bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the Changing Landscape of Cell-to-Cell Variation After CTCF Knockdown via Single Cell RNA-seq
Authors: Wang Wei , Ren Gang , Hong Ni , Jin Wenfei
Published: December 2019

Background

CCCTC-Binding Factor (CTCF), also known as 11-zinc finger protein, participates in many cellular processes, including insulator activity, transcriptional regulation and organization of chromatin architecture. Based on single cell flow cytometry and single cell RNA-FISH analyses, our previous study showed that deletion of CTCF binding site led to a significantly increase of cellular variation of its target gene. However, the effect of CTCF on genome-wide landscape of cell-to-cell variation is unclear.

Results

We knocked down CTCF in EL4 cells using shRNA, and conducted single cell RNA-seq on both wild type (WT) cells and CTCF-Knockdown (CTCF-KD) cells using Fluidigm C1 system. Principal component analysis of single cell RNA-seq data showed that WT and CTCF-KD cells concentrated in two different clusters on PC1, indicating gene expression profiles of WT and CTCF-KD cells were systematically different. Interestingly, GO terms including regulation of transcription, DNA binding, Zinc finger and transcription factor binding were significantly enriched in CTCF-KD-specific highly variable genes, indicating tissue-specific genes such as transcription factors were highly sensitive to CTCF level. The dysregulation of transcription factors potentially explain why knockdown of CTCF lead to systematic change of gene expression. In contrast, housekeeping genes such as rRNA processing, DNA repair and tRNA processing were significantly enriched in WT-specific highly variable genes, potentially due to a higher cellular variation of cell activity in WT cells compared to CTCF-KD cells. We further found cellular variation-increased genes were significantly enriched in down-regulated genes, indicating CTCF knockdown simultaneously reduced the expression levels and increased the expression noise of its regulated genes.

Conclusions

To our knowledge, this is the first attempt to explore genome-wide landscape of cellular variation after CTCF knockdown. Our study not only advances our understanding of CTCF function in maintaining gene expression and reducing expression noise, but also provides a framework for examining gene function.
Linking servant leadership to employee creativity
Authors: Yang Jin , Ma Cuiping , Gu Jibao , Liu Hefu
Published: December 2019

Purpose

This paper aims to put forth a model that accounts for the effect of servant leadership on employee creativity from a social identity perspective. Specifically, this paper aims to examine team identification as the mediating mechanism by which servant leadership influence employee creativity. This paper also intends to investigate the moderating influences of horizontal and vertical collectivism on the effectiveness of servant leadership on follower team identification.

Design/methodology/approach

Servant leadership, team identification, collectivism (consisted of horizontal and vertical collectivism) and employee creativity were assessed in an empirical study based on a sample of 451 employees from 11 banks in China.

Findings

Drawing on social identity theory, this study found that follower team identification partially mediates the relationship between servant leadership and employee creativity. In addition, results showed that horizontal collectivism moderates the relationship between servant leadership and follower team identification; the relationship was more positive when horizontal collectivism was high, rather than low; vertical collectivism also moderates the relationship between servant leadership and follower team identification; the relationship was more positive when vertical collectivism was low, rather than high. However, results of this study indicated that the moderated mediation effects of team identification on the relationship between servant leadership and employee creativity are nonsignificant.

Practical implications

First, this research affirmed the need to promote servant leadership in employment settings. Second, managers’ understandings of the instrumental role of servant leadership in showing interpersonal acceptance, offering encouragement and support and expressing trust would prove to be valuable because it could enhance employee creativity. Finally, the findings from this study should help managers gain a better understanding of the contextual factors.

Originality/value

The first contribution of the current study was to identify team identification as an important psychological process that can link servant leadership to employee creativity. Another important contribution of the current research was the identification of the boundary conditions (e.g. horizontal and vertical collectivism).
System dynamics analysis of supply chain financial management during capacity expansion
Authors: Oleghe Omogbai
Published: December 2019

Purpose

This study aims to describe in detail, a system dynamics-based study that was used to show how a large vertically integrated aquaculture company should approach its stepwise capacity expansion program, without undermining its financial performance or affecting the performance of the value chain.

Design/methodology/approach

The company and its aquaculture value chain are used as case study. A system dynamics model is developed on the basis of generic end-to-end agribusiness and aquaculture supply chain models. The model includes the unique dynamics relating to an aquaculture supply chain. Also modelled is the working capital management rules of the company, with the effects of the capacity expansion program on its working capital, market share and its supply chain obligations. The model is used to determine the long-term impact of the company’s working capital management under different modes of financing and rate of expanding the capacity.

Findings

For a large vertically integrated company that wants to increase its capacity, there is a systematic approach to working capital management that can be used to avoid financial distress or value chain distortion.

Research limitations/implications

Extended the scope of system dynamics modelling within multiple disciplines, namely, agribusiness supply chain finance, supply chain capacity investment, financial management in large companies, supply chain working capital management and aquaculture value chain.

Practical implications

The developed model can be used to manage supply chain working capital in large vertically integrated agribusinesses, and also to assess supply chain financial risk.

Originality/value

To enhance the model build, discrete event simulation was used to model aspects of the system. The eventual system dynamics-discrete event simulation model is a form of hybrid simulation modelling that was used to provide a deeper understanding of how supply chain financial decisions affect an entire value chain system.
Berth scheduling at marine container terminals
Authors: Kavoosi Masoud , Dulebenets Maxim A. , Abioye Olumide , Pasha Junayed , Theophilus Oluwatosin , Wang Hui , Kampmann Raphael , Mikijeljević Marko
Published: December 2019

Purpose

Marine transportation has been faced with an increasing demand for containerized cargo during the past decade. Marine container terminals (MCTs), as the facilities for connecting seaborne and inland transportation, are expected to handle the increasing amount of containers, delivered by vessels. Berth scheduling plays an important role for the total throughput of MCTs as well as the overall effectiveness of the MCT operations. This study aims to propose a novel island-based metaheuristic algorithm to solve the berth scheduling problem and minimize the total cost of serving the arriving vessels at the MCT.

Design/methodology/approach

A universal island-based metaheuristic algorithm (UIMA) was proposed in this study, aiming to solve the spatially constrained berth scheduling problem. The UIMA population was divided into four sub-populations (i.e. islands). Unlike the canonical island-based algorithms that execute the same metaheuristic on each island, four different population-based metaheuristics are adopted within the developed algorithm to search the islands, including the following: evolutionary algorithm (EA), particle swarm optimization (PSO), estimation of distribution algorithm (EDA) and differential evolution (DE). The adopted population-based metaheuristic algorithms rely on different operators, which facilitate the search process for superior solutions on the UIMA islands.

Findings

The conducted numerical experiments demonstrated that the developed UIMA algorithm returned near-optimal solutions for the small-size problem instances. As for the large-size problem instances, UIMA was found to be superior to the EA, PSO, EDA and DE algorithms, which were executed in isolation, in terms of the obtained objective function values at termination. Furthermore, the developed UIMA algorithm outperformed various single-solution-based metaheuristic algorithms (including variable neighborhood search, tabu search and simulated annealing) in terms of the solution quality. The maximum UIMA computational time did not exceed 306 s.

Research limitations/implications

Some of the previous berth scheduling studies modeled uncertain vessel arrival times and/or handling times, while this study assumed the vessel arrival and handling times to be deterministic.

Practical implications

The developed UIMA algorithm can be used by the MCT operators as an efficient decision support tool and assist with a cost-effective design of berth schedules within an acceptable computational time.

Originality/value

A novel island-based metaheuristic algorithm is designed to solve the spatially constrained berth scheduling problem. The proposed island-based algorithm adopts several types of metaheuristic algorithms to cover different areas of the search space. The considered metaheuristic algorithms rely on different operators. Such feature is expected to facilitate the search process for superior solutions.
Measuring the subgingival microbiota in periodontitis patients: Comparison of the surface layer and the underlying layers
Authors: Liu Guojing , Chen Feng , Cai Yu , Chen Zhibin , Luan Qingxian , Yu Xiaoqian
Published: December 2019

Periodontitis is a major cause of tooth loss in adults that initially results from dental plaque. Subgingival plaque pathogenesis is affected by both community composition and plaque structures, although limited data are available concerning the latter. To bridge this knowledge gap, subgingival plaques were obtained using filter paper (the fourth layer) and curette (the first‐third layers) sequentially and the phylogenetic differences between the first–third layers and the fourth layer were characterized by sequencing the V3–V4 regions of 16S rRNA. A total of 11 phyla, 148 genera, and 308 species were obtained by bioinformatic analysis, and no significant differences between the operational taxonomic unit numbers were observed for these groups. In both groups, the most abundant species were Porphyromonas gingivalis and Fusobacterium nucleatum. Actinomyces naeslundii, Streptococcus intermedius, and Prevotella intermedia possessed relatively high proportions in the first–third layers; while in the fourth layer, both traditional pathogens (Treponema denticola and Campylobacter rectus) and novel pathobionts (Eubacterium saphenum, Filifactor alocis, Treponema sp. HOT238) were prominent. Network analysis showed that either of them exhibited a scale‐free property and was constructed by two negatively correlated components (the pathogen component and the nonpathogen component), while the synergy in the nonpathogen component was lower in the first–third layers than that in the fourth layer. After merging these two parts into a whole plaque group, the negative/positive correlation ratio increased. With potential connections, the first–third layers and the fourth layer showed characteristic key nodes in bacterial networks.
Developmental temperature predicts the adult response to stressors in a free‐living passerine
Authors: Uehling Jennifer J. , Taff Conor C. , Winkler David W. , Vitousek Maren N.
Published: December 2019

Early‐life conditions can have substantial effects on the ways animals respond to stressors as adults. In particular, thermal conditions during development affect juveniles' responses to stressors, and there is evidence that these effects may extend into adulthood. However, these effects remain poorly understood, especially in free‐living organisms.

We test the prediction that ambient temperatures during laying, embryonic development and nestling development affect the hormonal mediators of the response to stressors in adults. To do so, we use a long‐term dataset of tree swallows (Tachycineta bicolor) with records from both natal development and adult breeding.

We found a strong, negative relationship between ambient temperature during early development (incubation) and an individual's corticosterone (CORT) response to stress later in life (while incubating her own young). Thermal conditions during other stages of natal development also showed a weak relationship with baseline CORT during provisioning.

In a post hoc analysis, we found no evidence that ambient temperature during development differentially influenced the survival and recruitment of juveniles with different CORT phenotypes.

Our results show that thermal conditions during development can have long‐term effects on how individuals respond to stressors.
The Hiroshima memory complex
Authors: Olesen Thomas
Published: December 2019

The atomic bomb attack on Hiroshima on August 6, 1945 is one of the most powerful global memories. While the literature on global memories has greatly expanded in recent decades, Hiroshima remains surprisingly understudied. In addressing this lacuna, this paper develops a new theoretical prism for the study of global memories. It argues that the Hiroshima memory cannot be understood in isolation, but rather as the hub in a broader memory complex. This complex is the result of symbolic dialogues that connect Hiroshima with such different events, situations, and memories as Nanjing, Pearl Harbor, the Cold War, and so on. The paper demonstrates how these dialogues have been forged, often in the context of substantial controversy. While distinctly sociological in orientation, the paper takes its main theoretical inspiration from cultural, literary, and history scholars such as Jan and Aleida Assmann, Sebastian Conrad, Astrid Erll, Ann Rigney, Michael Rothberg, Aby Warburg and Mikhael Bakhtin.
Long noncoding RNA SNHG7 contributes to cell proliferation, migration, invasion and epithelial to mesenchymal transition in non‐small cell lung cancer by regulating miR‐449a/TGIF2 axis
Authors: Pang Lingling , Cheng Yun , Zou Shenchun , Song Jie
Published: December 2019

Background

Non‐small cell lung cancer (NSCLC) is an intractable malignant lung cancer with high rates of metastasis and mortality. Currently, long noncoding RNA nuclear RNA host gene 7 (SNHG7) is recognized as a biomarker of multiple cancers. However, the role of SNHG7 in NSCLC requires further understanding.

Methods

The expression of SNHG7, miR‐449a and TGIF2 in NSCLC tumors and cells was examined by quantitative real time polymerase chain reaction (qRT‐PCR). Cell viability was measured by MTT assay. Cell migration and invasion was conducted using transwell assay. Protein expression of TGIF2, vimentin, N‐cadherin and E‐cadherin was detected by western blot. The interaction between miR‐449a and SNHG7 or TGIF2 was determined by luciferase reporter system, RIP and RNA pull‐down assay, respectively. Xenograft mice models were established by subcutaneously injecting A549 cells transfected with sh‐SNHG7 and sh‐control.

Results

SNHG7 expression was upregulated in NSCLC tumors and cells compared with normal tissues and cells. SNHG7 silencing repressed cell proliferation, migration, invasion and epithelial to mesenchymal transition (EMT) in NSCLC. Consistently, SNHG7 knockdown hindered tumor growth in vivo. The subsequent luciferase reporter system, RIP and RNA pull‐down assay validated the interaction between miR‐449a and SNHG7 or TGIF2. The rescue experiments displayed that miR‐449a inhibitor counteracted SNHG7 silencing induced inhibition on proliferation, migration, invasion and EMT. Similarly, restoration of TGIF2 reversed miR‐449a mediated inhibition on cell progression. In addition, the results indicated that SNHG7 could regulate cell progression by targeting miR‐449a/TGIF2 axis.

Conclusion

SNHG7 contributed to cell proliferation, migration, invasion and EMT in NSCLC by upregulating TGIF2 via sponging miR‐449a, representing a novel targeted therapy method for NSCLC.
Grafted muscle‐derived stem cells promote the therapeutic efficiency of epimysium conduits in mice with peripheral nerve gap injury
Authors: Xu Zhuqiu , Chen Zixiang , Feng Weifeng , Huang Minlu , Yang Xiaonan , Qi Zuoliang
Published: December 2019

Our research aimed to build allogeneic artificial conduits with epimysium and muscle‐derived stem cells (MDSCs) from the skeletal muscle of mice. We applied the conduit to repair peripheral nerve defects and estimated the effectiveness of the repair process. In the research, we prepared epimysium conduits with lumens to bridge repair a 5‐mm‐long sciatic nerve defect from C57 wild‐type mice and then transplanted green fluorescent protein (GFP)‐MDSCs and Matrigel suspensions into the conduit. Histological and functional assessments were performed 4 and 8 weeks after surgery. The tissue‐engineered conduit from muscle effectively repaired the nerve defect, while the group with GFP‐MDSCs showed improved histological examinations and functional assessments, and the newborn nerves highly expressed GFP. As the results suggested, autologous epimysium conduits represent a reliable method to repair peripheral nerve defects, and the addition of MDSCs promote the effectiveness of differentiating into multiple lineages. Our research simultaneously demonstrated the myogenic, neurogenic, and angiogenic potential of MDSCs in vivo for the first time.
Effects of land‐use change on functional and taxonomic diversity of Neotropical bats
Authors: Farneda Fábio Z. , Meyer Christoph F. J. , Grelle Carlos E. V.
Published: December 2019

Human land‐use changes are particularly extensive in tropical regions, representing one of the greatest threats to terrestrial biodiversity and a key research topic in conservation. However, studies considering the effects of different types of anthropogenic disturbance on the functional dimension of biodiversity in human‐modified landscapes are rare. Here, we obtained data through an extensive review of peer‐reviewed articles and compared 30 Neotropical bat assemblages in well‐preserved primary forest and four different human‐disturbed habitats in terms of their functional and taxonomic diversity. We found that disturbed habitats that are structurally less similar to primary forest (pasture, cropland, and early‐stage secondary forest) were characterized by a lower functional and taxonomic diversity, as well as community‐level functional uniqueness. These habitats generally retained fewer species that perform different ecological functions compared to higher‐quality landscape matrices, such as agroforestry. According to functional trait composition, different bat ensembles respond differently to landscape change, negatively affecting mainly gleaning insectivorous bats in pasture, narrow‐range species in cropland, and heavier animalivorous bats in secondary forest. Although our results highlight the importance of higher‐quality matrix habitats to support elevated functional and taxonomic bat diversity, the conservation of bat species that perform different ecological functions in the mosaic of human‐modified habitats also depends on the irreplaceable conservation value of well‐preserved primary forests. Our study based on a pooled analysis of individual studies provides novel insights into the effects of different human‐modified habitats on Neotropical bat assemblages.
Participation in leisure activities in adolescents with congenital heart defects
Authors: Majnemer Annette , Rohlicek Charles , Dahan‐Oliel Noemi , Sahakian Sossy , Mazer Barbara , Maltais Désirée B , Schmitz Norbert
Published: December 2019

Aim

To describe leisure participation in adolescents with congenital heart defects (CHD) and identify factors associated with intensity of participation.

Method

Eighty adolescents with CHD were recruited (39 males, 41 females; mean age [SD] 15y 8mo [1y 8mo] range 11y 5mo–19y 11mo) of whom 78 completed the Children’s Assessment of Participation and Enjoyment (CAPE) outcome measure of leisure participation. The measure has five subscales: recreational, active‐physical, social, skill‐based, and self‐improvement. Associations between the CAPE and age, sex, and development were examined. Motor ability (Movement Assessment Battery for Children, Second Edition), cognition (Leiter International Performance Scale‐Revised), behavior (Strengths and Difficulties Questionnaire), and motivation (Dimensions of Mastery Questionnaire) were assessed.

Results

Participants exhibited impaired motor (43.5%), behavioral (23.7%), and cognitive (29.9%) development. The most intense participation was in social (mean [SD] 3.3 [0.99]) and recreational (2.9 [0.80]) activity types on the CAPE. Male sex (p<0.05) and younger age were associated with greater physical activity (<15y: 1.87; ≥15y: 1.31, p<0.05). Greater engagement in social activities was related to better cognition (r=0.28, p<0.05), higher motor function (r=0.30–0.36, p<0.01), and fewer behavioral difficulties (r=−0.32 to −0.47, p<0.01). Cognitive ability (r=0.27, p<0.05), dexterity and aiming/catching (r=0.27–0.33, p<0.05), and behavior problems (r=0.38–0.49, p=0.001) were correlated with physical activity participation. Persistence in tasks, an aspect of motivation, correlated with physical (r=0.45, p<0.001) and social activity involvement (r=0.28, p<0.05).

Interpretation

Ongoing developmental impairments in adolescents with CHD are associated with decreased active‐physical and social engagement, putting them at risk of poor physical and mental health. Health promotion strategies should be considered.

What this paper adds

Adolescents with congenital heart defects (CHD) have limited engagement in active‐physical leisure activities.

Cognitive, motor, and behavioral impairments are associated with decreased participation in leisure in children with CHD.

Female sex and older age are associated with less engagement in leisure.

Mastery motivation correlates with participation, suggesting an avenue for intervention.
French Insights on Defining and Managing Talents
Authors: d'Armagnac Sophie , Guettiche Feirouz , Janand Anne , Klarsfeld Alain , Cloet Héloïse
Published: December 2019

Research on the topic of talent definition and talent management historically comes from Anglo‐American countries, but the importance of the specific context where these notions emerged often goes unacknowledged. The objective of this research is to clarify the meaning of talent as well as to examine talent‐management practices in France, investigating the possibility of a unique French approach rooted in a different initial context. Based on 39 interviews conducted among employees of 26 global French companies, this study highlights the French idiosyncrasies of the notion of talent: the reconsideration of traditional high‐potential profiles, the preference for insiders, concern about the effects of segmentation, and the role of talents in helping others develop into talents. Accordingly, the multidimensional concept of talent can be refined for a single dimension (the exclusive/inclusive one) and then extended by adding new dimensions. Finally, this article considers the implications of these findings for the managers of French companies, for human resources professionals, and for talents themselves.
Application of droplet digital PCR in diagnosing of X monosomy in mares
Authors: Szczerbal Izabela , Nowacka‐Woszuk Joanna , Kopp‐Kuhlman Christine , Mackowski Mariusz , Switonski Marek
Published: December 2019

Background

X monosomy is the most common disorder of sex development in horses. Although cytogenetic analysis is still the gold standard in the diagnosis of equine X monosomy, novel molecular techniques are being sought to quickly and reliably detect this chromosome abnormality.

Objectives

The goal of this study was to evaluate the usefulness of a novel variant of the PCR technique—namely, droplet digital PCR (ddPCR)—in the detection of X monosomy in mares.

Study design

A proof of concept of the usefulness of ddPCR in diagnosing an abnormal number of X chromosomes in mares.

Methods

We examined an infertile mare using cytogenetic (fluorescent in situ hybridisation—FISH) and molecular (droplet digital PCR—ddPCR) techniques. The X chromosome copy number in ddPCR was estimated via detection of the AMELX gene copy number. In addition, 70 mares homozygous for X‐linked microsatellite marker (LEX3) were examined by ddPCR. For all mares, a PCR search for the Y‐linked SRY gene was also performed.

Results

Cytogenetic analysis and ddPCR gave concordant results, indicating pure X monosomy in the studied mare. Of the 70 additional mares examined by ddPCR, a single copy of the X chromosome was found in two cases. All mares were SRY‐negative and thus both freemartinism, manifested by leucocyte XX/XY chimerism, and sex reversal syndrome (XX, SRY‐positive) could be excluded.

Main limitations

The ddPCR approach does not allow for unequivocal identification of mosaicism (63,X/64,XX or 65,XXX/64,XX), but may give an indication that further cytogenetic analysis is necessary.

Conclusion

The ddPCR approach appeared to be useful for diagnosing nonmosaic X monosomy in mares. If the number of X chromosome copies in a mare, as determined by ddPCR, differs from two (in our study, <1.8 or >2.2), additional cytogenetic investigation is recommended with the aim of detecting the mosaicism.
Predicting optimal combinations of by‐catch reduction devices in trawl gears: A meta‐analytical approach
Authors: Melli Valentina , Herrmann Bent , Karlsen Junita Diana , Feekings Jordan Paul , Krag Ludvig Ahm
Published: December 2019

Global efforts to reduce unwanted catches have led to the development of a vast array of by‐catch reduction devices (BRDs), in particular for mixed trawl fisheries. Some of these BRDs could likely benefit from being combined. However, the number of possible combinations would be prohibitive to be tested experimentally. Therefore, in this study we propose a meta‐analytical approach that combines the data available on BRDs tested independently in a fishery and predict the theoretical selectivity of all possible combinations of those devices. This allows to identify promising BRD combinations, worth experimental investigation and flexible trawl configurations, where the selectivity can be substantially modified by adding or removing one BRD, thus aiding fishermen in adapting to high variability in catch composition and quota availability. To illustrate the approach, we used BRDs developed for the well‐studied Nephrops (Nephrops norvegicus, Nephropidae) directed mixed trawl fishery in the Skagerrak and Kattegat seas. We predicted the selectivity of 100 BRD combinations for Nephrops, cod (Gadus morhua, Gadidae) and haddock (Melanogrammus aeglefinus, Gadidae), compared them in terms of absolute selectivity and performance under realistic catch scenarios, from both single‐ and multispecies perspectives, and identified 15 BRD combinations that could be worth future experimental investigation. The meta‐analytical approach makes best use of existing knowledge and leads to new insights about the potential for improvement and flexibility in trawl selectivity. This could benefit a variety of mixed trawl fisheries and help developing a new generation of more flexible gears, with multiple BRDs integrated in their structure.
The mitigation hierarchy for sharks: A risk‐based framework for reconciling trade‐offs between shark conservation and fisheries objectives
Authors: Booth Hollie , Squires Dale , Milner‐Gulland Eleanor Jane
Published: December 2019

Sharks and their cartilaginous relatives are one of the world's most threatened species groups. The primary cause is overfishing in targeted and bycatch fisheries. Reductions in fishing mortality are needed to halt shark population declines. However, this requires complex fisheries management decisions, which often entail trade‐offs between conservation objectives and fisheries objectives. We propose the mitigation hierarchy (MH)—a step‐wise precautionary approach for minimizing the impacts of human activity on biodiversity—as a novel framework for supporting these management decisions. We outline a holistic conceptual model for risks to sharks in fisheries, which includes biophysical, operational and socioeconomic considerations. We then demonstrate how this model, in conjunction with the MH, can support risk‐based least cost shark conservation. Through providing examples from real‐world fishery management problems, we illustrate how the MH can be applied to a range of species, fisheries and contexts, and explore some of the opportunities and challenges hereto. Finally, we outline next steps for research and implementation. This is important in the context of increasing international regulation of shark fishing and trade, which must lead to reductions in shark mortality, while managing trade‐offs between conservation objectives and the socioeconomic value of fisheries.
Molecular basis for the preferential recognition of β1,3‐1,4‐glucans by the family 11 carbohydrate‐binding module from Clostridium thermocellum
Authors: Ribeiro Diana O. , Viegas Aldino , Pires Virgínia M. R. , Medeiros‐Silva João , Bule Pedro , Chai Wengang , Marcelo Filipa , Fontes Carlos M. G. A. , Cabrita Eurico J. , Palma Angelina S. , Carvalho Ana Luísa
Published: December 2019

Understanding the specific molecular interactions between proteins and β1,3‐1,4‐mixed‐linked d‐glucans is fundamental to harvest the full biological and biotechnological potential of these carbohydrates and of proteins that specifically recognize them. The family 11 carbohydrate‐binding module from Clostridium thermocellum (CtCBM11) is known for its binding preference for β1,3‐1,4‐mixed‐linked over β1,4‐linked glucans. Despite the growing industrial interest of this protein for the biotransformation of lignocellulosic biomass, the molecular determinants of its ligand specificity are not well defined. In this report, a combined approach of methodologies was used to unravel, at a molecular level, the ligand recognition of CtCBM11. The analysis of the interaction by carbohydrate microarrays and NMR and the crystal structures of CtCBM11 bound to β1,3‐1,4‐linked glucose oligosaccharides showed that both the chain length and the position of the β1,3‐linkage are important for recognition, and identified the tetrasaccharide Glcβ1,4Glcβ1,4Glcβ1,3Glc sequence as a minimum epitope required for binding. The structural data, along with site‐directed mutagenesis and ITC studies, demonstrated the specificity of CtCBM11 for the twisted conformation of β1,3‐1,4‐mixed‐linked glucans. This is mediated by a conformation–selection mechanism of the ligand in the binding cleft through CH‐π stacking and a hydrogen bonding network, which is dependent not only on ligand chain length, but also on the presence of a β1,3‐linkage at the reducing end and at specific positions along the β1,4‐linked glucan chain. The understanding of the detailed mechanism by which CtCBM11 can distinguish between linear and mixed‐linked β‐glucans strengthens its exploitation for the design of new biomolecules with improved capabilities and applications in health and agriculture.

Database

Structural data are available in the Protein Data Bank under the accession codes 6R3M and 6R31.
New trade formations: precarity, pragmatic cosmopolitanism and long‐distance trade in the Caucasus
Authors: SKVIRSKAJA VERA
Published: December 2019

For many ordinary people responding to ongoing post‐Soviet precarity, domestic and transnational trade has become a common choice of livelihood. This article is about the small and medium sized traders who deal in cheap Chinese commodities in the Caucasus –particularly in Georgia and Armenia. It introduces the notion of ‘trade formations’ to account for the multiple ways in which cross‐cultural trade and microfinance practices, as well as stereotypes about national and regional groups and trading minorities, highlight the role of trust, reputation and everyday diplomacy in long‐distance commercial networks. While current trade networks are rooted in the cultures of trade practised under the Soviets, dispositions of pragmatic cosmopolitanism and defensive nationalism often determine who may or may not respond to post‐Soviet precarity by turning to transnational trade, embracing political and religious diversity, and overlooking hostilities, past and present.
Automated auditory detection of a rare, secretive marsh bird with infrequent and acoustically indistinct vocalizations
Authors: Schroeder Katie M. , McRae Susan B.
Published: December 2019

Autonomous recording units (ARUs) provide a non‐invasive and efficient method for acoustic detection of elusive species across large temporal and spatial scales. However, species with indistinct vocalization structures can be a considerable challenge for automated signal recognizers. We investigated the performance of ARUs and signal recognizers in identifying the broadband, short‐syllable, pulsed calls of a secretive, threatened marsh bird, the King Rail Rallus elegans. Other sympatric species in the same habitat also have repetitive calls within the same frequency range that can be difficult to distinguish. Following serial ARU deployments at specified sites in known breeding habitat, we conducted standardized callback surveys and nest searches to provide an independent measure of breeder density. To analyse recordings, we developed a signal recognizer based on user‐input training files to detect two common call types, kek and grunt. Detections that remained following manual review of recognizer output revealed a previously undescribed seasonal decline and crepuscular diel pattern in calling rate. The rate of the grunt call also predicted density. These patterns emerged despite the recognizer's low precision and high false‐positive rate, which were largely due to misclassification of other species' calls, although ambient noise and effective detection radius also limited the detectability of King Rail calls. We demonstrate that with informed ARU scheduling, improved ability to manipulate user‐specified parameters within signal detection software, and attention to quality control, even the simplest call structures can be located consistently in a diverse acoustic landscape. Our behavioural findings will inform improvements to auditory surveys and to management of King Rails across their range.
Identification and characterization of a Masculinizer homologue in the diamondback moth, Plutella xylostella
Authors: Harvey‐Samuel T. , Norman V. C. , Carter R. , Lovett E. , Alphey L.
Published: December 2019

Recently, a novel sex‐determination system was identified in the silkworm (Bombyx mori) in which a piwi‐interacting RNA (piRNA) encoded on the female‐specific W chromosome silences a Z‐linked gene (Masculinizer) that would otherwise initiate male sex‐determination and dosage compensation. Masculinizer provides various opportunities for developing improved genetic pest management tools. A pest lepidopteran in which a genetic pest management system has been developed, but which would benefit greatly from such improved designs, is the diamondback moth, Plutella xylostella. However, Masculinizer has not yet been identified in this species. Here, focusing on the previously described ‘masculinizing’ domain of B. mori Masculinizer, we identify P. xylostella Masculinizer (PxyMasc). We show that PxyMasc is Z‐linked, regulates sex‐specific alternative splicing of doublesex and is necessary for male survival. Similar results in B. mori suggest this survival effect is possibly through failure to initiate male dosage compensation. The highly conserved function and location of this gene between these two distantly related lepidopterans suggests a deep role for Masculinizer in the sex‐determination systems of the Lepidoptera.
Metabolic changes during malignant transformation in primary cells of oral lichen planus: Succinate accumulation and tumour suppression
Authors: Yang Qiaozhen , Sun Hongying , Wang Xiaxia , Yu Xuedi , Zhang Jie , Guo Bin , Hexige Saiyin
Published: December 2019

Oral squamous cell carcinoma (OSCC) is usually diagnosed at late stages, which leads to high morbidity. There are evidence that chronic inflammation (eg oral lichen planus [OLP]) was a risk factor of OSCC, but often misdiagnosed or ignored until invasion and metastasis. By applying precision medicine, the molecular microenvironment variations and relevant biomarkers for the malignant transformation from OLP to OSCC can be fully investigated. Several studies pointed out that the metabolic pathway were suppressed in OSCC. However, it remains unclear how the systemic profile of the metabolites change during the malignant transformation. In this study, we examined and compared the mucosa samples from 11 healthy individuals, 10 OLP patients and 21 OSCC patients. Based on the results, succinate, a key metabolite of the tricarboxylic acid cycle pathway, was accumulated in the primary cultured precancerous OLP keratinocytes and OSCC cells. Then, we found that succinate activated the hypoxia‐inducible factor‐1 alpha (HIF‐1α) pathway and induced apoptosis, which could also be up‐regulated by the tumour suppressor lncRNA MEG3. These results suggested the critical roles of succinate and MEG3 in the metabolic changes during malignant transformation from OLP to OSCC, which indicated that succinate, HIF1α and downstream proteins might serve as new biomarkers of precancerous OLP for early diagnosis and therapeutic monitoring. In addition, succinate or its prodrugs might become a potential therapy for the prevention or treatment of OSCC.
Increased proliferation of hepatic periportal ductal progenitor cells contributes to persistent hypermetabolism after trauma
Authors: Diao Li , Yousuf Yusef , Amini‐Nik Saeid , Jeschke Marc G.
Published: December 2019

Prolonged and persistent hypermetabolism and excessive inflammatory response after severe trauma is detrimental and associated with poor outcome. The predisposing pathology or signals mediating this complex response are essentially unknown. As the liver is the central organ mediating the systemic metabolic responses and considering that adult hepatic stem cells are on top of the hierarchy of cell differentiation and may pass epigenetic information to their progeny, we asked whether liver progenitor cells are activated, signal hypermetabolism upon post‐traumatic cellular stress responses, and pass this to differentiated progeny. We generated Sox9CreERT2: ROSA26 EYFP mice to lineage‐trace the periportal ductal progenitor cells (PDPCs) and verify the fate of these cells post‐burn. We observed increased proliferation of PDPCs and their progeny peaking around two weeks post‐burn, concomitant with the hepatomegaly and the cellular stress responses. We then sorted out PDPCs, PDPC‐derived hepatocytes and mature hepatocytes, compared their transcriptome and showed that PDPCs and their progeny present a significant up‐regulation in signalling pathways associated with inflammation and metabolic activation, contributing to persistent hypermetabolic and hyper‐inflammatory state. Furthermore, concomitant down‐regulation of LXR signalling in PDPCs and their progeny implicates the therapeutic potential of early and short‐term administration of LXR agonists in ameliorating such persistent hypermetabolism.
Repairing the effects of childhood trauma: The long and winding road
Authors: Palmer Christine J. , Williams Yorker , Harrington Ann
Published: December 2019

Accessible Summary

What is known on this subject?

Domestic and family violence contributes to mental distress and the development of mental illness and can reverberate throughout a person's life.

What this paper adds to existing knowledge?

Therapeutic work with people who experience domestic and family violence needs to take considerable time to allow the process to unfold.

Understanding the triggers that cause past traumas to be re‐experienced helps people to recognize and change their conditioned emotional responses.

What are the implications for practice?

Time needs to be invested to develop a secure and trusting relationship to enable a person to work through childhood experiences that have the potential to overwhelm.

It is important for adults who have experienced childhood trauma to have an opportunity to process the abuse to help minimize its intrusion in their lives.
Reciprocal relations between work stress and insomnia symptoms: A prospective study
Authors: Garefelt Johanna , Platts Loretta G. , Hyde Martin , Magnusson Hanson Linda L. , Westerlund Hugo , Åkerstedt Torbjörn
Published: December 2019

Work stress and poor sleep are closely related in cross‐sectional data, but evidence from prospective data is limited. We analysed how perceived stress and work stressors (work demands, decision authority and workplace social support) are related to key dimensions of insomnia over time, using structural equation modelling. Biennial measurements from a large sample of the working population in Sweden enabled us to analyse both the relationship from stress to sleep as well as that from sleep to stress. Overall, we found reciprocal relations between insomnia and all four stress measures. However, looking at the relation between each dimension of insomnia and each stress measure, there were some differences in direction of effects. In the direction from stress to sleep, all work stressors as well as perceived stress predicted both difficulties initiating sleep and difficulties maintaining sleep. The same was found for non‐restorative sleep, with the exception for decision authority. In the opposite direction, difficulties maintaining sleep predicted increased levels of work demands and perceived stress. Difficulties initiating sleep stood out among the insomnia symptoms as not predicting any of the stress measures, while non‐restorative sleep was the only symptom predicting all stress measures. The results advance the understanding of the stress−sleep relationship and indicate a potential vicious circle between insomnia and perceived stress as well as work stressors, suggesting that the workplace could be an arena for interventions to alleviate insomnia.
Social dynamics and sexual segregation of Australian humpback dolphins (Sousa sahulensis) in Moreton Bay, Queensland
Authors: Hawkins Elizabeth R. , Pogson‐Manning Lara , Jaehnichen Christian , Meager Justin J.
Published: December 2019

Understanding the social organization of coastal dolphins, particularly those that reside adjacent to major cities and urbanized regions, is important for understanding the vulnerability of populations to human impacts. We investigated the sexual segregation and social dynamics in a population of Australian humpback dolphins (Sousa sahulensis) inhabiting the near‐urban embayment of Moreton Bay, Queensland. Over 160 vessel‐based surveys, 148 adults were photographically identified. This included 116 assumed females and 32 assumed males. The population was sexually segregated (SSAS = 0.52, p < .001) and individuals preferred to associate with others of the same sex occupying the same spatial area (p < .025). Association indices between paired males were almost double those of females (, SD = 0.04 and , SD = 0.02, respectively). However, females were more gregarious than males and maintained a larger network of associates based on preferred companionships. The social network was also modular with five clusters identified, and a limited number of individuals had a disproportionate influence on connectivity between clusters. This highly fragmented social network implies that the population may be vulnerable to social disruptions from human impacts.
Perspectivism
Authors: Goodman Jeremy , Lederman Harvey
Published: December 2019

Consider the sentence “Lois knows that Superman flies, but she doesn't know that Clark flies”. In this paper we defend a Millian contextualist semantics for propositional attitude ascriptions, according to which ordinary uses of this sentence are true but involve a mid‐sentence shift in context. Absent any constraints on the relevant parameters of context sensitivity, such a semantics would be untenable: it would undermine the good standing of systematic theorizing about the propositional attitudes, trivializing many of the central questions of epistemology, the philosophy of mind, and the philosophy of action. In response to this problem, we prove a series of tenability results. We show that, given certain constraints on the parameters of context sensitivity, there is a broad class of principles of propositional attitude psychology whose good standing follows from corresponding claims about people's mental representations. But these constraints also have some surprising consequences: they are jointly incompatible with coarse‐grained theories of propositions, and they are in tension with a natural picture of how speakers and hearers coordinate on the interpretation of attitude ascriptions. In light of these consequences we explore different ways in which the contextualist picture might be developed, and argue that our preferred way compares favorably with Fregeanism and neo‐Russellianism.
Behavioral Public Administration: Past, Present, and Future
Authors: Bhanot Syon P. , Linos Elizabeth
Published: December 2019

The last decade has seen remarkable growth in the field of behavioral public administration, both in practice and in academia. In both domains, applications of behavioral science to policy problems have moved forward at breakneck speed; researchers are increasingly pursuing randomized behavioral interventions in public administration contexts, editors of peer‐reviewed academic journals are showing greater interest in publishing this work, and policy makers at all levels are creating new initiatives to bring behavioral science into the public sector. However, because the expansion of the field has been so rapid, there has been relatively little time to step back and reflect on the work that has been done and to assess where the field is going in the future. It is high time for such reflection: where is the field currently on track, and where might it need course correction?