bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining Monocyte Differentiation into Colonic and Ileal Macrophages
Authors: Gross-Vered Mor , Trzebanski Sébastien , Shemer Anat , Bernshtein Biana , Curato Caterina , Stelzer Gil , Salame Tomer-Meir , David Eyal , Boura-Halfon Sigalit , Chappell-Maor Louise , Levkovits Dena , Jung Steffen 
Published: July 2019

AbstractMonocytes are circulating short-lived macrophage precursors that are recruited on demand from the blood to sites of inflammation and challenge. In steady state, classical monocytes give rise to vasculature-resident cells that patrol the luminal side of the endothelium. In addition, classical monocytes feed macrophage compartments of selected organs, including barrier tissues, such as the skin and intestine, as well as the heart. Monocyte differentiation under conditions of inflammation has been studied in considerable detail. In contrast, monocyte differentiation under non-inflammatory conditions remains less well understood. Here we took advantage of a combination of cell ablation and precursor engraftment to investigate the generation of gut macrophages from monocytes. Collectively, we identify factors associated with the gradual adaptation of monocytes to tissue residency. Moreover, comparison of monocyte differentiation into the colon and ileum-resident macrophages revealed the graduated acquisition of gut segment-specific gene expression signatures.
Visual pigment evolution in Characiformes: the dynamic interplay of teleost whole-genome duplication, surviving opsins and spectral tuning
Authors: Escobar-Camacho Daniel , Carleton Karen L. , Narain Devika W. , Pierotti Michele E.R. 
Published: July 2019

AbstractVision represents an excellent model for studying adaptation, given the genotype-to-phenotype-map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we characterized the visual system of Neotropical Characiformes, which is the result of several spectral tuning mechanisms acting in concert including gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A1/A2-chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the characiform’s entire opsin gene repertoire is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS- and RH1-duplicates originated from a teleost specific whole-genome duplication as well as characiform-specific duplication events. Both LWS-opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS-paralogs has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. In addition, characiforms exhibited species-specific differences in opsin expression. Finally, we found interspecific and intraspecific variation in the use of A1/A2-chromophores correlating with the light environment. These multiple mechanisms may be a result of the highly diverse visual environments where Characiformes have evolved.
A unified role for membrane-cortex detachment during cell protrusion initiation
Authors: Welf Erik S. , Miles Christopher E. , Huh Jaewon , Driscoll Meghan K. , Isogai Tadamoto , Noh Jungsik , Weems Andrew D. , Chi Joseph , Pohlkamp Theresa , Dean Kevin , Fiolka Reto , Mogilner Alex , Danuser Gaudenz 
Published: July 2019

AbstractCell morphogenesis employs a diversity of membrane protrusions. They are discriminated by differences in force generation. Actin polymerization is the best studied mechanism of force generation, but growing interest in how variable molecular conditions and microenvironments alter morphogenesis has revealed other mechanisms, including intracellular pressure. Here, we show that local depletion of membrane cortex links is an essential step in the initiation of both pressure-based and actin-based protrusions. This observation challenges the quarter-century old Brownian ratchet model of actin-driven membrane protrusion, which requires an optimal balance of actin filament growth and membrane tethering. An updated model confirms membrane-filament detachment is necessary to activate the ratchet mechanism. These findings unify the regulation of different protrusion types, explaining how cells generate robust yet flexible strategies of morphogenesis.
Prefrontal somatostatin interneurons encode fear memory
Authors: Cummings Kirstie A. , Clem Roger L. 
Published: July 2019

AbstractTheories stipulate that memories are encoded within networks of cortical projection neurons (PNs). Conversely, GABAergic interneurons (INs) are thought to function primarily to inhibit PNs and thereby impose network gain control, an important but purely modulatory role. However, we found that associative fear learning potentiates synaptic transmission and cue-specific activity of medial prefrontal cortex (mPFC) somatostatin interneurons (SST-INs), and that activation of these cells controls both memory encoding and expression. Furthermore, the synaptic organization of SST- and parvalbumin (PV)-INs provides a potential circuit basis for SST-IN-evoked disinhibition of mPFC output neurons and recruitment of remote brain regions associated with defensive behavior. These data suggest that rather than constrain mnemonic processing, potentiation of SST-IN activity represents an important causal mechanism for conditioned fear.
Massively parallel kinetic profiling of natural and engineered CRISPR nucleases
Authors: Jones Stephen K. , Hawkins John A. , Johnson Nicole V. , Jung Cheulhee , Hu Kuang , Rybarski James R. , Chen Janice S. , Doudna Jennifer A. , Press William H. , Finkelstein Ilya J. 
Published: July 2019

AbstractEngineered Streptococcus pyogenes (Sp) Cas9s and Acidaminococcus sp. (As) Cas12a (formerly Cpf1) improve cleavage specificity in human cells. However, the fidelity, enzymatic mechanisms, and cleavage products of emerging CRISPR nucleases have not been profiled systematically across partially mispaired off-target DNA sequences. Here, we describe NucleaSeq— nuclease digestion and deep sequencing—a massively parallel platform that measures cleavage kinetics and captures the time-resolved identities of cleaved products for more than ten thousand DNA targets that include mismatches, insertions, and deletions relative to the guide RNA. The binding specificity of each enzyme is measured on the same DNA library via the chip-hybridized association mapping platform (CHAMP). Using this integrated cleavage and binding platform, we profile four SpCas9 variants and AsCas12a. Engineered Cas9s retain wtCas9-like off-target binding but increase cleavage specificity; Cas9-HF1 shows the most dramatic increase in cleavage specificity. Surprisingly, wtCas12a—reported as a more specific nuclease in cells—has cleavage specificity similar to wtCas9 in vitro. Initial cleavage position and subsequent end-trimming vary across nucleases, guide RNA sequences, and position and base identity of mispairs in target DNAs. Using these large datasets, we develop a biophysical model that reveals mechanistic insights into off-target cleavage activities by these nucleases. More broadly, NucleaSeq enables rapid, quantitative, and systematic comparison of the specificities and cleavage products of engineered and natural nucleases.
Estimates of genetic load suggest frequent purging of deleterious alleles in small populations
Authors: van der Valk Tom , de Manuel Marc , Marques-Bonet Tomas , Guschanski Katerina 
Published: July 2019

AbstractIt is commonly thought that declining populations will experience negative genetic consequences as a result of increased inbreeding. Here we estimated the average deleteriousness of derived alleles in a range of mammals and found that species with historically small population size and low genetic diversity often have lower genetic load than species with large population sizes. This is likely the result of genetic purging – the more efficient removal of partially deleterious recessive alleles from inbred populations. Our findings suggest that genetic purging occurs over long evolutionary time frames, and therefore rapid population declines are likely to dis-proportionally increase mutational load in species with high diversity, as they carry many deleterious alleles that can reach fixation before genetic purging can remove them.
The SMC complex, MukBEF, organizes theEscherichia colichromosome by forming an axial core
Authors: Mäkelä Jarno , Sherratt David J. 
Published: July 2019

AbstractStructural Maintenance of Chromosomes (SMC) complexes organize and individualize chromosomes ubiquitously, thereby contributing to their faithful segregation. Here we explore howEscherichia colichromosome organization emerges from the action of the SMC complex MukBEF, using quantitative imaging in cells with increased MukBEF occupancy on the chromosome. We demonstrate that theE. colichromosome is organized as series of loops around a thin axial MukBEF core whose length is ~1100 times shorter than the chromosomal DNA. The core is linear (1 μm), or circular (1.5 μm) in the absence of MatP, which displaces MukBEF from the 800 kbp replication termination region (ter). Our findings illustrate how MukBEF compacts the chromosome lengthwise and demonstrate how displacement of MukBEF fromterpromotes MukBEF enrichment with the replication origin.
Genomic signature of shifts in selection in a sub-alpine ant and its physiological adaptations
Authors: Cicconardi Francesco , Krapf Patrick , D’Annessa Ilda , Gamisch Alexander , Wagner Herbert C , Nguyen Andrew D , Economo Evan P , Mikheyev Alexander S , Guénard Benoit , Grabherr Reingard , Arthofer Wolfgang , di Marino Daniele , Steiner Florian M , Schlick-Steiner Birgit C 
Published: July 2019

AbstractUnderstanding how organisms adapt to extreme environments is fundamental and can provide insightful case studies for both evolutionary biology and climate-change biology. Here, we take advantage of the vast diversity of lifestyles in ants to identify genomic signatures of adaptation to extreme habitats such as high altitude. We hypothesised two parallel patterns would occur in a genome adapting to an extreme habitat: i) strong positive selection on genes related to adaptation and, ii) a relaxation of previous purifying selection. We tested this hypothesis by sequencing the high-elevation specialist Tetramorium alpestre and four other phylogenetic related species. In support of our hypothesis, we recorded a strong shift of selective forces in T. alpestre, in particular a stronger magnitude of diversifying and relaxed selection when compared to all other ants. We further disentangled candidate molecular adaptations in both gene expression and protein-coding sequence that were identified by our genome-wide analyses. In particular, we demonstrate that T. alpestre has i) a derived level of expression for stv and other heat-shock proteins in chill shock tests, and ii) enzymatic enhancement of Hex-T1, a rate-limiting regulatory enzyme that controls the entry of glucose into the glycolytic pathway. Together, our analyses highlight the adaptive molecular changes that support colonisation of high-altitude environments.
Predicting Meridian in Chinese Traditional Medicine Using Machine Learning Approaches
Authors: Wang Yinyin , Jafari Mohieddin , Tang Yun , Tang Jing 
Published: July 2019

AbstractPlant-derived nature products, known as herb formulas, have been commonly used in Traditional Chinese Medicine (TCM) for disease prevention and treatment. The herbs have been traditionally classified into different categories according to the TCM Organ systems known as Meridians. Despite the increasing knowledge on the active components of the herbs, the rationale of Meridian classification remains poorly understood. In this study, we took a machine learning approach to explore the classification of Meridian. We determined the molecule features for 646 herbs and their active components including structure-based fingerprints and ADME properties (absorption, distribution, metabolism and excretion), and found that the Meridian can be predicted by machine learning approaches with a top accuracy of 0.83. We also identified the top compound features that were important for the Meridian prediction. To the best of our knowledge, this is the first time that molecular properties of the herb compounds are associated with the TCM Meridians. Taken together, the machine learning approach may provide novel insights for the understanding of molecular evidence of Meridians in TCM.Author SummaryIn East Asia, plant-derived natural products, known as herb formulas, have been commonly used as Traditional Chinese Medicine (TCM) for disease prevention and treatment. According to the theory of TCM, herbs can be classified as different Meridians according to the balance of Yin and Yang, which are commonly understood as metaphysical concepts. Therefore, the scientific rational of Meridian classification remains poorly understood. The aim of our study was to provide a computational means to understand the classification of Meridians. We showed that the Meridians of herbs can be predicted by the molecular and chemical features of the ingredient compounds, suggesting that the Meridians indeed are associated with the properties of the compounds. Our work provided a novel chemoinformatics approach which may lead to a more systematic strategy to identify the mechanisms of action and active compounds for TCM herbs.
Hormones and the Human Alpha Female
Authors: Sumra Monika K. 
Published: July 2019

AbstractThe concept of the alpha female has become widely accepted as a form of female identity in the West. Though relationships between hormone concentrations and alpha-related traits have been demonstrated in alpha nonhuman primates, this has not been examined in the case of the human alpha female. The present study examined the associations of testosterone and cortisol, as well as 3 other hormones, estradiol, oxytocin, and progesterone derived from hair samples, with 11 variables related to the expression of the alpha female identity in a small non-random sample (N=126) of self-identified alpha and non-alpha women in North America. The results revealed statistically significant differences between these groups. When compared to non-alpha women, alpha women scored higher than non-alphas in measures for masculinity, leadership, low introversion, self-esteem, and exhibited lower hair cortisol levels. Alphas exhibited slightly lower estradiol and oxytocin levels than non-alphas though these differences were non-significant. Similar non-significant differences were also found in the case of sexual experience, sexual dominance, testosterone, and progesterone. Though cortisol was not associated with masculine traits, it was positively and significantly associated with leadership. Cortisol was also negatively and significantly associated with strength and a measure for femininity. Progesterone, testosterone, and oxytocin were positively and significantly associated with enjoying sex, as was oxytocin with playing a dominant role in sexual encounters. Surprisingly, testosterone was not associated with alpha status nor with the measure of masculinity, and estradiol was not associated with any of the variables. The results imply that women who identify as alpha may experience less physiological stress than non-alpha females as measured by their lower cortisol levels.
A SAP-LAP linkages framework for integrating Industry 4.0 and circular economy
Authors: Chauhan Chetna , Sharma Abhishek , Singh Amol 
Published: July 2019

PurposeIn the recent years, the two increasingly popular topics, namely, Industry 4.0 and circular economy (CE) have attracted the attention of many academicians and practitioners. However, the connection between CE and Industry 4.0 has not been much investigated in the literature. Motivated by this gap, the purpose of this paper is to integrate these two streams and attempt to understand the new paradigm of Industry 4.0 for resolving the issues pertaining to CE principles.Design/methodology/approachThe study uses situation, actor, process, learning, action, performance (SAP-LAP) linkages framework to analyze the applications of Industry 4.0 mechanisms in realizing the issues of current CE business models. This is done through the interpretation of the cross-interaction and self-interaction relationships among the different interfaces/elements of SAP-LAP.FindingsThe results suggest that top managers are the most essential actors for integrating the use of Industry 4.0 to achieve sustainability, in the light of CE. In addition, advanced technologies such as Internet of Things and cyber-physical systems are the most important Industry 4.0 actions that help in improving the CE performance parameters.Research limitations/implicationsThis qualitative study is an attempt to analyze and assess the strategic issues pertaining to Industry 4.0 standards in CE. The study identifies learnings (challenges/opportunities) and the corrective actions which are imperative toward achieving CE principles. This study will guide managers and policymakers to understand the importance of implementing Industry 4.0 for accomplishing CE principles.Originality/valueThis study integrates two important streams of literature – Industry 4.0 and CE. Thus, this paper offers insights about the importance of Industry 4.0 standards in achieving CE principles.
Diversity and return: the impact of diversity of board members’ education on performance
Authors: Boadi Isaac , Osarfo Daniel 
Published: July 2019

PurposeThis paper aims to examine the impact of diversity of board members’ educational qualifications on the financial performance of banks in Ghana.Design/methodology/approachThe present study applies system generalized methods of moments as an econometric model in carrying out the analysis. The study yielded a usable sample of 28 banks spanning from 2001 to 2016.FindingsThe paper concludes that the Ghanaian banking sector profit diverges and invalidates the convergence theory or “catch-up effect”. Specifically, educational qualifications of board members are relevant to banks’ financial performance. Across all the models used, board members with a first degree have a significant positive impact on performance. The opposite is the case for board members with Doctor of Philosophy (PhD).Research limitations/implicationsUnobservable characteristics such as entrepreneurial skills and intellectual competence experiences are excluded from the study because of the difficulties in measuring these variables. Notwithstanding, the exclusion of these characteristics does not invalidate the general outcome of the study.Originality/valueThe present study examines the impact of diversity of board members’ educational qualification on financial performance in the context of Sub-Saharan Africa, particularly Ghana. It also extends the existing literature by decomposing the banking sector into listed, non-listed, foreign and domestic banks.
A case study in developing an interdisciplinary learning experiment between architecture, building construction, and construction engineering and management education
Authors: Ali Ahmed K. 
Published: July 2019

Purpose
The purpose of this paper is to highlight the value of interdisciplinary learning specifically in the architecture (ARCH), building construction (BC) and construction management and engineering (CEM) disciplines within the USA’s higher education system. The study attempts to expand the existing literature on integrated design and construction education and offer an alternative model for academic students’ collaboration when restructuring curriculums is not possible in the short term.

Design/methodology/approach
The study adopted a qualitative research methodology, which involved designing a structured learning experiment, then followed it with collecting the “lived experience” of 31 participants from three majors according to the institution’s institution review board (IRB) office’s guidelines. The author hypothesized that students from different, but related disciplines working on a real-life project, would better understand the value of each other’s knowledge brought to the teamwork before graduation. The data were analyzed and compared to existing literature on integrated project delivery, and collaborative learning models. Data collection (surveys) was approved by the higher education’s IRB No. 13-021.

Findings
Despite the already-existing curriculum obstacles, the majority of students were very pleased with this collaborative experiment. The results confirmed many of the expectations about how students viewed each other’s discipline. The preconceived notions were dissipated at the end of the study, and students expressed more appreciation for each other’s field and expressed interest in learning more about the thought processes of other disciplines.

Research limitations/implications
Typical conflicting academic schedules were the greatest obstacle in this experiment. Architecture students often devote majority of their time to design studios and therefore are unable to fully engage in an integrated capstone project like this one as extracurricular. Because of the chosen research approach, the research results may lack generalizability. Therefore, researchers are encouraged to test the proposed propositions further.

Practical implications
It is possible to develop a successful collaborative experience in the architecture, engineering and construction higher education system without major restructuring of the curriculums. The impact on students’ learning experience is greater than the existing separated education model.

Originality/value
This paper fulfills an identified need to study how integrated design and construction education occurs without creating new dedicated programs or coursework.
Victims’ experiences and satisfaction with a family justice center
Authors: Melton Heather 
Published: July 2019

Purpose
The family justice center (FJC) model centralizes social and legal services available to intimate partner abuse (IPA) victims in order to facilitate their help-seeking and improve their experiences and the response to IPA. Little, yet promising, research has highlighted the effectiveness of this model. The purpose of this paper is to explore experiences of victims of IPA at one FJC.

Design/methodology/approach
In total, 24 respondents who utilized a FJC in a western county in the USA were interviewed using a survey that included both descriptive quantitative and qualitative questions. Descriptive analysis was performed on the quantitative portion and content analysis on the qualitative portion.

Findings
Most of the respondents used the FJC multiple times and for multiple services. Most were referred by a shelter or a hotline. The most common services used were housing services, followed by counseling. Overall, these respondents felt supported by FJC staff and were satisfied. However, some of the respondents who did indicate satisfaction in the quantitative portion of the survey expressed concerns in the qualitative portion.

Research limitations/implications
The study is limited by a small sample size; however, it has implications for recruitment, outreach and training as well as methodological implications for how FJCs should be evaluated.

Originality/value
This paper adds to the scant literature on FJCs and the FJC model.