bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of artifact removal approaches on TMS–EEG signal
Authors: Bertazzoli Giacomo , Esposito Romina , Mutanen Tuomas P. , Ferrari Clarissa , Ilmoniemi Risto J. , Miniussi Carlo , Bortoletto Marta
Published: January 2021

Transcranial magnetic stimulation (TMS)-evoked potentials (TEPs) allow one to assess cortical excitability and effective connectivity in clinical and basic research. However, obtaining clean TEPs is challenging due to the various TMS-related artifacts that contaminate the electroencephalographic (EEG) signal when the TMS pulse is delivered. Different preprocessing approaches have been employed to remove the artifacts, but the degree of artifact reduction or signal distortion introduced in this phase of analysis is still unknown. Knowing and controlling this potential source of uncertainty will increase the inter-rater reliability of TEPs and improve the comparability between TMS–EEG studies. The goal of this study was to assess the variability in TEP waveforms due to of the use of different preprocessing pipelines. To accomplish this aim, we preprocessed the same TMS–EEG data with four different pipelines and compared the results. The dataset was obtained from 16 subjects in two identical recording sessions, each session consisting of both left dorsolateral prefrontal cortex and left inferior parietal lobule stimulation at 100% of the resting motor threshold. Considerable differences in TEP amplitudes were found between the preprocessing pipelines. Topographies of TEPs from the different pipelines were all highly correlated (ρ>0.8) at latencies over 100 ms. By contrast, waveforms at latencies under 100 ms showed a variable level of correlation, with ρ ranging between 0.2 and 0.9. Moreover, the test–retest reliability of TEPs depended on the preprocessing pipeline. Taken together, these results take us to suggest that the choice of the preprocessing approach has a marked impact on the final TEP, and that caution should be taken when comparing TMS–EEG studies that used different approaches. Finally, we propose strategies to control this source of variability.
Association of a Common Genetic Variant with Parkinson’s Disease is Propagated through Microglia
Authors: Langston R. G. , Beilina A. , Reed X. , Singleton A. B. , Blauwendraat C. , Gibbs J. R. , Cookson M. R.
Published: January 2021

Studies of the genetic basis of Parkinson’s disease (PD) have identified many disease-associated genetic variants, but the mechanisms linking variants to pathogenicity are largely unknown. PD risk is attributed to both coding mutations in the Leucine-rich repeat kinase 2 (LRRK2) gene and to common non-coding variation upstream of theLRRK2locus. Here we show that the influence of genotype at non-coding variant rs76904798 onLRRK2expression is propagated specifically through microglia, in contrast to evaluations based on general rather than genotype-dependent expression. We find evidence of microglia-specific regulatory regions that may modulateLRRK2expression using single nuclei sequencing analyses of human frontal cortex and confirm these results in a human induced pluripotent stem cell-derived microglia model. Our study demonstrates that cell type is an important consideration in interrogation of the role of non-coding variation in disease pathogenesis.
Spontaneous neural synchrony links intrinsic spinal sensory and motor networks during unconsciousness
Authors: McPherson Jacob G. , Bandres Maria F.
Published: January 2021

Non-random functional connectivity during unconsciousness is a defining feature of supraspinal networks. However, its generalizability to intrinsic spinal networks remains incompletely understood. Previously, Barry et al. (2014) used fMRI to reveal bilateral resting state functional connectivity within sensory-dominant and, separately, motor-dominant regions of the spinal cord. Here, we record spike trains from large populations of spinal interneuronsin vivoin rats and demonstrate that spontaneous functional connectivity also links sensory- and motor-dominant regions during unconsciousness. The spatiotemporal patterns of connectivity could not be explained by latent afferent activity or by populations of interconnected neurons spiking randomly. We also document connection latencies compatible with mono- and di-synaptic interactions and putative excitatory and inhibitory connections. The observed activity is consistent with the hypothesis that salient, experience-dependent patterns of neural transmission introduced during behavior or by injury/disease are reactivated during unconsciousness. Such a spinal replay mechanism could shape circuit-level connectivity and ultimately behavior.
The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation
Authors: Wagner Alex H , Babb Lawrence , Alterovitz Gil , Baudis Michael , Brush Matthew , Cameron Daniel L , Cline Melissa , Griffith Malachi , Griffith Obi L , Hunt Sarah , Kreda David , Lee Jennifer , Lopez Javier , Moyer Eric , Nelson Tristan , Patel Ronak Y , Riehle Kevin , Robinson Peter N , Rynearson Shawn , Schuilenburg Helen , Tsukanov Kirill , Walsh Brian , Konopko Melissa , Rehm Heidi , Yates Andrew D , Freimuth Robert R , Hart Reece K
Published: January 2021

Maximizing the personal, public, research, and clinical value of genomic information will require that clinicians, researchers, and testing laboratories exchange genetic variation data reliably. Developed by a partnership among national information resource providers, public initiatives, and diagnostic testing laboratories under the auspices of the Global Alliance for Genomics and Health (GA4GH), the Variation Representation Specification (VRS, pronounced “verse”) is an extensible framework for the semantically precise and computable representation of variation that complements contemporary human-readable and flat file standards for variation representation. VRS objects are designed to be semantically precise representations of variation, and leverage this design to enable unique, federated identification of molecular variation. We describe the components of this framework, including the terminology and information model, schema, data sharing conventions, and a reference implementation, each of which is intended to be broadly useful and freely available for community use. The specification, documentation, examples, and community links are available athttps://vrs.ga4gh.org/.
Generalizable EEG encoding models with naturalistic audiovisual stimuli
Authors: Desai Maansi , Holder Jade , Villarreal Cassandra , Clark Nat , Hamilton Liberty S.
Published: January 2021

In natural conversations, listeners must attend to what others are saying while ignoring extraneous background sounds. Recent studies have used encoding models to predict electroencephalography (EEG) responses to speech in noise-free listening situations, sometimes referred to as “speech tracking” in EEG. Researchers have analyzed how speech tracking changes with different types of background noise. It is unclear, however, whether neural responses from noisy and naturalistic environments can be generalized to more controlled stimuli. If encoding models for noisy, naturalistic stimuli are generalizable to other tasks, this could aid in data collection from populations who may not tolerate listening to more controlled, less-engaging stimuli for long periods of time. We recorded non-invasive scalp EEG while participants listened to speech without noise and audiovisual speech stimuli containing overlapping speakers and background sounds. We fit multivariate temporal receptive field (mTRF) encoding models to predict EEG responses to pitch, the acoustic envelope, phonological features, and visual cues in both noise-free and noisy stimulus conditions. Our results suggested that neural responses to naturalistic stimuli were generalizable to more controlled data sets. EEG responses to speech in isolation were predicted accurately using phonological features alone, while responses to noisy speech were more accurate when including both phonological and acoustic features. These findings may inform basic science research on speech-in-noise processing. Ultimately, they may also provide insight into auditory processing in people who are hard of hearing, who use a combination of audio and visual cues to understand speech in the presence of noise.

Significance Statement

Understanding spoken language in natural environments requires listeners to parse acoustic and linguistic information in the presence of other distracting stimuli. However, most studies of auditory processing rely on highly controlled stimuli with no background noise, or with background noise inserted at specific times. Here, we compare models where EEG data are predicted based on a combination of acoustic, phonetic, and visual features in highly disparate stimuli – sentences from a speech corpus, and speech embedded within movie trailers. We show that modeling neural responses to highly noisy, audiovisual movies can uncover tuning for acoustic and phonetic information that generalizes to simpler stimuli typically used in sensory neuroscience experiments.
Sampling from Disentangled Representations of Single-Cell Data Using Generative Adversarial Networks
Authors: Yu Hengshi , Welch Joshua D.
Published: January 2021

Deep generative models, including variational autoencoders (VAEs) and generative adversarial networks (GANs), have achieved remarkable successes in generating and manipulating highdimensional images. VAEs excel at learning disentangled image representations, while GANs excel at generating realistic images. Here, we systematically assess disentanglement and generation performance on single-cell gene expression data and find that these strengths and weaknesses of VAEs and GANs apply to single-cell gene expression data in a similar way. We also develop MichiGAN1, a novel neural network that combines the strengths of VAEs and GANs to sample from disentangled representations without sacrificing data generation quality. We learn disentangled representations of two large singlecell RNA-seq datasets [13, 68] and use MichiGAN to sample from these representations. MichiGAN allows us to manipulate semantically distinct aspects of cellular identity and predict single-cell gene expression response to drug treatment.
Analysis of a “Split-and-Stuttering” Module of an Assembly Line Polyketide Synthase
Authors: Guzman Katarina M. , Yuet Kai P. , Lynch Stephen R. , Liu Corey W. , Khosla Chaitan
Published: January 2021

Notwithstanding the “one-module-one-elongation-cycle” paradigm of assembly line polyketide synthases (PKSs), some PKSs harbor modules that iteratively elongate their substrates through a defined number of cycles. While some insights into module iteration, also referred to as “stuttering”, have been derived throughin vivoandin vitroanalysis of a few PKS modules, a general understanding of the mechanistic principles underlying module iteration remains elusive. This report serves as the first interrogation of a stuttering module from atrans-AT subfamily PKS that is also naturally split across two polypeptides. Previous work has shown that Module 5 of the NOCAP (nocardiosisassociatedpolyketide) synthase iterates precisely three times in the biosynthesis of its polyketide product, resulting in an alltrans-configured triene moiety in the polyketide product. Here we describe the intrinsic catalytic properties of this NOCAP synthase module. Through complementary experimentsin vitroand inE. coli, the “split-and-stuttering” module was shown to catalyze up to five elongation cycles, although its dehydratase domain ceased to function after three cycles. Unexpectedly, the central olefinic group of this truncated product had acisconfiguration. Our findings set the stage for further in-depth analysis of a structurally and functionally unusual PKS module with contextual biosynthetic plasticity.

TOC/Abstract Graphic
Real-Time, Direct Classification of Nanopore Signals with SquiggleNet
Authors: Bao Yuwei , Wadden Jack , Erb-Downward John R. , Ranjan Piyush , Zhou Weichen , McDonald Torrin L. , Mills Ryan E. , Boyle Alan P. , Dickson Robert P. , Blaauw David , Welch Joshua D.
Published: January 2021

Oxford Nanopore sequencers provide results in real time as DNA passes through a nanopore and can eject a molecule after it has been partly sequenced. However, the computational challenge of deciding whether to keep or reject a molecule in real time has limited the application of this capability. We present SquiggleNet, the first deep learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than the DNA passes through the pore, allowing real-time classification and read ejection. When given the amount of sequencing data generated in one second, the classifier achieves significantly higher accuracy than base calling followed by sequence alignment. Our approach is also faster and requires an order of magnitude less memory than approaches based on alignment. SquiggleNet distinguished human from bacterial DNA with over 90% accuracy, generalized to unseen species, identified bacterial species in a human respiratory meta genome sample, and accurately classified sequences containing human long interspersed repeat elements.
Targeting primary and metastatic uveal melanoma with a G protein inhibitor
Authors: Onken Michael D. , Makepeace Carol M. , Kaltenbronn Kevin M. , Choi Joelle , Hernandez-Aya Leonel , Weilbaecher Katherine N. , Piggott Kisha D. , Rao P. Kumar , Yuede Carla M , Dixon Alethia J. , Osei-Owusu Patrick , Cooper John A. , Blumer Kendall J.
Published: January 2021

Uveal melanoma (UM) is the most common intraocular tumor in adults. Nearly half of UM patients develop metastatic disease and often succumb within months because effective therapy is lacking. A novel therapeutic approach has been suggested by the discovery that UM cell lines driven by mutant constitutively active Gq or G11 can be targeted by FR900359 (FR) or YM-254890, which are bioavailable, selective inhibitors of the Gq/11/14 subfamily of heterotrimeric G proteins. Here, we have addressed the therapeutic potential of FR for UM. We found that FR inhibited all oncogenic Gq/11 mutants reported in UM. FR arrested growth of all Gq/11-driven UM cell lines tested, but induced apoptosis only in a few. Similarly, FR inhibited growth of, but did not efficiently kill, UM tumor cells from biopsies of primary or metastatic tumors. FR evoked melanocytic redifferentiation of UM tumor cells with low (class 1), but not high (class 2), metastatic potential. FR administered systemically below its LD50 strongly inhibited growth of PDX-derived class 1 and class 2 UM tumors in mouse xenograft models, and reduced blood pressure transiently. FR did not regress xenografted UM tumors, or significantly affect heart rate, liver function, hematopoiesis, or behavior. These results indicated the existence of a therapeutic window in which FR can be explored for treating UM, and potentially other diseases caused by constitutively active Gq/11.
Regulation of neurofilament length and transport by a dynamic cycle of polymer severing and annealing
Authors: Uchida Atsuko , Peng Juan , Brown Anthony
Published: January 2021

Neurofilaments are space-filling cytoskeletal polymers that are transported into axons where they accumulate during development to expand axon caliber. We previously described novel severing and end-to-end annealing mechanisms in neurons that alter neurofilament length. To explore the functional significance of neurofilament length, we developed a long-term multi-field time-lapse method to track the movement of fluorescently tagged neurofilaments in axons of cultured neurons for up to 30 minutes. All filaments moved rapidly, but long filaments paused and reversed more often, resulting in little net movement, whereas short filaments moved persistently for long distances, pausing and reversing less often. Long filaments severed more frequently, generating shorter filaments, and short filaments annealed more frequently, generating longer filaments. Thus, neurofilament length is regulated by a dynamic cycle of severing and annealing and this influences neurofilament transport. Site-directed mutagenesis to mimic phosphorylation at four known phosphorylation sites in the head domain of neurofilament protein L generated shorter neurofilaments that moved more frequently. A non-phosphorylatable mutant had the opposite effect. Treatment of cultured neurons with activators of protein kinase A, which phosphorylates three of these sites, increased neurofilament severing. This effect was blocked by the non-phosphorylatable mutant. We propose that focal destabilization of intermediate filaments by N-terminal phosphorylation of their constituent polypeptides at specific locations along their length may be a general enzymatic mechanism for severing this class of cytoskeletal polymers. Our data suggest a novel mechanism for the control of neurofilament transport and accumulation in axons based on regulation of neurofilament polymer length.

Neurofilaments are space-filling cytoskeletal polymers that are transported into axons where they accumulate to expand axon caliber, which is an important determinant of axonal conduction velocity. We reported previously that neurofilaments can lengthen and shorten by novel end-to-end annealing and severing mechanisms. Here, we show that neurofilament annealing and severing are robust phenomena in cultured neurons that act antagonistically to dynamically regulate neurofilament length, which in turn regulates their transport. In addition, we present evidence for a novel enzymatic mechanism of intermediate filament severing based on site-directed phosphorylation of the neurofilament subunit proteins. We propose that modulation of neurofilament length by annealing and severing may be a mechanism for the regulation of neurofilament transport and accumulation in axons.
Tropism of SARS-CoV-2 for Developing Human Cortical Astrocytes
Authors: Andrews Madeline G. , Mukhtar Tanzila , Eze Ugomma C. , Simoneau Camille R. , Perez Yonatan , Mostajo-Radji Mohammed A. , Wang Shaohui , Velmeshev Dmitry , Salma Jahan , Kumar G. Renuka , Pollen Alex A. , Crouch Elizabeth E. , Ott Melanie , Kriegstein Arnold R.
Published: January 2021

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) readily infects a variety of cell types impacting the function of vital organ systems, with particularly severe impact on respiratory function. It proves fatal for one percent of those infected. Neurological symptoms, which range in severity, accompany a significant proportion of COVID-19 cases, indicating a potential vulnerability of neural cell types. To assess whether human cortical cells can be directly infected by SARS-CoV-2, we utilized primary human cortical tissue and stem cell-derived cortical organoids. We find significant and predominant infection in cortical astrocytes in both primary and organoid cultures, with minimal infection of other cortical populations. Infected astrocytes had a corresponding increase in reactivity characteristics, growth factor signaling, and cellular stress. Although human cortical cells, including astrocytes, have minimal ACE2 expression, we find high levels of alternative coronavirus receptors in infected astrocytes, including DPP4 and CD147. Inhibition of DPP4 reduced infection and decreased expression of the cell stress marker, ARCN1. We find tropism of SARS-CoV-2 for human astrocytes mediated by DPP4, resulting in reactive gliosis-type injury.
Adherence to quarantine protocols to prevent the spread of COVID-19: the mediating effect of intrinsic and extrinsic motivations
Authors: Suplico-Jeong Luz , Bautista Jr Reynaldo Altillo , Guillen Jr Nelson Borrega , Murad Noel Sajid
Published: January 2021

Purpose

Iloilo province was singled out as a model province in the Philippines because of its ability to prevent the spread of COVID-19. This study aims to examine the factors that influenced Iloilo residents' adherence to quarantine protocols.

Design/methodology/approach

A total of 334 Iloilo residents joined the survey. Using the theory of planned behavior (TPB), the results suggest a significant impact of attitude on adherence to quarantine protocols, while subjective norm, self-efficacy and controllability were not significant.

Findings

This study suggests that attitude predicts adherence to quarantine protocols. Further, the results showed that intrinsic motivation mediated the relationship between (1) attitude and adherence to quarantine protocols and (2) subjective norm and adherence to quarantine protocols. This implies that intrinsic motivation such as staying alive can encourage a resident to adhere to quarantine protocols.

Research limitations/implications

Subsequent research should also consider how to mitigate the effects of similar public health crises in the future.

Practical implications

The study implies that intrinsic motivation such as staying alive can encourage a resident to follow quarantine protocol given this pandemic.

Social implications

Health campaigns can lead to a more favorable attitude toward quarantine protocols adherence. Given the value of subjective norm, campaigns can also frame quarantine protocols adherence as socially responsible behavior. This can be used to target provinces with the highest risk of infection within the population. These insights can be used by local government units (LGUs), media and other stakeholders to encourage residents to adhere to quarantine protocols.

Originality/value

This study provides insights that can be used by the LGUs, media and other stakeholders to encourage residents to follow quarantine protocols.
Parent-adolescent communication on sexual and reproductive health among school adolescents of Woldia town, Ethiopia by the year 2019
Authors: Masresha Seteamlak Adane , Alen Gedefaw Diress
Published: January 2021

Purpose

The purpose of this paper is to assess the magnitude of parent-adolescent communication on sexual and reproductive health (SRH) issues and its association with gender and premarital sexual practice among school adolescents of Woldia town.

Design/methodology/approach

School-based cross-sectional study was conducted on 368 unmarried secondary and preparatory school adolescents (15–19 years) in Woldia town. Simple random sampling was employed to select study participants. Self-administered questionnaire was used. Data were entered by EPI-Data version 3.0.2 and analyzed by using SPSS version 20.

Findings

In this study, 56.3% of school adolescents had parental communication on sexual and reproductive health issues. The result of this study showed that adolescents who had history of sexual intercourse where 64% less likely to communicate with parents on sexual and reproductive health issues (AOR: 0.36 95% CI: 0.20, 0.65), but there was no association between gender and sexual and reproductive health communication between adolescent and parent (AOR: 1.06, 95% CI: 0.64, 1.75).

Originality/value

Parent-adolescent communication about sexual matters is one of the means that encourages adolescents to adopt responsible sexual behavior. Many children in Africa are uncomfortable to have a communication about sexual and reproductive health issues with their parents because the subject is a taboo topic in most homes.
Turbulent flow with nonequilibrium chemical reaction in single snorkel RH
Authors: Chen Shifu , Lei Hong , Wang Meng , Ding Changyou , Dou Weixue , Chang Lishan
Published: January 2021

Purpose

The reported mathematical models of gas–liquid flow in single snorkel Rheinstahl–Heraeus (SSRH) are based on the assumption of steady Ar-molten steel flow. The purpose of this paper is to develop a mathematical model to describe the unsteady turbulent flow (CO-Ar-molten steel) with nonequilibrium decarburization reaction.

Design/methodology/approach

On the base of the finite volume method, the computational fluid dynamics software CFX is used to predict the unsteady fluid flow, the spatial distributions of CO/argon gas and carbon element. The water model experiment and the industrial experiment are carried out to verify the mathematical models.

Findings

A two-way coupling model (T-WCM) based on algebraic slip model is developed to investigate the coupling phenomena. The related results show that T-WCM is more rigorous and accurate than one-way coupling model in predicting carbon content of molten steel. The amount of CO gas, which can enhance turbulent flow and mass transfer, is about three times the argon gas blown into SSRH.

Originality/value

CO gas is the key factor in investigating the transport phenomena. This study fully reveals the truth about the unsteady gas-liquid flow in SSRH. It is necessary to adopt T-WCM based on algebraic slip model to describe the CO-Ar-molten steel flow phenomenon.
The empowering role of hospitable telemedicine experience in reducing isolation and anxiety: evidence from the COVID-19 pandemic
Authors: Cheng Yusi , Wei Wei , Zhong Yunying , Zhang Lu
Published: January 2021

Purpose

This paper aims to explore how hospitable telemedicine services empowered patients during the COVID-19. Expanding from the technology aspect, this research integrated the philosophy of hospitality organizational culture by including factors related to human-human interaction as significant predictors for patients’ sense of empowerment (perceived competence and control) in coping with their emotional stress (anxiety and isolation).

Design/methodology/approach

Survey data were obtained from 409 general consumers who have used video-based virtual consultation since February 2020. Stepwise multiple regression and simple linear regression analyses were used for hypotheses testing.

Findings

The results reveal that the doctors’ reliability, responsiveness and empathy significantly predict patients’ perceived competence and control. Perceived usefulness and convenience of telemedicine technology enhance patients’ perceived competence and control. Patients’ sense of empowerment significantly reduces their anxiety and sense of isolation.

Research limitations/implications

To fully understand the role of hospitality in people’s telemedicine experiences, future studies are encouraged to not only examine the patients-clinicians interactions but also explore the patients-support staff interactions.

Practical implications

Health care providers’ “bed-side” manners empower patients in managing their emotional stress. Health care providers should be trained for their empathetic ability and communication skills. Strategies such as collaborating with hospitality schools and business schools can be implemented to help build medical student’s patient-centric attitudes and skills.

Originality/value

This paper provided empirical evidence for the value of hospitality in health care and offered useful suggestions for health care providers, especially by empowering vulnerable people during catastrophic events such as COVID-19.
Making #blacklivesmatter in universities: a viewpoint on social policy education
Authors: Bennett Bindi , Ravulo Jioji J. , Ife Jim , Gates Trevor G.
Published: January 2021

Purpose

The purpose of this viewpoint article is to consider the #BlackLivesMatter movement within the Aboriginal Australian struggle for equality, sovereignty and human rights. Indigenous sovereignty has been threatened throughout Australia's history of colonization. We provide a viewpoint and recommendations for social policy education and practice.

Design/methodology/approach

We provide commentary and interpretation based upon the lived experience of Black, Indigenous and Other People of Color (BIPOC) co-authors, co-authors who are Allies, extant literature and practice wisdom as social policy educators.

Findings

Universities are sources of knowledge production, transmission and consumption within society. We provide critical recommendations for what social policy education within universities can address human rights and the #BlackLivesMatter movement.

Originality/value

Culturally responsive inclusion for BIPOC has only just begun in Australia and globally within the context of the #BlackLivesMatter movement. This paper adds critical conversation and recommendations for what social policy programs might do better to achieve universities' teaching and learning missions.
The future is now: calling for a focus on temporal issues in information system research
Authors: Venkatesh Viswanath , Sykes Tracy Ann , Aljafari Ruba , Poole Marshall Scott
Published: January 2021

Purpose

As information systems (IS) phenomena continue to emerge and evolve in our ever-changing economic and social contexts, researchers need to increase their focus on time in order to enrich our theories. The purpose of this paper is to present broad suggestions for IS researchers about how they can direct some of their research efforts to consider, conceptualize and incorporate time into research endeavors and how they might be mindful about considering and specifying time-related scope conditions of their research efforts.

Design/methodology/approach

The authors synthesize empirical studies and discuss three distinct yet related frameworks of time and the benefits they can provide. The authors choose two research streams that reflect dynamic economic and social contexts – namely, enterprise systems and social networks – to illustrate how time and frameworks of time can be leveraged in our theory development and research design.

Findings

The authors demonstrate that limited research in IS has incorporated a rich conceptualization and/or discussion of time. The authors build on this gap to highlight guidelines that researchers can adopt to enrich their view of time.

Originality/value

Given the dynamic nature of IS phenomena and the increased availability of longitudinal data, the authors’ suggestions aim to urge and guide IS researchers about ways in which they can incorporate time into their theory and study designs.
Holding the government to account for its finances: the “Unsung” heroes of the UK parliament scrutiny unit
Authors: Ferry Laurence , Honeysett Larry , Midgley Henry
Published: January 2021

Purpose

This paper describes the role and remit of the Scrutiny Unit, which assists members of parliament (MPs) with the analysis of accounting data.

Design/methodology/approach

The analysis is developed through an understanding of the secondary literature and practical experience of the work of the Unit.

Findings

The Scrutiny Unit is an unappreciated and yet vital part of the way in which financial scrutiny operates within the UK parliament. It translates to MPs key financial and economic documents including the budget and accounts. It is a unique institution, covering the entire financial cycle of approval and accountability within parliament.

Originality/value

This is the first descriptive piece on the Unit in an accounting journal and contributes to our understanding of how financial accountability works within the UK parliament.
Genome‐enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats
Authors: DeLong Edward F.
Published: January 2021

As a young bacteriologist just launching my career during the early days of the ‘microbial revolution’ in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross‐disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize ‘wild’ bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited ‘How we did it’ perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene‐ and genome‐enabled surveys, and application of genome‐guided, cultivation‐independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!
Proton‐transfer‐reaction time‐of‐flight mass spectrometry (PTR‐TOF‐MS) as a tool for studying animal volatile organic compound (VOC) emissions
Authors: Portillo‐Estrada Miguel , Van Moorleghem Charlotte , Janssenswillen Sunita , Cooper Richard Joseph , Birkemeyer Claudia , Roelants Kim , Van Damme Raoul
Published: January 2021

Chemical sensing in vertebrates is crucial in their lives, and efforts are undertaken towards deciphering their chemical language. Volatile organic compounds (VOCs) are a group of chemicals believed to play an essential role in a wide variety of animal interactions. Therefore, understanding what animals sense themselves and untangling the ecological role of their volatile cues can be accomplished by analysing VOC emissions. A proton‐transfer‐reaction time‐of‐flight mass spectrometer (PTR‐TOF‐MS) is an instrument that measures VOCs in real‐time in an air sample. Since this technique acts as a hyper‐sensitive ‘nose’ it has a similar potential in deciphering the chemical language of vertebrates.

Here, we validate the use of PTR‐TOF‐MS as a tool to measure VOCs from vertebrates, which in turn will help resolve vertebrate interactions through VOCs. The instrument monitors and records the full spectrum of VOCs emitted by an individual with a high accuracy and low detection limit, including transient VOC emissions. We propose and test diverse measuring configurations that allow for measurement of VOC emissions from different vertebrates and their exudates: full body, specific parts of the body, urine and femoral pores. In addition, we test configurations for sudden and short‐lasting processes as VOCs emitted during adder skin shedding as well as the emissions of skin secretions upon mechanical and physiological stimulation in amphibia. Our configurations work in tandem with gas chromatography–mass spectrometry (GC‐MS) to allow compound structure verification.

We discuss the configurations and methodologies used and conclude with recommendations for further studies, such as the choice of chamber size and flow. We also report the results of the measurements on vertebrates—that are novel to science—and discuss their ecological meaning.

We argue that PTR‐TOF‐MS has a high potential to resolve important unanswered questions in vertebrate chemical ecology with great adaptability to a wide range of experimental set‐ups. If combined with a structure verification tool, such as GC‐MS, the creative deployment of PTR‐TOF‐MS in various future study designs will lead to the identification of ecologically relevant VOCs.
A review of seascape complexity indices and their performance in coral and rocky reefs
Authors: Lazarus Mai , Belmaker Jonathan
Published: January 2021

Seascape complexity is an important driver of ecological processes in marine systems. Today, high‐resolution, multiscale bathymetric data are being collected due to rapid advances in marine technologies and image processing, drastically improving the detailed mapping of the physical structure of the seascape. However, these data are rarely synthesized to create comprehensive complexity estimates, and complexity is still mostly measured using a small set of simple indices.

The aims of this study are to: (a) review existing seascape complexity indices and propose innovative indices designed to capture the marine organism perspective, (b) quantify the interrelationships among these complexity indices; (c) test the performance of these indices in explaining fish assemblage structure; and (d) provide R code to easily reproduce the indices. Seascape bottom topography for this study was quantified using digital depth recordings along transects in Mediterranean sub‐tropical rocky reefs and Red Sea tropical coral reefs. These were used to generate complexity indices that were then compared to visually surveyed fish assemblages.

We found that several common indices captured similar complexity facets, while an innovative family of structural diversity indices, representing the diversity of physical elements, captured distinct complexity facets not represented by existing indices. No single index was consistently superior; however, vertical relief was consistently included as a top predictor of fish assemblage structure. Interestingly, the most commonly used index, rugosity, was a poor predictor.

We suggest a new, distinct set of structural diversity indices that may explain considerable variation in fish assemblages. The results suggest that several indices may need to be combined to capture the full influence of complexity on marine diversity and caution against the use of a single ‘universal’ index. While bathymetric data are increasingly being collected at high resolutions and increasing scales, synthesizing these data requires the use of appropriate complexity indices. The guidelines and recommendations presented here, along with the supplemental R code, will facilitate progress towards a more complete representation of different complexity facets.
Chyle leak following pancreatico‐duodenectomy: a tertiary hepatopancreaticobiliary unit's experience and a proposed management algorithm
Authors: Russell Thomas , Tanase Andrei , Bowles Matthew , Briggs Christopher , Kanwar Aditya , Stell David , Aroori Somaiah
Published: January 2021

Background

Chyle leak (CL) is an uncommon complication of pancreatico‐duodenectomy (PD). Its incidence, risk factors, and effect on prognosis are not well described and optimum management remains debated. This study aims to calculate incidence of CL following PD and identify risk factors. Following a literature review, we have proposed a management algorithm.

Methods

This is a retrospective review of all patients who underwent PD between January 2006 and April 2020 at a tertiary hepatopancreaticobiliary unit in the UK. The following data were obtained: age, gender, American Society of Anesthesiologists grade, body mass index, co‐morbidities, duration of surgery, tumour histology, length of stay and mortality.

Results

A total of 560 patients were included. Seventeen developed CL (3.04%). Median age was 64 years (range 50–81). Sixteen (94.1%) patients still had their surgical drain in at the time of CL diagnosis. One (5.9%) did not and had free intra‐abdominal fluid on computed tomography; a diagnosis was made after an ultrasound‐guided drain had been inserted. CL patients were more likely to have higher body mass index (mean 30.5 kg/m2 (range 17–43) versus 26.7 kg/m2 (22–38)) (P = 0.02) and longer duration of operation (mean 6.2 h (range 4.3–9.0) versus 5.6 (3.0–11.0)) (P = 0.03). All cases of CL resolved without operative intervention. CL did not affect length of stay (median 10 days (range 4–41) versus 11 (4–34)).

Conclusions

In our series, 3.04% of patients who underwent PD developed CL. No patients required a return to theatre, and none had CL recurrence.
Comparative analysis of emergency general surgery on‐call structure and its impact on emergency appendicectomy outcomes
Authors: Gounder Jaya , Dissanayake Bhanuka , Burstow Matthew J. , Yuide Peter J. , Naidu Sanjeev , Lancashire Raymond P. , Chua Terence C.
Published: January 2021

Background

In Australia, there has been a shift from the traditional ‘on‐call’ surgical model to the ‘acute surgical unit’ (ASU) model to improve outcomes in acute general surgery. Using emergency appendicectomy as a standardized procedure, we aimed to identify the different patterns of care between these on‐call structures by comparing two metropolitan district hospitals; one that employs a traditional on‐call model and the other, which employ the ASU model.

Methods

Data on consecutive patients undergoing emergency appendectomies at the two hospitals (traditional and ASU model) between July 2018 and December 2018 were retrieved for retrospective review. Patient factors, preoperative factors, operative factors and post‐operative outcomes were collected and tabulated for comparative analysis between the traditional versus ASU model of care.

Results

Univariate analysis demonstrated that there were a greater proportion of consultant‐led cases (P < 0.001), a shorter time to theatre (P = 0.047) and a greater number of out‐of‐hours operations (P < 0.001) in the ASU model compared to the traditional model. A larger proportion of patients from the traditional model underwent a computed tomography scan as part of their diagnostic workup compared to the ASU model (P < 0.001). There was no difference in negative appendicectomy rates, intraoperative conversion rates, post‐operative complication rates or mean lengths of hospital stay between the two on‐call models.

Conclusion

The ASU and traditional on‐call model appears to achieve equivalent care outcomes for patients with acute appendicitis.
Hyperbaric oxygen therapy for the treatment of perianal fistulas in 20 patients with Crohn’s disease
Authors: Lansdorp Corine A. , Gecse Krisztina B. , Buskens Christianne J. , Löwenberg Mark , Stoker Jaap , Bemelman Willem A. , D’Haens Geert R.A.M. , van Hulst Rob A.
Published: January 2021

Background

Positive effects of hyperbaric oxygen on perianal fistulas in Crohn's disease have been reported.

Aim

To assess efficacy, safety and feasibility of hyperbaric oxygen in Crohn's disease patients with therapy‐refractory perianal fistulas.

Methods

Twenty consecutive patients were recruited at the out‐patient fistula clinic of the Amsterdam UMC. Crohn's disease patients with high perianal fistula(s) failing conventional treatment for over 6 months were included. Exclusion criteria were presence of a stoma, rectovaginal fistula(s) and recent changes in treatment regimens. Patients received treatment with 40 hyperbaric oxygen sessions and outcome parameters were assessed at Week 16.

Results

Seven women and 13 men were included (median age 34 years). At Week 16, median scores of perianal disease activity index and modified van Assche index (co‐primary outcome parameters) decreased from 7.5 (95% CI 6‐9) to 4 (95% CI 3‐6, P < 0.001), and from 9.2 (95% CI 7.3‐11.2) to 7.3 (95% CI 6.9‐9.7, P = 0.004) respectively. Perianal disease activity index scores ≤4 (representing inactive perianal disease) were observed in 13/20 patients (65%). Twelve patients showed a clinical response (60%) and four (20%) clinical remission, assessed with fistula drainage assessment. Median C‐reactive protein and faecal calprotectin levels decreased from 4.2 mg/mL (95% CI 1.6‐8) to 2.2 (95% CI 0.9‐4.3, P = 0.003) and from 399 µg/g (95% CI 52‐922) to 31 (95% CI 16‐245, P = 0.001), respectively.

Conclusions

We found significant clinical, radiological and biochemical improvement in Crohn's disease patients with therapy‐refractory perianal fistulas after treatment with hyperbaric oxygen.

Clinical trial registration: www.trialregister.nl/trial/6489.
The importance of co‐delivery of nanoparticle‐siRNA and anticancer agents in cancer therapy
Authors: Khelghati Nafiseh , Soleimanpour Mokhtarvand Jafar , Mir Mostafa , Alemi Forough , Asemi Zatollah , Sadeghpour Alireza , Maleki Masomeh , Samadi Kafil Hossein , Jadidi‐niaragh Farhad , Majidinia Maryam , Yousefi Bahman
Published: January 2021

According to global statistics, cancer is the second leading cause of death worldwide. Because of the heterogeneity of cancer, single‐drug therapy has many limitations due to low efficacy. Therefore, combination therapy with two or more therapeutic agents is being arisen. One of the most important approaches in cancer therapy is the shot down of key genes involved in apoptotic processes and cell cycle. In this regard, siRNA is a good candidate, a highly attractive method to suppressing tumor growth and invasion. Combination therapy with siRNAs and chemotherapeutic agents can overcome the multidrug resistance and increase apoptosis. The efficient delivery of siRNA to the target cell/tissue/organ has been a challenge. To overcome these challenges, the presence of suitable delivery systems by using nanoparticles is interesting. In this review, we discuss the current challenges for successful RNA interference. Also, we suggested proper a strategy for delivering siRNA that can be useful in targeting therapy. Finally, the combination of a variety of anticancer drugs and siRNA through acceptable delivery systems and their effects on cell cycle and apoptosis will be evaluated.
Identifying meaningful dietary intake and physical activity questions for individual and population health
Authors: Shinall Jennifer Bennett , Schlundt David G. , Sullivan Mikaela H. , Frank Hannah J. , Po'e Eli K. , Sommer Evan C. , Bonnet Kemberlee R. , Burgess Laura E. , Barkin Shari L. , Haws Kelly L.
Published: January 2021

We aimed to identify valid screening questions for adults regarding physical activity and dietary behaviours that (a) were correlated with BMI, (b) were deemed by patients and providers to be relevant to clinical care, and (c) have utility for longitudinal understanding of health behaviours in populations. The goal was to identify screening questions that could be implemented at annual health care visits. First, we identified dietary behaviour questions and solicited patient input. Next, we tested both physical activity and dietary behaviour questions in a large sample to test their potential utility. Finally, we used cognitive interviews with patients and physicians to narrow our assessment for clinical settings. We present a parsimonious and reliable six‐question scale of physical activity and dietary behaviours for research settings, as well as a three‐question scale for clinical settings. We demonstrate a robust relationship between these measures and obesity. Additionally, we present evidence that these measures may serve as a useful red flag for patients before they develop obesity. We provide a concise and useful tool for assessing patients' physical activity and dietary behaviours in a variety of research settings. We also highlight the importance of incorporating this tool into the clinical intake flow for inclusion in patients' Electronic Health Record.