bluuebunny/crossref_metadata_2025 huggingface dataset:
Secondary Analysis of Agreement Between Negative Timeline Follow Back Report and Negative Urine Toxicology in a Large Trial of Individuals with Opioid Use Disorder
Authors: Shulman Matisyahu , Choo Tse-Hwei , Scodes Jennifer , Pavlicova Martina , Novo Patricia , Campbell Aimee N.C. , Greiner Miranda , Lee Joshua D. , Rotrosen John , Nunes Edward V.
Published: May 2023

Objectives

Timeline follow-back (TLFB) is a self-report measure commonly used as a method of assessing historical drug use in both clinical and research settings. Our study considered rates of agreement between TLFB and an objective biological assay of opioid use.

Methods

We calculated the rates of agreement between negative report of opioid use for the most recent 8 days on TLFB and urine toxicology (UTOX) results in a large multisite opioid use disorder treatment trial.

Results

In total, 3986 assessments were provided by trial participants with both UTOX and TLFB during weeks 1 to 12, 2716 during weeks 13 to 24, and 325 at week 28. Rates of disagreement between negative TLFB and positive opioid UTOX were 2.33% of all assessments (21.68% of those with positive UTOX) over weeks 1 to 12, 2.06% of all assessment (25.00% of those with positive UTOX) over weeks 13 to 24, and 9.85% of all assessments (26.02% of those with positive UTOX) at week 28.

Conclusions

Negative TLFB seems to be generally associated with negative results on urine toxicology.
Reconstructive Surgery for the Neglected Tropical Diseases: Global Gaps and Future Directions
Authors: Pham Kala T. , Hotez Peter J. , Hamilton Kristy L.
Published: May 2023

Background:

Several neglected tropical diseases (NTDs) are highly disfiguring, particularly those in resource-poor countries that lack access to basic surgery. There has been a push to integrate surgery into treatment programs for NTDs. In this article, we provide an overview of the major disfiguring NTDs and discuss the processes and barriers that impede access to reconstructive surgical treatments or their integration into health systems.

Methods:

A review of the literature was conducted using the online database PubMed, from 2008 to 2021 with the specific diseases listed as NTDs either on the World Health Organization or the PLoS Neglected Tropical Disease websites. Reference lists of identified articles and reviews were also searched, as were databases from the World Health Organization’s Weekly Epidemiological Record.

Result:

Success in the surgical treatment and postoperative care of disfiguring NTDs would benefit from standardization and harmonization of surgical approaches and procedures. In some settings, reconstructive surgery should be used cautiously, emphasizing appropriate use of antibiotics, partnerships with global and local surgical teams, and local capacity building. Preventative hygiene approaches remain paramount in resource-poor areas.

Conclusions:

Surgery is a promising treatment for NTDs that result in disfigurement and disability. The expansion of local capacity building, with medical trips and surgical training of local health workers, together with the development of universal surgical protocols remain essential cornerstones for NTD reconstructive surgery. Antibiotics and drug management should comprise key first steps before turning to surgery.
Monitoring antihypertensive drug concentrations to determine nonadherence in hypertensive patients with or without a kidney transplant
Authors: Peeters Laura E.J. , Hesselink Dennis A. , Lafeber Melvin , Severs David , van den Hoogen Martijn W.F. , Sonneveld Michelle A.H. , Ramakers Christian R.B. , Bahmany Soma , van Gelder Teun , Koch Birgit C.P. , Versmissen Jorie
Published: May 2023

Background:

Nonadherence to antihypertensive drugs (AHDs) is a major contributor to pseudo-resistant hypertension. The primary objective of this study was to determine the prevalence of nonadherence to AHDs among patients visiting the nephrology and vascular outpatient clinics.

Methods:

Patients were eligible to participate in this prospective observational study if they used at least two AHDs that could be measured with a validated UHPLC-MS/MS method and had an office blood pressure at least 140 and/or at least 90 mmHg. For resistant hypertension, included patients had to use at least three AHDs including a diuretic or four AHDs. Adherence was assessed by measuring drug concentrations in blood. The complete absence of drug in blood was defined as nonadherence. A posthoc analysis was performed to determine the influence of a having a kidney transplant on the adherence rates.

Results:

One hundred and forty-two patients were included of whom 66 patients fulfilled the definition of resistant hypertension. The overall adherence rate to AHDs was 78.2% (n = 111 patients), with the highest adherence rate for irbesartan (100%, n = 9) and lowest adherence rate for bumetanide (n = 69%, n = 13). In further analysis, only kidney transplantation could be identified as an important factor for adherence (adjusted odds ratio = 3.35; 95% confidence interval 1.23–9.09). A posthoc analysis showed that patients with a kidney transplant were more likely to be adherent to AHDs (non-KT cohort 64.0% vs. KT-cohort 85.7%, χ2(2) = 10.34, P = 0.006).

Conclusion:

The adherence rate to AHDs in hypertensive patients was high (78.2%) and even higher after a kidney transplant (85.7%). Furthermore, patients after kidney transplant had a lower risk of being nonadherent to AHDs.
Accounting for antihypertensive medication in Mendelian randomization studies of blood pressure: methodological considerations in the Canadian Longitudinal Study on Aging
Authors: Mbutiwi Fiston Ikwa Ndol , Sylvestre Marie-Pierre
Published: May 2023

Background:

Mendelian randomization (MR) studies investigating determinants of blood pressure (BP) do not account for antihypertensive medication consistently, which may explain discrepancies across studies. We performed an MR study of the association between body mass index (BMI) and systolic BP (SBP) using five methods to account for antihypertensive medication and evaluated their impact on the estimation of the causal effect and on the assessment of the invalidity of the instruments used in MR.

Methods:

Baseline and follow-up data on 20 430 participants from the Canadian Longitudinal Study on Aging (CLSA) Comprehensive cohort (2011–2018) were used. The five methods to account for antihypertensive medication in the MR study were: no correction, adjustment for antihypertensive medication as a covariate in models, exclusion of treated individuals, addition of a constant value of 15 mmHg to measured values of SBP in treated individuals, and using hypertension as a binary outcome.

Results:

The magnitude of the estimated MR causal effect for SBP (mmHg) varied across the methods of accounting for antihypertensive medication effects ranging from 0.68 (effect per 1 kg/m2 increase in BMI) in scenario adjusting MR models for medication covariate to 1.35 in that adding 15 mmHg to measured SBP in treated individuals. Conversely, the assessment of the validity of the instruments did not differ across methods of accounting for antihypertensive medication.

Conclusions:

Methods to account for antihypertensive medication in MR studies may affect the estimation of the causal effects and must be selected with caution.
Microbiology and Antibiotic Resistance Profiles of Orbital Subperiosteal Abscesses: A Comparison of Pediatric, Adolescent, and Adult Populations
Authors: Gibbons Alison B. , Niknahad Ava , Bacorn Colin , Li Emily
Published: May 2023

Purpose:

The purpose of this study was to compare the microbiology and antibiotic resistance profiles of orbital subperiosteal abscesses (SPA) among 3 age cohorts.

Methods:

A retrospective study was conducted at a tertiary care center through a medical record search to identify patients with orbital cellulitis and SPA on imaging from January 1, 2000 to September 10, 2022. Patients were categorized into pediatric (<9 years old), adolescent (9–18 years old), and adult (>18 years old) cohorts. Primary outcomes included culture and antibiotic susceptibility results. Secondary outcomes included antibiotic therapy and surgical intervention.

Results:

Of the 153 SPA patients included, 62 (40.5%) were in the pediatric cohort (4 months–8 years, mean 5.0 ± 2.7), 51 (33.3%) were adolescent (9–18 years, 12.7 ± 2.8), and 40 (26.1%) were adult (19–95, 51.8 ± 19.3). Viridians group Streptococci were the most frequent organisms isolated across groups. The anaerobic infection rate was higher in the adult compared to the pediatric group (23.0% vs, 4.0%, p = 0.017), while that of the adolescent did not differ significantly from either. Pediatric patients carried a lower rate of clindamycin resistance than adolescent and adult cohorts, who shared similar rates (0 vs. 27.0% and 28.0%, respectively; p = 0.016). There were progressive increases in duration of intravenous antibiotic therapy (p < 0.195) and rate of surgical intervention (p < 0.001) going from younger to older cohorts.

Conclusion:

Organisms isolated from orbital SPA from the past 2 decades demonstrate a predominance of Streptococcal species. Older age may be associated with anaerobic infection, clindamycin resistance, and more aggressive management. Adolescent infections are more similar to adult rather than pediatric counterparts but may require less aggressive management than the former.
Delayed Optic Neuropathy Caused by Orbital Hyaluronic Filler Injection and Recovery Following Hyaluronidase Treatment
Authors: Lim Christina S. , Malhotra Raman
Published: May 2023

A 26-year-old female presented with left enophthalmos following orbital floor and medial wall fracture despite surgical repair. She underwent further exploration and surgical repair but the enophthalmos persisted at 3–4 mm. Following discussion, she received 2 ml of hyaluronic acid filler injection into the posterior orbit and intraconal space. There were no immediate postoperative complications with normal optic nerve function, and the enophthalmos improved by 2 mm. The optic nerve function remained normal at the 4-week review. She returned 30 months following the injection with left periorbital edema, subjective red desaturation, and reduced peripheral visual field. On examination, there was a left relative afferent pupillary defect, disc pallor, and reduced visual field defect on automated visual field test. Following transcutaneous orbital injection of hyaluronidase, there was a subjective improvement in red desaturation with an improved peripheral visual field. Here the authors present a case of compressive optic neuropathy of delayed onset following orbital hyaluronic acid filler injection.
A Case of Subcutaneous Sarcoidosis Treated With Intralesional Kenalog
Authors: Yousefian Faraz , Espinoza Liliana , Frandsen McKay , Yadlapati Sujitha , Eckert Auston , Bandino Justin
Published: May 2023

Sarcoidosis is a granulomatous disorder that is characterized by the development of noncaseating granulomas affecting multiple organ systems, most commonly the lungs and lymph nodes of the body. Aside from these organ systems, sarcoidosis can also affect the skin, eyes, central nervous system, liver, heart, kidneys, and musculoskeletal system. We present a patient with subcutaneous sarcoidosis, also known as Darier-Roussy disease, without extracutaneous findings. Patients may benefit from topical or intralesional steroids for localized involvement to decrease the size of the nodules while avoiding the adverse effects of systemic medications.
Work Related Demands and Resources as Predictors of Well-being at Work Among Healthcare Workers in Switzerland
Authors: Villiger Simone , Hämmig Oliver
Published: May 2023

Objective

The aim was to examine the effects of work-related demands and resources on well-being at work among employees in Swiss hospitals.

Methods

Self-reported survey data from 1840 employees of six hospitals/clinics were analyzed using multivariate linear regression analyses (all professions included).

Results

Of all demands, work-life imbalance had the strongest negative effect on well-being at work. The most relevant resource varied depending on the dimension of well-being: for job satisfaction it was good leadership, for work engagement job decision latitude and for satisfaction with relationships at work social support at work. The resources were more relevant for well-being at work than the demands. They also buffered against the negative effects of the demands.

Conclusions

To enhance well-being at work in hospitals, it is necessary to enable a good work-life balance and to strengthen work-related resources.
Factors Affecting Development of Chronic Obstructive Pulmonary Disease in Pneumoconiosis Cases: A Cross-sectional Study Between 2017 and 2022 in Turkey
Authors: Acun Pinar Merve , Sari Gülden , Koyuncu Adem , Şimşek Ceprail
Published: May 2023

Objectives

It was aimed to determine the factors affecting the development of chronic obstructive pulmonary disease (COPD) in pneumoconiosis cases

Methods

Pneumoconiosis cases were divided into two groups as those with only pneumoconiosis and those with coexistence of pneumoconiosis and COPD. Demographic data, smoking habits, pulmonary function test, radiological findings, and occupational risk factors of the cases were compared.

Results

Chronic obstructive pulmonary disease was detected in 134 of 465 pneumoconiosis cases (28.8%) included in the study. It was determined that patients who developed COPD were statistically significantly older, had longer exposure duration, had lower forced expiratory volume in 1 second, forced vital capacity, and forced expiratory volume in 1 second/forced vital capacity values, and had more pulmonary symptoms. Chronic obstructive pulmonary disease development was more common in sandblasting workers, dental technicians, and miners than in other occupations.

Conclusion

It has been shown that the risk of developing COPD is high in cases of pneumoconiosis, independent of smoking, especially in certain occupational groups.
Further evidence of biallelic variants in KCNK18 as a cause of intellectual disability and epilepsy with febrile seizure plus
Authors: Majethia Purvi , Harish Rhea , Narayanan Dhanya Lakshmi , B L Yatheesha , Sharma Suvasini , Shukla Anju
Published: May 2023

Introduction

KCNK18, a potassium channel subfamily K member 18 (MIM*613655), encodes for TWIK-related spinal cord K+ channel (TRESK) and is important for maintaining neuronal excitability. Monoallelic variants in KCNK18 are known to cause autosomal dominant migraine, with or without aura, susceptibility to, 13 (MIM#613656). Recently, biallelic missense variants in KCNK18 have been reported in three individuals from a non-consanguineous family with intellectual disability, developmental delay, autism spectrum disorder (ASD), and seizure.

Methods

Singleton exome sequencing was performed for the proband after detailed clinical evaluation to identify the disease-causing variants in concordance with the phenotype.

Results

We herein report an individual with intellectual disability, developmental delay, ASD, and epilepsy with febrile seizure plus with a novel homozygous stopgain variant, c.499C>T p.(Arg167Ter) in KCNK18.

Conclusion

This report further validates KCNK18 as a cause of autosomal recessive intellectual disability, epilepsy, and ASD.
Nanomedicine in kidney disease
Authors: Bishop Boaz , Sharma Swagat , Scott Evan A.
Published: May 2023

Purpose of review

The pathophysiological understanding of kidney-related disorders has profoundly increased; however, tissue-specific and cell-specific treatments in this field remain scarce. Advances in nanomedicine enable alteration of pharmacokinetics and targeted treatments improving efficiency and reducing toxicity. This review addresses recent developments of nanocarriers used for various purposes in the broad field of kidney disease, which may pave a path to therapeutic and diagnostic solutions for kidney disease.

Recent findings

Controlled delivery of antiproliferative medications enables improved treatment of polycystic kidney disease and fibrosis. Directed anti-inflammatory treatment mitigated glomerulonephritis and tubulointerstitial nephritis. Multiple injury pathways in AKI have been targeted, with therapeutic solutions for oxidative stress, mitochondrial dysfunction, local inflammation and improving self-repair mechanisms. In addition to such treatment development, noninvasive early detection methods (minutes after ischemic insult) have been demonstrated as well. Sustained release of therapies that reduce ischemia–reperfusion injury as well as new aspects for immunosuppression bring hope to improving kidney transplant outcomes. The latest breakthroughs in gene therapy are made achievable by engineering the targeted delivery of nucleic acids for new treatments of kidney disease.

Recent advances in nanotechnology and pathophysiological understanding of kidney diseases show potential for translatable therapeutic and diagnostic interventions in multiple etiologies of kidney disease.
Kidney clearance of fibroblast growth factor-23 in humans
Authors: Sharma Shilpa , Ix Joachim H.
Published: May 2023

Purpose of review

Recent studies have shed light on factors influencing FGF23 regulation in terms of its production and cleavage. However, less is known about FGF23 elimination from circulation. The kidney's role in FGF23 elimination will be the focus of this review.

Recent findings

Marked abnormalities in FGF23 physiology have been observed in persons with reduced kidney function compared with healthy persons and raise the question of whether the kidney may be directly regulating FGF23 concentrations. FGF23 concentrations rise dramatically after onset of acute kidney injury and early chronic kidney disease and are associated with poor clinical outcomes. New studies leveraging measurements of FGF23 in the aorta and renal veins concurrently demonstrate that the human kidney efficiently extracts both intact and C-terminal FGF23 from the circulation independent of kidney function and catabolize the hormone. Additionally, the kidney's reduction of PTH predicts the amount it will reduce both C-terminal and intact FGF23.

The human kidney removes both intact FGF23 and its C-terminal fragments. FGF23 catabolism within the kidney may be influenced by PTH concentrations, and other factors. Future studies to understand regulation of these hormones and the kidney's role in this interplay are timely.
A Targeted Analysis of Serial Cytokine Measures and Nonpulmonary Organ System Failure in Children With Acute Respiratory Failure: Individual Measures and Trajectories Over Time
Authors: Ardila Silvia M. , Weeks Heidi M. , Dahmer Mary K. , Kaciroti Niko , Quasney Michael , Sapru Anil , Curley Martha A. Q. , Flori Heidi R. ,   for the Biomarkers in Children with Acute Lung Injury (BALI) and Randomized Evaluation for Sedation Titration for Respiratory Failure (RESTORE) Study Investigators and Pediatric Acute Lung Injury and Sepsis Investigators (PALISI) Network
Published: May 2023

OBJECTIVES:

There is a need for research exploring the temporal trends of nonpulmonary organ dysfunction (NPOD) and biomarkers in order to identify unique predictive or prognostic phenotypes. We examined the associations between the number and trajectories of NPODs and plasma biomarkers of early and late inflammatory cascade activation, specifically plasma interleukin-1 receptor antagonist (IL-1ra) and interleukin-8 (IL-8), respectively, in the setting of acute respiratory failure (ARF).

DESIGN:

Secondary analysis of the Randomized Evaluation for Sedation Titration for Respiratory Failure clinical trial and Biomarkers in Acute Lung Injury (BALI) ancillary study.

SETTING:

Multicenter.

PATIENTS:

Intubated pediatric patients with ARF.

INTERVENTIONS:

NPODs were evaluated against plasma IL-1ra and IL-8 levels on individual days (1 to 4 d after intubation) and longitudinally across days.

MEASUREMENTS AND MAIN RESULTS:

Within the BALI cohort, 432 patients had at least one value for IL-1ra or IL-8 within days 0 through 5. 36.6% had a primary diagnosis of pneumonia, 18.5% had a primary diagnosis of sepsis and 8.1% died. Multivariable logistic regression models showed that increasing levels of both plasma IL-1ra and IL-8 were statistically significantly associated with increasing numbers of NPODs (IL-1ra: days 1–3; IL-8: days 1–4), independent of sepsis diagnosis, severity of oxygenation defect, age, and race/ethnicity. Longitudinal trajectory analysis identified four distinct NPOD trajectories and seven distinct plasma IL-1ra and IL-8 trajectories. Multivariable ordinal logistic regression revealed that specific IL-1ra and IL-8 trajectory groups were associated with greater NPOD trajectory group (p = 0.004 and p < 0.0001, respectively), independent of severity of oxygenation defect, age, sepsis diagnosis, and race/ethnicity.

CONCLUSIONS:

Both the inflammatory biomarkers and number of NPODs exhibit distinct trajectories over time with strong associations with one another. These biomarkers and their trajectory patterns may be useful in evaluating the severity of multiple organ dysfunction syndrome in critically ill children and identifying those phenotypes with time-sensitive, treatable traits.
Hematopoietic Stem Cell Transplantation for Myelodysplastic Syndromes
Authors: Sabile Jean , Pavletic Steven , Migdady Yazan
Published: May 2023

Myelodysplastic syndromes (MDSs) are characterized by a clonal proliferation of hematopoietic stem cells with potential life-threatening cytopenia(s) and transformation to acute myeloid leukemia. Individualized risk stratification is evolving with new molecular models, such as the Molecular International Prognostic Scoring System, for better estimation of leukemic transformation and overall survival. The only potential cure for MDSs is allogeneic transplant, although it is underutilized in MDSs because of advanced patient age and multiple comorbidities. Optimization of transplant relies on improved identification of high-risk patients pretransplant, using targeted therapies leading to deeper molecular response, developing lower toxicity conditioning regimens, engineering better molecular tools for early detection and relapse monitoring, and adding maintenance treatment strategies for high-risk patients posttransplant. This review provides an overview of transplant in MDSs with updates, future directions, and role for novel therapies.
Changing Characteristics of HIV-Positive Gay and Bisexual Men's Relationships in the Era of Biomedical Prevention
Authors: Broady Timothy R. , Chan Curtis , MacGibbon James , Mao Limin , Prestage Garrett , Clifton Brent , Paynter Heath , Bavinton Benjamin R. , Holt Martin
Published: May 2023

Objective:

To assess changes in personal and relationship characteristics among HIV-positive Australian gay and bisexual men (GBM) as rates of antiretroviral therapy and knowledge and confidence regarding the effectiveness of viral suppression in preventing HIV transmission have increased.

Design:

Repeated behavioral surveillance of GBM recruited from venues, events, and online in 7 Australian states and territories.

Methods:

HIV-positive participants were included. Trends in demographics, HIV treatment, and relationship characteristics were assessed with binary and multivariable logistic regression.

Results:

A total of 3643 survey responses (2016–2020) were included. Over time, HIV-positive GBM became less likely to identify as gay or report an Anglo-Australian ethnicity. The average length of time since HIV diagnosis increased and the frequency of attending HIV-related clinical appointments decreased. There were no changes in the reported number of recent sex partners or proportion reporting regular male partners over time. Among HIV-positive GBM in relationships, the proportion reporting HIV-positive partners decreased and the proportion reporting HIV-negative partners increased. Levels of condomless sex with regular partners increased over time; however, this was concentrated among HIV-positive GBM in serodiscordant relationships.

Conclusion:

Findings suggest that increased accessibility and trust in biomedical prevention strategies have contributed to broader relationship and sexual opportunities for HIV-positive GBM in Australia. Our findings suggest that future health promotion activities could highlight the social and relationship benefits of treatment as prevention to further increase trust in it as an HIV prevention strategy among GBM.
Traditional and faith-based healthcare in the management of psychotic disorders in Africa: in search for synergy
Authors: van der Zeijst Martine C.E. , Veling Wim , Chiliza Bonginkosi , Hoek Hans W.
Published: May 2023

Purpose of review

This review summarizes the current literature on the role of traditional and faith-based healthcare in the management of psychotic disorders in Africa.

Recent findings

In contemporary Africa, individuals with psychosis and traditional and faith healers (TFH) are pluralistic towards their understanding of psychosis and their help-seeking behaviour. Traditional healing is perceived to be helpful to patients with psychotic disorders and their family members and may have a positive influence on the course of psychosis in some selected individuals. Studies show that potentially harmful practices are commonly used by African TFH, but that these are associated with a lack of resources and are susceptible to training. Although various TFH and biomedical practitioners are open to collaboration, the many identified obstacles hinder actual partnerships. However, the few studies that have been conducted on collaborative care for patients with psychotic disorders on the continent, show positive outcomes.

Rather than harmonizing the two healing paradigms, synergistic collaboration between traditional/faith-based and biomedical mental healthcare in the management of individuals with psychosis seems to be possible within certain limits. Synergistic collaboration is more culturally syntonic and may actually contribute to bridging the treatment gap for mental disorders in present-day Africa.
No evidence of social learning in a socially roosting butterfly in an associative learning task
Authors: Moura Priscila A. , Cardoso Marcio Z. , Montgomery Stephen H.
Published: May 2023

Insects may acquire social information by active communication and through inadvertent social cues. In a foraging setting, the latter may indicate the presence and quality of resources. Although social learning in foraging contexts is prevalent in eusocial species, this behaviour has been hypothesized to also exist between conspecifics in non-social species with sophisticated behaviours, including
Heliconius
butterflies.
Heliconius
are the only butterfly genus with active pollen feeding, a dietary innovation associated with a specialized, spatially faithful foraging behaviour known as trap-lining. Long-standing hypotheses suggest that
Heliconius
may acquire trap-line information by following experienced individuals. Indeed,
Heliconius
often aggregate in social roosts, which could act as ‘information centres’, and present conspecific following behaviour, enhancing opportunities for social learning. Here, we provide a direct test of social learning ability in
Heliconius
using an associative learning task in which naive individuals completed a colour preference test in the presence of demonstrators trained to feed randomly or with a strong colour preference. We found no evidence that
Heliconius erato
, which roost socially, used social information in this task. Combined with existing field studies, our results add to data which contradict the hypothesized role of social learning in
Heliconius
foraging behaviour.
Quantifying optimal resource allocation strategies for controlling epidemics
Authors: Maity Biplab , Banerjee Swarnendu , Senapati Abhishek , Chattopadhyay Joydev
Published: May 2023

Frequent emergence of communicable diseases is a major concern worldwide. Lack of sufficient resources to mitigate the disease burden makes the situation even more challenging for lower-income countries. Hence, strategy development for disease eradication and optimal management of the social and economic burden has garnered a lot of attention in recent years. In this context, we quantify the optimal fraction of resources that can be allocated to two major intervention measures, namely reduction of disease transmission and improvement of healthcare infrastructure. Our results demonstrate that the effectiveness of each of the interventions has a significant impact on the optimal resource allocation in both long-term disease dynamics and outbreak scenarios. The optimal allocation strategy for long-term dynamics exhibits non-monotonic behaviour with respect to the effectiveness of interventions, which differs from the more intuitive strategy recommended in the case of outbreaks. Further, our results indicate that the relationship between investment in interventions and the corresponding increase in patient recovery rate or decrease in disease transmission rate plays a decisive role in determining optimal strategies. Intervention programmes with decreasing returns promote the necessity for resource sharing. Our study provides fundamental insights into determining the best response strategy when controlling epidemics in resource-constrained situations.
Integrating kelp genomic analyses and geological data to reveal ancient earthquake impacts
Authors: Vaux Felix , Fraser Ceridwen I. , Craw Dave , Read Stephen , Waters Jonathan M.
Published: May 2023

Detached buoyant kelp can disperse thousands of kilometres at sea and can colonize newly available shores in the wake of disturbances that wipe out competitors. Localized earthquake uplift can cause extirpation of intertidal kelp populations followed by recolonization. Sources of recolonizing kelp can be detectable in genomic structure of contemporary populations. Our field observations combined with LiDAR mapping identified a previously unrecognized zone of uplifted rocky coastline in a region that is slowly subsiding. Intertidal kelp (
Durvillaea antarctica
) on the uplifted section of coast is genetically distinctive from nearby populations, with genomic signatures most similar to that of kelp 300 km to the south. Genetic divergence between these locations suggests reproductive isolation for thousands of years. Combined geological and genetic data suggest that this uplift event occurred during one of four major earthquakes between 6000 and 2000 years ago, with one of the younger events most likely. Extirpation of the pre-existing kelp required sudden uplift of approximately 2 metres, precluding several small incremental uplift events. Our results show the power of integrating biological (genomic) analyses with geological data to understand ancient geological processes and their ecological impacts.
Teaching open and reproducible scholarship: a critical review of the evidence base for current pedagogical methods and their outcomes
Authors: Pownall Madeleine , Azevedo Flávio , König Laura M. , Slack Hannah R. , Evans Thomas Rhys , Flack Zoe , Grinschgl Sandra , Elsherif Mahmoud M. , Gilligan-Lee Katie A. , de Oliveira Catia M. F. , Gjoneska Biljana , Kalandadze Tamara , Button Katherine , Ashcroft-Jones Sarah , Terry Jenny , Albayrak-Aydemir Nihan , Děchtěrenko Filip , Alzahawi Shilaan , Baker Bradley J. , Pittelkow Merle-Marie , Riedl Lydia , Schmidt Kathleen , Pennington Charlotte R. , Shaw John J. , Lüke Timo , Makel Matthew C. , Hartmann Helena , Zaneva Mirela , Walker Daniel , Verheyen Steven , Cox Daniel , Mattschey Jennifer , Gallagher-Mitchell Tom , Branney Peter , Weisberg Yanna , Izydorczak Kamil , Al-Hoorie Ali H. , Creaven Ann-Marie , Stewart Suzanne L. K. , Krautter Kai , Matvienko-Sikar Karen , Westwood Samuel J. , Arriaga Patrícia , Liu Meng , Baum Myriam A. , Wingen Tobias , Ross Robert M. , O'Mahony Aoife , Bochynska Agata , Jamieson Michelle , Tromp Myrthe Vel , Yeung Siu Kit , Vasilev Martin R. , Gourdon-Kanhukamwe Amélie , Micheli Leticia , Konkol Markus , Moreau David , Bartlett James E. , Clark Kait , Brekelmans Gwen , Gkinopoulos Theofilos , Tyler Samantha L. , Röer Jan Philipp , Ilchovska Zlatomira G. , Madan Christopher R. , Robertson Olly , Iley Bethan J. , Guay Samuel , Sladekova Martina , Sadhwani Shanu ,   FORRT
Published: May 2023

In recent years, the scientific community has called for improvements in the credibility, robustness and reproducibility of research, characterized by increased interest and promotion of open and transparent research practices. While progress has been positive, there is a lack of consideration about how this approach can be embedded into undergraduate and postgraduate research training. Specifically, a critical overview of the literature which investigates how integrating open and reproducible science may influence
student outcomes
is needed. In this paper, we provide the first critical review of literature surrounding the integration of open and reproducible scholarship into teaching and learning and its associated outcomes in students. Our review highlighted how embedding open and reproducible scholarship appears to be associated with (i) students'
scientific literacies
(i.e. students’ understanding of open research, consumption of science and the development of transferable skills); (ii)
student engagement
(i.e. motivation and engagement with learning, collaboration and engagement in open research) and (iii) students'
attitudes towards science
(i.e. trust in science and confidence in research findings). However, our review also identified a need for more robust and rigorous methods within pedagogical research, including more interventional and experimental evaluations of teaching practice. We discuss implications for teaching and learning scholarship.
Optimizing crop rotations via Parrondo’s paradox for sustainable agriculture
Authors: Gokhale Chaitanya S. , Sharma Nikhil
Published: May 2023

Crop rotation, a sustainable agricultural technique, has been at humanity’s disposal since time immemorial and is practised globally. Switching between cover crops and cash crops helps avoid the adverse effects of intensive farming. Determining the optimum cash-cover rotation schedule for maximizing yield has been tackled on multiple fronts by agricultural scientists, economists, biologists and computer scientists, to name a few. However, considering the uncertainty due to diseases, pests, droughts, floods and impending effects of climate change is essential when designing rotation strategies. Analysing this time-tested technique of crop rotations with a new lens of Parrondo’s paradox allows us to optimally use the rotation technique in synchrony with uncertainty. While previous approaches are reactive to the diversity of crop types and environmental uncertainties, we make use of the said uncertainties to enhance crop rotation schedules. We calculate optimum switching probabilities in a randomized cropping sequence and suggest optimum deterministic sequences and judicious use of fertilizers. Our methods demonstrate strategies to enhance crop yield and the eventual profit margins for farmers. Conforming to translational biology, we extend Parrondo’s paradox, where two losing situations can be combined eventually into a winning scenario, to agriculture.
Non-random mating within an Island rookery of Hawaiian hawksbill turtles: demographic discontinuity at a small coastline scale
Authors: Horne John B. , Frey Amy , Gaos Alexander R. , Martin Summer , Dutton Peter H.
Published: May 2023

Hawksbill sea turtles (Eretmochelys imbricata) from the Hawaiian archipelago form a small and genetically isolated population, consisting of only a few tens of individuals breeding annually. Most females nest on the island of Hawai'i, but little is known about the demographics of this rookery. This study used genetic relatedness, inferred from 135 microhaplotype markers, to determine breeding sex-ratios, estimate female nesting frequency and assess relationships between individuals nesting on different beaches. Samples were collected during the 2017 nesting season and final data included 13 nesting females and 1002 unhatched embryos, salvaged from 41 nests, of which 13 had no observed mother. Results show that most females used a single nesting beach laying 1–5 nests each. From female and offspring alleles, the paternal genotypes of 12 breeding males were reconstructed and many showed high relatedness to their mates. Pairwise relatedness of offspring revealed one instance of polygyny but otherwise suggested a 1 : 1 breeding-sex ratio. Relatedness analysis and spatial-autocorrelation of genotypes indicate that turtles from different nesting areas do not regularly interbreed, suggesting that strong natal homing tendencies in both sexes result in non-random mating across the study area. Complexes of nearby nesting beaches also showed unique patterns of inbreeding across loci, further indicating that Hawaiian hawksbill turtles have demographically discontinuous nesting populations separated by only tens of km.
Exploring how members of illicit networks navigate investigative interviews
Authors: Neequaye David A. , Granhag Pär Anders , Luke Timothy J.
Published: May 2023

This study explored how members of an illicit network navigate investigative interviews probing their crimes. We examined how perceived disclosure outcomes, namely, the projected costs and benefits, affect what members choose to reveal. We recruited
N
= 22 groups, maximum of six participants per group. Each group assumed the role of an illicit network and planned for possible interviews with investigators probing into the legitimacy of a business the network owns. All participants underwent an interview after the group planning stage. The results indicated that network members navigate the dilemma interviews bring by disclosing information they perceive would likely yield beneficial (or desirable) rather than costly (or undesirable) outcomes. Additionally, much of the participants' sensitivity to potential costs and benefits was explained by the group of which they are a part: different networks likely respond to costs and benefits in unique ways. This work contributes to understanding how illicit networks manage information disclosure in investigative interviews.
Hypercontractivity meets random convex hulls: analysis of randomized multivariate cubatures
Authors: Hayakawa Satoshi , Oberhauser Harald , Lyons Terry
Published: May 2023

Given a probability measure

μ

on a set

X

and a vector-valued function

φ

, a common problem is to construct a discrete probability measure on

X

such that the push-forward of these two probability measures under

φ

is the same. This construction is at the heart of numerical integration methods that run under various names such as quadrature, cubature or recombination. A natural approach is to sample points from

μ

until their convex hull of their image under

φ

includes the mean of

φ

. Here, we analyse the computational complexity of this approach when

φ

exhibits a graded structure by using so-called hypercontractivity. The resulting theorem not only covers the classical cubature case of multivariate polynomials, but also integration on pathspace, as well as kernel quadrature for product measures.
Analytical investigation of a grain boundary model that accounts for slip system coupling in gradient crystal plasticity frameworks
Authors: Erdle H. , Böhlke T.
Published: May 2023

In this work, a physically based dislocation theory of plasticity is derived within an extended continuum mechanical context. An orientation-dependent grain boundary flow rule is introduced for the modelling of dislocation pile-up at grain boundaries and dislocation transmission through grain boundaries. With the conventional grain boundary modelling approach according to Gurtin (Gurtin. 2008
J. Mech. Phys. Solids
56
, 640–662. (
doi:10.1016/j.jmps.2007.05. 002
)) the single-crystal consistency check for the limit case of adjacent grains that hold no misorientation is not satisfied. In order to overcome this modelling shortcoming, a slip system coupling based on a geometric measure of slip system compatibility is introduced. In order to investigate the grain boundary modelling approaches, the analytical solution of a three-phase periodic laminate is used to study the interactions of dislocations and grain boundaries within the gradient crystal plasticity framework. With the developed grain boundary model two grain boundary states, i.e. microhard and microcontrolled, are observed for misaligned grains. This allows the modelling of slip activation at grain boundaries based on the dislocation pile-up stress.
Localization in musical steelpans
Authors: Bryde Petur , Mahadevan L.
Published: May 2023

The steelpan is a pitched percussion instrument that takes the form of a concave bowl with several localized dimpled regions of varying curvature. Each of these localized zones, called notes, can vibrate independently when struck, and produce a sustained tone of a well-defined pitch. While the association of the localized zones with individual notes has long been known and exploited, the relationship between the shell geometry and the strength of the mode confinement remains unclear. Here, we explore the spectral properties of the steelpan modelled as a vibrating elastic shell. To characterize the resulting eigenvalue problem, we generalize a recently developed theory of localization landscapes for scalar elliptic operators to the vector-valued case, and predict the location of confined eigenmodes by solving a Poisson problem. A finite-element discretization of the shell shows that the localization strength is determined by the difference in curvature between the note and the surrounding bowl. In addition to providing an explanation for how a steelpan operates as a two-dimensional xylophone, our study provides a geometric principle for designing localized modes in elastic shells.
Application of thrust layout optimization to masonry structures
Authors: Nanayakkara K. Isuru U. , Liew Andrew , Gilbert Matthew
Published: May 2023

A new automated analysis procedure designed to overcome limitations of the traditional thrust line analysis method for masonry gravity structures is presented. The procedure, termed thrust layout optimization (TLO), is capable of automatically identifying admissible thrust lines in masonry gravity structures comprising general arrangements of masonry blocks. The procedure employs a modified truss layout optimization with transmissible loads formulation, which means that an initial thrust line layout does not need to be specified in advance. Highly visual output is generated, allowing areas where tensile strength has been implicitly assumed to be clearly identified, which is beyond the scope of traditional thrust line analysis. Also, sliding failures can be modelled without difficulty. Finally, examples are used to demonstrate the efficacy of the TLO procedure; these show that thrust line bifurcations can be automatically identified in problems involving openings, and that there is no need to estimate the ineffective area in buttress wall problems, both issues for the traditional thrust line analysis method.
ICTV Virus Taxonomy Profile: Poxviridae 2023
Authors: McInnes Colin J. , Damon Inger K. , Smith Geoffrey L. , McFadden Grant , Isaacs Stuart N. , Roper Rachel L. , Evans David H. , Damaso Clarissa R. , Carulei Olivia , Wise Lyn M. , Lefkowitz Elliot J.
Published: May 2023

Poxviridae is a family of enveloped, brick-shaped or ovoid viruses. The genome is a linear molecule of dsDNA (128–375 kbp) with covalently closed ends. The family includes the sub-families Entomopoxvirinae, whose members have been found in four orders of insects, and Chordopoxvirinae, whose members are found in mammals, birds, reptiles and fish. Poxviruses are important pathogens in various animals, including humans, and typically result in the formation of lesions, skin nodules, or disseminated rash. Infections can be fatal. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Poxviridae, which is available at ictv.global/report/poxviridae.
An enrichment protocol and analysis pipeline for long read sequencing of the hepatitis B virus transcriptome
Authors: Ng Esther , Dobrica Mihaela-Olivia , Harris James M. , Wu Yanxia , Tsukuda Senko , Wing Peter A. C. , Piazza Paolo , Balfe Peter , Matthews Philippa C. , Ansari M. Azim , McKeating Jane A.
Published: May 2023

Hepatitis B virus (HBV) is one of the smallest human DNA viruses and its 3.2 Kb genome encodes multiple overlapping open reading frames, making its viral transcriptome challenging to dissect. Previous studies have combined quantitative PCR and Next Generation Sequencing to identify viral transcripts and splice junctions, however the fragmentation and selective amplification used in short read sequencing precludes the resolution of full length RNAs. Our study coupled an oligonucleotide enrichment protocol with state-of-the-art long read sequencing (PacBio) to identify the repertoire of HBV RNAs. This methodology provides sequencing libraries where up to 25 % of reads are of viral origin and enable the identification of canonical (unspliced), non-canonical (spliced) and chimeric viral-human transcripts. Sequencing RNA isolated from de novo HBV infected cells or those transfected with 1.3 × overlength HBV genomes allowed us to assess the viral transcriptome and to annotate 5′ truncations and polyadenylation profiles. The two HBV model systems showed an excellent agreement in the pattern of major viral RNAs, however differences were noted in the abundance of spliced transcripts. Viral-host chimeric transcripts were identified and more commonly found in the transfected cells. Enrichment capture and PacBio sequencing allows the assignment of canonical and non-canonical HBV RNAs using an open-source analysis pipeline that enables the accurate mapping of the HBV transcriptome.
NCTC3000: a century of bacterial strain collecting leads to a rich genomic data resource
Authors: Dicks Jo , Fazal Mohammed-Abbas , Oliver Karen , Grayson Nicholas E. , Turnbull Jake D. , Bane Evangeline , Burnett Edward , Deheer-Graham Ana , Holroyd Nancy , Kaushal Dorota , Keane Jacqueline , Langridge Gemma , Lomax Jane , McGregor Hannah , Picton Steve , Quail Michael , Singh Deepak , Tracey Alan , Korlach Jonas , Russell Julie E. , Alexander Sarah , Parkhill Julian
Published: May 2023

The National Collection of Type Cultures (NCTC) was founded on 1 January 1920 in order to fulfil a recognized need for a centralized repository for bacterial and fungal strains within the UK. It is among the longest-established collections of its kind anywhere in the world and today holds approximately 6000 type and reference bacterial strains – many of medical, scientific and veterinary importance – available to academic, health, food and veterinary institutions worldwide. Recently, a collaboration between NCTC, Pacific Biosciences and the Wellcome Sanger Institute established the NCTC3000 project to long-read sequence and assemble the genomes of up to 3000 NCTC strains. Here, at the beginning of the collection’s second century, we introduce the resulting NCTC3000 sequence read datasets, genome assemblies and annotations as a unique, historically and scientifically relevant resource for the benefit of the international bacterial research community.
Analysis of lncRNA, miRNA, mRNA-associated ceRNA networks in Autism
Authors: Azad Asal Tabatabaei , Mehrabi Mohammad-Reza , Zarinzad Yasamin , Noori Atefeh , Nemati Hossein , Shahbazi Amir , Badameh Parisa , Mohammadnezad kenari Seyed Roham , Arabzadeh Parham , Javanmard Amir-Reza
Published: May 2023

Autism is a multifactorial behavioral disease, which is caused by different environmental and genetic alterations. In this disease, various molecular pathways such as inflammation and cell-cell connections are affected. In this study, by analyzing RNA-seq data and bioinformatics approaches, candidate genes were selected for further analysis, and the expression of candidate genes in the blood samples of autistic people was compared to normal. Finally, the candidate genes showed potential as biological markers for prognosis in autism. Through the analysis of these candidate genes, the researchers were able to identify changes in the expression of certain genes that were associated with the disease. By understanding how these genes are involved in the disease, researchers can develop better treatments and diagnose the disease earlier.