bluuebunny/crossref_metadata_2025 huggingface dataset:
Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 Following the Largest Initial Epidemic Wave in the United States: Findings From New York City, 13 May to 21 July 2020
Authors: Pathela Preeti , Crawley Addie , Weiss Don , Maldin Beth , Cornell Jennifer , Purdin Jeff , Schumacher Pamela K , Marovich Stacey , Li Joyce , Daskalakis Demetre ,   NYC Serosurvey Team, Pacione Vinny , Abril Cesar , Chong Elena , Koehn John
Published: April 2021

Background

New York City (NYC) was the US epicenter of the spring 2020 coronavirus disease 2019 (COVID-19) pandemic. We present the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and correlates of seropositivity immediately after the first wave.

Methods

From a serosurvey of adult NYC residents (13 May to 21 July 2020), we calculated the prevalence of SARS-CoV-2 antibodies stratified by participant demographics, symptom history, health status, and employment industry. We used multivariable regression models to assess associations between participant characteristics and seropositivity.

Results

The seroprevalence among 45 367 participants was 23.6% (95% confidence interval, 23.2%–24.0%). High seroprevalence (>30%) was observed among black and Hispanic individuals, people from high poverty neighborhoods, and people in healthcare or essential worker industry sectors. COVID-19 symptom history was associated with seropositivity (adjusted relative risk, 2.76; 95% confidence interval, 2.65–2.88). Other risk factors included sex, age, race/ethnicity, residential area, employment sector, working outside the home, contact with a COVID-19 case, obesity, and increasing numbers of household members.

Conclusions

Based on a large serosurvey in a single US jurisdiction, we estimate that just under one-quarter of NYC adults were infected in the first few months of the COVID-19 epidemic. Given disparities in infection risk, effective interventions for at-risk groups are needed during ongoing transmission.
Detection of SARS-CoV-2 Virus on Stainless-Steel Surfaces: AOAC Performance Tested MethodSM 022102
Authors: Mehl Martin , Meinhardt Patricia , Lorenzen Erika , Knoll Caroline , Howaldt Patrizia , Geister Jennifer , Mergemeier Steffen , Lacorn Markus
Published: April 2021

Background

The SureFast® SARS-CoV-2 PLUS Test is a reverse transcription qPCR (RT-qPCR) assay for the direct, qualitative detection of novel coronavirus (SARS-CoV-2) RNA from stainless-steel environmental sample swabs.

Objective

To validate the SureFast SARS-CoV-2 PLUS Kit as part of the AOAC Research Institute’s Emergency Response Validation Performance Tested Method(s)SM program.

Method

The SureFast SARS-CoV-2 PLUS Kit was evaluated for specificity using in silico analysis of 15 764 SARS-CoV-2 sequences and 65 exclusivity organisms (both near neighbors and background organisms) using the ThermoBLAST program. The candidate method was evaluated in an unpaired study design for one environmental surface (stainless steel) and compared to the US Centers for Disease Control and Prevention 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel, Instructions for Use (Revision 4, Effective 6/12/2020).

Results

Results of the in silico analysis demonstrated 99.99% selectivity of the method in being able to detect target sequences of the known CoV-2 genomes and discriminate them from near neighbors. In the matrix study, the candidate method demonstrated statistically significant better recovery of the target analyte than the PCR detection reference method.

Conclusions

The SureFast SARS-CoV-2 PLUS Kit is a rapid and accurate method that can be utilized by food producers to detect the causative agent of COVID-19 on stainless-steel contact surfaces.

Highlights

SureFast SARS-CoV-2 PLUS test method is highly specific for primer/probe binding to the E target genome region for the SARS-CoV-2 virus, 99.99% binding specificity using in silico analysis.
Incidence of Benign Meningiomas in the United States: Current and Future Trends
Authors: Bhala Sonia , Stewart Douglas R , Kennerley Victoria , Petkov Valentina I , Rosenberg Philip S , Best Ana F
Published: April 2021

Background

Benign meningiomas are the most frequently reported central nervous system tumors in the United States, with increasing incidence in past decades. However, the future trajectory of this neoplasm remains unclear.

Methods

We analyzed benign meningioma incidence of cases identified by any means (eg, radiographically with or without microscopic confirmation) in US Surveillance, Epidemiology, and End Results cancer registries among groups aged 35 to 84 years during 2004-2017 by sex and race and ethnicity using age-period-cohort models. We employed age-period-cohort forecasting models to glean insights regarding the etiology, distribution, and anticipated future (2018-2027) public health impact of this neoplasm.

Results

In all groups, meningioma incidence overall increased through 2010, then stabilized. Temporal declines were statistically significant overall and in most groups. JoinPoint analysis of cohort rate-ratios identified substantial acceleration in White men born after 1963 (from 1.1% to 3.2% per birth year); cohort rate-ratios were stable or increasing in all groups and all birth cohorts. We forecast that meningioma incidence through 2027 will remain stable or decrease among groups aged 55-84 years but remain similar to current levels among groups aged 35-54 years. The case count of total meningioma burden in 2027 is expected to be approximately 30 470, similar to the expected case count of 27 830 in 2018.

Conclusions

Between 2004 and 2017, overall incidence of benign meningioma increased and then stabilized or declined. For 2018-2027, our forecast is incidence will remain generally stable in younger age groups but decrease in older age groups. Nonetheless, the total future burden will remain similar to current levels because the population is aging.
Restriction, Simplification, and Externalization: How German Refugee Accommodation Centres Deal with Diversity Related Uncertainty
Authors: Nagel Alexander-Kenneth
Published: April 2021

Since the very beginning of the so-called ‘refugee crisis’ European debates about the reception and accommodation of refugees have circled around religious issues: Some (of the most secularized) post-socialist countries rediscovered their Christian cultural heritage as an argument against the immigration of Muslims, and in Germany, reports on interreligious conflicts nurtured claims for a separation of refugees along with religious lines. The article draws from an extensive case study on religious diversity and practice in refugee accommodation centres in Lower Saxony. It focuses on the administrative staff and the social workers in these centres who face a high degree of uncertainty due to the multi-religious and multicultural constellations they encounter. To cope with this religious illiteracy and to transform uncertainty into certainty, they apply three kinds of strategies, namely Restriction of the scope of legitimate religious expression, Simplification of religious and cultural heterogeneity through culturalist stereotypes, and an Externalization of responsibilities to deal with religious differences, such as dietary needs.
Micra leadless pacemaker for bridge use after explantation of infected permanent pacemaker system: a case report
Authors: Narita Masahiko , Kunioka Shingo , Shirasaka Tomonori , Kamiya Hiroyuki
Published: April 2021

The extraction of a pacemaker (PM) lead may cause tricuspid regurgitation; however, in cases of device infection, surgical intervention or immediate PM system replacement is undesirable in the short term to prevent reinfection. We describe a case where Micra leadless PM was used as a bridge procedure to ensure an adequate period for antibacterial therapy and later replaced with a permanent PM system in the setting of PM pocket infection.
Extended-spectrum beta-lactamase-producing strains among diarrhoeagenicEscherichia coli—prospective traveller study with literature review
Authors: Kantele Anu , Lääveri Tinja
Published: April 2021

Background

Antibiotics are no longer the primary approach for treating all travellers’ diarrhoea (TD): most cases resolve without antibiotics and using them predisposes to colonization by multidrug-resistant bacteria. Data are accumulating on increasing resistance among TD pathogens, yet research into the most common agents, diarrhoeagenic Escherichia coli (DEC), remains limited.

Methods

A total of 413 travellers to the (sub)tropics were analyzed for travel-acquired diarrhoeal pathogens and ESBL-PE. To identify ESBL-producing DEC, ESBL-producing E. coli (ESBL-EC) isolates were subjected to multiplex qPCR for various DEC pathotypes: enteroaggregative (EAEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), enteroinvasive (EIEC) and enterohaemorrhagic (EHEC) E. coli.

For a literature review, we screened studies among travellers and locals in low- and middle-income countries (LMICs) on the frequency of ESBL-producing DEC, and among travellers, also DEC with resistance to ciprofloxacin, azithromycin, and rifamycin derivatives.

Results

Our rate of ESBL-EC among all DEC findings was 2.7% (13/475); among EAEC 5.7% (10/175), EPEC 1.1% (2/180), ETEC 1.3% (1/80) and EHEC (0/35) or EIEC 0% (0/5). The literature search yielded three studies reporting ESBL-EC frequency and thirteen exploring resistance to TD antibiotics among travel-acquired DEC. For EAEC and ETEC, the ESBL-EC rates were 10–13% and 14–15%, resistance to fluoroquinolones 0–42% and 0–40%, azithromycin 0–29% and 0–61%, and rifaximin 0% and 0–20%. The highest rates were from the most recent collections. Proportions of ESBL-producing DEC also appear to be increasing among locals in LMICs and even carbapenemase-producing DEC were reported.

Conclusion

ESBL producers are no longer rare among DEC, and the overall resistance to various antibiotics is increasing. The data predict decreasing efficacy of antibiotic treatment, threatening its benefits, for disadvantages still prevail when efficacy is lost.
Chaos at the Gates: The impacts of the COVID-19 pandemic and energy price shocks on South Korea’s gas industry amid energy transition
Authors: Sassi Francesco , Frassineti Francesca
Published: April 2021

South Korea was one of the first countries to be hit by the coronavirus infections. Having rapidly contained the health emergency in the immediate period, Seoul arguably mitigated the economic fallouts more successfully than the majority of advanced economies but could not avoid substantial losses. The far-reaching fallout of COVID-19 has been testing the country’s energy transition pathway, as actors involved are facing difficult decisions amid more stringent financial constraints to deliver their ambitious targets, including achieving carbon neutrality by 2050. Amid the combined effects of the pandemic and the global energy prices shocks, addressing the nexus between energy security on the supply side, affordability, and the safety of people’s lives and property, has become even more pressing. Against this backdrop, natural gas has tailored a special role to bridge the low carbon re-alignment of the entire Korean energy system, also in the face of the current and future challenges to Korea’s energy security. But long-drawn hurdles stemming from rather unsuccessful efforts to reform the gas system risk weakening its ability to cope with present uncertainties and heightened volatilities.
A warring style: A corpus stylistic analysis of the First World War poetry
Authors: Can Taner , Cangır Hakan
Published: April 2021

The poetry of the First World War bears poignant testimony to the unprecedented tragedies of human destructiveness. It has been the subject of numerous studies that looked at it from diverse perspectives, drawing from various contemporary psychological, historical, and literary theories. The present study can be regarded as yet another contribution to the existing picture of this rich and enduring field where literature and history are explored alongside. Informed by the emerging field of digital literary studies, this article aims to revisit the war experience through a computational analysis of the poetry of the Great War and explore how soldier-poets conveyed their emotions in the face of traumatic war experience. We adopted a top-down corpus-driven approach that moved from key semantic domains to lexical items and then to their collocates. First, we detected the key semantic domains of the genre through a corpus tool, Wmatrix. ‘Anatomy and physiology’, ‘religion and the supernatural’, and ‘senses’ were identified as the key semantic domains in our corpus. The unusual abundance of binaries led us to group and treat these lexical items as a separate category: ‘binary oppositions’. In the second phase of the research, we analysed these key semantic domains to foreground the frequent lexical items under each domain and explored the surrounding context of those items through their collocational networks exploiting another corpus tool, Lancsbox. Finally, we further investigated the frequent items and corresponding concordance lines to identify the common stylistic features in the Great War Poetry.
Above Time: Rabbi Nachman’sTzaddikand Enlightened Temporal Experience
Authors: Solomyak Olla
Published: April 2021

Rabbi Nachman of Bratslav describes the tzaddik (righteous person of spiritual enlightenment) as experiencing time in a distinctive, enlightened way: What is seventy years for the rest of us feels like a mere fifteen minutes for the tzaddik. Furthermore, even higher levels of enlightenment are possible—for a tzaddik on a higher level, what feels like seventy years for the first tzaddik is again but a mere fifteen minutes. This pattern continues, approaching a limit point which Rabbi Nachman calls “above time,” and which is the perspective on time of the Divine. How might Rabbi Nachman’s claims about enlightened temporal experience be understood? In this paper, my aim is to examine some ways of understanding what it might mean to ‘experience time more quickly’ or to ‘experience 70 years as 15 minutes’ in light of contemporary theories of the structure of temporal experience. I then present a novel interpretation of Rabbi Nachman’s claims which appeals to the contemporary notion of the specious present—a nonzero temporal interval experienced in a unified way as present.
The effect of herbs and spices on risk factors for cardiometabolic diseases: a review of human clinical trials
Authors: Gupta Kunal , Testa Hannah , Greenwood Tara , Kostek Megan , Haushalter Keally , Kris-Etherton Penny M , Petersen Kristina S
Published: April 2021

Herbs and spices are recommended to increase flavor and displace salt in the diet. Accumulating evidence suggests herbs and spices may improve risk factors for cardiometabolic diseases. In this narrative review, an overview of evidence from human clinical trials examining the effect of herbs and spices on risk factors for cardiometabolic diseases is provided. Human clinical trials examining supplemental doses of individual spices and herbs, or the active compounds, have yielded some evidence showing improvements to lipid and lipoprotein levels, glycemic control, blood pressure, adiposity, inflammation, and oxidative stress. However, cautious interpretation is warranted because of methodological limitations and substantial between-trial heterogeneity in the findings. Evidence from acute studies suggests intake of mixed herbs and spices as part of a high-saturated fat, high-carbohydrate meal reduces postprandial metabolic impairments, including lipemia, oxidative stress, and endothelial dysfunction. Limited studies have examined the postprandial metabolic effects of incorporating mixed herbs and spices into healthy meals, and, to our knowledge, no trials have assessed the effect of longer-term intake of mixed herbs and spices on risk factors for cardiometabolic diseases. To inform evidence-based guidelines for intake of herbs and spices for general health and cardiometabolic disease risk reduction, rigorously conducted randomized controlled trials are needed, particularly trials examining herb and spice doses that can be incorporated into healthy dietary patterns.
What are the overall implications of rising demand for organic fruits and vegetables? Evidence from theory and simulations
Authors: McFadden Brandon R , Bovay John , Mullally Conner
Published: April 2021

US consumers currently eat less fruits and vegetables (FV) than recommended by dietary guidelines. Inadequate FV consumption exists alongside rapid growth in demand for organic FV. Since the viable production area of FV is finite, organic and conventional FV are linked in production while serving as substitutes in consumption. Rising purchases of organic FV may have important implications for prices and quantities consumed in the conventional FV market. In this paper, we analyze the implications of rising demand for organic FV when organic and conventional FV are linked in supply and demand. More specifically, we use a multi-market equilibrium displacement model to examine the impact of rising demand for organic produce on prices and total quantities consumed of conventional and organic FV under two scenarios: product differentiation (i.e. organic versus conventional produce) while assuming that consumers have identical preferences that can be represented by a single market demand function for each good; and product differentiation with segmented markets, which allows for two types of consumers with unique demand functions. Both scenarios were simulated with and without an offsetting shift in demand for conventional FV. Our simulation results indicate that the increasing demand for organic FV may result in decreased consumption of combined conventional and organic FV, and that the direction of changes in FV consumption may vary by consumer segment. Under the most realistic assumptions, when one segment of consumers increases its demand for organic FV, this segment's overall consumption of organic plus conventional FV falls; the other segment's overall consumption rises. We provide sensitivity analyses and discuss caveats and directions for future research.
Management of MDA-5 antibody-positive dermatomyositis with interstitial lung disease—an Auckland case series
Authors: Dick Michael , Martin Julia , Tugnet Nicola
Published: April 2021

Objective

The aim was to present our experience of managing six cases of anti-melanoma differentiation-associated gene 5 (anti-MDA-5) DM with associated interstitial lung disease (ILD), presenting between June 2017 and October 2020.

Methods

The electronic notes were reviewed for six patients being followed up by the Rheumatology service at Auckland District Health Board. Three patients were initially diagnosed and treated in neighbouring Counties Manukau District Health Board and later transferred to Auckland District Health Board. All had different initial treating clinicians at a time before any predefined treatment algorithm. Emphasis was placed on initial diagnosis and treatment, subsequent disease activity and changes in management. Local management was compared retrospectively with existing evidence relating to the treatment of anti-MDA-5 DM with ILD. Ethical approval was not obtained, according to the New Zealand Health and Disability Ethics Committee exemption for audits and related activities.

Results

Six patients with a variety of clinical presentations were identified appropriately as having anti-MDA-5 DM with ILD. They were commenced on different immunosuppressive regimens, with treatment adjusted according to response and on-going disease activity. Four have achieved clinical and biochemical remission, a fifth has improving active disease, and the sixth is in the early stages of their illness.

Conclusion

Anti-MDA-5 DM is commonly associated with ILD. This can be rapidly progressive, with a poor prognosis in spite of treatment, particularly among Asian patients. Disease activity can seemingly be monitored with serum ferritin. The most effective management of this condition remains poorly researched; however, increasing retrospective evidence favours early aggressive multi-agent immunosuppression and a low threshold for escalation of therapy.
Cooperation without Consensus: Midwives’ Collaborations across Political Distance
Authors: Goldensher Liora O’Donnell
Published: April 2021

What happens when people not only talk to one another but collaborate closely and form strong relationships in conditions of political heterogeneity? This article analyzes data from ethnographic research in seven states with homebirth midwives who, reflecting the “strange coalition” of feminists and traditionalists that analysts have long described in this community, self-identify with a wide range of partisan political affiliations and with divergent positions on the key issue of professional midwifery licensure. Results show that this community’s use of a shared model of care as a boundary object to facilitate collaboration without consensus relies upon a focus on sameness and a bracketing of the ideological commitments that undergird practitioners’ investment in the model of care. When difference is directly engaged, collaboration across political difference becomes difficult to sustain. I argue that bridging ideological divides using boundary objects is politically costly.  Collaborative relationships and coalitions are made precarious and risk depoliticizing shared concerns when they are bound by a weakly structured, network-level object whose use demands the allocation of attention to sameness and the bracketing of difference and political disagreement.
Grazing behavior and production for lactating cows differing in residual feed intake while grazing spring and summer rangeland
Authors: Sprinkle James E , Ellison Melinda J , Hall John B , Yelich Joel V , Willmore Carmen M , Brennan Jameson R
Published: April 2021

The objectives were to determine if previously classified, efficient (LRFI, low-residual-feed intake, n = 12 × 2 yr) vs. inefficient (HRFI, high-residual-feed intake, n = 12 × 2 yr) lactating 2-yr-old Hereford × Angus cows differed in grazing behavior, body weight (BW), body condition score (BCS), and calf weaning weight while grazing rugged rangeland pastures. Cows were fitted with grazing halters containing both an accelerometer and a global positioning system (GPS) data logger during June 14 to July 4, 2016, August 2 to 25, 2016, May 23 to June 12, 2017, and August 5 to 28, 2017. GPS data were recorded at 7-min intervals in 2016 and 4-min intervals in 2017 and accelerometer data recorded at 25 times/s. Grazing time (GT), resting, walking, bite rate (BR), daily travel distance (DTD), elevation, and slope were analyzed with a mixed model that included fixed effects of RFI group, day, and RFI group × day and cow within treatment as the random effect. Cow BW, BCS, and calf weaning weight were analyzed by analysis of variance with treatment as the main effect. There were no differences (P > 0.10) due to RFI detected for BW, BCS, or calf weaning weights. During periods of mild heat load (MHL), HRFI cows spent more (P < 0.05) time resting during the day at lower elevations (P < 0.05) than LRFI cows. During a 6-d period in spring with only 2 h MHL, HRFI cows grazed 1.7 h/d longer than LRFI cows (P < 0.05); commencing grazing earlier in the morning and extending the grazing bout later. During the summer with > MHL, LRFI cows grazed more than HRFI cows 18% of the time (P < 0.10). The HRFI cows had greater GT than LRFI cows only 3% of the time (P < 0.10) during summer. There was no difference (P > 0.10) in BR between HRFI and LRFI cattle. The DTD tended (P < 0.10) to be greater for LRFI cattle during summer 2017. Over all sample periods, HRFI had greater walking than LRFI 15% of the time and LRFI exceeded HRFI cattle for walking 3% of the time (P < 0.10). The greater walking for HRFI was assumed to be associated with more search grazing. Metabolic heat load on hot summer days for HRFI cattle is presumed to have contributed to differences observed in grazing behavior. These results suggest that lactating cows with low-RFI phenotypes appear to be better adapted to grazing rugged rangelands in late summer during periods of MHL.
Dynamic Stabilization Surgery in Patients with Spinal Stenosis
Authors: Jung Jong-myung , Hyun Seung-Jae , Kim Ki-Jeong , Jahng Tae-Ahn
Published: April 2021

Study Design.

Retrospective cohort study.

Objectives.

The purpose of this study was to analyze the long-term results for patients with lumbar spinal stenosis (LSS) treated with dynamic stabilization (DS) and to consider how we can improve the results.

Summary of Background Data.

Few studies have reported long-term outcomes of DS surgery for LSS with or without spondylolisthesis.

Methods.

A single-center, single-surgeon consecutive series of LSS patients who underwent DS surgery with at least 5 years of follow-up were retrospectively reviewed. Twenty-seven patients were included in the LSS group and 38 patients in the spondylolisthesis group. Patient characteristics, operative data, radiographic parameters, clinical outcomes, and complications were analyzed at baseline and follow-up.

Results.

In the LSS group, all radiographic parameters (e.g., disc height, segmental lordosis, segmental range of motion [ROM] at the index level and proximal adjacent level, global lordosis, and global ROM) were maintained well until the last follow-up. In the spondylolisthesis group, global lordosis decreased from 36.5° ± 8.2° to 32.6° ± 6.0° at the last follow-up (P = 0.039), and global ROM decreased from 22.1° ± 6.9° to 18.8° ± 7.1° at the last follow-up (P = 0.012). In both groups, back pain, leg pain, and Oswestry Disability Index scores showed significant and sustained improvements. Screw loosening occurred in three patients (11.1%) in the LSS group and five patients (13.2%) in the spondylolisthesis group. Symptomatic adjacent segment degeneration (ASD) occurred in two patients (7.4%) in the LSS group and three patients (7.9%) in the spondylolisthesis group.

Conclusion.

Decompression and DS surgery for LSS with or without spondylolisthesis showed favorable long-term surgical outcomes with an acceptable rate of complications and ASD. However, an improved physiological DS system should be developed.

Level of Evidence: 4
Osmoregulatory ability predicts geographical range size in marine amniotes
Authors: Brischoux François , Lillywhite Harvey B. , Shine Richard , Pinaud David
Published: April 2021

Species that are distributed over wide geographical ranges are likely to encounter a greater diversity of environmental conditions than do narrowly distributed taxa, and thus we expect a correlation between size of geographical range and breadth of physiological tolerances to abiotic challenges. That correlation could arise either because higher physiological capacity enables range expansion, or because widely distributed taxa experience more intense (but spatially variable) selection on physiological tolerances. The invasion of oceanic habitats by amniotic vertebrates provides an ideal system with which to test the predicted correlation between range size and physiological tolerances, because all three lineages that have secondarily moved into marine habitats (mammals, birds, reptiles) exhibit morphological and physiological adaptations to excrete excess salt. Our analyses of data on 62 species (19 mammals, 18 birds, 24 reptiles) confirm that more-widely distributed taxa encounter habitats with a wider range of salinities, and that they have higher osmoregulatory ability as determined by sodium concentrations in fluids expelled from salt-excreting organs. This result remains highly significant even in models that incorporate additional explanatory variables such as metabolic mode, body size and dietary habits. Physiological data thus may help to predict potential range size and perhaps a species' vulnerability to anthropogenic disturbance.
Increased functional diversity warns of ecological transition in the Arctic
Authors: Frainer André , Primicerio Raul , Dolgov Andrey , Fossheim Maria , Johannesen Edda , Lind Sigrid , Aschan Michaela
Published: April 2021

As temperatures rise, motile species start to redistribute to more suitable areas, potentially affecting the persistence of several resident species and altering biodiversity and ecosystem functions. In the Barents Sea, a hotspot for global warming, marine fish from boreal regions have been increasingly found in the more exclusive Arctic region. Here, we show that this shift in species distribution is increasing species richness and evenness, and even more so, the functional diversity of the Arctic. Higher diversity is often interpreted as being positive for ecosystem health and is a target for conservation. However, the increasing trend observed here may be transitory as the traits involved threaten Arctic species via predation and competition. If the pressure from global warming continues to rise, the ensuing loss of Arctic species will result in a reduction in functional diversity.
The genetic architecture and evolution of life-history divergence among perennials in theMimulus guttatusspecies complex
Authors: Coughlan Jenn M. , Brown Maya Wilson , Willis John H.
Published: April 2021

Ecological divergence is a fundamental source of phenotypic diversity between closely related species, yet the genetic architecture of most ecologically relevant traits is poorly understood. Differences in elevation can impose substantial divergent selection on both complex, correlated suites of traits (such as life-history), as well as novel adaptations. We use theMimulus guttatusspecies complex to assess if the divergence in elevation is accompanied by trait divergence in a group of closely related perennials and determine the genetic architecture of this divergence. We find that divergence in elevation is associated with differences in life-history, as well as a unique trait, the production of rhizomes. The divergence between two perennials is largely explained by few mid-to-large effect quantitative trait loci (QTLs). However, the presence of QTLs with correlated, but opposing effects on multiple traits leads to some hybrids with transgressive trait combinations. Lastly, we find that the genetic architecture of the ability to produce rhizomes changes through development, wherein most hybrids produce rhizomes, but only later in development. Our results suggest that elevational differences may shape life-history divergence between perennials, but aspects of the genetic architecture of divergence may have implications for hybrid fitness in nature.
A sensory bias overrides learned preferences of bumblebees for honest signals in
Mimulus guttatus
Authors: Haber Ariela I. , Sims James W. , Mescher Mark C. , De Moraes Consuelo M. , Carr David E.
Published: April 2021

Insect pollinators readily learn olfactory cues, and this is expected to select for ‘honest signals' that provide reliable information about floral rewards. However, plants might alternatively produce signals that exploit pollinators' sensory biases, thereby relaxing selection for signal honesty. We examined the innate and learned preferences of
Bombus impatiens
for
Mimulus guttatus
floral scent phenotypes corresponding to different levels of pollen rewards in the presence and absence of the innately attractive floral volatile compound β-trans-bergamotene. Bees learned to prefer honest signals after foraging on live
M. guttatus
flowers, but only exhibited this preference when presented floral scent phenotypes that did not include β-trans-bergamotene. Our results suggest that a sensory bias for β-trans-bergamotene overrides the ability of
B. impatiens
to use honest signals when foraging on
M. guttatus
. This may represent a deceptive pollination strategy that allows plants to minimize investment in costly rewards without incurring reduced rates of pollinator visitation.
Biogeographic diversification of
Eranthis
(Ranunculaceae) reflects the geological history of the three great Asian plateaus
Authors: Xiang Kun-Li , Erst Andrey S. , Yang Jian , Peng Huan-Wen , Ortiz Rosa del C. , Jabbour Florian , Erst Tatyana V. , Wang Wei
Published: April 2021

The evolutionary history of organisms with poor dispersal abilities usually parallels geological events. Collisions of the Indian and Arabian plates with Eurasia greatly changed Asian topography and affected regional and global climates as well as biotic evolution. However, the geological evolution of Asia related to these two collisions remains debated. Here, we used
Eranthis
, an angiosperm genus with poor seed dispersal ability and a discontinuous distribution across Eurasia, to shed light on the orogenesis of the Qinghai–Tibetan, Iranian and Mongolian Plateaus. Our phylogenetic analyses show that
Eranthis
comprises four major geographical clades: east Qinghai–Tibetan Plateau clade (I-1), North Asian clade (I-2), west Qinghai–Tibetan Plateau clade (II-1) and Mediterranean clade (II-2). Our molecular dating and biogeographic analyses indicate that within
Eranthis
, four vicariance events correlate well with the two early uplifts of the Qinghai–Tibetan Plateau during the Late Eocene and the Oligocene–Miocene boundary and the two uplifts of the Iranian Plateau during the Middle and Late Miocene. The origin and divergence of the Mongolian Plateau taxa are related to the two uplifts of the Mongolian Plateau during the Middle and Late Miocene. Additionally, our results are in agreement with the hypothesis that the central part of Tibet only reached an altitude of less than 2.3 km at approximately 40 Ma. This study highlights that organismal evolution could be related to the formation of the three great Asian plateaus, hence contributing to the knowledge on the timing of the key tectonic events in Asia.
Detection of plasmid contigs in draft genome assemblies using customized Kraken databases
Authors: Gomi Ryota , Wyres Kelly L. , Holt Kathryn E.
Published: April 2021

Plasmids play an important role in bacterial evolution and mediate horizontal transfer of genes including virulence and antimicrobial resistance genes. Although short-read sequencing technologies have enabled large-scale bacterial genomics, the resulting draft genome assemblies are often fragmented into hundreds of discrete contigs. Several tools and approaches have been developed to identify plasmid sequences in such assemblies, but require trade-off between sensitivity and specificity. Here we propose using the Kraken classifier, together with a custom Kraken database comprising known chromosomal and plasmid sequences of

Klebsiella pneumoniae

species complex (KpSC), to identify plasmid-derived contigs in draft assemblies. We assessed performance using Illumina-based draft genome assemblies for 82 KpSC isolates, for which complete genomes were available to supply ground truth. When benchmarked against five other classifiers (Centrifuge, RFPlasmid, mlplasmids, PlaScope and Platon), Kraken showed balanced performance in terms of overall sensitivity and specificity (90.8 and 99.4 %, respectively, for contig count; 96.5 and >99.9 %, respectively, for cumulative contig length), and the highest accuracy (96.8% vs 91.8-96.6% for contig count; 99.8% vs 99.0-99.7 % for cumulative contig length), and F1-score (94.5 % vs 84.5-94.1 %, for contig count; 98.0 % vs 88.9-96.7 % for cumulative contig length). Kraken also achieved consistent performance across our genome collection. Furthermore, we demonstrate that expanding the Kraken database with additional known chromosomal and plasmid sequences can further improve classification performance. Although we have focused here on the KpSC, this methodology could easily be applied to other species with a sufficient number of completed genomes.
Designing a Clerkship Curriculum for Medical Students in Clinical and Medical Informatics in the Electronic Medical Record Era
Authors: Chartash David , Finnell John T
Published: April 2021

Introduction

The nature of practice in clinical and medical informatics has changed since the last recommended incorporation of the field into undergraduate medical education in 1998. The Regenstrief Institute and Indiana University have been offering a clerkship in clinical and medical informatics since 2008, and post-graduate medical education since the early 1970s.

Methods

Drawing on this existing educational program and the expertise at the institute, we developed a clerkship elective to support medical students in learning about the subspecialty in practice, as well as the state of the art in research. Student evaluation of the clerkship and satisfaction with curricular design elements was measured.

Results

A modular inverted classroom curriculum was designed and implemented using learning management systems and instructional technology available at Indiana University. Students were satisfied with the clerkship, and explicitly understood how curricular design contributed to their understanding of material. The curriculum was found flexible for multiple levels of learners, particularly those with advanced mastery of technical skills.

Discussion

This curriculum, and its packaged content to be imported into common learning management systems, offers a state of the art introduction to clinical and medical informatics for medical students, which supports student success and preferences during their clerkship elective period.

Educational Objectives

By the end of this activity, learners will be able to:’

Articulate the scope of clinical and medical informatics within medicine

Describe a problem pertinent to their clinical interests, and how a solution can be supported by health information technology, as well as more generally be assessed using clinical outcome measures

Demonstrate a knowledge of terminologies and standards found in clinical medicine, as well how they integrate to define and describe disease

Demonstrate an understanding of clinical decision making and the evaluation of discrete choice problems
Effects of bariatric surgery on functional connectivity of the reward and default mode network: a pre-registered analysis
Authors: Heinrichs Hannah S. , Beyer Frauke , Medawar Evelyn , Prehn Kristin , Ordemann Jürgen , Flöel Agnes , Witte A. Veronica
Published: April 2021

Obesity imposes serious health risks and involves alterations in resting-state functional connectivity of brain networks involved in eating behavior. Bariatric surgery is an effective treatment, but its effects on functional connectivity are still under debate. In this pre-registered study, we aimed to determine the effects of bariatric surgery on major resting-state brain networks (reward and default mode network) in a longitudinal controlled design. 33 bariatric surgery patients and 15 obese waiting-list control patients (37 females; aged 44.15 ± 11.86 SD years (range 21-68)) underwent magnetic resonance imaging at baseline, after 6 and 12 months. We conducted a pre-registered whole-brain time-by-group interaction analysis, and a time-by-group interaction analysis on within-network connectivity (https://osf.io/f8tpn/, https://osf.io/59bh7/). In exploratory analyses, we investigated the effects of weight loss and head motion. Bariatric surgery compared to waiting did not significantly affect functional connectivity (FWE-corrected p > 0.05), neither whole-brain nor within-network. In exploratory analyses, surgery-related BMI decrease (FWE-corrected p = 0.041) and higher average head motion (FWE-corrected p = 0.021) resulted in significantly stronger connectivity of the reward network with medial posterior frontal regions. This pre-registered well-controlled study did not support a strong effect of bariatric surgery, compared to waiting, on major resting-state brain networks after 6 months. Exploratory analyses indicated that head motion might have confounded the effects. Data pooling and more rigorous control of within-scanner head motion during data acquisition are needed to substantiate effects of bariatric surgery on brain organization.
Donor race has no role in predicting allograft and patient survival among kidney transplant recipients
Authors: Chong Kelly , Litvinovich Igor , Chen Shan Shan , Zhu Yiliang , Argyropoulos Christos , Ng Yue-Harn
Published: April 2021

A heated debate in creatinine-based estimated glomerular filtration rate (eGFR) calculation is the inclusion of race alongside biological factors, such as age and gender. Similarly, the race variable was included in the calculation of the Kidney Donor Risk Index (KDRI) as deceased donor kidneys from black donors have historically been shown to be associated with lower allograft or patient survival. Given the current climate of uncertainty with the use of race in nephrology, we sought to answer the question of whether removing the donor race variable from the KDRI would alter its validity to assess allograft and patient survival. Our modeling and analysis showed that removing donor race from the original KDRI did not alter the overall model predictability of allograft failure or patient mortality. Clinical risk factors included in the KDRI have largely accounted for differential risk between black and other donors. Adding donor race into the KDRI only shifts how risk is attributed to these clinical risk factors, without yielding better prediction of outcomes than the model without race.
Effect of Tocilizumab on “ventilator free days” composite outcome in SARS-CoV-2 patients. A retrospective competing risk analysis
Authors: Mady Ahmed F. , Abdulrahman Basheer , Ramadan Omar E. , Mumtaz Shahzad A. , Al-Odat Mohammed A. , Kuhail Ahmed , Altoraifi Rehab , Alshae Rayan , Alharthy Abdulrahman M. , Karakitsos Dimitrios , Aletreby Waleed Th.
Published: April 2021

Background

SARS-CoV-2 infection demonstrates a wide range of severity, the more severe cases demonstrate a cytokine storm with elevated serum interleukin-6, hence IL-6 receptor antibody Tocilizumab was tried for the management of severe cases.

Objectives

The effect of Tocilizumab treatment on the composite outcome of ventilator free days, among critically ill SARS-CoV-2 patients.

Method

Retrospective observational propensity score matching study, comparing mechanically ventilated patients upon ICU admission who received Tocilizumab to a control group. Utilizing competing risk analysis method, and reporting sub-distributional hazard ratio of a composite outcome of ventilator free days at day 28.

Results

29 patients in the intervention group were compared to 29 patients in the control group. Matched groups were similar at base line. The primary outcome of ventilator free days was higher in the intervention group (SHR 2.7, 95% CI: 1.2 – 6.3; p = 0.02), crude ICU mortality rate was not different between Tocilizumab and control groups (37.9% versus 62% respectively, p = 0.1), actual ventilator free days were significantly longer in Tocilizumab group (mean difference 4.7 days, 95% CI 1.1 – 8.3; p = 0.02). Sensitivity analysis by Cox regression showed a significantly lower hazard ratio of death in Tocilizumab group (HR 0.49, 95% CI: 0.25 – 0.97; p = 0.04). While there was no difference in grown positive cultures among groups (55.2% in Tocilizumab group versus 34.5% in the control, 95% CI of difference: −7.11% to 54.4%; p = 0.1).

Conclusion

Tocilizumab may improve the composite outcome of ventilator free days at day 28 among mechanically ventilated SARS-CoV-2 patients, it is associated with significantly longer actual ventilator free days, and insignificantly lower mortality and superinfection.
Intensity of home-based telework and work engagement during the COVID-19 pandemic
Authors: Nagata Tomohisa , Nagata Masako , Ikegami Kazunori , Hino Ayako , Tateishi Seiichiro , Tsuji Mayumi , Matsuda Shinya , Fujino Yoshihisa , Mori Koji ,   for the CORoNaWork project
Published: April 2021

Objective

The present study examined the relationship between the intensity of home-based telework and work engagement.

Methods

This cross-sectional study using a self-administrated questionnaire survey was conducted from December 22 to 25, 2020, in Japan. The subjects were asked single-item questions about the intensity of telework and three-item questions about work engagement using the Utrecht Work Engagement Scale. Coefficients were estimated using a multilevel regression model nested by prefecture of residence and adjusted for covariates.

Results

High-intensity (four or more days per week) telework was not associated with high work engagement for men or women. In contrast, low and moderate intensity (three days per week to once per month) were associated with high work engagement. The results were consistent when stratified by sex.

Conclusions

Reasonable-intensity telework may have beneficial effects on work engagement.

Clinical Significance

This study revealed that a reasonable intensity of telework may have beneficial effects on work engagement. A reasonable intensity is defined as low (once per week to once per month) or moderate intensity (two to three days per week) for both men and women.
Brain age prediction using fMRI network coupling in youths and associations with psychiatric symptoms
Authors: Lund Martina J. , Alnæs Dag , de Lange Ann-Marie , Andreassen Ole A. , Westlye Lars T. , Kaufmann Tobias
Published: April 2021

Objective

Magnetic resonance imaging (MRI) has shown that estimated brain age is deviant from chronological age in various common brain disorders. Brain age estimation could be useful for investigating patterns of brain maturation and integrity, aiding to elucidate brain mechanisms underlying these heterogeneous conditions. Here, we examined functional brain age in two large samples of children and adolescents and its relation to mental health.

Methods

We used resting-state fMRI data from the Philadelphia Neurodevelopmental Cohort (PNC; n=1126, age range 8-22 years) to estimate functional connectivity between brain networks, and utilized these as features for brain age prediction. We applied the prediction model to 1387 individuals (age range 8-22 years) in the Healthy Brain Network sample (HBN). In addition, we estimated brain age in PNC using a cross-validation framework. Next, we tested for associations between brain age gap and various aspects of psychopathology and cognitive performance.

Results

Our model was able to predict age in the independent test samples, with a model performance of r=0.54 for the HBN test set, supporting consistency in functional connectivity patterns between samples and scanners. Linear models revealed a significant association between brain age gap and psychopathology in PNC, where individuals with a lower estimated brain age, had a higher overall symptom burden. These associations were not replicated in HBN.

Discussion

Our findings support the use of brain age prediction from fMRI-based connectivity. While requiring further extensions and validations, the approach may be instrumental for detecting brain phenotypes related to intrinsic connectivity and could assist in characterizing risk in non-typically developing populations.