bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptation of the yeast gene knockout collection is near-perfectly predicted by fitness and diminishing return epistasis
Authors: Persson Karl , Stenberg Simon , Tamás Markus J. , Warringer Jonas 
Published: March 2022

ABSTRACTAdaptive evolution of clonally dividing cells and microbes is the ultimate cause of cancer and infectious diseases. The possibility of constraining the adaptation of cell populations, by inhibiting proteins that enhance their evolvability has therefore attracted substantial interest. However, our current understanding of how individual genes influence the speed of adaptation is limited, partly because accurately tracking adaptation for many experimental cell populations in parallel is challenging. Here we use a high throughput artificial laboratory evolution (ALE) platform to track the adaptation of >18.000 cell populations corresponding to single gene deletion strains in the haploid yeast deletion collection. We report that the fitness of gene knockout near-perfectly (R2=0.91) predicts their adaptation dynamics under arsenic exposure, leaving virtually no role for dedicated evolvability functions in the corresponding proteins. We tracked the adaptation of another >23.000 yeast gene knockout populations to a diverse range of selection pressures and generalised the almost perfect (R2=0.72 to 0.98) capacity of initial fitness to predict the rate of adaptation. Finally, we reconstruct mutations in the genes FPS1, ASK10, and ARR3, which together account for almost all arsenic adaptation in wildtype cells, in gene deletions covering a broad fitness range. We show that the predictability of arsenic adaptation can be understood almost entirely as a global epistasis phenomenon where excluding arsenic from cells, through these mutations, is more beneficial in cells with low arsenic fitness regardless of what causes the arsenic defects. The lack of genes with a meaningful effect on the adaptation dynamics of clonally reproducing cell populations diminishes the prospects of developing adjuvant drugs aiming to slow antimicrobial and chemotherapy resistance.
Identifying transcription factor-bound activators and silencers in the chromatin accessible human genome using ATAC-STARR-seq
Authors: Hansen Tyler J. , Hodges Emily 
Published: March 2022

ABSTRACTMassively parallel reporter assays test the capacity of putative gene regulatory elements to drive transcription on a genome-wide scale. Most gene regulatory activity occurs within accessible chromatin, and recently described methods have combined assays that capture these regions—such as assay for transposase-accessible chromatin using sequencing (ATAC-seq)—with self-transcribing active regulatory region sequencing (STARR-seq) to selectively assay the regulatory potential of accessible DNA (ATAC-STARR-seq). Here, we report a multi-omic approach that quantifies regulatory activity, chromatin accessibility, and transcription factor (TF) occupancy with one assay using ATAC-STARR-seq. Our strategy, including important updates to the ATAC-STARR-seq assay design and workflow, enabled high-resolution testing of ∼50 million unique DNA fragments tiling ∼101,000 accessible chromatin regions in human lymphoblastoid cells. We discovered that 30% of all accessible regions contain an activator, a silencer or both. We demonstrate that activators and silencers represent distinct functional groups that are enriched for unique sets of TF motifs and are marked by specific combinations of histone modifications. Using Tn5 cut-sites retained by the ATAC-STARR library, we performed TF footprinting and stratified these groups by the presence of specific TF footprints that are supported by chromatin immunoprecipitation data. We found that activators and silencers clustered by distinct TF footprint combinations are enriched for distinct gene regulatory pathways, and thus, represent distinct gene regulatory networks of human lymphoblastoid cell function. Altogether, these data highlight the multi-faceted capabilities of ATAC-STARR-seq to comprehensively investigate the regulatory landscape of the human genome all from a single DNA fragment source.
Bone Morphogenetic Protein (BMP) signaling regulates germline stem cell self-renewal in the newly formed Drosophila testis stem cell niche
Authors: Best Merci N , Fidler Ashley , Jones Marieke K , Wawersik Matthew 
Published: March 2022

AbstractBone morphogenetic proteins (BMPs) are a group of multifunctional cytokines and metabologens highly conserved in the transforming growth factor-β (TGF-β) superfamily. BMPs have an established role in controlling cell fate and tissue morphogenesis in a diverse range of organisms and are known to maintain stem cells in adult Drosophila testes. Additional studies in embryonic and larval testes suggest BMP regulates germ cell behavior. However, the roles of BMP signaling in controlling testis stem cell formation have yet to be directly examined. Here, we explore the pattern of BMP activation during embryonic testis niche morphogenesis as well as niche maturation in larval testes. We also assess the impact of altered BMP signaling on these stages of development. Our data suggest that BMP signaling is critical for promoting germ cell identity in primordial germ cells during embryonic niche formation. During niche maturation, we also find that that BMP signaling is both necessary and sufficient for maintenance of a self- renewing germline stem cell (GSC) population, and that newly formed cyst stem cells (CySCs) are a source of BMP activating ligand. As development progresses, however, BMP activation is no longer sufficient to alter GSC self-renewal. Collectively, our work promotes a more thorough understanding of BMP as a key mechanism controlling stem cell development in Drosophila testes that has implications for the development of other organ systems.
Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network
Authors: Wysocka Emilia M. , Page Matthew , Snowden James , Simpson T. Ian 
Published: March 2022

ABSTRACTDynamic modelling has considerably improved our understanding of complex molecular mechanisms. Ordinary differential equations (ODEs) are the most detailed and popular approach to modelling the dynamics of molecular systems. However, their application in signalling networks, characterised by multi-state molecular complexes, can be prohibitive. Contemporary modelling methods, such as rule-based (RB) modelling, have addressed these issues. The advantages of RB modelling over ODEs have been presented and discussed in numerous reviews. In this study, we conduct a direct comparison of the time courses of a molecular system founded on the same reaction network but encoded in the two frameworks. To make such a comparison, a set of reactions that underlie an ODE model was manually encoded in the Kappa language, one of the RB implementations. A comparison of the models was performed at the level of model specification and results were acquired through model simulations. Conforming to previous reports, we confirm that the Kappa model recapitulated the general dynamics of its ODE counterpart with minor differences. These differences occur whenever molecules have multiple sites binding the same interactor. Furthermore, activation of these molecules in the RB model is slower than in the ODE one but can be corrected by revision of the rate constants used in the relevant rules. As in previous reports on other molecular systems, we find that, also in the case of the DARPP-32 reaction network, the RB representation offers a more expressive and flexible syntax that facilitates access to fine details of the model, facilitating model reuse. In parallel with these analyses, this manuscript reports a refactored model of the DARPP-32 interaction network that can serve as a canvas for the development of a more complex interaction network to study this important molecular system.
Environmental predictors of electroactive bacterioplankton in small boreal lakes
Authors: Olmsted Charles N. , Ort Roger , Tran Patricia Q. , McDaniel Elizabeth A. , Roden Eric E. , Bond Daniel R. , He Shaomei , McMahon Katherine D. 
Published: March 2022

ABSTRACTExtracellular electron transfer (EET) by electroactive bacteria in anoxic soils and sediments is an intensively researched subject, but EET’s function in planktonic ecology has been less considered. Following the discovery of an unexpectedly high prevalence of EET genes in a bog lake’s bacterioplankton, we hypothesized that the redox capacities of dissolved organic matter (DOM) enrich for electroactive bacteria by mediating redox chemistry. We developed the bioinformatics pipeline FEET (Find EET) to identify and summarize EET proteins from metagenomics data. We then applied FEET to several bog and thermokarst lakes and correlated EET protein occurrence values with environmental data to test our predictions. Our results provide evidence that DOM participates in EET by bacterioplankton. We found a similarly high prevalence of EET genes in most of these lakes, where oxidative EET strongly correlated with DOM. Numerous novel clusters of multiheme cytochromes that may enable EET were identified. Taxa previously not considered EET-capable were found to carry EET genes. We conclude that EET and DOM interactions are of major ecological importance to bacterioplankton in small boreal lakes, and that EET, particularly by methylotrophs and phototrophs, should be further studied and incorporated into both conceptual and quantitative methane emission models of melting permafrost.
Complete sequencing of the mouse pseudoautosomal region, the most rapidly evolving ‘chromosome’
Authors: Kasahara Takaoki , Mekada Kazuyuki , Abe Kuniya , Ashworth Alan , Kato Tadafumi 
Published: March 2022

AbstractThe pseudoautosomal region (PAR) of mammalian sex chromosomes is a small region of sequence identity that allows pairing, crossover, recombination, and proper chromosome segregation during male meiosis. The structure of the mouse PAR is largely unknown. Here, we developed a new assembly method to robustly resolve repetitive sequences and employed highly accurate long-read sequencing data to reveal the entire PAR sequence. The PAR of the widely-used inbred strain C57BL/6J is ∼700 kb, comprising 10 protein- coding genes in a mass of complex repetitive sequences. A large segmental duplication exhibiting copy-number polymorphisms even among C57BL/6J littermates is present. High GC-content exons and short introns are common properties of PAR genes and are the consequence of maintaining gene function, while PAR is rapidly evolving. Elucidating the mouse PAR sequence completes the mouse euchromatic genome sequencing and enables the exploration of the function and evolution of the PAR using modern molecular genetic approaches.
Versican binds collagen via its G3 domain and regulates the organization and mechanics of collagenous matrices
Authors: Chen Dongning , Du Yu , Llewellyn Jessica , Bonna Arkadiusz , Zuo Biao , Janmey Paul A. , Farndale Richard W. , Wells Rebecca G. 
Published: March 2022

AbstractType I collagen is the most abundant structural protein in the body and, with other fibrillar collagens, forms the fibrous network of the extracellular matrix (ECM). Another group of ECM polymers, the glycosaminoglycans (GAGs) and GAG-modified proteoglycans, play important roles in regulating collagen behaviors and contribute to the compositional, structural and mechanical complexity of the ECM. While the binding between collagen and small leucine-rich proteoglycans (SLRPs) has been studied in detail, the interactions between collagen and the large bottlebrush proteoglycan versican are not well understood. Here, we report that versican binds collagen directly and regulates collagen structure and mechanics. Versican colocalizes with collagen fibers in vivo and binds to collagen via its C-terminal G3 domain (a non-GAG-modified domain present in all known versican isoforms) in vitro; it promotes the deposition of a highly-aligned collagen-rich matrix by fibroblasts. Versican also shows an unexpected effect on the rheology of collagen gels in vitro, causing decreased stiffness and attenuated shear strain stiffening, and the cleavage of versican in liver results in reduced tissue compression stiffening. Thus, versican is an important collagen binding partner, playing a role in modulating collagen organization and mechanics.
A four-dimensional model for the Ba–Ti–O dodecagonal quasicrystal
Authors: Yamada Tsunetomo 
Published: March 2022

A four-dimensional (4D) model is presented of the first oxide dodecagonal quasicrystal found in a Ba–Ti–O ultra-thin film on a Pt(111) single-crystal substrate. The 4D model, with a 4D dodecagonal lattice constant a

d
= 8.39 Å, was derived by considering a tile decoration model of dodecagonal Niizeki–Gähler tiling composed of squares, triangles and 30° rhombuses. The model consists of four kinds of occupation domain, and 4D positional vectors defining the shape of each occupation domain are given. Moreover, the atomic arrangement of two Ba–Ti–O periodic approximants, the sigma-phase approximant and a 25.6 Å approximant were derived from the 4D model by the introduction of linear phason strains.
Correlating structural complexity and acoustic noise performance of electric motors
Authors: Ibrahim Issah , Mohammadi Mohammad Hossain , Ghorbanian Vahid , Lowther David 
Published: March 2022

Purpose
Acoustic noise is a crucial performance index in the design of electrical machines. Due to the challenges associated with modelling a complete motor, the stator is often used to estimate the sound power in the prototyping stage. While this approach greatly reduces lengthy simulations, the actual sound power of the motor may not be known. But, from the acoustic noise standpoint, not much is known about the correlation between the stator and complete motor. This paper, therefore, aims to use the sound pressure levels of the stator and the full motor to investigate the existence of correlations in the interior permanent magnet synchronous motor.

Design/methodology/approach
A multiphysics simulation framework is proposed to evaluate the sound pressure levels of multiple motor geometries in a given design space. Then, a statistical analysis is performed on the calculated sound pressure levels of each geometry over a selected speed range to compare the correlation strength between the stator and the full model.

Findings
It was established that the stator and the complete motor model are moderately correlated. As such, a reliance on the stator sound power for design and optimization routines could yield inaccurate results.

Originality/value
The main contribution involves the use of statistical tools to study the relationship between sound pressure levels associated with the stator geometry and the complete electric motor by increasing the motor sample size to capture subtle acoustic correlation trends in the design space of the interior permanent magnet synchronous motor.
Experimental verification of STATCOM based on quasi impedance source inverter for power quality enhancement in the hybrid distributed generation system
Authors: R. Karthick , C. Ramakrishnan , S. Sridhar 
Published: March 2022

PurposeThis paper aims to introduce the quasi impedance source inverter (qZSI)-based static compensator (STATCOM), which is incorporated into the hybrid distributed power generation system for enhancement of power quality. The distributed power generation system includes the photovoltaic (PV), wind energy conversion system (WECS) and battery energy storage system.Design/methodology/approachThe WECS is used by the self-excited induction generator (SEIG) and the flywheel energy storage system (FESS). To regulate its terminal voltage and frequency, the SEIG requires adjustable volt-ampere reactive (VAR). A combination of a STATCOM and a fixed condenser bank usually serves to satisfy the VAR demand. The maximum correntropy criterion-based adaptive filter technique (AFT) is proposed to control the qZSI-STATCOM and to guarantee that the voltage at the SEIG terminal is harmonic-free while providing non-linear three-phase and single-phase loads.FindingsThe coordinated operation of the suggested voltage control and flywheel control systems ensures that load voltage and frequency are retained in their respective values at very low harmonic distortions regardless of wind speed and load variation. The simulation and experimental studies are carried out under different load conditions to validate the efficiencies of the PV-assisted STATCOM.Originality/valueTo improve system stability and minimize total costs, extra load current sensors can also be avoided. This paper proposes to control the SEIG terminal voltage and harmonic elimination in the standalone WECS systems using maximum correntropy criterion-based AFT with a fuzzy logic controller.
Oil price shocks on shale oil supply and energy security: a case study of the United States
Authors: Kazemzadeh Emad , Ahmadi Shadmehri Mohammad Taher , Ebrahimi Salari Taghi , Salehnia Narges , Pooya Alireza 
Published: March 2022

Purpose
The purpose of this study is to examine oil price shocks on US shale oil supply and energy security during the period 2000q1–2020q4.

Design/methodology/approach
In this study, the Shannon–Wiener index was used to calculate energy security, and then a structural vector autoregression (VAR) was applied to measure the effect of oil price shocks.

Findings
The results of the variance decomposition indicate that oil prices account for about 20% of changes in US shale oil production, while it explains only about 3% of changes in energy security. Finally, historical decomposition confirms the results of impulse response functions.

Originality/value
The novelty of this study is that so far, no study has examined the effect of oil price shock on shale oil production and energy security in the USA using the structural VAR model. This study also used the latest Shannon–Wiener index as a measure of energy security in the USA. The reason for selecting this index is that, in addition to considering the share of the total consumption of each primary energy, the share of energy imports from each country as well as the political risk of energy exporting countries to the USA are also included.
Strategic alliances and firms’ chances to survive “black swans” in B2B industries
Authors: Xue Rui , Li Lee 
Published: March 2022

Purpose
This study aims to propose that, in business-to-business (B2B) industries, number of strategic alliances firms established before a “black swan” event enhances their chances to survive the black swan, and the enhancements take place through moderation effects. Changes in firms’ core structures – their stated goals, authority structure, core technologies and marketing strategies – to adapt to business jolts have adverse effects on firm performance. Firms’ existing B2B strategic alliances moderate the effects negatively by outsourcing different goals, authority structures, core technologies and marketing strategies to partners who fit the changed environment.

Design/methodology/approach
This study collected quantitative data and analyzed the data with the regression method.

Findings
Using data from Chinese firms in five technology industries during the 2007–2009 economic crisis, this study finds that firms’ internal adaptation is negatively correlated with their performance during economic crises, and B2B strategic alliances negatively moderate this relationship.

Research limitations/implications
First, this study focuses on B2B strategic alliances, and it is not clear whether the findings apply to B2C industries, where strategic alliances may not be common. Perhaps firms can use other means of survival in addition to strategic alliances in B2C industries. Second, this study does not differentiate between fast-moving and slow-moving industries, and it is not clear whether strategic alliances play the same role in both industries. Third, this study does not differentiate firm ages and sizes. It remains unclear how large, established and small, young firms differ when facing crises. Finally, this study is based on the Chinese setting, and it is not clear whether the findings apply to other markets as well. These issues should be explored in future studies.

Practical implications
Changing firms’ core structures harms their performance during black swan crises because such crises are unpredictable, and planned changes may not adapt firms to crises. Managers should not attempt to change their core structures during crises. B2B strategic alliances provide an effective means for firms to survive crises.

Originality/value
This paper makes two contributions to the existing literature: First, this paper demonstrates that changes of one of the four core structures of a firm to cope with black swan events have negative impacts on firm performance. Second, this paper identifies the importance of holding a variety of strategic alliances previously to the black swan events to reduce the negative impacts of changing core structures.
Health‐related quality of life in patients with alopecia areata: Results of a Japanese survey with norm‐based comparisons
Authors: Ito Taisuke , Kamei Kazumasa , Yuasa Akira , Matsumoto Fumihiro , Hoshi Yayoi , Okada Masafumi , Noto Shinichi 
Published: March 2022

AbstractAlopecia areata (AA) is a non‐scarring hair loss disorder affecting approximately 2% of the global population. AA is reported to have a significant negative impact on the emotional and psychological well‐being of the patients. This study aimed to evaluate the health‐related quality of life (HRQoL) of Japanese patients with AA in comparison to the Japanese population norms (national standard values for Japanese) using Short Form Health Survey 36 Item Version 2.0 (SF‐36v2). The study also aimed to access the negative effect of AA on patients’ daily lives and the proportion of patients having anxiety and/or depression. This cross‐sectional, non‐interventional web‐based survey study included 400 participants aged 17–84 years currently suffering from medically diagnosed AA. The assessment tools integrated in the online questionnaire included SF‐36v2, the Dermatology Life Quality Index (DLQI), and the Hospital Anxiety and Depression Scale (HADS). All outcome measures from the tools were evaluated across the study population. SF‐36v2 subscale scores for patients with AA revealed lower scores specifically for mental health (45.7 ± 10.1 points), social functioning (45.8 ± 10.9 points), vitality (46.2 ± 9.8 points), and role emotional (46.9 ± 11.6 points) as compared to the Japanese population norms of 50 ± 10 points each. The DLQI questionnaire‐based analysis indicated that 32.1% of respondents showed a moderate to extremely large effect on their lives; and HADS‐A (anxiety) and HADS‐D (depression) scores categorized 46.0% and 41.8% respondents as doubtful‐to‐definite cases, respectively. Multivariate linear regression revealed that hair loss range, age, comorbidities, and depression significantly worsened DLQI scores. In conclusion, the results of this survey demonstrated that a significant decrease in the HRQoL scores was observed in Japanese patients with AA in comparison with the national norms. Hence, emphasis on mental health is crucial for AA management.