bluuebunny/crossref_metadata_2025_split huggingface dataset:
A synthesis of the biogeographical distribution of Rotifera in Africa
Authors: Smolak Radoslav , Walsh Elizabeth J , Brown Patrick D , Wallace Robert L 
Published: December 2022

Abstract
The rotifer fauna of Africa has been studied for &gt;100 years, but there has been no recent synthesis. We compiled data from 265 publications that reported information on African rotifers. Our dataset yielded information on the distribution of 765 taxa from ~1850 separate sites; these included both natural and artificial habitats such as lakes, ponds, puddles, oases, artificial systems, rivers and wetlands. A heat map of predicted rotifer biodiversity indicated that the greatest diversity should be present in the sub-Saharan region including a large hotspot in Mali and several smaller ones scattered in that region. Lakes Kariba, Tanganyika and Malawi showed high-predicted diversity, but surprisingly, Lake Victoria had lower diversity than expected. Two regions showed unusually high-predicted diversity: northwestern Algeria extending into Morocco and Egypt. Equatorial Africa is rich in habitats well suited for rotifers, yet their predicted biodiversity seems low. Latitude and elevation were negatively correlated with richness, while permanent water source and littoral zone were positively correlated according to generalized linear modeling results. Partial RDA analyses showed significant correlations among several environmental features and species occurrences. It is clear that more survey work remains to be done to achieve a better understanding of African rotifers.
Freezing Biological Time: A Modern Perspective on Organ Preservation
Authors: Criswell Tracy , Swart Corné , Stoudemire Jana , Brockbank Kelvin G M , Powell-Palm Matthew , Stilwell Reginald , Floren Michael 
Published: December 2022

Abstract
Transporting tissues and organs from the site of donation to the patient in need, while maintaining viability, is a limiting factor in transplantation medicine. One way in which the supply chain of organs for transplantation can be improved is to discover novel approaches and technologies that preserve the health of organs outside of the body. The dominant technologies that are currently in use in the supply chain for biological materials maintain tissue temperatures ranging from a controlled room temperature (+25 °C to +15 °C) to cryogenic (−120 °C to −196 °C) temperatures (reviewed in Criswell et al. Stem Cells Transl Med. 2022). However, there are many cells and tissues, as well as all major organs, that respond less robustly to preservation attempts, particularly when there is a need for transport over long distances that require more time. In this perspective article, we will highlight the current challenges and advances in biopreservation aimed at “freezing biological time,” and discuss the future directions and requirements needed in the field.
Performance of Akaike Information Criterion and Bayesian Information Criterion in Selecting Partition Models and Mixture Models
Authors: Liu Qin , Charleston Michael A , Richards Shane A , Holland Barbara R 
Published: December 2022

AbstractIn molecular phylogenetics, partition models and mixture models provide different approaches to accommodating heterogeneity in genomic sequencing data. Both types of models generally give a superior fit to data than models that assume the process of sequence evolution is homogeneous across sites and lineages. The Akaike Information Criterion (AIC), an estimator of Kullback–Leibler divergence, and the Bayesian Information Criterion (BIC) are popular tools to select models in phylogenetics. Recent work suggests that AIC should not be used for comparing mixture and partition models. In this work, we clarify that this difficulty is not fully explained by AIC misestimating the Kullback–Leibler divergence. We also investigate the performance of the AIC and BIC at comparing amongst mixture models and amongst partition models. We find that under nonstandard conditions (i.e. when some edges have small expected number of changes), AIC underestimates the expected Kullback–Leibler divergence. Under such conditions, AIC preferred the complex mixture models and BIC preferred the simpler mixture models. The mixture models selected by AIC had a better performance in estimating the edge length, while the simpler models selected by BIC performed better in estimating the base frequencies and substitution rate parameters. In contrast, AIC and BIC both prefer simpler partition models over more complex partition models under nonstandard conditions, despite the fact that the more complex partition model was the generating model. We also investigated how mispartitioning (i.e., grouping sites that have not evolved under the same process) affects both the performance of partition models compared with mixture models and the model selection process. We found that as the level of mispartitioning increases, the bias of AIC in estimating the expected Kullback–Leibler divergence remains the same, and the branch lengths and evolutionary parameters estimated by partition models become less accurate. We recommend that researchers are cautious when using AIC and BIC to select among partition and mixture models; other alternatives, such as cross-validation and bootstrapping, should be explored, but may suffer similar limitations [AIC; BIC; mispartitioning; partitioning; partition model; mixture model].
The protective effect of red cabbage on water-soluble fractions of spent crankcase oil-induced alterations in lipid function biomarkers and atherogenic indices in male Albino rats
Authors: Bekibele G E , Anacletus F C , Patrick-Iwuanyanwu K C , Nwaogazie I L 
Published: December 2022

AbstractSpent crankcase oil (SCO) contains a cocktail of metals and polycyclic aromatic hydrocarbons (PAHs), transferred to the associated water-soluble fractions (WSF); and low-dose heavy metals exposures could increase the triglycerides (TG), total cholesterol (TC), low-density lipoproteins (LDL), and very-low-density lipoproteins (VLDL) concentrations. Hence, this study estimated the changes in the lipid profile and atherogenic indices (AI) of male Wistar albino rats exposed to the WSF of SCO and treated with aqueous extracts (AE) of red cabbage (RC) for 60 and 90 days. Sixty-four male Wistar rats divided into 8 groups (8 animals each) were orally administered 1 mL of deionized water, 500 mg/kg AE of RC, 1 mL of 25%, 50%, and 100% WSF of SCO daily for 60 and 90 days, whereas alternate groups were given the stated percentages of the WSF and the AE. Serum TG, TC, LDL, and VLDL concentrations were then analyzed using appropriate kits and the AI estimated thereafter. Although the 60 days study presented a nonsignificant (P &lt; 0.05) difference in the TG, VLDL, and high density lipoprotein (HDL)-C levels in all the exposed and treated groups, a significantly (P &lt; 0.05) elevated TC and non-HDL was recorded for the 100% exposed group alone. Also, the LDL concentration of all exposed groups was higher than all treated groups. The findings at the 90th day was different, such that the 100% and 25% exposed only groups had elevated lipid profile (except HDL-C) concentrations and AI compared with other groups. RC extracts can act as good hypolipidemic agents in WSF of SCO hyperlipidemia potentiating events.
Single-Center Experience Using the Cardiohelp System for Neonatal and Pediatric Extracorporeal Membrane Oxygenation
Authors: Agasthya Nisha , Froehlich Curtis D. , Golecki Michael , Meyer Marisa , Ogino Mark T. , Froehlich Kendra , Beaty Christopher , McCants Sharon , Maul Timothy M. , Dirnberger Daniel R. 
Published: December 2022

OBJECTIVES:
Extracorporeal membrane oxygenation (ECMO) systems have continued to evolve and improve with the development of smaller and portable systems. The Cardiohelp (Maquet Getinge Cardiopulmonary AG, Rastatt, Germany) portable life support device is a compact ECMO system used widely in adults and for ECMO transport. Reports of its use in neonatal and pediatric centers remain limited. In this single-center retrospective review, we describe our institutional experience with the Cardiohelp.

DESIGN:
Single-center retrospective review.

SETTING:
Neonatal ICUs and PICUs in a tertiary-care children’s hospital.

PATIENTS:
Seventeen pediatric patients on ECMO.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Median (interquartile range, IQR) of patient age was 0.5 years (0–7 yr). Eleven of 17 patients were on veno-arterial ECMO, five on veno-venous ECMO, and one on veno-venoarterial ECMO. All veno-venous and veno-venoarterial runs (n = 6) were accomplished with bicaval, dual-lumen cannulae. Median duration on Cardiohelp was 113 hours (IQR 50–140 hr). Median anti-Xa level for patients was 0.43 IU/mL (IQR 0.35–0.47 IU/mL), with median heparin dose of 23.6 U/kg/hr (IQR 17.6–28.1 U/kg/hr). Median plasma-free hemoglobin was 41.4 mg/dL (IQR 30–60 mg/dL). Circuit change was required in three cases. Fourteen patients survived ECMO, with 13 patients surviving to discharge.

CONCLUSIONS:
We have used the Cardiohelp system to support 17 neonatal and pediatric ECMO patients, without complications. Further studies are warranted to compare complications, outcomes, and overall cost with other institutions and other existing ECMO systems.
Alteration in shear wave elastography is associated with acute kidney injury: A prospective observational pilot study
Authors: Xu Qiancheng , Qiang Banghong , Pan Youjun , Li Juan , Zha Lei , Lu Weihua , Wang Junli , Li Jianguo 
Published: December 2022

Abstract

Background
Kidney stiffness could change during kidney disease. We hypothesize that acute kidney injury (AKI) would increase renal stiffness. Therefore, evaluating kidney Young's modulus (YM, a measure of tissue stiffness) using shear wave elastography (SWE) might help to diagnose AKI.

Methods
This research was divided into two studies. Study A: Male C57BL/6 mice were used to observe kidney YM changes induced by sepsis-associated AKI, which was established by caecal ligation and puncture (CLP). Study B included 54 consecutive critically ill patients with or without AKI. Changes in renal YM were observed.

Results
Study A: CLP mice showed a significantly higher kidney YM compared to the sham group. The YM gradually increased from CLP 0-hour to CLP 24 hours. And, presented a fair relationship with the renal tubular injury score (R2 = 0.71) and serum creatinine (R2 = 0.73). Study B: YM was easily accessible and the intraclass correlation coefficient ranged from 0.62 to 0.84. Kidney YM was higher in AKI patients and gradually increased from non-AKI to AKI III patients. Furthermore, the YM in the upper, middle and lower poles renal cortex presented a fair relationship with kidney injury molecule-1 and neutrophil gelatinase-associated lipocalin (R2 ranging from 0.4 to 0.58). And the area under curves of the above five indicators for the diagnosis of AKI were 0.7, 0.73, 0.70, 0.74, and 0.79, respectively.

Conclusions
SWE-derived estimates of renal stiffness are higher in AKI patients and sepsis-associated AKI mice. However, it has no advantage over NGAL and KIM-1.

Trial registration: Chinese Clinical Trial Registry No: ChiCTR2200061725. Retrospectively registered on 1 July 2022, https://www.chictr.org.cn/showproj.aspx?proj=169359
Successful Islet Transplantation Into a Subcutaneous Polycaprolactone Scaffold in Mice and Pigs
Authors: Smink Alexandra M. , Rodriquez Samuel , Li Shiri , Ceballos Bryan , Corrales Nicole , Alexander Michael , Koster Taco , de Haan Bart J. , Lakey Jonathan R.T. , de Vos Paul 
Published: December 2022

Background.
Islet transplantation is a promising treatment for type 1 diabetes. It has the potential to improve glycemic control, particularly in patients suffering from hypoglycemic unawareness and glycemic instability. As most islet grafts do not function permanently, efforts are needed to create an accessible and replaceable site, for islet grafts or for insulin-producing cells obtained from replenishable sources. To this end, we designed and tested an artificial, polymeric subcutaneous transplantation site that allows repeated transplantation of islets.

Methods.
In this study, we developed and compared scaffolds made of poly(D,L,-lactide-co-ε-caprolactone) (PDLLCL) and polycaprolactone (PCL). Efficacy was first tested in mice‚ and then, as a proof of principle for application in a large animal model, the scaffolds were tested in pigs, as their skin structure is similar to that of humans.

Results.
In mice, islet transplantation in a PCL scaffold expedited return to normoglycemia in comparison to PDLLCL (7.7 ± 3.7 versus 16.8 ± 6.5 d), but it took longer than the kidney capsule control group. PCL also supported porcine functional islet survival in vitro. Subcutaneous implantation of PDLLCL and PCL scaffolds in pigs revealed that PCL scaffolds were more stable and was associated with less infiltration by immune cells than PDLLCL scaffolds. Prevascularized PCL scaffolds were therefore used to demonstrate the functional survival of allogenic islets under the skin of pigs.

Conclusions.
To conclude, a novel PCL scaffold shows efficacy as a readily accessible and replaceable, subcutaneous transplantation site for islets in mice and demonstrated islet survival after a month in pigs.
Australian Donation and Transplantation Biobank: A Research Biobank Integrated Within a Deceased Organ and Tissue Donation Program
Authors: Sharma Varun J. , Starkey Graham , D’Costa Rohit , James Fiona , Mouhtouris Effie , Davis Lisa , Wang Boa Zhong , Vago Angela , Raman Jaishankar , Mackay Laura K. , Opdam Helen , Jones Robert , Grayson M. Lindsay , Martin Dominique E. , Gordon Claire L. 
Published: December 2022

Background.
We aimed to facilitate the donation of tissue samples for research by establishing a centralized system integrated in the organ donation program for collection, storage, and distribution of samples (the Australian Donation and Transplantation Biobank [ADTB]).

Methods.
Feasibility of a research biobank integrated within the deceased organ and tissue donation program was assessed. DonateLife Victoria sought consent for ADTB donation after consent was received for organ donation for transplantation from the donor’s senior available next of kin. ADTB samples were collected during donation surgery and distributed fresh to researchers or stored for future research. The main outcome measures were ADTB donation rates, ADTB sample collection, ADTB sample use, and to identify ethical considerations.

Results.
Over 2 y, samples were collected for the ADTB from 69 donors (28% of 249 donors). Samples were obtained from the spleen (n = 59, 86%), colon (n = 57, 83%), ileum (n = 56, 82%), duodenum (n = 55, 80%), blood (n = 55, 80%), bone marrow (n = 55, 80%), skin (n = 54, 78%), mesenteric lymph nodes (n = 56, 81%), liver (n = 21, 30%), lung (n = 29, 42%), and lung-draining lymph node (n = 29, 42%). Heart (n = 20), breast (n = 1), and lower urinary tract (n = 1) samples were obtained in the second year. Five hundred fifty-six samples were used in 19 ethics-approved research projects spanning the fields of immunology, microbiology, oncology, anatomy, physiology, and surgery.

Conclusions.
The integration of routine deceased donation and transplantation activities with a coordinated system for retrieval and allocation of donor samples for use in a range of research projects is feasible and valuable.
Transplantation Amid a Pandemic: The Fall and Rise of Kidney Transplantation in the United States
Authors: Bisen Shivani S. , Zeiser Laura B. , Boyarsky Brian , Werbel William , Snyder Jon , Garonzik-Wang Jacqueline , Levan Macey L. , Segev Dorry L. , Massie Allan B. 
Published: December 2022

Background.
Following the outbreak of coronavirus disease 2019 (COVID-19) in the United States, the number of kidney waitlist additions and living-donor and deceased-donor kidney transplants (LDKT/DDKT) decreased substantially but began recovering within a few months. Since then, there have been several additional waves of infection, most notably, the Delta and Omicron surges beginning in August and December 2021, respectively.

Methods.
Using SRTR data, we compared observed waitlist registrations, waitlist mortality, waitlist removal due to deteriorating condition, LDKT, and DDKT over 5 distinct pandemic periods to expected events based on calculations from preepidemic data while accounting for seasonality and secular trends.

Results.
Although the number of daily waitlist additions has been increasing since May 2020, the size of the active waitlist has consistently declined, reaching a minimum of 52 556 on February 27, 2022. The recent Omicron surge knocked LDKT from 25% below baseline (incidence rate ratio [IRR] = 0.690.750.81) during the Delta wave to 38% below baseline (IRR = 0.580.620.67). DDKT, however, was less affected by the Omicron wave (IRR = 0.850.890.93 and 0.880.920.96 during the Delta and Omicron waves, respectively). Waitlist death decreased from 56% above baseline (IRR = 1.431.561.70) during Delta to 41% above baseline during Omicron, whereas waitlist removal due to deteriorating condition remained at baseline/expected levels during the Delta wave (IRR = 0.931.021.12) and the Omicron wave (IRR = 0.991.071.16).

Conclusions.
Despite exceptionally high COVID-19 incidence during the Omicron wave, the transplant system responded similarly to prior waves that imposed a lesser disease burden, demonstrating the transplant system’s growing adaptations and resilience to this now endemic disease.
Concepts in interaction: social engagement and inner experiences
Authors: Borghi Anna M. , Osińska Albertyna , Roepstorff Andreas , Raczaszek-Leonardi Joanna 
Published: December 2022

This theme issue aims to view the literature on concepts through a novel lens, that of social interaction and its influence on inner experiences. It discusses unsolved problems in literature on concepts, emphasizing the distinction between concrete versus abstract concepts and external versus internal grounding. This introductory article reflects the two research streams that the theme aims to bridge—in this area, the dimension of embodied interaction with others and how this influences the interaction with ourselves is still underexplored. In the first part, we discuss recent trends in social cognition, showing how interacting with others influences our concepts. In the second part, we address how social interactions become part of our inner world in a Vygotskian fashion. First, we illustrate how interoception, emotion and metacognition are connected with concepts and knowledge. Second, we deal with how language, in both its outer and inner form, can empower cognition and concepts. We also briefly describe how novel experimental and computational methods contribute to investigating the online use of concepts. Overall, this introductory article outlines the potentialities of an integrated and interactive approach that can give new, fresh life to a topic, that of concepts, which lies at the root of human cognition.
This article is part of the theme issue ‘Concepts in interaction: social engagement and inner experiences’.
On the social nature of abstraction: cognitive implications of interaction and diversity
Authors: Olsen Karsten , Tylén Kristian 
Published: December 2022

The human capacity for abstraction is remarkable. We effortlessly form abstract representations from varied experiences, generalizing and flexibly transferring experiences and knowledge between contexts, which can facilitate reasoning, problem solving and learning across many domains. The cognitive process of abstraction, however, is often portrayed and investigated as an individual process. This paper addresses how cognitive processes of abstraction—together with other aspects of human reasoning and problem solving—are fundamentally shaped and modulated by online social interaction. Starting from a general distinction between convergent thinking, divergent thinking and processes of abstraction, we address how social interaction shapes information processing differently depending on cognitive demands, social coordination and task ecologies. In particular, we suggest that processes of abstraction are facilitated by the interactive sharing and integration of varied individual experiences. To this end, we also discuss how the dynamics of group interactions vary as a function of group composition; that is, in terms of the similarity and diversity between the group members. We conclude by outlining the role of cognitive diversity in interactive processes and consider the importance of group diversity in processes of abstraction.
This article is part of the theme issue ‘Concepts in interaction: social engagement and inner experiences’.
The RNA-binding protein Adad1 is necessary for germ cell maintenance and meiosis in zebrafish
Authors: Islam Kazi Nazrul , Ajao Anuoluwapo , Henke Katrin , Siegfried Kellee R. 
Published: December 2022

AbstractThe double stranded RNA binding protein Adad1 (adenosine deaminase domain containing 1) is a member of theadenosinedeaminaseacting onRNAs (Adar) protein family with germ cell-specific expression. In mice, Adad1 is necessary for sperm differentiation, however its function outside of mammals has not been investigated. Here, through an N-ethyl-N-nitrosourea (ENU) based forward genetic screen, we identified anadad1mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish, however germ cells populated the gonad, proliferated, and entered meiosis in larval and juvenile fish. Although meiosis was initiated inadad1mutant testes, the spermatocytes failed to progress beyond the zygotene stage. Thus, Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using a label retaining cell (LRC) assay and found that the mutant testes had fewer LRCs compared to wild-type siblings, suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by adulthood. To identify potential molecular processes regulated by Adad1, we sequenced bulk mRNA from mutants and wild-type testes and found mis-regulation of genes involved in RNA stability and modification, pointing to a potential broader role in post-transcriptional regulation. Our findings suggest that Adad1 is an RNA regulatory protein required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.Author SummaryInfertility is a serious problem for millions of couples who wish to have children. Globally more than 10% of couples suffer from infertility due to genetic, epigenetic, and environmental factors. Among these about 50% of cases occur due to genetic factors such as aneuploidy and genetic mutations affecting development of the gametes (i.e. sperm and eggs). Although many genes are known to be involved in germ cell development, genetic causes of infertility are still largely unexplained. Therefore, it is imperative to investigate genes involved in reproductive processes. In this study, we report that theadad1gene is essential for germ cell maintenance and fertility in zebrafish. Our analysis of zebrafishadad1mutants demonstrates that it is required for maintenance of the germline stem cells and for completion of meiosis. This is in contrast to mouseAdad1, which functions later in gamete development to regulate differentiation of haploid sperm. Our work on zebrafishadad1has uncovered previously unknown roles ofadad1function in germline stem cell maintenance.