bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of Solentim verified in-situ plate seeding (VIPS™) enhances single-cell cloning efficiency
Authors: Ilyayev Nadia , Martel Catherine , Mazumder Mostafizur , Singh Nishi , Rahbar Ramtin
Published: June 2022

The primary goal in cell line development is to establish high-producer recombinant cell line(s) of single-cell origin. Traditionally, these cell lines are developed using limiting dilution cloning (LDC) method of single cell isolation, a rate-limiting, lengthy and labor-intensive process.

The Verified-In-Situ-Plate-Seeding (VIPS™) is an automated single-cell seeding and imaging equipment designed to accelerate cell line development workflow. In this study, VIPS™ was tested for efficiency and accuracy of single cell seeding in parallel with limiting dilution cloning (LDC). Three Chinese hamster ovary (CHO) derived cell lines with known clonal properties were tested under six different growth conditions (three growth media and two different kinds of microplates). Data showed VIPS™ and limiting dilution (LDC) have comparable cloning efficiency when CHO-M cells were tested. By contrast, the Verified In-Situ Plate Seeding (VIPS™) produced 6-8-fold more clones of single-cell origin than LDC when CHO-K1 or CHO-S cells were tested. Moreover, the verified In-Situ Plate Seeding (VIPS™) correctly identified single-cell and multiple-cells seeded wells with 65-72% and 52-81% accuracy, respectively. Taken together, the high throughput imaging and single-cell seeding capabilities of VIPS™ outperformed the rate-limiting LDC method and, therefore, has the potential to accelerate cell line development workflow.
Designed allosteric protein logic
Authors: Plaper Tjaša , Merljak Estera , Fink Tina , Lainšček Duško , Satler Tadej , Jazbec Vid , Benčina Mojca , Jerala Roman
Published: June 2022

Regulation of the activity of proteins enables control of complex cellular processes. Allosteric regulation has been introduced individually into few natural proteins. Here, we present a generally applicable regulation of diverse proteins called INSRTR (inserted peptide structure regulator), based on inserting a short unstructured peptide into a solvent-accessible loop that retains protein function. Function of the target protein can be inactivated by the addition of a peptide that forms a rigid coiled-coil dimer. This platform enables the construction of ON/OFF protein switches, their regulation by small molecules, and Boolean logic functions with a rapid response in mammalian cells. INSRTR can be used to regulate a wide range of proteins, as demonstrated on ten members of protein families with diverse biological activities including enzymes, signaling mediators, DNA binders/transcriptional regulators, fluorescent protein, and antibodies regulating chimeric antigen receptor. INSRTR platform presents an extraordinary potential for regulating biological systems and applications.

One sentence summary

Authors have designed a widely applicable system to activate or inactivate function of diverse proteins or form Boolean logic gates based on formation of a coiled-coil dimer within protein loops and demonstrated its implementation on a range of 10 diverse proteins.
Genetic architecture of trophic adaptations in cichlid fishes
Authors: DeLorenzo Leah , DeBrock Victoria , Baez Aldo Carmona , Ciccotto Patrick J. , Peterson Erin N. , Stull Clare , Roberts Natalie B. , Roberts Reade B. , Powder Kara E.
Published: June 2022

Since Darwin, biologists have sought to understand the evolution and origins of phenotypic adaptations. The skull is particularly diverse due to intense natural selection such as feeding biomechanics. We investigate the genetic and molecular origins of trophic adaptation using Lake Malawi cichlids, which have undergone an exemplary evolutionary radiation. We analyze morphological differences in the lateral and ventral head among an insectivore that eats by suction feeding, an obligate biting herbivore, and their F2 hybrids. We identify variation in a series of morphologies including mandible width, mandible length, and buccal length that directly affect feeding kinematics and function. Using quantitative trait loci (QTL) mapping, we find that many genes of small effects influence these craniofacial adaptations. Intervals for some traits are enriched in genes related to potassium transport and sensory systems, the latter suggesting correlation between feeding structures and sensory adaptations for foraging. Craniofacial phenotypes largely map to distinct genetic intervals, and morphologies in the head do not correlate. Together, these suggest that craniofacial traits are mostly inherited as separate modules, which confers a high potential for the evolution of morphological diversity. Though these traits are not restricted by genetic pleiotropy, functional demands of feeding and sensory structures likely introduce constraints on variation. In all, we provide insights into the quantitative genetic basis of trophic adaptation, identify mechanisms that influence the direction of morphological evolution, and provide molecular inroads to craniofacial variation.
Atomic-scale Quantum Chemical Calculation of Omicron Mutations Near Cleavage Sites of the Spike Protein
Authors: Adhikari Puja , Jawad Bahaa , Podgornik Rudolf , Ching Wai-Yim
Published: June 2022

The attachment of the Spike-protein in SARS-CoV-2 to host cells and the initiation of viral invasion are two critical processes in the viral infection and transmission processes in which the presence of unique furin (S1/S2) and TMPRSS2 (S2’) cleavage sites play a pivotal role. In this study, we provide detailed analysis of the impact of the BA.1 Omicron variant mutations, vicinal to these two cleavage sites using a novel computational method based on Amino acid – amino acid bond pair unit (AABPU), a specific protein structural unit in 3D as a proxy for quantifying the atomic interaction. We have identified several key features related to the electronic structure as well as bonding of the Omicron mutations near the cleavage sites that significantly increase the size of the relevant AABPUs and the fraction of the positive partial charge. These results of the ultra-large-scale quantum calculations enable us to conjecture on the biological role of Omicron mutations and their specific effects on cleavage sites, as well as identify the principles that can be of some value in analyzing other new variants or subvariants.
The identification of potent and selective antibodies for Serine/threonine-protein kinase TBK1, for use in immunoblot, immunofluorescence and immunoprecipitation
Authors: Alshafie Walaa , Fotouhi Maryam , Shlaifer Irina , Edwards Aled M. , Durcan Thomas M , McPherson Peter S. , Laflamme Carl
Published: June 2022

TBK1 is a serine-threonine kinase that has been linked to a number of diseases, including amyotrophic lateral sclerosis and frontotemporal dementia. Reproducible research on TBK1 has been hampered by the lack of well characterized antibodies. In this study, we characterized 11 commercial antibodies for immunoblot, immunofluorescence and immunoprecipitation, using a knock-out cell line as the control. For each application, we identified several potent and selective antibodies that will facilitate studies on TBK1.
Physiological Levels of Estrogen and Progesterone Modulate CR3 expression on, andNeisseria gonorrhoeaeInfection of, Primary, Human, Cervical Epithelial Cells
Authors: Edwards Trevor J. , Edwards Jennifer L.
Published: June 2022

Despite advances made in our understanding ofNeisseria gonorrhoeaepathogenesis, factors dictating the divergent presentation of gonococcal disease observed between men and women,in vivo, remain unclear. Clinical data indicate that gonococcal pathogenesis of the female genital tract is influenced by steroid hormones. Notwithstanding, there are limited data addressing how steroid hormones modulate gonococcal pathogenesis. Hence, we investigated the effect(s) of physiological concentrations of estrogens and progestogens onN. gonorrhoeaeviability and on complement-mediated infection of primary cervical cells. In contrast to previous studies that showed a bacteriostatic effect of non-physiological concentrations of steroid hormones on gonococci, our data indicate that physiological concentrations of estrogens and progestogens do not inhibit gonococcal growthin vitroor during infection of primary cervical cells. Estradiol promoted complement receptor 3 recruitment to the cervical cell surface and, thus, the ability of gonococci to associate with these cells. Progesterone-predominant assay conditions resulted in decreased expression of Opa proteins by gonococci, increased complement production by cervical cells, and increased iC3b opsonization of gonococci during cervical cell challenge. Collectively, our data support clinical observations and demonstrate that estrogens and progestogens distinctly modulate gonococcal cervical infection.
N-hydroxy pipecolic acid methyl ester is involved in Arabidopsis immunity
Authors: Mohnike Lennart , Huang Weijie , Worbs Brigitte , Feussner Kirstin , Zhang Yuelin , Feussner Ivo
Published: June 2022

The biosynthesis of N-hydroxy pipecolic acid (NHP) has been intensively studied, though knowledge on its metabolic turnover is still scarce. To close this gap, we discovered three novel metabolites via metabolite fingerprinting in Arabidopsis thaliana leaves. Exact mass information and fragmentation by mass spectrometry (MSMS) suggest a methylated derivative of NHP (MeNHP), a NHP-OGlc-hexosyl conjugate (NHP-OGlc-Hex) and an additional NHP-OGlc-derivative. All three compounds were formed in wildtype leaves but not present in the NHP deficient mutant fmo1-1. The identification of these novel NHP-based molecules was possible by a dual-infiltration experiment using a mixture of authentic NHP- and D9-NHP-standards for leaf infiltration followed by an UV-C treatment. Interestingly, the signal intensity of MeNHP and other NHP-derived metabolites increased in ugt76b1-1 mutant plants. This suggests a detour, for the inability to synthesize NHP-O-glucoside. For MeNHP, we unequivocally determined the site of methylation at the carboxylic acid function. MeNHP application by leaf infiltration leads to the detection of a MeNHP-OGlc as well as NHP, suggesting MeNHP-hydrolysis to NHP. This is in line with the observation that MeNHP-infiltration is able to rescue the fmo1-1 susceptible phenotype against Hyaloperonospora arabidopsidis Noco 2. Together these data suggest MeNHP as additional storage or transport form of NHP.

Highlight

In this work, we identify N-hydroxy pipecolic acid (NHP) metabolites including methyl ester and complex glycosides. The application of methyl ester is able to rescue the disease phenotype of the biosynthesis deficient mutant of NHP.
A discrete-time survival model for porcine epidemic diarrhea virus
Authors: Trostle Parker , Corzo Cesar A. , Reich Brian J. , Machado Gustavo
Published: June 2022

Since the arrival of porcine epidemic diarrhea virus (PEDV) in the United States in 2013, elimination and control programs have had partial success. The dynamics of its spread are hard to quantify, though previous work has shown that local transmission and the transfer of pigs within production systems are most associated with the spread of PEDV.

Our work relies on the history of PEDV infections in a region of the southeastern United States. This infection data is complemented by farm-level features and extensive industry data on the movement of both pigs and vehicles. We implement a discrete-time survival model and evaluate different approaches to modeling the local-transmission and network effects.

We find strong evidence in that the local-transmission and pig-movement effects are associated with the spread of PEDV, even while controlling for seasonality, farm-level features, and the possible spread of disease by vehicles. Our fully Bayesian model permits full uncertainty quantification of these effects. Our farm-level out-of-sample predictions have a receiver-operating characteristic area under the curve (AUC) of 0.779 and a precision-recall AUC of 0.097. The quantification of these effects in a comprehensive model allows stakeholders to make more informed decisions about disease prevention efforts.
Mitochondrial dysfunction triggers actin polymerization necessary for rapid glycolytic activation
Authors: Chakrabarti Rajarshi , Fung Tak Shun , Kang Taewook , Pallijeff Pieti W. , Suomalainen Anu , Usherwood Edward J. , Higgs Henry N.
Published: June 2022

Mitochondrial damage represents a dramatic change in cellular homeostasis, necessitating rapid responses. One rapid response is peri-mitochondrial actin polymerization, termed ADA (acute damage-induced actin). The consequences of ADA are not fully understood. Here we show that ADA is necessary for rapid glycolytic activation upon inhibition of mitochondrial ATP production in multiple cells, including mouse embryonic fibroblasts and effector CD8+ T lymphocytes, for which glycolysis is an important source of ATP and biosynthetic molecules. Treatments that induce ADA include CCCP, antimycin A, rotenone, oligomycin, and hypoxia. The Arp2/3 complex inhibitor CK666 or the mitochondrial sodium-calcium exchanger (NCLX) inhibitor CGP37157, applied simultaneously with the ADA stimulus, inhibit both ADA and the glycolytic increase within 5-min, suggesting that ADA is necessary for glycolytic stimulation. Two situations causing chronic reductions in mitochondrial ATP production, ethidium bromide treatment (to deplete mitochondrial DNA) and mutation to the NDUFS4 subunit of complex 1 of the electron transport chain, cause persistent peri-mitochondrial actin filaments of similar morphology to ADA. Both peri-mitochondrial actin loss and a 20% ATP decrease occur within 10 min of CK666 treatment in NDUFS4 knock-out cells. We propose that ADA is necessary for rapid glycolytic activation upon mitochondrial impairment, to re-establish ATP production.
Autonomous cycles of data analysis tasks for innovation processes in MSMEs
Authors: Gutiérrez Ana , Aguilar Jose , Ortega Ana , Montoya Edwin
Published: June 2022

Purpose

The authors propose the concept of “Autonomic Cycle for innovation processes,” which defines a set of tasks of data analysis, whose objective is to improve the innovation process in micro-, small and medium-sized enterprises (MSMEs).

Design/methodology/approach

The authors design autonomic cycles where each data analysis task interacts with each other and has different roles: some of them must observe the innovation process, others must analyze and interpret what happens in it, and finally, others make decisions in order to improve the innovation process.

Findings

In this article, the authors identify three innovation sub-processes which can be applied to autonomic cycles, which allow interoperating the actors of innovation processes (data, people, things and services). These autonomic cycles define an innovation problem, specify innovation requirements, and finally, evaluate the results of the innovation process, respectively. Finally, the authors instance/apply the autonomic cycle of data analysis tasks to determine the innovation problem in the textile industry.

Research limitations/implications

It is necessary to implement all autonomous cycles of data analysis tasks (ACODATs) in a real scenario to verify their functionalities. Also, it is important to determine the most important knowledge models required in the ACODAT for the definition of the innovation problem. Once determined this, it is necessary to define the relevant everything mining techniques required for their implementations, such as service and process mining tasks.

Practical implications

ACODAT for the definition of the innovation problem is essential in a process innovation because it allows the organization to identify opportunities for improvement.

Originality/value

The main contributions of this work are: For an innovation process is specified its ACODATs in order to manage it. A multidimensional data model for the management of an innovation process is defined, which stores the required information of the organization and of the context. The ACODAT for the definition of the innovation problem is detailed and instanced in the textile industry. The Artificial Intelligence (AI) techniques required for the ACODAT for the innovation problem definition are specified, in order to obtain the knowledge models (prediction and diagnosis) for the management of the innovation process for MSMEs of the textile industry.
“You must go here”: architecture, yelp and the tourist gaze
Authors: Lindsay Georgia , Sawyer Mark
Published: June 2022

Purpose

The Tourist Gaze has been debated, reimagined and applied to a variety of actors and settings. This paper helps investigate how contemporary architecture operates as subject and participant in gazing practices.

Design/methodology/approach

Using Yelp reviews of art museums in a regional US city, a thematic analysis of text reviews and image uploads was conducted.

Findings

Reviewers do refer to buildings as objects of the gaze; but they also connect their experience of the building to emotions and to actions and use the building to orient themselves spatially. This article demonstrates that contemporary buildings are important components of tourist experiences as objects of the gaze, but also as frames for gazing and as stages for tourist practices.

Research limitations/implications

The research implications are both topical and methodological: the paper demonstrates that contemporary (neo-modern) architecture is a vibrant avenue of research, and that social networking sites are a promising potential source of data for studying architecture in the social field.

Originality/value

This research uses an underexplored data set, Yelp reviews, to capture what people pay attention to and think others will find interesting about architecture. It also adds important layers to studies on the tourist gaze. First, it emphasizes that architecture is important to tourists not only as an object of the gaze but also as a site for affective experience, action and daily life. Second, it addresses some building styles beyond the historical ones that are foundational to the idea of the tourist gaze.
Sustainability evaluation of the prefabricated medical emergency buildings’ renovation scheme after the COVID-19
Authors: Teng Yue , Li Zhongfu , Cai Jin , Ju Min
Published: June 2022

Purpose

This study aims to focus on the sustainability of prefabricated medical emergency buildings (PMEBs) renovation after the epidemic, to address the problem that large numbers of PMEBs may be abandoned for losing their original architectural functions. This study develops an evaluation system to identify and measure sustainable factors for PMEBs’ renovation schemes. Qualitative and quantitative analysis of PMEBs’ renovation scheme was conducted based on cloud model evaluation method and selected the renovation scheme in line with sustainable development. The study promotes evaluation methods and decision-making basis for the renovation design of global PMEBs and realizes the use-value of building functions again.

Design/methodology/approach

By referring to the existing literature, design standards and expert visiting a set of evaluation index systems which combines the renovation of the PMEBs and the sustainability concept has been established, which calculates the balanced optimal comprehensive weight of each indicator utilizing combination weighting method, and quantifies the qualitative language of different PMEBs’ renovation schemes by experts through characteristics of the cloud model. This paper takes Huoshenshan hospital a representative PMEB during the epidemic period as an example, to verify the feasibility of the cloud model evaluation method.

Findings

The research results of this paper are that in the PMEBs’ renovation scheme structural reformative (T11) and corresponding nature with the original building (T13) have the most important influence; the continuity of architectural cultural value (T22) and regional development coherence (T23) are the key factors affecting the social dimension; the profitability of renovated buildings (T34) is the key factor affecting the economic dimension; the environmental impact (T41), resource utilization (T42) and ecological technology (T43) are the key factors in the environmental dimension.

Originality/value

This study contributes to the existing body of knowledge by supplementing a set of scientific evaluation methods to make up for the sustainability measurement of PMEBs’ renovation scheme. The main objective was to make renovated PMEBs meet the needs of urban sustainable development, retain the original cultural value of the buildings, meanwhile enhance their social and economic value and realize the renovation with the least impact on the environment.
Rule with an iron hand: powerful CEOs, influential shareholders and corporate performance in Russia
Authors: Zavertiaeva Marina , Ershova Tatiana
Published: June 2022

Purpose

This study examines whether CEO power influences the book-based and market-based performance of Russian companies when it is restricted by the presence of essential shareholders, namely, state and influential businessmen.

Design/methodology/approach

Managerial power is divided into structural, ownership, expert and prestige. The proposed power metrics include not only CEOs but also the board of directors' characteristics that may restrict or enhance CEO power. The empirical analysis is based on the sample of 90 large traded Russian firms, which shares are included in the Moscow Stock Exchange Broad Market Index (MICEX BMI), observed from 2012 to 2019.

Findings

Panel data analysis suggests that higher board ownership and tenure may restrict CEO power, which in turn would be beneficial for corporate performance. the authors also see that in companies owned by influential businessmen, CEO power influence on M/B value is more negative, while state ownership does not moderate it. CEO power metrics, based on political experience and tenure, affect corporate performance differently in companies affiliated with extractive industries.

Originality/value

First, the authors consider two channels through which a company in emerging markets may get additional resources: CEOs and influential owners. Second, the authors develop power metrics based on Finkelstein's managerial power classification (1992) and the idea of relative power proposed by Bebchuk et al. (2011). It allows identifying whether the board of directors' may constrain or enhance CEO power to raise corporate performance. Third, the authors analyze developing Russian markets that represent a good ground for testing the question, whereas empirical research on Russia is relatively scarce (Grosman and Leiponen, 2018). Fourth, the authors pay particular attention to the CEO power in the extractive industry, strategically important for the Russian economy.
Evaluating the role of microfinance institutions in enhancing the livelihood of urban poor
Authors: Hasan Nazia , Singh Anjani Kumar , Agarwal Manoj Kumar , Kushwaha Bijay Prasad
Published: June 2022

Purpose

The goal of this research is to look at how urban microfinance affects livelihood transformation in terms of poverty reduction, living standards, social well-being, empowerment and entrepreneurship.

Design/methodology/approach

This paper analyses the role of urban microfinance towards livelihood with special reference to Western Uttar Pradesh. Primary data were collected from 321 respondents who are users of a microfinance programme using a standardised questionnaire. The data were collected using a stratified random sampling technique, and the data were analysed using structural equation modelling.

Findings

Urban microfinance has a considerable impact on poverty reduction, the standard of living, social well-being, empowerment and entrepreneurship in the urban poor, according to the findings.

Research limitations/implications

The fact that the majority of the borrowers were uneducated was the most significant barrier to them filling out the questionnaire. Their anxiety was the most significant psychological obstacle to successfully answering the questions, and it took time. As a result, it is urged that proper counselling be conducted before the poor borrowers fill out the questionnaire.

Practical implications

The current study highlights the factors that lead to the utilisation of microfinance services. This research will aid MFIs in selecting the appropriate products and services for the urban poor. The results of this study will aid them in understanding and meeting the expectations of microfinance CEOs.

Originality/value

This is a first study conducted in Northern zone of India measuring the roles urban microfinance institutions (MFIs) in uplifting the livelihood of urban poor.
Management control systems. A non-family stakeholder perspective on the critical success factors influencing continuous stakeholder support during businesses succession
Authors: Rodriguez Serna Lil , Bowyer Dorothea Maria , Gregory Sheree K.
Published: June 2022

Purpose

Although the use of management control systems (MCS) is known to support organizational strategic success, the role played by MCS to monitor stakeholder satisfaction, thus minimizing stakeholder relationship severance, during uncertain events such as business succession remains underexplored. Thus, the authors investigate why succession creates uncertainty and how can stakeholders' concerns assist in contingently adapt the family businesses (FB) MCS to assist decision-making during succession.

Design/methodology/approach

The authors use a qualitative approach and a multiple-case study design. The authors conducted 30 in-depth interviews within 6 Australian FB SMEs. Interviewees included owners, successors, senior managers, customers and suppliers.

Findings

The authors' findings suggest that owners' perceptions, that intergenerational succession causes minimal stakeholder disruption, results in MCS not adapting to monitor the uncertain event. Other stakeholders, on the contrary, highlight the need for MCSs to evolve and adapt during the process to assist owners monitor stakeholder-derived success factors to secure the long-term sustainability of the FB.

Originality/value

The novelty of this research is based on the inclusion of non-family stakeholders, such as customers and suppliers, as part of the sample. This approach allowed for stronger conclusions and a broader overview of the succession issue.
Viscoelastic wave propagation for nearly constant Q transverse isotropy
Authors: Hao Qi , Greenhalgh Stewart , Huang Xingguo , Li Huijian
Published: June 2022

Constant Q, also called frequency‐independent Q, is a phenomenological assumption often used in practice for dissipative wave propagation in both forward and inverse seismic modelling. A constant Q dissipative model generally results in a temporal convolution‐type wave equation, which is computationally costly to solve by a time‐domain numerical modelling method. In this paper, we use the recently proposed weighting function method to derive the nearly constant Q wave equations in differential form for viscoelastic transversely isotropic media. These wave equations explicitly involve specified Q parameters, which is convenient for time‐domain waveform modelling and inversion. As numerical examples, we analyse the nearly constant Q behaviour of the proposed model , nearly constant Q wave reflection and wave propagation in a heterogeneous case.
Entrepreneurial Passion and Product Innovation Intensity in New Ventures: Mediating Effects of Exploration and Exploitation Activities
Authors: Ahsan Mujtaba , Adomako Samuel , Donbesuur Francis , Mole Kevin F.
Published: June 2022

In this paper, we examine the differential effects of entrepreneurial passion (EP) on product innovation intensity (PII) through the mediating mechanisms of exploration and exploitation activities. Using time‐lagged data from 260 new ventures from Ghana, we examine the direct relationships between the three domains of EP (i.e. inventing, developing and founding) and a new venture's PII. Further, we test the indirect relationships between the three domains of EP and PII through the mediating mechanisms of a new venture's exploration and exploitation activities. The empirical results provide a fine‐grained understanding of the relationship between EP, exploration and exploitation activities and PII. Implications for research and practice are also discussed.
Pickets, Protests and Purses in the American Civil Rights Movement
Authors: Casey Kathleen B.
Published: June 2022

At first glance, perhaps nothing seems more mundane and apolitical than a purse. But purses have always been much more than a fashion accessory. This article analyses how southern Black women – both the legendary and the lesser known – in the ‘classical’ phase of the Civil Rights Movement used purses to appear as respectable ladies' when their dress and comportment were under close surveillance. Yet they simultaneously used their purses as private, female‐controlled spaces that aided them in achieving a wide variety of social, economic and political objectives. In fact, many southern Black women used their purses to hide critical items needed to prepare themselves and protect their bodies as they voted, sat‐in, rode on public transportation and integrated schools. Using oral histories, memoirs, newspaper and magazine stories and photographs, this article argues that Black southern female activists used purses primarily as ‘toolkits’. In the process, it reveals that Black southern women's participation in the armed self‐defence movement is far more significant than scholars have appreciated.
Job match and housing tenure
Authors: Coulson N. Edward , D'Lima Walter , Jinkins David
Published: June 2022

Homeownership, though it brings both private and social benefits, entails substantial fixed costs. Standard personal financial advice suggests that homeownership should only be undertaken when one's job situation is stable and job movement is not likely in the near future. Little research has asked whether this advice is followed. Our goal is to rectify that omission. To test this hypothesis, we employ detailed information on workers and housing decisions from Danish administrative data. We construct a measure of job mismatch and find evidence, suggesting that homeowners are indeed better matched at their jobs than renters, and that an improved match leads renters to become homeowners. An examination of job durations suggests that homeownership is correlated with longer job duration both because of a direct causal effect and also due to an indirect effect through selection into homeownership.
Melanosis coli: A factor not associated with histological progression of colorectal polyps
Authors: Zhang Yan , Zhan Ting Ting , Dong Zhi Yu , Sun Hui Hui , Wang Jun Wen , Chen Ying , Xu Shu Chang
Published: June 2022

Objective

In this study we aimed to investigate the association of melanosis coli (MC) and the colorectal polyp detection rate (PDR).

Methods

In all, 1104 MC patients and 62 181 non‐MC participants were enrolled. And 2208 controls were matched by participants' age and gender, and quality of bowel preparation using the propensity score matching (PSM) method. Additionally, 490 polyps in MC and 980 in controls matched by age and gender, and size and location of polyps were analyzed. The association of PDR and pathological features of polyps with MC were also analyzed.

Results

MC patients showed a higher PDR (44.3% vs 39.3%, P = 0.006) and detection rate of low‐grade adenoma (45.4% vs 36.7%, P = 0.002) but fewer large polyps (≥10 mm) (18.8% vs 26.9%, P = 0.001), fewer polyps in the left colon (33.5% vs 40.0%, P = 0.018), and a lower detection rate of advanced adenoma/adenocarcinoma (17.4% vs 24.3%, P = 0.003) than the matched controls. On multivariate logistic regression analysis, MC was independently associated with an increased PDR (odds ratio 1.184, 95% confidence interval 1.045–1.343, P = 0.008). Analysis targeting polyps showed that there were significant differences in age, gender, location, and pathology (P < 0.001) between polyps with and without MC. However, after adjusting for participants' age and gender, size and location of polyps, there was no difference between the two groups in pathology (P = 0.635).

Conclusion

MC is independently associated with increased colorectal PDR, but not with histological progression of polyps.
A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins
Authors: Irestedt Martin , Thörn Filip , Müller Ingo A. , Jønsson Knud A. , Ericson Per G. P. , Blom Mozes P. K.
Published: June 2022

Biological specimens in natural history collections constitute a massive repository of genetic information. Many specimens have been collected in areas in which they no longer exist or in areas where present‐day collecting is not possible. There are also specimens in collections representing populations or species that have gone extinct. Furthermore, species or populations may have been sampled throughout an extensive time period, which is particularly valuable for studies of genetic change through time. With the advent of high‐throughput sequencing, natural history museum resources have become accessible for genomic research. Consequently, these unique resources are increasingly being used across many fields of natural history. In this paper, we summarize our experiences of resequencing hundreds of genomes from historical avian museum specimens. We publish the protocols we have used and discuss the entire workflow from sampling and laboratory procedures, to the bioinformatic processing of historical specimen data.
Chromosome‐level genome of Entada phaseoloides provides insights into genome evolution and biosynthesis of triterpenoid saponins
Authors: Lin Min , Jian Jian‐Bo , Zhou Zhu‐Qing , Chen Chun‐Hai , Wang Wen , Xiong Hui , Mei Zhi‐Nan
Published: June 2022

As a medicinal herbal plant, Entada phaseoloides has high levels of secondary metabolites, particularly triterpenoid saponins, which are important resources for scientific research and medical applications. However, the lack of a reference genome for this genus has limited research on its evolution and utilization of its medicinal potential. In this study, we report a chromosome‐scale genome assembly for E. phaseoloides using Illumina, Nanopore long reads and high‐throughput chromosome conformation capture technology. The assembled reference genome is 456.18 Mb (scaffold N50 = 30.9 Mb; contig N50 = 6.34 Mb) with 95.71% of the sequences anchored onto 14 pseudochromosomes. E. phaseoloides was estimated to have diverged from the Leguminosae lineage at ~72.0 million years ago. With the integration of transcriptomic and metabolomic data, gene expression patterns and metabolite profiling of E. phaseoloides were determined in different tissues. The pattern of gene expression and metabolic profile of the kernel were distinct from those of other tissues. Furthermore, the evolution of certain gene families involved in the biosynthesis of triterpenoid saponins and terpenes was analysed and offers new insights into the formation of these two metabolites. Four CYP genes, one UGT gene and related transcription factors were identified as candidate genes contributing to regulation of triterpenoid saponin biosynthesis. As the first high‐quality assembled reference genome in the genus Entada, it will not only provide new information for the evolutionary study of this genus and conservation biology of E. phaseoloides but also lay a foundation for the formation and utilization of secondary metabolites in medicinal plants.
Effectiveness evaluation of adjuvant concurrent chemoradiotherapy for patients with positron emission tomography‐staged esophageal squamous cell carcinoma after complete resection: A population‐based cohort study
Authors: Fang Hsin‐Yuan , Lin Yu‐Sen , Chen Chien‐Kuang , Chen Jian‐Xun , Lu Ting‐Yu , Huang Tzu‐Min , Hsieh Te‐Chun , Kuo Yu‐Cheng , Lin Chen‐Yuan , Lien Ming‐Yu , Chen Chi‐Ching , Li Chia‐Chin , Chien Chun‐Ru
Published: June 2022

Background

The role of adjuvant concurrent chemoradiotherapy (ACCRT) is unclear for patients with esophageal squamous cell carcinoma (ESCC) who receive esophagectomy with clean margins. We compared the survival of the ACCRT versus observation groups for these patients staged with positron emission tomography (PET) via a population‐based approach.

Methods

Eligible patients with locally advanced ESCC diagnosed between 2011 and 2017 were identified via the Taiwan Cancer Registry. We used propensity score (PS) weighting to balance observable potential confounders between groups. The hazard ratios (HR) of death and incidence of esophageal cancer mortality (IECM) were compared between the ACCRT and observation groups. We also evaluated overall survival (OS) in subgroups of either with or without lymph node metastases.

Results

Our primary analysis consisted of 105 patients in whom the covariates were well balanced after PS weighting. The HR for death when ACCRT was compared with observation was 0.58 (95% confidence interval 0.28–1.21, p = 0.15). The results were also not significantly different for IECM or in the subgroup analyses.

Conclusion

We found that for patients with PET‐staged ESCC who received esophagectomy with clean margins, the survival was not statistically different between ACCRT and observation. Further studies (randomized or larger sample size) are needed to clarify this issue.
Untangling the role of a novel agroecosystem as a habitat for declining farmland birds
Authors: Kämpfer Steffen , Löffler Franz , Brüggeshemke Jonas , Fartmann Thomas
Published: June 2022

As a result of agricultural industrialisation, traditionally managed habitats have dramatically declined throughout Europe. As a result, farmland specialists across several taxa have become increasingly threatened. Concurrently, altered farming practices have also contributed to the emergence of novel agricultural habitats, such as Christmas tree plantations, but knowledge of their impact on biodiversity is still scarce. In the following study, we analysed the drivers behind the territory selection of four declining farmland birds—Common linnet (Linaria cannabina), Tree pipit (Anthus trivialis), Woodlark (Lullula arborea) and Yellowhammer (Emberiza citrinella)—in a landscape dominated by Christmas tree plantations. Our study suggests that Christmas tree plantations provide well‐suited breeding conditions for the species and thus may represent important refuges in human‐modified landscapes. We found that all four species favoured young Christmas tree plantations (<6 years) for territory establishment. In particular, the territories of Tree pipit and Woodlark were characterised by a high proportion of young plantations, which provide open habitat structures rich in bare ground. However, older plantations (>6 years) were also of high importance for some of the model organisms, especially for Common linnet and Yellowhammer. The territory establishment of Yellowhammer was additionally favoured by brushwood plantations, clear‐cut/fringe vegetation and low‐growing shrubland. We attribute the high value of Christmas tree plantations mainly to the coexistence of open habitat structures rich in bare ground and less intensively managed stands, which both represent important foraging sites for the model organisms. At least in intensively used agricultural areas, Christmas tree plantations may represent important refuges for declining farmland birds. Therefore, further measures aiming to promote habitat quality while reducing the use of herbicides in the plantations should be addressed.
Root‐end resection with or without retrograde obturation after orthograde filling with two techniques: A micro‐CT study
Authors: Angerame Daniele , De Biasi Matteo , Lenhardt Massimiliano , Porrelli Davide , Bevilacqua Lorenzo , Generali Luigi , La Rosa Giusy Rita Maria , Pedullà Eugenio
Published: June 2022

To evaluate the filling ability of two orthograde obturation techniques followed by the apical resection with or without retrograde obturation through micro‐computed tomography (CT). Thirty‐two single‐rooted permanent teeth were prepared and randomised into four groups (n = 8) according to the orthograde obturation technique (single cone technique [SCT] and mineral trioxide aggregate placement) combined or not with retrograde obturation. The volume of voids (VoV) within the entire endodontic space, the apical 3 mm, and 1 mm after root resection was calculated by micro‐CT. Statistical analysis showed no significant difference among the groups regarding the total VoV in all root canals, as well as within the apical 1 mm after root resection. The SCT and apical resection without retrograde filling showed significantly better results in terms of VoV at the apical 3 mm after root resection. Within the study limitations, SCT associated with apical resection without retrograde preparation exhibited a similar or less amount of voids than the other groups.
3D geometric analysis of second mesiobuccal canal in permanent maxillary first molar tooth
Authors: Khadilkar Indrani , Nangia Divya , Chawla Amrita , Sharma Sidhartha , Kumar Vijay , Gupta Shalini , Logani Ajay
Published: June 2022

Cone‐beam computed tomography scans exhibiting a second mesiobuccal (MB2) canal were examined. The vertical distance of the MB2 orifice from the pulp floor (depth), inter‐orifice distance (IOD) of MB2 from mesiobuccal (MB) and palatal (P) orifices, the horizontal distance of the MB2 orifice from the line joining MB‐P orifices [mesial deviation (MD)] and root canal configuration (RCC) were evaluated on 330 scans. The Student's t‐test, ANOVA, Spearman's correlation and linear regression analysis were applied. The MB2 depth was 1.69 ± 0.86 mm. IOD (MB‐MB2, MB2‐P) was 2.18 ± 0.58 mm and 4.63 ± 1.06 mm, respectively. MD was 1.02 ± 0.37 mm. The predominant RCC was Vertucci's type II (75.5%). No correlation of depth with IOD of MB‐MB2 (rho = 0.0367, p = 0.506) was observed. Significant correlation of depth with IOD of MB2‐P (rho = 0.696, p < 0.001) and MD (rho = 0.174, p = 0.001) was established. No association of depth with age and IOD (MB‐MB2) was observed on linear regression analysis. However, a significant positive association was established with IOD (MB2‐P) (p < 0.001) and MD (p = 0.001).
Influence of minimally invasive access cavities on load capacity of root‐canal‐treated teeth: A systematic review and meta‐analysis
Authors: Rahbani Nobar Behrad , Dianat Omid , Rahbani Nobar Behnam , Kazem Majid , Hicks M. Lamar
Published: June 2022

This systematic review (PROSPERO‐CRD42020147333) aimed to compare the effects of conservative, ultraconservative and truss access cavities with traditional access cavities on the load capacity of root‐canal‐treated teeth. Online databases were searched until December 2021, and 25 ex vivo studies in which the effects of different access cavities on load capacity of permanent teeth had been investigated were included. Quality assessment was completed using a modified risk of bias tool for in vitro studies adapted from previous studies. Meta‐analysis was performed using the maximum‐likelihood‐based random‐effects model with similar groups. Conservative access cavities significantly improved the load capacity of maxillary premolars (p < 0.01 [−1.32, −0.028]) and molars (p < 0.05 [−0.89, −0.02]) compared to traditional access cavities. Additionally, truss access cavities significantly improved the load capacity of mandibular molars with (p < 0.05, [−1.18, −0.02]) mesio‐occluso‐distal cavity preparations. Higher levels of evidence are needed to determine the long‐term implications of minimal preparations for treatment outcomes.
Lower class people suffered more (but perceived fewer risk disadvantages) during the COVID‐19 pandemic
Authors: Zhang Yue , Ding Yi , Xie Xiaona , Guo Yongyu , van Lange Paul A. M.
Published: June 2022

Does COVID‐19 affect people of all classes equally? In the current research, we focus on the social issue of risk inequality during the early stages of the COVID‐19 pandemic. Using a nationwide survey conducted in China (N = 1,137), we predicted and found that compared to higher‐class individuals, lower‐class participants reported a stronger decline in self‐rated health as well as economic well‐being due to the COVID‐19 outbreak. At the same time, we examined participants' beliefs regarding the distribution of risks. The results demonstrated that although lower‐class individuals were facing higher risks, they expressed lesser belief in such a risk inequality than their higher‐class counterparts. This tendency was partly mediated by their stronger endorsement of system‐justifying beliefs. The findings provide novel evidence of the misperception of risk inequality among the disadvantaged in the context of COVID‐19. Implications for science and policy are discussed.
Reinke crystals: Hallmarks of adult Leydig cells in humans
Authors: Planinić Ana , Marić Tihana , Bojanac Ana Katušić , Ježek Davor
Published: June 2022

Background

Reinke crystals are structures pathognomonic for Leydig cells, which have the important function of testosterone production and are vital for male reproductive health. These crystalline inclusions are thought to be of protein origin; however, the molecular composition has not yet been resolved.

Objectives

This review summarizes all available information regarding Reinke crystal's characteristics and aims to produce a comprehensive guide for research on this topic as well as to determine and discuss potential Reinke‐protein candidates.

Methods

Pubmed was thoroughly searched for all publications regarding Reinke crystals and 137 publications were identified. All publications were surveyed and all relevant information was included in the review.

Results

Along with the cytoplasm, structures that resemble Reinke crystals were also observed in the nucleus, suggesting that their formation depends only on protein concentration. Variations in tissue processing protocols could impact Reinke crystal microscopic visualization, which is an important factor in diagnosing Leydig cell disorders such as Leydig cell tumors. Reinke crystals appear to be hallmarks of normally differentiated, adult, Leydig or Leydig‐like cells in humans, while some abnormal and nonhuman Leydig cells contain Reinke‐like paracrystalline inclusions or crystalloids.

Conclusions

These characteristics point to some differentially expressed proteins, which could be involved in Reinke crystal formation. Differential Reinke crystal and paracrystalline inclusion presence could also be due to small changes in protein structure or the cell environment. Further research is needed to solve the ongoing mystery of the Reinke crystal, which would enhance our knowledge of Leydig cell contribution in the pathogenesis of various male reproductive disorders and improve their diagnosis and treatment.