bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-fidelity, Large-scale Targeted Profiling of Microsatellites
Authors: Loh Caitlin A. , Shields Danielle A. , Schwing Adam , Evrony Gilad D. 
Published: November 2023

ABSTRACTMicrosatellites are highly mutable sequences that can serve as markers for relationships among individuals or cells within a population. The accuracy and resolution of reconstructing these relationships depends on the fidelity of microsatellite profiling and the number of microsatellites profiled. However, current methods for targeted profiling of microsatellites incur significant “stutter” artifacts that interfere with accurate genotyping, and sequencing costs preclude whole-genome microsatellite profiling of a large number of samples. We developed a novel method for accurate and cost-effective targeted profiling of a panel of > 150,000 microsatellites per sample, along with a computational tool for designing large-scale microsatellite panels. Our method addresses the greatest challenge for microsatellite profiling — “stutter” artifacts — with a low-temperature hybridization capture that significantly reduces these artifacts. We also developed a computational tool for accurate genotyping of the resulting microsatellite sequencing data that uses an ensemble approach integrating three microsatellite genotyping tools, which we optimize by analysis of de novo microsatellite mutations in human trios. Altogether, our suite of experimental and computational tools enables high-fidelity, large-scale profiling of microsatellites, which may find utility in diverse applications such as lineage tracing, population genetics, ecology, and forensics.
LiveMalasseziastrains isolated from the mucosa of patients with ulcerative colitis
Authors: Cho Yong-Joon , Yang Juan , Shin Seung Yong , Kim Hyo Keun , Rintarhat Piyapat , Park Minji , Sung Muhyeon , Lagree Kate , Underhill David M. , Lee Dong-Woo , Choi Chang Hwan , Yang Chul-Su , Jung Won Hee 
Published: November 2023

AbstractThe human gut is inhabited by a complex ecosystem of diverse microorganisms. While most studies on the gut microbiota have focused on bacteria, accumulating evidence has underscored the role of the mycobiota in inflammatory bowel disease (IBD). This study is the first to isolate and characterize liveMalassezia globosastrains from the intestinal mucosa of patients with ulcerative colitis.Malasseziaspecies primarily inhabit the human skin. We therefore compared theM. globosagut isolates with theM. globosaskin isolates and noted a striking disparity between them. The gut isolates led to a greater exacerbation of colitis in mice. Transcriptome analysis revealed that the gut isolates were more sensitive to normoxia than the skin isolates, suggesting adaptation to hypoxia prevalent in the intestinal environment. These findings provide novel insights into the potential impact ofM. globosaon the pathogenesis of IBD and the influence of niche-specific adaptations on its virulence.
Structural snapshots of phenuivirus cap-snatching and transcription
Authors: Williams Harry M. , Thorkelsson Sigurdur R. , Vogel Dominik , Busch Carola , Milewski Morlin , Cusack Stephen , Grünewald Kay , Quemin Emmanuelle R.J. , Rosenthal Maria 
Published: November 2023

ABSTRACTSevere fever with thrombocytopenia syndrome virus (SFTSV) is a human pathogen that is now endemic to several East Asian countries. The viral large (L) protein catalyzes viral transcription by stealing host mRNA caps via a process known as cap-snatching. Here, we establish anin vitrocap-snatching assay and present three high-quality electron cryo-microscopy (cryo-EM) structures of the SFTSV L protein in biologically relevant, transcription-specific states. In a priming-state structure, we show capped RNA bound to the L protein cap-binding domain (CBD). The L protein conformation in this priming structure is significantly different from published replication-state structures, in particular the N- and C-terminal domains. The capped-RNA is positioned in a way that it can feed directly into the RNA-dependent RNA polymerase (RdRp) ready for elongation. We also captured the L protein in an early-elongation state following primer-incorporation demonstrating that this priming conformation is retained at least in the very early stages of primer extension. This structural data is complemented byin vitrobiochemical and cell-based assays. Together, these insights further our mechanistic understanding of how SFTSV and other bunyaviruses incorporate stolen host mRNA fragments into their viral transcripts thereby allowing the virus to hijack host cell translation machinery.
Fecal transplant allows transmission of the gut microbiota in honey bees
Authors: Cabirol Amélie , Chhun Audam , Liberti Joanito , Kesner Lucie , Neuschwander Nicolas , Schaerli Yolanda , Engel Philipp 
Published: November 2023

AbstractThe gut of honey bees is colonized by symbiotic bacteria during the first days of adult life, once bees have emerged from their wax cells. Within five days, the gut microbiota becomes remarkably stable and consistent across individual bees. Yet, the modes of acquisition and transmission of the gut microbiota are to be confirmed. Few studies suggested bees could be colonized via contact with fecal matter in the hive and via social interactions. However, the composition of the fecal microbiota is still unknown. It is particularly unclear whether all bacterial species can be found viable in the feces and can therefore be transmitted to newborn nestmates. Using 16s rRNA gene amplicon sequencing we revealed that the composition of the honey bee fecal microbiota is strikingly similar to the microbiota of entire guts. We found that fecal transplantation resulted in gut microbial communities largely similar to those obtained from feeding gut homogenates. Our study shows that fecal sampling and transplantation are viable tools for the longitudinal analysis of bacterial community composition and host-microbe interactions. Our results also imply that contact of young bees with fecal matter in the hive is a plausible route for the acquisition of the core gut microbiota.
Tapping into the configurational paths to employee digital innovation in the realm of the dualistic AMO framework
Authors: Li Fumeng , Long Jiancheng 
Published: November 2023

PurposeEnterprises in the digital context attach importance to the participation of heterogeneous subjects in co-creation activities. As the core source of organizational innovation, employees are bound to assume responsibilities or provide role value in the process of digital innovation. While employee-driven digital innovation frameworks are being explored, together with research on employee innovation behavior mostly focusing on the “net effect” of single-level variables on outcomes.Design/methodology/approachFollowing the interaction logic of employee level and organizational level, this study applies ability, motivation and opportunity (AMO) theory and fuzzy set qualitative comparative analysis to explore the influence of various digitization related factors' conditional configuration on employees' digital innovation behavior.FindingsThe results indicate that type of “self-motivation with multiple supports”, “organization-driven with digital oriented” and “digital-driven with ambidextrous complementary” constitute the configuration that drives high digital innovation behavior, while type of “cognitive deficit with environmental slack” and “fuzzy motivation with opportunity misapplication” constitute the configuration that drives nonhigh digital innovation behavior.Originality/valueThis conclusion enriches the theoretical research on digital innovation that regards individuals as action potentials and provides important guidance for how to cultivate and activate employees' digital innovation behaviors in management practice.
Knowledge and experience of Zambian teaching faculties with scholarly communication and dissemination practices
Authors: Subaveerapandiyan A. , Tiwary Neelam , Kasonde Cecilia Christabel , Ugwulebo Jeremiah Emeka , Amees Mohammad 
Published: November 2023

Purpose
This paper aims to investigate the knowledge and experience of Zambian teaching faculties with scholarly communication and dissemination practices.

Design/methodology/approach
The researchers used a survey to quickly obtain information about a large sample of individuals of interest. The study population consisted of faculties from two Zambian public universities with research and publication experience. The researchers used random sampling techniques. A total of 125 valid responses were received from the selected population.

Findings
The findings show that most respondents agreed that publishing in open-access journals increased visibility and readership, had a more significant impact, facilitated collaboration and interdisciplinary research, was cost-effective and provided accessibility. Google Scholar was the most commonly used platform, followed by ResearchGate and ORCID.

Research limitations/implications
This study’s limitations focus on only two Zambian public universities. This study’s practical implications include improving the universities’ open-access policies and educating faculties on the benefits of open access.

Originality/value
This study’s originality lies in exploring the Zambian teaching faculties’ perceptions of open access and academic social networking sites. The results of this study can help universities and researchers in Zambia to understand the importance of scholarly communication and dissemination practices and help them implement effective policies for promoting open-access publishing, institutional repositories and academic social networking sites.
Do welfare regimes matter? Perceptions of welfare in contemporary word
Authors: Mäntyneva Päivi 
Published: November 2023

PurposeThis paper takes an ideal type of different welfare regimes as a starting point. It investigates with survey data people's experiences and expectations towards the welfare state and its functioning against various social risks. The paper discusses questions like, are there differences in perceptions between welfare regimes? And what is the role of the welfare state regime in explaining those differences?Design/methodology/approachThis research article is based on OECD survey data and classical welfare state classifications. The analysis of welfare regimes provides both a theoretical and methodological structure for study. The study-applied analysis of variance (one-way ANOVA) to test a hypothesis that regimes matter analyses more nuanced aspects of current and prospects to the near future welfare state provision.FindingsThis examination suggests that welfare regimes still matter even though the differences in averages were not as immense as expected. Perceptions in different welfare regimes also have priorities related to the willingness to pay more taxes in order to receive better access to services and financial support if needed. In Nordic countries, the acute priority based on survey data is investment in education and re-training. In Continental Europe, more financial support is needed for pensions. Overall, respondents representing emerging Eastern European and Mediterranean welfare regimes think that welfare provision should be financed more compared to other welfare regime respondents. Health is a universal and unifying issue, particularly in ageing welfare states, and brings health as a traditional and central question again.Originality/valueRespondents' perceptions work as people's voice and assessments are used to gain a contemporary understanding of welfare and about welfare state functioning.
How does institutional quality determine energy consumption? Empirical evidence from the South Asia region
Authors: Tabash Mosab I. , Farooq Umar , Ahmed Adel 
Published: November 2023

Purpose Due to an increase in energy demands, it has become vital to devise efficient energy policies. Literature has suggested multiple factors influencing the consumption of specific energy types. Among others, institutional quality (INQ) is another factor that can determine energy consumption. Given this, the current study aimed to investigate the impact of INQ on fossil fuel energy (FFE) and renewable energy consumption (REC).Design/methodology/approach The empirical analysis was conducted on 20 years (2000–2019) of data from South Asian economies, and regression among variables was established by employing the dynamic ordinary least square and fully modified ordinary least square models. The selection of both techniques is subject to the existence of cointegration identified by the Johansen cointegration test. Other pre-estimation techniques include cross-section dependence and unit root testing validating the estimation of coefficients in the long run.Findings The analysis mainly reveals the negative impact of INQ on FFE and the positive impact of INQ on REC. The authors further find the asymmetric impact of control variables including foreign direct investment inflow, economic growth, inflation rate, financial sector development and energy investment on the consumption of both types of energy.Research limitations/implications Given the positive influence of INQ on REC, it is recommended to focus on improving the efficiency of institutions specifically those that are directly linked with energy-related policies. A better INQ can ensure environmental sustainability by enhancing the consumption of renewable energy. Therefore, it is advised to exert more efforts to improve the INQ.Practical implications In view of the positive influence of INQ on REC, it is recommended to focus on improving the efficiency of institutions specifically that are directly linked with energy-related policies. A better INQ can ensure environmental sustainability by enhancing the consumption of renewable energy. Therefore, it is advised to exert more efforts for improving the INQ.Originality/value This study offers robustness to the empirical findings of existing literature on the INQ-REC nexus and complements the underdeveloped literature on the INQ-FFE relationship.
Exploring integrity in Australian public services: A method to benchmark public service codes of conduct
Authors: Moon Katie , Brunoro David , Connor James , Dickinson Helen , Huybers Twan 
Published: November 2023

AbstractIntegrity is an ongoing concern in the public sector. Contemporary examples include fraud incidents, ethical violations, theft, and a disregard of legal advice resulting in significant harms to the public. Public service integrity management systems are interconnected frameworks of legislation and institutions intended to reduce such incidents, including Codes of Conduct (CoCs). A CoC is typically defined as a written set of norms that outline virtuous or desired behaviours, often creating or linking to sanctions for violations. Despite matters of integrity and corruption being a high concern for citizens, no method exists to compare monitoring, reporting, and review of CoCs across jurisdictions. We developed and applied a method to assess CoC implementation using specific assessment criteria developed by reviewing available content across jurisdictions and the current literature on CoCs and integrity management. Our results reveal substantial inconsistency between jurisdictions and a lack of available or accessible data for many CoC elements. Our method serves both as a tool for analysis of the effectiveness of CoCs over time and as an assessment of how jurisdictions are currently reporting on their compliance with their own CoCs.Points for practitioners
A lack of evidence exists in terms of how CoCs are monitored, reported on, and reviewed.
As a first stage of a research program, we develop and apply a method to all Australian states, territories, and the Australian Public Service to compare the monitoring, reporting, and review activities undertaken by these jurisdictions.
Application of the method reveals opportunities for jurisdictions to improve the availability and accessibility of CoC data collection, reporting, and review.
Auditors General and Public Accounts Committees should consider this method as part of their works programs and potentially use it to inform their scrutiny programs and requirements for performance and annual reporting.
Public Service Commissions could find the data useful in adapting and improving their CoC monitoring, reporting, and review systems.
A rapid and non‐destructive identification for paper cup evidence based on shifted‐excitation Raman difference spectroscopy and SOM clustering
Authors: Tian Luchuan , Jiang Hong , Zhang Xin 
Published: November 2023

AbstractIn order to achieve rapid, non‐destructive, efficient, and accurate classification of paper cup samples, we propose a classification model that integrates shifted‐excitation Raman difference spectroscopy (SERDS) with self‐organizing map (SOM) and Bayesian optimization–support vector machine (BO‐SVM). We collected differential Raman data from 52 paper cup samples using SERDS, with an excitation wavelength range of 784–785 nm, a laser power of 440 mW, an integration time of 10 s, and a spectral range spanning from 280 to 2700 cm−1. Subsequently, principal component analysis (PCA) was applied to reduce the dimensionality of the data. The SOM clustering outcomes were utilized as the foundation for constructing the discriminant analysis (FDA) and BO‐SVM classification models. The primary constituent of the paper cup samples was identified as cellulose, while additional fillers such as talc, calcium carbonate, and kaolin were also present. The SOM clustering categorized the samples into seven distinct groups. The FDA model achieved a classification accuracy of 92.3%, and the BO‐SVM model reached a classification accuracy of 96.2%. The SOM clustering effectively discerned samples with different fillers, as evidenced by distinct peak numbers and shapes in the differential Raman spectra, thereby underscoring the practical significance of SOM clustering. In comparison with FDA, BO‐SVM exhibited enhanced classification accuracy and exceptional performance in handling outliers and linearly inseparable data, indicating its superior generalization capabilities.
Predicting visceral pleural invasion in lung adenocarcinoma presenting as part‐solid density utilizing a nomogram model combined with radiomics and clinical features
Authors: Wang Fen , Pan Xianglong , Zhang Teng , Zhong Yan , Wang Chenglong , Li Hai , Wang Jun , Guo Lili , Yuan Mei 
Published: November 2023

AbstractBackgroundTo develop and validate a preoperative nomogram model combining the radiomics signature and clinical features for preoperative prediction of visceral pleural invasion (VPI) in lung nodules presenting as part‐solid density.MethodsWe retrospectively reviewed 156 patients with pathologically confirmed invasive lung adenocarcinomas after surgery from January 2016 to August 2019. The patients were split into training and validation sets by a ratio of 7:3. The radiomic features were extracted with the aid of FeAture Explorer Pro (FAE). A CT‐based radiomics model was constructed to predict the presence of VPI and internally validated. Multivariable regression analysis was conducted to construct a nomogram model, and the performance of the models were evaluated with the area under the receiver operating characteristic curve (AUC) and compared with each other.ResultsThe enrolled patients were split into training (n = 109) and validation sets (n = 47). A total of 806 features were extracted and the selected 10 optimal features were used in the construction of the radiomics model among the 707 stable features. The AUC of the nomogram model was 0.888 (95% CI: 0.762–0.961), which was superior to the clinical model (0.787, 95% CI: 0.643–0.893; p = 0.049) and comparable to the radiomics model (0.879, 95% CI: 0.751–0.965; p > 0.05). The nomogram model achieved a sensitivity of 90.5% and a specificity of 76.9% in the validation dataset.ConclusionsThe nomogram model could be considered as a noninvasive method to predict VPI with either highly sensitive or highly specific diagnoses depending on clinical needs.
Using warming tolerances to predict understory plant responses to climate change
Authors: Wei Liping , Sanczuk Pieter , De Pauw Karen , Caron Maria Mercedes , Selvi Federico , Hedwall Per‐Ola , Brunet Jörg , Cousins Sara A. O. , Plue Jan , Spicher Fabien , Gasperini Cristina , Iacopetti Giovanni , Orczewska Anna , Uria‐Diez Jaime , Lenoir Jonathan , Vangansbeke Pieter , De Frenne Pieter 
Published: November 2023

AbstractClimate change is pushing species towards and potentially beyond their critical thermal limits. The extent to which species can cope with temperatures exceeding their critical thermal limits is still uncertain. To better assess species' responses to warming, we compute the warming tolerance (ΔTniche) as a thermal vulnerability index, using species' upper thermal limits (the temperature at the warm limit of their distribution range) minus the local habitat temperature actually experienced at a given location. This metric is useful to predict how much more warming species can tolerate before negative impacts are expected to occur. Here we set up a cross‐continental transplant experiment involving five regions distributed along a latitudinal gradient across Europe (43° N–61° N). Transplant sites were located in dense and open forests stands, and at forest edges and in interiors. We estimated the warming tolerance for 12 understory plant species common in European temperate forests. During 3 years, we examined the effects of the warming tolerance of each species across all transplanted locations on local plant performance, in terms of survival, height, ground cover, flowering probabilities and flower number. We found that the warming tolerance (ΔTniche) of the 12 studied understory species was significantly different across Europe and varied by up to 8°C. In general, ΔTniche were smaller (less positive) towards the forest edge and in open stands. Plant performance (growth and reproduction) increased with increasing ΔTniche across all 12 species. Our study demonstrated that ΔTniche of understory plant species varied with macroclimatic differences among regions across Europe, as well as in response to forest microclimates, albeit to a lesser extent. Our findings support the hypothesis that plant performance across species decreases in terms of growth and reproduction as local temperature conditions reach or exceed the warm limit of the focal species.
The association between trypsin‐like protease activity in the oral cavity and kidney function in Japanese workers
Authors: Iwasaki Masanori , Inoue Maki , Usui Michihiko , Ariyoshi Wataru , Nakashima Keisuke , Nagai‐Yoshioka Yoshie , Nishihara Tatsuji 
Published: November 2023

AbstractAimTo evaluate the association between trypsin‐like protease (TLP) activity in the oral cavity as an indicator of periodontal health status and kidney function in Japanese workers.Materials and MethodsThis cross‐sectional study included 1117 Japanese workers (mean age = 43.8 years). Tongue‐swab TLP activity was quantified as a* value (the redness intensity of the matrix disc of the TLP activity assessment kit; a larger value indicates more intense enzymatic activity in the samples and poorer periodontal health status). Kidney function was assessed using the estimated glomerular filtration rate (eGFR; a lower value indicates poorer kidney function). We performed ordinal logistic regression analyses to assess the association of the a* value with three eGFR categories: ≥90, 60–89 and <60 mL/min/1.73 m2.ResultsThe prevalence for each eGFR category was as follows: ≥90 (31.6%), 60–89 (63.8%) and <60 mL/min/1.73 m2 (4.6%). After adjusting for potential confounders, the a* value was found to be significantly associated with reduced kidney function. The multivariable‐adjusted odds ratio (95% confidence interval) for reduced kidney function was 1.12 (1.02–1.22) per unit increase in the a* value.ConclusionsHigher TLP activity was associated with reduced kidney function in Japanese workers.