bluuebunny/crossref_metadata_2025 huggingface dataset:
Manipulating the 3D organization of the largest synthetic yeast chromosome
Authors: Zhang Weimin , Lazar-Stefanita Luciana , Yamashita Hitoyoshi , Shen Michael J. , Mitchell Leslie A. , Kurasawa Hikaru , Lobzaev Evgenii , Fanfani Viola , Haase Max A. B. , Sun Xiaoji , Jiang Qingwen , Goldberg Gregory W. , Ichikawa David M. , Lauer Stephanie L. , McCulloch Laura H. , Easo Nicole , Jiaming Lin S. , Camellato Brendan R. , Zhu Yinan , Cai Jitong , Xu Zhuwei , Zhao Yu , Sacasa Maya , Accardo Ryan , Ahn Ju Young , Annadanam Surekha , Brammer Basta Leighanne A. , Bello Nicholas R. , Cai Lousanna , Cerritos Stephanie , Cornwell MacIntosh , D’Amato Anthony , Hacker Maria , Hersey Kenneth , Kennedy Emma , Kianercy Ardeshir , Kim Dohee , Lim Hong Seo , McCutcheon Griffin , McGirr Kimiko , Meaney Nora , Meyer Lauren , Moyer Ally , Nimer Maisa , Sabbatini Carla , Shores Lucas S. , Silvestrone Cassandra , Snee Arden , Spina Antonio , Staiti Anthony , Stuver Matt , Tian Elli , Whearty Danielle , Zhao Calvin , Zheng Tony , Zhou Vivian , Scheifele Lisa , Zeller Karen , Noyes Marcus B. , Bader Joel S. , Deutsch Samuel , Stracquadanio Giovanni , Aizawa Yasunori , Dai Junbiao , Boeke Jef D.
Published: April 2022

Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we reportde novosynthesis of the largest eukaryotic chromosome thus far,synIV, a 1,454,621-bpSaccharomyces cerevisiaechromosome resulting from extensive genome streamlining and modification. During the construction ofsynIV, we developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction and facilitated chromosome debugging. In addition to the drastic sequence changes made tosynIVby rewriting it, we further manipulated the three-dimensional structure ofsynIVin the yeast nucleus to explore spatial gene regulation within the nuclear space. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tetheredsynIVto the inner nuclear membrane via its hundreds ofloxPsymsites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of the largest synthetic yeast chromosome shed light on higher-order architectural design of the synthetic genomes.

Graphical abstract

Highlights

De novosynthesis of the largest eukaryotic chromosome,synIV

SynIVshows similar 3D structure to wild-type IV, despite thousands of changes made to it

“Inside-out” repositioning ofsynIVin nucleus shows minor transcriptional changes

Multipoint tetheringsynIVto inner nuclear membrane represses transcription of whole chromosome
Deterministic evolution and stringent selection during pre-neoplasia
Authors: Karlsson Kasper , Przybilla Moritz J. , Kotler Eran , Khan Aziz , Xu Hang , Karagyozova Kremena , Sockell Alexandra , Wong Wing H. , Liu Katherine , Mah Amanda , Lo Yuan-Hung , Lu Bingxin , Houlahan Kathleen E. , Ma Zhicheng , Suarez Carlos J. , Barnes Chris P. , Kuo Calvin J. , Curtis Christina
Published: April 2022

The earliest events during human tumor initiation, while poorly characterized, may hold clues to malignancy detection and prevention1. Here we model occult pre-neoplasia by bi-allelically inactivatingTP53, a common early event in gastric cancer, in human gastric organoids. Causal relationships between this initiating genetic lesion and resulting phenotypes were established using experimental evolution in multiple clonally derived cultures over two years.TP53loss elicited progressive aneuploidy, including copy number alterations and structural variants prevalent in gastric cancers, with evident preferred orders. Longitudinal single cell sequencing ofTP53deficient gastric organoids similarly indicates progression towards malignant transcriptional programs. Moreover, high-throughput lineage tracing with expressed cellular barcodes demonstrates reproducible dynamics whereby initially rare subclones with shared transcriptional programs repeatedly attain clonal dominance. This powerful platform for experimental evolution exposes stringent selection, clonal interference, and a striking degree of phenotypic convergence in pre-malignant epithelial organoids. These data imply predictability in the earliest stages of tumorigenesis and reveal evolutionary constraints and barriers to malignant transformation with implications for earlier detection and interception of aggressive, genome instable tumors.
Structure of phage λ Redβ177 annealase shows how it anneals DNA strands during single-strand annealing homologous DNA recombination
Authors: Newing Timothy , Brewster Jodi L. , Yu Haibo , Johnston Nikolas P. , Fitschen Lucy J. , Tolun Gökhan
Published: April 2022

The bacteriophage λ red recombination system catalyzes the single-strand annealing homologous DNA recombination reaction, in which Redβ annealase protein plays a critical role. Using cryogenic electron microscopy, we were able to determine a structure of a C-terminally truncated Redβ with the residues 1-177 bound to two complementary 27mer oligonucleotides forming an annealing intermediate, to a final resolution of 3.3 Å. This structure validates and rationalizes decades of experimental observations on the biochemistry of Redβ. Definition of the interaction surfaces between subunits explains not only the DNA binding properties of Redβ, but also its propensity to oligomerize into long helical filaments, which are also formed by almost all annealases and are known to be functionally important. In addition, this annealing intermediate structure provides a detailed picture of the hydrogen bonding network that positions the DNA strands in a planar orientation to facilitate base pairing. Residues 133-138, which are missing from our structure, form a flexible loop. Molecular dynamics simulations were used to model the range of motion of the flexible loop, which suggested that it has a crucial role in keeping the DNA strands in the DNA-binding groove long enough to allow homology searching. The combination of structural and computational observations has allowed us to propose a detailed mechanism for the action of Redβ. More than half a century after its discovery, our work shines a light not only on the structure and mechanisms of Redβ, but also of other proteins within the annealase superfamilies.

Significance Statement

Single-strand annealing homologous DNA recombination is a process that is conserved throughout evolution from bacteriophages to humans, highlighting its importance and indispensability. It is a process that repairs double-stranded DNA breaks and is particularly vital in dsDNA viruses. The Redβ protein from the bacteriophage lambda is the archetypal annealase protein, forming the basis of our knowledge about this class of proteins. Along with the exonuclease λExo, these two proteins not only form the model system for single-strand annealing homologous recombination, but are also used in thousands of laboratories worldwide for performing genetic manipulations. After its discovery in 1966, we report the first structure of the DNA-binding and oligomerization domain of Redβ, providing details about the mechanism of homologous DNA annealing.
Life-long Dietary Restrictions have Negligible or Damaging Effects on Late-life Cognitive Performance: A Key Role for Genetics in Outcomes
Authors: Ouellette Andrew R. , Hadad Niran , Deighan Andrew , Robinson Laura , O’Connell Kristen , Freund Adam , Churchill Gary A. , Kaczorowski Catherine C.
Published: April 2022

Several studies report that caloric restriction (CR) or intermittent fasting (IF) can improve cognition, while others report limited or no cognitive benefits. Here, we compare the effects of 20% CR, 40% CR, 1-day IF, and 2-day IF feeding paradigms to ad libitum controls (AL) on Y-maze working memory and contextual fear memory (CFM) in a large population of Diversity Outbred mice that model the genetic diversity of humans. While CR and IF interventions improve lifespan, we observed no enhancement of working memory or CFM in mice on these feeding paradigms, and report 40% CR to be damaging in the context of long-term memory. Using Quantitative Trait Loci mapping, we identified the gene Slc16a7 to be associated with late-life long-term memory outcomes in mice on lifespan promoting feeding paradigms. Limited utility of dieting and fasting on memory in mice that recapitulate genetic diversity in the human population highlights the need for anti-aging therapeutics that promote cognitive function, with a neuronal monocarboxylate transporter encoded by Slc16a7 highlighted as novel target.
Improvement of Gene Delivery and Mutation Efficiency in the CRISPR-Cas9 Wheat (Triticum aestivum L.) Genomics System via Biolistics
Authors: Tanaka Jaclyn , Minkenberg Bastian , Poddar Snigdha , Staskawicz Brian , Cho Myeong-Je
Published: April 2022

Discovery of the CRISPR-Cas9 gene editing system revolutionized the field of plant genomics. Despite advantages in ease of designing gRNA and the low cost of the CRISPR-Cas9 system, there are still hurdles to overcome in low mutation efficiencies, specifically in hexaploid wheat. In conjunction with gene delivery and transformation frequency, the mutation rate bottleneck has the potential to slow down advancements in genomic editing of wheat. In this study, nine bombardment parameter combinations using three gold particle sizes and three rupture disk pressures were tested to establish optimal stable transformation frequencies in wheat. Utilizing the best transformation protocol and a knockout cassette of the phytoene desaturase gene, we subjected transformed embryos to four temperature treatments and compared mutation efficiencies. The use of 0.6 μm gold particles for bombardment increased transformation frequencies across all delivery pressures. A heat treatment of 34°C for 24 hours resulted in the highest mutation efficiency with no or minimal reduction in transformation frequency. The 34°C treatment produced two M0 mutant events with albino phenotypes, requiring biallelic mutations in all three genomes of hexaploid wheat. Utilizing optimal transformation and heat treatment parameters greatly increases mutation efficiency and can help advance research efforts in wheat genomics.
The impact of foreign direct investment (FDI) on renewable and non-renewable energy in Bangladesh: does the global climate change emergencies required?
Authors: Elheddad Mohamed , Alfar Abdelrahman J.K. , Haloub Radi , Sharma Neetu , Gomes Patrick
Published: April 2022

Purpose

The purpose of this study is to identify the effects of MNCs measured by the foreign direct investment (FDI) inflows on the promotion of renewable energy consumption and non-renewable energy in Bangladesh. It is an emergency issue these days and makes some policy suggestions.

Design/methodology/approach

Based on the literature review, the study sets a time series models to empirically test FDI degrades the environmental quality in Bangladesh, using the parametric (GMM, IV estimations) and non-parametric approaches (quantile regression).

Findings

The main findings drawn from the empirical analysis are as follows. First, the FDI inflows lead to more CO2 emissions in the Bangladeshi economy. In other words, the MNCs promote the usages of non-renewable energy which causes an increase in pollution. Second, the FDI inwards discourage renewable energy consumption and in terms of magnitude, the negative impacts of FDI on renewable energy are higher than the positive effect of FDI on CO2 emissions. This makes the situation worse.

Research limitations/implications

This study is limited to Bangladesh and explores the total impact of FDI on the environment. For further investigation, it would be better to do a detailed investigation on the FDI-renewable and nonrenewable energy relationship. For instance, one could test which type of FDI promotes green energy consumption and which one is dirtier. So, the sectorial FDI effects on pollution.

Originality/value

Most past studies parametric techniques and did not compare the effects of FDI on renewable and non-renewable energy consumption, Unlike the previous empirical studies, this paper uses GMM and IV estimations for the parametric approach and quantile regression (QR) as a robustness check. Also, it is the first study that approves the crowding-out effect of non-renewable using the FDI channel.
Supportive culture and job involvement in public sector: the mediating role of participation in decision making and organizational learning
Authors: Saraf Pavan Kumar , Saha Shilpi , Anand Amitabh
Published: April 2022

Purpose

The purpose of this study is to determine whether participation in decision-making (PDM) and organizational learning (OL) act as mediating factors in the relationship between supportive culture and job involvement.

Design/methodology/approach

Data were collected from 712 employees working in different public sector undertakings (PSUs) across India. Necessary condition analysis (NCA) analysis and partial least square (PLS) analysis were used to test the proposed hypotheses.

Findings

The findings of the present study indicated that PDM and OL act as a full mediator respectively in the relationship between supportive culture (SC) and job involvement (JI). The SC was positively and significantly related to PDM and OL. However, SL did not have a significant impact on JI. In addition, higher PDM and OL were found to be significantly impacting JI.

Practical implications

The results suggest that PDM and OL facilitate the impact of SC on JI and may help organizations to retain their employees. The implications of these findings for all hierarchical levels in PSUs are discussed.

Originality/value

OL and PDM as mediators between SC and JI have received very little attention from the context of India. The results add to the growing literature of culture from a non-western context as this study is based on Indian samples. This study has taken care to provide unbiased responses by utilizing data from employees working in various functional units of the organizations.
The interplay between supervisor support and job performance: implications of social exchange and social learning theories
Authors: Zeb Ali , Goh Gerald Guan Gan , Javaid Mudaser , Khan Muhammad Nawaz , Khan Atta Ullah , Gul Shehnaz
Published: April 2022

Purpose

Social exchange theory and social learning theory are widely employed in many disciplines but there is little application on the intention to leave and job performance among academic staff. Therefore, this study intends to examine the relationships among supervisor support, intention to leave and job performance along with mediating role of self-confidence in a developing context.

Design/methodology/approach

Data were collected through questionnaires from the academic staff of private Pakistani universities. The model was tested using data collected from 295 respondents by using structural equation modeling (SEM) technique.

Findings

The results revealed that supervisor support influenced job performance positively through the mediating role of self-confidence. Conversely, supervisor support influenced intention to leave negatively through the mediating role of self-confidence. In addition, the results also showed the direct effect of supervisor support on employees' job performance and intention to leave.

Practical implications

The results of this study suggest that the supervisor must provide adequate support to the academic staff, which helps them to develop their self-confidence. In addition, self-confidence is helpful for the employees to improve their job performance and reduce their intention to leave.

Originality/value

The study contributes to theory building in the area of supervisor support by enriching the understanding of the processes carrying the effect of supervisor support on desirable workplace outcomes. In addition, the study also explicates the less understood nature of relationship between supervisor support, job performance, and intention to leave through the mediating role of self-confidence in the Pakistani context.
Strategic human resource practices and new product development performance: the mediating role of intellectual capital
Authors: Ghlichlee Behrooz , Goodarzi Amirhossein
Published: April 2022

Purpose

The paper investigates the effects of strategic human resource practices on intellectual capital and new product development performance in knowledge-based firms.

Design/methodology/approach

A quantitative approach was adopted to conduct the present study. The respondents were sampled from knowledge-based firms in Iran. Overall, 120 managers in 60 knowledge-based firms were selected using convenience sampling. A confirmatory factor analysis was conducted to ascertain the validity and reliability of the observed items, and a structural equation model was employed for testing the proposed hypotheses.

Findings

In the studied firms, strategic human resource practices have a positive and significant effect on intellectual capital. Moreover, the findings of this study indicate that those firms that use their intellectual capital have a higher new product development performance.

Research limitations/implications

The study focuses on knowledge-based firms in Iran, which limits the generalizability of the research results. Therefore, future studies should be carried out with samples from other settings and countries. Moreover, as the study was cross-sectional, the causal relationships could not be inferred directly.

Practical implications

With regard to key areas of improvement identified in this study, knowledge-based firms should focus on increasing new product development performance by improving employees' training, involving them in their job-related decision-making process, empowering employees to innovate, developing intellectual capital and monitoring the customer's satisfaction level of new products.

Originality/value

The study extends the intellectual capital literature by linking strategic human resource practices to new product development performance in knowledge-based firms via intellectual capital as a mediator.
Organizational structure in family firms: a systematic literature review
Authors: Ahmad Tipu Syed Awais
Published: April 2022

Purpose

This paper provides a review of the academic literature on organizational structure (OS) in family firms, highlighting the contribution to knowledge and identifying research gaps and possible avenues for future research.

Design/methodology/approach

Different databases were used to search the relevant literature on OS in family firms, including Scopus, ABI/Inform Global, Business Source Complete, and Emerald Insight. The systematic literature review presents an analysis of 52 studies on OS in family firms.

Findings

The literature largely reveals inconsistent findings in terms of the characteristics and outcomes of OS in family firms. The majority of the studies (21) are either survey-based or employ a case study approach (18), with relatively fewer studies (8) being conceptual in nature. A large number of the studies (34) were conducted in developed countries, whereas only nine were undertaken in developing countries. Moreover, 23 studies examine characteristics of OS, 23 studies explore the outcomes, while 15 investigate the antecedents of OS in family firms. The characteristics of OS in family firms relate to the degree of centralization and formalization. The antecedents or factors affecting OS in family firms include cultural values, family influence, need for succession, and ownership and management changes. The positive outcomes of OS include legacy building, enhancing entrepreneurial orientation, and efficiency. The negative outcomes of OS include exploitation of fewer opportunities, maintaining the status quo, and adverse effects on sustainability initiatives.

Originality/value

Existing reviews generally explore the highest level of OS in family firms. The current review complements this debate and reviews OS in family firms from the perspective of the lower and operational levels. As such, the current review is both timely and relevant, as it identifies limitations of the available literature as well as suggests avenues for future research.
Market power and efficiency of Indian banks: does the “quiet life” hypothesis hold?
Authors: Coccorese Paolo , Misra Biswa Swarup
Published: April 2022

Purpose

This paper investigates the relationship between market power and efficiency for Indian banks in order to test the validity of the quiet life hypothesis (QLH) during 2005–2019.

Design/methodology/approach

First, the bank-level DEA efficiency scores and three measures of the Lerner index: traditional, efficiency-adjusted, stochastic are estimated. Then, efficiency scores are regressed on Lerner indices plus a set of banking and economic control variables.

Findings

Robust evidence against the QLH is obtained. Moreover, the conventional Lerner index suggests that market power of Indian banks, as well as of the different bank groups, increased during the study period, due to a greater reduction in costs compared to that of the price of banking services. The efficiency scores also declined for the banking system as a whole, and for all bank groups except new private banks.

Originality/value

This is the first study testing the QLH for the different categories of Indian banks and also provides robust inferences by using both stochastic and non-stochastic measures of market power.
Hybridized neural network for upper limb movement detection using EEG signals
Authors: Sagar G.V.R.
Published: April 2022

Purpose

This paper aims to propose a new upper limb movement classification with two phases like pre-processing and classification. Investigation of human limb movements is a significant topic in biomedical engineering, particularly for treating patients. Usually, the limb movement is examined by analyzing the signals that occurred by the movements. However, only few attempts were made to explore the correlations among the movements that are recognized by the human brain.

Design/methodology/approach

The initial process is the pre-processing that is performed for detecting and removing noisy channels. The artifacts are marked by band-pass filtering that discovers the values below and above thresholds of 200 and –200 µV, correspondingly. It also discovers the trials with unusual joint probabilities, and the trials with unusual kurtosis are also determined using this method. After this, the pre-processed signals are subjected to a classification process, where the neural network (NN) model is used. The model finally classifies six movements like “elbow extension, elbow flexion, forearm pronation, forearm supination, hand open, and hand close,” respectively. To make the classification more accurate, this paper intends to optimize the weights of NN by a new hybrid algorithm known as bypass integrated jaya algorithm (BI-JA) that hybrids the concept of rider optimization algorithm (ROA) and JA. Finally, the performance of the proposed model is proved over other conventional models concerning certain measures like accuracy, sensitivity, specificity, and precision, false positive rate, false negative rate, false discovery rate, F1-score and Matthews correlation coefficient.

Findings

From the analysis, the adopted BI-JA-NN model in terms of accuracy was high at 80th population size was 7.85%, 3.66%, 7.53%, 2.09% and 0.52% better than Levenberg–Marquardt (LM)-NN, firefly (FF)-NN, JA-NN, whale optimization algorithm (WOA)-NN and ROA-NN algorithms. On considering sensitivity, the proposed method was 2%, 0.2%, 5.01%, 0.29% and 0.3% better than LM-NN, FF-NN, JA-NN, WOA-NN and ROA-NN algorithms at 50th population size. Also, the specificity of the implemented BI-JA-NN model at 80th population size was 7.47%, 4%, 7.05%, 2.1% and 0.5% better than LM-NN, FF-NN, JA-NN, WOA-NN and ROA-NN algorithms. Thus, the betterment of the presented scheme was proved.

Originality/value

This paper adopts the latest optimization algorithm called BI-JA to introduce a new upper limb movement classification with two phases like pre-processing and classification. This is the first work that uses BI-JA based optimization for improving the upper limb movement detection using electroencephalography signals.
Antecedents and consequences of group cognitive complexity: a conceptual review
Authors: Coman Andra , Fodor Oana C.
Published: April 2022

Purpose

The purpose of this paper is to examine the literature on the antecedents and consequences of group cognitive complexity (GCC) and integrate the empirical work by using the composition/compilation framework of emergence and the input-mediator-output-input (I-M-O-I) model of team effectiveness.

Design/methodology/approach

Through a systematic search in extant databases, the authors found 27 empirical studies exploring the antecedents and consequences of GCC.

Findings

The extant literature is dominated by a compilational approach on GCC, experimental designs and a focus on exploring the antecedents of GCC (group composition and processes mostly), thus providing useful insights for organizational interventions. The work on the implications of GCC for individual or organizational level outcomes is however scant. Future endeavors could rely more on a multilevel exploration of GCC, take a developmental rather than a one-shot approach and explore the impact of new ways of working on the emergence of GCC.

Originality/value

The authors propose an integration of extant empirical work on GCC by using two complementary frameworks: the I-M-O-I model and the composition/compilation framework. The authors highlight the implications for practice and draw future research directions.
A critical review of implementing lean and simulation to improve resource utilization and patient experience in outpatient clinics
Authors: Al-Kaf Abdulqader , Jayaraman Raja , Demirli Kudret , Simsekler Mecit Can Emre , Ghalib Hussam , Quraini Dima , Tuzcu Murat
Published: April 2022

Purpose

The purpose of this paper is to explore and critically review the existing literature on applications of Lean Methodology (LM) and Discrete-Event Simulation (DES) to improve resource utilization and patient experience in outpatient clinics. In doing, it is aimed to identify how to implement LM in outpatient clinics and discuss the advantages of integrating both lean and simulation tools towards achieving the desired outpatient clinics outcomes.

Design/methodology/approach

A theoretical background of LM and DES to define a proper implementation approach is developed. The search strategy of available literature on LM and DES used to improve outpatient clinic operations is discussed. Bibliometric analysis to identify patterns in the literature including trends, associated frameworks, DES software used, and objective and solutions implemented are presented. Next, an analysis of the identified work offering critical insights to improve the implementation of LM and DES in outpatient clinics is presented.

Findings

Critical analysis of the literature on LM and DES reveals three main obstacles hindering the successful implementation of LM and DES. To address the obstacles, a framework that integrates DES with LM has been recommended and proposed. The paper provides an example of such a framework and identifies the role of LM and DES towards improving the performance of their implementation in outpatient clinics.

Originality/value

This study provides a critical review and analysis of the existing implementation of LM and DES. The current roadblocks hindering LM and DES from achieving their expected potential has been identified. In addition, this study demonstrates how LM with DES combined to achieve the desired outpatient clinic objectives.
Photodegradation of plant litter cuticles enhances microbial decomposition by increasing uptake of non‐rainfall moisture
Authors: Logan J. Robert , Barnes Paul , Evans Sarah E.
Published: April 2022

Litter decomposition plays a central role in carbon cycling in terrestrial ecosystems worldwide. In drylands, which cover 40% of the Earth's land surface, photodegradation and biotic decomposition driven by non‐rainfall moisture are important mechanisms of litter decay, though studies have only recently begun examining interactions between these two processes. We describe a novel priming mechanism in which photodegradation and biotic decay of the cuticle of plant litter increase litter absorption of non‐rainfall moisture (fog, dew and water vapor), supporting greater microbial decomposition.

We used several field experiments in a coastal fog desert and a series of in situ observations to demonstrate a relationship between solar radiation, cuticle integrity, water absorption rates and mass loss.

Experimentally attenuating solar radiation for 36 months slowed mass loss, reduced cuticle degradation and decreased litter moisture uptake relative to litter under ambient sunlight controls. In a separate field experiment, removing the cuticle of recently senesced grass tillers increased mass loss fourfold over 6 months relative to controls. Tillers with degraded cuticles also absorbed 3.8 times more water following an overnight dew event than did those with intact cuticles. Finally, fungal growth was consistently greater on the sun‐facing side of in situ tillers than on the shaded side, coincident with greater cuticle degradation.

We present a conceptual model where the cuticle of plant litter acts as a water‐resistant barrier that is first degraded by solar radiation and surficial microbes, increasing litter's ability to absorb enough water during non‐rainfall moisture events to support substantial biotic decomposition inside the tissue. Considering how photodegradation and non‐rainfall moisture are both substantial drivers of litter decomposition in drylands, understanding how they interact under realistic field conditions will help us better predict how these systems are responding to changing climate regimes.

Read the free Plain Language Summary for this article on the Journal blog.
Yeast and fruit fly mutual niche construction and antagonism against mould
Authors: Chakraborty Amrita , Mori Boyd , Rehermann Guillermo , Hernández Garcia Armando , Lemmen‐Lechelt Joelle , Hagman Arne , Khalil Sammar , Håkansson Sebastian , Witzgall Peter , Becher Paul G.
Published: April 2022

A goal in insect–microbe ecology is to understand the mechanisms regulating species associations and mutualistic interactions.

The spotted wing drosophila Drosophila suzukii develops in ripening fruit, unlike other drosophilids that typically feed on overripe fruit, and is associated with the yeast Hanseniaspora uvarum.

We hypothesized that D. suzukii and H. uvarum engage in niche construction leading to a mutualistic relation, facilitating the exploitation of fruit and berries as larval substrate.

We show that H. uvarum proliferates on both ripe and on unripe raspberries, mediates attraction of D. suzukii larvae and adult flies, enhances egg‐laying in mated females and is a sufficient food substrate to support larval development. Moreover, H. uvarum suppresses the antagonistic grey mould, Botrytis cinerea in collaboration with D. suzukii larvae, and produces less ethanol than baker's yeast. H. uvarum thus creates favourable conditions for D. suzukii larval development, which is susceptible to ethanol and grey mould.

D. suzukii, on the other hand, vectors H. uvarum to suitable substrates such as raspberries, where larval feeding activity enhances growth of H. uvarum. Larval feeding also helps to suppress B. cinerea, which otherwise outcompetes H. uvarum on raspberry, in the absence of fly larvae.

In conclusion, H. uvarum enhances D. suzukii larval development on unripe berries, and D. suzukii promotes H. uvarum dispersal and growth on berries. Yeast and fly modify their shared habitat in reciprocal niche construction and mutual interaction.

Read the free Plain Language Summary for this article on the Journal blog.
Drastic shift in flowering phenology of F1 hybrids causing rapid reproductive isolation in Imperata cylindrica in Japan
Authors: Nomura Yasuyuki , Shimono Yoshiko , Mizuno Nobuyuki , Miyoshi Ikuya , Iwakami Satoshi , Sato Kazuhiro , Tominaga Tohru
Published: April 2022

Hybridization is a major source of phenotypic variation and a driving force for evolution. Although novel hybrid traits can often disrupt adaptive relationships between the parental phenotypes and their environments, how new hybrid traits disrupt local adaptation remains unclear. Here, we report how a new phenotype of hybrids between two Imperata cylindrica ecotypes contributes to rapid reproductive isolation from their parents and affects hybrid fitness.

We analysed 350 accessions of I. cylindrica collected from the 1980s to the 2010s throughout Japan to explore the genetic population structure of the hybrids. We surveyed the flowering periods, seed set, and germination of two ecotypes and their hybrids in both natural habitats and common gardens.

Genetic analyses of population structure revealed that the hybrid populations consisted of only F1 individuals, without advanced generation hybrids. The flowering phenology of the F1 plants was delayed until autumn, 5–6 months later than the parental ecotypes. The drastic shift in flowering phenology prevents F1s from backcrossing. In addition, it changes their seed dispersal time to winter. Germination is inhibited by low temperatures, and the seeds likely decay before the next spring, resulting in the absence of an F2 generation. We identified the environmental mismatch of the F1 population as a specific mechanism for the maintenance of an only F1 population.

Synthesis. We have demonstrated that this flowering phenology mismatch promotes reproductive isolation between the parents and F1s and affects various temporal components of the hybrids, resulting in a unique hybrid population consisting only of F1s. This system sheds light on the importance of hybrid traits in driving rapid reproductive isolation.
Intermediate dispersal hypothesis of species diversity: New insights
Authors: Yamaguchi Ryo
Published: April 2022

The origin and patterns of species diversity are fundamental themes in ecology and evolutionary biology. Insular systems play an important role in biogeography, and the species richness within an insular system has classically been considered as determined by the balance between the rate of speciation plus net migration and the rate of species extinction. A recent wave of studies integrating comprehensive phenotypic, phylogenetic, and environmental data is accumulating additional macroevolutionary insights at unprecedented scales. In this review, I summarize and discuss the hypothesis that intermediate dispersal ability leads to clades with high species diversity by recurrent speciation events (referred to as the intermediate dispersal hypothesis, IDH). Although some recent empirical and theoretical studies have supported the IDH, further integration of other ecological and evolutionary concepts spanning different timescales is needed to resolve long‐standing debates about the non‐linear relationship between diversification and organismal dispersal ability. This paper presents a framework for future studies that intend to test the IDH; I organize the factors that should be taken into account, including the indices for quantifying dispersal ability and species diversification, and methods of taxon sampling. The IDH requires more attention and could be used to unveil the diversity of extant species and how dispersal ability affects rates of speciation and extinction.
Early experience of the quality improvement award program in federally funded health centers
Authors: Jin Janel L. , Bolton Joshua , Nocon Robert S. , Huang Elbert S. , Hoang Hank , Sripipatana Alek , Chin Marshall H.
Published: April 2022

Objectives

To describe the Health Resources and Services Administration's Quality Improvement Award (QIA) program, award patterns, and early lessons learned.

Study Setting

1413 health centers were eligible for QIA from 2014 to 2018.

Study Design

We assessed cumulative QIA funding earned and modified funding excluding payments for per‐patient bonuses, electronic health record (EHR) use, patient‐centered medical home (PCMH) accreditation, and health information technology. We compared health centers on rural/urban location, PCMH accreditation, EHR reporting, and size.

Data Collection

Organizational and quality measures are reported in the Uniform Data System, QIA program data.

Principal Findings

Average cumulative funding was higher for health centers that were not rural (USD 380,387 [± USD 233,467] vs. USD 303,526 [± USD 164,272]), had PCMH accreditation (USD 401,675 [± USD 218,246] vs. USD 250,784 [± USD 144,404]), used their EHR for quality reporting (USD 374,214 (± USD 222,866) vs. USD 331,150 (± USD 198,689)), and were large (USD 435,473 (± USD 238,193) vs. USD 270,681 (± USD 114,484) an USD 231,917 (± USD 97,847) for small and medium centers, respectively). There were similar patterns, with smaller differences, for average modified payments.

Conclusions

QIA is an important feasible initiative to introduce value‐based payment principles to health centers. Early lessons for program design include announcing award criteria in advance and focusing on a smaller number of priority targets.
snpfiltr: An R package for interactive and reproducible SNP filtering
Authors: DeRaad Devon A.
Published: April 2022

Here, I describe the R package snpfiltr and demonstrate its functionality as the backbone of a customizable, reproducible single nucleotide polymorphism (SNP) filtering pipeline implemented exclusively via the widely adopted R programming language. SNPfiltR extends existing SNP filtering functionalities by automating the visualization of key parameters such as sequencing depth, quality, and missing data proportion, allowing users to visually optimize and implement filtering thresholds within a single, cohesive work session. All SNPfiltR functions require vcfr objects as input, which can be easily generated by reading a SNP data set stored in standard variant call format (vcf) into an R working environment using the function read.vcfR() from the R package vcfr. Performance and accuracy benchmarking reveal that for moderately sized SNP data sets (up to 50 M genotypes, plus associated quality information), SNPfiltR performs filtering with comparable accuracy and efficiency to current state of the art command‐line‐based programs. These results indicate that for most reduced‐representation genomic data sets, SNPfiltR is an ideal choice for investigating, visualizing, and filtering SNPs as part of a user friendly bioinformatic pipeline. The snpfiltr package can be downloaded from CRAN with the command install.packages(“snpfiltr”), and the current development version is available from GitHub at: (github.com/DevonDeRaad/SNPfiltR). Thorough documentation for SNPfiltR, including multiple comprehensive vignettes detailing realistic use‐cases, is available at the website: devonderaad.github.io/SNPfiltR/.
Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA
Authors: Suchan Tomasz , Chauvey Lorelei , Poullet Marine , Tonasso‐Calvière Laure , Schiavinato Stéphanie , Clavel Pierre , Clavel Benoit , Lepetz Sébastien , Seguin‐Orlando Andaine , Orlando Ludovic
Published: April 2022

Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post‐mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have recently gained popularity in ancient DNA research, the impact of USER‐treatment on capture efficacy still remains untested. In this study, we applied hyRAD capture to eight ancient equine subfossil specimens from France (1st–17th century CE), including horses, donkeys and their first‐generation mule hybrids. We found that USER‐treatment could reduce capture efficacy and introduce significant experimental bias. It differentially affected the size distribution of on‐target templates following capture with two distinct hyRAD probe sets in a manner that was not driven by differences in probe sizes and DNA methylation levels. Finally, we recovered unbalanced proportions of donkey‐specific and horse‐specific alleles in mule capture sequence data, due to the combined effects of USER‐treatment, probe sets and reference bias. Our work demonstrates that while USER‐treatment can improve the quality of ancient DNA sequence data, it can also significantly affect hyRAD capture outcomes, introducing bias in the sequence data that is difficult to predict based on simple molecular probe features. Such technical batch effects may prove easier to model and correct for using capture with synthetic probes of controlled sizes and diversity content.
China engages the Global South: From Bandung to the Belt and Road Initiative
Authors: Liu Hong
Published: April 2022

This article addresses China’s engagement with the Global South regarding the transnational transfer of knowledge and policy. It argues that China’s active participation in the Bandung Conference constituted historical capital in legitimating its (leadership) role in the Global South and as an alternative modernity. The past decade has witnessed the growing importance of the Global South for China. Apart from a geopolitical motive, China’s expanding economic ties with the developing world serve as an overarching framework facilitating transnational knowledge transfer, with the centrality of development reinforced by an institutionalization drive. The essay concludes that China’s engagement with the Global South in the context of the Belt and Road Initiative has been shaped by the complex logics of domestic political economy and changing global geopolitics, not all of which are within China’s control. A stakeholder‐centric approach, therefore, will be beneficial to all countries concerned.
Time to make some noise about a quiet revolution
Authors: Calvert Katrina , Leathersich Sebastian , Howat Paul , Van Der Wal Sarah
Published: April 2022

‘Tomorrow belongs to those who can hear it coming’ David Bowie. Language is a living entity that moves and changes. Use of gender‐neutral language in medical literature is increasingly common. It is time for obstetricians and gynaecologists in Australia and New Zealand to interrogate their own bias and desire to maintain the status quo, and to consider reasons for change.
Let's teach Kibot: Discovering discussion patterns between student groups and two conversational agent designs
Authors: Nguyen Ha
Published: April 2022

Conversational agents can deepen reasoning and encourage students to build on others' knowledge in collaborative learning. Embedding agents in group work, however, presents challenges where groups may ignore the agents, and this calls for designs where students perceive agents as learning partners. This study examines group interactions with two text‐based agents (ie, chatbots) that posed as an expert and a less knowledgeable peer in a high school marine biology lesson. Student messages (N = 1764) from 18 groups (52 students ages 14–15) received codes for reasoning, building on prior ideas, and responsiveness to the agents. Results indicate no differences between agents in how often each discussion move occurred. Interestingly, sequential pattern mining suggests that the less‐knowledgeable‐peer agent prompted groups to show questioning and building on others' ideas, similar to how students may act as peer tutors to the agent. Meanwhile, sequences with the expert agent resembled student‐teacher exchange, where groups responded to the agent's nudges and then provided reasoning. Findings illustrate the affordances of embedding humanized features in technology designs to promote discussion.

Practitioner notes

What is already known about this topic

Conversational agents can facilitate group discussions, but can get abused or ignored by student groups.

To engage students, agent designs can simulate the characteristics of familiar classroom figures, such as peers or teachers.

There are limited explorations of how student groups adapt their interactions to different agent designs in collaborative settings.

What the paper adds

Illustrations of the utilities of diversifying agent designs in collaborative learning.

Insights into the unique interaction patterns that student groups displayed to different designs, such as questioning and building on others' ideas with a less‐knowledgeable‐peer agent.

Implications for practice and/or policy

Embedding signs of humanness in classroom facilitation and technology design can foster responsiveness among users.

Pedagogy can consider adaptive designs to promote interaction sequences that contribute to learning (eg, questioning, expanding on prior ideas) at opportune moments.
Late recurrence of lymphoid malignancies after initial treatment for Hodgkin lymphoma – A study from the Danish Lymphoma Registry
Authors: Andersen Maja Dam , Hamilton‐Dutoit Stephen , Modvig Lena , Vase Maja , Christiansen Ilse , Christensen Jacob Haaber , Dahl‐Sørensen Rasmus Bo , Stoltenberg Danny , Kamper Peter , d'Amore Francesco
Published: April 2022

We analysed a large cohort of Hodgkin lymphoma (HL) patients in order to characterize: (1) the pattern of late recurrence of lymphoid malignancies (LR) after initial treatment for HL over a 35‐year period; (2) the clinicopathological parameters influencing the risk of LR; and (3) the outcome of patients experiencing LR. We reviewed data of 3350 HL patients diagnosed in Denmark between 1982 and 2018 and registered in the Danish National Lymphoma Registry (LYFO). LR was defined as a recurrence of lymphoid malignancy at least five years after initial diagnosis. LR occurred in 58 patients, with a cumulative incidence at 10, 15 and 20 years of 2.7%, 4.0% and 5.4% respectively. LR was more frequently observed in patients with nodular lymphocyte‐predominant HL (NLPHL) [hazard ratio (HR) 4.5; 95% confidence interval (CI): 2.4–8.4, p < 0.001]. In classical HL (cHL) patients, older age and lymphocytopenia were risk factors for LR with HRs of 1.04 per additional year (95% CI: 1.02–1.06) and 5.6 (95% CI: 2.7–11.5) respectively. Mixed cellularity histological subtype was a risk factor for LR, but only in females, with a HR of 5.4 (95% CI: 1.4–20.4, p = 0.014). In contrast to what was observed in NLPHL, LR in cHL was associated with an almost threefold increased risk of death compared with patients in continuous complete remission. Approximately one fifth (22.4%) of patients with LR experienced a second relapse.
Extracting firms' R&D processes from patent data to study inbound and coupled open innovation
Authors: Cammarano Antonello , Michelino Francesca , Caputo Mauro
Published: April 2022

The paper suggests a patent‐based methodology to study the implications of inbound and coupled open innovation adoption at the project level. The input–process–output–outcome model suggested in this work allows the analysis of firms' R&D projects and can be considered as an approach to investigate how companies achieve specific outputs and outcomes starting from certain inputs and employing open innovation practices. The methodology is tested on a sample of 35,857 patents of 214 worldwide companies from three top R&D spending industries. Results show that the model is able to delineate high performing applications of open innovation. Inbound open innovation is associated with exploitation activities and produces incremental or architectural innovation, with high innovation performance in terms of technological and market success. Coupled open innovation is linked to explorative behaviours aiming at getting radical innovation, but with a limited likelihood of the technology developed to be successful, at least in the short term.