bluuebunny/crossref_metadata_2025 huggingface dataset:
Postglacial migration across a large dispersal barrier outpaces regional expansion from glacial refugia: evidence from two conifers in the Pacific Northwest
Authors: Fernandez MC , Hu FS , Gavin DG , deLafontaine G , Heath KD
Published: January 2020

Understanding how climate refugia and migration over great distances have facilitated species survival during periods of past climate change is crucial for evaluating contemporary threats to biodiversity. In addition to tracking a changing climate, extant species must face complex, anthropogenically fragmented landscapes. The dominant conifer species in the mesic temperate forests of the Pacific Northwest are split by the arid rain-shadow of the Cascade Range into coastal and interior distributions, with continued debate over the origins of the interior populations. If the Last Glacial Maximum extirpated populations in the interior then postglacial migration across the arid divide would have been necessary to create the current distribution, whereas interior refugial persistence could have locally repopulated the disjunction. These alternative scenarios have significant implications for the postglacial development of the Pacific Northwest mesic forests and the impact of dispersal barriers during periods of climate change. Here we use genotyping-by-sequencing (ddRADseq) and phylogeographical modeling to show that the postglacial expansion of both mountain hemlock and western redcedar consisted largely of long-distance spread inland in the direction of dominant winds, with limited expansion from an interior redcedar refugium. Our results for these two key mesic conifers, along with fossil pollen data, address the longstanding question on the development of the Pacific Northwest mesic forests and contrast with many recent studies emphasizing the role of cryptic refugia in colonizing modern species ranges.

Statement of Significance

Understanding whether habitat fragmentation hinders range shifts as species track a changing climate presents a pressing challenge for biologists. Species with disjunct distributions provide a natural laboratory for studying the effects of fragmentation during past periods of climate change. We find that dispersal across a 50-200-km inhospitable barrier characterized the expansion of two conifer species since the last ice age. The importance of migration, and minimal contribution of more local glacial refugia, contrasts with many recent studies emphasizing the role of microrefugia in populating modern species distributions. Our results address a longstanding question on the development of the disjunct mesic conifer forests of the Pacific Northwest and offer new insights into the spatiotemporal patterns of refugial populations and postglacial vegetation development previously unresolved despite decades of paleoecological studies.
Mining the Selective Remodeling of DNA Methylation in Promoter Regions to Identify Robust Gene-Level Associations with Phenotype
Authors: Quan Yuan , Liang Fengji , Zhu Yuexing , Chen Ying , Xu Ruifeng , Xiong Jianghui
Published: January 2020

Epigenetics is an essential biological frontier linking genetics to the environment, where DNA methylation is one of the most studied epigenetic events. In recent years, through the epigenome-wide association study (EWAS), researchers have identified thousands of phenotype-related methylation sites. However, the overlap between identified phenotype-related DNA methylation sites are often quite small, and it might clue to methylation remodeling has a certain degree of randomness within the genome. Thus, the identification of robust gene-phenotype associations is crucial for interpreting pathogenesis. How to integrate the methylation values of different sites on the same gene and to mining the DNA methylation at the gene level remains a challenge. A recent study found that the DNA methylation difference of the gene body and promoter region has a strong correlation with gene expression. In this study, we proposed a Statistical difference of DNA Methylation between Promoter and Other Body Region (SIMPO) algorithm to extract DNA methylation values at the gene level. First, by choosing to smoke as an environmental exposure factor, our method led to significant improvements in gene overlaps (from 5% to 17%) between different datasets. In addition, the biological significance of these genes (∼23%) are significantly better than those identified by traditional probe-based methods (∼18%, P-value = 5.18e-03). Then, we selected two disease content (e.g., insulin resistance and Parkinson’s disease) to show that the biological efficiency of disease-related gene identification increased from 15.43% to 44.44% (P-value = 1.20e-28). Thus, our results declare that mining the selective remodeling of DNA methylation in promoter regions can identify robust gene-level associations with phenotype, and the characteristic remodeling of a given gene’s promoter region can reflect the essence of disease.
Exactly solvable models of stochastic gene expression
Authors: Ham Lucy , Schnoerr David , Brackston Rowan D. , Stumpf Michael P. H.
Published: January 2020

Stochastic models are key to understanding the intricate dynamics of gene expression. But the simplest models which only account for e.g. active and inactive states of a gene fail to capture common observations in both prokaryotic and eukaryotic organisms. Here we consider multistate models of gene expression which generalise the canonical Telegraph process, and are capable of capturing the joint effects of e.g. transcription factors, heterochromatin state and DNA accessibility (or, in prokaryotes, Sigma-factor activity) on transcript abundance. We propose two approaches for solving classes of these generalised systems. The first approach offers a fresh perspective on a general class of multistate models, and allows us to “decompose” more complicated systems into simpler processes, each of which can be solved analytically. This enables us to obtain a solution of any model from this class. We further show that these models cannot have a heavy-tailed distribution in the absence of extrinsic noise. Next, we develop an approximation method based on a power series expansion of the stationary distribution for an even broader class of multistate models of gene transcription. The combination of analytical and computational solutions for these realistic gene expression models also holds the potential to design synthetic systems, and control the behaviour of naturally evolved gene expression systems, e.g. in guiding cell-fate decisions.
Loss of vacuolar acidity results in iron sulfur cluster defects and divergent homeostatic responses during aging inSaccharomyces cerevisiae
Authors: Chen Kenneth L. , Ven Toby N. , Crane Matthew M. , Brunner Matthew L.C. , Pun Adrian K. , Helget Kathleen L. , Brower Katherine , Chen Dexter E. , Doan Ha , Dillard-Telm Justin D. , Huynh Ellen , Feng Yen-Chi , Yan Zili , Golubeva Alexandra , Hsu Roy A. , Knight Raheem , Levin Jessie , Mobasher Vesal , Muir Michael , Omokehinde Victor , Screws Corey , Tunali Esin , Tran Rachael K. , Valdez Luz , Yang Edward , Kennedy Scott R. , Herr Alan J. , Kaeberlein Matt , Wasko Brian M.
Published: January 2020

The loss of vacuolar/lysosomal acidity is an early event during aging that has been linked to mitochondrial dysfunction. However, it is unclear how loss of vacuolar acidity results in age-related dysfunction. Through unbiased genetic screens, we determined that increased iron uptake can suppress the mitochondrial respiratory deficiency phenotype of yeastvmamutants, which have lost vacuolar acidity due to genetic disruption of the vacuolar ATPase proton pump. Yeastvmamutants exhibited nuclear localization of Aft1, which turns on the iron regulon in response to iron sulfur cluster (ISC) deficiency. This led us to find that loss of vacuolar acidity with age in wildtype yeast causes ISC defects and a DNA damage response. Using microfluidics to investigate aging at the single cell level, we observe grossly divergent trajectories of iron homeostasis within an isogenic and environmentally homogeneous population. One subpopulation of cells fails to mount the expected compensatory iron regulon gene expression program, and suffers progressively severe ISC deficiency with little to no activation of the iron regulon. In contrast, other cells show robust iron regulon activity with limited ISC deficiency, which allows extended passage and survival through a period of genomic instability during aging. These divergent trajectories suggest that iron regulation and ISC homeostasis represent a possible target for aging interventions.
A probabilistic gene expression barcode for annotation of cell-types from single cell RNA-seq data
Authors: Grabski Isabella N. , Irizarry Rafael A.
Published: January 2020

Abstract

Single-cell RNA sequencing (scRNA-seq) quantifies gene expression for individual cells in a sample, which allows distinct cell-type populations to be identified and characterized. An important step in many scRNA-seq analysis pipelines is the annotation of cells into known cell-types. While this can be achieved using experimental techniques, such as fluorescence-activated cell sorting, these approaches are impractical for large numbers of cells. This motivates the development of data-driven cell-type annotation methods. We find limitations with current approaches due to the reliance on known marker genes or from overfitting because of systematic differences between studies or batch effects. Here, we present a statistical approach that leverages public datasets to combine information across thousands of genes, uses a latent variable model to define cell-type-specific barcodes and account for batch effect variation, and probabilistically annotates cell-type identity. The barcoding approach also provides a new way to discover marker genes. Using a range of datasets, including those generated to represent imperfect real-world reference data, we demonstrate that our approach substantially outperforms current reference-based methods, in particular when predicting across studies. Our approach also demonstrates that current approaches based on unsupervised clustering lead to false discoveries related to novel cell-types.
Low-cost microphysiological systems: Feasibility study of a tape-based barrier-on-chip system for small intestine modeling
Authors: Winkler Thomas E. , Feil Michael , Stronkman Eva F.G.J. , Matthiesen Isabelle , Herland Anna
Published: January 2020

We see affordability as a key challenge in making organs-on-chips accessible to a wider range of users, particularly outside the highest-resource environments. Here, we present an approach to barrier-on-a-chip fabrication based on double-sided pressure-sensitive adhesive tape and off-the-shelf polycarbonate. Besides a low materials cost, common also to PDMS or thermoplastics, it requires minimal (€ 100) investment in laboratory equipment, yet at the same time is suitable for upscaling to industrial roll-to-roll manufacture. We evaluate our microhpysiological system with an epithelial (C2BBe1) barrier model of the small intestine, studying the biological effects of permeable support pore size, as well as stimulation with a common food compound (chili pepper-derived capsaicinoids). The cells form tight and continuous barrier layers inside our systems, with comparable permeability but superior epithelial polarization compared to Transwell culture, in line with other perfused microphysiological models. Permeable support pore size is shown to weakly impact barrier layer integrity as well as the metabolic cell profile. Capsaicinoid response proves distinct between culture systems, but we show that impacted metabolic pathways are partly conserved, and that cytoskeletal changes align with previous studies. Overall, our tape-based microphysiolgical system proves to be a robust and reproducible approach to studying physiological barriers, in spite of its low cost.
Mutations in the tomato gibberellin receptors suppresses xylem proliferation and reduces water loss under water-deficit conditions
Authors: Illouz-Eliaz Natanella , Nissan Idan , Nir Ido , Ramon Uria , Shohat Hagai , Weiss David
Published: January 2020

Low gibberellin (GA) activity in tomato (Solanum lycopersicum) inhibits leaf expansion and reduces stomatal conductance. These lead to lower transpiration and improve water status under transient drought conditions. Tomato has three GIBBERELLIN-INSENSITIVE DWARF1 (GID1) GA receptors with overlapping activities and high redundancy. We have tested whether mutation in a single GID1 reduces transpiration without affecting growth and productivity. CRISPR-Cas9gid1mutants were able to maintain higher leaf water content under water-deficit conditions. Moreover, whilegid1aexhibited normal growth, it showed reduced whole plant transpiration and better recovery from dehydration. Mutation inGID1ainhibited xylem vessels proliferation that led to lower hydraulic conductance. In stronger GA mutants, we also found reduced xylem vessel expansion. These results suggest that low GA activity affects transpiration by multiple mechanisms; it reduces leaf area, promotes stomatal closure and reduces xylem proliferation and expansion and as a result, xylem hydraulic conductance. We further examined ifgid1aperform better than the control M82 in the field. Under these conditions, the high redundancy of GID1s was lost andgid1aplants were semi-dwarf, but their productivity was not affected. Althoughgid1adid not perform better under drought conditions in the field, it exhibited higher harvest index.

Highlight

The loss of the tomato gibberellin receptors GID1s reduced xylem proliferation and xylem hydraulic conductance. These contribute to the effect of low gibberellin activity on water loss under water-deficit condition.
Transfer of hepatocellular microRNA regulates cytochrome P450 2E1 in renal tubular cells
Authors: Matthews Olivia , Morrison Emma E , Tranter John D , Lewis Philip Starkey , Toor Iqbal S , Srivastava Abhishek , Sargeant Rebecca , Rollison Helen , Matchett Kylie P , Gray Gillian A , Goldring Chris , Park Kevin , Denby Laura , Dhaun Neeraj , Bailey Matthew A , Henderson Neil C , Williams Dominic , Dear James W
Published: January 2020

Extracellular microRNAs have been demonstrated to have the ability to enter kidney tubular cells and modify gene expression. We have used a Dicer-hepatocyte-specific microRNA conditional knock-out (Dicer-CKO) mouse to investigate functional microRNA transfer from liver to kidney under physiological conditions and in the context of drug toxicity. Dicer-CKO mice demonstrated a time-dependent decrease in the hepatocyte-derived microRNA, miR-122, in the kidney in the absence of other microRNA changes. During hepatotoxicity, miR-122 increased in kidney tubular cells; this was abolished in Dicer-CKO mice. Depletion of hepatocyte microRNAs increased expression and activity of the miR-122 target - cytochrome (CYP) P450 2E1 - in the kidney. Serum extracellular vesicles (ECVs) from mice with hepatotoxicity increased proximal tubular cell miR-122 and prevented cisplatin proximal tubular cell toxicity. miR-122 also increased in urinary ECVs during hepatotoxicity in humans. Transfer of microRNA was not restricted to liver injury – we detected miR-499 release with murine cardiac injury, and this correlated with an increase in the kidney. In summary, a physiological transfer of microRNA to the kidney exists, which is increased by liver injury. Regulation of renal drug response due to signalling by microRNA of hepatic origin represents a new paradigm for understanding and preventing nephrotoxicity.
Collective cell sorting requires contractile cortical waves in germline cells
Authors: Chanet Soline , Huynh Jean-René
Published: January 2020

Encapsulation of germline cells by layers of somatic cells forms the basic unit of female reproduction called primordial follicles in mammals and egg chambers inDrosophila. How germline and somatic tissues are coordinated for the morphogenesis of each separated unit remains poorly understood. Here, using improved live-imaging ofDrosophilaovaries, we uncovered periodic actomyosin waves at the cortex of germ cells. These contractile waves are associated with pressure release blebs, which project from germ cells into somatic cells. We demonstrate that these cortical activities, together with cadherin-based adhesion, are required to sort each germline cyst as one collective unit. Genetic perturbations of cortical contractility, blebs protrusion or adhesion between germline and somatic cells induced failures to encapsulate any germ cells or the inclusion of too many germ cells or even the mechanical split of germline cysts. Our results reveal that germ cells play an active role in the physical coupling with somatic cells to produce the female gamete.
Loyalty formation toward Halal food
Authors: Suhartanto Dwi , Marwansyah Marwansyah , Muflih Muhammad , Najib Moh Farid , Faturohman Irgiana
Published: January 2020

Purpose

The purpose of this paper is to integrate the Quality–Loyalty Model and the Religiosity–Loyalty Model to assess loyalty formation toward Halal food.

Design/methodology/approach

Data from 320 respondents were collected in Bandung Indonesia through a survey. A partial least-square modeling was employed to evaluate the association between food quality, religiosity, perceived value, satisfaction and loyalty.

Findings

This study discloses that the two integrated loyalty models are fit, indicating that incorporating these loyalty models provides a better comprehension of loyalty toward Halal food. Further, this study confirms the importance of both food quality and religiosity in determining loyalty.

Practical implications

This research offers an important finding for Halal food managers to develop customer loyalty through food quality and religiosity. This research recommends that Halal food managers, besides obtaining Halal certification, need to constantly innovate and adopt world food-quality standards to deal with customers’ constantly changing demands.

Originality/value

This research is the first that integrates the Quality–Loyalty Model and the Religiosity–Loyalty Model to get a better understanding of loyalty formation toward Halal food.
Does environmental concern drive Asian firms’ governance?
Authors: Mitra Aditi , Gaur Sanjaya Singh
Published: January 2020

Purpose

The sustainability issues faced by Asian firms, such as environmental destruction and depletion of resources, require the existing corporate social responsibility (COSR) models to be carefully examined and re-conceptualized. Both researchers and practitioners have indicated how social equity and having a long-term business perspective are imperative to address environmental concerns alongside fulfilling the wealth maximization goals among firms. The purpose of this study is to contribute to the literature by examining the interrelationships between COSR parameters among firms, with social equity perspective.

Design/methodology/approach

The data for this study comes from the Thomson Reuters Asset4 Index. The baseline sample of this study included 1,690 firms listed between 2011 and 2017. For hypothesis testing, fixed-effect panel analysis on 10,140 firm-year observations over seven years from 2011 to 2017 was conducted. These data points were drawn from four Asian countries (Malaysia, Thailand, Singapore and Hong Kong).

Findings

This study indicates that developed stock exchange markets among Asian markets such as Singapore and Hong Kong are transitioning from a strong focus on environmental issues to a more social equity-based economy, which is driving higher governance performance. This indicates the significance of the social dimension inherent in sustainable development and goes beyond just the ethical dimensions among the firms and the economy at large. The study also presents the challenges of re-modeling existing COSR framework among firms in Asia which do not have a clear road map on how to achieve environmental performance to achieve higher levels of human well-being, as well as the ethical considerations of achieving the wealth maximization goal.

Originality/value

This paper is unique in nature because it attempts to re-conceptualize the COSR models that support governance initiatives from an Asian market perspective by improving upon environmental performance, which in turn addresses critical issues around depleting resources and reducing wastage in the production process. The re-conceptualization model used in this study is based on the social exchange theory developed by George Homans in 1958. Accordingly, this study links the circular flow of resource procurement as well as production to the circular flow of resource replenishment seen in the chosen emerging Asian markets.
Sex counts: An examination of sexual service advertisements in a UK online directory
Authors: Kingston Sarah , Smith Nicola
Published: January 2020

Internationally, sex work research, public opinion, policy, laws, and practice are predicated on the assumption that commercial sex is a priori sold by women and bought by men. Scarce attention has been devoted to lesbian, gay, bisexual, transgender, or queer/questioning (LGBTQ) sex working as well as women who pay for sex. This is as much an empirical absence as it is a theoretical one, for the ideological claim that women comprise the “vast majority” of sex workers is rarely, if ever, exposed to empirical scrutiny. Focusing on the UK, we address this major gap in evidence in order to challenge the gendered and heterosexist logics that underpin contemporary debates. We do so by presenting large‐scale data gained from the quantitative analysis of 25,511 registered member profiles of an online escort directory. Our findings point to heterogeneity rather than homogeneity in the contemporary sex industry including in terms of gender identity, sexual orientation, and advertised client base. For example, while two‐thirds of advertisements self‐identify as “Female,” one in four are listed as “Male;” less than half list their sexual orientation as “Straight;” and nearly two‐thirds advertise to women clients. Our study thus challenges prevailing heteronormative assumptions about commercial sex, which erase LGBTQ sex workers and other non‐normative identities and practices, and which we argue have important political, practical, and theoretical consequences.
A review of surgical and peri‐operative factors to consider in emergency laparotomy care
Authors: Boyd‐Carson H. , Gana T. , Lockwood S. , Murray D. , Tierney G. M.
Published: January 2020

Patients undergoing emergency laparotomy are a heterogeneous group with regard to comorbidity, pre‐operative physiological state and surgical pathology. There are many factors to consider in the peri‐operative period for these patients. Surgical duration should be as short as possible for adequate completion of the procedure. This is of particular importance in the elderly and comorbid population. To date, there are limited data addressing the role of damage control surgery in emergency general surgery. Dual consultant‐led care in all stages of emergency laparotomy care is increasing, with increased presence out of hours and also for high‐risk patients. The role of the stoma care team should be actively encouraged in all patients who may require a stoma. Due to the emergent and unpredictable nature of surgical emergencies, healthcare teams may need to employ novel strategies to ensure early input from the stoma care team. It is important for all members of the medical teams to ensure that patients have given consent for both anaesthesia and surgery before emergency laparotomy. Small studies suggest that patients and their families are not aware of the high risk of morbidity and mortality following emergency laparotomy before operative intervention. Elderly patients should have early involvement from geriatric specialists and careful attention paid to assessment of frailty due to its association with mortality and morbidity. Additionally, the use of enhanced recovery programmes in emergency general surgery has been shown to have some impact in reducing length of stay in emergency surgical patients. However, the emergent nature of this surgery has been shown to be a detrimental factor in full implementation of enhanced recovery programmes. The use of a national database to collect data on patients undergoing emergency laparotomy and their processes of care has led to reduced mortality and length of stay in the UK. However, internationally, fewer data are available to draw conclusions.
Human factors and the safety of surgical and anaesthetic care
Authors: Marshall S. D. , Touzell A.
Published: January 2020

Safety of patients in the operating theatre relies on a cordial and efficient working relationship between all members of the theatre team. A team that communicates well, defines the roles of its members and is aware of their limitations will provide safe patient care. In this review, we will examine how human factors engineering – the science of how to design processes, equipment and environments to optimise the human contributions to performance – can be used to improve safety and efficiency of surgery. Although these are often dismissed as ‘common sense’, we will explain how these solutions emerge not from healthcare but from diverse disciplines such as psychology, design and engineering.
Advances in regional anaesthesia and acute pain management: a narrative review
Authors: Albrecht E. , Chin K. J.
Published: January 2020

Regional anaesthesia has undergone several exciting advances in the past few decades. Ultrasound‐guided techniques of peripheral nerve blockade have become the gold standard thanks to the associated improvements in efficacy, ease of performance and safety. This has increased the accessibility and utilisation of regional anaesthesia in the anaesthesia community at large and is timely given the mounting evidence for its potential benefits on various patient‐centred outcomes, including major morbidity, cancer recurrence and persistent postoperative pain. Ultrasound guidance has also paved the way for refinement of the technical performance of existing blocks concerning simplicity and safety, as well as the development of new regional anaesthesia techniques. In particular, the emergence of fascial plane blocks has further broadened the application of regional anaesthesia in the management of painful conditions of the thorax and abdomen. The preliminary results of investigations into these fascial plane blocks are promising but require further research to establish their true value and role in clinical care. One of the challenges that remains is how best to prolong regional anaesthesia to maximise its benefits while avoiding undue harm. There is ongoing research into optimising continuous catheter techniques and their management, intravenous and perineural pharmacological adjuncts, and sustained‐release local anaesthetic molecules. Finally, there is a growing appreciation for the critical role that regional anaesthesia can play in an overall multimodal anaesthetic strategy. This is especially pertinent given the current focus on eliminating unnecessary peri‐operative opioid administration.
Postoperative recovery: the importance of the team
Authors: Nilsson U. , Gruen R. , Myles P. S.
Published: January 2020

An ageing population and rising healthcare costs are challenging cost‐efficient hospital systems wanting to adapt, employing novel organisational structures designed to merge diverse skill sets. This needs not only physician and nursing leadership but also new models of care. Anaesthetists have expanded their role into the broader multidisciplinary field of peri‐operative medicine, emphasising collaboration and safety in health teams. A greater focus on patient‐centred care and shared decision making, along with validated metrics to quantify quality improvement activities, have emphasised the importance of comfort, patient satisfaction and quality of life after surgery. Shared decision‐making is more likely to be manifest in a flat hierarchy in which each member of the team brings their own experience and skills to optimise patient care. Successful surgery is best achieved by a coordinated, multidisciplinary team, embedded in a culture of collaboration and safety.
Role of patient‐centred outcomes after hospital discharge: a state‐of‐the‐art review
Authors: Ladha K. S. , Wijeysundera D. N.
Published: January 2020

The traditional approach for measuring outcomes after surgery involves ascertaining whether a patient survived surgery while avoiding major complications. This approach does not capture the full spectrum of events that are meaningful to patients, especially because mortality risks after elective surgery are relatively low, and different complication types vary considerably with respect to their impact on postoperative recovery. This review discusses the application, advantages, disadvantages and select examples of patient‐centred outcomes in peri‐operative medicine. When applied appropriately, these outcomes complement traditional clinical outcomes, identify important changes in postoperative function that impact patients without discernible complications and ensure that the definition of success after surgery is more meaningful to all relevant stakeholders.
Peri‐operative cardiac biomarker screening: a narrative review
Authors: Ruzycki S. M. , Prystajecky M. , Driedger M. R. , Kachra R.
Published: January 2020

Peri‐operative risk estimation has traditionally focused on assessing the likelihood of postoperative morbidity and mortality using pre‐operative functional assessment. Although this strategy is currently recommended by most major society guidelines, contemporary evidence suggests that cardiac biomarker measurement has important advantages over pre‐operative functional assessment. These advantages include superior predictive discrimination and inclusion of the postoperative course in risk estimation. In this review, we provide an overview of the evidence supporting the peri‐operative utilisation, compare risk estimation methods and discuss which patients may benefit most from cardiac biomarker screening. We also discuss protocols for biomarker screening and management of patients with abnormal results.
Initial response of understorey vegetation and tree regeneration to a mixed‐severity fire in old‐growth Araucaria–Nothofagus forests
Authors: Fuentes‐Ramirez Andres , Salas‐Eljatib Christian , González Mauro E , Urrutia‐Estrada Jonathan , Arroyo‐Vargas Paola , Santibañez Pablo
Published: January 2020

Questions

Fire is a key factor influencing Araucaria araucana forests, but the impact of fire severity on the understorey vegetation is not well understood. In this study we seek to answer the following questions: (a) how do initial plant diversity, composition and spatial distribution of the understorey vegetation change in response to different levels of fire severity; and (b) does the abundance of dominant tree species exhibit different patterns across a fire severity gradient shortly after fire?

Location

Old‐growth Araucaria araucana–Nothofagus pumilio forests in the Andes of south‐central Chile (38° S, 71° W) burned in 2015.

Methods

We evaluated the post‐fire plant regeneration across a fire severity gradient ranging from unburned forests to areas of high fire severity. One year after fire (in February 2016), we measured woody and herbaceous species richness, abundance, height, origin (native vs exotic species), life forms and the spatial pattern of plant recovery.

Results

Plant species richness and abundance were significantly higher within the unburned forest and low fire severity areas one year after fire, compared to areas of high and moderate fire severity. Overall, nearly 50% of the species present in the unburned forest were not found in areas of high severity, including the tree Nothofagus pumilio. Rapid vegetative resprouting of pioneer species such as Chusquea culeou resulted in an aggregated spatial distribution of plants after fire.

Conclusions

Plant diversity and the abundance of Araucaria araucana and Nothofagus pumilio were reduced in areas of high fire severity one year after fire. Exotic species were more abundant within areas of low severity, being likely mediated by cattle browsing. Our research makes clear the potential changes in forest composition and structure if dominant tree species are not capable of recovering after fire. We recommend the exclusion of cattle within fire‐affected areas and planting Nothofagus pumilio in areas of high fire severity.
Children Change Their Answers in Response to Neutral Follow‐Up Questions by a Knowledgeable Asker
Authors: Bonawitz Elizabeth , Shafto Patrick , Yu Yue , Gonzalez Aaron , Bridgers Sophie
Published: January 2020

Burgeoning evidence suggests that when children observe data, they use knowledge of the demonstrator's intent to augment learning. We propose that the effects of social learning may go beyond cases where children observe data, to cases where they receive no new information at all. We present a model of how simply asking a question a second time may lead to belief revision, when the questioner is expected to know the correct answer. We provide an analysis of the CHILDES corpus to show that these neutral follow‐up questions are used in parent–child conversations. We then present three experiments investigating 4‐ and 5‐year‐old children's reactions to neutral follow‐up questions posed by ignorant or knowledgeable questioners. Children were more likely to change their answers in response to a neutral follow‐up question from a knowledgeable questioner than an ignorant one. We discuss the implications of these results in the context of common practices in legal, educational, and experimental psychological settings.
Investigation into the effect of a plant‐derived stabiliser on the light and wash fastness of sulphur‐dyed cotton and nylon fabrics
Authors: Broadbent Peter J. , Mohtashim Quratulain , Rigout Muriel , Carr Chris M.
Published: January 2020

In this study, cotton fabric and nylon fabric were dyed with a range of commercial sulphur dyes and the light and wash fastness of the coloured fabrics was investigated. The effect of after‐treating the coloured cotton and nylon fabrics with a tannin‐based commercial product, Bayprotect Cl, in the presence or absence of sodium sulphate in the treatment bath, was found to significantly improve the light fastness of the sulphur‐dyed cotton, and the photoprotective effect was partially stable to ISO 105‐C06 washing. In addition, the tannin‐based after‐treatment also improved the colour stability of the dyed fabrics to the perborate‐based ISO 105‐C06 washing. The possible mechanisms for the improved fastness properties are also discussed. The application of sulphur dyes to nylon is potentially commercially useful but has been limited because of the reported poor light fastness of the dyeings. The photoprotective effect of the tannin‐based after‐treatment was investigated with a view to providing the necessary commercial performance. However, it was established that on this fibre, the light fastness improvement was marginal, and the associated wash fastness to oxidative bleach‐based ISO 105‐C06 washing was limited.
Emphysema is associated with the aggressiveness of COPD‐related adenocarcinomas
Authors: Lim Chun Geun , Shin Kyung Min , Lim Jae Kwang , Kim Hye Jung , Kim Won Hwa , Cho Seung Hyun , Kim Gab Chul , Lim Jiseun , Jeong Ji Yun , Cha Seung‐Ick
Published: January 2020

Objectives

To compare the differences in radiologic and pathologic features of surgically resected chronic obstructive pulmonary disease (COPD)‐related adenocarcinomas according to the presence of emphysema.

Methods

A total of 216 smokers with surgically resected lung adenocarcinoma were included in this retrospective study, and 102 patients were diagnosed with COPD. We classified COPD patients as emphysematous or non‐emphysematous group based on the emphysema severity on computed tomography (CT) and evaluated the differences in the CT and pathologic features between the two groups. The relationship between emphysema and disease‐free survival was assessed using a Kaplan–Meier curve.

Results

Lung adenocarcinomas in emphysema group presented a more aggressive pathologic grade and higher prevalence of solid lesions (vs subsolid lesions) on CT than those in non‐emphysematous group (P = 0.006 and <0.001, respectively). After adjustment for age, sex, smoking pack‐years and tumor size, emphysema group had a greater risk for higher histologic grade and higher prevalence of solid lesions than non‐emphysema group (odds ratio, 3.445; 95% confidence interval, 1.124‐10.564; P = 0.030, odds ratio, 6.192; 95% confidence interval, 1.804‐21.254; P = 0.004, respectively). Kaplan‐Meier survival curves showed that patients with emphysema had significantly impaired disease‐free survival compared with those without emphysema (median disease‐free survival = 37.0 vs 57.5 months, P = 0.038).

Conclusion

Adenocarcinomas in emphysema‐present COPD had more aggressive features of pathology and CT findings, and worse disease‐free survival than those without emphysema. These findings might provide an insight into the different pathobiology and prognostic implications of lung adenocarcinomas according to the presence of emphysema in patients with COPD.
Ureterostomy as an alternative to ileal conduits in pediatric kidney transplantation
Authors: Brubaker Aleah L. , Wu Hsi‐Yang , Lee Angela , Vuong Phoenix , Stoltz Daniel J. , Chaudhuri Abanti , James Gerri , Grimm Paul C. , Concepcion Waldo , Gallo Amy E.
Published: January 2020

Introduction

Urinary diversion in pediatric renal transplant candidates with bladders not amenable to primary reconstruction can be achieved by pre‐transplant ileal conduit creation. We performed cutaneous ureterostomies to limit pre‐transplant surgery, protect the peritoneum for dialysis, transplant patients sooner, and preserve ureter length for future surgical reconstruction.

Methods

We compared four pediatric transplant recipients with ureterostomies to four recipients with ileal conduits from 2009 to 2017.

Results

All patients with ileal conduits developed at least one urinary tract infection (UTI) within 1 year of transplant and three of four patients had recurrent UTIs within the first year. Two patients required ileal conduit revisions for redundant conduits and recurrent UTIs. Of the four ureterostomy patients, two patients had UTIs within one year of transplant. Two patients developed ureterostomy strictures requiring revision at the fascial level; one was associated with a UTI.

Conclusion

In our small case series, ureterostomy allowed for a single operative intervention with preservation of ureter length for later reconstruction. Ureterostomy is safe and recurrent UTI may be lower in the ureterostomy group. Long‐term evaluation of ureterostomy for urinary diversion in pediatric kidney transplant is warranted.
Going the distance for procurement of donation after circulatory death livers for transplantation—Does reimbursement reflect reality?
Authors: Montgomery John R. , Highet Alexandra , Hobeika Mark J. , Englesbe Michael J. , McElroy Lisa M.
Published: January 2020

Donation after circulatory death (DCD) liver transplantation (LT) has increased slowly over the past decade. Given that transplant surgeons generally determine liver offer acceptance, understanding surgeon incentives and disincentives is paramount. The purpose of this study was to assess aggregate travel distance per successful DCD versus deceased after brain death (DBD) liver procurement as a surrogate for surgeon time expenditure and opportunity cost. All consecutive liver offers made to Michigan Medicine from 2006 to 2017 were analyzed. Primary outcome was the summative travel distance (spent on all attempted procurements) per successful liver procurement that resulted in LT. Donation after circulatory death liver offer acceptance was lower than DBD liver offers, as was proportion of successful procurements among accepted offers. Overall, 10 275 miles were travelled for accepted DCD liver offers, resulting in 23 successful procurements (mean 447 miles per successful DCD liver procurement). For accepted DBD liver offers, 197 299 miles were travelled, resulting in 863 successful procurements (mean 229 miles per successful DBD liver procurement). On average, each successful DCD liver procurement required 218 more miles of travel than each successful DBD liver procurement. Current reimbursement policies poorly reflect increased surgeon travel (and time) expenditures between DCD and DBD liver offers.
Aplasia cutis congenita of the scalp: Histopathologic features and clinicopathologic correlation in a case series
Authors: Gassenmaier Maximilian , Bösmüller Hans , Metzler Gisela
Published: January 2020

Background

Aplasia cutis congenita (ACC) is a rare and heterogeneous disorder characterized by congenital absence of skin. The scalp is the most commonly affected site and lesions may overlie deeper ectodermal abnormalities. The exact etiology is still unknown, and histopathologic features are poorly defined.

Methods

A series of 10 cases from nine patients was analyzed to characterize the clinicopathologic spectrum and age‐related changes of ACC of the scalp. Hematoxylin and eosin, S100, Elastica van Gieson, and Weigert elastic stains were performed, and clinical information was retrieved from archived medical files.

Results

Patient ages ranged from 1 day to 39 years (median 57 months). All cases resembled deep‐reaching scars with almost complete loss of all adnexal structures. Isolated residual hair follicles were present in 8/10 and sweat glands and ducts in 2/10 cases. The subcutis was thinned or absent. Elastic fibers were always more fragmented than in normal tissue, and the thickness and density increased over time. There was no gain of adnexal structures with increasing age.

Conclusions

ACC represents a congenital scarring alopecia with permanent loss of skin appendages. Histopathologic changes resemble a deep‐reaching scar with fragmented elastic fibers and differentiate ACC from all other forms of non‐traumatic congenital alopecias.
SCN8A encephalopathy: Mechanisms and models
Authors: Meisler Miriam H.
Published: January 2020

De novo mutations of the neuronal sodium channel SCN8A have been identified in approximately 2% of individuals with epileptic encephalopathy. These missense mutations alter the biophysical properties of sodium channel Nav1.6 in ways that lead to neuronal hyperexcitability. We generated two mouse models carrying patient mutations N1768D and R1872W to examine the effects on neuronal function in vivo. The conditional R1872W mutation is activated by expression of CRE recombinase, permitting characterization of the effects of the mutation on different classes of neurons and at different points in postnatal development. Preclinical drug testing in these mouse models provides support for several new therapies for this devastating disorder. In contrast with the gain‐of‐function mutations in epilepsy, mutations of SCN8A that result in partial or complete loss of function are associated with intellectual disability and other disorders.
Predicting the impact of sodium channel mutations in human brain disease
Authors: Noebels Jeffrey L.
Published: January 2020

Genetic alteration of the sodium channel provides a remarkable opportunity to understand how epilepsy and its comorbidities arise from a molecular disease of excitable membranes, and a chance to create a better future for children with epileptic encephalopathy. In a single cell, the channel reliably acts as a voltage‐sensitive switch, enabling axon impulse firing, whereas at a network level, it becomes a variable rheostat for regulating dynamic patterns of neuronal oscillations, including those underlying cognitive development, seizures, and even premature lethality. Despite steady progress linking genetic variation of the channels with distinctive clinical syndromes, our understanding of the intervening biologic complexity underlying each of them is only just beginning. More research on the functional contribution of individual channel subunits to specific brain networks and cellular plasticity in the developing brain is needed before we can reliably advance from precision diagnosis to precision treatment of inherited sodium channel disorders.
Phenotypic spectrum and genetics of SCN2A‐related disorders, treatment options, and outcomes in epilepsy and beyond
Authors: Wolff Markus , Brunklaus Andreas , Zuberi Sameer M.
Published: January 2020

Pathogenic variants in the SCN2A gene are associated with a variety of neurodevelopmental phenotypes, defined in recent years through multicenter collaboration. Phenotypes include benign (self‐limited) neonatal and infantile epilepsy and more severe developmental and epileptic encephalopathies also presenting in early infancy. There is increasing evidence that an important phenotype linked to the gene is autism and intellectual disability without epilepsy or with rare seizures in later childhood. Other associations of SCN2A include the movement disorders chorea and episodic ataxia. It is likely that as genetic testing enters mainstream practice that new phenotypic associations will be identified. Some missense, gain of function variants tend to present in early infancy with epilepsy, whereas other missense or truncating, loss of function variants present with later‐onset epilepsies or intellectual disability only. Knowledge of both mutation type and functional consequences can guide precision therapy. Sodium channel blockers may be effective antiepileptic medications in gain of function, neonatal and infantile presentations.
Phenotypic and genetic spectrum of SCN8A‐related disorders, treatment options, and outcomes
Authors: Gardella Elena , Møller Rikke S.
Published: January 2020

Pathogenic variants in SCN8A have originally been described in patients with developmental and epileptic encephalopathy (DEE). However, recent studies have shown that SCN8A variants can be associated with a broader phenotypic spectrum, including the following: (1) Patients with early onset, severe DEE, developing severe cognitive and motor regression, pyramidal/extrapyramidal signs, and cortical blindness. Severe SCN8A‐DEE is characterized by intractable seizures beginning in the first months of life. The seizures are often prolonged focal hypomotor and occur in clusters, with prominent vegetative symptoms (apnea, cyanosis, mydriasis), evolving to clonic or bilateral tonic‐clonic manifestations. Spasm‐like episodes, cortical myoclonus, and recurrent episodes of status epilepticus are also common. Electroencephalograms (EEGs) show progressive background deterioration and multifocal abnormalities, predominant in the posterior regions. (2) Sporadic and familial patients with mild‐to‐moderate intellectual disability, discrete neurological signs, and treatable epilepsy. EEG is abnormal in half of the cases, showing multifocal or diffuse epileptiform abnormalities. (3) Familial cases with benign infantile seizures, sometimes associated with paroxysmal dyskinesia later in life, with no other neurological deficits, normal cognition, and usually normal interictal EEG. (4) Patients without epilepsy but with cognitive and/or behavioral disturbances, or with movement disorders. Extrapyramidal features, such as dyskinesia, ataxia, and choreoathetosis are common in all groups. Early death has been reported in about 5% of the patients, most often in the subgroup of severe DEE. Premature death occurs during early childhood and often for causes other than sudden unexpected death in epilepsy. All epilepsy subgroups exhibit better seizure control with sodium channel blockers, usually at supratherapeutic doses in the severe cases. In severe SCN8A‐DEE, ketogenic diet often has a good effect, whereas levetiracetam has a negative effect, if any. The familial SCN8A‐related epilepsies show an autosomal dominant pattern of inheritance, whereas the vast majority of SCN8A‐DEEs occur de novo.