bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of protein interactions of grapevine fanleaf virus RNA-dependent RNA polymerase during infection of Nicotiana benthamiana by affinity purification and tandem mass spectrometry
Authors: Osterbaan Larissa J. , Hoyle Victoria , Curtis Michelle , DeBlasio Stacy , Rivera Keith D. , Heck Michelle , Fuchs Marc
Published: May 2021

The RNA-dependent RNA polymerase (1EPol) is involved in replication of grapevine fanleaf virus (GFLV, Nepovirus, Secoviridae) and causes vein clearing symptoms in Nicotiana benthamiana. Information on protein 1EPol interaction with other viral and host proteins is scarce. To study protein 1EPol biology, three GFLV infectious clones, i.e. GHu (a symptomatic wild-type strain), GHu-1EK802G (an asymptomatic GHu mutant) and F13 (an asymptomatic wild-type strain), were engineered with protein 1EPol fused to a V5 epitope tag at the C-terminus. Following

Agrobacterium tumefaciens

-mediated delivery of GFLV clones in N. benthamiana and protein extraction at seven dpi, when optimal 1EPol:V5 accumulation was detected, two viral and six plant putative interaction partners of V5-tagged protein 1EPol were identified for the three GFLV clones by affinity purification and tandem mass spectrometry. This study provides insights into the protein interactome of 1EPol during GFLV systemic infection in N. benthamiana and lays the foundation for validation work.
Geographical and temporal distribution of SARS-CoV-2 globally: An attempt to correlate case fatality rate with the circulating dominant SARS-CoV-2 clades
Authors: Sarkar Rakesh , Chawla-Sarkar Mamta , Majumdar Swagata , Lo Mahadeb , Chattopadhyay Shiladitya
Published: May 2021

Uncontrolled high transmission is driving the continuous evolution of SARS-CoV-2, leading to the nonstop emergence of the new variants with varying sensitivity to the neutralizing antibodies and vaccines.Wehave analysed of 8,82,740 SARS-CoV-2 genome sequences, collected and sequenced during late December 2019 to 25 March 2021 from all across the world. The findings revealed differences in temporal and spatial distribution,and predominance of various clades/variants among six different continents.We found no clear association between the pathogenic potential of the various clades by comparing the case fatality rate (CFR) of 170 countries with the predominant SARS-CoV-2 clades in those countries, demonstrating the insignificance of the clade specific mutations on case fatality. Overall, relying on a large-scale dataset,this study illustratedthe time-basedevolution andprevalence of various clades/variantsamong different geographic regions.The study may help in designing continent specific vaccines in the future.
Development and performance of a population-based risk stratification model for COVID-19
Authors: Vela Emili , Carot-Sans Gerard , Clèries Montse , Monterde David , Acebes Xènia , Comella Adrià , Eroles Luís García , Coca Marc , Valero-Bover Damià , Piera-Jiménez Jordi , Pérez Sust Pol
Published: May 2021

The shortage of recently approved vaccines against the severe acute respiratory syndrome coronavirus (SARS-CoV-2) has highlighted the need for evidence-based tools to prioritize healthcare resources for people at higher risk of severe coronavirus disease 2019 (COVID-19). Current evidence indicates that age is far from accurate in identifying the risk of severe illness; furthermore, the count of individual risk factors has limited applicability to population-based “stratify-and-shield” strategies. We developed a COVID-19 risk stratification system that allows allocating people into four mutually-exclusive risk categories based on multivariate models for hospital admissions, transfer to intensive care unit (ICU), and mortality among the general population. The model was developed using clinical, hospital, and epidemiological data from the entire population of Catalonia (North-East Spain; 7.5 million people) and validated using an independent dataset of 218,329 individuals with PCR-confirmed COVID-19, who were infected after developing the model. This showed high discrimination capacity, with an area under the curve of the receiving operating characteristics of 0.85 (95% CI 0.85 – 0.85) for hospital admissions, 0.86 (0.86 – 0.97) for ICU transfers, and 0.96 (0.96 – 0.96) for deaths. Our results provide clinicians and policymakers with an evidence-based tool for prioritizing COVID-19 healthcare resources other population groups aside from those with higher exposure to SARS-CoV-2 and frontline workers.
Using Biological Constraints to Improve Prediction in Precision Oncology
Authors: Omar Mohamed , Dinalankara Wikum , Mulder Lotte , Coady Tendai , Zanettini Claudio , Imada Eddie Luidy , Younes Laurent , Geman Donald , Marchionni Luigi
Published: May 2021

Many gene signatures have been developed by applying machine learning (ML) onomicsprofiles, however, their clinical utility is often hindered by limited interpretability and unstable performance in different datasets. Here, we show the importance of embedding prior biological knowledge in the decision rules yielded by ML approaches to build robust classifiers. We tested this by applying different ML algorithms on gene expression data to predict three difficult cancer phenotypes: bladder cancer progression to muscle invasive disease; response to neoadjuvant chemotherapy in triple-negative breast cancer, and prostate cancer metastatic progression. We developed two sets of classifiers:mechanistic, by restricting the training process to features capturing a specific biological mechanism; andagnostic, in which the training didn’t use anya prioribiological information. Mechanistic models had a similar or better performance to their agnostic counterparts in the testing data, with enhanced stability, robustness, and interpretability. Our findings support the use of biological constraints to develop robust and interpretable gene signatures with high translational potential.

Motivation

Omics-based gene signatures often suffer from overfitting and reduced performance when tested on independent data. This usually results from the discrepancy between the high number of features compared to the much smaller number of samples used in the training process, which results in the machine learning algorithm perfectly fitting the training data with a subsequent deterioration in performance in independent cohorts. We introduce a mechanistic framework to mitigate overfitting and improve interpretability by constraining the training process to simple rank-based decision rules recapitulating relevant, cancer-related, biological mechanisms. Our approach aims at reducing the number of training variables to a pre-defined set of biologically important features in the form of gene pairs. The classification mechanism depends entirely on the relative ordering of these pairs, making it robust to data preprocessing techniques, improving the overall interpretability of the resulting models with significant translational implications. Most importantly, these pairs are configured in such a way that the decision rules resulting from the genes relative order embed and recapitulate specific biological mechanism, inherently enhancing the classifiers interpretability.
Out-of-Distribution Generalization from Labeled and Unlabeled Gene Expression Data for Drug Response Prediction
Authors: Sharifi-Noghabi Hossein , Harjandi Parsa Alamzadeh , Zolotareva Olga , Collins Colin C. , Ester Martin
Published: May 2021

Data discrepancy between preclinical and clinical datasets poses a major challenge for accurate drug response prediction based on gene expression data. Different methods of transfer learning have been proposed to address this data discrepancy. These methods generally use cell lines as source domains and patients, patient-derived xenografts, or other cell lines as target domains. However, they assume that they have access to the target domain during training or fine-tuning and they can only take labeled source domains as input. The former is a strong assumption that is not satisfied during deployment of these models in the clinic. The latter means these methods rely on labeled source domains which are of limited size. To avoid these assumptions, we formulate drug response prediction as an out-of-distribution generalization problem which does not assume that the target domain is accessible during training. Moreover, to exploit unlabeled source domain data, which tends to be much more plentiful than labeled data, we adopt a semi-supervised approach. We propose Velodrome, a semi-supervised method of out-of-distribution generalization that takes labeled and unlabeled data from different resources as input and makes generalizable predictions. Velodrome achieves this goal by introducing an objective function that combines a supervised loss for accurate prediction, an alignment loss for generalization, and a consistency loss to incorporate unlabeled samples. Our experimental results demonstrate that Velodrome outperforms state-of-the-art pharmacogenomics and transfer learning baselines on cell lines, patient-derived xenografts, and patients. Finally, we showed that Velodrome models generalize to different tissue types that were well-represented, under-represented, or completely absent in the training data. Overall, our results suggest that Velodrome may guide precision oncology more accurately.
Mechanical counterbalance of kinesin and dynein motors in microtubular network regulates cell mechanics, 3D architecture, and mechanosensing
Authors: Zhovmer Alexander S. , Manning Alexis , Smith Chynna , Hayes James. B. , Burnette Dylan T. , Cartagena-Rivera Alexander X. , Singh Rakesh K. , Tabdanov Erdem D.
Published: May 2021

Microtubules (MTs) and MT motor proteins form active 3D networks made of unstretchable cables with rod-like bending mechanics that provide cells with a dynamically changing structural scaffold. In this study, we report an antagonistic mechanical balance within the dynein-kinesin microtubular motor system. Dynein activity drives microtubular network inward compaction, while isolated activity of kinesins bundles and expands MTs into giant circular bands that deform the cell cortex into discoids. Furthermore, we show that dyneins recruit MTs to sites of cell adhesion increasing topographic contact guidance of cells, while kinesins antagonize itviaretraction of MTs from sites of cell adhesion. Actin-to-microtubules translocation of septin-9 enhances kinesins-MTs interactions, outbalances activity of kinesins over dyneins and induces discoid architecture of cells. These orthogonal mechanisms of MT network reorganization highlight the existence of an intricate mechanical balance between motor activities of kinesins and dyneins that controls cell 3D architecture, mechanics, and cell-microenvironment interactions.
Single-cell RNA-sequencing reveals thoracolumbar vertebra heterogeneity and rib-genesis in pigs
Authors: Li Jianbo , Wang Ligang , Yu Dawei , Hao Junfeng , Zhang Longchao , Adeola Adeniyi C. , Mao Bingyu , Gao Yun , Wu Shifang , Zhu Chunling , Zhang Yongqing , Ren Jilong , Mu Changgai , Irwin David M. , Wang Lixian , Hai Tang , Xie Haibing , Zhang Yaping
Published: May 2021

Thoracolumbar vertebra (TLV) and rib primordium (RP) development is a common evolutionary feature across vertebrates although whole-organism analysis of TLV and RP gene expression dynamics has been lacking. Here we investigated the single-cell transcriptomic landscape of thoracic vertebra (TV), lumbar vertebra (LV), and RP cells from a pig embryo at 27 days post-fertilization (dpf) and identified six cell types with distinct gene-expression signatures. In-depth dissection of the gene-expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and rib development. Further analysis of cell-type-specific and strand-specific expression uncovered the extremely high levels of HOXA10 3’-UTR sequence specific to osteoblast of LV cells, which may function as anti-HOXA10-antisense by counteracting the HOXA10-antisense effect to determine TLV transition. Thus, this work provides a valuable resource for understanding embryonic osteogenesis and angiogenesis underlying vertebrate TLV and RP development at the cell-type-specific resolution, which serves as a comprehensive view on the transcriptional profile of animal embryo development.
Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes
Authors: Liu Ying , Demina Tatiana A. , Roux Simon , Aiewsakun Pakorn , Kazlauskas Darius , Simmonds Peter , Prangishvili David , Oksanen Hanna M. , Krupovic Mart
Published: May 2021

The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counter defense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered four distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine and anoxic environments.
Growth hormone transgenesis affects thermal tolerance in zebrafish (Danio rerio)
Authors: Almeida Daniela Volcan , Figueiredo Marcio Azevedo , Marins Luis Fernando
Published: May 2021

In fish, growth hormone (GH)-transgenesis may modify physiological mechanisms of adaptation when challenged by biotic and abiotic stressors. Thus, we evaluated whether GH overexpression can alter the thermal tolerance of adult and juvenile GH-transgenic zebrafish (Danio rerio). This study compared the thermal tolerance in non-transgenic (NT) and GH-transgenic (T) zebrafish exposed to 13 °C, 39 °C, or 28 °C (control) for 96 h. Mortality rate was checked every 12 h in juvenile (8 week-old) and adult males (6 month-old). Exposure to different temperatures revealed that GH overexpression increases the tolerance of transgenic juveniles exposed to 13 °C and diminishes the tolerance of juveniles and adults, when exposed to 39 °C. Additionally, we have analyzed transcriptional expression from the heat shock proteins (HSPs), which are mainly involved in the thermal tolerance mechanism. The mRNA level analysis results revealed that, under controlled conditions (28 °C), GH-transgenesis upregulates the expression of hsp47, hsp70, hsp90a and heat shock transcription factor (hsf1a) in transgenic juveniles, although the same result was not observed in transgenic adults. Exposure to low temperature did not alter the expression of any analyzed gene, both in adults and in juveniles. Exposure to 39 °C decreased the expression of all genes analyzed, in GH-transgenic adults. Furthermore, the HSP expression pattern was analyzed via hierarchical clustering. This analysis revealed two major clusters illustrating the dependency of gene changes related to age. These results indicate that the GH overexpression can alter thermal tolerance of fish, depending of age and temperature.

Highlights

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GH-transgenesis increased the survival rate of juveniles at low temperature;

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High temperature is more lethal for juvenile ande adult GH-transgenic zebrafish;

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GH-transgenesis increased expression of hsf1a, hsp47, and hsp70 genes in juvenile zebrafish;

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hsf1a, hsp47, hsp70, hsp90a, and hsp90b genes expression is diminished in adult zebrafish GH-transgenesis exposure at high temperature.

Abstract Figure
Large protein complex interfaces have evolved to promote cotranslational assembly
Authors: Badonyi Mihaly , Marsh Joseph A
Published: May 2021

Assembly pathways of protein complexes should be precise and efficient to minimise misfolding and unwanted interactions with other proteins in the cell. One way to achieve this efficiency is by seeding assembly pathways during translation via the cotranslational assembly of subunits. While recent evidence suggests that such cotranslational assembly is widespread, little is known about the properties of protein complexes associated with the phenomenon. Here, using a combination of proteome-specific protein complex structures and publicly available ribosome profiling data, we show that cotranslational assembly is particularly common between subunits that form large intermolecular interfaces. To test whether large interfaces have evolved to promote cotranslational assembly, as opposed to cotranslational assembly being a non-adaptive consequence of large interfaces, we compared the sizes of first and last translated interfaces of heteromers in bacterial, yeast, and human complexes. We detect a clear preference in N-terminal interfaces, which will be translated first and thus more likely to form cotranslationally, to be larger than C-terminal interfaces, suggesting that large interfaces have evolved as a means to maximise the chance of successful cotranslational subunit binding.
IRIXS Spectrograph: an ultra high-resolution spectrometer for tender RIXS
Authors: Bertinshaw Joel , Mayer Simon , Dill Frank-Uwe , Suzuki Hakuto , Leupold Olaf , Jafari Atefeh , Sergueev Ilya , Spiwek Manfred , Said Ayman , Kasman Elina , Huang Xianrong , Keimer Bernhard , Gretarsson Hlynur
Published: May 2021

The IRIXS Spectrograph represents a new design of an ultra-high-resolution resonant inelastic X-ray scattering (RIXS) spectrometer that operates at the Ru L
3-edge (2840 eV). First proposed in the field of hard X-rays by Shvyd'ko [(2015), Phys. Rev. A, 91, 053817], the X-ray spectrograph uses a combination of laterally graded multilayer mirrors and collimating/dispersing Ge(111) crystals optics in a novel spectral imaging approach to overcome the energy resolution limitation of a traditional Rowland-type spectrometer [Gretarsson et al. (2020), J. Synchrotron Rad.
27, 538–544]. In combination with a dispersionless nested four-bounce high-resolution monochromator design that utilizes Si(111) and Al2O3(110) crystals, an overall energy resolution better than 35 meV full width at half-maximum has been achieved at the Ru L
3-edge, in excellent agreement with ray-tracing simulations.
Flow control method by applying flexible shells procedure in transonic flow
Authors: Saber M.R. , Djavareshkian M.H.
Published: May 2021

Purpose

In the present research, the effect of the flexible shells method in unsteady viscous flow around airfoil has been studied. In the presented algorithm, due to the interaction of the aerodynamic forces and the structural stiffness (fluid-structural interaction), a geometrical deformation as the bump is created in the area where the shock occurs. This bump causes instead of compressive waves, a series of expansion waves that produce less drag and also improve the aerodynamic performance to be formed. The purpose of this paper is to reduce wave drag throughout the flight range. By using this method, we can be more effective than recent methods throughout the flight because if there is a shock, a bump will form in that area, and if the shock does not occur, the shape of the airfoil will not change.

Design/methodology/approach

In this simulation pressure-based procedure to solve the Navier-Stokes equation with collocated finite volume formulation has been developed. For this purpose, a high-resolution scheme for fluid and structure simulation in transonic flows with an arbitrary Lagrangian-Eulerian method is considered. To simulate Navier-Stokes equations large eddy simulation model for compressible flow is used.

Findings

A new concept has been defined to reduce the transonic flow drag. To reduce drag force and increase the performance of airfoil in transonic flow, the shell can be considered flexible in the area of shock on the airfoil surface. This method refers to the use of smart materials in the aircraft wing shell.

Originality/value

The value of the paper is to develop a new approach to improve the aerodynamic performance and reduce drag force and the efficiency of the method throughout the flight. It is noticeable that the new algorithm can detect the shock region automatically; this point was disregarded in the previous studies. It is hoped that this research will open a door to significantly enhance transonic airfoil performance.
Industry 4.0 disruption: assessing the need for adaptive capability
Authors: Rangaswamy Uma Shankar
Published: May 2021

Purpose

Considering the advent of Industry 4.0, organizations need to undergo digital transformation to survive disruptions owing to rapid technological changes. Accordingly, organizations should develop their adaptive capability to respond to these technological advancements and move ahead with their digital transformation journey.

Design/methodology/approach

Based on the author’s insights as a practitioner on digital transformation and based on existing theoretical frameworks, the author presents a conceptual framework on the determinants of adaptive capability required for digital transformation.

Findings

Organizations should develop their adaptive capability through improved learning capabilities and effective knowledge management system. They should also focus on exploring innovations and ideas and discard unwanted business processes to meet Industry 4.0 disruptions and achieve digital transformation.

Originality/value

This study has been done based on the author's academic research on adaptive capability and personal insights after engaging in several digital transformation engagements.
State, institutional entrepreneurship and the creation of the biopharmaceutical industry in a developing country
Authors: Babaee Ali , Mashayekhi Ali N. , HamidiMotlagh Rouholah
Published: May 2021

Purpose

This study aims to explore the emergence and development of new industries, especially in the context of developing countries, by considering industry emergence and development as a large-scale institutional change or transition.

Design/methodology/approach

The authors conducted an inductive case study research on the emergence of the biopharmaceutical industry in a developing country. The data on the emergence and development of Iran’s biopharmaceutical industry during 1990 and 2018 were collected through semi-structured interviews, participation in meetings, visits to companies and analysis of archival texts. The data analysis was an inductive and iterative process.

Findings

In the emergence and development of the biopharmaceutical industry, there have been a few key agents, institutional entrepreneurs (IEs), in both the state and private sectors, who played main roles. Moreover, the most important type of knowledge which has been crucial for the decision-making of IEs has been informal, tacit and institutional knowledge. Furthermore, the authors identified a mechanism, inter-institutional circulation, as being most effective in the transfer of institutional knowledge among IEs.

Originality/value

The originality of this study is applying insights from institutional entrepreneurship and knowledge management literature to the extant literature on industry emergence and development.
Effects of process parameters on compressive property of FDM with ABS
Authors: Nathaphan Supphachai , Trutassanawin Worrasid
Published: May 2021

Purpose

This work aims to investigate the interaction effects of printing process parameters of acrylonitrile butadiene styrene (ABS) parts fabricated by fused deposition modeling (FDM) technology on both the dimensional accuracy and the compressive yield stress. Another purpose is to determine the optimum process parameters to achieve the maximum compressive yield stress and dimensional accuracy at the same time.

Design/methodology/approach

The standard cylindrical specimens which produced from ABS by using an FDM 3D printer were measured dimensions and tested compressive yield stresses. The effects of six process parameters on the dimensional accuracy and compressive yield stress were investigated by separating the printing orientations into horizontal and vertical orientations before controlling five factors: nozzle temperature, bed temperature, number of shells, layer height and printing speed. After that, the optimum process parameters were determined to accomplish the maximum compressive yield stress and dimensional accuracy simultaneously.

Findings

The maximum compressive properties were achieved when layer height, printing speed and number of shells were maintained at the lowest possible values. The bed temperature should be maintained 109°C and 120°C above the glass transition temperature for horizontal and vertical orientations, respectively.

Practical implications

The optimum process parameters should result in better FDM parts with the higher dimensional accuracy and compressive yield stress, as well as minimal post-processing and finishing techniques.

Originality/value

The important process parameters were prioritized as follows: printing orientation, layer height, printing speed, nozzle temperature and bed temperature. However, the number of shells was insignificant to the compressive property and dimensional accuracy. Nozzle temperature, bed temperature and number of shells were three significant process parameters effects on the dimensional accuracy, while layer height, printing speed and nozzle temperature were three important process parameters influencing compressive yield stress. The specimen fabricated in horizontal orientation supported higher compressive yield stress with wide processing ranges of nozzle and bed temperatures comparing to the vertical orientation with limited ranges.
Development of a classifier with analysis of feature selection methods for COVID-19 diagnosis
Authors: Chauhan Hetal , Modi Kirit , Shrivastava Saurabh
Published: May 2021

Purpose

The COVID-19 pandemic situation is increasing day by day and has affected the lifestyle and economy worldwide. Due to the absence of specific treatment, the only way to control a pandemic is by stopping its spread. Early identification of affected persons is urgently in demand. Diagnostic methods applied in hospitals are time-consuming, which delay the identification of positive patients. This study aims to develop machine learning-based diagnosis model which can predict positive cases and helps in decision-making.

Design/methodology/approach

In this research, the authors have developed a diagnosis model to check coronavirus positivity based on an artificial neural network. The authors have trained the model with clinically assessed symptoms, patient-reported symptoms, other medical histories and exposure data of the person. The authors have explored filter-based feature selection methods such as Chi2, ANOVA F-score and Mutual Information for improving performance of a classification model. Metrics used to evaluate performance of the model are accuracy, precision, sensitivity and F1-score.

Findings

The authors got highest classification performance with model trained with features ranked according to ANOVA FS method. Highest scores for accuracy, sensitivity, precision and F1-score of predictions are 0.93, 0.99, 0.94 and 0.93, respectively. The study reveals that most relevant predictors for COVID-19 diagnosis are sob severity, cough severity, sob presence, cough presence, fatigue and number of days since symptom onset.

Originality/value

Treatment for COVID-19 is not available to date. The best way to control this pandemic is the isolation of positive persons. It is very much necessary to identify positive persons at an early stage. RT-PCR test used to check COVID-19 positivity is the time-consuming, expensive and laborious method. Current diagnosis methods used in hospital demand more medical resources with increasing cases of coronavirus that introduce shortage of resources. The developed model provides solution to the problem cheaper and faster decreases the immediate need for medical resources and helps in decision-making.
Public good overprovision by a manipulative provider
Authors: Celik Gorkem , Shin Dongsoo , Strausz Roland
Published: May 2021

We study contracting between a public good provider and users with private valuations of the good. We show that, once the provider extracts the users' private information, she benefits from manipulating the collective information received from all users when communicating with them. We derive conditions under which such manipulation determines the direction of distortions in public good provision. If the provider is non‐manipulative, the public good is always underprovided, whereas overprovision occurs with a manipulative provider. With overprovision, not only high‐valuation users, but also low‐valuation users may obtain positive rents—users may prefer facing a manipulative provider.
Specialist residential dementia care for people with severe and persistent behaviours: A ten‐year retrospective review
Authors: Gresham Meredith , Morris Thomas , Min Chao Sabrina , Lorang Catriona , Cunningham Colm
Published: May 2021

Very severe behavioural and psychological symptoms of dementia (BPSD) have low prevalence but disproportionately poor outcomes for persons with dementia, others and systems of care, including inappropriate use of medication, tenuous accommodation, poor quality of life and increased costs. The Australian Government has established new Special Dementia Care Programmes (SDCPs) to provide interim care for up to 12 months for those with severe and persistent BPSD unsuitable for mainstream aged care. This 10‐year retrospective review describes environmental design, governance, clinical processes, characteristics and outcomes for 80 residents of a similar‐aged care mental health partnership SDCP. A key finding was that average length of stay was slightly over 12 months. All surviving residents except one were able to be transferred to mainstream aged care services. Doses of regular and PRN antipsychotic and anxiolytic medications were significantly reduced. SDCPs may have the potential to improve care and outcomes for this group of vulnerable older people.
Violent masculinities
Authors: SALEM TOMAS , LARKINS ERIKA ROBB
Published: May 2021

Historically, policing in Rio de Janeiro has been shaped by the equation of racialized violence and masculinity. Attempts to reform the police have paradoxically drawn on forms of male violence that are centered on the rational and professional use of force and on “softer” practices, such as dialogue and collaboration, symbolically coded as feminine. The failure of police reform reflects the cultural salience of understandings of masculinity centered around violence within the police, historical patterns of policing in Rio, and political actors’ strategic cultivation of male violence. Through Rio de Janeiro's failed attempt at police reform, we theorize the relation between racialized state violence, authoritarian political projects, and transgressive forms of male violence, arguing that an important appeal of authoritarianism lies in its promise to carve out a space for performing what we callwild masculinity. [masculinity,race,police,violence,gender,politics,favela,Rio de Janeiro,Brazil]
Use of contrast enhanced ultrasound in testicular diseases: A comprehensive review
Authors: Tenuta Marta , Sesti Franz , Bonaventura Ilaria , Mazzotta Paola , Pofi Riccardo , Gianfrilli Daniele , Pozza Carlotta
Published: May 2021

Background

Contrast‐enhanced ultrasound (CEUS) is a sonographic technique that increases the diagnostic accuracy of ultrasound and color Doppler ultrasound (CDUS) when studying testicular abnormalities. However, its role in clinical practice is still debatable because there are no accepted standards regarding how and when this technique should be used for patients with testicular disease.

Objectives

To perform a nonsystematic review of the current literature to highlight the strength and flaws of performing CEUS and to provide a critical overview of current research evidence on this topic.

Materials and methods

A thorough search of published peer‐reviewed studies in PubMed was performed using proper keywords.

Results

Strong enhancement of neoplastic lesions (both benign and malignant) during CEUS aids in differential diagnosis with non‐neoplastic lesions, which usually appears either nonenhanced or enhanced in a manner similar to that of the surrounding parenchyma. CEUS enhancement has a high predictive value in the identification of neoplastic lesions, whereas a similar or complete absence of enhancement may be interpreted as strong evidence of benignity, although there are exceptions. Literature on quantitative analysis is still scarce, though promising, particularly in distinguishing benign from malignant neoplasms. Furthermore, CEUS may be useful in many emergency situations, such as acute scrotum, blunt scrotal trauma, and focal infarction of the testis. Finally, CEUS can help increase the probability of sperm recovery in azoospermic males.

Discussion and conclusion

CEUS is a safe, easy‐to‐perform, and cost‐effective diagnostic tool that can provide a more accurate diagnosis in testicular lesions and acute scrotal disease. However, further studies with larger cohorts are required to refine the differential diagnosis between benign and malignant neoplasms. Finally, these preliminary results can instigate the development of innovative research on pre‐testicular sperm extraction to increase the chances of sperm recovery.
A constructivism of desire: Conceptualising the politics of assemblage with Deleuze and Guattari
Authors: Roberts Tom
Published: May 2021

Assemblage theory has made a significant impact on the theoretical landscape of human geography over the past decade, providing the discipline with a “radically constructivist” account of social and cultural life that is no longer anchored to the process of human meaning‐making. Despite this growing popularity, however, geographers have recently voiced concerns about the critical efficacy of contemporary assemblage approaches, which often rely on the application of scientific terms like emergence and complexity to social and cultural processes. This temptation to overemphasise the physics of assemblage is problematic, I argue, because it tends to obfuscate the concept’s political significance and leads to accusations of a lack of criticality. In this paper I revisit the philosophy of Deleuze and Guattari with the aim of bringing the political implications of the assemblage concept into sharper focus. While more commonly associated with A thousand plateaus, I trace the conceptual genealogy of Deleuze and Guattari's assemblage concept through to their earlier collaboration Anti‐Oedipus, where the two philosophers develop a novel framework for political theory based on a radically constructivist model of desire. In doing so, I show how Deleuze and Guattari's political commitment to re‐think desire in machinic terms is what makes assemblage theory both a critique of capitalist subjectivity and a provocation to think the conditions of social and cultural life beyond the human.
Effects of land‐use on fruit bat distribution in different habitats along the slopes of Mt. Kilimanjaro, Tanzania
Authors: Vogeler Anna‐Valeska Bettina , Tschapka Marco
Published: May 2021

Tropical ecosystems are currently degrading at unprecedented speed, mostly due to rapid human population growth. This affects the associated biodiversity, which frequently results in damage to or loss of ecosystem functions. Due to high species richness and ecological diversity, bats are essential ecosystem elements. Our objective was to determine effects of land‐use categories on species abundance, richness and diversity of the guild of fruit bats (Chiroptera: Pteropodidae) on Mt. Kilimanjaro, a biodiversity hotspot in Tanzania. We surveyed five habitat types, including two natural habitats lower montane forest and savanna, and three disturbed habitats, coffee plantations, Chagga homegardens, and maize fields. We captured 629 frugivorous bats and (1) compared diversity and species abundance among the habitat types and (2) assessed factors driving the differences in guild structure along an elevational gradient. Species accumulation curves were asymptotic for all habitats, suggesting an adequate sampling effort. Non‐metric multidimensional scaling analysis indicated strong differentiation of fruit bat guilds among habitats. Highest species richness was recorded in lower montane forest and Chagga homegardens, which therefore represent habitats of high value for these bats. Nevertheless, even in the intensively used coffee plantations and maize fields we found a high abundance of bats from most species despite a low abundance of food resources. Our results suggest that bats do not perceive moderately sized plantations as a hostile matrix, but rather use them as flyways between fragments and patches of secondary vegetation. Further, we suggest that within plantations, trees likeFicusspp. increase bat activity.
Sinus laser therapy versus sinus lay open in the management of sacrococcygeal pilonidal disease
Authors: Abdelnaby Mahmoud , Fathy Mohammad , Emile Sameh Hany , Arnous Mohamed , Balata Mohamed , Abdelmawla Ahmed , Abdallah Emad
Published: May 2021

Aim

There is no standard method for the management of sacrococcygeal pilonidal disease (SPND); however, surgery remains the gold standard treatment. Wide surgical excision of the sinus is the traditional surgical treatment of SPND, yet it is associated with extended healing time and delayed recovery. This study aimed to compare the outcomes of sinus laser therapy (SiLaT) and sinus lay open in the management of SPND.

Methods

Patients with SPND who were treated with SiLaT or lay open were retrospectively reviewed. The main outcome measures were the success of surgery in terms of complete healing at 12 months postoperatively, time to complete healing, complications, operation time and quality of life (QoL).

Results

A total of 139 patients with a mean age of 25 years were included to the study. Sixty‐two patients underwent SiLaT and 77 underwent lay open. Six patients experienced recurrence after SiLaT while there was no recorded recurrence after the lay open technique (P = 0.007). Sinus lay open had a shorter operation time than SiLaT (P < 0.0001). On the other hand, SiLaT was followed by a shorter healing time, lower incidence of delayed wound healing, better cosmetic outcome, and higher QoL scores compared to the lay open group. The complication rates were comparable between the two groups.

Conclusion

Sinus lay open was associated with better success than SiLaT. On the other hand, SiLaT was associated with quicker healing, better cosmesis, better QoL and longer operation time. The complication rate of the two procedures was comparable.
The long‐term incidence of dysplasia and colorectal cancer in a Crohn’s colitis population‐based cohort
Authors: Gatenby Grace , Glyn Tamara , Pearson John , Gearry Richard , Eglinton Tim
Published: May 2021

Aim

The risk of developing colorectal cancer (CRC) in Crohn's disease (CD) has been variably reported. Chronic inflammation is associated with an increased risk of neoplasia; variable outcomes in CD possibly reflect the heterogeneous nature of the disease. The aim of this work was to characterize the risk of CRC in a New Zealand population‐based cohort of CD patients with colonic inflammation.

Method

A review of all participants with CD in the population‐based Canterbury Inflammatory Bowel Disease Study was conducted. Data on demographics, endoscopic surveillance, presence of dysplasia/neoplasia and oncological outcome were extracted. The age‐adjusted standardized incidence ratio (SIR) was used to compare the incidence of CRC in the cohort with the incidence of CRC in the New Zealand population in 2006.

Results

Data on 649 patients with CD were collected. Four hundred and thirty‐six participants (58% female) with ileocolonic or colonic CD were included for analysis. CRC was diagnosed in 13 patients (62% female). The median age at CRC diagnosis was 58.5 years, and the mean duration of CD prior to diagnosis of CRC was 20.4 years. When compared with the New Zealand population (using census data), the overall age‐adjusted SIR was 4.1 (95% CI 2.4–7.1).

Conclusion

This population‐based cohort of patients with colonic CD shows a significantly increased risk of CRC compared with the general population. This is consistent with the colonic location of inflammation increasing the risk of neoplasia. Inclusion of patients with isolated upper gastrointestinal/ileal CD in similar studies may mask the truly increased risk for patients with long‐standing colonic inflammation.
Risk of non‐fatal overdose and polysubstance use in a longitudinal study with people who inject drugs in Tijuana, Mexico
Authors: Rivera Saldana Carlos D. , Abramovitz Daniela , Meacham Meredith C. , Gonzalez‐Zuniga Patricia , Rafful Claudia , Rangel Gudelia , Strathdee Steffanie A. , Cepeda Javier
Published: May 2021

Introduction

Among people who inject drugs (PWID), polysubstance use has been associated with fatal and non‐fatal overdose (NFOD). However, the risk of overdose due to the cumulative number of various recently used drug types remains unexplored. We estimated the risk of NFOD for different polysubstance use categories among PWID in Tijuana, Mexico.

Methods

Data came from 661 participants followed for 2 years in Proyecto El Cuete‐IV, an ongoing prospective cohort of PWID. A multivariable Cox model was used to assess the cumulative impact of polysubstance use on the time to NFOD. We used the Cochran‐Armitage test to evaluate a dose–response relationship between number of polysubstance use categories and NFOD.

Results

We observed 115 NFOD among 1029.2 person‐years of follow‐up (incidence rate: 11.2 per 100 person‐years; 95% confidence interval [CI] 9.3‐13.3). Relative to those who used one drug class, the adjusted hazard ratio of NFOD for individuals reporting using two drug classes was 1.11 (95% CI 0.69‐1.79), three drug classes was 2.00 (95% CI 1.16‐3.44) and for those reporting three compared to two was 1.79 (95% CI 1.09‐2.97). A significant Cochran‐Armitage trend test (P < 0.001) suggested a dose–response relationship.

Discussion and Conclusions

Polysubstance use was associated with increased risk of NFOD with a dose–response relationship over 2 years. We identified a subgroup of PWID at high risk of NFOD who reported concurrent use of opioids, stimulants and benzodiazepines. Prioritising tailored harm reduction and overdose prevention interventions for PWID who use multiple substances in Tijuana is needed.
From puzzles to portraits: Enhancing situation awareness during natural disasters using a design science approach
Authors: Vemprala Naga , Liu Charles Zhechao , Choo Kim‐Kwang Raymond
Published: May 2021

During emergency situations, a quick and concise summary from the deluge of messages improves “situation awareness” and enables informed decisions. However, this is challenging due to the volume, variety, and veracity of information. Grounded in the Situation Awareness Theory, this study presents a streamlined protocol to process millions of social media messages and render them in an easily comprehensible format for various stakeholders to gain deeper insights. Specifically, using a design science approach, we develop a set of artifacts using incremental hierarchical clustering and enhanced text summarization algorithm to produce informative summaries under crisis situations. We implemented our protocol on 2.5 and 3 million tweets collected during the two major hurricanes in 2017 and 2018. The results show that our protocol can derive critical information not captured by Twitter's search tools and mainstream news media and significantly improve on accuracy and efficiency when compared to other contemporary tools.
Adoptive Parenting Cognitions in the Era of Open Adoption: Is Shared Fate Theory Still Relevant?
Authors: Lo Albert Y. H. , Cashen Krystal K. , Grotevant Harold D.
Published: May 2021

Objective

To reexamine shared fate theory by validating the original measure of “acknowledgment of differences” (AOD) and testing the theory's relations in the current era of open adoptions.

Background

Shared fate theory states adoptive parents who acknowledge differences between adoptive and nonadoptive parenthood are better able to empathize with their child and promote open communication about adoption. The theory has not been validated in the context of modern adoption practices, such as birth family contact.

Method

Confirmatory factor analyses examined the validity of the original measure of AOD using a sample of 190 adoptive mothers whose families varied in level of birth family contact. Regression analyses examined the relation between AOD and empathy and communication 8 years later, as well as whether level of birth family contact moderated these relations.

Results

Results provided evidence for the validity of the measure of AOD. AOD in mothers significantly predicted empathy and communication 8 years later, with little evidence for moderation by level of birth family contact.

Conclusion

AOD has implications for parenting practices and remains an important adoptive parenting cognition, regardless of level of birth family contact.

Implications

AOD is a still relevant area of intervention for practitioners working with adoptive families.
Rent burden determinants in hot and cold housing markets of Davidson and Shelby counties, Tennessee
Authors: Samarin Mikhail , Sharma Madhuri
Published: May 2021

Rent burden is a situation when a renter‐occupied household spends a sizable portion of its income on housing costs. Using census tracts as the scale of analysis, this article examines rent burden determinants in Shelby and Davidson counties, the two largest of Tennessee. These counties differ substantially in terms of their housing markets, demographics, and the state of their economy. Mapping reveals distinct spatial patterns of rent burden and its geographic extent. Correlations and spatial regression analyses suggest that in both counties, a lack of access to an automobile, crowded living, and the presence of children in households similarly associate with higher rent burden. In contrast, educational attainment, race, and a lack of medical insurance do not demonstrate such consensus. Compared to Davidson County, race is a less crucial predictor of rent burden in Shelby County, likely due to its predominantly African American composition across different income groups. Besides, the positive effect of education is more pronounced in Shelby County. Results indicate that rent burden tends to be more of a socioeconomic class issue in Shelby County, whereas it is not as strongly associated with the socially disadvantaged in Davidson County.
Physicochemical properties of acid‐soluble collagens from different tissues of large yellow croaker (Larimichthys crocea)
Authors: Sun Le‐Chang , Du Han , Wen Jia‐Xin , Zhong Chan , Liu Guang‐Ming , Miao Song , Cao Min‐Jie
Published: May 2021

Acid‐soluble collagens (ASCs) were extracted and characterised from different tissues of large yellow croaker (Larimichthys crocea). The yields of ASCs in bones, skins, scales and muscles were 3.22 ± 0.47%, 42.30 ± 1.15%, 2.82 ± 0.31% and 0.89 ± 0.12%, respectively. SDS‐PAGE and ATR‐FTIR analysis showed that all ASCs were type I collagen with intact triple helical structure and consisted of α1,3‐chain, α2‐chain, β‐chain and γ‐chain. Quantitative analysis of SDS‐PAGE revealed that the ratio of β‐chains in ASC from scales was lower than other tissues. The imino acid contents of ASC from bones, skins, scales and muscles were 169, 167, 162 and 173 residues/1000 residues, respectively. The maximum transition temperature (Tm) of ASC from scales was 30.15 °C, lower than the other three ASCs, indicated that the thermal stability of collagen was affected by both the content of imino acid and β‐chains. The results also implied that thermal stability of ASC might exist the tissue specificity among different fish species.