A , Lawston-Parker P , Basara J
Published: March 2021

Cyclone Kelvin made landfall in northwest Australia as a category 1 storm on 18 February 2018. After landfall, tropical cyclones typically weaken due to the exhaustion of a moisture supply. Cyclone Kelvin continued to intensify with winds gusting to 100 knots and significant flooding well inland. A distinct eye feature also formed well after landfall. An analysis of meteorological satellite, MERRA2 reanalysis, and Global Data Assimilation System (GDAS) data was employed in a case study of Cyclone Kelvin. Using a cyclone phase diagram, it is confirmed that a warm core structure was maintained as Cyclone Kelvin continued to move inland, even through a period of brief inland intensification.
Modulation of global sea surface temperature on tropical cyclone rapid intensification frequency
Authors: Hong Jiacheng , Wu Qiaoyan
Published: March 2021

Rapid intensification (RI; ≥30 knots within 24 h) is an essential characteristic of a CAT 4–5 hurricane (≥115 knots). Between 1980 and 2018, interannual variability in CAT 4–5 hurricanes was strongly correlated with RI, both globally and in individual basins. The annual number of tropical cyclone RI events is a useful measure of global intense CAT 4–5 hurricanes. Here, singular value decomposition analysis was applied to sea surface temperature and the number of RI events throughout the world as calculated from best track data. The first two modes explained ~70% of the total covariance. The mode that dominated variability in global RI occurrence was primarily modulated by the El Niño southern oscillation and the Pacific decadal oscillation. The first mode indicated decreased RI activity in the North Atlantic and increased RI activity in the North Pacific except between 10°–30° N and 125°–135° E, and the corresponding sea surface temperature pattern matched the positive El Niño southern oscillation and Pacific decadal oscillation phases. For the second mode, RI occurrence increased in most parts of the active RI region though with some exceptions, and this was linked with global warming. These results suggest that interannul variability in TC RI events and the associated CAT 4–5 hurricanes are modulated by climate variability in the global scale.
Investigation on hot forging strategy for 5CrNiMoV via high-throughput experiment and machine learning
Authors: Wang Yongshan , Sun Zhiren , Hu Zhiqiang , Wang Kaikun
Published: March 2021

Hot deformation conditions have important influence on the final properties of 5CrNiMoV steel. Based on the developed high-throughput forging equipment, a combined method of high-throughput simulation and machine learning was put forward to efficiently explore the best deformation conditions for 5CrNiMoV steel. A dataset containing 960 sets of data was established, describing the average grain size, damage, and dynamic recrystallization volume fraction of samples, strain rates and temperatures. The RFR (Random Forest Regression) model was trained and used to predict the optimal hot deformation conditions of 5CrNiMoV steel. Based on the searching space and the screening strategies, the optimal hot deformation conditions of 5CrNiMoV at different strains was successfully achieved. The results show that the designed strategy could be used to improve the research efficiency for better production processes and provide a certain theoretical reference for further experimental verification.
Code Review as a Simple Trick to Enhance Reproducibility, Accelerate Learning, and Improve the Quality of Your Team’s Research
Authors: Vable Anusha M , Diehl Scott F , Glymour M Maria
Published: March 2021

Programming for data wrangling and statistical analysis is an essential technical tool of modern epidemiology, yet many epidemiologists receive limited formal training in strategies to optimize the quality of our code. In complex projects, coding mistakes are easy to make, even for skilled practitioners. Such mistakes can lead to invalid research claims that reduce the credibility of the field. Code review is a straightforward technique used by the software industry to reduce the likelihood of coding bugs. The systematic implementation of code review in epidemiologic research projects could not only improve science but also decrease stress, accelerate learning, contribute to team building, and codify best practices. In the present article, we argue for the importance of code review and provide some recommendations for successful implementation for 1) the research laboratory, 2) the code author (the initial programmer), and 3) the code reviewer. We outline a feasible strategy for implementation of code review, though other successful implementation processes are possible to accommodate the resources and workflows of different research groups, including other practices to improve code quality. Code review isn’t always glamorous, but it is critically important for science and reproducibility. Humans are fallible; that’s why we need code review.
Favorable Crisscrossing Pattern With Polydioxanone: Barbed Thread Lifting in Constructing Fibrous Architecture
Authors: Song Jennifer Kim , Chang Jiyeon , Cho Kae Won , Choi Chang Yong
Published: March 2021

Background

The longevity of polydioxanone (PDO)-barbed lifting threads remains controversial.

Objectives

The authors sought to assess the longevity extension effect of a crisscross implantation pattern in PDO-barbed thread lifting.

Methods

To acquire the desired outcome in PDO-barbed thread lifting, the authors suggested a paradigm shift to incorporate biochemical factors in enforcing the physico-mechanical lift. A nude mouse model was employed to evaluate their theory to compare the conventional fan-shaped protocols in barbed thread lifting with an architectural construction of intersections of fibrous capsule in a crisscross pattern. Three fragments of monofilament PDO-barbed–lifting threads were implanted in the dorsal skin of 12 nude mice. The pattern of implantation was fan-shaped in the control group and crisscross in the experimental group. Tissue specimens containing tangential areas of threads were harvested, fixed, and paraffin-embedded. Samples were horizontally cut and histologically analyzed employing hematoxylin and eosin, Massons’ Trichrome, and Sirius red staining. Fibrotic areas and the width of fibrosis from the thread were also analyzed.

Results

Fibrous capsulations around the barbed area of the PDO-barbed lifting threads were threefold greater than those around the barb-free areas of the threads. In the crisscross implantation pattern, width and density of the fibrotic areas were fivefold greater than those of the fan-shaped areas. Induction of fibrous capsules around the PDO-barbed thread was markedly condensed in the crisscross areas.

Conclusions

This study provides the basis for a more logical implantation pattern in PDO-barbed lifting threads for facial rejuvenation. By generating controlled multiple crisscross patterns, we can create more intense fibrogenesis, reduce tension applied on each barbed thread, and, therefore, extend the longevity of the result.

Level of Evidence: 4
VCFShark: how to squeeze a VCF file
Authors: Deorowicz Sebastian , Danek Agnieszka , Kokot Marek
Published: March 2021

Variant Call Format (VCF) files with results of sequencing projects take a lot of space. We propose the VCFShark, which is able to compress VCF files up to an order of magnitude better than the de facto standards (gzipped VCF and BCF). The advantage over competitors is the greatest when compressing VCF files containing large amounts of genotype data. The processing speeds up to 100 MB/s and main memory requirements lower than 30 GB allow to use our tool at typical workstations even for large datasets.

Availability and implementation

https://github.com/refresh-bio/vcfshark.

Supplementary information

Supplementary data are available at Bioinformatics online.
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches
Authors: Rossier Victor , Warwick Vesztrocy Alex , Robinson-Rechavi Marc , Dessimoz Christophe
Published: March 2021

Motivation

Assigning new sequences to known protein families and subfamilies is a prerequisite for many functional, comparative and evolutionary genomics analyses. Such assignment is commonly achieved by looking for the closest sequence in a reference database, using a method such as BLAST. However, ignoring the gene phylogeny can be misleading because a query sequence does not necessarily belong to the same subfamily as its closest sequence. For example, a hemoglobin which branched out prior to the hemoglobin alpha/beta duplication could be closest to a hemoglobin alpha or beta sequence, whereas it is neither. To overcome this problem, phylogeny-driven tools have emerged but rely on gene trees, whose inference is computationally expensive.

Results

Here, we first show that in multiple animal and plant datasets, 18–62% of assignments by closest sequence are misassigned, typically to an over-specific subfamily. Then, we introduce OMAmer, a novel alignment-free protein subfamily assignment method, which limits over-specific subfamily assignments and is suited to phylogenomic databases with thousands of genomes. OMAmer is based on an innovative method using evolutionarily informed k-mers for alignment-free mapping to ancestral protein subfamilies. Whilst able to reject non-homologous family-level assignments, we show that OMAmer provides better and quicker subfamily-level assignments than approaches relying on the closest sequence, whether inferred exactly by Smith-Waterman or by the fast heuristic DIAMOND.

Availabilityand implementation

OMAmer is available from the Python Package Index (as omamer), with the source code and a precomputed database available at https://github.com/DessimozLab/omamer.

Supplementary information

Supplementary data are available at Bioinformatics online.
Phenotypic response to a major hurricane in Anolis lizards in urban and forest habitats
Authors: Avilés-Rodríguez Kevin J , Winchell Kristin M , De León Luis F , Revell Liam J
Published: March 2021

Little is known about the synergistic impacts of urbanization and hurricanes on synanthropes. We compared morphological traits of the lizard Anolis cristatellus on Puerto Rico sampled before the 2017 category 5 Hurricane Maria and 4 and 11 months after the hurricane. We measured limb lengths, toepad size and the number of subdigital scales, termed lamellae, that facilitate adhesion. We hypothesized that the hurricane should have selected for longer limbs and larger toepads with more lamellae, which are traits that other research has suggested to increase clinging performance. Given prior work demonstrating that urban lizards of this species tend to share this phenotype, we also predicted increased phenotypic overlap between post-hurricane urban–forest pairs. Instead, we found that forest and urban populations alike had smaller body sizes, along with a small size-adjusted decrease in most traits, at 4 months after the hurricane event. Many traits returned to prehurricane values by 11 months post-hurricane. Toe morphology differed in the response to the hurricane between urban and forest populations, with significantly decreased trait values in forest but not in urban populations. This difference could be attributable to the different biomechanical demands of adhesion to anthropogenic substrates compared with natural substrates during intense winds. Overall, more research will be required to understand the impacts of hurricanes on urban species and whether differential natural selection can result.
Private active cyber defense and (international) cyber security—pushing the line?
Authors: Broeders Dennis
Published: March 2021

Private sector Active Cyber Defence (ACD) lies on the intersection of domestic security and international security and is a recurring subject, often under the more provocative flag of ‘hack back’, in the American debate about cyber security. This article looks at the theory and practice of private cyber security provision and analyses in more detail a number of recent reports and publications on ACD by Washington DC based commissions and think tanks. Many of these propose legalizing forms of active cyber defence, in which private cyber security companies would be allowed to operate beyond their own, or their clients’ networks, and push beyond American law as it currently stands. Generally, public-private governance solutions for security problems have to manage a balance between (i) questions of capacity and assigning responsibilities, (ii) the political legitimacy of public–private security solutions and (iii) the mitigation of their external effects. The case of private active cyber defence reveals a strong emphasis on addressing the domestic security (and political) problem, while failing to convincingly address the international security problems. The proposals aim to create a legitimate market for active cyber defence, anchored to the state through regulation and certification as a way to balance capacity, responsibilities and domestic political legitimacy. A major problem is that even though these reports anticipate international repercussions and political pushback, against what is likely be received internationally as an escalatory and provocative policy, they offer little to mitigate it.
Prognostic value of right ventricular dilatation in patients with COVID-19: a multicentre study
Authors: Soulat-Dufour Laurie , Fauvel Charles , Weizman Orianne , Barbe Thomas , Pezel Théo , Mika Delphine , Cellier Joffrey , Geneste Laura , Panagides Vassili , Marsou Wassima , Deney Antoine , Attou Sabir , Delmotte Thomas , Ribeyrolles Sophie , Chemaly Pascale , Karsenty Clement , Giordano Gauthier , Gautier Alexandre , Duceau Baptiste , Sutter Willy , Chaumont Corentin , Guilleminot Pierre , Sagnard Audrey , Pastier Julie , Trimaille Antonin , Bonnet Guillaume , Canu Marjorie , Coisne Augustin , Cohen Ariel
Published: March 2021

Aims

Although cardiac involvement has prognostic significance in coronavirus disease 2019 (COVID-19) and is associated with severe forms, few studies have explored the prognostic role of transthoracic echocardiography (TTE). We investigated the link between TTE parameters and prognosis in COVID-19.

Methods and results

Consecutive patients with COVID-19 admitted to 24 French hospitals were retrospectively included. Comprehensive data, including clinical and biological parameters, were recorded at admission. Focused TTE was performed during hospitalization, according to clinical indication. Patients were followed for a primary composite outcome of death or transfer to intensive care unit (ICU) during hospitalization. Among 2878 patients, 445 (15%) underwent TTE. Most of these had cardiovascular risk factors, a history of cardiovascular disease, and were on cardiovascular treatments. Dilatation and dysfunction were observed in, respectively, 12% (48/412) and 23% (102/442) of patients for the left ventricle, and in 12% (47/407) and 16% (65/402) for the right ventricle (RV). Primary composite outcome occurred in 44% (n = 196) of patients [9% (n = 42) for death without ICU transfer and 35% (n = 154) for admission to ICU]. RV dilatation was the only TTE parameter associated with the primary outcome. After adjustment, male sex [hazard ratio (HR) 1.56, 95% confidence interval (CI) 1.09 − 2.25; P = 0.02], higher body mass index (HR 1.10, 95% CI 1.02 − 1.18; P = 0.01), anticoagulation (HR 0.53, 95% CI 0.33 − 0.86; P = 0.01), and RV dilatation (HR 1.66, 95% CI 1.05 − 2.64; P = 0.03) remained independently associated with the primary outcome.

Conclusion

Echocardiographic evaluation of RV dilatation could be useful for assessing risk of severe COVID-19 developing in hospitalized patients.
Influence of low-level-laser therapy on the stability of orthodontic mini-screw implants. A systematic review and meta-analysis
Authors: Michelogiannakis Dimitrios , Jabr Luay , Barmak Abdul Basir , Rossouw Paul Emile , Kotsailidi Elli Anna , Javed Fawad
Published: March 2021

Background

The influence of low-level-laser therapy (LLLT) on the stability of orthodontic mini-screw implants (MSIs) has not been systematically reviewed.

Objectives

The aim was to assess the influence of LLLT on the stability of orthodontic MSIs.

Methods

An unrestricted search of indexed databases was performed.

Selection criteria

Randomized controlled clinical trials (RCTs) investigating the influence of LLLT on orthodontic MSI stability.

Data collection and analysis

Two authors independently performed study retrieval and selection, and data extraction. The risk of bias (RoB) of individual studies was assessed using the Cochrane RoB Tool for RCTs. Meta-analyses were performed separately for RCTs using periotest and resonance frequency analysis (RFA) to measure MSI stability; and a random effects model was applied. Subgroup analyses were performed based on the time-points of MSI stability evaluation. The quality of available evidence was evaluated using the Grades of Recommendation, Assessment, Development, and Evaluation approach.

Results

Initially, 1332 articles were screened. Six RCTs with a split-mouth design were included. The periotest was used in 4 RCTs and 2 RCTs used RFA to measure MSI stability. All RCTs had a low RoB. Subgroup analyses based on periotest indicated that MSIs treated with LLLT had significantly higher stability than untreated MSIs at 21 and 30 days [weighted mean difference (MD) = −2.76, confidence interval (CI): [−4.17, −1.36], P-value = 0.0001) and at 60 days (weighted MD = −3.47, CI: [−4.58, −2.36], P < 0.00001); and the level of certainty was high. Subgroup analyses based on RFA showed higher stability of MSIs treated with than without LLLT at 56 and 60 days (standardized MD = 0.82, CI: [0.32, 1.32], P = 0.001), and at 70 and 90 days (standardized MD = 0.86, CI: [0.36, 1.36], P = 0.0007); and the level of certainty was moderate.

Limitations

Due to limited number of relevant studies, it was not possible to perform sensitivity analysis, subgroup analyses for patient and intervention-related characteristics, and reporting biases assessment.

Conclusions

The role of LLLT on the secondary stability of MSIs placed in patients undergoing OT remains debatable.

Clinical Trial Registration

PROSPERO (CRD42021230291).
Bacterial communities are more sensitive to ocean acidification than fungal communities in estuarine sediments
Authors: Su Xiaoxuan , Yang Xiaoru , Li Hu , Wang Hongtao , Wang Yingmu , Xu Jianxin , Ding Kai , Zhu Yong-guan
Published: March 2021

Ocean acidification (OA) in estuaries is becoming a global concern, and may affect microbial characteristics in estuarine sediments. Bacterial communities in response to acidification in this habitat have been well discussed; however, knowledge about how fungal communities respond to OA remains poorly understood. Here, we explored the effects of acidification on bacterial and fungal activities, structures and functions in estuarine sediments during a 50-day incubation experiment. Under acidified conditions, activities of three extracellular enzymes related to nutrient cycling were inhibited and basal respiration rates were decreased. Acidification significantly altered bacterial communities and their interactions, while weak alkalization had a minor impact on fungal communities. We distinguished pH-sensitive/tolerant bacteria and fungi in estuarine sediments, and found that only pH-sensitive/tolerant bacteria had strong correlations with sediment basal respiration activity. FUNGuild analysis indicated that animal pathogen abundances in sediment were greatly increased by acidification, while plant pathogens were unaffected. High-throughput quantitative PCR-based SmartChip analysis suggested that the nutrient cycling-related multifunctionality of sediments was reduced under acidified conditions. Most functional genes associated with nutrient cycling were identified in bacterial communities and their relative abundances were decreased by acidification. These new findings highlight that acidification in estuarine regions affects bacterial and fungal communities differently, increases potential pathogens and disrupts bacteria-mediated nutrient cycling.
Assessing evidence for adaptive evolution in two hearing-related genes important for high-frequency hearing in echolocating mammals
Authors: Wang Hui , Zhao Hanbo , Chu Yujia , Feng Jiang , Sun Keping
Published: March 2021

High-frequency hearing is particularly important for echolocating bats and toothed whales. Previously, studies of the hearing-related genes Prestin, KCNQ4, and TMC1 documented that adaptive evolution of high-frequency hearing has taken place in echolocating bats and toothed whales. In this study, we present two additional candidate hearing-related genes, Shh and SK2, that may also have contributed to the evolution of echolocation in mammals. Shh is a member of the vertebrate Hedgehog gene family and is required in the specification of the mammalian cochlea. SK2 is expressed in both inner and outer hair cells, and it plays an important role in the auditory system. The coding region sequences of Shh and SK2 were obtained from a wide range of mammals with and without echolocating ability. The topologies of phylogenetic trees constructed using Shh and SK2 were different; however, multiple molecular evolutionary analyses showed that those two genes experienced different selective pressures in echolocating bats and toothed whales compared to nonecholocating mammals. In addition, several nominally significant positively selected sites were detected in the nonfunctional domain of the SK2 gene, indicating that different selective pressures were acting on different parts of the SK2 gene. This study has expanded our knowledge of the adaptive evolution of high-frequency hearing in echolocating mammals.
Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion
Authors: Haeussler Simon , Yeroslaviz Assa , Rolland Stéphane G , Luehr Sebastian , Lambie Eric J , Conradt Barbara
Published: March 2021

Mitochondrial dynamics plays an important role in mitochondrial quality control and the adaptation of metabolic activity in response to environmental changes. The disruption of mitochondrial dynamics has detrimental consequences for mitochondrial and cellular homeostasis and leads to the activation of the mitochondrial unfolded protein response (UPRmt), a quality control mechanism that adjusts cellular metabolism and restores homeostasis. To identify genes involved in the induction of UPRmt in response to a block in mitochondrial fusion, we performed a genome-wide RNAi screen in Caenorhabditis elegans mutants lacking the gene fzo-1, which encodes the ortholog of mammalian Mitofusin, and identified 299 suppressors and 86 enhancers. Approximately 90% of these 385 genes are conserved in humans, and one-third of the conserved genes have been implicated in human disease. Furthermore, many have roles in developmental processes, which suggests that mitochondrial function and their response to stress are defined during development and maintained throughout life. Our dataset primarily contains mitochondrial enhancers and non-mitochondrial suppressors of UPRmt, indicating that the maintenance of mitochondrial homeostasis has evolved as a critical cellular function, which, when disrupted, can be compensated for by many different cellular processes. Analysis of the subsets “non-mitochondrial enhancers” and “mitochondrial suppressors” suggests that organellar contact sites, especially between the ER and mitochondria, are of importance for mitochondrial homeostasis. In addition, we identified several genes involved in IP3 signaling that modulate UPRmt in fzo-1 mutants and found a potential link between pre-mRNA splicing and UPRmt activation.
A selection-based next generation sequencing approach to develop robust, genotype-specific mutation profiles in Saccharomyces cerevisiae
Authors: Lamb Natalie A , Bard Jonathan E , Buck Michael J , Surtees Jennifer A
Published: March 2021

Distinct mutation signatures arise from environmental exposures and/or from defects in metabolic pathways that promote genome stability. The presence of a particular mutation signature can therefore predict the underlying mechanism of mutagenesis. These insults to the genome often alter dNTP pools, which itself impacts replication fidelity. Therefore, the impact of altered dNTP pools should be considered when making mechanistic predictions based on mutation signatures. We developed a targeted deep-sequencing approach on the CAN1 gene in Saccharomyces cerevisiae to define information-rich mutational profiles associated with distinct rnr1 backgrounds. Mutations in the activity and selectivity sites of rnr1 lead to elevated and/or unbalanced dNTP levels, which compromises replication fidelity and increases mutation rates. The mutation spectra of rnr1Y285F and rnr1Y285A alleles were characterized previously; our analysis was consistent with this prior work but the sequencing depth achieved in our study allowed a significantly more robust and nuanced computational analysis of the variants observed, generating profiles that integrated information about mutation spectra, position effects, and sequence context. This approach revealed previously unidentified, genotype-specific mutation profiles in the presence of even modest changes in dNTP pools. Furthermore, we identified broader sequence contexts and nucleotide motifs that influenced variant profiles in different rnr1 backgrounds, which allowed specific mechanistic predictions about the impact of altered dNTP pools on replication fidelity.
Natural History and Risk Stratification of Recurrent Crohn’s Disease After Ileocolonic Resection: A Multicenter Retrospective Cohort Study
Authors: Joustra Vincent , Duijvestein Marjolijn , Mookhoek Aart , Bemelman Willem , Buskens Christianne , Koželj Matic , Novak Gregor , Hindryckx Pieter , Mostafavi Nahid , D’Haens Geert
Published: March 2021

Background

Prediction of endoscopic postoperative recurrence (POR) and prophylactic treatment based on clinical risk profile have thus far been inconclusive. This study aimed to examine the association between clinical risk profile and the development of endoscopic POR in a Crohn’s disease population without postoperative treatment and to identify individual risk factors of endoscopic POR.

Methods

Medical records of 142 patients with Crohn’s disease during follow-up after ileocecal or ileocolonic resection without prophylactic treatment at 3 referral centers were reviewed. Endoscopic POR was defined as a modified Rutgeerts score ≥i2b. Clinical risk profiles were distilled from current guidelines. Both uni- and multivariate logistic regression analysis were used to assess the relationship between risk profiles and endoscopic POR.

Results

Endoscopic POR was observed in 68 out of 142 (47.9%) patients. Active smoking postsurgery (odds ratio [OR], 3.01; 95% confidence interval [CI], 1.24-7.34; P = 0.02), a Montreal classification of A3 (OR, 3.05; 95% CI, 1.07-8.69; P = 0.04), and previous bowel resections (OR, 2.58; 95% CI, 1.07-6.22; P = 0.03) were significantly associated with endoscopic POR. No significant association was observed between endoscopic POR and any guideline defined as a high-/low-risk profile. However, patients with a combination of any 3 or more European Crohns & Colitis Organisation– (OR, 4.87; 95% CI, 1.30-18.29; P = 0.02) or British Society of Gastroenterology–defined (OR 3.16; 95% CI, 1.05-9.49; P = 0.04) risk factors showed increased odds of developing endoscopic POR.

Conclusions

Our results suggest that patients with a combination of any 3 or more European Crohns & Colitis Organisation– or British Society of Gastroenterology–defined risk factors would probably benefit from immediate prophylactic treatment.
Nonhypoalbuminemic Inflammatory Bowel Disease in Dogs as Disease Model
Authors: Hernandez Juan , Rouillé Elodie , Chocteau Florian , Allard Marie , Haurogné Karine , Lezin Florence , Hervé Julie M , Bach Jean-Marie , Abadie Jérôme , Lieubeau Blandine
Published: March 2021

Background

The incidence of inflammatory bowel disease (IBD) is increasing worldwide, emphasizing the need of relevant models, as dogs spontaneously affected by IBD may be, for better knowledge of the disease’s physiopathology.

Methods

We studied 22 client-owned dogs suffering from IBD without protein loss and 14 control dogs. Biopsies were obtained from the duodenum, ileum, and colon. Inflammatory grade was assessed by histopathology, immunohistochemistry, and chemokine analysis. The expression of Toll-like receptors (TLR) in mucosa was immunohistochemically evaluated. Antibody levels against bacterial ligands (lipopolysaccharide [LPS] and flagellin) were measured in sera using enzyme-linked immunoassay.

Results

Dogs with IBD showed low to severe clinical disease. Histopathologically, the gut of dogs with IBD did not exhibit significant alterations compared with controls except in the colon. The number of CD3+ T lymphocytes was decreased in the ileum and colon of dogs with IBD compared with controls, whereas the numbers of Foxp3+, CD20+, and CD204+ cells were similar in the 2 groups. Three chemokines, but no cytokines, were detected at the protein level in the mucosa, and the disease poorly affected their tissue concentrations. Dogs with IBD exhibited higher serum reactivity against LPS and flagellin than controls but similar immunoreactivity against the receptors TLR4 and TLR5. In addition, TLR2 and TLR9 showed similar expression patterns in both groups of dogs.

Conclusions

Our data described dysregulated immune responses in dogs affected by IBD without protein loss. Despite fairly homogeneous dog cohorts, we were still faced with interindividual variability, and new studies with larger cohorts are needed to validate the dog as a model.