bluuebunny/crossref_metadata_2025 huggingface dataset:
Utilization of municipal solid waste compost for the improvement of microbial biomass, n-mineralization and fertility of soil under maize crop
Authors: Bibi Hamida , Basit Abdul , Shams Dilawar Farhan , Khan Muhammad Zafarullah , Iqbal Mudassar , Ullah Sajid
Published: August 2023

The experiment was conducted to assess the influence of municipal solid waste compost on microbial activity of soil after harvesting of maize crop and to determine the effect of municipal solid waste compost on N mineralization. A field experiment to test the effect of solid waste compost on fertility, microbial biomass and nitrogen (N) mineralization was conducted at Agriculture Research Institute Tarnab, Peshawar during spring 2017. A maize crop was selected as test crop for this experiment. The experiment was carried out in a Randomized Complete Block (RCBD) design with three replications. Maize variety (Azam) was sown in March 2017. Plot size was 5 × 3 m. Municipal solid waste compost was applied as treatment in each plot with different rates. The data showed maximum N mineralization (7.6 µg g-1 soil) at the treatment T2 where only NPK dose was applied while minimum N was mineralized at treatment T1 control where no NPK and MSW compost was applied, Then the application of MSW compost influenced N mineralization at large extent (6.4 µg g-1 soil) in treatment T4 where MSW compost was applied at 12 t ha-1 followed by the treatment T6 (6.1 µg g-1 soil) where MSW compost was applied at 24 t ha-1. Applying MSW compost influence microbial activities and increase soil organic carbon.
Importance of Information Availability, its effects on Business & the proposed Model
Authors: Alvi Bilal , Qureshi M. Wasim , Karim Shakir
Published: August 2023

Many a time the irony one can face is the unavailability of the resources when they are needed the most causing unavoidable/irreversible loss. These kinds of scenarios can cost organizations their business. Enterprises suffered and are still suffering a huge loss in terms of revenue, customers’ dissatisfaction and more.  Though availability is one of the three basic components of security besides Confidentiality and Integrity, it could not get its due share and remained under the back- drop. In this paper, the importance of the information availability and its key determinants are discussed, analyzed and a conceptual model is proposed. The model is validated by carrying out an in-depth study of three major multinational oil enterprises of Pakistan. The study proved that if information availability is taken care in true sense, success in business could be assured.
How Do Young Provisional Drivers Who Crash Early Compare With Those Who Only Crash Later?
Authors: Siskind Victor
Published: August 2023

Much attention has been given to the elevated crash rates of young novice drivers when first driving unsupervised, particularly in the initial six months, but less to the question of whether those who crash during that period are in any way different from those who only crash subsequently. This question was examined in a large cohort of New South Wales novices aged under 25 years at their first licensing, which occurred in the financial year 2007/08. Only post-learner drivers were considered, and divided into three driver groups, early crashers within the first six months, late crashers whose first crash was later, and non-crashers. All factors derivable from the routine records provided were analysed including metropolitan residence and aggregate socio-economic status as determined by post-code of residence. Overall, the largest differences were between those who crashed and those who did not. Females were under-represented among both early and late crashers. Age, aggregate socio-economic status, and metropolitan residence at first licensing did not differ between early and late crashers, but late crashers had spent less time driving supervised. Early crashers had crashed and incurred traffic citations, including for serious offences, more frequently than late crashers, with more crashes judged at-fault. However, exclusion of offences occurring on the same day as a crash reduced the difference between early and late crashers. The difference between crashers and non-crashers was reduced but remained significant.
Can I Stop? Considering Opportunities to Influence Multidisciplinary Factors That Result in Crashes
Authors: Zurlinden Hendrik , Gaffney John , Hovenden Elizabeth
Published: August 2023

In previous decades significant gains were made in reducing the number of road traffic related fatalities in Victoria and Australia. However, in absolute terms this reduction started plateauing despite substantial investment in road safety countermeasures. This trend is not well aligned with the goal to achieve zero fatalities by 2050. Through practical traffic management experience, a study tour of nine countries and a literature review, we have gained valuable insights into the changing dynamics of roads. We have identified opportunities to improve road safety by adapting to larger/heavier vehicles, denser traffic, changing travel patterns and evolving demographics. These opportunities include: vehicle-centred crash avoidance in addition to crash consequence mitigation strategies; reduced traffic complexity; reduced cognitive workload; and targeted dynamic information of inclement weather and traffic conditions. Improved road surface friction, braking, tyres and vehicle stability can reduce crashes and their impacts. This article aims at stimulating broader discussions among experts for the development of next-generation road safety strategies.
PERAN PUSAT PERPUSTAKAAN DAN PENYEBARAN TEKNOLOGI PERTANIAN DALAM TUJUAN PEMBANGUNAN BERKELANJUTAN
Authors: Rufaidah Vivit Wardah , Iskak Penny Ismiati
Published: August 2023

The Sustainable Development Goals (SDGs) are aligned with Indonesia's national development priorities set out in the National Medium Term Development Plan. Of the 169 SDGs targets, around 57 percent of SDGs are in line with national development priorities. Agriculture is closely related to achieving SDGs. Agricultural development driven by the Ministry of Agriculture of the Republic of Indonesia is included in second goal and 8th on achieving SDGs in Indonesia. The second goal is to eliminate hunger, achieve  food security, good nutrition, and improve sustainable agriculture. Whereas, the 8th goal is to promote inclusive and sustainable economic growth, productive and comprehensive employment opportunities, and decent work for all. In the second quarter of 2017, the agricultural sector contributed 13.92 percent (up 0.33 percent from the first quarter of 2017) to economic growth. In addition to absorbing labor (31.86% of the workforce), agriculture also provides food, industrial raw materials, feed and bio-energy and contributes to foreign exchange of US $ 8.24 billion. Innovation is very important in the success of agricultural development. Information plays an important role in the application of innovation by agricultural actors. The Indonesian Center for Agricultural Library and Agricultural Technology Dissemination plays a role in providing information related to agricultural innovation and promoting agricultural literacy in the community. The activities of agricultural literacy conducted by PUSTAKA include: 1) agricultural literacy workshop among students and extension workers, 2) increasing video collections of agricultural technology, 3) agricultural literacy in Taman Baca, 4) building Kid Corner and completing it with library material in agriculture , 5) visit Agricultural Technology and Science Parks, 6) exhibitions, and 7) technical guidance for farmers by presenting resource persons who are experts in agriculture. Through agricultural literacy, the community have been able to utilize information resources such as iTani, the Agricultural Publication Repository and the agricultural information provider website. In the end, it is expected that the community will more quickly adopt agricultural innovations.
WEBSITE PERPUSTAKAAN SEBAGAI MEDIA PROMOSI LEMBAGA RISET
Authors: Sutarsyah Sutarsyah
Published: August 2023

Website perpustakaan lembaga riset dipandang sebagai cerminan atas layanan dan sumber-sumber yang dimiliki oleh sebuah perpustakaan dan lembaga induknya, Website perpustakaan menjadi salah satu media promosi yang dapat mengangkat citra perpustakaan dan akan membangun image perpustakaan. Artikel ini bertujuan untuk mengetahui sejauh mana website yang efektif  sebagai media promosi dan mengenal profil website perpustakaan Lembaga Pemerintah Non Kementerian (LPNK)   Ristekdikti. Metode yang digunakan yaitu metode survei, survei dilakukan terhadap 6  website perpustakaan dari  enam lembaga penelitian LPNK lingkup Ristekdikti di Indonesia  LIPI, LAPAN, BPPT, BSN, BAPETEN, BATAN, dan ditinjau website menarik sebagai media promosi mengacu pada 7 aspek website efektif yaitu;  context, content, community, customization, communication, connection, commerce.  Hasil kajian menunjukkan dari aspek context, tampilan interface dengan  warna background didominasi putih  dan teks didominasi hitam ada pada website perpustakaan BSN, Batan, Bapeten, PDII-LIPI sedangkan dua website lainnya warna background didominasi abu-abu dengan tulisan biru muda, dan putih yaitu BPPT dan Lapan. Tampilan gambar variatif terdapat pada website Batan, Bapeten, Lapan, PDII-LIPI, sedangkan dua website lainnya tampilan gambarnya kurang variatif yaitu pada website perpustakaan BSN dan BPPT. Dari aspek content hanya ada 2 website memuat  video yaitu website BPPT dan PDII-LIPI yaitu film tentang profil Perpustakaan BPPT & PDDITV. Dari aspek Community, hanya ada satu website yang memfasilitasi yaitu web PDII-LIPI dengan adanya media Login forum. Sedangkan dari aspek customization dan communication  ke-6 website tidak memfasilitasinya. Dari aspek connection yang memiliki tautan kepada website dengan tema yang sama yaitu website perpustakaan Batan, Bapeten. Lapan, PDII-LIPI. Sedangkan dari aspek commerce/komersial , hanya website Perpustakaan BSN yang menyediakan menu pemesanan  SNI.
THE INFLUENCE OF THE CONCENTRATION OF CHLORINE-CONTAINING CONDENSING AGENTS IN THE SYNTHESIS OF CARBOXYLIC ACID ANILIDESТ
Authors: Shteinberg Leon
Published: August 2023

Chlorine-containing condensing agents (PCl3, TiCl4, SiCl4) are widely used in the synthesis of carboxylic acid arylamides by the reaction of arylamines with carboxylic acids in stoichiometric amounts, and often in excess (40–150 mol % relative to the latter). To find the optimal amount of the condensing agent used, the acylation of aniline with 3-hydroxy-2-naphthoic acid in boiling ortho-xylene was studied in the PCl3 concentration range of 0–10 mol % from 3-hydroxy-2-naphthoic acid. It has been established that phosphorus tri-chlorochloride plays the role of a condensing agent and a catalyst, while 3-hydroxy-2-naphthoic acid anilide is formed along two routes with different rates, which can be separated kinetically. The first route includes the rapid synthesis of acid chloride, its interaction with aniline to obtain the target product. The second route is implemented due to phosphorous acid, which is formed from phosphorus trichloride and is a true acylation catalyst.

The maximum yield of anilide 3-hydroxy-2-naphthoic acid decreases with increasing catalyst concentration, approximately propor-tional to the amount of aniline phosphite formed from it in the mass, which, apparently, is not reactive when interacting with the starting acid.

Similar patterns were also found in the acylation of aniline with benzoic and salicylic acids in the presence of phosphorus trichloride; benzoic acid in the presence of titanium tetrachloride; 3-hydroxy-2-naphthoic acid in the presence of silicon tetrachloride. They allow a new look at the role of these products (PCl3, TiCl4, SiCl4) as condensing agents and/or ca­talysts in the synthesis of amides of carboxylic acids.

Taking into account the obtained results, in practice it is better to use PCl3 as a catalyst in an amount not exceeding 2–2.5%, or even to replace it with phosphorous acid. This allows to completely get rid of the release of hydrogen chloride, significantly reduce the consumption rates for raw materials, simplify the entire technological process, reduce the amount of waste, ensure the yield of 3-hydroxy-2-naphthoic acid anilide close to quantitative, create a direct catalytic amidation technology that fully meets the criteria «green» chemistry processes.
Phylogeography of the Cow Knob Salamander (Plethodon punctatus Highton): populations on isolated Appalachian mountaintops are disjunct but not divergent
Authors: Graham Matthew R. , Flint William D. , Powell Alexsis M. , Fet Victor , Pauley Thomas K.
Published: August 2023

Although many studies have examined how taxa responded to Pleistocene climate fluctuations in the Appalachian Mountains, impacts on high-elevation endemics of Central Appalachia are not yet understood. We use mitochondrial (ND4 & Cytb) and nuclear (GAPD) DNA sequences to investigate the phylogeography of the Cow Knob Salamander (Plethodon punctatus), a woodland species from Central Appalachian highlands thought to have origins in the Pleistocene. Data from 72 tail tips representing 25 sites revealed that the species comprises two geographically cohesive mitochondrial clades with a narrow, putative contact zone on Shenandoah Mountain. Molecular clock estimates indicate the clades diverged in the Middle Pleistocene. The population size of the Southern clade appears to have remained stable for at least 50,000 years. Despite spanning several isolated mountain systems, the Northern clade has exceptionally low genetic diversity, probably due to recent demographic expansion. Palaeodemographic hypothesis testing supported a scenario in which a founder effect characterized the Northern clade as it diverged from the Southern clade. Species distribution models predicted no suitable habitat for the species during the Last Glacial Maximum. Ultimately, Pleistocene glacial climates may have driven the species from the northern half of its current range, with recolonization events by members of the Northern clade as climates warmed. Density dependent processes may now maintain a narrow contact zone between the two clades.
Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets
Authors: Li Wanxin , Mirone Jules , Prasad Ashok , Miolane Nina , Legrand Carine , Dao Duc Khanh
Published: August 2023

Conventional dimensionality reduction methods like Multidimensional Scaling (MDS) are sensitive to the presence of orthogonal outliers, leading to significant defects in the embedding. We introduce a robust MDS method, called DeCOr-MDS (Detection and Correction of Orthogonal outliers using MDS), based on the geometry and statistics of simplices formed by data points, that allows to detect orthogonal outliers and subsequently reduce dimensionality. We validate our methods using synthetic datasets, and further show how it can be applied to a variety of large real biological datasets, including cancer image cell data, human microbiome project data and single cell RNA sequencing data, to address the task of data cleaning and visualization.
Collective behavior and self-organization in neural rosette morphogenesis
Authors: Miotto Mattia , Rosito Maria , Paoluzzi Matteo , de Turris Valeria , Folli Viola , Leonetti Marco , Ruocco Giancarlo , Rosa Alessandro , Gosti Giorgio
Published: August 2023

Neural rosettes develop from the self-organization of differentiating human pluripotent stem cells. This process mimics the emergence of the embryonic central nervous system primordium, i.e., the neural tube, whose formation is under close investigation as errors during such process result in severe diseases like spina bifida and anencephaly. While neural tube formation is recognized as an example of self-organization, we still do not understand the fundamental mechanisms guiding the process. Here, we discuss the different theoretical frameworks that have been proposed to explain self-organization in morphogenesis. We show that an explanation based exclusively on stem cell differentiation cannot describe the emergence of spatial organization, and an explanation based on patterning models cannot explain how different groups of cells can collectively migrate and produce the mechanical transformations required to generate the neural tube. We conclude that neural rosette development is a relevant experimental 2Din-vitromodel of morphogenesis because it is a multi-scale self-organization process that involves both cell differentiation and tissue development. Ultimately, to understand rosette formation, we first need to fully understand the complex interplay between growth, migration, cytoarchitecture organization, and cell type evolution.
Targeting alternative splicing in cancer immunotherapy
Authors: Han Nan , Liu Zhaoqi
Published: August 2023

Tumor immunotherapy has made great progress in cancer treatment but still faces several challenges, such as a limited number of targetable antigens and varying responses among patients. Alternative splicing (AS) is an essential process for the maturation of nearly all mammalian mRNAs. Recent studies show that AS contributes to expanding cancer-specific antigens and modulating immunogenicity, making it a promising solution to the above challenges. The organoid technology preserves the individual immune microenvironment and reduces the time/economic costs of the experiment model, facilitating the development of splicing-based immunotherapy. Here, we summarize three critical roles of AS in immunotherapy: resources for generating neoantigens, targets for immune-therapeutic modulation, and biomarkers to guide immunotherapy options. Subsequently, we highlight the benefits of adopting organoids to develop AS-based immunotherapies. Finally, we discuss the current challenges in studying AS-based immunotherapy in terms of existing bioinformatics algorithms and biological technologies.
Is there a role for bradykinin in cerebral malaria pathogenesis?
Authors: Pinheiro Alessandro de Sa , Kazura James W. , Pinheiro Ana Acacia , Schmaier Alvin H.
Published: August 2023

Malaria is a parasitic disease of global health significance and a leading cause of death in children living in endemic regions. Although various Plasmodium species are responsible for the disease, Plasmodium falciparum infection accounts for most severe cases of the disease in humans. The mechanisms of cerebral malaria pathogenesis have been studied extensively in humans and animal malaria models; however, it is far from being fully understood. Recent discoveries indicate a potential role of bradykinin and the kallikrein kinin system in the pathogenesis of cerebral malaria. The aim of this review is to highlight how bradykinin is formed in cerebral malaria and how it may impact cerebral blood-brain barrier function. Areas of interest in this context include Plasmodium parasite enzymes that directly generate bradykinin from plasma protein precursors, cytoadhesion of P. falciparum infected red blood cells to brain endothelial cells, and endothelial cell blood-brain barrier disruption.
Left atrial appendage aneurysm in pediatrics: Case study and literature review
Authors: Norozi Kambiz , Subasri Mathushan , Diaz Luis Altamirano , Honjo Osami
Published: August 2023

Left atrial appendage aneurysm (LAAA) is a rare cardiac pathology that is often identified in adulthood. There are a myriad of presentations related to atrial appendage enlargement, but most are asymptomatic. Pediatric cases of LAAA are extremely rare. We report a case of an incidental giant LAAA found in a healthy 6-year-old boy. He was successfully treated with surgical resection. A review of the literature shows that the presentation of LAAA in pediatrics likely involves cardiac or respiratory symptoms but can also be incidental findings. Similar to adults, diagnosis requires cardiac imaging, with echocardiography being the mainstay. Surgical intervention is indicated in symptomatic and most asymptomatic patients to prevent complications. More research is warranted into the optimal timing of surgery and alternative surgical approaches for complex cases.
Identification of potential angiogenic biomarkers in human follicular fluid for predicting oocyte maturity
Authors: Chen Hsuan-Ting , Wu Wen-Bin , Lin Jun-Jin , Lai Tsung-Hsuan
Published: August 2023

Background

Angiogenesis in folliculogenesis contributes to oocyte developmental competence in natural and in vitro fertilization (IVF) cycles. Therefore, the identification of key angiogenic factors in follicular fluid (FF) during folliculogenesis is clinically significant and important for in vitro fertilization. This study aims to identify the key angiogenic factors in FF for predicting oocyte maturity during in vitro fertilization.

Materials and methods

Forty participants who received ovarian stimulation using a GnRH antagonist protocol in their first in vitro fertilization treatment were recruited. From each patient, two follicular samples (one preovulatory follicle, > 18 mm; one mid-antral follicle, < 14 mm) were collected without flushing during oocyte retrieval. In total, 80 FF samples were collected from 40 patients. The expression profiles of angiogenesis-related proteins in FF were analyzed via Luminex high-performance assays. Recorded patient data included antral follicle count, anti-müllerian hormone, age, and BMI. Serum samples were collected on menstrual cycle day 2, the trigger day, and the day of oocyte retrieval. Hormone concentrations including day 2 FSH/LH/E2/P4, trigger day E2/LH/P4, and retrieval day E2/LH/P4 were measured by chemiluminescence assay.

Results

Ten angiogenic factors were highly expressed in FF: eotaxin, Gro-α, IL-8, IP-10, MCP-1, MIG, PAI-1 (Serpin), VEGF-A, CXCL-6, and HGF. The concentrations of eotaxin, IL-8, MCP1, PAI-1, and VEGF-A were significantly higher in preovulatory follicles than those in mid-antral follicles, while the Gro-α and CXCL-6 expressional levels were lower in preovulatory than in mid-antral follicles (p < 0.05). Logistic regression and receiver operating characteristic (ROC) analysis revealed that VEGF-A, eotaxin, and CXCL-6 were the three strongest predictors of oocyte maturity. The combination of VEGF-A and CXCL-6 predicted oocyte maturity with a higher sensitivity (91.7%) and specificity (72.7%) than other combinations.

Conclusion

Our findings suggest that VEGF-A, eotaxin, and CXCL-6 concentrations in FF strongly correlate with oocyte maturity from the mid-antral to preovulatory stage. The combination of VEGF-A and CXCL-6 exhibits a relatively good prediction rate of oocyte maturity during in vitro fertilization.
Flow characteristics of the Hornád River and the anthropogenic impact of the Ružín dam for the period 1973–2020
Authors: Nagy Patrik , Kubiak-Wójcicka Katarzyna , Káposztásová Daniela , Zeleňákova Martina , Vranay František
Published: August 2023

The aim of the study is to analyse the monthly and annual variability of the flow of the Hornad River in the years 1973–2020. The research showed that an upward trend in annual air temperature, precipitation and flows was recorded throughout the catchment area. The analysis of the annual Richard-Baker Index (RBI) and flow variability (Cv) showed a clear downward trend in the variability indexes Cv and Richard-Baker Index in the analyzed multi-year period only at the Kysak station, which is located downstream of the dam. No such changes were observed at the remaining Margecany and Spisska Nova Ves stations, which are located above the dam. The analysis of average monthly Richard-Baker Index values over the course showed greater variation. Between 1973 and 2020, the Richard-Baker Index values ranged from 0 to 0.49 at the Spisska Nova Ves and Margecany hydrological stations, while at the Kysak station, the Richard-Baker Index ranged from 0 to 0.57, indicating large changes in short-term flows. The maximum Richard-Baker Index value occurred in June 1973 (0.57) at the Kysak station. At the hydrological stations above the Ruzin reservoir, the maximum RBI values were recorded in as well as in July 2008 (0.49) at the Margecany station (0.49) and at the Spisska Nova Ves station (0.48), which was the result of very high precipitation (above 170 mm during a month). The values of the Richard-Baker Index at the Kysak station depended on the possibility of water retention in the Ružín I and Ružín II reservoirs and flow control below the dam.
Construction of a carbon neutral enterprise environmental performance assessment model based on transformer-GRU
Authors: Chen Yanqing
Published: August 2023

Introduction

Carbon-neutral enterprise environmental performance assessment is an important method for evaluating the impact and benefits of enterprises on the environment during the process of achieving carbon neutrality. This paper proposes a method for evaluating the environmental performance of carbon-neutral enterprises using the Transformer-GRU model.

Methods

The proposed method combines the Transformer and GRU models to accurately predict and analyze the environmental performance of carbon-neutral enterprises. The Transformer model is used to extract features, and the GRU model is used for sequence modeling, which improves the model's prediction accuracy and generalization ability. The method is validated using actual enterprise data for experimental verification.

Results

The experiments show that the proposed method has significant practical significance in evaluating the environmental performance of carbon-neutral enterprises. The method accurately predicts and analyzes the enterprise's carbon emissions, energy consumption, wastewater and gas discharge, and solid waste treatment.

Discussion

The proposed method provides a new approach for evaluating the environmental performance of carbon-neutral enterprises. The combination of the Transformer and GRU models can effectively improve the accuracy and generalization ability of the model. The method can be used to help enterprises evaluate their environmental performance and make decisions to achieve carbon neutrality.
Genetics, environmental stress, and amino acid supplementation affect lactational performance via mTOR signaling pathway in bovine mammary epithelial cells
Authors: Li Bin , Khan Muhammad Zahoor , Khan Ibrar Muhammad , Ullah Qudrat , Cisang Zhuo-Ma , Zhang Nan , Wu Dan , Huang Bingjian , Ma Yulin , Khan Adnan , Jiang Nan , Zahoor Muhammad
Published: August 2023

Mammary glands are known for their ability to convert nutrients present in the blood into milk contents. In cows, milk synthesis and the proliferation of cow mammary epithelial cells (CMECs) are regulated by various factors, including nutrients such as amino acids and glucose, hormones, and environmental stress. Amino acids, in particular, play a crucial role in regulating cell proliferation and casein synthesis in mammalian epithelial cells, apart from being building blocks for protein synthesis. Studies have shown that environmental factors, particularly heat stress, can negatively impact milk production performance in dairy cattle. The mammalian target of rapamycin complex 1 (mTORC1) pathway is considered the primary signaling pathway involved in regulating cell proliferation and milk protein and fat synthesis in cow mammary epithelial cells in response to amino acids and heat stress. Given the significant role played by the mTORC signaling pathway in milk synthesis and cell proliferation, this article briefly discusses the main regulatory genes, the impact of amino acids and heat stress on milk production performance, and the regulation of mTORC signaling pathway in cow mammary epithelial cells.
Comparative analysis of the complete mitogenome of Geoffroea decorticans: a native tree surviving in the Atacama Desert
Authors: Contreras-Díaz Roberto , Carevic Felipe S. , van den Brink Liesbeth
Published: August 2023

Chañar (Geoffroea decorticans (Gill., ex Hook. & Arn.) Burkart) has been highly significant for indigenous people in the Atacama Desert for over 3,000 years. Through evolutionary processes, the G. decorticans mitogenome likely underwent changes facilitating its adaptation to the extreme conditions of the Atacama Desert. Here, we compare the mitochondrial genome of G. decorticans with those of other Papilionoideae family species. The complete mitogenome of G. decorticans was sequenced and assembled, making it the first in the genus Geoffroea. The mitogenome contained 383,963 base pairs, consisting of 33 protein coding genes, 21 transfer RNA genes, and 3 ribosomal RNA genes. The Chañar mitogenome is relatively compact, and has two intact genes (sdh4 and nad1) which were not observed in most other species. Additionally, Chañar possessed the highest amount of mitochondrial DNA of plastid origin among angiosperm species. The phylogenetic analysis of the mitogenomes of Chañar and 12 other taxa displayed a high level of consistency in taxonomic classification, when compared to those of the plastid genome. Atp8 was subjected to positive selection, while the ccmFc and rps1 were subjected to neutral selection. This study provides valuable information regarding its ability to survive the extreme environmental conditions of the Atacama Desert.
Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs
Authors: Fiedler Lisa , Middendorf Martin , Bernt Matthias
Published: August 2023

A wide range of scientific fields, such as forensics, anthropology, medicine, and molecular evolution, benefits from the analysis of mitogenomic data. With the development of new sequencing technologies, the amount of mitochondrial sequence data to be analyzed has increased exponentially over the last few years. The accurate annotation of mitochondrial DNA is a prerequisite for any mitogenomic comparative analysis. To sustain with the growth of the available mitochondrial sequence data, highly efficient automatic computational methods are, hence, needed. Automatic annotation methods are typically based on databases that contain information about already annotated (and often pre-curated) mitogenomes of different species. However, the existing approaches have several shortcomings: 1) they do not scale well with the size of the database; 2) they do not allow for a fast (and easy) update of the database; and 3) they can only be applied to a relatively small taxonomic subset of all species. Here, we present a novel approach that does not have any of these aforementioned shortcomings, (1), (2), and (3). The reference database of mitogenomes is represented as a richly annotated de Bruijn graph. To generate gene predictions for a new user-supplied mitogenome, the method utilizes a clustering routine that uses the mapping information of the provided sequence to this graph. The method is implemented in a software package called DeGeCI (De Bruijn graph Gene Cluster Identification). For a large set of mitogenomes, for which expert-curated annotations are available, DeGeCI generates gene predictions of high conformity. In a comparative evaluation with MITOS2, a state-of-the-art annotation tool for mitochondrial genomes, DeGeCI shows better database scalability while still matching MITOS2 in terms of result quality and providing a fully automated means to update the underlying database. Moreover, unlike MITOS2, DeGeCI can be run in parallel on several processors to make use of modern multi-processor systems.
Childhood-onset systemic lupus erythematosus: characteristics and the prospect of glucocorticoid pulse therapy
Authors: Pan Lu , Liu Jinxiang , Liu Congcong , Guo Lishuang , Punaro Marilynn , Yang Sirui
Published: August 2023

Childhood-onset systemic lupus erythematosus (cSLE) is an autoimmune disease that results in significant damage and often needs more aggressive treatment. Compared to adult-onset SLE, cSLE has a stronger genetic background and more prevalent elevated type I Interferon expression. The management of cSLE is more challenging because the disease itself and treatment can affect physical, psychological and emotional growth and development. High dose oral glucocorticoid (GC) has become the rule for treating moderate to severe cSLE activity. However, GC-related side effects and potential toxicities are problems that cannot be ignored. Recent studies have suggested that GC pulse therapy can achieve disease remission rapidly and reduce GC-related side effects with a reduction in oral prednisone doses. This article reviews characteristics, including pathogenesis and manifestations of cSLE, and summarized the existing evidence on GC therapy, especially on GC pulse therapy in cSLE, followed by our proposal for GC therapy according to the clinical effects and pathogenesis.
No association between incidence of type 1 diabetes and rotavirus vaccination in Swedish children
Authors: Rangert Amanda , Oldin Carin , Golsäter Marie , Ludvigsson Johnny , Åkesson Karin
Published: August 2023

Background

Rotavirus infection is a potential trigger of type 1 diabetes (T1D) and rotavirus vaccination is hypothesized to decrease the incidence of T1D. In Sweden, rotavirus vaccination was introduced in 2014 in two regions and from 2019, nationwide. This study aims to investigate the association between rotavirus vaccination and incidence of T1D in Swedish children and whether rotavirus vaccination is associated with a change in clinical manifestation at diabetes onset.

Methods

A nationwide register-based study with all Swedish children <15 years of age, diagnosed with T1D 2009-2019 was conducted. 7893 children were retrieved. Nationwide vaccine coverage was collected from Child Health Services. Three vaccine groups were created: I: Vaccination start 2014; II: Gradual vaccination start 2016-2018; III: No vaccination. Incidence rates of T1D before (2009-2014) and after (2014-2019) introduction of rotavirus vaccine were compared.

Findings

The mean incidence of T1D in children <15 years was 42·61 per 100 000 during the observed period. When comparing the years before and after 2014 the incidence rate ratio (IRR) for children <5 years was 0·86 in group I (p=0·10), 0·85 (p=0·05) in group II and 0·87 (p=0·06) in group III. A similar IRR reduction was also seen among older children who received no vaccine. Children developing or not developing T1D were vaccinated to the same extent. No differences regarding clinical manifestation at onset associated with rotavirus vaccination were seen.

Interpretation

There is no association between rotavirus vaccination in children and incidence or clinical manifestation of T1D.
Dual role of peripheral B cells in multiple sclerosis: emerging remote players in demyelination and novel diagnostic biomarkers
Authors: Torres Iglesias Gabriel , Fernández-Fournier Mireya , López-Molina MariPaz , Piniella Dolores , Laso-García Fernando , Gómez-de Frutos Mari Carmen , Alonso-López Elisa , Botella Lucía , Chamorro Beatriz , Sánchez-Velasco Sara , Puertas Inmaculada , Tallón Barranco Antonio , Nozal Pilar , Díez-Tejedor Exuperio , Gutiérrez-Fernández María , Otero-Ortega Laura
Published: August 2023

Introduction

Multiple sclerosis is an inflammatory and demyelinating disease caused by a pathogenic immune response against the myelin sheath surfaces of oligodendrocytes. The demyelination has been classically associated with pathogenic B cells residing in the central nervous system that release autoreactive antibodies against myelin. The aim of the present study was to investigate whether extracellular vesicles (EVs) mediate delivery of myelin autoreactive antibodies from peripheral B cells against oligodendrocytes in multiple sclerosis (MS) and to analyze whether these EVs could mediate demyelination in vitro. We also studied the role of these EV-derived myelin antibodies as a diagnostic biomarker in MS.

Methods

This is a prospective, observational, and single-center study that includes patients with MS and two control groups: patients with non-immune white matter lesions and healthy controls. We isolated B-cell-derived EVs from the blood and cerebrospinal fluid (CSF) and analyzed their myelin antibody content. We also studied whether antibody-loaded EVs reach oligodendrocytes in patients with MS and the effect on demyelination of B-cell-derived EVs containing antibodies in vitro.

Results

This study enrolled 136 MS patients, 23 white matter lesions controls, and 39 healthy controls. We found autoreactive myelin antibodies in EVs that were released by peripheral B cells, but not by populations of B cells resident in CSF. We also identified a cut-off of 3.95 ng/mL of myelin basic protein autoantibodies in EVs from peripheral B cells, with 95.2% sensitivity and 88.2% specificity, which allows us to differentiate MS patients from healthy controls. EV-derived myelin antibodies were also detected in the oligodendrocytes of MS patients. Myelin antibody-loaded EVs from B cells induced myelin markers decrease of oligodendrocytes in vitro.

Discussion

Peripheral reactive immune cells could contribute remotely to MS pathogenesis by delivering myelin antibodies to oligodendrocytes. EV-derived myelin antibodies could play a role as diagnostic biomarker in MS.
Customizably designed multibodies neutralize SARS-CoV-2 in a variant-insensitive manner
Authors: Abreu Cecilia , Ortega Claudia , Olivero-Deibe Natalia , Carrión Federico , Gaete-Argel Aracelly , Valiente-Echeverría Fernando , Soto-Rifo Ricardo , Milan Bonotto Rafaela , Marcello Alessandro , Pantano Sergio
Published: August 2023

The COVID-19 pandemic evolves constantly, requiring adaptable solutions to combat emerging SARS-CoV-2 variants. To address this, we created a pentameric scaffold based on a mammalian protein, which can be customized with up to 10 protein binding modules. This molecular scaffold spans roughly 20 nm and can simultaneously neutralize SARS-CoV-2 Spike proteins from one or multiple viral particles. Using only two different modules targeting the Spike’s RBD domain, this construct outcompetes human antibodies from vaccinated individuals’ serum and blocks in vitro cell attachment and pseudotyped virus entry. Additionally, the multibodies inhibit viral replication at low picomolar concentrations, regardless of the variant. This customizable multibody can be easily produced in procaryote systems, providing a new avenue for therapeutic development and detection devices, and contributing to preparedness against rapidly evolving pathogens.
The challenge of making the right choice: patient avatars in the era of cancer immunotherapies
Authors: Kayser Charlotte , Brauer Annika , Susanne Sebens , Wandmacher Anna Maxi
Published: August 2023

Immunotherapies are a key therapeutic strategy to fight cancer. Diverse approaches are used to activate tumor-directed immunity and to overcome tumor immune escape. The dynamic interplay between tumor cells and their tumor(immune)microenvironment (T(I)ME) poses a major challenge to create appropriate model systems. However, those model systems are needed to gain novel insights into tumor (immune) biology and a prerequisite to accurately develop and test immunotherapeutic approaches which can be successfully translated into clinical application. Several model systems have been established and advanced into so-called patient avatars to mimic the patient´s tumor biology. All models have their advantages but also disadvantages underscoring the necessity to pay attention in defining the rationale and requirements for which the patient avatar will be used. Here, we briefly outline the current state of tumor model systems used for tumor (immune)biological analysis as well as evaluation of immunotherapeutic agents. Finally, we provide a recommendation for further development to make patient avatars a complementary tool for testing and predicting immunotherapeutic strategies for personalization of tumor therapies.
Interferome signature dynamics during the anti-dengue immune response: a systems biology characterization
Authors: Usuda Júlia Nakanishi , Plaça Desirée Rodrigues , Fonseca Dennyson Leandro M. , Marques Alexandre H. C. , Filgueiras Igor Salerno , Chaves Victor Gabriel Bastos , Adri Anny Silva , Torrentes-Carvalho Amanda , Hirata Mario Hiroyuki , Freire Paula Paccielli , Catar Rusan , Cabral-Miranda Gustavo , Schimke Lena F. , Moll Guido , Cabral-Marques Otavio
Published: August 2023

Dengue virus (DENV) infection manifests as a febrile illness with three distinct phases: early acute, late acute, and convalescent. Dengue can result in clinical manifestations with different degrees of severity, dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. Interferons (IFNs) are antiviral cytokines central to the anti-DENV immune response. Notably, the distinct global signature of type I, II, and III interferon-regulated genes (the interferome) remains uncharacterized in dengue patients to date. Therefore, we performed an in-depth cross-study for the integrative analysis of transcriptome data related to DENV infection. Our systems biology analysis shows that the anti-dengue immune response is characterized by the modulation of numerous interferon-regulated genes (IRGs) enriching, for instance, cytokine-mediated signaling (e.g., type I and II IFNs) and chemotaxis, which is then followed by a transcriptional wave of genes associated with cell cycle, also regulated by the IFN cascade. The adjunct analysis of disease stratification potential, followed by a transcriptional meta-analysis of the interferome, indicated genes such as IFI27, ISG15, and CYBRD1 as potential suitable biomarkers of disease severity. Thus, this study characterizes the landscape of the interferome signature in DENV infection, indicating that interferome dynamics are a crucial and central part of the anti-dengue immune response.
Novel opportunities from bioimaging to understand the trafficking and maturation of intracellular pulmonary surfactant and its role in lung diseases
Authors: Garcia María José , Amarelle Luciano , Malacrida Leonel , Briva Arturo
Published: August 2023

Pulmonary surfactant (PS), a complex mixture of lipids and proteins, is essential for maintaining proper lung function. It reduces surface tension in the alveoli, preventing collapse during expiration and facilitating re-expansion during inspiration. Additionally, PS has crucial roles in the respiratory system’s innate defense and immune regulation. Dysfunction of PS contributes to various respiratory diseases, including neonatal respiratory distress syndrome (NRDS), adult respiratory distress syndrome (ARDS), COVID-19-associated ARDS, and ventilator-induced lung injury (VILI), among others. Furthermore, PS alterations play a significant role in chronic lung diseases such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). The intracellular stage involves storing and releasing a specialized subcellular organelle known as lamellar bodies (LB). The maturation of these organelles requires coordinated signaling to organize their intracellular organization in time and space. LB’s intracellular maturation involves the lipid composition and critical processing of surfactant proteins to achieve proper functionality. Over a decade ago, the supramolecular organization of lamellar bodies was studied using electron microscopy. In recent years, novel bioimaging tools combining spectroscopy and microscopy have been utilized to investigate the in cellulo intracellular organization of lamellar bodies temporally and spatially. This short review provides an up-to-date understanding of intracellular LBs. Hyperspectral imaging and phasor analysis have allowed identifying specific transitions in LB’s hydration, providing insights into their membrane dynamics and structure. A discussion and overview of the latest approaches that have contributed to a new comprehension of the trafficking and structure of lamellar bodies is presented.
Midgut serine proteinases participate in dietary adaptations of the castor (Eri) silkworm Samia ricini Anderson transferred from Ricinus communis to an ancestral host, Ailanthus excelsa Roxb
Authors: Kashung Sochanngam , Bhardwaj Parul , Saikia Mahaswetta , Mazumdar-Leighton Sudeshna
Published: August 2023

Dietary change influenced the life-history traits, nutritional utilization, and midgut serine proteinases in the larvae of the domesticated polyphagous S. ricini, transferred from R. communis (common name: castor; family Euphorbiaceae; the host plant implicated in its domestication) to A. excelsa (common name: Indian tree of heaven; family Simaroubaceae; an ancestral host of wild Samia species). Significantly higher values for fecundity and body weight were observed in larvae feeding on R. communis (Scr diet), and they took less time to reach pupation than insects feeding on A. excelsa (Scai diet). Nevertheless, the nutritional index for efficiency of conversion of digested matter (ECD) was similar for larvae feeding on the two plant species, suggesting the physiological adaptation of S. ricini (especially older instars) to an A. excelsa diet. In vitro protease assays and gelatinolytic zymograms using diagnostic substrates and protease inhibitors revealed significantly elevated levels (p ≤ 0.05) of digestive trypsins, which may be associated with the metabolic costs influencing slow growth in larvae feeding on A. excelsa. RT-PCR with semidegenerate serine proteinase gene-specific primers, and cloning and sequencing of 3′ cDNA ends identified a large gene family comprising at least two groups of putative chymotrypsins (i.e., Sr I and Sr II) resembling invertebrate brachyurins/collagenases with wide substrate specificities, and five groups of putative trypsins (i.e., Sr III, Sr IV, Sr V, Sr VII, and Sr VIII). Quantitative RT-PCR indicated that transcripts belonging to the Sr I, Sr III, Sr IV, and Sr V groups, especially the Sr IV group (resembling achelase I from Lonomia achelous), were expressed differentially in the midguts of fourth instars reared on the two plant species. Sequence similarity indicated shared lineages with lepidopteran orthologs associated with expression in the gut, protein digestion, and phytophagy. The results obtained are discussed in the context of larval serine proteinases in dietary adaptations, domestication, and exploration of new host plant species for commercial rearing of S. ricini.
Immune reconstitution inflammatory syndrome, a controversial burden in the East African context: a systematic review and meta-analysis
Authors: Geteneh Alene , Andualem Henok , Belay Demeke Mesfin , Kiros Mulugeta , Biset Sirak
Published: August 2023

Introduction

It is well established that starting antiretroviral therapy (ART) increases a patient's life expectancy among HIV-positive individuals. Considering the HIV pandemic, the major concern is initiation of ARTs to the large segment of HIV infected population, not adverse events from immune restoration. The prevalence of HIV-associated immune reconstitution inflammatory syndrome (IRIS) is poorly estimated due to Africa's underdeveloped infrastructure, particularly in Eastern Africa. Therefore, this study compiled data regarding the magnitude and associated factors of IRIS in the context of Eastern Africa.

Methods

The electronic databases such as Google Scholar, PubMed, Web of Science, and free Google access were searched till 5 June 2021, and the search was lastly updated on 30 June 2022 for studies of interest. The pooled prevalence, and associated factors with a 95% confidence interval were estimated using the random effects model. The I2 and Egger's tests were used for heterogeneity and publication bias assessment, respectively.

Results

The development of HIV-associated IRIS in Eastern Africa was estimated to be 18.18% (95% CI 13.30–23.06) in the current review. The two most common predictors of IRIS associated with Eastern Africa were the lower pre-ART CD4 T-cell count of 50 cells/μl and the low baseline body mass index level. Therefore, attention should be focused on the early detection and care of HIV-associated IRIS to reduce the morbidity and death caused by IRIS.