bluuebunny/crossref_metadata_2025_split huggingface dataset:
SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes
Authors: Tadrent Nachida , Dedeine Franck , Hervé Vincent 
Published: February 2023

Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM, GUNC), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Importantly, these additional MAGs showed no significant difference compared to the other ones in terms of completeness, contamination, genome size nor relative abundance. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.
Local approaches and ineffectivity in reducing stunting in children: A case study of policy in Indonesia
Authors: Meher Cashtri , Zaluchu Fotarisman , Eyanoer Putri Chairani 
Published: February 2023

Background: Stunting is a global issue. Indonesia has to cope with this stunting issue very seriously because it has the highest number among Southeast Asian countries and is included in the countries with the highest number of stunting sufferers in the world. One of the important points that requires intervention is to fulfill the nutrition of both the pregnant women and children under the age of five. Policy and implications: The central government has issued the national policy to prevent stunting in children and determined the national and regional parties in charge of the program. The government commitment is shown through the fund allocation arrangement for village development aimed to prevent and overcome stunting. Theoretically, it all seemed to be conducted according to each responsibility of the parties in charge. However, the effort is generally still bureaucratic, in a form of campaign, and has not solved the issue of fulfilling nutrition at the local level. Recommendations: Based on field experience and literature, the goal to reduce stunting significantly will be achievable if local approaches are applied. The local issue on nutrition intake can be intervened specifically by applying local approaches in understanding the community consumption behavior pattern and delivering education on nutrition. The government should abandon a too-generic approach (one-size-fits-all) which has been used so far. Conclusion: Intervention of nutrition intake through local approaches is crucial considering that stunting prevalence is still very high. As the organization for the program to prevent stunting is supported by fund allocation, in the future the government should encourage local intervention efforts through the cooperation with higher education, local non-governmental organisations, or partners that understand local context more on nutrition issues in respective regions. To observe this, stunting prevention in Indonesia should develop more local approaches in campaign material and education to local society.
Analysis of the spatial inequality in residential quality indicators: the 22 urban regions of Tehran Metropolis
Authors: Zarghamfard Moslem , Bahadori Behnaz , Hoseinzadeh Robab , Safaralizadeh Esmaiel 
Published: February 2023

Research objective: the present study seeks to assess and analyze the status of residential quality indicators in the 22 urban regions of the Tehran metropolis.
Methodology: 79 residential quality variables are classified into the four indicators of physical, economic, ecological, and socio-cultural indices. Shannon entropy model, the coefficient of variation, TOPSIS, hotspot analysis, and Moran spatial autocorrelation were used for data analysis.
Results: Results of the present study indicated a TOPSIS score of 0.58 for the integrated indicators which revealed region 1 had the best and region 15 had the worst status. In fact, a sort of divergence and heterogeneity rules residential quality indicators in Tehran urban regions, so that among the 22 urban regions of the city, around 4.5% were advantaged while 13.6% were relatively advantaged, 77.3% were semi- advantaged, and 4.5% were less advantaged. Results of statistical spatial analysis also indicate that the advantaged clusters were located in northern and northeastern parts of the city while the less advantaged and extremely less advantaged clusters were more focused in the southern and southeastern parts of the city, and residential quality indicators followed a cluster pattern.
Conclusion: A spatial difference and inequality in residential quality index distribution were observed in the 22 urban regions of Tehran so that the regions located in the southern and southeastern parts of the city had an unfavorable status in terms of residential quality indicators while the northern and northeastern regions were more advantaged in this regard.
será que a voz que ouvimos por dentro é a mesma que as pessoas ouvem por fora?
Authors: Carvalho Magda Costa 
Published: February 2023

This text was written after hearing a childlike question about voice, a question asked by Lara, a girl at a “basic” school in a rural area of the Azores islands that resulted in a diferent way of understanding the motives and intentions that are implicit in the way we practice community of philosphical inquiry with children and adults. This question also unveiled important aspects of the way we construct ourselves as adults who believe in the importance of teaching philosophy in elementary school. This text describes an attempt to follow the trail of inquiry triggered by Lara’s question, and documents three moments or possibilities of re-questioning. These moments – which are not understood as forming an orderly sequence, but rather represent inroads into the initial question – emerge as possibilities marked by the rhythm of inquiry that followed. Those questions were: What do we hear when we talk about voice? What do we say when we talk about listening? And what do we think about when we share voices and listen actively? The text invites us to focus on voice as a concept aligned with a certain paradigmatic model of thinking commonly referred to as “philosophy,”and also invites us to consider the concept of listening as a construct that returns us to the origins of western philosophy. Finally, the text invites us to consider different ways of understanding voice and listening as based on the idea of thinking as an in-between space of sharing, focusing specifically on activities centering philosophical dialogue with children.
Stable emission of solar laser power under non-continuous solar tracking conditions
Authors: Catela Miguel , Liang Dawei , Vistas Cláudia R. , Garcia Dário , Costa Hugo , Tibúrcio Bruno D. , Almeida Joana 
Published: February 2023

Solar laser technology typically requires a highly accurate solar
tracking system that operates continuously, which increases energy
consumption and reduces the system’s lifetime. We propose a multi-rod
solar laser pumping approach to enhance solar laser stability under
non-continuous solar tracking conditions. Using a heliostat, solar
radiation is redirected toward a first-stage parabolic concentrator.
At its focus, an aspheric lens further concentrates the solar rays
onto five Nd:YAG rods positioned within an elliptical-shaped pump
cavity. Numerical analysis using Zemax and LASCAD software showed that
the tracking error width at 10% laser power loss for the five
6.5 mm diameter and 15 mm length rods was 2.20°, which
is 50% higher than that of the solar laser in previous non-continuous
solar tracking experiments. 2.0% solar-to-laser conversion efficiency
was also attained.
Metalens integrated receiver to reduce the effect of angle of arrival jitter in free space optical communication
Authors: Islam Md Shafiqul , Shahverdi Kaveh , Boyraz Ozdal 
Published: February 2023

In this paper, we propose a metalens integrated receiver for free space optical communication, which provides robust performance in the presence of angle of arrival fluctuations jitter. As a proof of concept, we show that our proposed receiver can tolerate up to a 2.5 mrad angle of arrival fluctuations with a detector radius of 20 µm before reaching a 3 dB power penalty. We design a meta unit cell to realize the optimized phase profile and present a quasi-3D full wave simulation of the proposed architecture. The system shows steady signal power and bit error rate in the presence of angle of arrival fluctuation.
Real-time noise-free inline self-interference incoherent digital holography with temporal geometric phase multiplexing
Authors: Choi Kihong , Lee Jae-Won , Shin Jungyeop , Hong Keehoon , Park Joongki , Kim Hak-Rin 
Published: February 2023

In this paper, we propose a real-time incoherent digital holographic (IDH) recording system free from bias and twin-image noises. A motionless three-step polarization-encoded phase-shifter operating at 99 Hz is realized with two electrically controllable birefringence-mode liquid crystal cells operating in tandem with a geometric phase lens and polarizers. Based on the proposed optical configuration, a coaxial straight-line self-interference IDH recording system is devised. Notably, the elimination of bias and twin-image noise from three phase-shifted images is demonstrated as a proof of concept. Moreover, complex-valued holographic video acquisitions with a resolution greater than 20 megapixels are demonstrated, with an effective acquisition frequency of 33 Hz.
Comparison of new psychiatric diagnoses among Finnish children and adolescents before and during the COVID-19 pandemic: A nationwide register-based study
Authors: Gyllenberg David , Bastola Kalpana , Wan Mohd Yunus Wan Mohd Azam , Mishina Kaisa , Liukko Emmi , Kääriälä Antti , Sourander Andre 
Published: February 2023

Background
Coronavirus Disease 2019 (COVID-19) restrictions decreased the use of specialist psychiatric services for children and adolescents in spring 2020. However, little is known about the pattern once restrictions eased. We compared new psychiatric diagnoses by specialist services during pandemic and pre-pandemic periods.

Methods and findings
This national register study focused on all Finnish residents aged 0 to 17 years from January 2017 to September 2021 (approximately 1 million a year). The outcomes were new monthly diagnoses for psychiatric or neurodevelopmental disorders in specialist services. These were analyzed by sex, age, home location, and diagnostic groups. The numbers of new diagnoses from March 2020 were compared to predictive models based on previous years. The predicted and observed levels in March to May 2020 showed no significant differences, but the overall difference was 18.5% (95% confidence interval 12.0 to 25.9) higher than predicted in June 2020 to September 2021, with 3,821 more patients diagnosed than anticipated. During this period, the largest increases were among females (33.4%, 23.4 to 45.2), adolescents (34.4%, 25.0 to 45.3), and those living in areas with the highest COVID-19 morbidity (29.9%, 21.2 to 39.8). The largest increases by diagnostic groups were found for eating disorders (27.4%, 8.0 to 55.3), depression and anxiety (21.0%, 12.1 to 51.9), and neurodevelopmental disorders (9.6%, 3.0 to 17.0), but psychotic and bipolar disorders and conduct and oppositional disorders showed no significant differences and self-harm (−28.6, −41.5 to −8.2) and substance use disorders (−15.5, −26.4 to −0.7) decreased in this period. The main limitation is that data from specialist services do not allow to draw conclusions about those not seeking help.

Conclusions
Following the first pandemic phase, new psychiatric diagnoses in children and adolescents increased by nearly a fifth in Finnish specialist services. Possible explanations to our findings include changes in help-seeking, referrals and psychiatric problems, and delayed service access.
Serum biomarkers and anti-flavivirus antibodies at presentation as indicators of severe dengue
Authors: Bernal Cynthia , Ping Sara , Rojas Alejandra , Caballero Oliver , Stittleburg Victoria , de Guillén Yvalena , Langjahr Patricia , Pinsky Benjamin A. , Von-Horoch Marta , Luraschi Patricia , Cabral Sandra , Sánchez María Cecilia , Torres Aurelia , Cardozo Fátima , Waggoner Jesse J. 
Published: February 2023

Background
Dengue is the most common vector-borne viral disease worldwide. Most cases are mild, but some evolve into severe dengue (SD), with high lethality. Therefore, it is important to identify biomarkers of severe disease to improve outcomes and judiciously utilize resources.

Methods/Principal findings
One hundred forty-five confirmed dengue cases (median age, 42; range <1–91 years), enrolled from February 2018 to March 2020, were selected from an ongoing study of suspected arboviral infections in metropolitan Asunción, Paraguay. Cases included dengue virus types 1, 2, and 4, and severity was categorized according to the 2009 World Health Organization guidelines. Testing for anti-dengue virus IgM and IgG and serum biomarkers (lipopolysaccharide binding protein and chymase) was performed on acute-phase sera in plate-based ELISAs; in addition, a multiplex ELISA platform was used to measure anti-dengue virus and anti-Zika virus IgM and IgG. Complete blood counts and chemistries were performed at the discretion of the care team. Age, gender, and pre-existing comorbidities were associated with SD vs. dengue with/without warning signs in logistic regression with odds ratios (ORs) of 1.07 (per year; 95% confidence interval, 1.03, 1.11), 0.20 (female; 0.05,0.77), and 2.09 (presence; 1.26, 3.48) respectively. In binary logistic regression, for every unit increase in anti-DENV IgG in the multiplex platform, odds of SD increased by 2.54 (1.19–5.42). Platelet count, lymphocyte percent, and elevated chymase were associated with SD in a combined logistic regression model with ORs of 0.99 (1,000/μL; 0.98,0.999), 0.92 (%; 0.86,0.98), and 1.17 (mg/mL; 1.03,1.33) respectively.

Conclusions
Multiple, readily available factors were associated with SD in this population. These findings will aid in the early detection of potentially severe dengue cases and inform the development of new prognostics for use in acute-phase and serial samples from dengue cases.
Story Listening and Experience in Early Childhood, Donna Schatt and Patrick Ryan (2021)
Authors: Wilson Michael 
Published: February 2023

Review of: Story Listening and Experience in Early Childhood, Donna Schatt and Patrick Ryan (2021)
Cham: Palgrave Macmillan, 214 pp.,
ISBN 978-3-03065-357-6, h/bk, £79.99
The Page Is Printed, Carrie Smith (2021)
The Catch: Fishing for Ted Hughes, Mark Wormald (2022)
Authors: Gowar Mick 
Published: February 2023

Review of: The Page Is Printed, Carrie Smith (2021)
Liverpool: Liverpool University Press, 256 pp.,
ISBN 978-1-80085-535-9, h/bk, £90.00

The Catch: Fishing for Ted Hughes, Mark Wormald (2022)
London: Bloomsbury, 336 pp.,
ISBN 978-1-52664-424-4, h/bk, £20.00
Association of the structure of the glucocorticoid receptor and single nucleotide <i>NR3C1</i> gene polymorphisms with metabolic disorders
Authors: Brovkina S. S. , Dzherieva I. S. , Volkova N. I. , Shkurat T. P. , Goncharova Z. A. , Mashkina E. V. , Reshetnikov I. B. 
Published: February 2023

Glucocorticoid therapy is widely used in the treatment of various pathologies. Sensitivity to glucocorticoids (GC) has a serious impact not only on the effectiveness of their action, but also on the severity of side effects, the formation of risk factors and the development of cardiovascular diseases (CVD). Variability of sensitivity to GC causes different phenotypes and severity of metabolic disorders underlying CVD. Among them, one can distinguish a decrease in muscle mass and strength, obesity, glucose and lipid metabolism impairment, and others. Glucocorticoids carry out their effects by binding to the glucocorticoid receptor (GR), and therefore this is considered a critical point in their action. This review presents data on the significance of the glucocorticoid receptor structure, examines the main single nucleotide polymorphisms (SNP) of the NR3C1 gene associated with hypersensitivity or relative resistance to glucocorticoids in the context of metabolic disorders and the development of CVD. The association of the four most studied SNP of the GR gene with metabolic risks is described in detail: BclI (rs41423247), N363S (rs56149945), ER22/23EK (rs6189/rs6190), GR-9ß (rs6198). Their determination can contribute to clarifying the prognosis of both the effectiveness of GC and the development of metabolic disorders, and subsequent early correction of CVD risk factors.
The impact of carbohydrate metabolism disorders on the early and long-term clinical outcomes of patients with COVID-19 according to the AKTIV and AKTIV 2 registries
Authors: Salukhov V. V. , Arutyunov G. P. , Tarlovskaya E. I. , Batluk T. I. , Bashkinov R. A. , Samus I. V. , Melnikov E. S. , Trubnikova M. A. , Arutyunov A. G. 
Published: February 2023

BACKGROUND: Numerous studies indicate a high incidence of various disorders of carbohydrate metabolism against the new coronavirus infection. These disorders aggravate the course of infection and increase mortality. Thereby, analysis of risk factors for unfavorable outcomes and assessment of the long-term consequences of COVID-19 in patients with impaired carbohydrate metabolism is of great importance.AIM: To investigate the association between carbohydrate metabolism disorders in COVID-19 patients and mortality, course of infection, long-term consequences, as well as to identify risk factors for an unfavorable disease course.MATERIALS AND METHODS: A retrospective analysis of data from the combined multicenter non-interventional real-world AKTIV and AKTIV 2 registries was performed. The sample included 9290 patients who had COVID-19 with varying severity from June 29, 2020, to November 29, 2020 (AKTIV) and from October 01, 2020, to March 30, 2021 (AKTIV 2). The patients were divided into 3 groups: Group 1 — patients with intact carbohydrate metabolism, n=6606; Group 2 — patients with newly diagnosed hyperglycemia (NDH), n=1073; Group 3 — patients with a history of type 2 diabetes mellitus (DM2), n=1611. The groups were assessed for clinical and laboratory parameters, comorbidities, mortality, carbohydrate metabolic status, and well-being during the infection and at 12 months.RESULTS: The prevalence of carbohydrate metabolism disorders (CMD) was 28,9%, with DM2 patients accounting for 17,3% and patients with newly diagnosed hyperglycemia (NDH) for 11,6%. The mortality rate of patients with hyperglycemia of any origin was 10.6%, which was significantly higher compared to patients without hyperglycemia (3,9%). The probability of lethal outcome increased 2,48-fold in the group of patients with DM2 and 2,04-fold in the group of patients with NDH. At the same time, the probability of a lethal outcome decreased 2,94-fold in patients without CMD. At 12 months, patients with CMD showed a significantly higher frequency and longer persistence of complaints. This trend was more pronounced in patients with DM2 than in those with NDH. Only 1,7% of patients from the NDH group had type 2 diabetes and were receiving oral hypoglycemic medications one year after the infection. A prognostic model was developed to determine the risk of lethal outcome. The model included such known predictors as concomitant ischemic heart disease, history of myocardial infarction or stroke, blood glucose level, and age.CONCLUSION: Carbohydrate metabolism disorders aggravate the course of COVID-19 and increase mortality. One year after infection, patients with DM2 and NDH were more likely to have symptoms typical for post-COVID syndrome, and NDH resolved in most cases after the infection.
Ultrastructural characterization of Minutocellus polymorphus (Cymatosiraceae, Bacillariophyta) and first record from the Eastern Pacific
Authors: Hernández-Márquez Sinuhé , Zamudio-Resendiz María Eugenia , Núñez-Reséndiz María Luisa , Escarcega-Bata Alexis , Sentíes Abel 
Published: February 2023

Abstract
The diatom Minutocellus polymorphus is a widely studied species because it is an ideal model for toxicity tests since it grows rapidly. Although the gross morphology has been extensively described, the ultrastructural characters associated with its importance, are unknown. It is also the only species in the genus that has been documented in the North American Atlantic, but unknown on the Eastern Pacific coasts. In a collection made in Acapulco Bay, Guerrero, Mexico, cells morphologically identical to M. polymorphus were isolated. From cultures and observations in transmission electron microscope, a first description of the ultrastructure of the genus is provided, and from sequences of 18S, we confirmed its taxonomic identity as M. polymorphus. However, more detailed studies are needed to continue increasing the knowledge about the ultrastructure of diatoms on the Mexican Pacific coasts, where they are previously unknown.
First record of phytomyxid infection of the non-native seagrass Halophila stipulacea in Puerto Rico
Authors: Kaldy James E. , Sullivan Cayla , Dieppa Angel , Cappielo Cosme Ivelisse , Orizondo Lugo Marco , Schiebout Michael 
Published: February 2023

Abstract

Halophila stipulacea is an invasive seagrass in the Caribbean Sea that also harbors a phytomyxid endoparasite. Phytomyxean parasites are known to cause disease in agricultural crops and are documented to form galls in some seagrass species. Here we make the first report of phytomyxid infection of Halophila stipulacea in the Bahía de Jobos in Salinas, Puerto Rico. We found phytomyxid infected H. stipulacea at 3 of 5 sites examined, expanding the documented range of the Marinomyxa marina phytomyxid infection by almost 400 km from where it was first documented in 2018. Presence of the endoparasite has not impeded H. stipulacea dispersal and continued expansion of H. stipulacea will likely spread both the host seagrass and the endoparasite.