bluuebunny/crossref_metadata_2025 huggingface dataset:
Is there an association between peptic ulcer disease and osteoporosis: a systematic review and cumulative analysis
Authors: Zhao Shankun , Ding Lingzhi , Xie Qiang , Zhang Jingsheng , Yang Suqing , Xu Weifang , Yang Jianhong , Xu Yan , Zheng Changjun
Published: November 2020

Background

Mounting studies have emerged indicating that patients with peptic ulcer disease (PUD) are at a high risk of developing osteoporosis, but the evidence has not been previously synthesized. The present study aims to examine whether patients with PUD have a significantly higher prevalence of osteoporosis than the healthy normal subjects.

Methods

Four electronic databases were systematically searched for eligible studies up to February 2020. The association between PUD and osteoporosis was evaluated by calculating the relative risk (RR) with a 95% confidence interval (CI).

Results

Six observational studies were finally included, enrolling a total of 216 122 individuals. Synthetic results from the six included studies providing the number of cases for both sexes demonstrated that PUD was significantly associated with an increased risk of osteoporosis (95% CI, 1.37–1.89; P < 0.001). In line with this finding, the combined effect from the three studies independently reporting the male subjects also yielded to a positive relationship between PUD and osteoporosis (RR = 2.08; 95% CI,1.10–3.93; P = 0.023). However, when restricted to female participants, pooled results indicated that women patients with PUD would not suffer significantly more risk of osteoporosis than the general women population (RR = 1.36; 95% CI, 0.84–2.21, P = 0.212).

Conclusions

This is the first study for quantifying the positive association between PUD and the risk of osteoporosis by conducting a meta-analysis. In clinical practice, assessment of the bone mineral density and antiosteoporosis treatments are recommended for those potential patients with PUD.
Utilizing an Evidence-Based Practice Approach to Examining Infusion Therapy Practices in Non-hospital Outpatient Ambulatory Clinic Settings
Authors: Trentadue Mary Beth , Rafter Deborah , Weiss Suzanne , Phelan Cynthia H.
Published: November 2020

The types of infusion therapy services provided in ambulatory care settings are expanding. The Infusion Therapy Standards of Practice can be applied across service locations/care settings; however, no specific literature was found to indicate how these recommendations have been applied in ambulatory care settings. This article demonstrates how an Ambulatory Care Shared Governance Practice Council led a systemwide evidence-based practice (EBP) initiative to improve infusion therapy over an 18-month period (May 2017 to December 2018). The initiative, based on the Iowa Model Revised, strengthened the nurses understanding of EBP and successfully standardized infusion therapy care across ambulatory care settings.
Changing the Culture of Pediatric Palliative Care at the Bedside
Authors: Drach Laura L. , Cook Michelle , Shields Susan , Burger Kristina J.
Published: November 2020

The benefits of palliative care services have been widely documented; however, many organizations are unable to financially support the number of professionals needed to meet the growing demand. Nurses receive minimal training in palliative care, and the resulting knowledge gap can lead to a lack of confidence when providing the essential aspects of palliative care. Recognizing the needs of patients and staff, one organization created a Palliative Care Champions Program to support and educate bedside staff. The Champions received initial and ongoing education, allowing them to function as liaisons to the Palliative Care Team while providing education and mentorship to staff. A program evaluation tool measuring Champion comfort and confidence in the provision of palliative care has shown positive results. Champions reported an increase in confidence in their ability to identify appropriate consults and mentor staff, as well as an increase in comfort in being considered an expert in palliative care. Consults to the Palliative Care service increased by 28% within the first 12 months of program implementation. The Palliative Care Champions Program framework can be easily adapted to fit the needs of other organizations.
The Impact of Terbutaline as Adjuvant Therapy in the Treatment of Severe Asthma in the Pediatric Emergency Department
Authors: Adair Erik , Dibaba Daniel , Fowke Jay H. , Snider Mark
Published: November 2020

Objective

Parenteral β-agonists are often used as adjuvant treatment for severe asthma exacerbations in pediatric patients. We wanted to determine if the addition of a single dose of parenteral terbutaline to our asthma protocol resulted in fewer pediatric intensive care unit (PICU) admissions.

Methods

Patients were identified using a retrospective cohort analysis from a single, tertiary care, urban children's hospital. Patients presenting directly to our emergency department aged 2 to 18 years were included if they had a diagnosis of severe asthma exacerbation, defined by an initial Respiratory Clinical Score (RCS) of 9 or higher. A total of 787 patients were identified during the study timeframe (December 16, 2017, to December 31, 2018), and of those, 651 patients met study criteria and were included in the analysis. The χ2 test was used to establish P values for categorical variables. For normally distributed variables, a t test was used. For nonnormally distributed variables, the Kruskal-Wallis test was used. A P value of 0.05 or less was interpreted as statistically significant.

Results

Patients who received terbutaline had an increased risk of admission to the PICU (P < 0.001). This association was lost after controlling for age, sex, continuous albuterol use, and intramuscular epinephrine use (P = 0.362). Patients receiving terbutaline in the emergency department also had a higher risk of admission to the hospital (odds ratio, 1.55; confidence interval, 1.08–2.22; P = 0.020) as compared with their nonterbutaline counterparts. Overall, patients in the terbutaline group had a higher initial RCS at presentation. Upon further analysis, patients with the same RCS at presentation were more likely to be admitted if they received terbutaline than those who did not. There was no statistically significant difference in length of stay (P = 0.298) and BiPAP/CPAP use (P = 0.107). The patients on terbutaline were relatively more likely to require oxygen (P = 0.003) and intramuscular epinephrine (P = 0.010) than the patients not on terbutaline.

Conclusions

Terbutaline administration given to pediatric patients experiencing a severe asthma exacerbation was not associated with decreased PICU or general hospital floor admission. The study is limited given that it was a retrospective analysis. Further randomized controlled trials are needed to assess the role of terbutaline in severe acute asthma exacerbations in pediatric patients.
Health-Related Quality of Life in Patients With ANCA-Associated Vasculitis and Sinonasal Involvement
Authors: Cazzador Diego , Padoan Roberto , Colangeli Roberta , Pendolino Alfonso Luca , Felicetti Mara , Zanoletti Elisabetta , Emanuelli Enzo , Martini Alessandro , Doria Andrea , Nicolai Piero , Schiavon Franco
Published: November 2020

Background/Objective

The aim of this study was to assess the impact of sinonasal morbidity on quality of life (QoL) in antineutrophil cytoplasmic antibody–associated vasculitis (AAV).

Methods

This cross-sectional case-control study enrolled 71 patients—44 AAV cases with (ear, nose, and throat [ENT]–AAV) or without ENT involvement (non–ENT-AAV) undergoing multidisciplinary evaluations and 27 chronic rhinosinusitis (CRS) cases. Three validated QoL questionnaires (Sino-Nasal Outcomes Test-22 [SNOT-22], Nasal Obstruction Symptom Evaluation [NOSE], and Short-Form 36) were administered, and the 3 groups were compared.

Results

The ENT-AAV patients were significantly younger (p = 0.01), with less antineutrophil cytoplasmic antibody positivity frequency (p = 0.035) and lower renal involvement (p = 0.003) than the non–ENT-AAV patients.

The SNOT-22 questionnaire demonstrated significantly greater sinonasal morbidity in ENT-AAV patients compared with CRS patients (p < 0.001). The NOSE score of ENT-AAV patients was comparable to those of CRS patients, but higher than that of non–ENT-AAV patients (p < 0.001). The SNOT-22 and NOSE scores positively correlated with disease activity (p = 0.037; p = 0.004, respectively). Short-Form 36 domain-by-domain analysis revealed a significantly poorer QoL in ENT-AAV patients, especially with physical functioning being progressively impaired in CRS, non–ENT-AAV, and ENT-AAV patients (p < 0.001). No significant differences in QoL came to light when AAV patients were stratified according to current systemic o local treatments.

Conclusions

The QoL in AAV patients is significantly reduced, especially in the presence of ENT involvement. The AAV-related nasal morbidity is consistent and comparable to that reported by CRS patients. It significantly affects patients' QoL and in particular social functioning, leading to limitation in daily/work activities. Organ-focused questionnaires and multidisciplinary management are warranted to pursue a treat-to-target approach in these patients.
Importance of Ultrasound Education in Undergraduate Medical Curriculum
Authors: Zervides Constantinos , Kefala-Karli Pelagia , Sassis Leandros
Published: November 2020

Ultrasound imaging modality is a tool used in clinical practice and is being introduced gradually in the undergraduate curriculum of several medical schools worldwide. This study aims to assess medical students' perception regarding the integration of ultrasound training as part of undergraduate education. A questionnaire was given to first-year medical students after a 2-hour-long session, which was developed to introduce them in the fundamental physics theory and function of ultrasound equipment in the clinical practice. Analysis of the results indicated that students acknowledged that ultrasound training would improve their knowledge of internal medicine (P = 0.027) and of different diagnostic modalities (P = 0.019), and enhance their medical decision making (P = 0.0004). Moreover, students found beneficial the ultrasound education regarding correlating clinical knowledge with basic sciences (P = 0.0004). The study pointed out that the majority of first-year students have the opinion that the integration of ultrasound training in the medical program is valuable in medical education and patient care. However, work is needed to determine how to provide an optimal learning environment and to assess the competency of the training sessions.
Posterior Cranial Vault Distraction (PCVD): Common Complication Rates and Strategies of Prevention and Management
Authors: Hassan Abbas M. , Chappell Ava G. , Murthy Nikhil , Stoehr Jenna R. , Alden Tord , Gosain Arun K.
Published: November 2020

Background:

Posterior cranial vault distraction (PCVD) is a well-established procedure to treat infants with craniosynostosis. Craniofacial surgeons have seen an evolution in the complications following PCVD. This report aims to demonstrate the rates of common complications from PCVD, and to identify strategies for prevention and management of these complications.

Methods:

A formal literature review of studies on postoperative complications from PCVD was conducted to identify the breadth of reported complications from PCVD and rates of occurrence.

Results:

A total of 776 articles were captured by our search strategy. Nineteen original articles met inclusion criteria, with a total of 342 patients. The average rate of reported complications was 25%, range (0%–100%). The most commonly reported complication was postoperative infection (23.7%), followed by cerebrospinal fluid leak (20.3%) and device failure (15.3%). Postoperative infection, device exposure, iatrogenic vascular injury, cerebrospinal fluid leak, and other complications have the potential to disrupt distraction and increase morbidity and mortality.

Conclusions:

By continuing to identify and evaluate complications, prevention strategies can be determined and standardized to decrease complications from PCVD. These efforts uphold the ultimate goal for surgeons involved in the treatment of craniosynostosis: to provide safe, effective surgical care.
A Novel IRF6 Variant Detected in a Family With Nonsyndromic Cleft Lip and Palate by Whole Exome Sequencing
Authors: Wang Yanyang , Ma Cui , Jiang Chanyuan , Zhang Yongbiao , Wu Di
Published: November 2020

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common congenital craniofacial malformation, and its harmful effects on affected individuals and families are apparent. The causative genes and their mechanisms are not completely clear, although several studies have been conducted. Accordingly, in the present study, we recruited a Han Chinese family with hereditary NSCL/P to explore the possible causative variants of this disease using whole exome sequencing. Bioinformatics screening and analysis, mutation function prediction, species conservation analysis, and homology protein modeling were used to identify the variants and evaluate their influence. A mutation in the interferon regulatory factor 6 (IRF6) gene (c.961C>T; p.Val321Met) was detected as a candidate causative variant and predicted to be deleterious. The codon was found to be conserved in many species, and the residue change caused by this mutation changed the structure of IRF6 to a certain degree. The findings suggest that this IRF6 variant is probably the pathogenic cause of NSCL/P in this family. Our results further provide evidence that IRF6 variants play a role in the etiology of NSCL/P.
Usefulness of Tranexamic Acid Administration During Sagittal Split Ramus Osteotomy
Authors: Yoshida Mitsuhiro , Ono Shigehiro , Shimizu Yoshitaka , Oue Kana , Mukai Akari , Doi Mitsuru , Irifune Masahiro
Published: November 2020

Tranexamic acid has been used to reduce intraoperative bleeding; however, its effect on anti-inflammation and the amount of drainage after orthognathic surgery is yet to be determined. Therefore, we aimed to examine the effect of tranexamic acid on intraoperative bleeding volume and operation time, amount of drainage, and anti-inflammation after orthognathic surgery. Forty healthy women who underwent bilateral sagittal split ramus osteotomy under general anesthesia participated in this study. The amount of intraoperative bleeding, the operation time, the amount of drainage, and the C-reactive protein level were compared between patients intravenously administered with tranexamic acid before surgery (before-surgery group) and those administered with the drug after surgery (after-surgery group). All data were analyzed using the Student t-test. Results were considered to be statistically significant when P < 0.05. Although no significant difference was found in the amount of drainage between the groups (P > 0.05), significant variations were detected in the amount of bleeding during surgery (before-surgery group: 161.7 ± 45.3 mL versus after-surgery group: 270.2 ± 24.0 mL; P = 0.0009), operation time (before-surgery group: 141.3 ± 16.8 min versus after-surgery group: 166.8 ± 24.9 min; P = 0.03), and postoperative C-reactive protein level (before-surgery group: 3.77 ± 0.40 mg/dL versus after-surgery group: 5.02 ± 0.75 mg/dL; P = 0.012) between the groups. In conclusion, administering tranexamic acid before surgery was found to significantly decrease bleeding, reduce operation time, and suppress postoperative inflammation.
Unraveling Ariadne’s Thread Into the Labyrinth of aMCI
Authors: Giannouli Vaitsa , Tsolaki Magda
Published: November 2020

Background:

People with amnestic mild cognitive impairment (aMCI) face many daily challenges as memory loss is their predominant cognitive impairment.

Objectives:

This study examined whether financial capacity can be influenced by comorbid depression in patients with multiple-domain aMCI.

Materials and Methods:

The participants included 120 patients in 4 groups: multiple-domain aMCI with and without depressive symptoms, and nondemented elders with and without depression. Participants were examined with the Mini-Mental State Examination, the 15-item Geriatric Depression Scale, and the Legal Capacity for Property Law Transactions Assessment Scale.

Results:

The findings extend earlier work in other groups of older patients and indicate that the performance of patients with multiple-domain aMCI in cognitive functioning and financial capacity is severely impaired when depression coexists, resembling the performance of patients with mild Alzheimer disease.

Conclusions:

The results support special care for individuals with depression as this condition severely influences financial capacity in aMCI.
Alterations in the Retinal Vascular Network and Structure in MOG Antibody-Associated Disease: An Optical Coherence Tomography Angiography Study
Authors: Yu Jian , Huang Yongheng , Quan Chao , Zhou Lei , ZhangBao Jingzi , Wu Kaicheng , Zong Yuan , Zhou Xujiao , Wang Min
Published: November 2020

Background:

To determine retinal vessel density in patients with myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD).

Methods:

Twenty-five patients with MOGAD and 20 healthy participants were enrolled. Patients with MOGAD were divided into myelin oligodendrocyte glycoprotein antibody (MOG-Ab)-positive eyes with a history of optic neuritis (ON; MOG-Ab-ON+ group) or without a history of ON (MOG-Ab-ON− group). Visual function, retinal vessel densities, and thickness were measured.

Results:

The retinal nerve fiber layer, parafoveal ganglion cell and inner plexiform layers, and vessel densities in the peripapillary and parafoveal areas were significantly decreased in the MOG-Ab-ON+ eyes compared with healthy eyes and MOG-Ab-ON− eyes (all P < 0.05). An increasing number of ON episodes was associated with greater decreases in these variables (all P < 0.05). Visual field mean deviation was not significantly decreased in patients with a history of 1 or 2 episodes of ON, although the relative decreases in retinal nerve fiber layer thickness, parafoveal ganglion cell and inner plexiform layer thickness, peripapillary vessel density, and parafoveal vessel density reached 33.1%, 23.2%, 17.0%, and 11.5% (all P < 0.05), respectively, in eyes with 2 episodes of ON. The mean deviation was significantly correlated with peripapillary vessel density (P < 0.05) after adjustment for other variables. Best-corrected visual acuity was not significantly correlated with optical coherence tomography variables (all P > 0.05).

Conclusions:

MOG-Ab-associated ON was associated with significant decreases in retinal structure and vessel density, without significant deteriorations in visual function. The peripapillary vessel density might predict the visual outcomes in patients with MOG-Ab-associated ON.
Neurosarcoidosis and Ocular Inflammation: A Case Series and Literature Review
Authors: Desai Aishwary , Chaon Benjamin , Berkenstock Meghan
Published: November 2020

Objective:

To describe the ocular findings of neurosarcoidosis (NS) through a case series and review the current literature on the ocular complications of NS.

Methods:

Case series of 4 patients with a literature review.

Results:

Ophthalmic involvement in NS includes scleritis, cranial nerve palsies, uveitis, optic nerve granulomas, and occlusive retinal vasculitis.

Conclusion:

NS is an uncommon, but potentially life-threatening, manifestation of sarcoidosis with ocular involvement up to 25% of patients. Patients presenting with neuro-ophthalmic manifestations of sarcoidosis are more likely to have other sites of involvement requiring ophthalmologists to maintain a high index of suspicion for systemic disease.
Cerebral Venous Sinus Thrombosis in the COVID-19 Pandemic
Authors: Medicherla Chaitanya B. , Pauley Rachel A. , de Havenon Adam , Yaghi Shadi , Ishida Koto , Torres Jose L.
Published: November 2020

Background:

Recent studies have noted concern for increased thromboembolic events in the setting of Coronavirus Disease 2019 (COVID-19). Cerebral venous sinus thrombosis (CVST) is a form of thromboembolism that has been observed as a neuro-ophthalmologic complication of COVID-19.

Methods:

Review of the scientific literature.

Results:

In this article, we report an overview of CVST epidemiology, clinical presentation, diagnostics, disease pathophysiology, and management in the setting of COVID-19.

Conclusion:

CVST is an uncommon thromboembolic event with variable phenotypes and multiple etiologies. Neurologic complications can be severe, including significant visual deficits and death. Current observations suggest that the risk of CVST may be profoundly impacted by this novel COVID-19 pandemic, thus prompting increased attention to disease presentation, pathogenesis, and management.
Segmental Imaging of the Trochlear Nerve: Anatomic and Pathologic Considerations
Authors: Agarwal Nivedita , Ahmed Ali Karim , Wiggins Richard H. , McCulley Timothy J. , Kontzialis Marinos , Macedo Leonardo L. , Choudhri Asim F. , Ditta Lauren C. , Ishii Masaru , Gallia Gary L. , Aygun Nafi , Blitz Ari M.
Published: November 2020

Background:

The trochlear nerve (the fourth cranial nerve) is the only cranial nerve that arises from the dorsal aspect of the midbrain. The nerve has a lengthy course making it highly susceptible to injury. It is also the smallest cranial nerve and is often difficult to identify on neuroimaging.

Evidence Acquisition:

High-resolution 3-dimensional skull base MRI allows for submillimeter isotropic acquisition and is optimal for cranial nerve evaluation. In this text, the detailed anatomy of the fourth cranial nerve applicable to imaging will be reviewed.

Results:

Detailed anatomic knowledge of each segment of the trochlear nerve is necessary in patients with trochlear nerve palsy. A systematic approach to identification and assessment of each trochlear nerve segment is essential. Pathologic cases are provided for each segment.

Conclusions:

A segmental approach to high-resolution 3-dimensional MRI for the study of the trochlear nerve is suggested.
Cognitive impairment in patients diagnosed with tramadol dependence compared to healthy controls
Authors: Elrassas Hanan H. , Elsayed Yasser A. , El Nagar Zeinab M. , Abdeen Mai S. , Mohamed Aya T.
Published: November 2020

Cognitive impairment is one of the consequences of substance use. We aimed to estimate the prevalence and correlates of cognitive impairment among patients with tramadol dependence in comparison with healthy controls. The sample consisted of 30 patients with tramadol dependence and 30 healthy controls. Cognitive functions were assessed using Benton Visual Retention Test- revised, Trail Making Test A and B and Wechsler Memory Scale. Patients were also subjected to the Structured Clinical Interview for diagnostic and statistical manual of mental disorders-fourth edition (DSM-IV) Axis I Disorder, the Structured Clinical Interview for DSM-IV Axis II Disorders and the Addiction Severity Index. Results showed that tramadol-dependence patients performed significantly worse than controls regarding cognitive functions, mainly manifested in impaired visual memory, visual reconstruction ability and processing, delayed memory, attention and processing speed, and visual, auditory, immediate, delayed and working memory. We found a nonsignificant negative correlation between cognitive performance and the age of patients or duration of tramadol use. Patients with tramadol dependence were more likely to have cognitive impairment than controls. This may have important clinical implications in determining the right academic and vocational programs for these individuals and adding skills training (e.g. problem solving) to their standard psychosocial treatment.
Integrative research perspectives on marine conservation
Authors: Hillebrand Helmut , Jacob Ute , Leslie Heather M.
Published: November 2020

Whereas the conservation and management of biodiversity has become a key issue in environmental sciences and policy in general, the conservation of marine biodiversity faces additional challenges such as the challenges of accessing field sites (e.g. polar, deep sea), knowledge gaps regarding biodiversity trends, high mobility of many organisms in fluid environments, and ecosystem-specific obstacles to stakeholder engagement and governance. This issue comprises contributions from a diverse international group of scientists in a benchmarking volume for a common research agenda on marine conservation. We begin by addressing information gaps on marine biodiversity trends through novel approaches and technologies, then linking such information to ecosystem functioning through a focus on traits. We then leverage the knowledge of these relationships to inform theory aiming at predicting the future composition and functioning of marine communities. Finally, we elucidate the linkages between marine ecosystems and human societies by examining economic, management and governance approaches that contribute to effective marine conservation in practice.

This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.
Linking dimensions of data on global marine animal diversity
Authors: Webb Thomas J. , Vanhoorne Bart
Published: November 2020

Recent decades have seen an explosion in the amount of data available on all aspects of biodiversity, which has led to data-driven approaches to understand how and why diversity varies in time and space. Global repositories facilitate access to various classes of species-level data including biogeography, genetics and conservation status, which are in turn required to study different dimensions of diversity. Ensuring that these different data sources are interoperable is a challenge as we aim to create synthetic data products to monitor the state of the world's biodiversity. One way to approach this is to link data of different classes, and to inventory the availability of data across multiple sources. Here, we use a comprehensive list of more than 200 000 marine animal species, and quantify the availability of data on geographical occurrences, genetic sequences, conservation assessments and DNA barcodes across all phyla and broad functional groups. This reveals a very uneven picture: 44% of species are represented by no record other than their taxonomy, but some species are rich in data. Although these data-rich species are concentrated into a few taxonomic and functional groups, especially vertebrates, data are spread widely across marine animals, with members of all 32 phyla represented in at least one database. By highlighting gaps in current knowledge, our census of marine diversity data helps to prioritize future data collection activities, as well as emphasizing the importance of ongoing sustained observations and archiving of existing data into global repositories.

This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.
The crossover from microscopy to genes in marine diversity: from species to assemblages in marine pelagic copepods
Authors: Laakmann Silke , Blanco-Bercial Leocadio , Cornils Astrid
Published: November 2020

An accurate identification of species and communities is a prerequisite for analysing and recording biodiversity and community shifts. In the context of marine biodiversity conservation and management, this review outlines past, present and forward-looking perspectives on identifying and recording planktonic diversity by illustrating the transition from traditional species identification based on morphological diagnostic characters to full molecular genetic identification of marine assemblages. In this process, the article presents the methodological advancements by discussing progress and critical aspects of the crossover from traditional to novel and future molecular genetic identifications and it outlines the advantages of integrative approaches using the strengths of both morphological and molecular techniques to identify species and assemblages. We demonstrate this process of identifying and recording marine biodiversity on pelagic copepods as model taxon. Copepods are known for their high taxonomic and ecological diversity and comprise a huge variety of behaviours, forms and life histories, making them a highly interesting and well-studied group in terms of biodiversity and ecosystem functioning. Furthermore, their short life cycles and rapid responses to changing environments make them good indicators and core research components for ecosystem health and status in the light of environmental change.

This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.
Acoustic indexes for marine biodiversity trends and ecosystem health
Authors: Pieretti Nadia , Danovaro Roberto
Published: November 2020

Acoustic approaches have been recently proposed to investigate critical ecological issues, such as biodiversity loss and different typologies of impacts, including climate change. However, the extensive use of acoustic monitoring is hampered by the lack of algorithms enabling the discrimination among different sound sources (e.g. geophysical, anthropogenic and biological). Eco- and bioacoustic indexes have been applied to provide non-invasive information on the temporal and spatial patterns of marine biodiversity and on the anthropogenic impact on marine life. Here, we review the potential of acoustic tools in expanding the monitoring of marine ecosystems from a current three-dimensional perception to a four-dimensional dimension. We also explore the use of acoustic indexes, mostly developed in terrestrial ecology, for the investigation of different marine ecosystems. Their appraisal, strengths and limits, and potential for future investigations in the biological exploration of the oceans are also discussed.

This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.
Projecting marine developmental diversity and connectivity in future oceans
Authors: Marshall Dustin J. , Alvarez-Noriega Mariana
Published: November 2020

Global change will alter the distribution of organisms around the planet. While many studies have explored how different species, groups and traits might be re-arranged, few have explored how dispersal is likely to change under future conditions. Dispersal drives ecological and evolutionary dynamics of populations, determining resilience, persistence and spread. In marine systems, dispersal shows clear biogeographical patterns and is extremely dependent on temperature, so simple projections can be made regarding how dispersal potentials are likely to change owing to global warming under future thermal regimes. We use two proxies for dispersal—developmental mode and developmental duration. Species with a larval phase are more dispersive than those that lack a larval phase, and species that spend longer developing in the plankton are more dispersive than those that spend less time in the plankton. Here, we explore how the distribution of different development modes is likely to change based on current distributions. Next, we estimate how the temperature-dependence of development itself depends on the temperature in which the species lives, and use this estimate to project how developmental durations are likely to change in the future. We find that species with feeding larvae are likely to become more prevalent, extending their distribution poleward at the expense of species with aplanktonic development. We predict that developmental durations are likely to decrease, particularly in high latitudes where durations may decline by more than 90%. Overall, we anticipate significant changes to dispersal in marine environments, with species in the polar seas experiencing the greatest change.

This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.
Life in fluctuating environments
Authors: Bernhardt Joey R. , O'Connor Mary I. , Sunday Jennifer M. , Gonzalez Andrew
Published: November 2020

Variability in the environment defines the structure and dynamics of all living systems, from organisms to ecosystems. Species have evolved traits and strategies that allow them to detect, exploit and predict the changing environment. These traits allow organisms to maintain steady internal conditions required for physiological functioning through feedback mechanisms that allow internal conditions to remain at or near a set-point despite a fluctuating environment. In addition to feedback, many organisms have evolved feedforward processes, which allow them to adjust in anticipation of an expected future state of the environment. Here we provide a framework describing how feedback and feedforward mechanisms operating within organisms can generate effects across scales of organization, and how they allow living systems to persist in fluctuating environments. Daily, seasonal and multi-year cycles provide cues that organisms use to anticipate changes in physiologically relevant environmental conditions. Using feedforward mechanisms, organisms can exploit correlations in environmental variables to prepare for anticipated future changes. Strategies to obtain, store and act on information about the conditional nature of future events are advantageous and are evidenced in widespread phenotypes such as circadian clocks, social behaviour, diapause and migrations. Humans are altering the ways in which the environment fluctuates, causing correlations between environmental variables to become decoupled, decreasing the reliability of cues. Human-induced environmental change is also altering sensory environments and the ability of organisms to detect cues. Recognizing that living systems combine feedback and feedforward processes is essential to understanding their responses to current and future regimes of environmental fluctuations.

This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.
Modern models of trophic meta-communities
Authors: Gross Thilo , Allhoff Korinna T. , Blasius Bernd , Brose Ulrich , Drossel Barbara , Fahimipour Ashkaan K. , Guill Christian , Yeakel Justin D. , Zeng Fanqi
Published: November 2020

Dispersal and foodweb dynamics have long been studied in separate models. However, over the past decades, it has become abundantly clear that there are intricate interactions between local dynamics and spatial patterns. Trophic meta-communities, i.e. meta-foodwebs, are very complex systems that exhibit complex and often counterintuitive dynamics. Over the past decade, a broad range of modelling approaches have been used to study these systems. In this paper, we review these approaches and the insights that they have revealed. We focus particularly on recent papers that study trophic interactions in spatially extensive settings and highlight the common themes that emerged in different models. There is overwhelming evidence that dispersal (and particularly intermediate levels of dispersal) benefits the maintenance of biodiversity in several different ways. Moreover, some insights have been gained into the effect of different habitat topologies, but these results also show that the exact relationships are much more complex than previously thought, highlighting the need for further research in this area.

This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.
The territories of governance
: unpacking the ontologies and geophilosophies of fixed to flexible ocean management, and beyond
Authors: Peters Kimberley
Published: November 2020

This paper offers a conceptual contribution to understanding ocean governance and the management of spaces for the protection of marine biodiversity, organization of extractive industries, the arrangement of global shipping and other ‘blue-economy’ uses. Rather than focus on one type of management technique (such as a Marine Protected Area (MPA) or example of Marine Spatial Planning), or a site- or species-specific case study of governance, this paper offers a
theoretical
tracking of the uncharted territories of governance that foreground ocean management approaches. The literature on ocean governance and management techniques predominantly derive from scientific disciplines (which provide the basis for planning) and policy-related social science fields, leaving a lacuna in more critical discussions of ways of knowing and understanding the world that drive it. The paper argues the need to critically understand the ontologies (the regimes of what we believe exists) and geophilosophies (the geographically informed modes of thinking)
of territory
that underscore ocean management to make sense of its past successes and failures, its present functioning and its future directions. This paper argues that without critical consideration of the kinds of thinking—the ontologies and geophilosophies—that drive ocean management, it will lack the transformative potential many hope it will achieve for sustainable development.

This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.
Boceprevir, calpain inhibitors II and XII, and GC-376 have broad-spectrum antiviral activity against coronaviruses in cell culture
Authors: Hu Yanmei , Ma Chunlong , Szeto Tommy , Hurst Brett , Tarbet Bart , Wang Jun
Published: November 2020

As the COVID-19 pandemic continues to fold out, the morbidity and mortality are increasing daily. Effective treatment for SARS-CoV-2 is urgently needed. We recently discovered four SARS-CoV-2 main protease (Mpro) inhibitors including boceprevir, calpain inhibitors II and XII and GC-376 with potent antiviral activity against infectious SARS-CoV-2 in cell culture. Despite the weaker enzymatic inhibition of calpain inhibitors II and XII against Mprocompared to GC-376, calpain inhibitors II and XII had more potent cellular antiviral activity. This observation promoted us to hypothesize that the cellular antiviral activity of calpain inhibitors II and XII might also involve the inhibition of cathepsin L in addition to Mpro. To test this hypothesis, we tested calpain inhibitors II and XII in the SARS-CoV-2 pseudovirus neutralization assay in Vero E6 cells and found that both compounds significantly decreased pseudoviral particle entry into cells, indicating their role in inhibiting cathepsin L. The involvement of cathepsin L was further confirmed in the drug time-of-addition experiment. In addition, we found that these four compounds not only inhibit SARS-CoV-2, but also SARS-CoV, MERS-CoV, as well as human coronaviruses (CoVs) 229E, OC43, and NL63. The mechanism of action is through targeting the viral Mpro, which was supported by the thermal shift binding assay and enzymatic FRET assay. We further showed that these four compounds have additive antiviral effect when combined with remdesivir. Altogether, these results suggest that boceprevir, calpain inhibitors II and XII, and GC-376 are not only promising antiviral drug candidates against existing human coronaviruses, but also might work against future emerging CoVs.
Generalized neural decoders for transfer learning across participants and recording modalities
Authors: Peterson Steven M. , Steine-Hanson Zoe , Davis Nathan , Rao Rajesh P. N. , Brunton Bingni W.
Published: November 2020

Objective

Advances in neural decoding have enabled brain-computer interfaces to perform increasingly complex and clinically-relevant tasks. However, such decoders are often tailored to specific participants, days, and recording sites, limiting their practical long-term usage. Therefore, a fundamental challenge is to develop neural decoders that can robustly train on pooled, multi-participant data and generalize to new participants.

Approach

We introduce a new decoder, HTNet, which uses a convolutional neural network with two innovations: (1) a Hilbert transform that computes spectral power at data-driven frequencies and (2) a layer that projects electrode-level data onto predefined brain regions. The projection layer critically enables applications with intracranial electrocorticography (ECoG), where electrode locations are not standardized and vary widely across participants. We trained HTNet to decode arm movements using pooled ECoG data from 11 of 12 participants and tested performance on unseen ECoG or electroencephalography (EEG) participants; these pretrained models were also subsequently fine-tuned to each test participant.

Main results

HTNet outperformed state-of-the-art decoders when tested on unseen participants, even when a different recording modality was used. By fine-tuning these generalized HTNet decoders, we achieved performance approaching the best tailored decoders with as few as 50 ECoG or 20 EEG events. We were also able to interpret HTNet’s trained weights and demonstrate its ability to extract physiologically-relevant features.

Significance

By generalizing to new participants and recording modalities, robustly handling variations in electrode placement, and allowing participant-specific fine-tuning with minimal data, HTNet is applicable across a broader range of neural decoding applications compared to current state-of-the-art decoders.
Accelerated Simulation of Large Reaction Systems Using a Constraint-Based Algorithm
Authors: Burke Paulo E. P. , Costa Luciano da F.
Published: November 2020

Simulation of reaction systems has been employed along decades for a better understanding of such systems. However, the ever-growing gathering of biological data implied in larger and more complex models that are computationally challenging for current discrete-stochastic simulation methods. In this work, we propose a constraint-based algorithm to simulate such reaction systems, called the Constraint-Based Simulation Algorithm (CBSA). The main advantage of the proposed method is that it is intrinsically parallelizable, thus being able to be implemented in GPGPU architectures. We show through examples that our method can provide valid solutions when compared to the well-known Stochastic Simulation Algorithm (SSA). An analysis of computational efficiency showed that the CBSA tend to outperform other considered methods when dealing with a high number of molecules and reaction channels. Therefore, we believe that the proposed method constitutes an interesting alternative when simulating large chemical reaction systems.
Mutagenesis and homology modeling reveal a predicted pocket of lysophosphatidylcholine acyltransferase 2 to catch Acyl-CoA
Authors: Hamano Fumie , Matoba Kazuaki , Hashidate-Yoshida Tomomi , Suzuki Tomoyuki , Miura Kiyotake , Hishikawa Daisuke , Harayama Takeshi , Yuki Koichi , Kita Yoshihiro , Noda Nobuo N. , Shimizu Takao , Shindou Hideo
Published: November 2020

Platelet-activating factor (PAF) is a potent proinflammatory phospholipid mediator that elicits various cellular functions and promotes several pathological conditions, including anaphylaxis and neuropathic pain. PAF is biosynthesized by two types of lyso-PAF acetyltransferases: lysophosphatidylcholine acyltransferase 1 (LPCAT1) and LPCAT2, which are constitutive and inducible forms of lyso-PAF acetyltransferase, respectively. Because LPCAT2 mainly produces PAF under inflammatory conditions, understanding the structure of LPCAT2 is important for developing specific drugs against PAF-related inflammatory diseases. Although the structure of LPCAT2 has not been determined, the crystal structure was reported forThermotoga maritimaPlsC, an enzyme in the same enzyme family as LPCAT2. In this study, we identified residues in mouse LPCAT2 essential for its enzymatic activity and a potential acyl-coenzyme A (CoA)-binding pocket, based on homology modeling of mouse LPCAT2 with PlsC. We also found that Ala115 of mouse LPCAT2 was important for acyl-CoA selectivity. In conclusion, these results predict the structure of mouse LPCAT2. Our findings have implications for the future development of new drugs against PAF-related diseases.
Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice
Authors: Hamza Bashar , Miller Alex B. , Meier Lara , Stockslager Max , King Emily M. , Ng Sheng Rong , DeGouveia Kelsey L. , Mulugeta Nolawit , Calistri Nicholas L. , Strouf Haley , Lin Lin , Chin Christopher R. , Weinberg Robert A. , Shalek Alex K. , Jacks Tyler , Manalis Scott
Published: November 2020

Existing pre-clinical methods for acquiring dissemination kinetics of rare circulating tumor cells (CTCs) en route to forming metastases have not been capable of providing a direct measure of CTC intravasation rate and subsequent half-life in the circulation. Here, we demonstrate an approach for measuring endogenous CTC kinetics by continuously exchanging CTC-containing blood over several hours between un-anesthetized, tumor-bearing mice and healthy, tumor-free counterparts. By tracking CTC transfer rates using an autochthonous small cell lung cancer model, we extrapolated half-life times in the circulation of 50-100 seconds and intravasation rates between 4,000 and 27,000 CTCs/hour – an average daily shedding rate equivalent to ∼0.07% of the total number of primary tumor cells in the lung. Additionally, transfer of 1-2% of daily-shed CTCs from late-stage tumor-bearing mice generated macrometastases in healthy recipient mice. We envision that our technique will help further elucidate the role of CTCs and the rate-limiting steps in metastasis.
Sequential dynein effectors regulate axonal autophagosome motility in a maturation-dependent pathway
Authors: Cason Sydney E. , Carman Peter , Duyne Claire Van , Goldsmith Juliet , Dominguez Roberto , Holzbaur Erika L.F.
Published: November 2020

Autophagy is a degradative pathway required to maintain neuronal homeostasis. Neuronal autophagosomes form constitutively at the axon terminal and mature via lysosomal fusion during dynein-mediated transport to the soma. How the dynein-autophagosome interaction is regulated during maturation is unknown. Here, we identify a series of handoffs between dynein effectors as autophagosomes transit along the axons of primary neurons. In the distal axon, JIP1 initiates autophagosomal transport, while autophagosomes in the mid-axon require HAP1 and Huntingtin for motility. We demonstrate that HAP1 is a bonafide dynein activator, binding the dynein-dynactin complex via canonical and noncanonical interactions. JIP3 is found on most axonal autophagosomes but specifically regulates the transport of acidified autolysosomes. Inhibiting autophagosomal transport disrupts maturation, while inhibiting autophagosomal maturation perturbs the association and function of dynein effectors. Thus maturation and transport are tightly linked. These results describe a novel maturation-based dynein effector handoff on neuronal autophagosomes that is key to autophagosomal motility, cargo degradation, and the maintenance of axonal health.

Neuronal autophagosomes form in the distal axon and mature via fusion with lysosomes during their dynein-driven transport to the soma. Dynein is regulated on autophagosomes by distinct effector proteins—JIP1, HAP1, and JIP3—depending on location and autophagosomal maturity. In this sequential pathway, transport and maturation state are tightly linked to maintain neuronal health.