bluuebunny/crossref_metadata_2025 huggingface dataset:
Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq data
Authors: Andreani Tommaso , Slot Linda M. , Gabillard Samuel , Struebing Carsten , Reimertz Claus , Veeranagouda Yaligara , Bakker Aleida M. , Olfati-Saber Reza , Toes Rene’ E. M. , Scherer Hans U. , Augé Franck , Šimaitė Deimantė
Published: March 2022

Multiple methods have recently been developed to reconstruct full-length B-cell receptors (BCRs) from single-cell RNA-seq (scRNA-seq) data. This need emerged from the expansion of scRNA-seq techniques, the increasing interest in antibody-based drug development and the importance of BCR repertoire changes in cancer and autoimmune disease progression. However, a comprehensive assessment of performance-influencing factors like the sequencing depth, read length or the number of somatic hypermutations (SHMs) as well as guidance regarding the choice of methodology are still lacking. In this work, we evaluated the ability of six available methods to reconstruct full-length BCRs using one simulated and three experimental SMART-seq datasets. In addition, we validated that the BCRs assembled in silico recognize their intended targets when expressed as monoclonal antibodies. We observed that methods like BALDR, BASIC and BRACER showed the best overall performance across the tested datasets and conditions whereas only BASIC demonstrated acceptable results on very short read libraries. Furthermore, the de novo assembly-based methods BRACER and BALDR were the most accurate in reconstructing BCRs harboring different degrees of SHMs in the variable domain, while TRUST4, MiXCR and BASIC were the fastest. Finally, we propose guidelines to select the best method based on the given data characteristics.
m6A RNA methylation impairs gene expression variability and reproductive thermotolerance inArabidopsis
Authors: Wang Ling , Zhuang Haiyan , Fan Wenwen , Zhang Xia , Dong Haihong , Yang Hongxing , Cho Jungnam
Published: March 2022

Plants are more susceptible to high temperature stress during reproductive development, which can cause drastic yield loss of fruit and seed crops. Unfortunately, the underlying mechanism remains largely unknown. Here we suggest that m6A RNA methylation level increases in the reproductive tissues ofArabidopsisand negatively regulates gene expression variability. It has been suggested that stochasticity of gene expression can be advantageous to fitness of living organisms under environmental challenges. Indeed, reduced gene expression variability in flowers was associated with compromised transcriptional activation of heat-responsive genes. Importantly, disruption of an RNA demethylaseAtALKBH10Bled to lower gene expression variability, hypo-responsiveness of heat-activated genes, and strong reduction of plant fertility. Overall, our work proposes a novel mechanism that m6A RNA modification mediates the bet-hedging strategy of plants challenged by heat stress.
A Cellular Taxonomy of the Adult Human Spinal Cord
Authors: Yadav Archana , Matson Kaya J.E. , Li Li , Hua Isabelle , Petrescu Joana , Kang Kristy , Alkaslasi Mor R. , Lee Dylan I. , Hasan Saadia , Galuta Ahmad , Dedek Annemarie , Ameri Sara , Parnell Jessica , Alshardan Mohammad M. , Qumqumji Feras Abbas , Alhamad Saud M. , Wang Alick Pingbei , Poulen Gaetan , Lonjon Nicolas , Vachiery-Lahaye Florence , Gaur Pallavi , Nalls Mike A. , Qi Yue A. , Ward Michael E. , Hildebrand Michael E. , Mery Pierre-Francois , Bourinet Emmanuel , Bauchet Luc , Tsai Eve C. , Phatnani Hemali , Le Pichon Claire E. , Menon Vilas , Levine Ariel J.
Published: March 2022

The mammalian spinal cord functions as a community of glial and neuronal cell types to accomplish sensory processing, autonomic control, and movement; conversely, the dysfunction of these cell types following spinal cord injury or disease states can lead to chronic pain, paralysis, and death. While we have made great strides in understanding spinal cellular diversity in animal models, it is crucial to characterize human biology directly to uncover specialized features of basic function and to illuminate human pathology. Here, we present a cellular taxonomy of the adult human spinal cord using single nucleus RNA-sequencing with spatial transcriptomics and antibody validation. We observed 29 glial clusters, including rare cell types such as ependymal cells, and 35 neuronal clusters, which we found are organized principally by anatomical location. To demonstrate the potential of this resource for understanding human disease, we analyzed the transcriptome of spinal motoneurons that are prone to degeneration in amyotrophic lateral sclerosis (ALS) and other diseases. We found that, compared with all other spinal neurons, human motoneurons are defined by genes related to cell size, cytoskeletal structure, and ALS, thereby supporting a model of a specialized motoneuron molecular repertoire that underlies their selective vulnerability to disease. We include a publicly available browsable web resource with this work, in the hope that it will catalyze future discoveries about human spinal cord biology.
Transcriptome analysis reveals robust transcriptional reprogramming during early stages of Cicer-Ascochyta interaction
Authors: Singh Ritu , Dwivedi Aditi , Singh Yeshveer , Kumar Kamal , Ranjan Aashish , Verma Praveen Kumar
Published: March 2022

Ascochyta blight (AB) caused by a filamentous fungus Ascochyta rabiei is a major threat to global chickpea production. The mechanisms underlying chickpea response to A. rabiei remain elusive. Here, we investigated the comparative transcriptional dynamics of AB-resistant and susceptible chickpea genotypes upon A. rabiei infection to understand the early host defence response. Our findings revealed that AB-resistant plants underwent rapid and extensive transcriptional reprogramming compared to susceptible host. At early stage (24-hpi), mainly cell wall remodeling and secondary metabolite pathways were highly activated, while DEGs related with signaling components viz. protein kinases, transcription factors, and hormonal pathways show remarkable upsurge at 72-hpi, especially in resistant genotype. Notably, our data suggests imperative role of JA, ET, and ABA signaling in providing immunity against A. rabiei. Furthermore, gene co-expression networks and modules corroborated the importance of cell wall remodeling, signal transduction and phytohormone pathways. The hub genes such as MYB14, PRE6 and MADS-SOC1 discovered in these modules might be the master regulators governing chickpea immunity. Overall, we not only provide novel insights for comprehensive understanding of immune signaling components mediating AB resistance/susceptibility at early Cicer-Ascochyta interactions, but also offer a valuable resource for developing AB-resistant chickpea.

Highlights

Comparative transcriptomic and co-expression analysis of AB-resistant and susceptible chickpea genotypes reveals high-amplitude transcriptional dynamics in resistant plants, and also identifies TFs, PKs and phytohormone-crosstalk as core regulators for AB-resistance.
Knockout of TSPO delays and reduces amyloid, Tau, astrocytosis and behavioral dysfunctions in Alzheimer’s disease
Authors: Ceyzériat Kelly , Meyer Léa , Bouteldja Farha , Tsartsalis Stergios , Amossé Quentin , Middleton Ryan J. , Liu Guo-Jun , Banati Richard B. , Zilli Thomas , Garibotto Valentina , Millet Philippe , Tournier Benjamin B.
Published: March 2022

The 18kDa translocator protein (TSPO) is up-regulated in glial cells in neurodegenerative diseases. In Alzheimer’s disease (AD) animal models, TSPO is first overexpressed in astrocytes and then in microglia. However, the precise role of TSPO in the onset and progression of pathology and symptoms characteristic of the disease remains unknown. Here, we report that in the absence of TSPO in 3xTgAD mice the expected disease onset is significantly delayed and a reduction is seen in the hippocampal load of poorly and highly aggregated forms of Tau (−44% and −82%, respectively) and Aβ42 (−25% and −95%, respectively), at 9 months of age. In addition, the astrocyte reactivity was decreased in 3xTgAD.TSPO−/− mice with a reduction in the morphologic complexity and the size of astrocytes in the dorso-dorsal hippocampus and the hilus. Functionally, the absence of TSPO ameliorated the cognitive consequences of adeno-associated virus-induced Tau over-expression in the hippocampus. This suggests that TSPO plays an important role in the active disease progression of AD. TSPO-inhibiting drugs thus merit further exploration as to their potential to reduce the rate of neurodegenerative disease progression.
Differences in homologous recombination and maintenance of heteropolyploidy between Haloferax volcanii and Haloferax mediterranei
Authors: Dattani Ambika , Sharon Itai , Shtifman-Segal Ella , Robinzon Shachar , Gophna Uri , Allers Thorsten , Altman Neta
Published: March 2022

Polyploidy, the phenomenon of having more than one copy of the genome in an organism, is common among haloarchaea. While providing short-term benefits for DNA repair, polyploidy is generally regarded as an ‘evolutionary trap’ that by the notion of the Muller’s ratchet will inevitably conclude in the species’ decline or even extinction due to a gradual reduction in fitness. In most reported cases of polyploidy in archaea, the genetic state of the organism is considered as homoploidy i.e. all copies of the genome are identical. Here we demonstrate that while this is indeed the prevalent genetic status in the halophilic archaeon H. volcanii, its close relative H. mediterranei maintains a prolonged heteroploidy state in a non-selective environment once a second allele is introduced. Moreover, a strong genetic linkage was observed between two distant loci in H. mediterranei indicating a low rate of homologous recombination while almost no such linkage was shown in H. volcanii indicating a high rate of recombination in the latter species.

We suggest that H. volcanii escapes Muller’s ratchet by means of an effective chromosome-equalizing gene-conversion mechanism facilitated by highly active homologous recombination, whereas H. mediterranei must elude the ratchet via a different, yet to be elucidated mechanism.
Detection of Parasites in Microbiomes using Metagenomics
Authors: Kirstahler Philipp , Aarestrup Frank M. , Pamp Sünje Johanna
Published: March 2022

Despite a yearly death toll of up to one million people due to parasite-related infections, parasites are still neglected in genomics research. While there is progress in the detection of bacteria and viruses using metagenomics in the context of infectious diseases, there are still challenges in metagenomics-based detection of parasites. Here, we implement a workflow for the detection of parasites from metagenomics data. We employ stringent cut off criteria to limit false positive detections. We analysed a total of 7.120 metagenomics samples of which 359 originated from gut microbiomes of livestock (pigs and chicken) from nine countries, and 6.761 from gut microbiomes of humans (adults and infants) from 25 countries. Five parasite-related genera were detected in livestock, of which Blastocystis sp. was detected in 71% of all pig herds and Eimeria in 83% of all chicken flocks. Distinct gut bacterial taxa were associated with Blastocystis sp. abundance in pigs. Nine parasite-related genera were detected in humans. Blastocystis sp. subtypes ST1, ST2, and ST3 were detected in all countries, and ST3 was most predominant. A higher overall prevalence of Blastocystis sp. was observed in low-income countries as compared to high-income countries, and a higher diversity of Blastocystis subtypes (ST1, ST2, ST3, ST4, ST6, ST7, ST8) was detected in high-income countries as compared to low-income countries. The prevalence of Blastocystis sp. in infant gut microbiome samples was lower as compared to adults. Overall, metagenomics-based analysis may be a promising tool for parasite detection from complex microbiome samples in clinical and veterinary medicine.

Metagenomics could become the preferred method for parasite detection for a wide range of biological samples. Current parasite detection methods often rely on microscopic examination of the sample or using specific PCR. Metagenomics-based analyses may allow for a faster and more convenient way of detecting parasites in humans and animals, as this approach could serve as a one-for-all untargeted approach for pathogen detection, including bacteria, viruses, and parasites.
Moderation: concept and operationalisation in UK universities
Authors: Poole Brian
Published: March 2022

Purpose

The purpose of this paper is to examine the way “moderation” is defined and operationalised at UK universities. It is hoped that this investigation provides pointers for modifications in university documentation and practices, as well as indicates possible areas for future research.

Design/methodology/approach

This paper begins with a review of relevant scholarly literature, first tracing the history of the concept of moderation (essentially meaning the avoidance of extremes) in western thought and then proceeding to show how moderation is understood and operationalised in UK universities. Relevant documentation from 10 UK universities, all in the public domain, is analysed to show both commonalities and differences in definition and operationalisation of moderation.

Findings

This paper shows that universities differ in their understanding of the scope of moderation, with some seeing it as covering the evaluation of draft assessment artifacts. It is also noted that the distinction between moderation and marking is not always expressed in university documentation in ways that distinguish between the two with maximal clarity.

Research limitations/implications

Limitations include the relatively small sample of documents examined. Conversely, ancient universities (e.g. Edinburgh), long-established universities (e.g. Manchester) and 1992 and more recent universities (e.g. Manchester Metropolitan University and Suffolk) are contained in the sample, so moderation practices from across the sector are included.

Practical implications

The main findings are that some universities see moderation as including drafting, redrafting and approval of assessment artifacts, whereas others do not. In addition, although all universities stress that moderation and marking are separate activities, some documentation discusses both the activities in tandem; thus, undermining the contention that they are discrete. Both these findings have implications for UK university documentation in terms of both document structure and precise wording.

Originality/value

The approach taken, in which a sample of publicly available university documents is scrutinised and evaluated, casts a new light on understandings of “moderation”, which is a term and concept that may not always be examined critically by lecturers and quality assurance professionals involved in higher education.
Investigating the role of crowdsourcing in improving the quality of production processes: a systematic literature review
Authors: Grimaldi Michele , Vermicelli Silvia , Cricelli Livio
Published: March 2022

Purpose

In recent years, crowdsourcing – an open and innovative model for outsourcing tasks to a crowd – has become popular for production processes, allowing organizations and firms in different industries to access external skills and expertise efficiently. Companies have opened their innovation processes to crowds outside their boundaries, and users and customers are often involved in developing products in line with market needs. This work aims to investigate the link between crowdsourcing, production and quality to better understand this new interesting phenomenon.

Design/methodology/approach

An explicit and systematic method for reviewing the literature was used. Through the selection and analysis of the relevant articles in the field, this paper presents a comprehensive overview of the pros and cons, risks and opportunities, disadvantages, or concerns, as addressed in the literature, for the adoption of crowdsourcing in the production processes.

Findings

It identifies where, how and to what extent crowdsourcing can be applied profitably within the production of products and services, highlighting how crowdsourcing could affect product and process quality. Finally, some directions for future research are outlined from the analysis conducted.

Originality/value

This work applied the systematic literature review to investigate and evaluate the actual use and impact of crowdsourcing on the production process, focusing on quality enhancement contribution.
Australia's LGBTIQ Research Data Landscape
Authors: Saxby Karinna
Published: March 2022

The past decades have seen rapid changes in societal attitudes and policy surrounding members of the LGBTIQ  community, however this community continues to experience adverse social and economic outcomes relative to their cisgendered heterosexual counterparts. Understanding the LGBTIQ data landscape is essential to promote scholarship in this space and highlight avenues for future data collection. Here I provide an overview of the 17 national data surveys in Australia that capture information on either sexual or gender diversity and are either repeated or longitudinal samples. For each dataset, I provide details on questions pertaining to sexual and gender diversity, indicative sample sizes and age ranges, scope of survey, and data custodians. Altogether, I find thatcollection of information on sexual and gender diverse (SGD) populations in Australia is poor and terminology varies widely. Only seven datasets capture information on both sexual and gender diversity and, of these, none are nationally representative, and only one is a longitudinal sample. Altogether, this review highlights the need for large‐scale, representative and longitudinal data capture of SGD populations in Australia.
Clinicopathological indicators for TERT promoter mutation in papillary thyroid carcinoma
Authors: Na Hee Young , Yu Hyeong Won , Kim Woochul , Moon Jae Hoon , Ahn Chang Ho , Choi Sang Il , Kim Yeo Koon , Choi June Young , Park So Yeon
Published: March 2022

Objective

Mutations in the telomerase reverse transcriptase (TERT) promoter have been reported as a convincing prognostic factor in papillary thyroid carcinomas (PTCs). We aimed to investigate the frequency of TERT promoter mutations in patients with thyroid cancer and identify the clinicopathological factors associated with them in PTCs.

Design

A total of 1086 consecutive cases of thyroid cancer composed of mostly PTCs were included in this study. TERT promoter and BRAF mutations were detected by pyrosequencing and their associations with clinicopathological features of tumour were analyzed.

Results

TERT promoter mutations were observed in 1.9% of PTCs, 6.7% of follicular thyroid carcinomas, 8.3% of Hurthle cell carcinomas and 25.0% of poorly differentiated thyroid carcinomas and in a single case of anaplastic thyroid carcinoma. In PTCs, aggressive clinicopathological features, higher stage and BRAF V600E mutation were all found to be associated with TERT promoter mutations. Distant metastasis and disease recurrence were more frequent in TERT promoter‐mutated PTCs. In multivariate analysis, age ≥55 years, tall cell variant, mitoses ≥3/10 high‐power fields, tumour necrosis, and gross extrathyroidal extension (ETE) were identified as independent factors associated with TERT promoter mutations in PTCs.

Conclusions

This study revealed a relatively low frequency of TERT promoter mutations in Korean patients with PTC. Certain clinicopathological features including old age, tall cell variant, increased mitoses, tumour necrosis and gross ETE were found to be indicative of TERT promoter mutations in PTCs, suggesting that mutational analysis in a particular group of PTCs can be effective in regions with low mutation rates.
Colour‐patterned fabric defect detection based on an unsupervised multi‐scale U‐shaped denoising convolutional autoencoder model
Authors: Zhang Hongwei , Liu Shuting , Tan Quanlu , Lu Shuai , Yao Le , Ge Zhiqiang
Published: March 2022

This study proposes an unsupervised, learning‐based, reconstructed scheme and a residual analysis‐based defect detection model for colour‐patterned fabric defect detection problems in the clothing process industry. It solves the challenging problems of existing supervised fabric defect detection methods, such as high costs in manually labelling samples and designing features, unstable generalisation ability and scarcity of defective samples. First, for a specific texture, the training set was constructed by collecting easily accessible defect‐free colour‐patterned fabric images. Second, a multi‐scale U‐shaped denoising convolutional autoencoder was modelled using defect‐free samples, which can reconstruct the newly tested colour‐patterned fabric images automatically. Subsequently, a residual map between the original image and corresponding reconstructed image was calculated. Finally, the defective areas were detected and accurately localised by further opening operations. The experimental results indicated that the proposed method is valid and robust for detecting defects in various colour‐patterned fabrics. Moreover, with the YDFID‐1 dataset, compared with other models, the intersection over union index of the model proposed in the current paper was improved by at least 3.95%.
Exports to China and Local Employment in South Korea
Authors: Kim Jiyoung , Go Sun
Published: March 2022

We estimate the effect of exports to China on local employment in South Korea, exploiting variations in trade and employment across 220 South Korean municipalities between 2007 and 2017. To identify the effect of exports on employment, we use a novel instrument: China's exports to the US. This isolates the demand‐side factors for South Korean exports to China from the supply‐side factors that lead to biased estimations using ordinary least squares regressions. The results of a two‐stage least squares estimation using municipality‐level data confirm that increased exports to China contribute to a rise in employment in South Korean local labor markets. This effect occurs mostly in the service and construction industries rather than in the manufacturing sector.
Who is @ease? Visitors’ characteristics and working method of professionally supported peer‐to‐peer youth walk‐in centres, anonymous and free of charge
Authors: Leijdesdorff Sophie M. J. , Rosema Stefanie , Klaassen Rianne M. C. , Popma Arne , van Amelsvoort Therese
Published: March 2022

Aim

Although mental disorders often emerge early in life, only a minority of young people receive timely and appropriate mental health care. A worldwide youth mental health movement aims to prevent development and persistence of psychiatric disorders. As part of this movement, the first four @ease centres were opened in the Netherlands. @ease is a youth driven, professionally supported initiative, providing peer‐to‐peer counselling, anonymous and free of charge, for people aged 12–25.

Methods

Data consist of a detailed description of the working method of @ease, combined with characteristics of all young people accessing the services between its inception (January 2018) and July 2020.

Results

Young‐adult peers, including experts by experience, served as counsellors after training in listening, motivational interviewing and solution‐focused strategies. They were supervised by a diverse group of healthcare professionals. A total of 291 visitors, aged 21 on average, were satisfied to very satisfied with @ease's services. Psychosocial distress, social functioning and quality of life measures at first visit showed moderate to severe levels of impairment, and almost half of all visitors reported skipping classes. One third reported parental mental illness, 28% suicidal ideations, and 11% had made specific plans. Less than a third of visitors had received mental health care in the 3 months prior to their visit.

Conclusion

This study showed the need for and feasibility of a youth driven, professionally supported organization offering peer‐to‐peer counselling in the Netherlands. Its flexible and individualized working method enables @ease to normalize problems when possible and intervene when necessary.
A supervised learning‐based approach for focused web crawling for IoMT using global co‐occurrence matrix
Authors: Rajiv S , Navaneethan C
Published: March 2022

Irrelevant search results for a given topic end up wasting search engine users' time. A learning focused web crawler downloads relevant URLs for a given topic using machine‐learning algorithms. The dynamic nature of the web is a challenge in related computation for focused web crawlers. Studies have shown that the learning focused crawler utilizes term frequency‐inverse document frequency (TF‐IDF) to compute the relevance between a web page and a given topic. The TF‐IDF detects similarity of the given topic to its co‐occurrence on the web page. The necessity of efficient mechanism to compute the relevance of URLs syntactically and semantically has led to the proposal of this paper with a word embedding approach to compute the relevance of the web page. The global vector representation cosine similarity is calculated between a topic and the web page contents. The calculated cosine similarity is provided as input to the trained random forest classifier to predict the relevancy of the web page. The evaluation results proved that the proposed crawler produced an average of 0.41 and of 0.59, which outperformed other learning‐focused crawlers on support vector machines, Naive Bayes and artificial neural networks.
Permeability and corrosion resistance of the porous alumina doped by Y2O3 with monodispersed PMMA as pore former
Authors: Li Yanjun , Cao Weidi , Zhao Lianfeng , Liu Donghua , Chen Jin , Cai Yanzhi , Ding Donghai , Xiao Guoqing
Published: March 2022

Porous alumina, with monodispersed PMMA as pore former and Y2O3 as sintering additive, was prepared via a gel casting route with Isobam as a gelling agent. The effects of PMMA addition on its properties, including apparent porosity, bulk density, strength, permeability, and corrosion resistance to acid/alkali, were investigated. With PMMA addition increased, the apparent porosity and permeability were increased obviously, while strength and corrosion resistance to acid/alkali were deteriorated due to increased porosity. Higher firing temperature resulted in lower porosity, higher strength, lower permeability, and better corrosion resistance to acid/alkali. Coarser raw powders resulted in lower strength and higher permeability due to the coarser structure and larger pores of the fabricated samples. Because Y2O3 was used as a sintering additive, and no silica was introduced, the resulting samples possess better corrosion resistance to acid and alkali, especially much better corrosion resistance to alkali, than those reported with silica introduced.
Patterns of parental care and movement in divided broods of golden‐winged warblers
Authors: Peterson Sean M. , Streby Henry M. , Kramer Gunnar R. , Feura Jared M. , Andersen David E.
Published: March 2022

Post‐fledging brood division is a poorly understood, yet widespread suite of avian behaviours that includes both division of parental care and spatial division of a brood. For most species, the differences in parental care between adult males and females and the behavioural mechanisms explaining spatial patterns of brood division are unknown. We studied brood division in golden‐winged warblers Vermivora chrysoptera to describe the spatial and behavioural characteristics of brood division and assess hypotheses describing the potential benefits of brood division. Female golden‐winged warblers are known to travel farther from their nests than males within the post‐fledging period, although the mechanism resulting in this spatial pattern is unknown. From 2010 to 2012, we monitored radio‐marked golden‐winged warbler fledglings from fledging until independence from adult care at three sites in the western Great Lakes region of North America. We observed no significant differences in provisioning, parental attendance, daily distance traveled and fledgling begging between male‐ and female‐reared sub‐broods. We also did not observe a relationship between parental sex and fledgling sex or mass. However, female‐reared sub‐broods exhibited a unique period of relatively consistent directional movement on days 8–10 after fledging, which resulted in females traveling farther from the nests than males. Our observations were not fully consistent with any previously proposed hypotheses about the benefits of brood division. Brood division is a complex behaviour that may have a suite of benefits, including predation defense and provisioning efficiency, that are not fully understood.
Risk factors for incomplete excision of cutaneous squamous cell carcinoma: a large cohort study
Authors: Marsidi N. , Ottevanger R. , Bouwes Bavinck J.N. , Krekel ‐ Taminiau N.M.A. , Goeman J.J. , Genders R.E.
Published: March 2022

Background

The standard treatment for cutaneous squamous cell carcinoma (cSCC) is surgical excision. Failure to radically remove a cSCC is a risk for recurrence, progression and metastasis.

Objectives

This study investigates several risk factors for incomplete excision of cSCC.

Methods

All consecutive patients in a single institution treated with wide local excision for primary cSCC over a 10‐year period were included in this study. Risk factors such as: gender, age, immunosuppression, tumour size, location, differentiation grade, tumour depth, perineural and lymphovascular invasion (PNI and LVI) were extracted from the database. Univariable and (if applicable) multivariable logistic regression analysis were used to identify risk factors (P < 0.05). Generalized estimating equations (GEEs) were used for multiple tumours within the same patients.

Results

A total of 566 patients with 1159 cSCC were identified. Univariable and multivariable logistic regression analysis showed that depth beyond the dermis (OR: 5.7 95% CI: 3.1–10.5) was the only risk factor for incomplete excision of cSCC. Immunosuppression was only a risk factor in the deep plane (OR: 2.5, 95% CI: 1.3–4.6).

Conclusion

Tumour depth beyond the dermis is the most important risk factor for incomplete excision of cSCC. Immunosuppression is a risk factor in the deep plane but its relevance is uncertain. Immunosuppression is not consistently included in the current cSCC staging systems, but care should be taken when treating these patients.
The informed majority could help make research into Alzheimer's disease fairer and more efficient
Authors: Daly Timothy
Published: March 2022

See the Reply by Michael J. DiStefano et al.
Reply to: The informed majority could help make research into Alzheimer's disease fairer and more efficient
Authors: DiStefano Michael J. , Alexander G. Caleb , Anderson Gerard F.
Published: March 2022

This letter comments on the letter by Timothy Daly.
Altered T‐cell subset distribution in the viral reservoir in HIV‐1‐infected individuals with extremely low proviral DNA (LoViReTs)
Authors: Gálvez Cristina , Urrea Víctor , Garcia‐Guerrero Maria del Carmen , Bernal Sílvia , Benet Susana , Mothe Beatriz , Bailón Lucía , Dalmau Judith , Martinez Andrea , Nieto Aroa , Leal Lorna , García Felipe , Clotet Bonaventura , Martinez‐Picado Javier , Salgado Maria
Published: March 2022

Background

HIV cure strategies aim to eliminate viral reservoirs that persist despite successful antiretroviral therapy (ART). We have previously described that 9% of HIV‐infected individuals who receive ART harbor low levels of provirus (LoViReTs).

Methods

We selected 22 LoViReTs matched with 22 controls ART suppressed for more than 3 years with fewer than 100 and more than 100 HIV‐DNA copies/106 CD4+ T cells, respectively. We measured HIV reservoirs in blood and host genetic factors. Fourteen LoViReTs underwent leukapheresis to analyze replication‐competent virus, and HIV‐DNA in CD4+ T‐cell subpopulations. Additionally, we measured HIV‐DNA in rectum and/or lymph node biopsies from nine of them.

Results

We found that LoViReTs harbored not only lower levels of total HIV‐DNA, but also significantly lower intact HIV‐DNA, cell‐associated HIV‐RNA, and ultrasensitive viral load than controls. The proportion of intact versus total proviruses was similar in both groups. We found no differences in the percentage of host factors. In peripheral blood, 71% of LoViReTs had undetectable replication‐competent virus. Minimum levels of total HIV‐DNA were found in rectal and lymph node biopsies compared with HIV‐infected individuals receiving ART. The main contributors to the reservoir were short‐lived transitional memory and effector memory T cells (47% and 29%, respectively), indicating an altered distribution of the HIV reservoir in the peripheral T‐cell subpopulations of LoViReTs.

Conclusion

In conclusion, LoViReTs are characterized by low levels of viral reservoir in peripheral blood and secondary lymphoid tissues, which might be explained by an altered distribution of the proviral HIV‐DNA towards more short‐lived memory T cells. LoViReTs can be considered exceptional candidates for future interventions aimed at curing HIV.
Mineral and glycerol concentrations in drinking water on body weight loss and acid‐base balance in feed‐deprived Holstein bulls
Authors: Wilms Juliette N. , Carvalho Isabela P. , van Empel Mireille , Martín‐Tereso Javier
Published: March 2022

Situations in which cattle are feed‐deprived over extensive periods of time are common in the context of transport and is an animal welfare concern which may also compromise growth and carcass yield grade. This study investigated how the main components of an oral rehydration solution would affect BW loss and blood parameters in feed‐deprived bulls. Three dose–response experiments were performed with 24 bulls each (n = 6 per treatment) to study the effect of mineral concentration in Study I (0, 100, 200 and 300 mOsm/kg), the K+ to Na+ ratio in Study II (25:75, 40:60, 60:40 and 75:25), and glycerol concentration in Study III (0%, 1%, 2% and 4% of the final solution). The blocking factor was initial BW and treatments were randomly assigned within each block. Measurements included fluid intakes, BW, and blood parameters at 0, 24 and 48 h relative to the start of feed deprivation. In Study I, increasing mineral concentration in solution linearly decreased BW losses at 48 h. At 24 and 48 h, serum urea linearly decreased with increasing mineral concentration. At 48 h, blood K+ and Na+ linearly increased, resulting in increased blood osmolarity. Additionally, at 24 h feed deprivation, blood pH linearly increased with increasing osmolality. In Study II, BW losses decreased with increasing K+ to Na+ ratio at 24 h, but not at 48 h. No effect of the K+ to Na+ ratio was found on blood parameters, apart from a trend for a linear decrease of blood osmolarity at 48 h. In Study III, serum urea tended to linearly decrease with increasing glycerol inclusion at 24 h, while blood glucose linearly increased with glycerol inclusion at 24 and 48 h. These combined results indicated that a solution with an osmolality of 200 mOsm/kg and a high K+ to Na+ ratio would effectively mitigate BW losses and maintain blood acid–base balance, whereas high glycerol inclusion sustained blood glucose in feed‐deprived bulls.
Detection of spoilage-causing yeasts and bacteria in tchapalo, the Ivorian traditional sorghum beer
Authors: Attchelouwa C.K. , Kouakou-Kouamé C.A. , Ouattara L. , Amoikon T.L.S. , N’guessan F.K. , Marcotte S. , Charmel M. , Djè M.K.
Published: March 2022

In this study, we aimed to analyse the spoilage potential of the isolated yeast, LAB and AAB species. Thus, 11 strains were inoculated at 0·3% (v/v) into a sterile filtered tchapalo and stored for 3 days at ambient temperature (27–30°C). All the tested strains grew well or remained stable except for Limosilactobacillus fermentum and Pediococcus acidilactici, which decreased throughout the storage time. A significant decrease of total soluble solids was observed only for Saccharomyces cerevisiae (from 7·8 to 5·8 °Brix) and Meyerozyma guilliermondii (from 7·8 to 5·5 °Brix). The tchapalo samples inoculated with the LAB strains Weissella paramesenteroides, P. acidilactici, L. fermentum and the yeast strain Candida tropicalis were judged similar to the control by the panellists. However, the strains of Lacticaseibacillus paracasei and Latilactobacillus curvatus (LAB), S. cerevisiae, M. guilliermondii and Kluyveromyces marxianus (yeasts) and Acetobacter pasteurianus and A. cerevisiae (AAB) induced the spoilage of the tchapalo appearance, smell and/or taste. In the spoiled tchapalo quantitative and qualitative modification of some volatile compounds (VOCs), such as lilac aldehyde, ethyl acetate, ethyl hexanoate, ethyl octanoate and phenethyl acetate, were observed. These results provide information about the microorganisms that need to be removed to extend the shelf life of tchapalo.
A conserved MYB transcription factor is involved in regulating lipid metabolic pathways for oil biosynthesis in green algae
Authors: Shi Meicheng , Yu Lihua , Shi Jianan , Liu Jin
Published: March 2022

Green algae can accumulate high levels of triacylglycerol (TAG), yet knowledge remains fragmented on the regulation of lipid metabolic pathways by transcription factors (TFs).

Here, via bioinformatics and in vitro and in vivo analyses, we revealed the roles of a myeloblastosis (MYB) TF in regulating TAG accumulation in green algae.

CzMYB1, an R2R3‐MYB from Chromochloris zofingiensis, was transcriptionally upregulated upon TAG‐inducing conditions and correlated well with many genes involved in the de novo fatty acid synthesis, fatty acid activation and desaturation, membrane lipid turnover, and TAG assembly. Most promoters of these genes were transactivated by CzMYB1 in the yeast one‐hybrid assay and contained the binding elements CNGTTA that were recognized by CzMYB1 through the electrophoretic mobility shift assay. CrMYB1, a close homologue of CzMYB1 from Chlamydomonas reinhardtii that recognized similar elements for binding, also transcriptionally correlated with many lipid metabolic genes. Insertional disruption of CrMYB1 severely suppressed the transcriptional expression of CrMYB1, as well as of key lipogenic genes, and impaired TAG level considerably under stress conditions.

Our results reveal that this MYB, conserved in green algae, is involved in regulating global lipid metabolic pathways for TAG biosynthesis and accumulation.
Coupling-based Convergence Assessment of some Gibbs Samplers for High-Dimensional Bayesian Regression with Shrinkage Priors
Authors: Biswas Niloy , Bhattacharya Anirban , Jacob Pierre E. , Johndrow James E.
Published: March 2022

We consider Markov chain Monte Carlo (MCMC) algorithms for Bayesian high-dimensional regression with continuous shrinkage priors. A common challenge with these algorithms is the choice of the number of iterations to perform. This is critical when each iteration is expensive, as is the case when dealing with modern data sets, such as genome-wide association studies with thousands of rows and up to hundreds of thousands of columns. We develop coupling techniques tailored to the setting of high-dimensional regression with shrinkage priors, which enable practical, non-asymptotic diagnostics of convergence without relying on traceplots or long-run asymptotics. By establishing geometric drift and minorization conditions for the algorithm under consideration, we prove that the proposed couplings have finite expected meeting time. Focusing on a class of shrinkage priors which includes the ‘Horseshoe’, we empirically demonstrate the scalability of the proposed couplings. A highlight of our findings is that less than 1000 iterations can be enough for a Gibbs sampler to reach stationarity in a regression on 100,000 covariates. The numerical results also illustrate the impact of the prior on the computational efficiency of the coupling, and suggest the use of priors where the local precisions are Half-t distributed with degree of freedom larger than one.
Characterization of the novel HLA‐DQB1*02:197 allele by sequencing‐based typing
Authors: Cargou Marine , Elsermans Vincent , Top Isabelle , Guidicelli Gwendaline , Visentin Jonathan
Published: March 2022

HLA‐DQB1*02:197 differs from HLA‐DQB1*02:01:01:01 by one nucleotide substitution in codon 18 in exon 2.
Transient Regulating Characteristics of V-Port Ball Valve in Opening and Closing Process
Authors: Lin Zhe , Wang Dongrui , Tao Junyu , Zhu Zuchao , Guo Xiaomei
Published: March 2022

V-port ball valves have been widely utilized as a control device in various fluid transmission systems, achieving the function of throttling and controlling the flow direction effectively. However, the flow characteristics for a V-port ball valve in the opening and closing processes are unclear, especially the influence of different cone angles on the valve regulation process. The present work investigates the transient regulation performance and internal flow characteristics with different cone angles of a V-port ball valve in its opening and closing processes experimentally and numerically. The results reveal that the performance parameters involving the flow rate, pressure, and flow coefficient in the opening process are greater than those in the closing process; subsequently, they become the same after stabilization. The V-port cone angle affects the flow rate, pressure, and flow coefficient significantly. The maximum flow rate and flow coefficient increases with the increase in the cone angle. The inlet pressure and the initial opening in which the outlet pressure begins to reduce decrease with an increase in the cone angle. In the valve regulation process, the interaction between the flow and the cone leading edge produces a large flow variation. As the cone angle increases, the variation degree at the leading edge weakens. The current conclusions can provide a reference for the design and optimization of V-port ball valves.
Impact of SARS-CoV-2 Variants on the Analytical Sensitivity of rRT-PCR Assays
Authors: Chen Yuqing , Han Yanxi , Yang Jing , Ma Yu , Li Jinming , Zhang Rui
Published: March 2022

Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with enhanced transmissibility, pathogenicity, and immune escape ability have ravaged many countries and regions, which has brought substantial challenges to pandemic prevention and control. Real-time reverse transcriptase PCR (rRT-PCR) is widely used for SARS-CoV-2 detection but may be limited by the continuous evolution of the virus.
The Explorer's Guide to Biology: A Free Multimedia Educational Resource to Promote Deep Learning and Understanding of the Scientific Process
Authors: Green Noah H. , Walter Mike , Anderton Brittany N.
Published: March 2022

Here, we describe a new open-access digital resource for teaching and learning life science, The Explorer’s Guide to Biology (available at
explorebiology.org
). Biology can often feel like a daunting subject where learners must comprehend a sea of facts before they can participate in meaningful discussions regarding core biology concepts or biological research.
Bacterial Competition Systems Share a Domain Required for Inner Membrane Transport of the Bacteriocin Pyocin G from Pseudomonas aeruginosa
Authors: Atanaskovic Iva , Sharp Connor , Press Cara , Kaminska Renata , Kleanthous Colin
Published: March 2022

Nuclease bacteriocins are potential antimicrobials for the treatment of antibiotic-resistant bacterial infections. While the mechanism of outer membrane translocation is beginning to be understood, the mechanism of inner membrane transport is not known.
Complete Genome Sequence of
Kluyvera
sp. CRP, a Cellulolytic Strain Isolated from Red Panda Feces (Ailurus fulgens)
Authors: Wai A. C. H. , Lai G. K. K. , Griffin S. D. J. , Leung F. C. C.
Published: March 2022

The enterobacterium genus
Kluyvera
is widely distributed in the environment and a rare source of infection in humans.
Kluyvera
sp. strain CRP was isolated from feces of a healthy, captive Chinese red panda (
Ailurus fulgens
), and its complete genome (5,157,963 bp, 54.80% GC content) was established through hybrid assembly.
Canyon Vortices: Application of the Theory of Topographic Vortices to the Phenomenon of Ice Rings in Baikal
Authors: Zyryanov V. N. , Chebanova M. K. , Zyryanov D. V.
Published: March 2022

A phenomenon of ice rings in Lake Baikal is considered. A hydrodynamic theory is proposed according to which geostrophic vortices form under ice in the area near the ice rings. These vortices are due to bed relief, namely, underwater canyons; therefore, they are referred to as canyon vortices. It is shown that a divergent ring vortex forms under ice in the ring domain at the crossing of a vertical cylindrical Stewartson layer on the lateral surface of the canyon geostrophic vortex and under-ice horizontal Ekman layer in the form of a horizontal vortex torus, and the melting of ice below in the form of a ring is due to the formation of this vortex torus.
Guideline Values for the Content of Chemical Elements in Soils of Urban Functional Zones: A Review
Authors: Semenkov I. N. , Koroleva T. V.
Published: March 2022

Abstract—

The Russian soil quality assessment system, where the guideline values for the content of heavy metals and metalloids derived for arable lands (mostly, in terms of the general sanitary indicator of harmfulness) are applied to soils of the residential area and the protected area of water supply sources, can be updated using international experience, e.g., substantiation of generic values for urban functional zones since, with a few exceptions, the Russian soil quality guidelines are the same for all soils of the country. In order to assess the applicability of foreign approaches to Russian realities, we have thoroughly analyzed the original and most developed legislation systems of the soil quality control in cities of Germany, Canada, and the United States, as well as the systems of Australia, New Zealand, Republic of South Africa, and the countries of the European Union, where the values are land use specific. In this paper, we summarize the principles of soil quality assessment for the contents of chemical elements, brief the methodology used in different countries and the consequences of exceeding the standards, and highlight some clues for improving the Russian soil quality assessment system. The Russian soil quality assessment system can be improved and updated by substantiating (i) the land use specific standards for cities with the focus on actual subjects of standardization (the health of ecosystems, children, or adults); (ii) the standards for different geochemical environments taking into account the specific features of migration of substances; and (iii) the standards for the soil materials used to construct lawns and roadside areas. In addition, we suggest (i) developing a comprehensive system of management decisions for the case when soil quality standards are exceeded; (ii) legitimizing the concept of historical pollution that existed before the commencement of business activities; and (iii) establishing the minimum volume of soil and the depth or set of soil horizons to be remediated or removed due to pollution.
Carbonate Groundwater—An Ore-Preserving Factor at Uranium Deposits of The Khiagda Ore Field (Republic of Buryatia)
Authors: Solodov I. N. , Nesterova M. V.
Published: March 2022

The article presents factual material substantiating the mixed supply regime of the ore-bearing aquifer at uranium deposits of the Khiagda ore field. There are two competing flows: infiltration of oxygen-containing meteoric waters and exfiltration of deep carbonate bicarbonate–magnesium groundwaters containing epigenetic reducing agents in the form of gases and dissolved organic matter of the petroleum series. Exfiltration prevails over infiltration. Carbonate groundwater containing epigenetic reducing agents forms a constantly acting reductive geochemical barrier that works as an ore-preserving factor.