bluuebunny/crossref_metadata_2025 huggingface dataset:
The Impact of COVID-19 on Clinical Nurse Specialists and Patients With Cancer
Authors: Forster Alice S. , Zylstra Janine , von Wagner Christian , Hirst Yasemin , Forster Martin , Walshe Rebecca , Kazzaz Zainab , Steptoe Andrew , Birchall Martin , Patani Neill
Published: August 2022

Purpose/Aims

Uptake and delivery of cancer services across the United Kingdom have been significantly impacted by the COVID-19 pandemic. This study aimed to understand the impact of the pandemic on the working practices of clinical nurse specialists and their patient interactions across different cancer specialties.

Design

We performed a cross-sectional survey exploring nurses' experiences of delivering care during the pandemic, as well as their perceptions of the concerns that cancer patients were experiencing.

Methods

Clinical nurse specialists working in London cancer services were invited to complete an online questionnaire. Nurses' experiences and their perceptions of patients' concerns were analyzed descriptively.

Results

Fifty-four nurses participated. Almost half had been redeployed to other clinical areas during the pandemic (n = 19). COVID-19 discussions added 5 to 10 minutes on average to most consultations, with nurses either working longer/unpaid hours (34%) or spending less time talking to patients about cancer (39%) to deal with this. Approximately 50% of nurses would have liked additional information and support from their hospital.

Conclusions

Clinical nurse specialist time and resources have been stretched during the COVID-19 pandemic. Hospitals need to work with nursing staff to ensure the specific information needs of cancer patients are being met.
A multi-centre observational study of HIV, tuberculosis and risk of chronic lung disease in urban West Africa
Authors: Fink Douglas L. , Oladele David A. , Slack Abigail J. , Odubela Oluwatosin , Musari-Martins Tomilola , Okechukwu Adaobi , Adetayo Kemi , Opaneye Sola , Abubakar Rufai , David Agatha , Cai James , Quaderi Shumonta , Abubakar Ibrahim , Ezechi Oliver , Hurst John R. , Lipman Marc , Salako Babatunde
Published: August 2022

Objective:

HIV and tuberculosis (TB) are risk factors for non-communicable chronic lung disease (CLD). Despite the high prevalence of these infections in West Africa, there are no studies that compare CLD between people with HIV and HIV-negative populations in this setting. This study sought to quantify the contribution of HIV and TB infection in addition to conventional CLD risk factors, such as tobacco and biofuel exposure, to CLD in urban West Africa.

Design:

A multi-centre cross-sectional study was conducted in three community clinics in Lagos, Nigeria between 2018 and 2019.

Methods:

Spirometry, questionnaires and clinical records were used to estimate prevalence of CLD and association with risk factors.

Results:

In total, 148 HIV-negative individuals and 170 HIV-positive individuals completed the study. Current cigarette (11 of 318, 3.5%) and lifetime domestic biofuel (6 of 318, 1.8%) exposures were low. Airway obstruction (33 of 170, 19.4% vs. 12 of 148, 8.1%, P = 0.004) and CLD (73 of 170, 42.9% vs. 34 of 148, 23%, P < 0.0001) were more prevalent in people with HIV compared with the HIV-negative group. HIV infection [odds ratio 2.35 (1.33, 4.17), P = 0.003] and history of TB [odds ratio 2.09 (1.04, 4.20), P = 0.038] were independently associated with increased risk of CLD.

Conclusion:

HIV and TB far outweigh conventional risk factors, including tobacco and domestic biofuel exposure, as drivers of non-communicable CLD in urban West Africa. Current global policy for CLD may have limited impact on CLD in this setting. Enhanced prevention, diagnosis and management strategies for incident HIV and TB infections are likely to have a significant impact on long-term lung health in sub-Saharan Africa.
Reciprocating Rasp for Use in Mandibular Anterior Subapical Osteotomy
Authors: Zhang Wenbin , Shen Steve Guofang , Shi Jun
Published: August 2022

The article describes a reciprocating rasp used in the mandibular anterior subapical osteotomy. Over the past 2 years, reciprocating rasp osteotomy was introduced in the Oral and Craniomaxillofacial Surgery Department of Shanghai Ninth People’s Hospital. No complication such as bleeding, wound infection, or tissue necrosis has been encountered. The use of reciprocating rasp avoids iatrogenic damage to adjacent structures and reduces the time spent operating mandibular anterior subapical osteotomy. Therefore, it is recommended for mandibular anterior subapical osteotomy.
Modification of LeFort I Osteotomy for Correction of Severe Maxillary Cant Associated With Fibrous Dysplasia
Authors: Anehosur Venkatesh , Acharya Priyanka , Suresh Amal , Kumar Niranjan
Published: August 2022

Differential superior reposition of maxilla following LeFort I osteotomy in the correction of maxillary cant poses a greater challenge especially when associated with the pathology like fibrous dysplasia which completely obliterates the antrum. Purpose of this paper is to highlight the modification of LeFort I osteotomy and hypothesis is to assess its difficulty index in modifying the standard steps, in executing the maxillary separation at various to correct the gross facial asymmetry to achieve a favorable outcome. Multiphased management involved scrupulous clinical planning, advanced imaging by computed tomgraphy scans, stereolithographic models to debulk the lesion. The second phase included pre surgical orthodontic evaluation along with correction of severe maxillary cant adopting a modified LeFort 1 osteotomy technique and standard bilateral sagittal split osteotomy, thereby simultaneously attaining functional stability and esthetic harmony.
Driving Ability Evaluation and Rehabilitation for People With Alzheimer’s Disease and Related Dementias
Authors: Liu Ziming , Grant Jordan , Simpson Skylar P. , Khattak Asad , Anderson Joel G. , Gao Zhiming , Zhao Xiaopeng
Published: August 2022

Worldwide, it is estimated that around 50 million older adults have Alzheimer’s disease and related dementias (ADRD). Cognitive deficits associated with ADRD may affect a driver’s perception and decision-making and potentially cause safety concerns. Despite much research, there lacks a comprehensive cognitive evaluation to determine the driving capability of a person with ADRD and it is unclear what are the most effective training and interventions that help to enhance driving performance for these individuals. The purpose of this article is to conduct a comprehensive literature survey to review and summarize studies of driving performance evaluation and intervention for people with ADRD and discuss perspectives for future studies. Although many studies have investigated the correlations between driving behaviors and cognitive performances for people with ADRD, it remains unclear how driving behaviors and cognitive performances are associated with psychophysiological measures. We discussed the need to develop regular driving evaluation and rehabilitation protocol for people with ADRD. We also highlighted the potential benefit to combine driving tests with psychophysiological measures to assist in characterizing personalized cognitive evaluation in the behavioral evaluation process.
Establishing a national reference laboratory for antimicrobial resistance using a whole-genome sequencing framework: Nigeria’s experience
Authors: Okeke Iruka N. , Aboderin Aaron O. , Egwuenu Abiodun , Underwood Anthony , Afolayan Ayorinde O. , Kekre Mihir , Oaikhena Anderson O. , Odih Erkison Ewomazino , Omotayo Hamzat T. , Dada-Adegbola Hannah , Ogunleye Veronica O. , Ikhimiukor Odion O. , Aanensen David M. , Ihekweazu Chikwe
Published: August 2022

Whole-genome sequencing (WGS) is finding important applications in the surveillance of antimicrobial resistance (AMR), providing the most granular data and broadening the scope of niches and locations that can be surveilled. A common but often overlooked application of WGS is to replace or augment reference laboratory services for AMR surveillance. WGS has supplanted traditional strain subtyping in many comprehensive reference laboratories and is now the gold standard for rapidly ruling isolates into or out of suspected outbreak clusters. These and other properties give WGS the potential to serve in AMR reference functioning where a reference laboratory did not hitherto exist. In this perspective, we describe how we have employed a WGS approach, and an academic–public health system collaboration, to provide AMR reference laboratory services in Nigeria, as a model for leapfrogging to national AMR surveillance.
Accurate 3D Positron Range Correction Method for Heterogeneous Material Densities in PET
Authors: Li Chong , Scheins Jürgen , Tellmann Lutz , Issa Ahlam , Wei Long , Shah N. Jon , Lerche Christoph
Published: August 2022

Objective

The positron range is a fundamental, detector-independent physical limitation to special resolution in positron emission tomography (PET) as it causes a significant blurring of the reconstructed PET images. A major challenge for positron range correction methods is to provide accurate range kernels that inherently incorporate the generally inhomogeneous stopping power, especially at tissue boundaries. In this work, we propose a novel approach to generate accurate three-dimensional (3-D) blurring kernels both in homogenous and heterogeneous media to improve PET spatial resolution.

Approach

In the proposed approach, positron energy deposition was approximately tracked along straight paths, depending on the positron stopping power of the underlying material. The positron stopping power was derived from the attenuation coefficient of 511keV gamma photons according to the available PET attenuation maps. Thus, the history of energy deposition is taken into account within the range of kernels. Special emphasis was placed on facilitating the very fast computation of the positron annihilation probability in each voxel.

Results

Positron path distributions of 18F in low-density polyurethane were in high agreement with Geant4 simulation at an annihilation probability larger than 10−2∼10−3 of the maximum annihilation probability. The Geant4 simulation was further validated with measured 18F depth profiles in these polyurethane phantoms. The tissue boundary of water with cortical bone and lung was correctly modeled. Residual artifacts from the numerical computations were in the range of 1%. The calculated annihilation probability in voxels shows an overall difference of less than 20% compared to the Geant4 simulation.

Significance

The proposed method significantly improves spatial resolution for non-standard isotopes by providing accurate range kernels, even in the case of significant tissue inhomogeneities.
Attention Deficit Hyperactivity Disorder and the gut microbiome: An ecological perspective
Authors: Cickovski Trevor , Mathee Kalai , Aguirre Gloria , Tatke Gorakh , Hermida Alejandro , Narasimhan Giri , Stollstorff Melanie
Published: August 2022

Attention Deficit Hyperactivity Disorder (ADHD) is an increasingly prevalent neuropsychiatric disorder characterized by hyperactivity, inattention, and impulsivity. Symptoms emerge from underlying deficiencies in neurocircuitry, and recent research has suggested a role played by the gut microbiome. The gut microbiome is a complex ecosystem of interdependent taxa with an exponentially complex web of interactions involving these taxa, plus host gene and reaction pathways, some of which involve neurotransmitters with roles in ADHD neurocircuitry. Studies have analyzed the ADHD gut microbiome using macroscale metrics such as diversity and composition, and have proposed several biomarkers. Few studies have delved into the complex underlying dynamics ultimately responsible for the emergence of such metrics, leaving a largely incomplete, sometimes contradictory, and ultimately inconclusive picture.

We aim to help complete this picture by venturing beyond taxa abundances and into taxa relationships (i.e. cooperation and competition), using a publicly available gut microbiome dataset from 30 Control (15 female, 15 male) and 28 ADHD (15 female, 13 male) undergraduate students. We conduct our study in two parts. We first perform the same macroscale analyses prevalent in ADHD gut microbiome literature (diversity, differential, biomarker, and composition) to observe the degree of correspondence, or any new trends. We then estimate two-way ecological relationships by producing Control and ADHD Microbial Co-occurrence Networks (MCNs), using SparCC correlations (p < 0.01). We perform community detection to find clusters of taxa estimated to mutually cooperate along with their centroids, and centrality calculations to estimate taxa most vital to overall gut ecology. We conclude by summarizing our results, and provide conjectures on how they can guide future experiments, some methods for improving our experiments, and general implications for the field.
Maximizing the impact of limited vaccine supply under different epidemic conditions: a two-city monkeypox modelling analysis
Authors: Knight Jesse , Tan Darrell H.S. , Mishra Sharmistha
Published: August 2022

background

In the current global monkeypox outbreak, many jurisdictions have been faced with limited vaccine supply, motivating interest in efficient allocation. We sought to explore optimal vaccine allocation between two linked transmission networks over a short-term time horizon, across a range of epidemic conditions.

methods

We constructed a deterministic compartmentalsveirmodel of monkeypox transmission. We parameterized the model to reflect two representative, weakly connectedgbmsmsexual networks (cities) in Ontario. We simulated roll-out of 5000 vaccine doses over 15 days, starting 60 days after epidemic seeding with 10 imported cases. Within this model, we varied: the relative city (network) sizes, epidemic potentials (R0), between-city mixing, and distribution of imported/seed cases between cities. In each context (combination of varied factors), we then identified the “optimal” allocation of doses between cities — resulting in the fewest cumulative infections by day 120.

results

Under our modelling assumptions, we found that a fixed supply of vaccines could generally avert more infections over short-term time horizons when prioritized to: a larger transmission network, a network with more initial infections, and/or a network with greaterR0. Greater between-city mixing decreased the influence of initial seed cases, and increased the influence of cityR0on optimal allocation. Under mixed conditions (e.g. fewer seed cases but greaterR0), optimal allocation saw doses shared between cities, suggesting that proximity-based and risk-based vaccine prioritization can work in combination to minimize transmission.

interpretation

Prioritization of limited vaccine supply based on network-level risk factors can help minimize transmission during an emerging epidemic. Such prioritization should be grounded in an understanding of context-specific drivers of risk, and should acknowledge the potential connectedness of multiple transmission networks.
Cell-associated Transcriptional Alterations in the Retinal of Alzheimer’s Disease
Authors: Ngolab Jennifer , Mark Adam , Buchanan Justin , Korouri Shaina , Priessl Sebastian , Rosenthal Sara Brin , Wang Allen , Fisch Kathleen M. , Rissman Robert A.
Published: August 2022

Current approaches for studying pathologic changes in the retina associated with Alzheimer’s Disease (AD) remain heterogeneous, limiting the use of retinal amyloid-beta as a viable biomarker for AD. Transcriptomic profiling of the retina has provided cell-specific insight into AD progression in the brain yet is lacking in the retina. In this study, we implemented a non-biased approach through next generation sequencing to profile frozen archived retinal tissues from autopsy/pathologically confirmed AD and non-diagnosed cases (NonAD). A total of 37,211 nuclei were isolated from frozen retinal tissue punches originating from AD, and 31,326 were isolated from non-diagnosed cases. Gene expression patterns specific to the retinal region and major retinal cell types were represented in both tissue groups. AD-associated genes were differentially expressed in AD retinal glial cells, including microglia. A greater percentage of microglial nuclei from AD retinal nuclei expressed TYRO protein tyrosine kinase-binding protein (TYROBP) compared to nonAD retinal nuclei. However, compared to microglia from single retinal cell datasets from elderly non-diseased individuals, TYROBP expression is highly expressed in the single cell data set, indicating TYROBP transcripts reside within the cytoplasm. However, other AD-associated genes were differentially expressed in AD nuclei such as DOCK2, PICALM, and PLCG2 compared to non-diseased single-cell microglia, implicating a role of these genes in the AD retina. To summarize, we extracted a high number of nuclei from frozen retinal tissue that retain specific gene markers for cell classification and highlighted candidate AD-associated genes in retinal microglia that may be viable in future AD retinal studies.
Single-cell RNA sequencing highlights a reduced function of natural killer and cytotoxic T cell in recovered COVID-19 pregnant women
Authors: Aziz Nor Haslinda Abd , Salker Madhuri S. , Lankapalli Aditya Kumar , Shafiee Mohammed Nasir , Kocak Ersoy , Pal Surya Sekhar , Khalid Omer , Kasim Norhana Mohd , Kalok Aida , Fuad Norashikin Abdul , Ossowski Stephan , Casadei Nicolas ,   Deutsche COVID-19 OMICS Initiative (DeCOI), Brucker Sara Y , Riess Olaf , Singh Yogesh
Published: August 2022

Pregnancy is a complex phenomenon during which women undergo immense immunological change throughout this period. Having an infection with the SARS-CoV-2 virus leads to an additional burden on the highly stretched immune response. Some studies suggest that age-matched pregnant women are more prone to SARS-CoV-2 infection compared with normal healthy (non-pregnant) women, while alternative evidence proposed that pregnant women are neither susceptible nor develop severe symptoms. This discrepancy in different findings regarding the immune responses of pregnant women infected with SARS-CoV-2 virus is not well understood. In this study, we investigated how SARS-CoV-2 viral infection could modulate the immune landscape during the active infection phase and recovery in pregnant females. Using flow cytometry, we identified that intermediate effector CD8+ T cells were increased in pregnant women who had recovered from COVID-19 as opposed to those currently infected. Similarly, an increase in CD4+ T helper cells (early or late) during the recovered phase was observed during the recovery phase compared with infected pregnant women or healthy pregnant women, whilst infected pregnant women had a reduced number of late effector CD4+ T cells. CD3+CD4- CD8-NKT cells that diminished during active infection in contrast to healthy pregnant women were significant increase in recovered COVID-19 recovered pregnant women. Further, our single-cell RNA sequencing data revealed that infection of SARS-CoV-2 had changed the gene expression profile of monocytes, CD4+ effector cells and antibody producing B cells in convalescent as opposed to healthy pregnant women. Additionally, several genes with cytotoxic function, interferon signalling type I & II, and pro- and anti-inflammatory functions in natural killer cells and CD8+ cytotoxic T cells were compromised in recovered patients compared with healthy pregnant women. Overall, our study highlights that SARS-CoV-2 infection deranged the adaptive immune response in pregnant women and could be implicated in pregnancy complications in ongoing pregnancies.
A syntenin inhibitor blocks endosomal entry of SARS-CoV-2 and a panel of RNA viruses
Authors: Lindqvist Richard , Benz Caroline , Sereikaite Vita , Maassen Lars , Laursen Louise , Jemth Per , Strømgaard Kristian , Ivarsson Ylva , Överby Anna K.
Published: August 2022

Viruses are dependent on interactions with host factors in order to efficiently establish an infection and replicate. Targeting such interactions provides an attractive strategy to develop novel antivirals. Syntenin is a protein known to regulate the architecture of cellular membranes by its involvement in protein trafficking, and has previously been shown to be important for HPV infection. Here we show that a highly potent and metabolically stable peptide inhibitor that binds to the PDZ1 domain of syntenin inhibits SARS-CoV-2 infection by blocking the endosomal entry of the virus. Furthermore, we found that the inhibitor also hampered chikungunya infection, and strongly reduced flavivirus infection, which are completely dependent on receptor mediated endocytosis for their entry. In conclusion, we have identified a novel pan-viral inhibitor that efficiently target a broad range of RNA viruses.
First-sight recognition of touched objects shows that chicks can solve the Molyneux’s problem
Authors: Versace Elisabetta , Freeland Laura , Wang Shuge , Emmerson Michael G.
Published: August 2022

If a congenitally blind person learns to distinguish between a cube and a sphere by touch, would they immediately recognise these objects by sight if their vision is restored? This question, posed by Molyneux in 1688, has puzzled philosophers and scientists. We overcame ethical and practical difficulties in the study of cross-modal recognition by using inexperienced chicks. We hatched chicks in darkness, exposed them to tactile smooth vs. bumpy stimuli in darkness and then tested them in a visual recognition task. At first sight, chicks previously exposed to smooth stimuli approached the smooth stimulus significantly more than those exposed to the bumpy stimuli. This shows that cross-modal recognition does not require multimodal experience. At least in precocial species, supra-modal brain areas already function at birth.
Muscle-derived Cues are Required to Specify Proprioceptor Pool Identity
Authors: Norovich Amy L. , Brenner-Morton Susan , Jessell Thomas M.
Published: August 2022

The formation of spinal sensory-motor circuits requires the diversification of proprioceptive sensory neurons (pSNs). During embryonic development, pSNs acquire molecular identities aligned with the limb muscle that they supply, but the extent of pSN “pool” diversity and how it is established are poorly understood. We find that the gene v-set transmembrane domain-2b (vstm2b) is preferentially expressed in pSN pools supplying dorsal limb muscle targets along the proximodistal extent of the limb. Genetic removal of muscle precursor cells from the developing limb greatly reduces the number of pSNs expressing vstm2b, demonstrating a requirement for limb muscle in specifying pSN pool identity. Comparison of dorsal and ventral muscle precursors identifies spatially restricted expression of the genes lumican (lum), decorin (dcn), and BMP binding endothelial regulator (bmper), demonstrating that dorsal and ventral muscle groups possess distinct molecular identities early in embryonic development. Together, these findings show that limb muscle is required for the specification of pSN pool identity and define early molecular correlates of dorsoventral muscle identity that are positioned to drive neuronal diversity.
Dauer fate in aCaenorhabditis elegansBoolean network model
Authors: Kandoor Alekhya Abhiram , Fierst Janna L.
Published: August 2022

Cellular fates are determined by genes interacting across large, complex biological networks. A critical question is how to identify causal relationships spanning distinct signaling pathways and underlying organismal phenotypes. Here, we address this question by constructing a Boolean model of a well-studied developmental network and analyzing information flows through the system. Depending on environmental signalsCaenorhabditis elegansdevelop normally to sexual maturity or enter a reproductively delayed, developmentally quiescent ‘dauer’ state, progressing to maturity when the environment changes. The developmental network that starts with environmental signal and ends in the dauer/no dauer fate involves genes across 4 signaling pathways including cyclic GMP, Insulin/IGF-1, TGF-β and steroid hormone synthesis. We identified three stable motifs leading to normal development, each composed of genes interacting across the Insulin/IGF-1, TGF-Beta and steroid hormone synthesis pathways. Three genes known to influence dauer fate,daf-2, daf-7andhsf-1, acted as driver nodes in the system. Using causal logic analysis, we identified a five gene cyclic subgraph integrating the information flow from environmental signal to dauer fate. Perturbation analysis showed that a multifactorial insulin profile determined the stable motifs the system entered and interacted withdaf-12as the switchpoint driving the dauer/no dauer fate. Our results show that complex organismal systems can be distilled into abstract representations that permit full characterization of the causal relationships driving developmental fates. Analyzing organismal systems from this perspective of logic and function has important implications for studies examining the evolution and conservation of signaling pathways.
Identification of transcriptional landscapes and functions of the inhibition of ARHGEF2 in hepatocellular carcinoma cells
Authors: Zhang Min , He David C , Chung Andrew
Published: August 2022

The RHO guanine exchange factor ARHGEF2 has exchange activity toward RHOA, which is essential for the development of cancers such as liver cancer. However, the potential functions and mechanisms of ARHGEF2 in the progression of liver cancer are largely unknown. In this study, we identified the transcriptional landscapes of hepatocellular carcinoma cells treated with ARHGEF2 shRNAs. The gene enrichment assays such as KEGG and GO were used to further analyze the potential signaling pathways. Moreover, the PPI network and Reactome map were used to further identify the biological processes. The results showed that Alzheimer’s disease disease (AD) and Cushing syndrome (CS) are the major signaling pathways involved in the ARHGEF2-shRNAs treated hepatocellular carcinoma cells. We identified the top ten interactive genes including ICAM1, APOE, LDLR, NAT10, HSPA1A, EDN1, CACNA1C, KCNMA1, SNAI1, and ELN. Our study may provide novel mechanisms for the treatment of liver cancer by inhibiting ARHGEF2.
A touchscreen device for behavioral testing in pigs
Authors: Ao Will , Grace Megan , Floyd Candace L. , Vonder Haar Cole
Published: August 2022

Pigs are becoming more common research models due to their utility in studying neurological conditions such as traumatic brain injury, Alzheimer’s disease, and Huntington’s Disease. However, behavioral tasks often require a large apparatus and are not automated, which may disinterest researchers in using important functional measures. To address this, we developed a touchscreen that pigs could be trained on for behavioral testing. A rack-mounted touchscreen monitor was placed in an enclosed, weighted audio rack. A pellet dispenser was operated by a radio frequency transceiver to deliver fruit-flavored sugar pellets from across the testing room. Programs were custom written in Python and executed by a Raspberry Pi. A behavioral shaping program was designed to train pigs to interact with the screen and setup responses for future tasks. Pigs rapidly learned to interact with the screen. To demonstrate efficacy in more complex behavior, two pigs were trained on a delay discounting tasks and two pigs on a color discrimination task. The device held up to repeated testing of large pigs and could be adjusted to the height of minipigs. The device can be easily recreated and constructed at a relatively low cost. Research topics ranging from brain injury to pharmacology to vision could benefit from behavioral tasks designed to specifically interrogate relevant function. More work will be needed to develop tests which are of specific relevance to these disciplines.
The neighborhood of interaction in human crowds is neither metric nor topological, but visual
Authors: Wirth Trenton D. , Dachner Gregory C. , Rio Kevin W. , Warren William H.
Published: August 2022

Global patterns of collective motion in bird flocks, fish schools, and human crowds are thought to emerge from local interactions within a neighborhood of interaction, the zone in which an individual is influenced by their neighbors. Both topological and metric neighborhoods have been reported in birds, but this question has not been addressed in humans. With a topological neighborhood, an individual is influenced by a fixed number of nearest neighbors, regardless of their physical distance; whereas with a metric neighborhood, an individual is influenced by all neighbors within a fixed radius. We test these hypotheses experimentally with participants walking in real and virtual crowds, by manipulating the crowd’s density. Our results rule out a strictly topological neighborhood, are approximated by a metric neighborhood, but are best explained by a visual neighborhood with aspects of both. This finding has practical implications for modeling crowd behavior and understanding crowd disasters.
Circadian rhythms in multiple behaviors depend on sex, neuropeptide signaling, and ambient light
Authors: Wahba Lari Rays , Perez Blanca , Nikhil KL , Herzog Erik D. , Jones Jeff R.
Published: August 2022

Organisms have evolved circadian (near-24 h) rhythms in behavior to anticipate daily opportunities and challenges such as mating and predation. However, the ethological investigation of circadian behavioral rhythms has been traditionally limited to studying easy-to-measure behaviors at higher temporal resolution or difficult-to-measure behaviors with limited temporal resolution. Our ability to simultaneously record circadian rhythms in multiple behaviors has also been limited by currently available technology. We thus sought to examine eight overt, ethologically-relevant behaviors never before studied simultaneously as a function of time of day: eating, drinking, grooming, rearing, nesting, digging, exploring, and resting. To address the hypothesis that the daily patterning of these behaviors depends on neuropeptide signaling, sex, and ambient light, we used high-throughput machine learning to automatically score millions of video frames of freely-behaving male and female wild-type and vasoactive intestinal peptide (Vip)-deficient mice. Automated frame-by-frame predictions of the eight behaviors correlated highly with consensus labels by trained human classifiers. We discovered reliable daily rhythms in many previously unreported behaviors that peaked at stereotyped times of day and persisted in constant darkness. Surprisingly, nesting and digging rhythms differed dramatically in both phase and amplitude between male and female mice. InVip-deficient mice, daily rhythms in most behaviors were low amplitude and peaked earlier in the day in a light:dark cycle, while rhythms in all behaviors peaked randomly throughout the day in constant darkness. We also found that for most behaviors, time budgets predominantly differed by light cycle, but transition probabilities predominantly differed with VIP signaling and by sex. We conclude that machine learning can be used to reveal novel sex, neuropeptide, and light-dependent behaviors at time scales from seconds to days.
Isolation and characterization of autophagic bodies from yeast
Authors: Kawamata Tomoko , Makino Shiho , Kagohashi Yoko , Sasaki Michiko , Ohsumi Yoshinori
Published: August 2022

Autophagy is a major cellular degradation pathway that is highly conserved among eukaryotes. The identification of cargos captured by autophagosomes is critical to our understanding of the physiological significance of autophagy in cells. In the yeast S. cerevisiae, cells deficient in the vacuolar lipase Atg15 accumulate autophagic bodies (ABs) within the vacuole following the induction of autophagy. As ABs contain cytosolic components including proteins, RNAs, and lipids, their purification allows the identification of material targeted by autophagy for degradation. In this study, we demonstrate a method to purify intact ABs from vacuoles that retain membrane integrity and contain autophagic cargos. This technique offers a valuable tool for the identification of the cargos of autophagy, examination of autophagic cargo selectivity, and biochemical characterization of autophagosome membranes.
Expression of complexes I, II and IV in the SGNs of noise-stimulated rats was decreased, and mitochondrial energy metabolism was disturbed, mediating the damage and degeneration of SGNs
Authors: Ding Zhong Jia , Wang Yin , Wang Ren Feng , Mi Wen Juan , Qiu Jian Hua , Zha Ding Jun
Published: August 2022

Noise-induced hearing impairment can mediate delayed injury of spiral neurons (SGNs), resulting in degeneration of nerve fibers, synaptic degeneration and even death of SGNs. We believe that delayed injury is related to mitochondrial energy metabolism disorders. Therefore, we investigated ATP and the electron transport chain (ETC) in rat SGNs after noise injury and found that with prolonged injury time, ATP synthesis and the expression of complexes II and IV decreased, indicating the functional decline of the ETC. The maintenance of ETC function is related to subunit import and assembly of the complex. The disulfide relay mechanism controlled by the apoptosis inducing factor/coiled-coil-helix-coiled-coil-helix domain-containing protein 4(AIF/CHCHD4) pathway can regulate mitochondrial protein import. The results showed that AIF expression in SGNs decreased after noise exposure, indicating that noise damage to SGNs can restore intramitochondrial protein input by downregulating the AIF/CHCHD4 pathway, hindering ETC function; insufficient ETC function is a possible reason for the delayed injury of SGNs.
Distinct non-coding RNA cargo of extracellular vesicles from M1 and M2 human primary macrophages
Authors: Pantazi Paschalia , Clements Toby , Venø Morten , Abrahams Vikki M , Holder Beth
Published: August 2022

Macrophages are important antigen presenting cells which can release extracellular vesicles (EVs) carrying functional cargo including non-coding RNAs. Macrophages can be broadly classified into M1 ‘classical’ and M2 ‘alternatively-activated’ macrophages. M1 macrophages have been linked with inflammation-associated pathologies, whereas a switch towards an M2 phenotype indicates resolution of inflammation and tissue regeneration. Here, we provide the first comprehensive analysis of the small RNA cargo of EVs from human M1 and M2 primary macrophages. Using small RNA sequencing, we identified several types of small non-coding RNAs in M1 and M2 macrophage EVs including miRNAs, isomiRs, tRNA fragments, piRNA, snRNA, snoRNA and Y-RNA fragments. Distinct differences were observed between M1 and M2 EVs, with higher relative abundance of miRNAs, and lower abundance of tRNA fragments in M1 compared to M2 EVs. MicroRNA-target enrichment analysis identified several gene targets involved in gene expression and inflammatory signalling pathways. EVs were also enriched in tRNA fragments, primarily originating from the 5’ end or the internal region of the full length tRNAs, many of which were differentially abundant in M1 and M2 EVs. Similarly, several other small non-coding RNAs, namely piRNAs, snRNAs, snoRNAs and Y-RNA fragments, were differentially enriched in M1 and M2 EVs; we discuss their putative roles in macrophage EVs. In conclusion, we show that M1 and M2 macrophages release EVs with distinct RNA cargo, which has the potential to contribute to the unique effect of these cell subsets on their microenvironment.
Acquisition and processing methods of whole-brain layer-fMRI VASO and BOLD: The Kenshu dataset
Authors: Koiso Kenshu , Müller Anna K , Akamatsu Kazuaki , Dresbach Sebastian , Wiggins Christopher J , Gulban Omer Faruk , Goebel Rainer , Miyawaki Yoichi , Poser Benedikt A , Huber Laurentius
Published: August 2022

Cortical depth-dependent functional magnetic resonance image (fMRI), also known as layer-fMRI, has the potential to capture directional neural information flow of brain computations within and across large-scale cortical brain networks. E.g., layer-fMRI can differentiate feedforward and feedback cortical input in hierarchically organized brain networks.

Recent advancements in 3D-EPI sampling approaches and MR contrast generation strategies have allowed proof-of-principle studies showing that layer-fMRI can provide sufficient data quality for capturing laminar changes in functional connectivity. These studies have however not shown how reliable the signal is and how repeatable the respective results are. It is especially unclear whether whole-brain layer-fMRI functional connectivity protocols are widely applicable across common neuroscience-driven analysis approaches. Moreover, there are no established preprocessing fMRI methods that are optimized to work for whole-brain layer-fMRI datasets.

In this work, we aimed to serve the field of layer-fMRI and build tools for future routine whole-brain layer-fMRI in application-based neuroscience research. We have developed publicly available sequences, acquisition protocols, and processing pipelines for whole-brain layer-fMRI. These protocols are validated across 60 hours of scanning in nine participants. Specifically, we identified and exploited methodological advancements for maximizing tSNR efficiency and test-retest reliability.

We are sharing an extensive multi-modal whole-brain layer-fMRI dataset (20 scan hours of movie-watching in a single participant) for the purpose of benchmarking future method developments: The Kenshu dataset. With this dataset, we are also exemplifying the usefulness of whole brain layer-fMRI for commonly applied analysis approaches in modern cognitive neuroscience fMRI studies. This includes connectivity analyses, representational similarity matrix estimations, general linear model analyses, principal component analysis clustering, etc. We believe that this work paves the road for future routine measurements of directional functional connectivity across the entire brain.

Graphical Abstract
“New career” profiles for young adults incorporating traditional and protean career orientations and competencies
Authors: Kim Sujin , Hood Michelle , Creed Peter , Bath Debra
Published: August 2022

Purpose

Using latent profile analysis, the authors explored the career profiles of young adult tertiary students (N = 468, 73.9% women; mean age 20 years) to determine the relative importance of traditional career orientation (TCO) and protean career orientation (PCO) beliefs for them.

Design/methodology/approach

Young adults studying at university can aspire to traditional career experiences as they believe organizations will support their professional and career development. However, since the development of newer career models, the TCO model has received little research attention compared to the PCO.

Findings

The authors found that the dominant profile exhibited average levels of TCO, PCO and career competencies, and that this mixed profile was associated with more mature career identity development and greater organizational commitment. A second profile, with low TCO, average PCO and career competencies, showed a similar level of career maturity to the mixed profile, but exhibited less organizational commitment. A third profile, with average TCO, low PCO and career competencies, especially vocational identity awareness, was related to less career development and organizational commitment.

Originality/value

The findings suggest that a mixed traditional-protean orientation is common in young adult tertiary students and that the development of a vocational identity is important for positive career outcomes, regardless of orientation.
An examination of the influence of urban violence on rental value of residential property in Kaduna metropolis
Authors: Odebode Adedayo Ayodeji , Aro Shittu Oluwakayode , Agboola Alirat Olayinka
Published: August 2022

Purpose

The paper aims to examine the influence of urban violence on residential property rental value in Kaduna metropolis. This is motivated by the spate of insurgency and the attendant destructions of land and properties in the past few years in the study area.

Design/methodology/approach

This paper adopted a survey of key sites of urban violence and also a total enumeration of all the 67-estate surveying and valuation firms in the study area to elicit from them vital information on trends on rental from 2011 to 2019. The data obtained were analyzed using both descriptive and inferential methods of statistical analysis.

Findings

The result of this study revealed that among other sources of urban violence, violence fueled by ethnic affiliations/convictions is the only significant factor that influenced rental value of residential property in the study area. The regression analysis shows that ethnic violence accounted for 21.6% of the variability observed in residential property rental value over the period of study. Furthermore, the correlation result showed that ethnic violence is negatively correlated (−0.458) and significantly related to residential property rental value.

Practical implications

This study concluded that the emergence of urban violence in Kaduna metropolis contributed to a fall in the rental value of residential property in the study area. This study thus suggested policy directions that could engender harmonious coexistence among different ethnic groups in the study area.

Originality/value

This study is expected to enhance improvement in residential property rental value in Kaduna metropolis through increase assurance to security of lives and property.
Multi-objective particle swarm optimization algorithm using Cauchy mutation and improved crowding distance
Authors: Li Qingxia , Zeng Xiaohua , Wei Wenhong
Published: August 2022

Purpose

Multi-objective is a complex problem that appears in real life while these objectives are conflicting. The swarm intelligence algorithm is often used to solve such multi-objective problems. Due to its strong search ability and convergence ability, particle swarm optimization algorithm is proposed, and the multi-objective particle swarm optimization algorithm is used to solve multi-objective optimization problems. However, the particles of particle swarm optimization algorithm are easy to fall into local optimization because of their fast convergence. Uneven distribution and poor diversity are the two key drawbacks of the Pareto front of multi-objective particle swarm optimization algorithm. Therefore, this paper aims to propose an improved multi-objective particle swarm optimization algorithm using adaptive Cauchy mutation and improved crowding distance.

Design/methodology/approach

In this paper, the proposed algorithm uses adaptive Cauchy mutation and improved crowding distance to perturb the particles in the population in a dynamic way in order to help the particles trapped in the local optimization jump out of it which improves the convergence performance consequently.

Findings

In order to solve the problems of uneven distribution and poor diversity in the Pareto front of multi-objective particle swarm optimization algorithm, this paper uses adaptive Cauchy mutation and improved crowding distance to help the particles trapped in the local optimization jump out of the local optimization. Experimental results show that the proposed algorithm has obvious advantages in convergence performance for nine benchmark functions compared with other multi-objective optimization algorithms.

Originality/value

In order to help the particles trapped in the local optimization jump out of the local optimization which improves the convergence performance consequently, this paper proposes an improved multi-objective particle swarm optimization algorithm using adaptive Cauchy mutation and improved crowding distance.
Lean supply chain management and Industry 4.0: a systematic literature review
Authors: Rossini Matteo , Powell Daryl John , Kundu Kaustav
Published: August 2022

Purpose

Even though the integration of Lean Supply Chain Management (LSCM) and Industry 4.0 (I4.0) technologies is relatively recent, it has been receiving a lot of attention. Partly because it is a recent field of practise and research and partly because the number of works developed in this field has grown rapidly, it is important to frequently update the perspectives on this field of investigation. Thus, this study aims to review the integration between LSCM and I4.0 analysing relationship at operative, tactical and strategic levels.

Design/methodology/approach

Systematic literature review was conducted to identify and explain the integration of LSCM and I4.0 from scientific sources that were published before March 2021.

Findings

The analysis of the literature revealed the level of integration of LSCM and I4.0 is present at different managerial levels. Moreover, when the integration is detailed at different managerial levels, it appears that LSCM paves the way for the adoption of I4.0 at a strategic level, while I4.0 technologies promise to enhance LSCM practices at the operational level.

Research limitations/implications

The main contribution of this study is the framework which shows that LSCM paves the way for the adoption of I4.0 at a strategic level, while I4.0 technologies promise to enhance LSCM practices at the operational level.

Originality/value

This study develops a new perspective of the articles published under the thematic of LSCM and I4.0. Additionally, it proposes a framework of analysis that can be used by future researchers. Finally, it shows the most recent implementations of LSCM and I4.0, exposing the current trends, improvements and also the main gaps.
Capturing cross-border logistics for analysis and improvement
Authors: Bandaranayake Namal , Kiridena Senevi , Kulatunga Asela K.
Published: August 2022

Purpose

Achieving swift and even flow of cargo through the border, the ultimate objective of cross-border logistics (CBL) requires the close coordination and collaboration of a multitude of stakeholders, as well as optimally configured systems. To achieve and sustain competitiveness in a dynamic international trade environment, CBL processes must undergo periodic analysis, improvement and optimization. This study aims to develop a modelling framework to capture CBL processes for analysis and improvement.

Design/methodology/approach

Relying on the extant literature, a meta-model is developed incorporating significant perspectives required to model CBL processes. Popular process modelling notations are evaluated against the meta-model and their ease of comprehension is also evaluated. The selected notation through evalution is augmented with addendums for a comprehensive depiction of CBL processes.

Findings

The capacity of role activity diagrams (RADs) to depict all perspectives, including interactions in a single diagram, makes them particularly suitable for modelling CBL processes. RADs have been complemented with physical flow diagrams and methods to capture temporal dimension, enabling a comprehensive view of CBL processes laying the foundation for insightful analysis.

Research limitations/implications

The meta-model developed in this paper paves the way to develop an analysis framework which requires further research.

Originality/value

The lack of well-accepted modelling notations for studying CBL processes prompts researchers to search and adapt different formalisms. This study has filled this gap by proposing a comprehensive modelling framework able to capture CBL processes at different granularities in rich detail. Not only does the developed meta-model aid in selecting the notation, it is also useful in analysing the constituent elements of CBL processes.