bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
Authors: Martin Samuel , Heavens Darren , Lan Yuxuan , Horsfield Samuel , Clark Matthew D , Leggett Richard M 
Published: May 2021

AbstractBackgroundAdaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms recently implemented in Oxford Nanopore’s own control software. By examining the first few hundred bases of a DNA molecule as it passes through a pore, software can determine if the molecule is sufficiently interesting to sequence in its entirety. If not, the molecule is ejected from the pore by reversing the voltage across it, freeing the pore for a new molecule. User supplied sequences define the targets to be sequenced or ejected. Here we explore the potential of using adaptive sampling for enrichment of rarer species within metagenomic samples.ResultsWe created a synthetic mock community consisting of seven bacterial species at different proportions ranging from 1.2% to 47% and used this as the basis for a series of enrichment and depletion experiments. To investigate the effect of DNA length on adaptive sampling efficiency, we created sequencing libraries with mean read lengths of 1.7 kbp, 4.7 kbp, 10.6 kbp, and 12.8 kbp and enriched or depleted for individual and multiple species over a series of sequencing runs. Across all experiments enrichment ranged from 1.67-fold for the most abundant species with the shortest read length to 13.87-fold for the least abundant species with the longest read length. Factoring in the reduction to sequence output associated with repeatedly rejecting molecules reduces the calculated efficiency of this enrichment to between 0.96-fold and 4.93-fold. We note that reducing ejections due to false negatives (approximately 36%) would significantly increase efficiency. We used the relationship between abundance, molecule length and enrichment factor to produce a mathematical model of enrichment based on molecule length and relative abundance, whose predictions correlated strongly with experimental data. A web application is provided to allow researchers to explore model predictions in advance of performing their own experiments.ConclusionsOur data clearly demonstrates the benefit for enriching low abundant species in adaptive sampling metagenomic experiments, especially with longer molecules, and our mathematical model can be used to determine whether a given experimental DNA sample is suitable for adaptive sampling. Notably, repeated voltage reversals have no effect on pore stability.
Simple-to-use CRISPR-SpCas9/SaCas9/AsCas12a vector series for genome editing inSaccharomyces cerevisiae
Authors: Okada Satoshi , Doi Goro , Nakagawa Shitomi , Kusumoto Emiko , Ito Takashi 
Published: May 2021

AbstractGenome editing using the CRISPR/Cas system has been implemented for various organisms and becomes increasingly popular even in the genetically tractable budding yeastSaccharomyces cerevisiae. Since each CRISPR/Cas system recognizes only the sequences flanked by its unique protospacer adjacent motif (PAM), a certain single system often fails to target a region of interest due to the lack of PAM, thus necessitating the use of another system with a different PAM. Three CRISPR/Cas systems with distinct PAMs, namely SpCas9, SaCas9, and AsCas12a, have been successfully used in yeast genome editing and their combined use should expand the repertoire of editable targets. However, currently available plasmids for these systems were individually developed under different design principles, thus hampering their seamless use in the practice of genome editing. Here we report a series of Golden Gate Assembly-compatible backbone vectors designed under a unified principle to exploit the three CRISPR/Cas systems in yeast genome editing. We also created a software to assist the design of genome-editing plasmids for individual target sequences using the backbone vectors. Genome editing with these plasmids demonstrated practically sufficient efficiency in both insertion of gene fragments to essential genes and complete deletion of an open reading frame. The backbone vectors with the software would thus provide a versatile toolbox to facilitate the seamless use of SpCas9, SaCas9, and AsCas12a in various types of genome manipulation, especially those that are difficult to perform with conventional techniques in yeast genetics.
Mesenchymal stem cell subpopulations and their heterogeneity of response to inductions revealed by single-cell RNA-seq
Authors: Hou Wenhong , Duan Li , Huang Changyuan , Li Xingfu , Xu Xiao , Qin Pengfei , Hong Ni , Wang Daping , Jin Wenfei 
Published: May 2021

AbstractMesenchymal stem/stromal cells (MSCs) are promising cell source for regenerative medicine and treatment of autoimmune disorders. Comparing MSCs from different tissues at single cell level is fundamental for optimizing clinical applications. Here we analyzed single cell RNA-seq data of MSCs from 4 tissues, namely umbilical cord, bone marrow, synovial tissue and adipose tissue. We identified 3 major cell subpopulations, namely osteo-MSCs, chondro-MSCs, adipo/myo-MSCs, across all MSC samples. MSCs from umbilical cord exhibited the highest immunosuppression, potentially indicating it is the best immune modulator for autoimmune diseases. The differentiation potentials of MSC subpopulations, which are strongly associated with their subtypes and tissue sources, showed pronounced subpopulation differences. We found MSC subpopulations expanded and differentiated when their subtypes consist with induction directions, while the other subpopulations shrank. We identified the genes and transcription factors underlying each induction at single cell level and subpopulation level, providing better targets for improving induction efficiency.
Diverse DNA modification in marine prokaryotic and viral communities
Authors: Hiraoka Satoshi , Sumida Tomomi , Hirai Miho , Toyoda Atsushi , Kawagucci Shinsuke , Yokokawa Taichi , Nunoura Takuro 
Published: May 2021

AbstractChemical modifications of DNA, including methylation, play an important role in prokaryotes and viruses. However, our knowledge of the modification systems in environmental microbial communities, typically dominated by members not yet cultured, is limited. Here, we conducted ‘metaepigenomic’ analyses by single-molecule real-time sequencing of marine microbial communities. In total, 233 and 163 metagenomic assembly genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTases were not associated with the defense mechanism. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative motifs in the methylation system that are highly conserved in Alphaproteobacteria, illuminating the co-evolutionary history of the methylation system and host genome. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses.
The K18-hACE2 Transgenic Mouse Model Recapitulates Non-Severe and Severe COVID-19 in Response to Infectious Dose of SARS-CoV-2 Virus
Authors: Dong Wenjuan , Mead Heather , Jaramillo Sierra , Barr Tasha , Kollath Daniel S. , Coyne Vanessa K. , Stone Nathan E. , Jones Ashley , Zhang Jianying , Li Aimin , Wang Li-Shu , Milanes-Yearsley Martha , Keim Paul S , Barker Bridget Marie , Caligiuri Michael , Yu Jianhua 
Published: May 2021

AbstractA comprehensive analysis and characterization of a SARS-CoV-2 infection model that mimics non-severe and severe COVID-19 in humans is warranted for understating the virus and developing preventive and therapeutic agents. Here, we characterized the K18-hACE2 mouse model expressing human (h)ACE2 in mice, controlled by the human keratin 18 (K18) promoter, in epithelia, including airway epithelial cells where SARS-CoV-2 infections typically start. We found that intranasal inoculation with higher viral doses (2×103 and 2×104 PFU) of SARS-CoV-2 caused lethality of all mice and severe damage of various organs, including lungs, liver, and kidney, while lower doses (2×101 and 2×102 PFU) led to less severe tissue damage and some mice recovered from the infection. In this humanized hACE2 mouse model, SARS-CoV-2 infection damaged multiple tissues, with a dose-dependent effect in most tissues. Similar damage was observed in biopsy samples from COVID-19 patients. Finally, the mice that recovered after infection with a low dose of virus also survived rechallenge with a high dose of virus. Compared to other existing models, the K18-hACE2 model seems to be the most sensitive COVID-19 model reported to date. Our work expands the information available about this model to include analysis of multiple infectious doses and various tissues with comparison to human biopsy samples from COVID-19 patients. In conclusion, the K18-hACE2 mouse model recapitulates both severe and non-severe COVID-19 in humans and can provide insight into disease progression and the efficacy of therapeutics for preventing or treating COVID-19.ImportanceThe pandemic of COVID-19 has reached 112,589,814 cases and caused 2,493,795 deaths worldwide as of February 23, 2021, has raised an urgent need for development of novel drugs and therapeutics to prevent the spread and pathogenesis of SARS-CoV-2. To achieve this goal, an animal model that recapitulates the features of human COVID-19 disease progress and pathogenesis is greatly needed. In this study, we have comprehensively characterized a mouse model of SARS-CoV-2 infection using K18-hACE2 transgenic mice. We infected the mice with low and high doses of SARS-CoV-2 virus to study the pathogenesis and survival in response to different infection patterns. Moreover, we compared the pathogenesis of the K18-hACE2 transgenic mice with that of the COVID-19 patients to show that this model could be a useful tool for the development of anti-viral drugs and therapeutics.
Japanese Dermatological Association Guidelines: Outlines of Guidelines for Cutaneous Squamous Cell Carcinoma 2020
Authors: Ansai Shin‐ichi , Umebayashi Yoshihiro , Katsumata Noriyuki , Kato Hiroshi , Kadono Takafumi , Takai Toshihiro , Namiki Takeshi , Nakagawa Masahiro , Soejima Toshinori , Koga Hiroshi , Sugaya Makoto ,   The Squamous Cell Carcinoma Guidelines Committee of the Japanese Skin Cancer Society
Published: May 2021

AbstractIn consideration of the development of treatment options for squamous cell carcinoma (SCC), the Japanese Skin Cancer Society issued the first guidelines of SCC in 2007 and revised them in 2015. Here, we report the English version of the 2020 edition of the Japanese SCC guidelines. The first half of this article is an overview of SCC including actinic keratosis and Bowen’s disease, and the second half discusses three clinical questions: (i) treatment of actinic keratosis; (ii) determination of the resection margin of the primary lesion; and (iii) treatment of radically incurable cases, as contemporary problems encountered in treating SCC. In these evaluations, all processes were implemented according to the Grading of Recommendations, Assessment, Development, Evaluation system. Also, items of recommendation concerning each clinical question were determined by a multidisciplinary expert panel consisting of dermatologists, plastic/reconstructive surgeons, radiologists, and oncologists through a comprehensive literature search and systematic reviews.
Observation policy for sentinel node metastasis of melanoma: Comparative study with completion lymph node dissection in Japanese patients
Authors: Matsui Yu , Sasaki Jin , Takatsuka Sumiko , Takenouchi Tatsuya 
Published: May 2021

AbstractBased on the results of international multicenter randomized trials, completion lymph node dissection for patients with sentinel lymph node‐positive melanoma is no longer routinely recommended. However, clinicians should take into consideration racial and medical resource differences when applying this evidence to clinical practice in Japan. To evaluate the clinical validity of the observation policy of omitting completion lymph node dissection, we retrospectively surveyed patients with sentinel lymph node‐positive melanoma between 2002 and 2020 at Niigata Cancer Center Hospital. A total of 59 patients were categorized into the observation group (n = 19) and completion lymph node dissection group (n = 40). Newly developed anticancer agents, including targeted therapy and immunotherapy, were more commonly used in the observation group than in the completion lymph node dissection group as either adjuvant therapy (31.6% vs. 5.0%) or post‐recurrence therapy (100% vs. 34.8%). The median overall survival in the observation group (not reached) was significantly longer than that in the completion lymph node dissection group (95.0 months; p = 0.02), which was mainly attributed to the difference in post‐recurrence overall survival. There was no significant difference in recurrence‐free survival between the two groups (p = 0.63). Although the use of new anticancer agents leads to bias, this study demonstrates that observation without prompt completion lymph node dissection provides a favorable overall survival without increasing the risk of recurrence compared with completion lymph node dissection. The observation policy for patients with sentinel lymph node‐positive melanoma patients is considered to be clinically valid in real‐world medical practice.
Practical algorithm to inform clinical decision‐making in the topical treatment of atopic dermatitis
Authors: Luger Thomas , Adaskevich Uladzimir , Anfilova Maryna , Dou Xia , Murashkin Nikolay N. , Namazova‐Baranova Leyla , Nitochko Oleg , Reda Ashraf , Svyatenko Tetyana V. , Tamay Zeynep , Tawara Mohammad , Vishneva Elena A. , Vozianova Svitlana , Wang Hua , Zhao Zuotao 
Published: May 2021

AbstractAtopic dermatitis is a chronic relapsing, inflammatory skin disorder associated with skin barrier dysfunction, the prevalence of which has increased dramatically in developing countries. In this article, we propose a treatment algorithm for patients with mild‐to‐moderate and severe atopic dermatitis flares in daily clinical practice. An international panel of 15 dermatology and allergy experts from eight countries was formed to develop a practical algorithm for the treatment of patients with atopic dermatitis, with a particular focus on topical therapies. In cases of mild‐to‐moderate atopic dermatitis involving sensitive skin areas, the topical calcineurin inhibitor pimecrolimus should be applied twice daily at the first signs of atopic dermatitis. For other body locations, patients should apply a topical calcineurin inhibitor, either pimecrolimus or tacrolimus, twice daily at the first signs of atopic dermatitis, such as pruritus, or twice weekly in previously affected skin areas. Emollients should be used regularly. Patients experiencing acute atopic dermatitis flares in sensitive skin areas should apply a topical corticosteroid twice daily or alternate once‐daily topical corticosteroid/topical calcineurin inhibitor until symptoms improve. Following improvement, topical corticosteroid therapy should be discontinued and patients switched to a topical calcineurin inhibitor. Maintenance therapy should include the use of pimecrolimus once daily for sensitive areas and tacrolimus for other body locations. This treatment algorithm can help guide clinical decision‐making in the treatment of atopic dermatitis.
Gender Politics after Corbynism
Authors: Dean Jonathan , Maiguashca Bice 
Published: May 2021

AbstractThis article examines Corbynism's gender politics, and its relationship with feminism. We note that in the early years of the Corbyn period there were starkly opposed positions on the gender dynamics and feminist‐friendliness of the Corbyn project. This, in turn, reflected wider factional divisions, often mapping onto different articulations of the relationship between feminism, race/whiteness, and trans rights. We then describe how initial prospects for the cultivation of a more gender‐sensitive left politics were ultimately undermined by two key developments: first, a discursive terrain in which feminism increasingly became pitted against the Corbynite left; and second, a defensiveness within the Corbyn project that made it resistant to immanent critique. We conclude by arguing that the failure of pro‐Corbyn feminists to gain much traction must be contextualised within the dynamics of personalisation, instrumentalisation and polarisation that increasingly shape our political culture.
Obese societies: Reconceptualising the challenge for public health
Authors: Blue Stanley , Shove Elizabeth , Kelly Michael P. 
Published: May 2021

AbstractThe prevalence of obesity and related health problems has increased sharply in recent decades. Dominant medical, economic, psychological, and especially epidemiological accounts conceptualise these trends as outcomes of individuals’ lifestyles – whether freely chosen or determined by an array of obesogenic factors. As such, they rest on forms of methodological individualism, causal narratives, and a logic of substitution in which people are encouraged to set currently unhealthy ways of life aside. This article takes a different approach, viewing trends in obesity as consequences of the dynamic organisation of social practices across space and time. By combining theories of practice with emerging accounts of epigenetics, we explain how changing constellations of practices leave their marks on the body. We extend the concept of biohabitus to show how differences in health, well‐being, and body shape are passed on as relations between practices are reproduced and transformed over time. In the final section, we take stock of the practical implications of these ideas and conclude by making the case for extended forms of enquiry and policy intervention that put the organisation of practices front and centre.
The Recognition of Excessive blood loss At ChildbirTh (REACT) Study: a two‐phase exploratory, sequential mixed methods inquiry using focus groups, interviews and a pilot, randomised crossover study
Authors: Hancock A , Weeks AD , Furber C , Campbell M , Lavender T 
Published: May 2021

ObjectivesTo explore how childbirth‐related blood loss is evaluated and excessive bleeding recognised; and to develop and test a theory of postpartum haemorrhage (PPH) diagnosis.DesignTwo‐phase, exploratory, sequential mixed methods design using focus groups, interviews and a pilot, randomised crossover study.SettingTwo hospitals in North West England.SampleWomen (following vaginal birth with and without PPH), birth partners, midwives and obstetricians.MethodsPhase 1 (qualitative): 8 focus groups and 20 one‐to‐one, semi‐structured interviews were conducted with 15 women, 5 birth partners, 11 obstetricians, 1 obstetric anaesthetist and 19 midwives (n = 51). Phase 2 (quantitative): 11 obstetricians and ten midwives (n = 21) completed two simulations of fast and slow blood loss using a high‐fidelity childbirth simulator.ResultsResponses to blood loss were described as automatic, intuitive reactions to the speed, nature and visibility of blood flow. Health professionals reported that quantifying volume was most useful after a PPH diagnosis, to validate intuitive decisions and guide ongoing management. During simulations, PPH treatment was initiated at volumes at or below 200 ml (fast mean blood loss 79.6 ml, SD 41.1; slow mean blood loss 62.6 ml, SD 27.7). All participants treated fast, visible blood loss, but only half treated slow blood loss, despite there being no difference in volumes (difference 18.2 ml, 95% CI −5.6 to 42.2 ml, P = 0.124).ConclusionsExperience and intuition, rather than blood loss volume, inform recognition of excessive blood loss after birth. Women and birth partners want more information and open communication about blood loss. Further research exploring clinical decision‐making and how to support it is required.Tweetable abstractDuring a PPH, clinical decision‐making is intuitive with clinicians treating as soon as excessive loss is recognised.
Matricide, parricide, and filicide: Are major mental disorders or personality disorders involved? Assessment of criminal responsibility in Brazilian cases
Authors: Valença Alexandre Martins , Carvalho de Oliveira Gustavo , Telles Lisieux Elaine de Borba , da Silva Antonio Geraldo , da Silva Jorge Adelino Rodrigues , Barros Alcina Juliana Soares , Nardi Antonio Egidio 
Published: May 2021

AbstractViolence committed by individuals with severe mental disorders has become a growing focus of interest among physicians, law enforcement officials, and the general population. Homicide involving relatives, specially parricide, matricide, and filicide, despite the relatively low incidence of these crimes, may be enigmatic, so forensic psychiatrist are frequently called on the courts to answer questions about insanity and criminal responsibility. The current study aims to describe Brazilian cases of parricide, matricide, and filicide associated with presence of major mental disorders and personality disorders, discussing the assessment of criminal responsibility in each case. The case series described were specifically related to people with mental illness, as bipolar disorder, schizophrenia, and borderline personality with comorbidity of drug abuse. Two of them were considered not guilty by reason of insanity, and the other one was considered partially criminally responsible, according to Brazilian Law and Forensic Psychiatric Reports of the cases. The justice determined compulsory psychiatric treatment for all of them. The question of criminal responsibility of individuals with mental disorders is challenging for criminal justice, psychiatry, and society. Adequate treatment is mandatory to prevent crimes involving mental disorders, as shown in literature. The verification of criminal responsibility is essential for persons’ adequate referral in any system of criminal law, thus protecting human rights and referring those who need psychiatric treatment.
Prehemodialysis hyponatremia and extracellular water: Is it simply too much water?
Authors: Chhabra Roohi , Davenport Andrew 
Published: May 2021

AbstractObservational hemodialysis (HD) studies report an association between hyponatremia and increased mortality. As volume overload is also associated with mortality, we wished to determine whether hyponatremia is linked to increased extracellular water (ECW). We measured ECW, total body water (TBW) and body composition predialysis with multifrequency bioimpedance, arm strength with pinch gauge and hand grip strength (PS, HGS), standard biochemistry profiles, comorbidity and clinical frailty scores (CFS). We reviewed 324 patients, 195 (60.2%) male, mean age 62.3 ± 15.6 years. Thirty‐eight (11.7%) patients were hyponatremic (sodium ≤135 mmol/L), ECW/height2 was not different, but ECW/TBW (0.409 ± 0.016 vs. 0.402 ± 0.016, p < 0.01), C reactive protein (CRP) (9(4–6) vs. 5(2–12) g/L, p < 0.05), CFS (5(4–6) vs. 4(3–6), p < 0.05) were higher in hyponatremic patients, whereas appendicular lean mass index (8.6 ± 1.7 vs. 9.4 ± 1.8 kg/m2, p < 0.01), serum albumin (36.3 ± 5.5 vs. 38.8 ± 5.0 g/L, p < 0.01) and PS (3.7(2.7–4.7) vs. 4.7 (3.2–6.5) kg, p < 0.05)) were lower. Both serum sodium, and serum sodium after adjustment for glucose were associated with serum creatinine (β 4.26, (95% confidence limits [CL] 1.9–6.7), β 3.98 (CL 1.6–6.4), both p = 0.001, respectively) and negatively with CRP (β −0.76, [CL] ‐1.5 to −0.5), β −0.72 (CL −1.44 to −0.12), p = 0.036, p = 0.046, respectively) in a multivariable model. Hyponatremic HD patients did not simply have an increased ECW, as the increased ECW/TBW and ECW/ICW ratios were more likely secondary to loss of muscle mass and strength, associated with increased CRP and reduced albumin, suggesting that hyponatremia is associated with inflammation, loss of muscle mass and increasing frailty.