bluuebunny/crossref_metadata_2025 huggingface dataset:
Invited Commentary: Intermittent Opioid Use and Ischemic Placental Disease—Clarifying Associations With Adverse Pregnancy Outcomes
Authors: Ananth Cande V , Brandt Justin S
Published: September 2021

Discomfort and, to a lesser extent, pain are common complaints during pregnancy, and some patients may turn to opioids for pain relief. Esposito et al. (Am J Epidemiol. 2022;191(5):759–768) report associations between intermittent exposure to opioids during pregnancy and the risk of ischemic placental disease—a syndrome that includes preeclampsia, placental abruption, births that are small for gestational age, and preterm delivery. They found that early opioid exposure in pregnancy was associated with a modestly increased risk for abruption, births that are small for gestational age, and preterm delivery, and both early and late exposures were associated with the greatest risk for these outcomes. Surprisingly, preeclampsia was not associated with opioid use. Through quantitative bias analysis, the authors cleverly tackle a number of biases to assess their roles in explaining the associations, including unmeasured confounding, outcome misclassification, and residual confounding; none exerted strong influences on the associations. Although the findings appear fairly robust on the surface, the lack of association between intermittent opioid use and preeclampsia, and important differences in characteristics of patients in the opioid-exposed group compared with the unexposed group, suggest that further study is needed to clarify the relationship between intermittent opioid use, lifestyle factors, and ischemic placental disease risk.
Jewish American Literature Against the World
Authors: Schreier Benjamin
Published: September 2021

By way of a brief genealogy of the Jewish American literary field and through the lens of recent attempts to imagine how comparative literature-based thinking about a concept of “world literature” can be critically productive for Jewish literary study, this article analyzes Jewish American literary studies’ prestige problem. Because it has persistently failed to theorize the intellectual and methodological assumptions underlying its practice, Jewish American literary study remains burdened by the essentialist implications of an ethnological historicism. This article ultimately argues that Jewish American literary study needs to take more seriously the possibilities offered by a materialist epistemology rather than the Jewish studies-based historicist ontology it has mostly taken for granted.

“My hope is that a Jewish American epistemology can operate outside the penumbra of a tired and played-out concept of ethnicity—a term that unavoidably, if spectrally, posits a biologistic object at the heart of its historicist project—even as it might still claim the mantle of Jewish-y-ness.”
American Magazines and the Cultural Production of Blackness
Authors: Young John K
Published: September 2021

Eurie Dahn’s Jim Crow Networks (2021) and E. James West’s Ebony Magazine and Lerone Bennett Jr. (2020) offer compelling examples of the two main literary historical approaches to periodical studies: A survey of several different types of magazines in relation to the social networks through which they were produced, distributed, and read, and a deep dive into the editorial orientation of a particular magazine, as shaped by a dominant individual presence. Both studies present detailed accounts of how these periodicals’ publics and counterpublics resisted (and sometimes reinforced) prevailing conceptions of racialized identity at important points in the twentieth century. But the material circumstances of those productions risk being misrepresented by the model of the network, so this review essay argues for the Bakhtinian chronotope as a more expressive metaphor for the temporal dimension of the magazine experience. This approach enables a more fully historicist understanding of how the various important literary figures represented here were perceived by their original periodical readers.
‘Except God, no substance can be conceived’: Spinoza on other substances
Authors: Noorloos Ruben
Published: September 2021

This paper argues that Spinoza held substances other than God to be inconceivable. It uses this claim to develop a novel response to the Problem of Other Substances (Garrett 1979, Barry 2019), the problem of explaining why some of Spinoza’s proofs for God’s existence cannot be used to prove the existence of a non-divine substance instead.
Endotoxin in Aerosol Particles from Metalworking Fluids Measured with a Sioutas Cascade Impactor
Authors: Dahlman-Höglund Anna , Schiöler Linus , Andersson Marianne , Mattsby-Baltzer Inger , Lindgren Åsa
Published: September 2021

Objectives

The aim of this study was to characterize personal occupational exposure to endotoxin in size-separated airborne particles of MWF aerosol, using a Sioutas cascade impactor (SCI).

Methods

Exposure to inhalable fractions of MWF aerosol and endotoxin was measured by personal sampling of 52 individuals over an 8-h work shift using a PAS-6 sampler in parallel with a SCI (<0.25, 0.25–0.5, 0.5–1.0, 1.0–2.5, and 2.5–10 µm). Aerosol mass concentration was measured for each worker with a real-time instrument (DataRAM) during a full shift. Samples of MWF were collected from the machines and central tanks during the work shift.

Results

A total of 117 measurements of inhalable MWF aerosols were made among 52 workers. The geometric mean of inhalable MWF aerosol was 0.16 mg m−3 air. The geometric mean of endotoxin concentration on the inhalable sampler was 0.15 EU m−3. Airborne endotoxin was found on all size fractions from the impactor, with the major part seen in the fraction (2.5–10 µm). There was a correlation between the inhalable fraction of endotoxin measured by the PAS-6 sampler and on the SCI sampler (2.5–10 µm), estimated to be 0.51 for all samples (P < 0.0001). The concentration of endotoxin varied between the MWFs, as did the proportion of Gram-negative bacteria among the culturable bacteria (>80% in one MWF and <1.5% in the other three).

Conclusions

The personal exposure to inhalable fractions of endotoxin contained in the MWF aerosol were low, where most of the endotoxin were found in fraction (2.5–10 µm), measured by SCI. There are differences between factories and MWF systems regarding the distribution of endotoxin and so results from one context should not be generalized to other plants and systems. Compressed air was used for less than 10 min shift−1. The mixed-effect model showed that working with open machines and grinding as cutting task were important determinants of exposure to inhalable aerosol. It is important to keep occupational exposure to aerosols low with the help of good ventilation systems, enclosed machines, and organization of work.
Monthlong Intubated Patient with Life-Threatening COVID-19 and Cerebral Microbleeds Suffers Only Mild Cognitive Sequelae at 8-Month Follow-up: A Case Report
Authors: Backman Linda , Möller Marika C , Thelin Eric P , Dahlgren Daniel , Deboussard Catharina , Östlund Gunilla , Lindau Maria
Published: September 2021

Objective

To elaborate on possible cognitive sequelae related to COVID-19, associated cerebrovascular injuries as well as the general consequences from intensive care. COVID-19 is known to have several, serious CNS-related consequences, but neuropsychological studies of severe COVID-19 are still rare.

Methods

M., a 45-year-old man, who survived a severe COVID-19 disease course including Acute Respiratory Distress Syndrome (ARDS), cerebral microbleeds, and 35 days of mechanical ventilation, is described. We elaborate on M’s recovery and rehabilitation process from onset to the 8-month follow-up. The cognitive functions were evaluated with a comprehensive screening battery at 4 weeks after extubation and at the 8-month follow-up.

Results

Following extubation, M. was delirious, reported visual hallucinations, and had severe sleeping difficulties. At about 3 months after COVID-19 onset, M. showed mild to moderate deficits on tests measuring processing speed, working memory, and attention. At assessments at 8 months, M. performed better, with results above average on tests measuring learning, memory, word fluency, and visuospatial functions. Minor deficits were still found regarding logical reasoning, attention, executive functioning, and processing speed. There were no lingering psychiatric symptoms. While M. had returned to a part-time job, he was not able to resume previous work-tasks.

Conclusion

This case-study demonstrates possible cognitive deficits after severe COVID-19 and emphasizes the need of a neuropsychological follow-up, with tests sensitive to minor deficits. The main findings of this report provide some support that the long-term prognosis for cognition in severe COVID-19 may be hopeful.
Overexpression of AGR2vH, an oncogenic AGR2 spliced transcript, potentiates tumorigenicity and proteomic alterations in cholangiocarcinoma cell
Authors: Yosudjai Juthamas , Inpad Chaturong , Pothipan Phattarin , Saisomboon Saowaluk , Surangkul Damrasamon , Phimsen Suchada , Hongsrichan Nuttanan , Wongkham Sopit , Jirawatnotai Siwanon , Roytrakul Sittiruk , Kaewkong Worasak
Published: September 2021

The upregulation of anterior gradient 2 (AGR2) has been observed in cholangiocarcinoma (CCA) cells, nras-mutant zebrafish, and specimens derived from CCA patients. Our previous study reported AGR2 splicing into AGR2vH to facilitate CCA cell aggressiveness, while this work aims to investigate the molecular mechanisms underlying AGR2vH. First, AGR2vH upregulation was demonstrated in CCA tissues derived from patients. For in vitro studies, established AGR2vH-overexpressing KKU-213A cells were found to exhibit increased proliferation and clonogenicity. In vivo tumorigenicity assessed in a mouse model represented higher tumorigenic potential in AGR2vH-overexpressing cell xenograft mice. Next, LC-MS/MS was analyzed, indicating that AGR2vH may be associated with CCA cell proliferation via Wnt/β-catenin signaling pathway activation, which was verified by β-catenin expression and nuclear translocation. The current results provide evidence that AGR2vH upregulation promotes tumorigenicity in CCA cells linked with an alteration of CCA cell proteome.
Perceived risk structures the space use of competing carnivores
Authors: Rodriguez Curras Mauriel , Donadío Emiliano , Middleton Arthur D , Pauli Jonathan N
Published: September 2021

Competition structures ecological communities. In carnivorans, competitive interactions are disproportionately costly to subordinate carnivores who must account for the risk of interspecific killing when foraging. Accordingly, missed opportunity costs for meso-carnivores imposed by risk can benefit the smallest-bodied competitors. However, the extent to which the risk perpetuates into spatial partitioning in hierarchically structured communities remains unknown. To determine how risk-avoidance behaviors shape the space-use of carnivore communities, we studied a simple community of carnivores in northern Patagonia, Argentina: pumas (Puma concolor; an apex carnivore), culpeo foxes (Lycalopex culpaeus; a meso-carnivore), and chilla foxes (Lycalopex griseus; a small carnivore). We used multi-species occupancy models to quantify the space use within the carnivore community and giving-up densities to understand the behaviors that structure space use. Notably, we applied an analytical framework that tests whether the actual or perceived risk of predation most strongly influences the space use of subordinate carnivores although accounting for their foraging and vigilance behaviors. We found that there was a dominance hierarchy from the apex carnivore through the meso-carnivore to the subordinate small carnivore, which was reflected in space. Although both meso- and small carnivores exhibited similar predator avoidance behavioral responses to apex carnivores, the habitat associations of apex carnivores only altered meso-carnivore space use. The biases in risk management we observed for meso-carnivores likely translates into stable co-existence of this community of competing carnivores. We believe our analytical framework can be extended to other communities to quantify the spatial-behavioral tradeoffs of risk.
Emergence and repeatability of leadership and coordinated motion in fish shoals
Authors: Georgopoulou Dimitra G , King Andrew J , Brown Rowan M , Fürtbauer Ines
Published: September 2021

Studies of self-organizing groups like schools of fish or flocks of birds have sought to uncover the behavioral rules individuals use (local-level interactions) to coordinate their motion (global-level patterns). However, empirical studies tend to focus on short-term or one-off observations where coordination has already been established or describe transitions between different coordinated states. As a result, we have a poor understanding of how behavioral rules develop and are maintained in groups. Here, we study the emergence and repeatability of coordinated motion in shoals of stickleback fish (Gasterosteus aculeatus). Shoals were introduced to a simple environment, where their spatio-temporal position was deduced via video analysis. Using directional correlation between fish velocities and wavelet analysis of fish positions, we demonstrate how shoals that are initially uncoordinated in their motion quickly transition to a coordinated state with defined individual leader-follower roles. The identities of leaders and followers were repeatable across two trials, and coordination was reached more quickly during the second trial and by groups of fish with higher activity levels (tested before trials). The rapid emergence of coordinated motion and repeatability of social roles in stickleback fish shoals may act to reduce uncertainty of social interactions in the wild, where individuals live in a system with high fission-fusion dynamics and non-random patterns of association.
A network embedding framework based on integrating multiplex network for drug combination prediction
Authors: Yu Liang , Xia Mingfei , An Qi
Published: September 2021

Drug combination is a sensible strategy for disease treatment because it improves the treatment efficacy and reduces concomitant side effects. Due to the large number of possible combinations among candidate compounds, exhaustive screening is prohibitive. Currently, a large number of studies have focused on predicting potential drug combinations. However, these methods are not entirely satisfactory in terms of performance and scalability. In this paper, we proposed a Network Embedding frameWork in MultIplex Network (NEWMIN) to predict synthetic drug combinations. Based on a multiplex drug similarity network, we offered alternative methods to integrate useful information from different aspects and to decide the quantitative importance of each network. For drug combination prediction, we found seven novel drug combinations that have been validated by external sources among the top-ranked predictions of our model. To verify the feasibility of NEWMIN, we compared NEWMIN with other five methods, for which it showed better performance than other methods in terms of the area under the precision-recall curve and receiver operating characteristic curve.
Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation
Authors: Wang Tao , Liu Yongzhuang , Yin Quanwei , Geng Jiaquan , Chen Jin , Yin Xipeng , Wang Yongtian , Shang Xuequn , Tian Chunwei , Wang Yadong , Peng Jiajie
Published: September 2021

Quantitative trait locus (QTL) analyses of multiomic molecular traits, such as gene transcription (eQTL), DNA methylation (mQTL) and histone modification (haQTL), have been widely used to infer the functional effects of genome variants. However, the QTL discovery is largely restricted by the limited study sample size, which demands higher threshold of minor allele frequency and then causes heavy missing molecular trait–variant associations. This happens prominently in single-cell level molecular QTL studies because of sample availability and cost. It is urgent to propose a method to solve this problem in order to enhance discoveries of current molecular QTL studies with small sample size. In this study, we presented an efficient computational framework called xQTLImp to impute missing molecular QTL associations. In the local-region imputation, xQTLImp uses multivariate Gaussian model to impute the missing associations by leveraging known association statistics of variants and the linkage disequilibrium (LD) around. In the genome-wide imputation, novel procedures are implemented to improve efficiency, including dynamically constructing a reused LD buffer, adopting multiple heuristic strategies and parallel computing. Experiments on various multiomic bulk and single-cell sequencing-based QTL datasets have demonstrated high imputation accuracy and novel QTL discovery ability of xQTLImp. Finally, a C++ software package is freely available at https://github.com/stormlovetao/QTLIMP.
NiPTUNE: an automated pipeline for noninvasive prenatal testing in an accurate, integrative and flexible framework
Authors: Duboc Véronique , Pratella David , Milanesio Marco , Boudjarane John , Descombes Stéphane , Paquis-Flucklinger Véronique , Bottini Silvia
Published: September 2021

Noninvasive prenatal testing (NIPT) consists of determining fetal aneuploidies by quantifying copy number alteration from the sequencing of cell-free DNA (cfDNA) from maternal blood. Due to the presence of cfDNA of fetal origin in maternal blood, in silico approaches have been developed to accurately predict fetal aneuploidies. Although NIPT is becoming a new standard in prenatal screening of chromosomal abnormalities, there are no integrated pipelines available to allow rapid, accurate and standardized data analysis in any clinical setting. Several tools have been developed, however often optimized only for research purposes or requiring enormous amount of retrospective data, making hard their implementation in a clinical context. Furthermore, no guidelines have been provided on how to accomplish each step of the data analysis to achieve reliable results. Finally, there is no integrated pipeline to perform all steps of NIPT analysis.

To address these needs, we tested several tools for performing NIPT data analysis. We provide extensive benchmark of tools performances but also guidelines for running them. We selected the best performing tools that we benchmarked and gathered them in a computational pipeline. NiPTUNE is an open source python package that includes methods for fetal fraction estimation, a novel method for accurate gender prediction, a principal component analysis based strategy for quality control and fetal aneuploidies prediction. NiPTUNE is constituted by seven modules allowing the user to run the entire pipeline or each module independently. Using two cohorts composed by 1439 samples with 31 confirmed aneuploidies, we demonstrated that NiPTUNE is a valuable resource for NIPT analysis.
The substitution spectra of coronavirus genomes
Authors: Forni Diego , Cagliani Rachele , Pontremoli Chiara , Clerici Mario , Sironi Manuela
Published: September 2021

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has triggered an unprecedented international effort to sequence complete viral genomes. We leveraged this wealth of information to characterize the substitution spectrum of SARS-CoV-2 and to compare it with those of other human and animal coronaviruses.

We show that, once nucleotide composition is taken into account, human and most animal coronaviruses display a mutation spectrum dominated by C to U and G to U substitutions, a feature that is not shared by other positive-sense RNA viruses. However, the proportions of C to U and G to U substitutions tend to decrease as divergence increases, suggesting that, whatever their origin, a proportion of these changes is subsequently eliminated by purifying selection. Analysis of the sequence context of C to U substitutions showed little evidence of apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC)-mediated editing and such contexts were similar for SARS-CoV-2 and Middle East respiratory syndrome coronavirus sampled from different hosts, despite different repertoires of APOBEC3 proteins in distinct species. Conversely, we found evidence that C to U and G to U changes affect CpG dinucleotides at a frequency higher than expected. Whereas this suggests ongoing selective reduction of CpGs, this effect alone cannot account for the substitution spectra. Finally, we show that, during the first months of SARS-CoV-2 pandemic spread, the frequency of both G to U and C to U substitutions increased. Our data suggest that the substitution spectrum of SARS-CoV-2 is determined by an interplay of factors, including intrinsic biases of the replication process, avoidance of CpG dinucleotides and other constraints exerted by the new host.
ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features
Authors: Hippe Kyle , Lilley Cade , William Berkenpas Joshua , Chandana Pocha Ciri , Kishaba Kiyomi , Ding Hui , Hou Jie , Si Dong , Cao Renzhi
Published: September 2021

Motivation

The Estimation of Model Accuracy problem is a cornerstone problem in the field of Bioinformatics. As of CASP14, there are 79 global QA methods, and a minority of 39 residue-level QA methods with very few of them working on protein complexes. Here, we introduce ZoomQA, a novel, single-model method for assessing the accuracy of a tertiary protein structure/complex prediction at residue level, which have many applications such as drug discovery. ZoomQA differs from others by considering the change in chemical and physical features of a fragment structure (a portion of a protein within a radius $r$ of the target amino acid) as the radius of contact increases. Fourteen physical and chemical properties of amino acids are used to build a comprehensive representation of every residue within a protein and grade their placement within the protein as a whole. Moreover, we have shown the potential of ZoomQA to identify problematic regions of the SARS-CoV-2 protein complex.

Results

We benchmark ZoomQA on CASP14, and it outperforms other state-of-the-art local QA methods and rivals state of the art QA methods in global prediction metrics. Our experiment shows the efficacy of these new features and shows that our method is able to match the performance of other state-of-the-art methods without the use of homology searching against databases or PSSM matrices.

Availability

http://zoomQA.renzhitech.com
Ferroptosis-related lncRNA pairs to predict the clinical outcome and molecular characteristics of pancreatic ductal adenocarcinoma
Authors: Tang Rong , Wu Zijian , Rong Zeyin , Xu Jin , Wang Wei , Zhang Bo , Yu Xianjun , Shi Si
Published: September 2021

Ferroptosis is a form of regulated cell death initiated by oxidative perturbations that can be blocked by iron chelators and lipophilic antioxidants, and ferroptosis may be the silver bullet treatment for multiple cancers, including immunotherapy- and chemotherapy-insensitive cancers such as pancreatic ductal adenocarcinoma (PDAC). Numerous studies have noted that long non-coding RNAs (lncRNAs) regulate the biological behaviour of cancer cells by binding to DNA, RNA and protein. However, few studies have reported the role of lncRNAs in ferroptosis processes and the function of ferroptosis-associated lncRNAs.

The primary objective of the present study was to identify ferroptosis-related lncRNAs using bioinformatic approaches combined with experimental validation. The second objective was to construct a prognostic model to predict the overall survival of patients with PDAC. The present study identified ferroptosis-related lncRNAs using a bioinformatic approach and validated them in an independent pancreatic cancer cohort from Fudan University Shanghai Cancer Center. The lncRNA SLCO4A1-AS1 was identified as a novel molecule mediating ferroptosis resistance in vitro. A novel algorithm was used to construct a ‘0 or 1’ matrix-based prognosis model, which showed promising diagnostic accuracy for potential clinical translation (area under the curve = 0.89 for the 2-year survival rate). Notably, molecular subtypes classified by the risk scores of the model did not belong to any previously reported subtypes of PDAC. The immune microenvironment, metabolic activities, mutation landscape and ferroptosis sensitivity were significantly distinct between patients with different risk scores. Sensitivity (IC50) to 30 common anticancer drugs was analysed between patients with different risks, and imatinib and axitinib were found to be potential drugs for the treatment of patients with lower risk scores. Overall, we developed an accurate prognostic model based on the expression patterns of ferroptosis lncRNAs, which may contribute greatly to the evaluation of patient prognosis, molecular characteristics and treatment modalities and could be further translated into clinical applications.
A versatile and scalable single-cell data integration algorithm based on domain-adversarial and variational approximation
Authors: Hu Jialu , Zhong Yuanke , Shang Xuequn
Published: September 2021

Single-cell technologies provide us new ways to profile transcriptomic landscape, chromatin accessibility, spatial expression patterns in heterogeneous tissues at the resolution of single cell. With enormous generated single-cell datasets, a key analytic challenge is to integrate these datasets to gain biological insights into cellular compositions. Here, we developed a domain-adversarial and variational approximation, DAVAE, which can integrate multiple single-cell datasets across samples, technologies and modalities with a single strategy. Besides, DAVAE can also integrate paired data of ATAC profile and transcriptome profile that are simultaneously measured from a same cell. With a mini-batch stochastic gradient descent strategy, it is scalable for large-scale data and can be accelerated by GPUs. Results on seven real data integration applications demonstrated the effectiveness and scalability of DAVAE in batch-effect removing, transfer learning and cell-type predictions for multiple single-cell datasets across samples, technologies and modalities. Availability: DAVAE has been implemented in a toolkit package “scbean” in the pypi repository, and the source code can be also freely accessible at https://github.com/jhu99/scbean. All our data and source code for reproducing the results of this paper can be accessible at https://github.com/jhu99/davae_paper.
BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer
Authors: Huang Neng , Nie Fan , Ni Peng , Gao Xin , Luo Feng , Wang Jianxin
Published: September 2021

Long-read sequencing technology enables significant progress in de novo genome assembly. However, the high error rate and the wide error distribution of raw reads result in a large number of errors in the assembly. Polishing is a procedure to fix errors in the draft assembly and improve the reliability of genomic analysis. However, existing methods treat all the regions of the assembly equally while there are fundamental differences between the error distributions of these regions. How to achieve very high accuracy in genome assembly is still a challenging problem. Motivated by the uneven errors in different regions of the assembly, we propose a novel polishing workflow named BlockPolish. In this method, we divide contigs into blocks with low complexity and high complexity according to statistics of aligned nucleotide bases. Multiple sequence alignment is applied to realign raw reads in complex blocks and optimize the alignment result. Due to the different distributions of error rates in trivial and complex blocks, two multitask bidirectional Long short-term memory (LSTM) networks are proposed to predict the consensus sequences. In the whole-genome assemblies of NA12878 assembled by Wtdbg2 and Flye using Nanopore data, BlockPolish has a higher polishing accuracy than other state-of-the-arts including Racon, Medaka and MarginPolish & HELEN. In all assemblies, errors are predominantly indels and BlockPolish has a good performance in correcting them. In addition to the Nanopore assemblies, we further demonstrate that BlockPolish can also reduce the errors in the PacBio assemblies. The source code of BlockPolish is freely available on Github (https://github.com/huangnengCSU/BlockPolish).
INTERCAAT: identifying interface residues between macromolecules
Authors: Grudman Steven , Fajardo J Eduardo , Fiser Andras
Published: September 2021

The Interface Contact definition with Adaptable Atom Types (INTERCAAT) was developed to determine the atomic interactions between molecules that form a known three dimensional structure. First, INTERCAAT creates a Voronoi tessellation where each atom acts as a seed. Interactions are defined by atoms that share a hyperplane and whose distance is less than the sum of each atoms’ Van der Waals radii plus the diameter of a solvent molecule. Interacting atoms are then classified and interactions are filtered based on compatibility. INTERCAAT implements an adaptive atom classification method; therefore, it can explore interfaces between a variety macromolecules.

Availability and implementation

Source code is freely available at: https://gitlab.com/fiserlab.org/intercaat.

Supplementary information

Supplementary data are available at Bioinformatics online.
Morphology of migration: associations between wing shape, bill morphology and migration in kingbirds (Tyrannus)
Authors: Macpherson Maggie P , Jahn Alex E , Mason Nicholas A
Published: September 2021

Morphology is closely linked to locomotion and diet in animals. In animals that undertake long-distance migrations, limb morphology is under selection to maximize mobility and minimize energy expenditure. Migratory behaviours also interact with diet, such that migratory animals tend to be dietary generalists, whereas sedentary taxa tend to be dietary specialists. Despite a hypothesized link between migration status and morphology, phylogenetic comparative studies have yielded conflicting findings. We tested for evolutionary associations between migratory status and limb and bill morphology across kingbirds, a pan-American genus of birds with migratory, partially migratory and sedentary taxa. Migratory kingbirds had longer wings, in agreement with expectations that selection favours improved aerodynamics for long-distance migration. We also found an association between migratory status and bill shape, such that more migratory taxa had wider, deeper and shorter bills compared to sedentary taxa. However, there was no difference in intraspecific morphological variation among migrants, partial migrants and residents, suggesting that dietary specialization has evolved independently of migration strategy. The evolutionary links between migration, diet and morphology in kingbirds uncovered here further strengthen ecomorphological associations that underlie long-distance seasonal movements in animals.
Phenotypic and genomic differences between biomes of the South America marsh rat,Holochilus brasiliensis
Authors: Prado Joyce R , Percequillo Alexandre R , Pirani Renata M , Thomaz Andrea T
Published: September 2021

Abiotic factors can influence genetic and phenotypic divergence in several ways, and identifying the mechanisms responsible for generating this variation is challenging. However, when evaluated in combination, ecological characteristics and genetic and phenotypic information can help us to understand how habitat preferences can influence morphological and genetic patterns exhibited by taxa distributed between distinct biomes, such as the Atlantic Forest and Pampas biomes in South America. By combining distributional, environmental, phenotypic and genomic information from a habitat-specialist semi-aquatic rodent (Holochilus brasiliensis), we quantified the relationship between ecological niche differences and the phenotypic and genetic variation. The results demonstrate notable segregation among the ecological niches of H. brasiliensis within each biome, although we could not refute the hypothesis of niche similarity or equivalency. Such differences are consistent with a solid morphometric variation associated with the size of these rodents. However, the ecological and morphometric differentiation is not accompanied by the same pattern of genetic variation. Despite differences in the connectivity patterns in both biomes, the genetic differences corroborate a consistent level of migration history between biomes. Additionally, the association tests show that the environment explains a small and non- significant part of the genetic variation but a significant portion of the morphometric variation.
Genital coupling and copulatory wounding in the Drosophila auraria species complex (Diptera: Drosophilidae)
Authors: Onuma Moe , Kamimura Yoshitaka , Sawamura Kyoichi
Published: September 2021

Animal genitalia have changed substantially and rapidly during evolution, and functionally interacting anatomical structures complementarily match between the sexes. Several hypotheses have been proposed to explain how such structure-matching evolved. A test of these hypotheses would require a detailed analysis of male and female genitalia among closely related species and a comparison of the functional aspects of the interacting structures between the sexes. Therefore, here we document genital coupling and copulatory wounds in the four species of the Drosophila auraria complex. The position of the protrusion of the median gonocoxite of males relative to the female terminalia differed among the species, which may reflect differences in protrusion morphology. Species-specific female structures were discovered on the membrane between the genitalia and analia and on the vaginal wall. The former makes contact with the protrusion, and the latter makes contact with appendages of the aedeagus. Copulatory wounds, which are produced during copulation, were seen at three locations on females: depressions near the genital orifice, the membrane between the genitalia and analia, and the vaginal wall. Some of the copulatory wounds were located at sites that could potentially make contact with the species-specific structures that we identified. We speculate that the female structures that differ between species of the D. auraria complex evolved in concert with the genitalia of male conspecifics.
Prey preference of a wasp determined by nest size supports the role of natural selection in body size evolution in Cassidinae leaf beetles
Authors: Shinohara Tadashi , Takami Yasuoki
Published: September 2021

The prey preference of a predator can impose natural selection on prey phenotypes, including body size. Despite evidence that large body size protects against predation in insects, the determinants of body size variation in Cassidinae leaf beetles are not well understood. We examined the prey preference of the digger wasp Cerceris albofasciata, a specialist predator of adult Cassidinae leaf beetles, and found evidence for natural selection on prey body size. The wasp hunted prey smaller than the size of their nest entrance. However, the wasp preferred larger prey species among those that could be carried into their nest. Thus, the benefits of large prey and the cost associated with nest expansion might determine the prey size preference. As expected from the prey species preference, the wasp preferred small individuals of the largest prey species, Thlaspida biramosa, and large individuals of the smallest prey species, Cassida piperata, resulting in natural selection on body sizes. In intermediate-sized prey species, however, there was no evidence for selection on body size. Natural selection on body size might explain the variation of prey morphologies that increase body size, such as explanate margins, in this group.
Two distinct Sertoli cell states are regulated via germ cell crosstalk†
Authors: Gewiss Rachel L , Law Nathan C , Helsel Aileen R , Shelden Eric A , Griswold Michael D
Published: September 2021

Sertoli cells are a critical component of the testis environment for their role in maintaining seminiferous tubule structure, establishing the blood-testis barrier, and nourishing maturing germ cells in a specialized niche. This study sought to uncover how Sertoli cells are regulated in the testis environment via germ cell crosstalk in the mouse. We found two major clusters of Sertoli cells as defined by their transcriptomes in Stages VII–VIII of the seminiferous epithelium and a cluster for all other stages. Additionally, we examined transcriptomes of germ cell-deficient testes and found that these existed in a state independent of either of the germ cell-sufficient clusters. Altogether, we highlight two main transcriptional states of Sertoli cells in an unperturbed testis environment, and a germ cell-deficient environment does not allow normal Sertoli cell transcriptome cycling and results in a state unique from either of those seen in Sertoli cells from a germ cell-sufficient environment.
Understanding the Attraction: Prison Tourism and the Public Gaze
Authors: Urquhart Diane
Published: September 2021

Research undertaken in three decommissioned English prisons offers fresh insight into public attraction. Employing interviews with prison tourists, it reveals dark incentives rooted in historical and cultural representations of punishment, an inherent desire to look beyond the prison walls, and a fascination towards a concept I define as Abstract Death and Suffering.
GORD and Barrett’s oesophagus after bariatric procedures: multicentre prospective study
Authors: Genco Alfredo , Castagneto-Gissey Lidia , Gualtieri Loredana , Lucchese Marcello , Leuratti Luca , Soricelli Emanuele , Casella Giovanni
Published: September 2021

Introduction

Gastro-oesophageal reflux disease (GORD) after bariatric surgery is a debated topic. This study investigated the prevalence of GORD and associated oesophageal complications following bariatric procedures—namely, adjustable gastric banding (AGB), sleeve gastrectomy (SG), Roux-en-Y gastric bypass (RYGB), and one-anastomosis gastric bypass (OAGB).

Methods

This was a prospective multicentre study designed to evaluate the long-term effects of bariatric surgery on GORD. Patients were studied at baseline, at >10 years following AGB, SG, and RYGB, and at >3 years following OAGB (due to the more recent recognition of OAGB as a standard bariatric procedure). Patients were assessed by endoscopy and GORD symptom evaluation.

Results

A total of 241 patients were enrolled. A minimum follow-up of 10 years was completed by 193 patients following AGB (57 patients), SG (95 patients), and RYGB (41 patients), and of >3 years by 48 subjects following OAGB. GORD symptoms increased following AGB and SG (from 14 to 31.6 per cent and from 26.3 to 58.9 per cent, respectively; P < 0.0001), improved following RYGB (from 36.6 to 14.6 per cent; P < 0.0001), and were unchanged following OAGB. The overall prevalence of erosive oesophagitis was greater in the SG group (74.7 per cent) than in the AGB (42.1 per cent), RYGB (22 per cent), and OAGB (22.9 per cent) groups (P < 0.0001). Barrett’s oesophagus was found only in patients who had SG (16.8 per cent). Biliary-like gastric stagnation was found in a greater proportion of SG and OAGB patients (79.7 and 69.4 per cent, respectively) than in other treatment groups (P < 0.0001). The prevalence of biliary-type reflux into the oesophagus was higher in patients who underwent SG (74.7 per cent), compared with other treatment groups.

Conclusion

Bariatric surgery leads to gastro-oesophageal complications of variable severity, particularly SG, which can result in a large proportion of patients developing Barrett’s oesophagus.
Impact of the COVID-19 pandemic on early outcomes after colorectal cancer surgery
Authors: Polson Robin , Abdelqader Bushra , Chung Wen Yuan , Sangal Sam
Published: September 2021

This study aimed to identify whether changes to service made during the COVID-19 pandemic have had an impact on postoperative tumour histopathological grading and, therefore, prognosis. There was a significant increase in time between initial referral and surgery during the first and second waves compared with before the pandemic. However, despite the delay from initial referral to surgery, histology of the surgical specimens showed no significant difference between any of the three groups.
Genetic diversity in micro-endemic plants from highland grasslands in southern Brazil
Authors: Souza Analu , Giudicelli Giovanna C , Teixeira Marcelo C , Turchetto Caroline , Bonatto Sandro L , Freitas Loreta B
Published: September 2021

Population genetic structure results from the interaction between historical events, current ecological conditions and life traits. The genetic structure and gene flow between populations are important to species dynamics, mainly for rare and endangered species that are more vulnerable to landscape changes and fragmentation. Here we evaluated the genetic diversity, population structure and gene exchange in Petunia bonjardinensis, P. reitzii and P. saxicola, three rare species endemic to subtropical highland grasslands in southern South America. We analysed the genetic diversity and structure considering historical events, such as founder effect and climate changes, and biological traits of each species. We also estimated the conservation status for these three species. We collected samples from all adult individuals and occurrence sites that could be found at the same flowering season and genotyped them for 13 nuclear microsatellite markers. Our results indicate that rarity is probably historical for these species, given that we found no genetic evidence for recent bottlenecks. Petunia bonjardinensis, with the largest occurrence area and population sizes, displayed the higher diversity indices. The other two showed lower genetic diversity and are geographically most restricted. Gene exchange among these species was low, although they share some ancestral genetic polymorphism. Historical migration, founder effects and Pleistocene climate cycles ae the main factors explaining genetic diversity, and this was also influenced by reproductive biology and recent habitat loss, whereas the landscape influences the structure. Based on IUCN criteria, the three species are endangered, and the main risk for their survival is probably anthropic activity in the occurrence area. We recommend an urgent programme for the preservation of these species in situ and ex situ.
Another step towards defining the genetic landscape of rhabdomyolysis
Authors: Ravenscroft Gianina , Cabrera-Serrano Macarena
Published: September 2021

This scientific commentary refers to ‘MLIP causes recessive myopathy with rhabdomyolysis, myalgia and baseline high serum creatine kinase’, by Lopes Abath Neto et al. (doi:10.1093/brain/awab275).
Crosstalk between gut microbiota and sepsis
Authors: Niu Mengwei , Chen Peng
Published: September 2021

Sepsis is an overwhelming inflammatory response to microbial infection. Sepsis management remains a clinical challenge. The role of the gut microbiome in sepsis has gained some attention. Recent evidence has demonstrated that gut microbiota regulate host physiological homeostasis mediators, including the immune system, gut barrier function and disease susceptibility pathways. Therefore, maintenance or restoration of microbiota and metabolite composition might be a therapeutic or prophylactic target against critical illness. Fecal microbiota transplantation and supplementation of probiotics are microbiota-based treatment methods that are somewhat limited in terms of evidence-based efficacy. This review focuses on the importance of the crosstalk between the gastrointestinal ecosystem and sepsis to highlight novel microbiota-targeted therapies to improve the outcomes of sepsis treatment.
Mentorship and Relationality
Authors: Bordeaux Clementine
Published: September 2021

To be a good relative, as defined by Dakota scholar Ella Cara Deloria (1889–1971), means to follow cultural protocols of kinship in the shaping of relationships. In this article, the author utilizes Deloria’s employment of “being a good relative” within a Lakota/Dakota understanding and Indigenous studies’ articulations of relationality to discuss mentorship. Utilizing the Indigenous studies’ methodology of self-reflexivity, the author provides an analysis of mentorship experiences within different university settings.
Cortical Serotonergic and Catecholaminergic Denervation in MPTP-Treated Parkinsonian Monkeys
Authors: Masilamoni Gunasingh Jeyaraj , Weinkle Allison , Papa Stella M , Smith Yoland
Published: September 2021

Decreased cortical serotonergic and catecholaminergic innervation of the frontal cortex has been reported at early stages of Parkinson’s disease (PD). However, the limited availability of animal models that exhibit these pathological features has hampered our understanding of the functional significance of these changes during the course of the disease. In the present study, we assessed longitudinal changes in cortical serotonin and catecholamine innervation in motor-symptomatic and asymptomatic monkeys chronically treated with low doses of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Densitometry and unbiased stereological techniques were used to quantify changes in serotonin and tyrosine hydroxylase (TH) immunoreactivity in frontal cortices of 3 control monkeys and 3 groups of MPTP-treated monkeys (motor-asymptomatic [N = 2], mild parkinsonian [N = 3], and moderate parkinsonian [N = 3]). Our findings revealed a significant decrease (P < 0.001) in serotonin innervation of motor (Areas 4 and 6), dorsolateral prefrontal (Areas 9 and 46), and limbic (Areas 24 and 25) cortical areas in motor-asymptomatic MPTP-treated monkeys. Both groups of symptomatic MPTP-treated animals displayed further serotonin denervation in these cortical regions (P < 0.0001). A significant loss of serotonin-positive dorsal raphe neurons was found in the moderate parkinsonian group. On the other hand, the intensity of cortical TH immunostaining was not significantly affected in motor asymptomatic MPTP-treated monkeys, but underwent a significant reduction in the moderate symptomatic group (P < 0.05). Our results indicate that chronic intoxication with MPTP induces early pathology in the corticopetal serotonergic system, which may contribute to early non-motor symptoms in PD.
Verbal and General IQ Associate with Supragranular Layer Thickness and Cell Properties of the Left Temporal Cortex
Authors: Heyer D B , Wilbers R , Galakhova A A , Hartsema E , Braak S , Hunt S , Verhoog M B , Muijtjens M L , Mertens E J , Idema S , Baayen J C , de Witt Hamer P , Klein M , McGraw M , Lein E S , de Kock C P J , Mansvelder H D , Goriounova N A
Published: September 2021

The left temporal lobe is an integral part of the language system and its cortical structure and function associate with general intelligence. However, whether cortical laminar architecture and cellular properties of this brain area relate to verbal intelligence is unknown. Here, we addressed this using histological analysis and cellular recordings of neurosurgically resected temporal cortex in combination with presurgical IQ scores. We find that subjects with higher general and verbal IQ scores have thicker left (but not right) temporal cortex (Brodmann area 21, BA21). The increased thickness is due to the selective increase in layers 2 and 3 thickness, accompanied by lower neuron densities, and larger dendrites and cell body size of pyramidal neurons in these layers. Furthermore, these neurons sustain faster action potential kinetics, which improves information processing. Our results indicate that verbal mental ability associates with selective adaptations of supragranular layers and their cellular micro-architecture and function in left, but not right temporal cortex.