bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring public concerns for sharing and governance of personal health information: a focus group study
Authors: McCormick Jennifer B , Hopkins Margaret A
Published: December 2021

Objective

Researchers are increasingly collecting large amounts of deidentified data about individuals to address important health-related challenges and answer fundamental questions. Current US federal regulations permit researchers to use already collected and stored deidentified health-related data from a variety of sources without seeking consent from patients. The objective of this study was to investigate public views on the policies and processes institutions have in place for accessing, using, and sharing of data.

Materials and Methods

We conducted 5 focus groups with individuals living within a 20-mile radius of the local academic medical center. We also held a focus group with undergraduates at a local university.

Results

A total of 37 individuals participated, ages 18–76. Most participants were not surprised that researchers accessed and used deidentified personal information for research, and were supportive of this practice. Transparency was important. Participants wanted to know when their data were accessed, for what purpose, and by whom. Some wanted to have some control over the use of their data valuing the chance to opt-out. Finally, participants supported establishment of an advisory council or group with responsibility for deciding what data were used, who was accessing those data, and whether data could be shared.

Discussion and Conclusions

The trust people have in their local institutions should be considered fragile, and institutions should not take that trust for granted. How institutions choose to govern patients’ data and what voices are included in decisions about use and access are critical to maintaining the trust of the public.
Enhancing research informatics core user satisfaction through agile practices
Authors: Post Andrew R , Luther Jared , Loveless J Maxwell , Ward Melanie , Hewitt Shirleen
Published: December 2021

Objective

The Huntsman Cancer Institute Research Informatics Shared Resource (RISR), a software and database development core facility, sought to address a lack of published operational best practices for research informatics cores. It aimed to use those insights to enhance effectiveness after an increase in team size from 20 to 31 full-time equivalents coincided with a reduction in user satisfaction.

Materials and Methods

RISR migrated from a water-scrum-fall model of software development to agile software development practices, which emphasize iteration and collaboration. RISR’s agile implementation emphasizes the product owner role, which is responsible for user engagement and may be particularly valuable in software development that requires close engagement with users like in science.

Results

All RISR’s software development teams implemented agile practices in early 2020. All project teams are led by a product owner who serves as the voice of the user on the development team. Annual user survey scores for service quality and turnaround time recorded 9 months after implementation increased by 17% and 11%, respectively.

Discussion

RISR is illustrative of the increasing size of research informatics cores and the need to identify best practices for maintaining high effectiveness. Agile practices may address concerns about the fit of software engineering practices in science. The study had one time point after implementing agile practices and one site, limiting its generalizability.

Conclusions

Agile software development may substantially increase a research informatics core facility’s effectiveness and should be studied further as a potential best practice for how such cores are operated.
Budget-constrained coalition strategies with discounting
Authors: Bozzone Lia , Naumov Pavel
Published: December 2021

Discounting future costs and rewards is a common practice in accounting, game theory and machine learning. In spite of this, existing logics for reasoning about strategies with cost and resource constraints do not account for discounting. The article proposes a sound and complete logical system for reasoning about budget-constrained strategic abilities that incorporates discounting into its semantics.
Relentless and complex transits from a planetesimal debris disc
Authors: Farihi J , Hermes J J , Marsh T R , Mustill A J , Wyatt M C , Guidry J A , Wilson T G , Redfield S , Izquierdo P , Toloza O , Gänsicke B T , Aungwerojwit A , Kaewmanee C , Dhillon V S , Swan A
Published: December 2021

This article reports quasi-continuous transiting events towards WD 1054–226 at d = 36.2 pc and V = 16.0 mag, based on simultaneous, high-cadence, multiwavelength imaging photometry using ULTRACAM over 18 nights from 2019 to 2020 March. The predominant period is 25.02 h and corresponds to a circular orbit with blackbody Teq = 323 K, where a planetary surface can nominally support liquid water. The light curves reveal remarkable night-to-night similarity, with changes on longer time-scales, and lack any transit-free segments of unocculted starlight. The most pronounced dimming components occur every 23.1 min – exactly the 65th harmonic of the fundamental period – with depths of up to several per cent, and no evident colour dependence. Myriad additional harmonics are present, as well as at least two transiting features with independent periods. High-resolution optical spectra are consistent with stable, photospheric absorption by multiple, refractory metal species, with no indication of circumstellar gas. Spitzer observations demonstrate a lack of detectable dust emission, suggesting that the otherwise hidden circumstellar disc orbiting WD 1054–226 may be typical of polluted white dwarfs, and detected only via favourable geometry. Future observations are required to constrain the orbital eccentricity, but even if periastron is near the Roche limit, sublimation cannot drive mass loss in refractory parent bodies, and collisional disintegration is necessary for dust production.
Use of mycophenolate mofetil for systemic sclerosis and systemic sclerosis-associated interstitial lung disease: Information from a Japanese hospital claims database
Authors: Funatogawa Takashi , Narita Yusuke , Tamura Aya , Mii Kazuma , Sugitani Yasuo , Uchida Tomoaki
Published: December 2021

Objectives

Limited information is available on patients with systemic sclerosis (SSc) or SSc-associated interstitial lung disease (SSc-ILD) receiving mycophenolate mofetil (MMF) in Japan. The dose, treatment duration, and patient characteristics of SSc and SSc-ILD patients receiving MMF were investigated.

Methods

We used data from a Japanese hospital claims database (2008–2020).

Results

Data on 486 SSc patients ≥18 years old receiving MMF were captured; 314 had SSc complicated with ILD. The most common initial daily doses were 1000 mg (SSc, 39.5%; SSc-ILD, 38.1%) and 500 mg (SSc, 36.6%; SSc-ILD, 34.6%). The most common maximum daily doses were 1000 mg (SSc, 33.3%; SSc-ILD, 34.9%), 1500 mg (SSc, 24.4%; SSc-ILD, 23.1%), and 2000 mg (SSc, 23.8%; SSc-ILD, 24.4%). Doses ranged from 250 to 3000 mg/day and were similar for SSc and SSc-ILD patients. Over 27% of patients received treatment for >1 year. There was a gradual decrease in steroid doses during MMF treatment.

Conclusions

Our study suggests that the off-label use of MMF for SSc and SSc-ILD has been increasing annually since 2015 in Japan. The doses used in patients with SSc and SSc-ILD were similar to the approved doses of MMF for lupus nephritis in Japan.
Alpha and theta oscillations are inversely related to progressive levels of meditation depth
Authors: Katyal Sucharit , Goldin Philippe
Published: December 2021

Meditation training is proposed to enhance mental well-being by modulating neural activity, particularly alpha and theta brain oscillations, and autonomic activity. Although such enhancement also depends on the quality of meditation, little is known about how these neural and physiological changes relate to meditation quality. One model characterizes meditation quality as five increasing levels of ‘depth’: hindrances, relaxation, concentration, transpersonal qualities and nonduality. We investigated the neural oscillatory (theta, alpha, beta and gamma) and physiological (respiration rate, heart rate and heart rate variability) correlates of the self-reported meditation depth in long-term meditators (LTMs) and meditation-naïve controls (CTLs). To determine the neural and physiological correlates of meditation depth, we modelled the change in the slope of the relationship between self-reported experiential degree at each of the five depth levels and the multiple neural and physiological measures. CTLs reported experiencing more ‘hindrances’ than LTMs, while LTMs reported more ‘transpersonal qualities’ and ‘nonduality’ compared to CTLs, confirming the experiential manipulation of meditation depth. We found that in both groups, theta (4–6 Hz) and alpha (7–13 Hz) oscillations were related to meditation depth in a precisely opposite manner. The theta amplitude positively correlated with ‘hindrances’ and increasingly negatively correlated with increasing meditation depth levels. Alpha amplitude negatively correlated with ‘hindrances’ and increasingly positively with increasing depth levels. The increase in the inverse association between theta and meditation depth occurred over different scalp locations in the two groups—frontal midline in LTMs and frontal lateral in CTLs—possibly reflecting the downregulation of two different aspects of executive processing—monitoring and attention regulation, respectively—during deep meditation. These results suggest a functional dissociation of the two classical neural signatures of meditation training, namely, alpha and theta oscillations. Moreover, while essential for overcoming ‘hindrances’, executive neural processing appears to be downregulated during deeper meditation experiences.
Two decades of suspect evidence for adaptive molecular evolution—negative selection confounding positive-selection signals
Authors: Chen Qipian , Yang Hao , Feng Xiao , Chen Qingjian , Shi Suhua , Wu Chung-I , He Ziwen
Published: December 2021

There has been a large literature in the last two decades affirming adaptive DNA sequence evolution between species. The main lines of evidence are from (i) the McDonald-Kreitman (MK) test, which compares divergence and polymorphism data, and (ii) the phylogenetic analysis by maximum likelihood (PAML) test, which analyzes multispecies divergence data. Here, we apply these two tests concurrently to genomic data of Drosophila and Arabidopsis. To our surprise, the >100 genes identified by the two tests do not overlap beyond random expectation. Because the non-concordance could be due to low powers leading to high false negatives, we merge every 20–30 genes into a ‘supergene’. At the supergene level, the power of detection is large but the calls still do not overlap. We rule out methodological reasons for the non-concordance. In particular, extensive simulations fail to find scenarios whereby positive selection can only be detected by either MK or PAML, but not both. Since molecular evolution is governed by positive and negative selection concurrently, a fundamental assumption for estimating one of these (say, positive selection) is that the other is constant. However, in a broad survey of primates, birds, Drosophila and Arabidopsis, we found that negative selection rarely stays constant for long in evolution. As a consequence, the variation in negative selection is often misconstrued as a signal of positive selection. In conclusion, MK, PAML and any method that examines genomic sequence evolution has to explicitly address the variation in negative selection before estimating positive selection. In a companion study, we propose a possible path forward in two stages—first, by mapping out the changes in negative selection and then using this map to estimate positive selection. For now, the large literature on positive selection between species has to await reassessment.
Non-bacterial thrombotic endocarditis in pancreatic cancer and other high-risk malignancies: the case for prophylactic treatment
Authors: Spurgeon Laura , Ispoglou Sissi
Published: December 2021

Non-bacterial thrombotic endocarditis (NBTE) typically affects patients with underlying adenocarcinoma, often of pancreatic origin. If untreated, it can lead to serious morbidity and mortality, including recurrent ischaemic stroke. NBTE is frequently missed or confused with infective endocarditis, leading to inappropriate management. We present the case of a 54-year-old male with newly diagnosed pancreatic malignancy (CA19–9 >120 000) who suffered recurrent deep-vein-thromboses and multiple ischaemic strokes despite full anticoagulation therapy. Transoesophageal echocardiography was correctly performed, but only after a second stroke was NBTE considered. We recommend early clinical suspicion and investigation for NBTE in patients with known or suspected malignancy presenting with neurological symptoms consistent with stroke. Initial calculations indicate this could also be cost-effective. Further, the patient’s significantly elevated tumour-markers and NBTE-severity raise the possibility of a link; if further research established a reliable relationship, routine surveillance of high-risk malignancies could identify patients who might benefit from earlier echocardiography and anticoagulation management.
A comprehensive review of the pyrolysis process: from carbon nanomaterial synthesis to waste treatment
Authors: Devi Mamta , Rawat Sachin , Sharma Swati
Published: December 2021

Thermally induced chemical decomposition of organic materials in the absence of oxygen is defined as pyrolysis. This process has four major application areas: (i) production of carbon materials, (ii) fabrication of pre-patterned micro and nano carbon-based structures, (iii) fragmentation of complex organic molecules for analytical purposes and (iv) waste treatment. While the underlying process principles remain the same in all cases, the target products differ owing to the phase and composition of the organic precursor, heat-treatment temperature, influence of catalysts and the presence of post-pyrolysis steps during heat-treatment. Due to its fundamental nature, pyrolysis is often studied in the context of one particular application rather than as an independent operation. In this review article, an effort is made to understand each aspect of pyrolysis in a comprehensive fashion, ensuring that all state-of-the-art applications are approached from the core process parameters that influence the ensuing product. Representative publications from recent years for each application are reviewed and analyzed. Some classical scientific findings that laid the foundation of the modern-day carbon material production methods are also revisited. In addition, classification of pyrolysis, its history and nomenclature and the plausible integration of different application areas are discussed.
Tax policy in the UK post-Brexit
Authors: Freedman Judith , Loutzenhiser Glen
Published: December 2021

Tax matters figured prominently in the Brexit debate. Current signs are, however, that the UK government is not planning the creation of a post-Brexit ‘Singapore on Thames’ as some had predicted. In fact, we are seeing increases to the main corporation tax rate in response to broader international tax developments and the fiscal upheaval caused by the pandemic. Prior to Brexit, the UK already enjoyed considerable freedom in respect of direct taxes including income tax and corporation tax, but less so for VAT; it has more freedom to change the VAT now, if desired, and has already introduced some relatively small amendments to reflect the new state of play. At this point, the government has exercised its new-found freedoms on tax in quite limited ways—most notably in creating freeports which will benefit from special advantageous customs and tax rules, refocusing R&D tax relief towards activity conducted in the UK, making relatively minor changes to tonnage tax, alcohol duties, and air passenger duty, and removing some narrow EU-focused corporation tax measures. However, these new-found tax freedoms come with new-found restrictions, costs, and challenges for both taxpayers and the UK government. There are significant changes on the tax administration front, which generally complicates matters for HMRC as it will have to rely on less extensive and less convenient treaty and OECD avenues of cooperation. On VAT, teething issues as well as longer-term complications have arisen post-Brexit for businesses and consumers. Provisions remain to control the extent of fiscal state aid, albeit in a less restrictive way under the new subsidy control mechanism in the UK/EU Trade and Co-operation Agreement. The strong overall message is that financial and international pressures and constraints are more important to the direction of tax policy than the fact that the UK has left the EU.
Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections
Authors: Leigh Deborah M , Peranić Karla , Prospero Simone , Cornejo Carolina , Ćurković-Perica Mirna , Kupper Quirin , Nuskern Lucija , Rigling Daniel , Ježić Marin
Published: December 2021

Intra-host dynamics are a core component of virus evolution but most intra-host data come from a narrow range of hosts or experimental infections. Gaining broader information on the intra-host diversity and dynamics of naturally occurring virus infections is essential to our understanding of evolution across the virosphere. Here we used PacBio long-read HiFi sequencing to characterize the intra-host populations of natural infections of the RNA mycovirus Cryphonectria hypovirus 1 (CHV1). CHV1 is a biocontrol agent for the chestnut blight fungus (Cryphonectria parasitica), which co-invaded Europe alongside the fungus. We characterized the mutational and haplotypic intra-host virus diversity of thirty-eight natural CHV1 infections spread across four locations in Croatia and Switzerland. Intra-host CHV1 diversity values were shaped by purifying selection and accumulation of mutations over time as well as epistatic interactions within the host genome at defense loci. Geographical landscape features impacted CHV1 inter-host relationships through restricting dispersal and causing founder effects. Interestingly, a small number of intra-host viral haplotypes showed high sequence similarity across large geographical distances unlikely to be linked by dispersal.
Dexmedetomidine Clearance Decreases with Increasing Drug Exposure: Implications for Current Dosing Regimens and Target-controlled Infusion Models Assuming Linear Pharmacokinetics
Authors: Alvarez-Jimenez Ricardo , Weerink Maud A. S. , Hannivoort Laura N. , Su Hong , Struys Michel M. R. F. , Loer Stephan A. , Colin Pieter J.
Published: December 2021

Background

Numerous pharmacokinetic models have been published aiming at more accurate and safer dosing of dexmedetomidine. The vast majority of the developed models underpredict the measured plasma concentrations with respect to the target concentration, especially at plasma concentrations higher than those used in the original studies. The aim of this article was to develop a dexmedetomidine pharmacokinetic model in healthy adults emphasizing linear versus nonlinear kinetics.

Methods

The data of two previously published clinical trials with stepwise increasing dexmedetomidine target-controlled infusion were pooled to build a pharmacokinetic model using the NONMEM software package (ICON Development Solutions, USA). Data from 48 healthy subjects, included in a stratified manner, were utilized to build the model.

Results

A three-compartment mamillary model with nonlinear elimination from the central compartment was superior to a model assuming linear pharmacokinetics. Covariates included in the final model were age, sex, and total body weight. Cardiac output did not explain between-subject or within-subject variability in dexmedetomidine clearance. The results of a simulation study based on the final model showed that at concentrations up to 2 ng · ml–1, the predicted dexmedetomidine plasma concentrations were similar between the currently available Hannivoort model assuming linear pharmacokinetics and the nonlinear model developed in this study. At higher simulated plasma concentrations, exposure increased nonlinearly with target concentration due to the decreasing dexmedetomidine clearance with increasing plasma concentrations. Simulations also show that currently approved dosing regimens in the intensive care unit may potentially lead to higher-than-expected dexmedetomidine plasma concentrations.

Conclusions

This study developed a nonlinear three-compartment pharmacokinetic model that accurately described dexmedetomidine plasma concentrations. Dexmedetomidine may be safely administered up to target-controlled infusion targets under 2 ng · ml–1 using the Hannivoort model, which assumed linear pharmacokinetics. Consideration should be taken during long-term administration and during an initial loading dose when following the dosing strategies of the current guidelines.

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Preoperative Point-of-Care Ultrasound to Identify Frailty and Predict Postoperative Outcomes: A Diagnostic Accuracy Study
Authors: Canales Cecilia , Mazor Einat , Coy Heidi , Grogan Tristan R. , Duval Victor , Raman Steven , Cannesson Maxime , Singh Sumit P.
Published: December 2021

Background

Frailty is increasingly being recognized as a public health issue, straining healthcare resources and increasing costs to care for these patients. Frailty is the decline in physical and cognitive reserves leading to increased vulnerability to stressors such as surgery or disease states. The goal of this pilot diagnostic accuracy study was to identify whether point-of-care ultrasound measurements of the quadriceps and rectus femoris muscles can be used to discriminate between frail and not-frail patients and predict postoperative outcomes. This study hypothesized that ultrasound could discriminate between frail and not-frail patients before surgery.

Methods

Preoperative ultrasound measurements of the quadriceps and rectus femoris were obtained in patients with previous computed tomography scans. Using the computed tomography scans, psoas muscle area was measured in all patients for comparative purposes. Frailty was identified using the Fried phenotype assessment. Postoperative outcomes included unplanned intensive care unit admission, delirium, intensive care unit length of stay, hospital length of stay, unplanned skilled nursing facility admission, rehospitalization, falls within 30 days, and all-cause 30-day and 1-yr mortality.

Results

A total of 32 patients and 20 healthy volunteers were included. Frailty was identified in 18 of the 32 patients. Receiver operating characteristic curve analysis showed that quadriceps depth and psoas muscle area are able to identify frailty (area under the curve–receiver operating characteristic, 0.80 [95% CI, 0.64 to 0.97] and 0.88 [95% CI, 0.76 to 1.00], respectively), whereas the cross-sectional area of the rectus femoris is less promising (area under the curve–receiver operating characteristic, 0.70 [95% CI, 0.49 to 0.91]). Quadriceps depth was also associated with unplanned postoperative skilled nursing facility discharge disposition (area under the curve 0.81 [95% CI, 0.61 to 1.00]) and delirium (area under the curve 0.89 [95% CI, 0.77 to 1.00]).

Conclusions

Similar to computed tomography measurements of psoas muscle area, preoperative ultrasound measurements of quadriceps depth shows promise in discriminating between frail and not-frail patients before surgery. It was also associated with skilled nursing facility admission and postoperative delirium.

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Thomas Arthur Steitz. 23 August 1940—9 October 2018
Authors: Ramakrishnan V. , Henderson Richard
Published: December 2021

Thomas A. Steitz was among the foremost of the generation that was responsible for an explosion in our understanding of the structure and function of biological macromolecules. His research career was one of sustained excellence over six decades, and spanned the range from determining the structures of important metabolic enzymes to understanding the structural basis of how genetic information residing in our DNA is used to make the proteins they encode. This latter effort culminated in the structure of the ribosome, for which he shared the Nobel Prize in Chemistry in 2009.
Strategizing COVID-19 lockdowns using mobility patterns
Authors: Buchel Olha , Ninkov Anton , Cathel Danise , Bar-Yam Yaneer , Hedayatifar Leila
Published: December 2021

During the COVID-19 pandemic, governments have attempted to control infections within their territories by implementing border controls and lockdowns. While large-scale quarantine has been the most successful short-term policy, the enormous costs exerted by lockdowns over long periods are unsustainable. As such, developing more flexible policies that limit transmission without requiring large-scale quarantine is an urgent priority. Here, the dynamics of dismantled community mobility structures within US society during the COVID-19 outbreak are analysed by applying the Louvain method with modularity optimization to weekly datasets of mobile device locations. Our networks are built based on individuals' movements from February to May 2020. In a multi-scale community detection process using the locations of confirmed cases, natural break points from mobility patterns as well as high risk areas for contagion are identified at three scales. Deviations from administrative boundaries were observed in detected communities, indicating that policies informed by assumptions of disease containment within administrative boundaries do not account for high risk patterns of movement across and through these boundaries. We have designed a multi-level quarantine process that takes these deviations into account based on the heterogeneity in mobility patterns. For communities with high numbers of confirmed cases, contact tracing and associated quarantine policies informed by underlying dismantled community mobility structures is of increasing importance.
Habituation of common vampire bats to biologgers
Authors: Kline Emma , Ripperger Simon P. , Carter Gerald G.
Published: December 2021

Rapid advancements in biologging technology have led to unprecedented insights into animal behaviour, but testing the effects of biologgers on tagged animals is necessary for both scientific and ethical reasons. Here, we measured how quickly 13 wild-caught and captively isolated common vampire bats (Desmodus rotundus) habituated to mock proximity sensors glued to their dorsal fur. To assess habituation, we scored video-recorded behaviours every minute from 18.00 to 06.00 for 3 days, then compared the rates of grooming directed to the sensor tag versus to their own body. During the first hour, the mean tag-grooming rate declined dramatically from 53% of sampled time (95% CI = 36–65%,n= 6) to 16% (8–24%,n= 9), and down to 4% by hour 5 (1–6%,n= 13), while grooming of the bat's own body did not decline. When tags are firmly attached, isolated individual vampire bats mostly habituate within an hour of tag attachment. In two cases, however, tags became loose before falling off causing the bats to dishabituate. For tags glued to fur, behavioural data are likely to be impacted immediately after the tag is attached and when it is loose before it falls off.
Hot and sour: parasite adaptations to honeybee body temperature and pH
Authors: Palmer-Young Evan C. , Raffel Thomas R. , Evans Jay D.
Published: December 2021

Host temperature and gut chemistry can shape resistance to parasite infection. Heat and acidity can limit trypanosomatid infection in warm-blooded hosts and could shape infection resistance in insects as well. The colony-level endothermy and acidic guts of social bees provide unique opportunities to study how temperature and acidity shape insect–parasite associations. We compared temperature and pH tolerance between three trypanosomatid parasites from social bees and a related trypanosomatid from poikilothermic mosquitoes, which have alkaline guts. Relative to the mosquito parasites, all three bee parasites had higher heat tolerance that reflected body temperatures of hosts. Heat tolerance of the honeybee parasiteCrithidia mellificaewas exceptional for its genus, implicating honeybee endothermy as a plausible filter of parasite establishment. The lesser heat tolerance of the emergingLotmaria passimsuggests possible spillover from a less endothermic host. Whereas both honeybee parasites tolerated the acidic pH found in bee intestines, mosquito parasites tolerated the alkaline conditions found in mosquito midguts, suggesting that both gut pH and temperature could structure host–parasite specificity. Elucidating how host temperature and gut pH affect infection—and corresponding parasite adaptations to these factors—could help explain trypanosomatids' distribution among insects and invasion of mammals.
Consumer trait responses track change in resource supply along replicated thermal gradients
Authors: Moffett E. R. , Fryxell D. C. , Lee F. , Palkovacs E. P. , Simon K. S.
Published: December 2021

Rising temperatures may alter consumer diets through increased metabolic demand and altered resource availability. However, current theories assessing dietary shifts with warming do not account for a change in resource availability. It is unknown whether consumers will increase consumption rates or consume different resources to meet increased energy requirements and whether the dietary change will lead to associated variation in morphology and nutrient utilization. Here, we used populations of
Gambusia affinis
across parallel thermal gradients in New Zealand (NZ) and California (CA) to understand the influence of temperature on diets, morphology and stoichiometric phenotypes. Our results show that with increasing temperature in NZ, mosquitofish consumed more plant material, whereas in CA mosquitofish shifted towards increased consumption of invertebrate prey. In both regions, populations with plant-based diets had fuller guts, longer relative gut lengths, superior-orientated mouths and reduced body elemental %C and N/P. Together, our results show multiple pathways by which consumers may alter their feeding patterns with rising temperatures, and they suggest that warming-induced changes to resource availability may be the principal determinant of which pathway is taken.
Evaluation of Vaccination Strategies for the metropolitan area of Madrid
Authors: Singh David E. , Lucerón Carmen Olmedo , Sánchez Aurora Limia , Guzman-Merino Miguel , Duran Christian , Delgado-Sanz Concepción , Gomez-Barroso Diana , Carretero Jesus , Marinescu Maria-Cristina
Published: December 2021

Background

This work analyses the impact of different vaccination strategies on the propagation of COVID-19 within the Madrid metropolitan area starting the 27th of December 2020 and ending in the Summer of 2021. The predictions are based on simulation using EpiGraph, an agent-based COVID-19 simulator.

Methods

We briefly summarize the different interconnected models of EpiGraph and then we provide a comprehensive description of the vaccination model. We evaluate different vaccination strategies, and we validate the simulator by comparing the simulation results with real data from the metropolitan area of Madrid during the third wave.

Results

We consider the different COVID-19 propagation scenarios on a social environment consisting of the ten largest cities in the Madrid metropolitan area, with 5 million individuals. The results show that the strategy that fares best is to vaccinate the elderly first with the two doses spaced 56 days apart; this approach reduces the final infection rate and the number of deaths by an additional 6% and 3% with respect to vaccinating the elderly first at the interval between doses recommended by the vaccine producer.

Conclusion

Results show that prioritizing the vaccination of young individuals would significantly increase the number of deaths. On the other hand, spacing out the first and second dose by 56 days would result in a slight reduction in the number of infections and deaths. The reason is the increase in the number of vaccinated individuals at any time during the simulation.
Students Attitudes Surrounding STEM: A Social Cognitive Career Theory Instrument for High School
Authors: McDonough EmilyKate , Sawyer Kayle S. , Wilks Jessica , Jacque Berri
Published: December 2021

To broaden participation in science, technology, engineering, and math (STEM), we must understand the factors that shape perspectives and beliefs around career selection. Good measurement of these factors is crucial to quantify how effectively educational interventions impact student attitudes towards STEM. Adolescents are particularly suited for quantifying intervention efficacy because students build their identities during these formative years and make important career choices. To better quantify intervention efficacy at the high school level, we developed an instrument entitled Student Attitudes Surrounding STEM (SASS), which builds upon the social cognitive career theory (SCCT) framework for understanding career selection. Questionnaire responses were collected from 932 high school students and split into samples of 400 for exploratory factor analysis and 532 for confirmatory factor analysis. The 37 questions clustered into six factors: Self-Efficacy-Experience, Self-Efficacy-Academic, Outcome Expectations, Interests, Negative Perceptions of Scientists, and Career Awareness. Adequate construct validity for the factors indicated in the SASS model was suggested by the fit indices and theoretical considerations. Furthermore, the analyses supported criterion validity, internal consistency, and test-retest reliability. This tool represents a novel integration of three latent variables into SCCT: Negative Perceptions of Scientists, Career Awareness, and an experience factor for Self-Efficacy.
Neural synchronization is strongest to the spectral flux of slow music and depends on familiarity and beat salience
Authors: Weineck Kristin , Wen Olivia Xin , Henry Molly J.
Published: December 2021

Neural activity in the auditory system synchronizes to sound rhythms, and brain–environment synchronization is thought to be fundamental to successful auditory perception. Sound rhythms are often operationalized in terms of the sound’s amplitude envelope. We hypothesized that – especially for music – the envelope might not best capture the complex spectro-temporal fluctuations that give rise to beat perception and synchronized neural activity. This study investigated 1) neural synchronization to different musical features, 2) tempo-dependence of neural synchronization, and 3) dependence of synchronization on familiarity, enjoyment, and ease of beat perception. In this electroencephalography study, 37 human participants listened to tempo-modulated music (1–4 Hz). Independent of whether the analysis approach was based on temporal response functions (TRFs) or reliable components analysis (RCA), the spectral flux of music – as opposed to the amplitude envelope – evoked strongest neural synchronization. Moreover, music with slower beat rates, high familiarity, and easy-to-perceive beats elicited the strongest neural response. Our results demonstrate the importance of spectro-temporal fluctuations in music for driving neural synchronization, and highlight its sensitivity to musical tempo, familiarity, and beat salience.
Th1, Th2 and Th17 inflammatory pathways synergistically correlate with cardiometabolic processes. A case study in COVID-19
Authors: Michels James R. , Nazrul Mohammad Shaheed , Adhikari Sudeep , Wilkins Dawn , Pavel Ana B.
Published: December 2021

A predominant source of complication in SARS-CoV-2 patients arises from thecytokine storm, an elevated expression of inflammatory helper T-cell associated cytokines that can lead to tissue damage and organ failure. The high inflammatory burden of this viral infection often results in cardiovascular comorbidities. A better understanding of the interaction between thecytokine stormand cardiovascular proteins might inform medical decisions and therapeutic approaches. We hypothesized that all major helper T-cell inflammatory pathways (Th1, Th2 and Th17) synergistically contribute to cardiometabolic modifications in serum of COVID-19 patients. We proved our hypothesis by integrating Th1, Th2 and Th17 cytokines to predict expression of cardiometabolic proteins profiled by OLINK proteomics.
Dynamics of alpha suppression and enhancement may be related to resource competition in cross-modal cortical regions
Authors: Clements Grace M. , Gyurkovics Mate , Low Kathy A. , Beck Diane M. , Fabiani Monica , Gratton Gabriele
Published: December 2021

In the face of multiple sensory streams, there may be competition for processing resources in multimodal cortical area devoted to establishing representations. In such cases, alpha oscillations may serve to maintain the relevant representations and protect them from interference, whereas theta oscillations may facilitate their updating when needed. It can be hypothesized that these oscillations would differ in response to an auditory stimulus when the eyes are open or closed, as intermodal resource competition may be more prominent in the former than in the latter case. Across two studies we investigated the role of alpha and theta power in multimodal competition using an auditory task with the eyes open and closed, respectively enabling and disabling visual processing in parallel with the incoming auditory stream. In a passive listening task (Study 1a), we found alpha suppression following a pip tone with both eyes open and closed, but subsequent alpha enhancement only with closed eyes. We replicated this eyes-closed alpha enhancement in an independent sample (Study 1b). In an active auditory oddball task (Study 2), we again observed the eyes open/eyes closed alpha pattern found in Study 1 and also demonstrated that the more attentionally demanding oddball trials elicit the largest oscillatory effects. Theta power did not interact with eye status in either study. We propose a hypothesis to account for the findings in which alpha may be endemic to multimodal cortical areas in addition to visual ones.
A comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia
Authors: Darolti Iulia , Almeida Pedro , Wright Alison E. , Mank Judith E.
Published: December 2021

Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here we apply different analytical methodologies to the same dataset to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made de novo genome assemblies for the focal species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.
Bee communities in canola are affected by landscape context and farm management
Authors: Olsson Rachel L. , Pfeiffer Vera W. , Lee Benjamin W. , Crowder David W.
Published: December 2021

Bees are key pollinators that promote greater yield and seed quality of oilseed crops such as canola. Canola acreage has increased over 1,000% in the past decade in the Pacific Northwest USA, providing a major pulse of sugar-rich nectar and pollen resources that may affect bee health and community structure. However, because canola does not require insect pollination for seed production, few studies have examined the biodiversity of pollinators taking advantage of these resources, or the floral traits of canola that affect pollinators across variable landscapes. Here, we conducted pollinator surveys at canola farms across the inland Northwest region of the USA. We surveyed bee biodiversity and abundance, and assessed how these metrics correlated with landscape context, canola production practices, and floral traits of various canola varieties. We found that bee communities differed between sites and across growing seasons, with sweat bees more abundant later in the season, and mining bees more abundant earlier in the season. We also found that bees were more abundant overall on farms with less floral nectar and with less developed landscape surrounding the sampling area. Bee diversity was greater in spring canola than winter canola, and floral traits were also correlated with differing bee community diversity. This research provides important information for canola growers and land managers and offers a framework for future research in pollinator management in the inland Northwest.
Hunchback activates Bicoid in post-mitotic Pair1 neurons to regulate synapse number
Authors: Lee Kristen M , Linskens Amanda M , Doe Chris Q
Published: December 2021

The proper formation and function of neural circuits is crucial for cognition, sensation, and behavior. Neural circuits are highly-specific, and this specificity is dependent on neurons developing key features of their individual identities: morphology, anatomical location, molecular expression and biophysiological properties. Previous research has demonstrated that a neurons identity is, in part, generated by the temporal transcription window the neuron is born in, and the homeodomain transcription factors expressed in the mature neuron. However, whether temporal transcription factors and homeodomain transcription factors regulate neural circuit formation, maintenance and function remains unknown. Here, we utilize a well-characterized neural circuit in the Drosophila larvae, the Pair1 neuron. We determined that in the Pair1 neuron, the temporal transcription factor Hunchback activates the homeodomain transcription factor Bicoid (Bcd). Both Hunchback and Bcd are expressed in Pair1 throughout larval development. Interestingly, Hunchback and Bcd were not required in Pair1 for neurotransmitter identity or axonal morphology, but were required for synapse density. We found that these transcription factors were functioning post-mitotically in Pair1 to regulate synapse density. Additionally, knocking down Hunchback and Bcd in Pair1 neurons disrupted the behavioral output of the circuit. We utilized the genetic tool TransTango to determine that Hunchback function in Pair1 is to repress forming synapses with erroneous neurons. To our knowledge, these data are the first to show Hunchback activating Bcd expression, as well as the first to demonstrate a role for Hunchback and Bcd post-mitotically.
The Atypical Antipsychotic Quetiapine Induces Multiple Antibiotic Resistance in Escherichia coli
Authors: Kyono Yasuhiro , Ellezian Lori , Hu YueYue , Eliadis Kanella , Moy Junlone , Hirsch Elizabeth B. , Federle Michael J. , Flowers Stephanie A.
Published: December 2021

Atypical antipsychotic (AAP) medication is a critical tool for treating symptoms of psychiatric disorders. While AAPs primarily target dopamine (D2) and serotonin (5HT2A and 5HT1A) receptors, they also exhibit intrinsic antimicrobial activity as an off-target effect. Because AAPs are often prescribed to patients for many years, a potential risk associated with long-term AAP use is the unintended emergence of bacteria with antimicrobial resistance (AMR). Here, we show that exposure to the AAP quetiapine at estimated gut concentrations promotes AMR in Escherichia coli after six weeks. Quetiapine-exposed isolates exhibited an increase in minimal inhibitory concentrations (MICs) for ampicillin, tetracycline, ceftriaxone, and levofloxacin. By whole genome sequencing analysis, we identified mutations in genes that confer AMR, including the repressor for the multiple antibiotic resistance mar operon (marR), and real-time RT-qPCR analysis showed increased levels of marA, acrA, and tolC mRNAs and a reduced level of ompF mRNA in the isolates carrying marR mutations. To determine the contribution of each marR mutation to AMR, we constructed isogenic strains carrying individual mutant marR alleles in the parent background and re-evaluated their resistant phenotypes using MIC and RT-qPCR assays. While marR mutations induced a robust activity of the mar operon, they resulted in only a modest increase in MICs. Interestingly, although these marR mutations did not fully recapitulate the AMR phenotype of the quetiapine-exposed isolates, we show that marR mutations promote growth fitness in the presence of quetiapine. Our findings revealed an important link between the use of AAPs and AMR development in E. coli.