bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interacting effects of cold snaps, rain, and agriculture on the fledging success of a declining aerial insectivore
Authors: Garrett Daniel R. , Pelletier Fanie , Garant Dany , Bélisle Marc 
Published: July 2021

AbstractClimate change predicts the increased frequency, duration, and intensity of inclement weather periods, such as unseasonably low temperatures (i.e., cold snaps) and prolonged precipitation. Many migratory species have advanced the phenology of important life history stages, and as a result will likely be exposed to these periods of inclement spring weather more often, thus risking reduced fitness and population growth. For declining avian species, including aerial insectivores, anthropogenic landscape changes such as agricultural intensification are another driver of population declines. These landscape changes may affect the foraging ability of food provisioning parents, and reduce the survival of nestlings exposed to inclement weather, through for example pesticide exposure impairing thermoregulation and punctual anorexia. Breeding in agro-intensive landscapes may thus exacerbate the negative effects of inclement weather under climate change. We observed that a significant reduction in the availability of insect prey occurred when daily maximum temperatures fell below 18.3°C, and thereby defined any day where the maximum temperature fell below this value as a day witnessing a cold snap. We then combined daily information on the occurrence of cold snaps and measures of precipitation to assess their impact on the fledging success of Tree Swallows (Tachycineta bicolor) occupying a nest box system placed across a gradient of agricultural intensification. Estimated fledging success of this declining aerial insectivore was 36.2% lower for broods experiencing four cold snap days during the 12 days post hatching period versus broods experiencing none, and this relationship was worsened when facing more precipitation. We further found that the overall negative effects of a brood experiencing periods of inclement weather was exacerbated in more agro-intensive landscapes. Our results indicate that two of the primary hypothesized drivers of many avian population declines may interact to further increase the rate of declines in certain landscape contexts.
Inbreeding and learning affect fitness and colonization of new host plants, a behavioral innovation in the spider miteTetranychus urticae
Authors: Nieberding Caroline M. , Kaisin Aubin , Visser Bertanne 
Published: July 2021

AbstractHabitat fragmentation increases the isolation of natural populations resulting in reduced genetic variability and increased species extinction risk. Behavioral innovation through learning, i.e., the expression of a new learned behavior in a novel context, can help animals colonize new suitable and increasingly fragmented habitats. It has remained unclear, however, how reduced genetic variability affects learning for colonizing more or less suitable habitats. Here, we show that inbreeding in a subsocial invertebrate, the spider miteTetranychus urticae, reduces novel host plant colonization and reproductive fitness. When provided with the possibility to learn from previous experience with a host plant species, outbred mites showed aversive learning ability, but inbred mites did not adapt their behavior. We further found a putative general cost of learning in both inbred and outbred mites. Our results reveal that inbreeding affects the learning component of behavioral innovation for host plant colonization.
Protracted speciation under the state-dependent speciation and extinction approach
Authors: Hua Xia , Herdha Tyara , Burden Conrad 
Published: July 2021

ABSTRACTHow long does speciation take? What are the speciation processes that generated a species group? The answers to these important questions in evolutionary biology lie in the genetic difference not only among species, but also among lineages within each species. With the advance of genome sequencing in non-model organisms and the statistical tools to improve accuracy in inferring evolutionary histories among recently diverged lineages, we now have the lineage-level trees to answer these questions. However, we do not yet have an analytical tool for inferring speciation processes from these trees. What is needed is a model of speciation processes that generates both the trees and species identities of extant lineages. The model should allow calculation of the probability that certain lineages belong to certain species and have an evolutionary history consistent with the tree. Here we propose such a model and test the model performance on both simulated data and real data. We show that maximum likelihood estimates of the model are highly accurate and give estimates from real data that generate patterns consistent with observations. We discuss how to extend the model to account for different rates and types of speciation processes across lineages in a species group. By linking evolutionary processes on lineage level to species level, the model provides a new phylogenetic approach to study not just when speciation happened, but how speciation happened.
Probing molecular specificity with deep sequencing and biophysically interpretable machine learning
Authors: Tomas Rube H. , Rastogi Chaitanya , Feng Siqian , Kribelbauer Judith F. , Li Allyson , Becerra Basheer , Melo Lucas A. N. , Do Bach Viet , Li Xiaoting , Adam Hammaad H. , Shah Neel H. , Mann Richard S. , Bussemaker Harmen J. 
Published: July 2021

ABSTRACTQuantifying sequence-specific protein-ligand interactions is critical for understanding and exploiting numerous cellular processes, including gene regulation and signal transduction. Next-generation sequencing (NGS) based assays are increasingly being used to profile these interactions with high-throughput. However, these assays do not provide the biophysical parameters that have long been used to uncover the quantitative rules underlying sequence recognition. We developed a highly flexible machine learning framework, called ProBound, to define sequence recognition in terms of biophysical parameters based on NGS data. ProBound quantifies transcription factor (TF) behavior with models that accurately predict binding affinity over a range exceeding that of previous resources, captures the impact of DNA modifications and conformational flexibility of multi-TF complexes, and infers specificity directly from in vivo data such as ChIP-seq without peak calling. When coupled with a new assay called Kd-seq, it determines the absolute affinity of protein-ligand interactions. It can also profile the kinetics of kinase-substrate interactions. By constructing a biophysically robust foundation for profiling sequence recognition, ProBound opens up new avenues for decoding biological networks and rationally engineering protein-ligand interactions.
Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates
Authors: Shirai Masaki , Nara Takuya , Takahashi Haruko , Takayama Kazuya , Chen Yuan , Hirose Yudai , Fujii Masashi , Awazu Akinori , Shimoda Nobuyoshi , Kikuchi Yutaka 
Published: July 2021

AbstractCpG methylation in genomic DNA is well known as a repressive epigenetic marker in eukaryotic transcription, and DNA methylation of the promoter regions is correlated with silencing of gene expression. In contrast to the promoter regions, the function of DNA methylation during transcription termination remains to be elucidated. A recent study has revealed that mouse DNA methyltransferase 3a (Dnmt3a) mainly functions inde novomethylation in the promoter and gene body regions (including transcription termination sites (TTSs)) during development. To investigate the relationship between DNA methylation overlapping the TTSs and transcription termination, we employed two strategies: informatic analysis using already deposited datasets ofDnmt3a-/-mouse cells and the zebrafish model system. Bioinformatic analysis using methylome and transcriptome data showed that hypomethylated differentially methylated regions overlapping the TTSs were associated with increased read counts and chimeric transcripts downstream of TTSs inDnmt3a-/-Agouti-related protein neurons, but not inDnmt3a-/-embryonic stem cells and mouse embryonic fibroblasts. We experimentally detected increased read-through and chimeric transcripts downstream of hypomethylated TTSs in zebrafish maternal-zygoticdnmt3aa-/-mutant. This study is the first to identify transcription termination defects in DNA hypomethylated TTSs inDnmt3a-/-vertebrates.
Twisting to freedom: The evolution of copulation termination techniques across 48 species of sepsids (Diptera, Sepsidae)
Authors: Tuan Mindy Jia Min , Araujo Diego Pitta , Puniamoorthy Nalini , Woodford Jeremy M , Meier Rudolf 
Published: July 2021

AbstractStudies of insect mating behaviour usually focus on what happens before and during copulation. Few pay close attention to the actions needed to end copulation. However, genital separation after copulation is likely to be an important cause of mechanical stress and injuries because it often involves the withdrawal of heavily armoured male intromittent organs from membranous female reproductive tracts. Difficult and/or slow separations can also reduce male and female fitness by increasing their exposure to predation. We here report the results of a comparative study of separation behaviour in 48 species of Sepsidae (Diptera) and one outgroup. We find a surprising amount of qualitative and quantitative behavioural variability within and between species. We characterize and reconstruct three types of behaviours: 1) The sepsid ancestor likely used ‘back-off; a gentle separation technique that does not involve any pulling or twisting (https://youtu.be/EbkJvOaubZ0). 2) This potentially gave rise to the most common ‘pull’ technique where the male turns 180 degrees and pulls in an opposite direction from the female (https://youtu.be/oLf4xGpkk1s). This separation can be quick and straightforward, but in some species the ‘pull’ is slow and protracted and we routinely find dead males and/or females attached to their living partners in the latter (difficult: https://youtu.be/MbYPbXN6jr0; failure: https://youtu.be/leTiXefFzCc). 3) Finally, several species use ‘twist’, a new technique where the male rotates >360 degrees from the initial mounting position (https://youtu.be/WMUXbIPyLbk). We document that species capable of using ‘twist’ have shorter and less variable separation times than those using “pull”. However, many species capable of ‘twist’ also retain the ability to use ‘pull’ (‘back-off’/’pull’= 8%; ‘pull’ only= 41%; ‘twist’/ ‘pull’= 24%; ‘twist’ only = 27%). Overall, our study suggests that separation behaviour can vary among closely related species and highlights the significance of studying variable behavioural traits in a phylogenetic context.
Individually Unique Dynamics of Cortical Connectivity Reflect the Ongoing Intensity of Chronic Pain
Authors: Mayr Astrid , Jahn Pauline , Deak Bettina , Stankewitz Anne , Devulapally Vasudev , Witkovsky Viktor , Dietrich Olaf , Schulz Enrico 
Published: July 2021

AbstractBackgroundChronic pain diseases are characterised by an ongoing and fluctuating endogenous pain, yet it remains to be elucidated how this is reflected by the dynamics of ongoing functional cortical connections. The present study addresses this disparity by taking the individual perspective of pain patients into account, which is the varying intensity of endogenous pain.MethodsTo this end, we investigated the cortical encoding of 20 chronic back pain patients and 20 chronic migraineurs in four repeated fMRI sessions. During the recording, the patients were asked to continuously rate their pain intensity. A brain parcellation approach subdivided the whole brain into 408 regions. A 10 s sliding-window connectivity analysis computed the pair-wise and time-varying connectivity between all brain regions across the entire recording period. Linear mixed effects models were fitted for each pair of brain regions to explore the relationship between cortical connectivity and the observed trajectory of the patients’ fluctuating endogenous pain.ResultsTwo pain processing entities were taken into account: pain intensity (high, middle, low pain) and the direction of pain intensity changes (rising vs. falling pain). Overall, we found that periods of high and increasing pain were predominantly related to low cortical connectivity. For chronic back pain this applies to the pain intensity-related connectivity for limbic and cingulate areas, and for the precuneus. The change of pain intensity was subserved by connections in left parietal opercular regions, right insular regions, as well as large parts of the parietal, cingular and motor cortices. The change of pain intensity direction in chronic migraine was reflected by decreasing connectivity between the anterior insular cortex and orbitofrontal areas, as well as between the PCC and frontal and ACC regions.ConclusionsInterestingly, the group results were not mirrored by the individual patterns of pain-related connectivity, which is suggested to deny the idea of a common neuronal core problem for chronic pain diseases. In a similar vein, our findings are supported by the experience of clinicians, who encounter patients with a unique composition of characteristics: personality traits, various combinations of symptoms, and a wide range of individual responses to treatment. The diversity of the individual cortical signatures of chronic pain encoding results adds to the understanding of chronic pain as a complex and multifaceted disease. The present findings support recent developments for more personalised medicine.
Rethinking habitat occupancy modeling and the role of diel activity in an anthropogenic world
Authors: Rivera Kimberly , Fidino Mason , Farris Zach J. , Magle Seth B. , Murphy Asia , Gerber Brian D. 
Published: July 2021

ABSTRACTCurrent methods to model species habitat use through space and diel time are limited. Development of such models is critical when considering rapidly changing habitats where species are forced to adapt to anthropogenic change, often by shifting their diel activity across space. We use an occupancy modeling framework to develop a new model, the multi-state diel occupancy model (MSDOM), which can evaluate species diel activity against continuous response variables which may impact diel activity within and across seasons or years. We used two case studies, fosa in Madagascar and coyote in Chicago, USA, to conceptualize the application of this model and to quantify the impacts of human activity on species spatial use in diel time. We found support that both species varied their habitat use by diel states—in and across years, and by human disturbance. Our results exemplify the importance of understanding animal diel activity patterns and how human disturbance can lead to temporal habitat loss. The MSDOM will allow more focused attention in ecology and evolution studies on the importance of the short temporal scale of diel time in animal-habitat relationships and lead to improved habitat conservation and management.
Genome of the parasitoid wasp Dinocampus coccinellae reveals extensive duplications, accelerated evolution, and independent origins of thelytokous parthenogeny and solitary behavior
Authors: Sethuraman Arun , Tovar Alicia , Welch Walker , Dettmers Ryan , Arce Camila , Skaggs Timothy , Rothenberg Alexander , Saisho Roxane , Summerhays Bryce , Cartmill Ryan , Grenier Christy , Vasquez Yumary , Vansant Hannah , Obrycki John 
Published: July 2021

AbstractDinocampus coccinellae (Hymenoptera: Braconidae) is a generalist parasitoid wasp that parasitizes >50 species of predatory lady beetles (Coleoptera: Coccinellidae), with thelytokous parthenogeny as its primary mode of reproduction. Here we present the first high quality genome of D. coccinellae using a combination of short and long read sequencing technologies, followed by assembly and scaffolding of chromosomal segments using Chicago+ HiC technologies. We also present a first-pass ab initio genome annotation, and resolve timings of divergence and evolution of (1) solitary behavior vs eusociality, (2) arrhenotokous vs thelytokous parthenogenesis, and (3) rates of gene loss and gain among Hymenopteran lineages. Our study finds (1) at least two independent origins of eusociality and solitary behavior among Hymenoptera, (2) two independent origins of thelytokous parthenogenesis from ancestral arrhenotoky, and (3) accelerated rates of gene duplications, loss, and gain along the lineages leading to D. coccinellae. Our work both affirms the ancient divergence of Braconid wasps from ancestral Hymenopterans and accelerated rates of evolution in response to adaptations to novel hosts, including polyDNA viral co-evolution.
A transferable IncC-IncX3 hybrid plasmid co-carrying blaNDM-4, tet(X4), and tmexCD3-toprJ3 confers resistance to carbapenem and tigecycline
Authors: Hirabayashi Aki , Dao Trung Duc , Takemura Taichiro , Hasebe Futoshi , Trang Le Thi , Thanh Nguyen Ha , Tran Hoang Huy , Shibayama Keigo , Kasuga Ikuro , Suzuki Masato 
Published: July 2021

AbstractTigecycline is a last-resort antimicrobial that exhibits promising activity against carbapenemase-producing Enterobacterales (CPE). However, mobile tigecycline resistance genes, tet(X) and tmexCD-toprJ, have emerged in China and have spread possibly worldwide. Tet(X) family proteins, Tet(X3) to Tet(X14), function as tigecycline-inactivating enzymes, and TMexCD-TOprJ complexes function as efflux pumps for tigecycline. Here, we report a CPE isolate co-harboring both emerging tigecycline resistance factors for the first time. A carbapenem- and tigecycline-resistant Klebsiella aerogenes NUITM-VK5 was isolated from an urban drainage in Vietnam in 2021 and a plasmid pNUITM-VK5_mdr co-carrying tet(X4) and tmexCD3-toprJ3 along with the carbapenemase gene blaNDM-4 was identified in NUITM-VK5. pNUITM-VK5_mdr was transferred to Escherichia coli by conjugation and simultaneously conferred high-level resistance against multiple antimicrobials, including carbapenems and tigecycline. An efflux pump inhibitor canceled TMexCD3-TOprJ3-mediated tigecycline resistance, suggesting that both tigecycline resistance factors independently and additively contribute to the high-level resistance. The plasmid had the IncX3 and IncC replicons and was estimated to be a hybrid of plasmids with different origins. Unlike IncX3 plasmids, IncC plasmids are stably maintained in an extremely broad range of bacterial hosts in humans, animals, and environment. Thus, future global spread of multidrug-resistance plasmids such as pNUITM-VK5_mdr poses a public health crisis.
Can a technology firm desire too much of a good thing? The double-edged sword effects of technology orientation on performance
Authors: Zhani Najlae , Mouri Nacef , Hamdi Ahmed 
Published: July 2021

PurposeThis paper aims to investigate the underlying mechanisms that come into play in the relationship between technology orientation (TO) and performance in technology firms. In doing so, this paper explores how different levels of TO affect firm innovativeness, how different levels of firm innovativeness affect performance and the moderating role of risk-taking propensity in the relationship between innovativeness and performance.Design/methodology/approachData were collected from 112 information technology firms. Control variables include firm size and age and industry effects. The model was tested using PLS-based SEM.FindingsResults show that in technology firms, innovativeness plays a mediating role in the relationship between TO and firm performance, the relationship between TO and firm innovativeness is curvilinear, the relationship between innovativeness and performance is curvilinear and risk-taking propensity moderates the curvilinear relationship between innovativeness and performance.Originality/valueThe shape of the relationships in the mediating paths between TO, innovativeness and performance, is curvilinear (inverted U-shaped). Managers in technology firms focused on bolstering the TO and/or innovativeness should be cognizant of the fact that beyond a certain level, they might actually be doing more harm than good. Additionally, managers seeking to reinforce the relationship between innovativeness and performance need to be sensitive to the role that risk-taking propensity plays in this relationship.
Offering a preventive solution to defects in commercial building facility system using BIM
Authors: Eskandari Narges , Noorzai Esmatullah 
Published: July 2021

Purpose
Commercial building facility systems are costly, and due to the complexity of operation and maintenance (O&M), some failures can cause irreversible expensive damage. Currently, few capabilities of building information modeling (BIM) have been used in the facility maintenance operation. The purpose of this paper is to use a tool for making it easier to predict preventable defects in commercial building facility systems by examining a complete BIM.

Design/methodology/approach
To this end, a list of frequent defects in the facility system was achieved by a review of commercial building literature. Then, by examining a complete BIM model, the available methods and tools for O&M facilities during the operation period are identified and analyzed.

Findings
The results of the paper show that the solution presented based on total productive maintenance (TPM) subsets can effectively prevent facility system defects during the operation and maintenance period. An expert team assesses the validation of results.

Originality/value
The findings can help facility managers to adopt measures using TPM methods to prevent defects through an integrated BIM platform. The examination is based on case studies, surveys, expert experience and a thorough literature review.
Do creditors value corporate social responsibility disclosure? Evidence from Ghana
Authors: Boachie Christopher , Tetteh Joseph Emmanuel 
Published: July 2021

Purpose
Drawing on risk mitigation theory, this study aims to examine the link between corporate social responsibility (CSR) disclosure and the cost of debt financing (CDF). In particular, this paper seeks to determine whether firms with higher CSR disclosure scores have a lower CDF.

Design/methodology/approach
This paper uses a panel data analysis of non-financial Ghanaian firms listed on the Ghana Stock Exchange from 2006 to 2019. The CSR index constructed from firms’ annual reports and sustainability reports is used as a proxy for the extent of CSR information disclosures by Ghanaian companies.

Findings
The empirical results demonstrate that CDF is positively related to CSR disclosure scores. Besides, the results show that the levels of long-term debt increase with CSR disclosure in a highly risky industry. However, the finding does not meet the lenders’ expectations in terms of CSR attracting favourable debt financing sources.

Research limitations/implications
The research is based only on the quantity of the CSR information disclosed by Ghanaian companies and does not account for the quality of the CSR disclosures. The empirical model omits some control variables such as the age of the firm and external business conditions. The results should not be generalized, as the sample was based on three listed industries in Ghana for 2006–2019.

Originality/value
This study extends the scope of previous studies by examining the importance of CSR disclosures in financing decisions. More precisely, it focuses on the relatively little explored relationship between the extent of CSR disclosures and access to debt financing. Moreover, this study focuses on the rather interesting empirical setting of Ghana, which is characterized by its low level of CSR awareness. Achieving a better understanding of the effects of CSR information is useful for corporate managers desiring to meet lenders’ expectations and attract debt financing sources.