bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts
Authors: Cholet Fabien , Ijaz Umer Z. , Smith Cindy J. 
Published: April 2020

SummaryReverse‐transcriptase‐quantitative PCR (RT‐Q‐PCR) and RT‐PCR amplicon sequencing, provide a convenient, target‐specific, high‐sensitivity approach for gene expression studies and are widely used in environmental microbiology. Yet, the effectiveness and reproducibility of the reverse transcription step has not been evaluated. Therefore, we tested a combination of four commercial reverse transcriptases with two priming techniques to faithfully transcribe 16S rRNA and amoA transcripts from marine sediments. Both enzyme and priming strategy greatly affected quantification of the exact same target with differences of up to 600‐fold. Furthermore, the choice of RT system significantly changed the communities recovered. For 16S rRNA, both enzyme and priming had a significant effect with enzyme having a stronger impact than priming. Inversely, for amoA only the change in priming strategy resulted in significant differences between the same samples. Specifically, more OTUs and better coverage of amoA transcripts diversity were obtained with GS priming indicating this approach was better at recovering the diversity of amoA transcripts. Moreover, sequencing of RNA mock communities revealed that, even though transcript α diversities (i.e., OTU counts within a sample) can be biased by the RT, the comparison of β diversities (i.e., differences in OTU counts between samples) is reliable as those biases are reproducible between environments.
Subsistence and complexity of antimicrobial resistance on a community‐wide level
Authors: Perri Riccardo , Kolvenbach Boris A. , Corvini Philippe F. X. 
Published: April 2020

SummaryThere are a multitude of resistance strategies that microbes can apply to avoid inhibition by antimicrobials. One of these strategies is the enzymatic modification of the antibiotic, in a process generally termed inactivation. Furthermore, some microorganisms may not be limited to the mere inactivation of the antimicrobial compounds. They can continue by further enzymatic degradation of the compounds' carbon backbone, taking nutritional and energetic advantage of the former antibiotic. This driving force to harness an additional food source in a complex environment adds another level of complexity to the reasonably well‐understood process of antibiotic resistance proliferation on a single cell level: It brings bioprotection into play at the level of microbial community. Despite the possible implications of a resistant community in a host and a lurking antibiotic failure, knowledge of degradation pathways of antibiotics and their connections is scarce. Currently, it is limited to only a few families of antibiotics (e.g. β‐lactams and sulfonamides). In this article, we discuss the fluctuating nature of the relationship between antibiotic resistance and the biodegradation of antibiotics. This distinction mainly depends on the genetic background of the microbe, as general resistance genes can be recruited to function in a biodegradation pathway.
The Multitude and the Machine: Productivism, Populism, Posthumanism
Authors: Pitts Frederick Harry 
Published: April 2020

AbstractThere has been a proliferating literature on postcapitalist and post‐work futures in recent years, underpinned by policy proposals like the basic income and a reduction in working hours. It has gained increasing uptake within left electoral politics and policy making. The generational potency of these ideas require that we understand their theoretical roots. This article considers the interplay between the work of Michael Hardt and Antonio Negri and the new postcapitalism exemplified by the likes of Paul Mason and Aaron Bastani, as well as its relationship with intellectual currents around Corbynism and the wider contemporary left. Through a discussion of their latest book, Assembly, it will be seen that Hardt and Negri both inform, and are increasingly informed by, the postcapitalist and post‐work thinking popular on the left today—in particular at its ‘posthumanist’ fringes. However, this recent work is characterised by a series of tactical redirections that, rather than indicating renewal, reflect the potential collapse of this utopian framework for the future in the face of a rapidly unravelling global political context. Whilst the determinist understanding of social transformation cannot permit these setbacks, this shines a light on more general shifts in left strategy and analysis.
Inter‐professional practice in the prevention and management of child and adolescent self‐harm: foster carers’ and residential carers’ negotiation of expertise and professional identity
Authors: Jennings Stephen , Evans Rhiannon 
Published: April 2020

AbstractInter‐professional collaboration remains a significant concern within healthcare and social care. However, there has been scant attention paid to practices at the interface of clinicians and carers, namely foster carers and residential carers. The present study considers child and adolescent self‐harm management and prevention practices as a site of empirical interest due to reports that multi‐agency teams are not effectively operating. Drawing upon a grounded theory approach, data were generated via semi‐structured interviews and focus groups with residential carers (n = 15) and foster carers (n = 15) in Wales. Themes were developed through axial coding. The results present two central themes to explain the nature and perceived causes of inter‐professional discord. First, there are clear contestations in expertise, with carers challenging clinicians’ propositional knowledge in favour of their own experiential expertise. However, participants simultaneously endorse medical dominance, which contributes to their sense of disempowerment and marginalisation. Second, is the preclusion of carers’ professional identity, primarily due to inadequate professionalisation procedures. Meanwhile, the privileging of their parenting role is perceived to support the perpetuation of courtesy stigma. Carers are then compelled to undertake the effortful labour of legitimisation. Together these thematic insights provide direction on mechanisms to improve inter‐professional interactions, notably around training and accreditation.
Risk factors for the recurrence of obstetrical anal sphincter injury and the role of a mediolateral episiotomy: an analysis of a national registry
Authors: van Bavel J , Ravelli ACJ , Abu‐Hanna A , Roovers JPWR , Mol BW , de Leeuw JW 
Published: April 2020

ObjectiveThe assessment of risk factors, including mediolateral episiotomy (MLE), for the recurrence of obstetric anal sphincter injury (rOASI).DesignPopulation‐based cohort study.SettingData from the nationwide database of the Dutch Perinatal Registry (Perined).PopulationA cohort of 391 026 women at term, of whom 9943 had an OASI in their first delivery and had a second vaginal delivery of a liveborn infant in cephalic position.MethodsPossible risk factors were tested for statistical significance using univariate and multivariate logistic regression analysis.Main outcome measuresRate of rOASI.ResultsThe rate of rOASI was 5.8%. Multivariate analysis identified a birthweight of ≥4000 g (adjusted OR, aOR, 2.1, 95% CI 1.6–2.6) and a duration of second stage of ≥30 minutes (aOR 1.8, 95% CI 1.4–2.3) as statistically significant risk factors for rOASI. Mediolateral episiotomy was associated with a statistically significant lower rate of rOASI in spontaneous vaginal delivery (SVD) (aOR 0.4, 95% CI 0.3–0.5) and in operative vaginal delivery (OVD) (aOR 0.2, 95% CI 0.1–0.5).ConclusionsWomen with a history of OASI have a higher rate of OASI in their next delivery. Duration of the second stage of ≥30 minutes and a birthweight of ≥4000 g are significantly associated with an increased rate of rOASI. Mediolateral episiotomy is associated with a significantly lower rate of rOASI in both SVD and OVD.Tweetable abstractMediolateral episiotomy is associated with a significant lower recurrence rate of OASI in women with an OASI in their first delivery.
Updates on understanding of probiotic lactic acid bacteria responses to environmental stresses and highlights on proteomic analyses
Authors: Mbye Mustapha , Baig Mohd Affan , AbuQamar Synan F. , El‐Tarabily Khaled A. , Obaid Reyad S. , Osaili Tareq M. , Al‐Nabulsi Anas A. , Turner Mark S. , Shah Nagendra P. , Ayyash Mutamed M. 
Published: April 2020

AbstractProbiotics are defined as live microorganisms that improve the health of the host when administered in adequate quantities. Nonetheless, probiotics encounter extreme environmental conditions during food processing or along the gastrointestinal tract. This review discusses different environmental stresses that affect probiotics during food preparation, storage, and along the alimentary canal, including high temperature, low temperature, low and alkaline pH, oxidative stress, high hydrostatic pressure, osmotic pressure, and starvation. The understanding of how probiotics deal with environmental stress and thrive provides useful information to guide the selection of the strains with enhanced performance in specific situations, in food processing or during gastrointestinal transit. In most cases, multiple biological functions are affected upon exposure of the cell to environmental stress. Sensing of sublethal environmental stress can allow for adaptation processes to occur, which can include alterations in the expression of specific proteins.
Effect of nintedanib on non‐small cell lung cancer in a patient with idiopathic pulmonary fibrosis: A case report and literature review
Authors: Shiratori Toshihiro , Tanaka Hisashi , Tabe Chiori , Tsuchiya Junichiro , Ishioka Yoshiko , Itoga Masamichi , Taima Kageaki , Takanashi Shingo , Tasaka Sadatomo 
Published: April 2020

Nintedanib has been approved for the treatment of idiopathic pulmonary fibrosis (IPF). In addition, in EU countries, nintedanib plus docetaxel is used for patients with advanced non‐small cell lung cancer (NSCLC) after first‐line chemotherapy. Here, we report a case of advanced NSCLC in a patient with IPF successfully treated with nintedanib monotherapy. A 69‐year‐old man was diagnosed with NSCLC complicated by IPF. After three lines of chemotherapy, he still had progressive disease. Because his IPF had also progressed, requiring supplemental oxygen, we decided to start best supportive care and introduced nintedanib to treat his IPF. One month later, we observed a partial remission of the primary tumor and pleural disseminations without severe adverse events. Nintedanib monotherapy might therefore be an effective therapeutic choice for NSCLC in patients with IPF who are unable to tolerate cytotoxic chemotherapy.Key points
Efficacy of nintedanib administered in a NSCLC patient with IPF.
Nintedanib monotherapy might be a therapeutic option for NSCLC patients with IPF who are unable to tolerate chemotherapy.
Reporting Bias and Monitoring in Clean Development Mechanism Projects*
Authors: Chen Hui , Letmathe Peter , Soderstrom Naomi 
Published: April 2020

ABSTRACTThe Clean Development Mechanism (CDM) is a flexible carbon market mechanism managed by the United Nations. The program grants tradable carbon emissions credits (Certified Emission Reductions) for carbon‐reducing projects in developing countries. A project can only be admitted to the program if it is not financially profitable, and thus would not take place without the emission credits granted through the CDM. In this paper, we examine how monitoring reduces incentives of companies to bias the reported expected financial viability of potential CDM projects to gain admission to the program. We find that reported rates of return, which are a key factor for admission to the program, tend to be downwardly biased and are negatively associated with the expected benefits stemming from forecasted greenhouse gas reductions. However, monitoring from various sources mitigates some of the distorted incentives and related reporting bias. Furthermore, the monitoring effect becomes much stronger after 2008, when the CDM Executive Board implemented a series of measures to strengthen the additionality testing that provides guidance for program applications.
Keratinocyte cancer with incidental perineural invasion: A registry analysis of management and 5‐year outcomes
Authors: Adams Agnieszka , De’Ambrosis Brian , Panizza Ben , Belt Paul , Emmett James , Warren Tim , Whiteman David C. 
Published: April 2020

AbstractBackground/ObjectivesPerineural invasion within keratinocyte cancer is a hallmark of tumour aggression, and a definitive treatment paradigm for this condition remains undetermined. Our aim was to investigate the treatment and outcomes of keratinocyte cancer with incidental perineural invasion within two skin cancer databases to refine treatment protocols.MethodsWe retrospectively assessed the Queensland Perineural Invasion Registry for surgery, histopathology, adjuvant radiotherapy and recurrence of keratinocyte cancer five years post‐definitive treatment. We also reviewed the Princess Alexandra Hospital Head and Neck clinical perineural invasion database, specifically looking at surgical margins and adjuvant radiotherapy of cutaneous squamous cell carcinoma (cSCC) with incidental perineural invasion in the primary lesion.ResultsThere was no recurrence at 5 years in the Perineural Invasion Registry. Basal cell carcinoma (BCC) lesions with nerves <0.1 mm were more commonly treated with surgery alone, compared to lesions with nerves ≥0.1 mm which were offered adjuvant radiotherapy. Of the total BCC lesions with incidental perineural invasion, those with perineural margins ≥5 mm and peripheral tumour margins ≥3 mm were predominantly treated with surgery alone. Eighty‐nine per cent of cSCC lesions with incidental perineural invasion were treated with surgery and adjuvant radiotherapy.ConclusionSurgery alone is suitable for BCC lesions with incidental perineural invasion. The majority of BCC lesions achieved ≥5 mm perineural and ≥3 mm peripheral tumour margins. Future research can guide if adjuvant radiation is required for BCC with perineural invasion. The treatment of cSCC with incidental perineural invasion with surgery alone remains undetermined.
Short‐term outcomes following intrauterine transfusions for fetal anaemia: A retrospective cohort study
Authors: Urutherakumar Varshinee , Welsh Alec , Henry Amanda 
Published: April 2020

BackgroundIntrauterine transfusion (IUT) is the accepted standard for management of severe fetal anaemia. However, fetal transfusion may be associated with procedural complications such as fetal demise. There is a paucity of recent data on outcomes for severe fetal anaemia in Australia as compared with published outcomes from large international centres.AimsTo review the indications for and the procedural, obstetric and neonatal outcomes following intrauterine transfusion for fetal anaemia conducted at the New South Wales Fetal Therapy Centre (NSW FTC).Materials and MethodsRetrospective cohort study conducted between 2005 and 2017 of the outcomes of 85 IUT procedures (39 pregnancies). Data collected included maternal demographics, procedural and obstetric details and short‐term neonatal outcomes.ResultsComplete outcome data were available for 36/39 pregnancies. Red cell antibodies were the main indication for fetal transfusion (79%, predominantly D, Kell and other Rhesus antibodies) with parvovirus accounting for 8% of procedures. IUT was associated with a pregnancy loss rate of 1.2%/procedure, amounting to 2.6%/pregnancy. Fetal losses were limited to those complicated by hydrops prior to IUT (3/10 hydrops vs 0/26 non‐hydropic; P = 0.003).ConclusionsProcedural outcomes at NSW FTC compare favourably with international centres (1.1–8.7% procedural loss rate). However, this comparison is limited, as no procedures were performed during the last 24 months of the study. Given this, a nationwide audit is recommended to help guide appropriate centralisation of procedures and thereby maximise clinician experience and outcome.
Letter: pregnant women with IBD are more likely to be adherent to biologic therapies than other medications
Authors: Laube Robyn , Selinger Christian P. 
Published: April 2020

LINKED CONTENTThis article is linked to Lee et al papers. To view these articles, visit https://doi.org/10.1111/apt.15596 and https://doi.org/10.1111/apt.15599.
MC1R c.310G>‐ and c.871G > A determine the coat color of Kumamoto sub‐breed of Japanese Brown cattle
Authors: Matsumoto Hirokazu , Kojya Masatake , Takamuku Hiroko , Kimura Satoshi , Kashimura Atsushi , Imai Saki , Yamauchi Kenji , Ito Shuichi 
Published: April 2020

AbstractCoat color is one of the important factors characterizing breeds for domestic animals. Melanocortin 1 receptor (MC1R) is a representative responsible gene for this phenotype. Two single‐nucleotide polymorphisms (SNPs) in bovine MC1R gene, c.296T > C and c.310G>‐, have been well characterized, but these SNPs are not enough to explain cattle coat color. As far as we know, MC1R genotypes of Kumamoto sub‐breed of Japanese Brown cattle have not been analyzed. In the current study, genotyping for c.296T > C and c.310G>‐ was performed to elucidate the role of MC1R in determining the coat color of this sub‐breed. As a result, most animals were e/e genotype, suggesting the coat color of this sub‐breed is derived from the e allele of MC1R gene. However, we found six animals with E/e genotype, which coat color would be black theoretically. Subsequently, sequence comparison was performed with these animals to identify other polymorphisms affecting coat color, elucidating that these animals possessed the A allele of c.871G > A commonly. c.871G > A was a non‐synonymous mutation in the seventh transmembrane domain, suggesting alteration of the function and/or the structure of MC1R protein. Our data indicated that the A allele of c.871G > A might be a loss‐of‐function mutation.
Concentration patterns of antibacterial factors and immunoglobulin A antibody in foremilk fractions of healthy cows
Authors: Kitano Nana , Isobe Naoki , Noda Jun , Takahashi Toshihiko 
Published: April 2020

AbstractAntibacterial factors act as innate immune components, which respond as soon as bacteria enter a living organism. To prevent and treat mastitis in cattle, understanding the concentrations of these substances inside the udder is important; however, they remain to be studied. In this investigation, the concentration of lingual antimicrobial peptide (LAP), S100 protein (S100A7), lactoferrin (LF), and immunoglobulin antibody were measured in the different fractions of foremilk. Lactating Holstein cows were examined, and 10 foremilk fractions were obtained from sequential samples up to 150 ml. The LAP concentrations in milk samples increased until 25 ml. The LF concentrations increased up to the 10 ml fraction, then stabilized at low level after the 50 ml fraction. For S100A7, some fractions had significantly higher (p < .05) concentrations than the 5 or 10 ml fractions. The IgA antibody concentration increased up to the 5 ml fraction, then after 50 ml fraction showed relatively low concentrations. This investigation determined the concentration patterns of LAP, LF, S100A7, and IgA antibody secreted in milk inside the udders of healthy lactating cows as baseline data. These distinct concentration patterns might indicate various protective responses.
Long‐term risk of hip or forearm fractures in older occasional users of benzodiazepines
Authors: Carrier Hélène , Cortaredona Sébastien , Philipps Viviane , Jacqmin‐Gadda Hélène , Tournier Marie , Verdoux Hélène , Verger Pierre 
Published: April 2020

AimsThis article sought to study the association between patterns of benzodiazepine (BZD) use and the risk of hip and forearm fractures in people aged 50 and 75 years or more.MethodsIn a representative cohort of the French National Health Insurance Fund of individuals aged 50 years or older (n = 106 437), we followed up BZD dispensing (reflecting their patterns of use) and the most frequent fall‐related fractures (hip and forearm) for 8 years. We used joint latent class models to simultaneously identify BZD dispensing trajectories and the risk of fractures in the entire cohort and in those 75 years or older). We used a survival model to estimate the adjusted hazard ratios (aHRs) between these trajectories and the risk of fractures.ResultsIn the entire cohort, we identified 5 BZD trajectories: non‐users (76.7% of the cohort); occasional users (15.2%); decreasing users (2.6%); late increasing users (3.0%); and early increasing users (2.4%). Compared with non‐users, fracture risk was not increased in either occasional users (aHR = 0.99, 95% confidence interval [CI] 0.99–1.00) or in decreasing users (aHR = 0.90, 95% CI 0.74–1.08). It was significantly higher in early increasing users (aHR = 1.86, 95% CI 1.62–2.14) and in late increasing users (aHR = 1.39, 95% CI 1.15–1.60). We observed similar trajectories and risk levels in the people older than 75 years.ConclusionOccasional BZD use, which is compatible with current recommendations, was not associated with an excess risk of the most frequent fall‐related fractures in people older than 50 or 75 years.
Molecular and immunohistochemical analysis of BRAF gene in primary cutaneous melanoma: Discovery of novel mutations
Authors: Fatnassi‐Mersni Ghaya , Arfaoui Amira Toumi , Cherni Marwa , Jones Mariem , Zeglaoui Faten , Ouzari Hadda Imen , Rammeh Soumaya 
Published: April 2020

AbstractBackgroundDetermination of BRAF status is mandatory for targeted therapy but it is not currently available in most developing countries.AimWe aimed to analyze BRAF mutations in a series of cutaneous melanoma of Tunisian patients and to compare BRAF V600E mutation detection by immunohistochemistry to DNA sequencing.Patients and methodsArchival formalin fixed paraffin embedded tissues from 28 patients with primary cutaneous melanoma were evaluated for the BRAF mutations by Sanger sequencing and immunohistochemistry.ResultsBRAF mutations were detected in 19/28 (68%) of analyzed tumors. The sensitivity and specificity of immunohistochemistry compared to DNA sequencing for identification of the BRAF V600E mutation were 100%. We found five novel mutations, one of them had deleterious effect.ConclusionThe present study shows an intermediate frequency of mutations of the BRAF gene in cutaneous melanoma of Tunisian patients, and supports the use of immunohistochemistry as a screening test for the assessment of the BRAF V600E status in the management of melanoma in clinical practice.
An unusual variant of lichen nitidus: Generalized follicular spinous with perifollicular granulomas
Authors: Taneja Neha , Mehta Nikhil , Arava Sudheer , Gupta Vishal 
Published: April 2020

AbstractSeveral unusual variants of lichen nitidus are described in the literature. Spinous follicular lichen nitidus with perifollicular granulomas is one such variant characterized by generalized follicular as well as nonfollicular keratotic papules, which show perifollicular granulomas on histopathology as well as a lichenoid granulomatous tissue reaction typical of lichen nitidus. Owing to its atypical clinical and histopathologic manifestations, it raises several clinical possibilities and can be a diagnostic challenge. We report this rare variant of lichen nitidus in a 19‐year‐old female, and discuss its clinical and histopathological differential diagnosis.