bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue
Authors: Ziemski Michal , Adamov Anja , Kim Lina , Flörl Lena , Bokulich Nicholas A 
Published: September 2022

Abstract

Motivation
The volume of public nucleotide sequence data has blossomed over the past two decades and is ripe for re- and meta-analyses to enable novel discoveries. However, reproducible re-use and management of sequence datasets and associated metadata remain critical challenges. We created the open source Python package q2-fondue to enable user-friendly acquisition, re-use and management of public sequence (meta)data while adhering to open data principles.

Results
q2-fondue allows fully provenance-tracked programmatic access to and management of data from the NCBI Sequence Read Archive (SRA). Unlike other packages allowing download of sequence data from the SRA, q2-fondue enables full data provenance tracking from data download to final visualization, integrates with the QIIME 2 ecosystem, prevents data loss upon space exhaustion and allows download of (meta)data given a publication library. To highlight its manifold capabilities, we present executable demonstrations using publicly available amplicon, whole genome and metagenome datasets.

Availability and implementation
q2-fondue is available as an open-source BSD-3-licensed Python package at https://github.com/bokulich-lab/q2-fondue. Usage tutorials are available in the same repository. All Jupyter notebooks used in this article are available under https://github.com/bokulich-lab/q2-fondue-examples.

Supplementary information
Supplementary data are available at Bioinformatics online.
Morphogenesis of the female reproductive tract along antero-posterior and dorso-ventral axes is dependent on Amhr2+ mesenchyme in mice
Authors: Jia Shuai , Wilbourne Jillian , Crossen McKenna J , Zhao Fei 
Published: September 2022

Abstract
Morphogenesis of the female reproductive tract is regulated by the mesenchyme. However, the identity of the mesenchymal lineage that directs the morphogenesis of the female reproductive tract has not been determined. Using in vivo genetic cell ablation, we identified Amhr2+ mesenchyme as an essential mesenchymal population in patterning the female reproductive tract. After partial ablation of Amhr2+ mesenchymal cells, the oviduct failed to develop its characteristic coiling due to decreased epithelial proliferation and tubule elongation during development. The uterus displayed a reduction in size and showed decreased cellular proliferation in both epithelial and mesenchymal compartments. More importantly, in the uterus, partial ablation of Amhr2+ mesenchyme caused abnormal lumen shape and altered the direction of its long axis from the dorsal-ventral axis to the left–right axis (i.e., perpendicular to the dorsal-ventral axis). Despite these morphological defects, epithelia underwent normal differentiation into secretory and ciliated cells in the oviduct and glandular epithelial cells in the uterus. These results demonstrated that Amhr2+ mesenchyme can direct female reproductive tract morphogenesis by regulating epithelial proliferation and lumen shape without affecting the differentiation of epithelial cell types.
PMCA1 depletion in mouse eggs amplifies calcium signaling and impacts offspring growth
Authors: Savy Virginia , Stein Paula , Shi Min , Williams Carmen J 
Published: September 2022

Abstract
Egg activation in mammals is triggered by oscillations in egg intracellular calcium (Ca2+) level. Ca2+ oscillation patterns can be modified in vitro by changing the ionic composition of culture media or in vivo by conditions affecting mitochondrial function, such as obesity and inflammation. In mice, disruption of Ca2+ oscillations in vitro impacts embryo development and offspring growth. Here we tested the hypothesis that, even without in vitro manipulation, abnormal Ca2+ signaling following fertilization impacts offspring growth. Plasma membrane Ca2+ ATPases (PMCA) extrude cytosolic Ca2+ to restore Ca2+ homeostasis. To disrupt Ca2+ signaling in vivo, we conditionally deleted PMCA1 (cKO) in oocytes. As anticipated, in vitro fertilized cKO eggs had increased Ca2+ exposure relative to controls. To assess the impact on offspring growth, cKO females were mated to wild type males to generate pups that had high Ca2+ exposure at fertilization. Because these offspring would be heterozygous, we also tested the impact of global PMCA1 heterozygosity on offspring growth. Control heterozygous pups that had normal Ca2+ at fertilization were generated by mating wild type females to heterozygous males; these control offspring weighed significantly less than their wild type siblings. However, heterozygous offspring from cKO eggs (and high Ca2+ exposure) were larger than heterozygous controls at 12 week-of-age and males had altered body composition. Our results show that global PMCA1 haploinsufficiency impacts growth and support that abnormal Ca2+ signaling after fertilization in vivo has a long-term impact on offspring weight. These findings are relevant for environmental and medical conditions affecting Ca2+ handling and for design of culture conditions and procedures for domestic animal and human assisted reproduction.
Disentangling a 40-year-old taxonomic puzzle: the phylogenetic position of Mimulicalyx (Lamiales)
Authors: Zhao Fei , Liu Bing , Liu Su , Min Dao-Zhang , Zhang Ting , Cai Jie , Zhou Xin-Xin , Chen Bin , Olmstead Richard G , Xiang Chun-Lei , Li Bo 
Published: September 2022

Abstract
With the disintegration of the traditionally circumscribed Scrophulariaceae, the phylogenetic placements of most genera formerly placed in that family have been resolved. However, the familial placement of the monotypic genus Mimulicalyx has not been included in any published molecular phylogenetic study. Here, we adopt a two-step approach to resolve the phylogenetic placement of Mimulicalyx using three datasets: (1) a 71 619 bp plastome alignment of Lamiales; (2) a dataset of six plastid DNA regions (atpB, matK, ndhF, rbcL, rps16 and trnL-trnF) for Phrymaceae; and (3) a dataset of the nuclear ribosomal internal and external transcribed spacer regions (nrITS, ETS) for Phrymaceae. Our analyses reveal that Mimulicalyx is a member of the tribe Mimuleae in Phrymaceae. Generic level phylogenetic relationships within Phrymaceae are further discussed, and a dichotomous key to the 15 genera currently recognized is provided.
Environmental and geographical biases in plant specimen data from the Colombian Andes
Authors: Vargas Carlos A , Bottin Marius , Särkinen Tiina , Richardson James E , Raz Lauren , Garzon-Lopez Carol X , Sanchez Adriana 
Published: September 2022

AbstractSpecimen records are a major source of species information for biodiversity research. However, specimen records currently available may be geographically or environmentally biased. Detailed knowledge of biases is useful for understanding and accounting for errors they introduce into analyses of biodiversity patterns. Here we study geographical and environmental biases in online records representing the flora of the Colombian Andes and explore their effect on sample completeness at different spatial scales. We found a strong geographical and environmental sampling bias. Plant records were concentrated close to cities where herbaria and researchers are located. The highlands &gt; 2000 m are better sampled, whereas mid- and lowlands remain poorly sampled (i.e. montane and lowland forest). Sampling completeness (SC) median across the Colombian Andes is &lt; 75% at the scales studied. We explore possible causes of sampling bias, identify critical gaps and priority areas for plant sampling and make recommendations for strategies to increase SC and reduce biases.
Dual-MEG interbrain synchronization during turn-taking verbal interactions between mothers and children
Authors: Lin Jo-Fu Lotus , Imada Toshiaki , Meltzoff Andrew N , Hiraishi Hirotoshi , Ikeda Takashi , Takahashi Tetsuya , Hasegawa Chiaki , Yoshimura Yuko , Kikuchi Mitsuru , Hirata Masayuki , Minabe Yoshio , Asada Minoru , Kuhl Patricia K 
Published: September 2022

AbstractVerbal interaction and imitation are essential for language learning and development in young children. However, it is unclear how mother–child dyads synchronize oscillatory neural activity at the cortical level in turn-based speech interactions. Our study investigated interbrain synchrony in mother–child pairs during a turn-taking paradigm of verbal imitation. A dual-MEG (magnetoencephalography) setup was used to measure brain activity from interactive mother–child pairs simultaneously. Interpersonal neural synchronization was compared between socially interactive and noninteractive tasks (passive listening to pure tones). Interbrain networks showed increased synchronization during the socially interactive compared to noninteractive conditions in the theta and alpha bands. Enhanced interpersonal brain synchrony was observed in the right angular gyrus, right triangular, and left opercular parts of the inferior frontal gyrus. Moreover, these parietal and frontal regions appear to be the cortical hubs exhibiting a high number of interbrain connections. These cortical areas could serve as a neural marker for the interactive component in verbal social communication. The present study is the first to investigate mother–child interbrain neural synchronization during verbal social interactions using a dual-MEG setup. Our results advance our understanding of turn-taking during verbal interaction between mother–child dyads and suggest a role for social “gating” in language learning.
Alterations in resting-state functional connectivity associated to the age-related decline in time-based prospective memory
Authors: Morand Alexandrine , Segobin Shailendra , Lecouvey Grégory , Gonneaud Julie , Eustache Francis , Rauchs Géraldine , Desgranges Béatrice 
Published: September 2022

AbstractTime-based prospective memory (TBPM) is defined as the ability to remember to perform intended actions at a specific time in the future. TBPM is impaired in aging, and this decline has been associated with white-matter alterations within the superior fronto-occipital fasciculus. In the present study, we used resting-state functional magnetic resonance imaging from 22 healthy young (26 ± 5.2 years) and 23 older (63 ± 6.1 years) participants to investigate how age-related alterations in resting-state functional connectivity are related to TBPM performance, and whether these alterations are associated with the white-matter disruptions we have previously observed with diffusion tensor imaging. Whole-brain analyses revealed lower resting-state functional connectivity in older participants compared with younger ones, which in turn correlated with TBPM performance. These correlations were mainly located in the salience network and the parietal part of the frontoparietal network. Our findings suggest that resting-state functional connectivity alterations contribute to the age-related decline in TBPM.
A microcircuit model involving parvalbumin, somatostatin, and vasoactive intestinal polypeptide inhibitory interneurons for the modulation of neuronal oscillation during visual processing
Authors: Wagatsuma Nobuhiko , Nobukawa Sou , Fukai Tomoki 
Published: September 2022

AbstractVarious subtypes of inhibitory interneurons contact one another to organize cortical networks. Most cortical inhibitory interneurons express 1 of 3 genes: parvalbumin (PV), somatostatin (SOM), or vasoactive intestinal polypeptide (VIP). This diversity of inhibition allows the flexible regulation of neuronal responses within and between cortical areas. However, the exact roles of these interneuron subtypes and of excitatory pyramidal (Pyr) neurons in regulating neuronal network activity and establishing perception (via interactions between feedforward sensory and feedback attentional signals) remain largely unknown. To explore the regulatory roles of distinct neuronal types in cortical computation, we developed a computational microcircuit model with biologically plausible visual cortex layers 2/3 that combined Pyr neurons and the 3 inhibitory interneuron subtypes to generate network activity. In simulations with our model, inhibitory signals from PV and SOM neurons preferentially induced neuronal firing at gamma (30–80 Hz) and beta (20–30 Hz) frequencies, respectively, in agreement with observed physiological results. Furthermore, our model indicated that rapid inhibition from VIP to SOM subtypes underlies marked attentional modulation for low-gamma frequency (30–50 Hz) in Pyr neuron responses. Our results suggest the distinct but cooperative roles of inhibitory interneuron subtypes in the establishment of visual perception.
The Impact of Extended Treatment With Artemether-lumefantrine on Antimalarial Exposure and Reinfection Risks in Ugandan Children With Uncomplicated Malaria: A Randomized Controlled Trial
Authors: Whalen Meghan E , Kajubi Richard , Goodwin Justin , Orukan Francis , Colt McKenzie , Huang Liusheng , Richards Kacey , Wang Kaicheng , Li Fangyong , Mwebaza Norah , Aweeka Francesca T , Parikh Sunil 
Published: September 2022

Abstract

Background
Artemether-lumefantrine (AL) is the most widely used artemisinin-based combination therapy in Sub-Saharan Africa and is threatened by the emergence of artemisinin resistance. Dosing is suboptimal in young children. We hypothesized that extending AL duration will improve exposure and reduce reinfection risks.

Methods
We conducted a prospective, randomized, open-label pharmacokinetic/pharmacodynamic study of extended duration AL in children with malaria in high-transmission rural Uganda. Children received 3-day (standard 6-dose) or 5-day (10-dose) AL with sampling for artemether, dihydroartemisinin, and lumefantrine over 42-day clinical follow-up. Primary outcomes were (1) comparative pharmacokinetic parameters between regimens and (2) recurrent parasitemia analyzed as intention-to-treat.

Results
A total of 177 children aged 16 months to 16 years were randomized, contributing 227 total episodes. Terminal median lumefantrine concentrations were significantly increased in the 5-day versus 3-day regimen on days 7, 14, and 21 (P &lt; .001). A predefined day 7 lumefantrine threshold of 280 ng/mL was strongly predictive of recurrence risk at 28 and 42 days (P &lt; .001). Kaplan–Meier estimated 28-day (51% vs 40%) and 42-day risk (75% vs 68%) did not significantly differ between 3- and 5-day regimens. No significant toxicity was seen with the extended regimen.

Conclusions
Extending the duration of AL was safe and significantly enhanced overall drug exposure in young children but did not lead to significant reductions in recurrent parasitemia risk in our high-transmission setting. However, day 7 levels were strongly predictive of recurrent parasitemia risk, and those in the lowest weight-band were at higher risk of underdosing with the standard 3-day regimen.

Clinical Trial Registration
ClinicalTrials.gov number NCT03453840.
Approaching evolutionary communication
Authors: Lull James 
Published: September 2022

AbstractThe determining roles played by communication in the ongoing evolution of our species remain largely unexplored in communications-related disciplines. An unhelpful controversy that raged over E. O. Wilson’s sociobiology last century contributed to the problem and is reconsidered here in terms of the fault lines that run between natural science, social science, and politics. The article describes paths for future theoretical development by focusing first on the link between human communications behavior and evolutionary psychology. With an emphasis on understanding the crisis of community facing the world today, evolutionary communication is proposed as a theoretical alternative to limited proximate perspectives afforded by cultural analysis alone. The inherent interdisciplinary nature of communication makes the field a prime candidate for conducting research grounded in the deep-time explanatory framework of evolutionary theory and the epistemological assumptions of scientific humanism.
Comparison of the 6-minute walk distance measured on a 30 m track with guidance of a healthcare professional and those measured with a mobile application outdoors by participants themselves: a validation study
Authors: Klompstra Leonie , Lans Charlotta , Mercke Emil , Strömberg Anna , Jaarsma Tiny 
Published: September 2022

Abstract
To improve the practical application of measuring exercise capacity, the purpose of this study was to compare the 6 min walk distance (6MWD) obtained at a 30 m track with the guidance of healthcare professionals vs. the 6MWD obtained by participants themselves using an app. In total, 37 participants performed both tests. The mean of the differences between the 6MWD on the tests was −4 ± 45 m (95% limits of agreement: 84 to −99 m). The overall agreement between the two 6MWD measures was 97% with an intraclass correlation coefficient of 0.96 (95% confidence interval: 0.91–0.98, P &lt; 0.001). The use of an app is feasible, reliable, and valid to assess the 6MWD.
Instructing Use of an Effective Strategy Improves Recognition Memory in Healthy Adults
Authors: Bender Andrew R , Driver Charles C , Hertzog Christopher , Raz Naftali 
Published: September 2022

AbstractObjectivesAge-related memory decrements correlate with metacognitive declines, including knowledge and deployment of effective mnemonic encoding strategies. However, whether imparting such strategy suffices for mitigating memory differences is unclear.MethodIn a longitudinal study of 276 healthy adults aged 18–79 years, we tested associative and working memory, and assessed beliefs regarding mnemonic strategies. Testing was repeated every 2 years, 5 times. Starting with the third occasion, we instructed participants to use an effective mnemonic strategy (sentence generation). Using continuous-time dynamic modeling, we assessed changes in the item and associative recognition, intervention effects, and their relations with age, sex, meta-memory beliefs, working memory, and metabolic health.ResultsYounger age, better working memory, and stronger belief in effective mnemonic strategies predicted better recognition, whereas instructional intervention attenuated associative memory deficits, with some persistence over time.DiscussionThe present findings show merely imparting effective strategies holds promise for mitigating age-related associative memory deficits.
The effects of domestic and EU incentives on corporate investment toward ecological transition: a propensity score matching approach
Authors: Becchetti Leonardo , Mancini Sara , Solferino Nazaria 
Published: September 2022

AbstractWe investigate the effects of domestic and European Union (EU) incentives on different types of corporate investment in ecological transition in Italian firms including a large representative sample of small companies and the universe of companies above 250 employees. We perform propensity score matching tests exploiting revealed information of firms that declare to use the incentives for specific ecological transition investments compared to a synthetic counterfactual of “twin” companies matched on selected characteristics. Our findings show that domestic and EU incentives significantly increase green investment for both small and medium/large-sized companies, the impact being highest when we consider investment in energy-saving plants and for carbon emission reduction.
LIMA to LAD grafting returns patient survival to age-matched population: 20-year outcomes of MIDCAB surgery
Authors: Manuel Lucy , Fong Laura S , Betts Kim , Bassin Levi , Wolfenden Hugh 
Published: September 2022

AbstractOBJECTIVESPrevious studies have demonstrated the safety and excellent short-term and mid-term survival after minimally invasive direct coronary artery bypass (MIDCAB). We reviewed the long-term outcomes up to 20 years, including overall survival and freedom from reintervention.METHODSConsecutive patients who underwent MIDCAB between February 1997 and August 2020 were identified. Demographic details, operative information and long-term outcomes were obtained. The Australian National Death Index database was accessed to obtain long-term mortality data.RESULTSA total of 271 patients underwent an MIDCAB procedure during the study period. There were no intraoperative deaths and only one 30-day mortality (0.4%). The mean length of follow-up was 9.82 ± 8.08 years. Overall survival at 5-, 10-, 15- and 20-year survival was 91.9%, 84.7%, 71.3% and 56.5%, respectively. Patients with single-vessel disease [left anterior descending artery (LAD) only] had significantly better survival compared to patients with multivessel disease (P = 0.0035). During long-term follow-up, there were no patients who required repeat revascularization of the LAD territory. Sixty-nine patients died with the cause of death in 15 patients (21.7%) being attributable to ischaemic heart disease. An analysis comparing the isolated LAD disease MIDCAB cohort survival with the expected survival among an age/gender/year matched sample of the Australian reference population, using the standardized mortality ratio, demonstrated that the rate of survival returned to that of the reference population (standardized mortality ratio = 0.94).CONCLUSIONSMIDCAB is a safe and effective revascularization strategy which can be successfully performed in a carefully selected patient population with low morbidity and excellent long-term results. The survival of MIDCAB patients returns to that of their age/gender/year-matched counterparts within the normal population and hence should be offered as an alternative to coronary stenting when counselling patients with ischaemic heart disease.
Nasopharyngeal Carriage of Pneumococcus in Children in England up to 10 Years After 13-Valent Pneumococcal Conjugate Vaccine Introduction: Persistence of Serotypes 3 and 19A and Emergence of 7C
Authors: Tiley Karen S , Ratcliffe Helen , Voysey Merryn , Jefferies Kimberley , Sinclair Gemma , Carr Melanie , Colin-Jones Rachel , Smith David , Bowman Jaclyn , Hart Thomas , Kandasamy Rama , Hinds Jason , Gould Katherine , Berbers Guy , Tcherniaeva Irina , Robinson Hannah , Plested Emma , Aley Parvinder , Snape Matthew D 
Published: September 2022

AbstractBackgroundMonitoring changes in pharyngeal carriage of pneumococcus in children following 13-valent pneumococcal conjugate vaccine (PCV13) introduction in the United Kingdom in 2010 informs understanding of patterns of invasive pneumococcal disease (IPD) incidence.MethodsNasopharyngeal swabs from healthy children vaccinated with PCV13 according to schedule (2, 4, and 12 months) were cultured and serotyped. Results for children aged 13–48 months were compared between 2014–2015 and 2017–2019 and with children aged 6–12 months (2017–2020). Blood was obtained from a subset of children for pneumococcal serotype-specific immunoglobulin G (IgG).ResultsTotal pneumococcal carriage at 13–48 months was 47.9% (473/988) in 2014–2015 and 51.8% (412/795) in 2017–2019 (P = .10); at age 6–12 months this value was 44.6% (274/615). In 2017–2019, 2.9% (95% confidence interval, 1.8%–4.3%) of children aged 13–48 months carried PCV13 serotypes (mainly 3 [1.5%] and 19A [0.8%]) and &gt;20% carried the additional 20-valent PCV (PCV20) serotypes. Similar proportions of children had IgG ≥0.35 IU/mL for each serotype in 2014–2015 and 2017–2019. Serotype 7C carriage increased significantly (P &lt; .01) between 2014–2015 and 2017–2019. Carriage of PCV20 serotypes 8 and 12F, both major causes of IPD, was rare.ConclusionsIntroduction of PCV20, if licensed for children, could significantly change the composition of pneumococcal serotypes carried in the pharynx of UK children.Clinical Trials RegistrationNCT03102840.