bluuebunny/crossref_metadata_2025 huggingface dataset:
Selection for increased tibia length in mice alters skull shape through parallel changes in developmental mechanisms
Authors: Unger Colton M. , Devine Jay , Hallgrímsson Benedikt , Rolian Campbell
Published: October 2020

Bones in the vertebrate cranial base and limb skeleton grow by endochondral ossification, under the control of growth plates. Mechanisms of endochondral ossification are conserved across growth plates, which increases covariation in size and shape among bones, and in turn may lead to correlated changes in skeletal traits not under direct selection. We used micro-CT and geometric morphometrics to characterize shape changes in the cranium of the Longshanks mouse, which was selectively bred for longer tibiae. We show that Longshanks skulls became longer, flatter, and narrower in a stepwise process. Moreover, we show that these morphological changes likely resulted from developmental changes in the growth plates of the Longshanks cranial base, mirroring changes observed in its tibia. Thus, indirect and non-adaptive morphological changes can occur due to developmental overlap among distant skeletal elements, with important implications for interpreting the evolutionary history of vertebrate skeletal form.
HiCORE: Hi-C analysis for identification of core chromatin loops with higher resolution and reliability
Authors: Lee Hongwoo , Seo Pil Joon
Published: October 2020

Genome-wide chromosome conformation capture (3C)-based high-throughput sequencing (Hi-C) has enabled identification of genome-wide chromatin loops. Because the Hi-C map with restriction fragment resolution is intrinsically associated with sparsity and stochastic noise, Hi-C data are usually binned at particular intervals; however, the binning method has limited reliability, especially at high resolution. Here, we describe a new method called HiCORE, which provides simple pipelines and algorithms to overcome the limitations of single-layered binning and predict core chromatin regions with 3D physical interactions. In this approach, multiple layers of binning with slightly shifted genome coverage are generated, and interacting bins at each layer are integrated to infer narrower regions of chromatin interactions. HiCORE predicts chromatin looping regions with higher resolution and contributes to the identification of the precise positions of potential genomic elements.

Author Summary

The Hi-C analysis has enabled to obtain information on 3D interaction of genomes. While various approaches have been developed for the identification of reliable chromatin loops, binning methods have been limitedly improved. We here developed HiCORE algorithm that generates multiple layers of bin-array and specifies core chromatin regions with 3D interactions. We validated our algorithm and provided advantages over conventional binning method. Overall, HiCORE facilitates to predict chromatin loops with higher resolution and reliability, which is particularly relevant in analysis of small genomes.
Inhibiting the mitochondrial pyruvate carrier does not ameliorate synucleinopathy in the absence of inflammation or metabolic deficits
Authors: Peelaerts Wouter , Bergkvist Liza , George Sonia , Johnson Michaela , Meyerdirk Lindsay , Ku Emily , Steiner Jennifer A. , Madaj Zachary , Ma Jiyan , Becker Katelyn , Nilsson K. Peter R. , Colca Jerry , Brundin Patrik
Published: October 2020

Epidemiological studies suggest a link between type-2 diabetes and Parkinson’s disease (PD) risk. Treatment of type-2 diabetes with insulin sensitizing drugs lowers the risk of PD. We previously showed that the insulin sensitizing drug, MSDC-0160, ameliorates pathogenesis in some animal models of PD. MSDC-0160 reversibly binds the mitochondrial pyruvate carrier (MPC) protein complex, which has an anti-inflammatory effect and restores metabolic deficits. Since PD is characterized by the deposition of α-synuclein (αSyn), we hypothesized that inhibiting the MPC might directly inhibit αSyn aggregationin vivoin mammals. To answer if modulation of MPC can reduce the development of αSyn assemblies, and reduce neurodegeneration, we treated two chronic and progressive mouse models; a viral vector-based αSyn overexpressing model and a pre-formed fibril (PFF) αSyn seeding model with MSDC-0160. These two models present with distinct types of αSyn pathology but lack inflammatory or autophagy deficits. Contrary to our hypothesis, we found that a modulation of MPC in these models did not reduce the accumulation αSyn aggregates or mitigate neurotoxicity. Instead, MSDC-0160 changed the post-translational modification and aggregation features of the αSyn. These results are consistent with the lack of a direct effect on MPC modulation on synuclein clearance in these models.
Genome-wide association study reveals the genetic architecture of 27 yield-related traits in tomato
Authors: Ye Jie , Wang Xin , Wang Wenqian , Yu Huiyang , Ai Guo , Li Changxing , Sun Pengya , Wang Xianyu , Li Hanxia , Ouyang Bo , Zhang Junhong , Zhang Yuyang , Giovannoni James J. , Fei Zhangjun , Ye Zhibiao
Published: October 2020

Tomato (Solanum lycopersicum) is a highly valuable vegetable crop and yield is one of the most important traits. Uncovering the genetic architecture of yield-related traits in tomato is critical for the management of vegetative and reproductive development, thereby enhancing yield. Here we perform a comprehensive genome-wide association study for 27 yield-related traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many reported and novel genes related to vegetative and reproductive development, were identified, and these loci explained an average of ∼8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection, especially during tomato improvement. Furthermore, a candidate gene,SlALMT15that encodes an aluminum-activated malate transporter, was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation through increasing photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding.
Single-cell multimodal profiling of proteins and chromatin accessibility using PHAGE-ATAC
Authors: Fiskin Evgenij , Lareau Caleb A , Eraslan Gökcen , Ludwig Leif S , Regev Aviv
Published: October 2020

Multi-modal measurements of single cell profiles are a powerful tool for characterizing cell states and regulatory mechanisms. While current methods allow profiling of RNA along with either chromatin or protein levels, connecting chromatin state to protein levels remains a barrier. Here, we developed PHAGE-ATAC, a method that uses engineered camelid single-domain antibody (‘nanobody’)-displaying phages for simultaneous single-cell measurement of surface proteins, chromatin accessibility profiles, and mtDNA-based clonal tracing through a massively parallel droplet-based assay of single-cell transposase-accessible chromatin with sequencing (ATAC-seq). We demonstrate PHAGE-ATAC for multimodal analysis in primary human immune cells and for sample multiplexing. Finally, we construct a synthetic high-complexity phage library for selection of novel antigen-specific nanobodies that bind cells of particular molecular profiles, opening a new avenue for protein detection, cell characterization and screening with single-cell genomics.
Endogenous Galectin-3 is Required for Skeletal Muscle Repair
Authors: Cerri Daniel Giuliano , Rodrigues Lilian Cataldi , Alves Vani Maria , Machado Juliano , Bastos Víctor Alexandre Félix , do Carmo Kettelhut Isis , Alberici Luciane Carla , Stowell Sean R. , Costa Maria Cristina R. , Cummings Richard D. , Dias-Baruffi Marcelo
Published: October 2020

Skeletal muscle has the intrinsic ability to self-repair through a multifactorial process, but many aspects of its cellular and molecular mechanisms are not fully understood. There is increasing evidence that some members of the mammalian β-galactoside-binding protein family (galectins) are involved in the muscular repair process (MRP), including galectin-3 (Gal-3). However, there are many questions about the role of this protein on muscle self-repair. Here, we demonstrate that endogenous Gal-3 is required for: i) muscle repairin vivousing a chloride-barium myolesion mouse model, and ii) mouse primary myoblasts myogenic programming. Injured muscle from Gal-3 knockout mice (GAL3KO) showed persistent inflammation associated with compromised muscle repair and the formation of fibrotic tissue on the lesion site. InGAL3KOmice, osteopontin expression remained high even after 7 and 14 days of the myolesion, while MyoD and myogenin had decreased their expression. InGAL3KOmouse primary myoblast cell culture, Pax7 detection seems to sustain even when cells are stimulated to differentiation and MyoD expression is drastically reduced. These findings suggest that the detection and temporal expression levels of these transcriptional factors appear to be altered in Gal-3-deficient myoblast cell culture compared to Wild Type (WT) cells. We observed Gal-3 expression in WT states, bothin vivoandin vitro, in sarcoplasm/cytoplasm and myonuclei; as differentiation proceeds, Gal-3 expression is drastically reduced, and its location is confined to the sarcolemma/plasma cell membrane. We also observed a change in the temporal-spatial profile of Gal-3 expression and muscle transcription factors levels during the myolesion. Overall, these results demonstrate that endogenous Gal-3 is required for the skeletal muscle repair process.
Phages weaponize their bacteria with biosynthetic gene clusters
Authors: Dragoš Anna , Andersen Aaron J.C. , Lozano-Andrade Carlos N. , Kempen Paul J. , Kovács Ákos T. , Strube Mikael Lenz
Published: October 2020

Bacteria produce many different specialized metabolites, which are encoded by biosynthetic gene clusters (BGCs). Despite high industrial relevance owing to broad bioactive potential of these metabolites, their ecological roles remain largely unexplored. We analyze all available genomes for BGCs of phage origin. The BGCs predominantly reside within temperate phages infecting certain commensal and pathogenic bacteria. Nearly all phage BGCs encode bacteriocins, which appear to serve as a strong proxy for phage specificity. Using the gut-associated bacteriumBacillus subtilis, we demonstrate how a temperate phage equips its host with a functional BGC, providing it with a competitive fitness advantage over close relatives. Therefore, certain temperate phages use BGCs to weaponize their bacteria against close relatives, leading to evolutionary benefits from lysogeny to the infected host, and hence, to the phage itself. Our study is a large step towards understanding the natural role of specialized metabolites, as well as mutualistic phage-host relationships.
Advax adjuvant formulations promote protective immunity against aerosolMycobacterium tuberculosisin the absence of deleterious inflammation and reactogenicity
Authors: Quan Diana H. , Counoupas Claudio , Nagalingam Gayathri , Pinto Rachel , Petrovsky Nikolai , Britton Warwick J. , Triccas James A.
Published: October 2020

The development of safe and effective adjuvants is a critical goal of vaccine development programs. In this report, we defined the immunostimulatory profile and protective effect against aerosolMycobacterium tuberculosisinfection of vaccine formulations incorporating the semi-crystalline adjuvant δ-inulin (Advax). Advax formulated with CpG oligonucleotide and the QS-21 saponin (AdvaxCpQS) was the most effective combination, demonstrated by the capacity of CysVac2/AdvaxCpQSto significantly reduce the bacterial burden in the lungs ofM. tuberculosis-infected mice. CysVac2/AdvaxCpQSprotection was associated with rapid influx of neutrophils, macrophages and monocytes to the site of vaccination and the induction of antigen-specific IFN-γ+/IL-2+/TNF+polyfunctional CD4+T cells in the lung. When compared to the highly potent adjuvant combination of monophosphoryl lipid A and dimethyldioctadecylammonium bromide (MPL/DDA), AdvaxCpQSimparted a similar level of protective efficacy yet without the profound stimulation of inflammatory cytokines and vaccination site ulceration observed with MPL/DDA. Addition of DDA to CysVac2/ AdvaxCpQSfurther improved the protective effect of the vaccine, which correlated with increased polyfunctional CD4+T cells in the lung but with no increase in vaccine reactogenicity. The data demonstrate that Advax formulations can decouple protective tuberculosis immunity from reactogenicity, making them ideal candidates for human application.

Highlights

Advax adjuvant formulations improve pulmonary protection against aerosolMycobacterium tuberculosisinfection

Different combinations of adjuvant components markedly influence the level of protection observed

Protection is associated with the rapid influx of myeloid cells to the site of vaccination and the induction of antigen-specific polyfunctional CD4+T cells in the lung.

Advax formulations abrogate vaccine-site ulceration and inflammatory cytokine production
The history and evolution of the Denisovan-EPAS1haplotype in Tibetans
Authors: Zhang Xinjun , Witt Kelsey , Ko Amy , Yuan Kai , Xu Shuhua , Nielsen Rasmus , Huerta-Sanchez Emilia
Published: October 2020

Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high altitude environments on the Tibetan Plateau. Specifically, theEPAS1gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here we leverage data fromEPAS1in 78 Tibetan individuals to interrogate which of these two introgression events introduced theEPAS1beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 43,000 (15,700–60,000) years ago, and selection started 12,000 (1,925-50,000) years ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.
Investigating autism associated genes inC. elegansreveals candidates with a role in social behaviour
Authors: Rawsthorne Helena , Calahorro Fernando , Holden-Dye Lindy , O’ Connor Vincent , Dillon James
Published: October 2020

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterised by a triad of behavioural impairments and includes disruption in social behaviour. ASD has a clear genetic underpinning and hundreds of genes are implicated in its aetiology. However, how single penetrant genes disrupt activity of neural circuits which lead to affected behaviours is only beginning to be understood and less is known about how low penetrant genes interact to disrupt emergent behaviours. Investigations are well served by experimental approaches that allow tractable investigation of the underpinning genetic basis of circuits that control behaviours that operate in the biological domains that are neuro-atypical in autism. The model organismC. elegansprovides an experimental platform to investigate the effect of genetic mutations on behavioural outputs including those that impact social biology. Here we use progeny-derived social cues that modulateC. elegansfood leaving to assay genetic determinants of social behaviour. We used the SAFRI Gene database to identifyC. elegansorthologues of human ASD associated genes. We identified a number of mutants that displayed selective deficits in response to progeny. The genetic determinants of this complex social behaviour highlight the important contribution of synaptopathy and implicates genes within cell signalling, epigenetics and phospholipid metabolism functional domains. The approach overlaps with a growing number of studies that investigate potential molecular determinants of autism inC. elegans. However, our use of a complex, sensory integrative, emergent behaviour provides routes to enrich new or underexplored biology with the identification of novel candidate genes with a definable role in social behaviour.
The role of innovation in the relationship between university–industry collaboration in R&D and ISO 9001
Authors: Aldabbas Hazem , Pinnington Ashly , Lahrech Abdelmounaim
Published: October 2020

Purpose

This study aims to investigate the relationship between university–industry collaboration (U-I-C) in research and development (R&D) and quality management and explore how the relationship is mediated by innovation.

Design/methodology/approach

Based on panel data consisting of 109 countries spanning over a five year period (2013-2017) this study investigates, through structural equation modelling, how this relationship is mediated by innovation.

Findings

The main finding is that there are positive significant direct effects between U-I-C and innovation and between innovation and international organization for standardization (ISO) 9001. Furthermore, the strength and significance of these relations are highly affected by the classification of income in these countries, which ranges from high and upper-middle to lower-middle categories. This paper concludes that countries in the high-income category have higher achievement in U-I-C in R&D, innovation and ISO 9001 when compared to the upper and lower-middle-income categories.

Originality/value

This paper demonstrates in the empirical study the value of collaboration in R&D between government, industry and academia, as it can encourage scientific research and contribute to quality management and innovation. This research is one of the very few studies to assess the country’s income classification effect on U-I-C in R&D, innovation and ISO 9001. It is recommended that more research is conducted on how countries not ranked in the high-income category could benefit from U-I-C in R&D to enhance innovation and quality management.
Numerical analysis of reinforced concrete beams strengthened in shear using carbon fiber reinforced polymer materials
Authors: Barour Sabiha , Zergua Abdesselam
Published: October 2020

Purpose

This paper aims to analyze the performance of reinforced concrete (RC) beams strengthened in shear with carbon fiber-reinforced polymer (CFRP) sheets subjected to four-point bending.

Design/methodology/approach

ANSYS software is used to build six models. In addition, SOILD65, LINK180, SHELL181 and SOLID185 elements are used, respectively, to model concrete, steel reinforcement, polymer and steel plate support. A comparative study between the nonlinear finite element and analytical models, including the ACI 440.2 R-08 and FIB14 models as well as experimental data, is also carried out.

Findings

The comparative study of the nonlinear finite element results with analytical models shows that the difference between the predicted load capacity ranges from 4.44%–24.49% in the case of the ACI 440.2 R-08 model, while the difference for FIB14 code ranges from 2.69%–26.03%. It is clear that there is a good agreement between the nonlinear finite element analysis (NLFEA) results and the different expected CFRP codes.

Practical implications

This model can be used to explore the behavior and predict the RC beams strengthened in shear with different CFRP properties. They could be used as a numerical platform in contrast to expensive and time-consuming experimental tests.

Originality/value

On the basis of the results, a good match is found between the model results and the experimental data at all stages of loading the tested samples. Load capacities as well as load deflection curves are also presented. It is concluded that the differences between the loads at failure ranged from 0.09%–6.16% and 0.56%–4.98%, comparing with experimental study. In addition, the increase in compressive strength produces an increase in the ultimate load capacity of the beam. The difference in the ultimate load capacity was less than 30% when compared with the American Concrete Institute and FIB14 codes.
Behavior and detection method influence detection probability of a translocated, endangered amphibian
Authors: Hammond Talisin T. , Curtis Michelle J. , Jacobs Leah E. , Tobler Mathias W. , Swaisgood Ronald R. , Shier Debra M.
Published: October 2020

Accurate estimates of survival are crucial for many management decisions in translocation programs. Maximizing detection probabilities and reducing sampling biases for released animals can aid in estimates of survival. One important source of sampling bias is an animal’s behavior. For example, individuals that are consistently more exploratory or active may be more likely to be detected visually. Behavioral traits can be related to survival after reintroduction, and because many pre‐release treatments aim to manipulate animal behavior, it is critical to tease apart relationships between behavior and detection probability. Here, we assessed the repeatability (intra‐individual consistency and inter‐individual variation) of behavioral traits for an endangered amphibian, the mountain yellow‐legged frog (Rana muscosa). Because new technological tools offer one potential solution for reducing sampling biases while increasing detection, we also tested whether a long‐range passive integrated transponder (PIT) tag reader could enhance surveys for these individuals after translocation into the wild. After confirming that ex situ bred R. muscosa exhibit repeatable behavioral traits (repeatability = 0.25–0.41) and releasing these frogs (N = 196) into the wild, we conducted post‐release surveys visually and with the long‐range PIT tag reader. Integrating the long‐range reader into surveys improved detection probability four‐fold in comparison to visual surveys alone (~0.09 to ~0.36). Moreover, mark–recapture modeling revealed that tag reader detection probability was not biased toward detecting individuals of specific behavioral types, while visual detection was significantly related to behavioral traits. These results will enable a more accurate understanding of individual differences in post‐release success in translocations. This may be particularly important for amphibian species, which can be difficult to detect and are expected to increasingly be involved in human‐managed breeding and translocation programs due to their vulnerable conservation status.
The association of smoking status with SARS‐CoV‐2 infection, hospitalization and mortality from COVID‐19: a living rapid evidence review with Bayesian meta‐analyses (version 7)
Authors: Simons David , Shahab Lion , Brown Jamie , Perski Olga
Published: October 2020

Aims

To estimate the association of smoking status with rates of (i) infection, (ii) hospitalization, (iii) disease severity and (iv) mortality from SARS‐CoV‐2/COVID‐19 disease.

Design

Living rapid review of observational and experimental studies with random‐effects hierarchical Bayesian meta‐analyses. Published articles and pre‐prints were identified via MEDLINE and medRxiv.

Setting

Community or hospital, no restrictions on location.

Participants

Adults who received a SARS‐CoV‐2 test or a COVID‐19 diagnosis.

Measurements

Outcomes were SARS‐CoV‐2 infection, hospitalization, disease severity and mortality stratified by smoking status. Study quality was assessed (i.e. ‘good’, ‘fair’ and ‘poor’).

Findings

Version 7 (searches up to 25 August 2020) included 233 studies with 32 ‘good’ and ‘fair’ quality studies included in meta‐analyses. Fifty‐seven studies (24.5%) reported current, former and never smoking status. Recorded smoking prevalence among people with COVID‐19 was generally lower than national prevalence. Current compared with never smokers were at reduced risk of SARS‐CoV‐2 infection [relative risk (RR) = 0.74, 95% credible interval (CrI) = 0.58–0.93, τ = 0.41]. Data for former smokers were inconclusive (RR = 1.05, 95% CrI = 0.95–1.17, τ = 0.17), but favoured there being no important association (21% probability of RR ≥ 1.1). Former compared with never smokers were at somewhat increased risk of hospitalization (RR = 1.20, CrI = 1.03–1.44, τ = 0.17), greater disease severity (RR = 1.52, CrI = 1.13–2.07, τ = 0.29) and mortality (RR = 1.39, 95% CrI = 1.09–1.87, τ = 0.27). Data for current smokers were inconclusive (RR = 1.06, CrI = 0.82–1.35, τ = 0.27; RR = 1.25, CrI = 0.85–1.93, τ = 0.34; RR = 1.22, 95% CrI = 0.78–1.94, τ = 0.49, respectively), but favoured there being no important associations with hospitalization and mortality (35% and 70% probability of RR ≥ 1.1, respectively) and a small but important association with disease severity (79% probability of RR ≥ 1.1).

Conclusions

Compared with never smokers, current smokers appear to be at reduced risk of SARS‐CoV‐2 infection, while former smokers appear to be at increased risk of hospitalization, increased disease severity and mortality from COVID‐19. However, it is uncertain whether these associations are causal.
Rates of neonatal morbidity by maternal region of birth and gestational age in New South Wales, Australia 2003‐2016
Authors: Berman Ye’elah , Ibiebele Ibinabo , Randall Deborah , Torvaldsen Siranda , Nippita Tanya A. , Bowen Jennifer , Baldwin Heather J. , Todd Stephanie M. , Morris Jonathan M. , Ford Jane B. , Patterson Jillian A.
Published: October 2020

Introduction

Research suggests that neonatal morbidity differs by maternal region of birth at different gestational ages. This study aimed to determine the overall and gestation‐specific risk of neonatal morbidity by maternal region of birth, after adjustment for maternal, infant and birth characteristics, for women giving birth in New South Wales, Australia, from 2003 to 2016.

Material and methods

The study utilized a retrospective cohort study design using linked births, hospital and deaths data. Modified Poisson regression was used to determine risk with 95% confidence intervals (95% CI) of neonatal morbidity by maternal region of birth, overall and at each gestational age, compared with Australian or New Zealand‐born women giving birth at 39 weeks.

Results

There were 1 074 930 live singleton births ≥32 weeks’ gestation that met the study inclusion criteria, and 44 394 of these were classified as morbid, giving a neonatal morbidity rate of 4.13 per 100 live births. The gestational age‐specific neonatal morbidity rate declined from 32 weeks’ gestation, reaching a minimum at 39 weeks in all maternal regions of birth. The unadjusted neonatal morbidity rate was highest in South Asian‐born women at most gestations. Adjusted rates of neonatal morbidity between 32 and 44 weeks were significantly lower for babies born to East (adjusted relative risk [aRR] 0.65, 95% CI 0.62‐0.68), South‐east (aRR 0.76, 95% CI 0.73‐0.79) and West Asian‐born (aRR 0.93, 95% CI 0.88‐0.98) mothers, and higher for babies of Oceanian‐born (aRR 1.11, 95% CI 1.04‐1.18) mothers, compared with Australian or New Zealand‐born mothers. Babies of African, Oceanian, South Asian and West Asian‐born women had a lower adjusted risk of neonatal morbidity than Australian or New Zealand‐born women until 37 or 38 weeks’ gestation, and thereafter an equal or higher risk in the term and post‐term periods.

Conclusions

Maternal region of birth is an independent risk factor for neonatal morbidity in New South Wales.
Perioperative outcomes in patients undergoing robot‐assisted partial nephrectomy: Comparative assessments between complex and non‐complex renal tumors
Authors: Motoyama Daisuke , Sato Ryo , Watanabe Kyohei , Matsushita Yuto , Watanabe Hiromitsu , Matsumoto Rikiya , Ito Toshiki , Sugiyama Takayuki , Otsuka Atsushi , Miyake Hideaki
Published: October 2020

Introduction

The aim of this study was to investigate the effects of renal tumor complexity on perioperative outcomes in patients receiving robot‐assisted partial nephrectomy (RAPN).

Methods

This study included 153 consecutive patients with cT1 renal masses undergoing RAPN and analyzed their perioperative outcomes, particularly tumor complexity. In this series, cT1b, completely endophytic, hilar, and cystic tumors were considered complex tumors. Patients with tumors that met at least one of the complex criterion were placed in the complex tumor group; patients with tumors that did not meet any of the complex criteria were placed in the non‐complex tumor group.

Results

Of the 153 patients, 54 (35.3%) had complex tumors; specifically, 18 (11.8%) had cT1b tumors, 15 (9.8%) had completely endophytic tumors, 28 (18.3%) had hilar tumors, and 8 (5.2%) had cystic tumors. The non‐complex group included 99 patients (64.7%). The complex tumor group had significantly longer warm ischemia and console times than the non‐complex tumor group, but there was no significant difference between them in the achievement of the trifecta. Both warm ischemia and console times were significantly correlated with the number of complex factors. Multivariate analyses of complex factors demonstrated that completely endophytic and cT1b tumors were independently associated with warm ischemia time and console time, respectively.

Conclusions

For patients with complex tumors, RAPN may be a feasible procedure with acceptable perioperative outcomes. However, special attention should be paid to long warm ischemia and console times, particularly in those with completely endophytic and/or cT1b tumors.
Preference for inorganic sources of calcium and phosphorus by sheep as a function of need
Authors: Pedernera Mariana , Mereu Alessandro , Cromer Elaina , Villalba Juan J.
Published: October 2020

We hypothesized that ruminants discriminate among different mineral supplements and modify their selection as a function of need. Forty lambs were offered four‐way choices among P, Ca, and Mg sources: monosodium phosphate (MSP), Magnesium phosphate (MGP), Monocalcium phosphate (MCP), and Dicalcium phosphate (DCP); and two‐way choices between DCP and the other mineral sources (Baseline). Subsequently, lambs were randomly assigned to four groups (10 lambs/group) and fed rations such that levels of Ca and P were low (LCa_LP), adequate (NCa_NP), low in Ca and adequate in P (LCa_NP), or adequate in Ca and low in P (NCa_LP). Four‐ and two‐way choice tests were repeated (Post‐deficiency). During Baseline, lambs ate and preferred MSP > MGP>DCP = MCP (p < .0001), showing that they discriminated among minerals. This pattern remained during four‐way Post‐deficiency tests, but lambs in LCa_LP, LCa_NP, and NCa_LP showed increased preference for MCP, MGP, and DCP, respectively, relative to other groups and Baseline (p < .05). Some mineral preference also changed in relation to serum concentration of P and Ca. Thus, lambs discriminated among minerals and some groups modified their preferences from Baseline to Post‐deficiency choice tests, likely influenced by mineral needs, which in turn contributed to rectify mineral imbalances.
Leukocyte immunoglobulin-like receptor A3 is increased in IBD patients and functions as an anti-inflammatory modulator
Authors: Lan X , Liu F , Ma J , Chang Y , Lan X , Xiang L , Shen X , Zhou F , Zhao Q
Published: October 2020

Growing evidence shows that a homozygous 6·7-kb deletion of the novel anti-inflammatory molecule leukocyte immunoglobulin-like receptor A3 (LILRA3) is associated with many autoimmune disorders. However, its effects on pathogenesis of inflammatory bowel disease (IBD) have yet not been clarified. LILRA3 is mainly expressed in monocytes, whereas its effects on biological behaviors of monocytes have not been systematically reported. In our study, to investigate the association between LILRA3 polymorphism and IBD susceptibility, LILRA3 polymorphism was assessed in 378 IBD patients and 509 healthy controls. Quantitative real time PCR (qRT–PCR), Western blot and immunohistochemistry (IHC) were employed to detect the LILRA3 expression in IBD patient blood and intestinal samples. The human U937 monocyte cell line was employed to establish LILRA3 over-expressing cells and the effects of LILRA3 on the biological behaviors of U937 cells were systematically explored. Although no association of the polymorphism with IBD development was found, LILRA3 expression was markedly increased in IBD patients compared with healthy controls. Over-expression of LILRA3 in monocytes led to significant decreases in secretion of interferon (IFN)-γ, tumor necrosis factor (TNF)-α and interleukin (IL)-6. Additionally, LILRA3 abated monocyte migration by reducing the expression of several chemokines and enhanced monocyte phagocytosis by increasing CD36 expression. Furthermore, LILRA3 promoted monocyte proliferation through a combination of Akt and extracellular receptor kinase/mitogen-activated protein kinase (Erk/MEK) signaling pathways. We report for the first time, to our knowledge, that LILRA3 is related to IBD and functions as an anti-inflammatory modulator in U937 cells.
Underwater endoscopic papillectomy for residual tumor after endoscopic papillectomy: First report
Authors: Mori Yuki , Kurita Akira , Yazumi Shujiro
Published: October 2020

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The German bank–growth nexus revisited: savings banks and economic growth in Prussia†
Authors: Lehmann‐Hasemeyer Sibylle , Wahl Fabian
Published: October 2020

This article provides evidence that smaller, regional public financial intermediaries contributed to Germany's industrial development, using a new dataset of the foundation year and location of Prussian savings banks. This extends the bank–growth nexus beyond its traditional focus on large universal banks. Since savings banks were public financial intermediaries, our results further suggest that state intervention can be successful in the financial sector, particularly at the early stages of industrial development when capital requirements are manageable, and access to international capital markets is limited.
Genome‐wide postnatal changes in immunity following fetal inflammatory response
Authors: Costa Daniel , Bonet Núria , Solé Amanda , González de Aledo‐Castillo José Manuel , Sabidó Eduard , Casals Ferran , Rovira Carlota , Nadal Alfons , Marin Jose Luis , Cobo Teresa , Castelo Robert
Published: October 2020

The fetal inflammatory response (FIR) increases the risk of perinatal brain injury, particularly in extremely low gestational age newborns (ELGANs, < 28 weeks of gestation). One of the mechanisms contributing to such a risk is a postnatal intermittent or sustained systemic inflammation (ISSI) following FIR. The link between prenatal and postnatal systemic inflammation is supported by the presence of well‐established inflammatory biomarkers in the umbilical cord and peripheral blood. However, the extent of molecular changes contributing to this association is unknown. Using RNA sequencing and mass spectrometry proteomics, we profiled the transcriptome and proteome of archived neonatal dried blood spot (DBS) specimens from 21 ELGANs. Comparing FIR‐affected and unaffected ELGANs, we identified 782 gene and 27 protein expression changes of 50% magnitude or more, and an experiment‐wide significance level below 5% false discovery rate. These expression changes confirm the robust postnatal activation of the innate immune system in FIR‐affected ELGANs and reveal for the first time an impairment of their adaptive immunity. In turn, the altered pathways provide clues about the molecular mechanisms triggering ISSI after FIR, and the onset of perinatal brain injury.

Databases

EGAS00001003635 (EGA); PXD011626 (PRIDE).
Climate and land‐use change will lead to a faunal “savannization” on tropical rainforests
Authors: Sales Lilian P. , Galetti Mauro , Pires Mathias M.
Published: October 2020

Humans have fragmented, reduced or altered the biodiversity in tropical forests around the world. Climate and land‐use change act synergistically, increasing drought and fire frequencies, converting several tropical rainforests into derived savannas, a phenomenon known as “savannization.” Yet, we lack a full understanding of the faunal changes in response to the transformation of plant communities. We argue that the composition of vertebrate assemblages in ecotone regions of forest–savanna transitions from South America will be increasingly replaced by open savanna species, a phenomenon we name “faunal savannization.” We combined projections from ecological niche models, habitat filter masks and dispersal simulations to forecast the distribution of 349 species of forest‐ and savanna‐dwelling mammal species across South America. We found that the distribution of savanna species is likely to increase by 11%–30% and spread over lowland Amazon and Atlantic forests. Conversely, forest‐specialists are expected to lose nearly 50% of their suitable ranges and to move toward core forest zones, which may thus receive an influx of more than 60 species on the move. Our findings indicate that South American ecotonal faunas might experience high rates of occupancy turnover, in a process parallel to that already experienced by plants. Climate‐driven migrations of fauna in human‐dominated landscapes will likely interact with fire‐induced changes in plant communities to reshape the biodiversity in tropical rainforests worldwide.
Climate change‐mediated temperature extremes and insects: From outbreaks to breakdowns
Authors: Harvey Jeffrey A. , Heinen Robin , Gols Rieta , Thakur Madhav P.
Published: October 2020

Insects are among the most diverse and widespread animals across the biosphere and are well‐known for their contributions to ecosystem functioning and services. Recent increases in the frequency and magnitude of climatic extremes (CE), in particular temperature extremes (TE) owing to anthropogenic climate change, are exposing insect populations and communities to unprecedented stresses. However, a major problem in understanding insect responses to TE is that they are still highly unpredictable both spatially and temporally, which reduces frequency‐ or direction‐dependent selective responses by insects. Moreover, how species interactions and community structure may change in response to stresses imposed by TE is still poorly understood. Here we provide an overview of how terrestrial insects respond to TE by integrating their organismal physiology, multitrophic, and community‐level interactions, and building that up to explore scenarios for population explosions and crashes that have ecosystem‐level consequences. We argue that TE can push insect herbivores and their natural enemies to and even beyond their adaptive limits, which may differ among species intimately involved in trophic interactions, leading to phenological disruptions and the structural reorganization of food webs. TE may ultimately lead to outbreak–breakdown cycles in insect communities with detrimental consequences for ecosystem functioning and resilience. Lastly, we suggest new research lines that will help achieve a better understanding of insect and community responses to a wide range of CE.
PCAT18, as a novel differentially regulated long noncoding RNA in adult acute myeloid leukemia patients revealed by next‐generation sequencing
Authors: Zhang Jihong , Zhang Henan , Wang Xiaohui , Zhao Yue , Fu Yu , Liu Xuan
Published: October 2020

Introduction

Long noncoding RNAs (lncRNAs) play significant roles in the carcinogenesis and progression of human tumors. The aim of this work was to evaluate the expression level of lncRNAs in adult acute myeloid leukemia (AML) patients and to explore the function of candidate lncRNA PCAT18 in clinical diagnosis and prognosis of AML.

Methods

Noncoding RNA screening was performed by second‐generation sequencing on adult newly diagnosed AML patients and healthy controls. GO and KEGG pathway analysis were performed for functional analysis of differentially regulated lncRNAs. The expression of candidate lncRNA PCAT18 was detected by real‐time PCR. In K‐562 and THP‐1 cells, proliferation, and cell cycle analysis were performed using CCK‐8 assay and Cell Cycle Assay Kit.

Results

The lncRNA expression profile of AML patients and healthy controls showed that six upregulated (>5‐fold) and eight downregulated (<0.2‐fold) lncRNAs. The candidate lncRNA PCAT18 showed higher expression in AML patients with NPM1 mutation and favorable‐risk. RT‐PCR revealed a significant increase of PCAT18 expression comparing to control cells. PCAT18 overexpression obviously promoted cell proliferation and PCAT18 knockdown decreased cell proliferation. The fraction of the S phases was increased in the PCAT18 overexpression group and decreased in the PCAT18 knockdown group.

Conclusions

The candidate lncRNA PCAT18 in our study was firstly found upregulated in AML samples, that its overexpression promoted cell proliferation and G1/S transition. Further study of PCAT18 and its target mRNAs are needed to confirm the mechanism of PCAT18 in AML. PCAT18 may act as diagnostic and prognosis biomarker for AML.
Mitigating strategies and nursing response for cancer care management during the COVID‐19 pandemic: an Italian experience
Authors: Zeneli A. , Altini M. , Bragagni M. , Gentili N. , Prati S. , Golinucci M. , Rustignoli M. , Montalti S.
Published: October 2020

Aim

To describe our response to the COVID‐19 emergency in a cancer centre to enable other nursing organizations to determine which elements could be useful to manage a surge of patients in their own setting.

Background

The COVID‐19 pandemic represents one of the most challenging healthcare scenarios faced to date. Managing cancer care in such a complex situation requires a coordinated emergency action plan to guarantee the continuity of cancer treatments for patients by providing healthcare procedures for patients, caregivers and healthcare professionals in a safe environment.

Procedures

We describe the main strategies and role of nurses in implementating such procedures.

Results

Nurses at our hospital were actively involved in COVID‐19 response defined by the emergency action plan that positively contributed to correct social distancing and to the prevention of the spread of the virus.

Implications for nursing and health policies

Lessons learned from the response to phase I of COVID‐19 have several implications for future nursing and health policies in which nurses play an active role through their involvement in the frontline of such events. Key policies include a coordinated emergency action plan permitting duty of care within the context of a pandemic, and care pathway revision. This requires the rapid implementation of strategies and policies for a nursing response to the new care scenarios: personnel redistribution, nursing workflow revision, acquisition of new skills and knowledge, effective communication strategies, infection control policies, risk assessment and surveillance programmes, and continuous supplying of personal protective equipment. Finally, within a pandemic context, clear nursing policies reinforcing the role of nurses as patient and caregiver educators are needed to promote infection prevention behaviour in the general population.
Association between maternal height and mode of delivery in nulliparous Japanese women
Authors: Kuritani Yoshihiro , Hayashi Shusaku , Yamamoto Ryo , Mitsuda Nobuaki , Ishii Keisuke
Published: October 2020

Aim

The primary aim of this study was to examine the association between maternal height and mode of delivery in nulliparous Japanese women. The secondary aim was to examine the association between maternal height and maternal and neonatal morbidities.

Methods

This retrospective cohort study included women who gave birth at Osaka Women's and Children's Hospital, a tertiary perinatal center in Japan, from January 2015 to December 2017. Nulliparous Japanese women with singleton gestation, who went into labor at term were included in the study. The primary outcome was mode of delivery, and the secondary outcomes were maternal and neonatal morbidities. The relationships between maternal height and the outcomes were evaluated using multivariate logistic regression analysis adjusted for potential confounders. Maternal height was categorized into five groups with 5‐cm increments for the analysis.

Results

A total of 1593 women were analyzed in this study. Shorter women had higher rate of cesarean delivery (CD) than taller women. There were no significant differences in the rates of operative vaginal delivery, maternal morbidity and neonatal morbidity among the maternal‐height groups. The adjusted odds ratios (95% confidential interval) of maternal heights of <150 cm, 150–154 cm, 160–164 cm and ≥165 cm for CD, compared with a maternal height of 155–159 cm, were 3.56 (1.79–7.09), 1.68 (1.06–2.64), 0.63 (0.40–1.00) and 0.57 (0.30–1.01), respectively.

Conclusion

Shorter nulliparous Japanese women were more likely to undergo intrapartum CD. However, the rates of maternal and neonatal morbidities in shorter women were similar to those in taller women.
Magnetization transfer and diffusion tensor imaging in dogs with intervertebral disk herniation
Authors: Shinn Richard L. , Pancotto Theresa E. , Stadler Krystina L. , Werre Stephen R. , Rossmeisl John H.
Published: October 2020

Background

Quantitative magnetic resonance imaging (QMRI) techniques of magnetization transfer ratio (MTR) and diffusion tensor imaging (DTI) provide microstructural information about the spinal cord.

Objective

Compare neurologic grades using the modified Frankel scale with MTR and DTI measurements in dogs with thoracolumbar intervertebral disk herniation (IVDH).

Animals

Fifty‐one dogs with thoracolumbar IVDH.

Methods

Prospective cohort study. Quantitative MRI measurements of the spinal cord were obtained at the region of compression. A linear regression generalized estimating equations model was used to compare QMRI measurements between different neurological grades after adjusting for age, weight, duration of clinical signs, and lesion location.

Results

Grade 5 (.79  ×  10−3 mm2/s [median], .43−.91 [range]) and axial (1.47 × 10−3 mm2/s, .58−1.8) diffusivity were lower compared to grades 2 (1.003, .68−1.36; P = .02 and 1.81 × 10−3 mm2/s, 1.36−2.12; P < .001, respectively) and 3 (1.07 × 10−3 mm2/s, .77−1.5; P = .04 and 1.92 × 10−3 mm2/s, 1.83−2.37;P < .001, respectively). Compared to dogs with acute myelopathy, chronic myelopathy was associated with higher mean (1.02 × 10−3 mm2/s, .77−1.36 vs. .83 × 10−3 mm2/s, .64−1.5; P = .03) and radial diffusivity (.75 × 10−3 mm2/s, .38−1.04 vs. .44 × 10−3 mm2/s, .22−1.01; P = .008) and lower MTR (46.76, 31.8−56.43 vs. 54.4, 45.2−62.27; P = .004) and fractional anisotropy (.58, .4−0.75 vs. .7, .46−.85; P = .02). Fractional anisotropy was lower in dogs with a T2‐weighted intramedullary hyperintensity compared to those without (.7, .45−.85 vs. .54, .4−.8; P = .01).

Conclusion and Clinical Relevance

Mean diffusivity and AD could serve as surrogates of severity of spinal cord injury and are complementary to the clinical exam in dogs with thoracolumbar IVDH.