bluuebunny/crossref_metadata_2025 huggingface dataset:
Social Contact Mode and 15-Year Episodic Memory Trajectories in Older Adults With and Without Hearing Loss: Findings From the English Longitudinal Study of Ageing
Authors: Rafnsson Snorri Bjorn , Maharani Asri , Tampubolon Gindo
Published: February 2021

Objectives

Frequent social contact benefits cognition in later life although evidence is lacking on the potential relevance of the modes chosen by older adults, including those living with hearing loss, for interacting with others in their social network.

Method

11,418 participants in the English Longitudinal Study of Ageing provided baseline information on hearing status and social contact mode and frequency of use. Multilevel growth curve models compared episodic memory (immediate and delayed recall) at baseline and longitudinally in participants who interacted frequently (offline only or offline and online combined), compared to infrequently, with others in their social network.

Results

Frequent offline (B = 0.23; SE = 0.09) and combined offline and online (B = 0.71; SE = 0.09) social interactions predicted better episodic memory after adjustment for multiple confounders. We observed positive, longitudinal associations between combined offline and online interactions and episodic memory in participants without hearing loss (B = 0.50, SE = 0.11) but not with strictly offline interactions (B = 0.01, SE = 0.11). In those with hearing loss, episodic memory was positively related to both modes of engagement (offline only: B = 0.79, SE = 0.20; combined online and offline: B = 1.27, SE = 0.20). Sensitivity analyses confirmed the robustness of these findings.

Discussion

Supplementing conventional social interactions with online communication modes may help older adults, especially those living with hearing loss, sustain, and benefit cognitively from, personal relationships.
Comprehensive palaeomagnetic study of San Borja and Jaraguay monogenetic volcanic fields, Baja California (28–30°N): considerations on latitudinal corrections
Authors: Mahgoub A N , García-Amador B I , Alva-Valdivia L M
Published: February 2021

We report 24 palaeomagnetic directions and 10 high-quality Thellier-derived palaeointensity (PI) values, obtained from 27 sites located in Baja California Peninsula, northwestern Mexico. Sampling was done in four rock units (magnesian andesites, calc-alkaline lavas, ignimbrites, adakites) belonging to San Borja and Jaraguay monogenetic volcanic fields. These units have erupted between ∼15 and 2.6 Ma (previous K-Ar and 40Ar/39Ar data); hence results are presented in two consecutive periods: middle-late Miocene and Pliocene. The identified main magnetic minerals in the sampled sites are titanomagnetite, magnetite and minor hematite, of variable grain size, present as intergrowths or surrounding grains, which reflect varying oxidation/reduction conditions during emplacement of high-temperature magmas. Based on previous geological and geophysical records, the kinematic evolution was carefully considered in the region, allowing for the independent restoration of the palaeoposition of each sampled site. Previous palaeodirections were also evaluated and corrected for tectonic motion in order to combine them with present data. Accordingly, a number of 15 and 36 directional data are used to calculate palaeopole position for Pliocene and middle-late Miocene periods, respectively, selected from a total of 74 data points. Pliocene (Plat = 87.8°, Plong = 147.5°, K = 41.06, A95 = 6.0°) and middle-late Miocene (Plat = 86.0°, Plong = 172.7°, K = 41.08, A95 = 3.8°) palaeopole positions, calculated after tectonic corrections, are not statistically different from expected North American reference pole. Tectonic correction for Middle-late Miocene virtual geomagnetic poles plays an important role in reducing the resultant tilting from 2.7° to –0.8°. PI mean were calculated for Pliocene and middle-late Miocene periods at 29.2 ± 9.1 and 23.2 ± 6.3 μT, respectively. Compiling global filtered PI data, together with our results, indicates that the strength of the geomagnetic field during middle-late Miocene was weak (virtual dipole moment = 5.0 ± 2.2 × 1022 Am2) compared to Pliocene (6.4 ± 2.8 × 1022 Am2), and also relative to the present-day value (7.6 × 1022 Am2). This indicates the global nature of the low dipole moment during the middle-late Miocene period. However, issues related to the spatio-temporal distribution of PI data still present an obstacle to validating these suggestions; therefore, more reliable data are still needed.
Effectiveness and Safety of Nonmedical Switch From Adalimumab Originator to SB5 Biosimilar in Patients With Inflammatory Bowel Diseases: Twelve-Month Follow-Up From the TABLET Registry
Authors: Tapete Gherardo , Bertani Lorenzo , Pieraccini Alberto , Lynch Erica Nicola , Giannotta Martina , Morganti Riccardo , Biviano Ivano , Naldini Sara , Mumolo Maria Gloria , De Nigris Francesca , Calella Francesca , Bagnoli Siro , Minciotti Moira , Maltinti Simona , Rentini Silvia , Ceccarelli Linda , Lionetti Paolo , Milla Monica , Costa Francesco
Published: February 2021

Background

Few data are currently available about SB5 in inflammatory bowel diseases (IBD). The aim of this study was to assess the effectiveness and safety of SB5 in a cohort of patients with IBD in stable remission switched from the adalimumab (ADA) originator and in a cohort of patients with IBD naïve to ADA.

Methods

We prospectively enrolled patients with IBD who started ADA treatment with SB5 (naïve cohort) and those who underwent a nonmedical switch from the ADA originator to SB5 (switching cohort). Clinical remission and safety were assessed at baseline and at 3, 6, and 12 months. In addition, in a small cohort of patients who were switched, we assessed the ADA serum trough levels and antidrug antibodies at baseline, 3, and 6 months.

Results

In the naïve cohort, the overall remission rate at 12 months was 60.42%, whereas in the switching cohort it was 89.02%. Fifty-three (36.3%) patients experienced an adverse event, and injection site pain was the most common; it was significantly more frequent in the switching cohort (P = 0.001). No differences were found in terms of ADA serum trough levels at baseline, 3, and 6 months after switching. No patient developed antidrug antibodies after the switch.

Conclusions

We found that SB5 seemed effective and safe in IBD, both in the naïve cohort and in the switching cohort. Further studies are needed to confirm these data in terms of mucosal healing.
Measuring patient voice matters: setting the scene for patient-reported indicators
Authors: de Bienassis Katherine , Kristensen Solvejg , Hewlett Emily , Roe David , Mainz Jan , Klazinga Niek
Published: February 2021

Background

Achieving people-centred health care systems requires new and innovative strategies to capture information about whether, and to what degree, health care is successful in improving health from the perspective of the patient. Patient-reported outcome measures (PROMs) and Patient-reported experience measures (PREMs) can bring some of these new insights, and are increasingly used in research, clinical care, and policymaking.

Methods

This paper reflects the ongoing discussions and findings of the OECD PaRIS Working Group on Patient-reported Indicators for Mental Health Care.

Results

The OECD has been measuring quality of care for mental health conditions over the last 14 years through the Health Care Quality and Outcomes (HCQO) program; nonetheless, information on how persons with mental health problems value the services they receive, and impact of the services, remains limited. As of 2018, a survey from the OECD showed that only five of the twelve countries surveyed (Australia, Israel, Netherlands, Sweden, United Kingdom) reported PROMs and PREMs collection on a regular basis in mental health settings. The paper details some of the challenges specific to the collection and use of PROMs and PREMs in mental health care, and examples from countries which have implemented comprehensive programmes to gather information about PROMs and PREMs for individuals receiving mental health services.

Conclusions

Given the health and economic impact of mental ill-health across all OECD countries, there is significant value to being able to assess the quality and outcomes of care in this area using internationally-comparable measures. Continued international harmonisation of PROMs and PREMs for mental health through international coordination is a key way to facilitate the sharing of national experiences, promote the use of PROMs and PREMs, and create meaningful indicators for national and international benchmarking.
Efficacy and safety of subsequent molecular targeted therapy after immuno-checkpoint therapy, retrospective study of Japanese patients with metastatic renal cell carcinoma (AFTER I-O study)
Authors: Tomita Yoshihiko , Kimura Go , Fukasawa Satoshi , Numakura Kazuyuki , Sugiyama Yutaka , Yamana Kazutoshi , Naito Sei , Kabu Koki , Tajima Yohei , Oya Mototsugu
Published: February 2021

Objectives

Guidelines for treatment of mRCC recommend nivolumab monotherapy (NIVO) for treated patients, and nivolumab plus ipilimumab combination therapy (NIVO+IPI) for untreated IMDC intermediate and poor-risk mRCC patients. Although molecular-targeted therapies (TTs) such as VEGFR-TKIs and mTORi are recommended as subsequent therapy after NIVO or NIVO+IPI, their efficacy and safety remain unclear.

Methods

Outcome of Japanese patients with mRCC who received TT after NIVO (CheckMate 025) or NIVO+IPI (CheckMate 214) were retrospectively analyzed. Primary endpoints were investigator-assessed ORR of the first TT after either NIVO or NIVO+IPI. Secondary endpoints included TFS, PFS, OS and safety of TTs.

Results

Twenty six patients in CheckMate 025 and 19 patients in CheckMate 214 from 20 centers in Japan were analyzed. As the first subsequent TT after NIVO or NIVO+IPI, axitinib was the most frequently treated regimen for both CheckMate 025 (54%) and CheckMate 214 (47%) patients. The ORRs of TT after NIVO and NIVO+IPI were 27 and 32% (all risks), and median PFSs were 8.9 and 16.3 months, respectively. During the treatment of first TT after either NIVO or NIVO+IPI, 98% of patients experienced treatment-related adverse events, including grade 3–4 events in 51% of patients, and no treatment-related deaths occurred.

Conclusions

TTs have favorable antitumor activity in patients with mRCC after ICI, possibly via changing the mechanism of action. Safety signals of TTs after ICI were similar to previous reports. These results indicate that sequential TTs after ICI may contribute for long survival benefit.
Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize
Authors: Luo Jin-Hong , Wang Min , Jia Gui-Fang , He Yan
Published: February 2021

Heterosis has been extensively utilized to increase productivity in crops, yet the underlying molecular mechanisms remain largely elusive. Here, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize F1 hybrid B73×Mo17 and its two parental lines to ascertain the contribution of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and distribution of m6A remained unchanged, a greater number of genes had gained an m6A modification in the hybrid. Superior variations were observed at the m6A modification and translational efficiency levels when compared with mRNA abundance between the hybrid and parents. In the hybrid, the vast majority of genes with m6A modification exhibited a non-additive expression pattern, the percentage of which was much higher than that at levels of mRNA abundance and translational efficiency. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulation of gene expression make distinct contributions to heterosis in hybrid maize. Overall, this integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation of gene expression in hybrid maize, and paves the way for exploring molecular mechanisms underlying hybrid vigor.
Are there radio-loud and radio-quiet gamma-ray bursts?
Authors: Osborne Joshua A , Bagheri Fatemeh , Shahmoradi Amir
Published: February 2021

The potential existence of two separate classes of Long-duration Gamma-Ray Bursts (LGRBs) with and without radio afterglow emission, corresponding to radio-bright/loud and radio-dark/quiet populations, has been recently argued and favoured in the GRB literature. The radio-quiet LGRBs have been found to have, on average, lower total isotropic gamma-ray emissions (Eiso) and shorter intrinsic prompt gamma-ray durations (e.g. T90z). In addition, a redshift −T90z anticorrelation has been discovered among the radio-loud LGRBs, which is reportedly missing in the radio-quiet class. Here, we discuss the significance of the differences between the energetics and temporal properties of the two proposed classes of radio-loud and radio-quiet LGRBs. We show that much of the proposed evidence in support of the two distinct radio populations of LGRBs can be explained away in terms of selection effects and sample incompleteness. Our arguments are based on the recent discovery of the relatively strong, highly significant positive correlation between the total isotropic emission (Eiso) and the intrinsic prompt duration (T90z) that is present in both populations of short-hard and long-soft GRBs, predicted, quantified, and reported for the first time by Shahmoradi (2013a;2013b) and Shahmoradi & Nemiroff (2015).
A self-supervised, physics-aware, Bayesian neural network architecture for modelling galaxy emission-line kinematics
Authors: Dawson James M , Davis Timothy A , Gomez Edward L , Schock Justus
Published: February 2021

In the upcoming decades, large facilities, such as the SKA, will provide resolved observations of the kinematics of millions of galaxies. In order to assist in the timely exploitation of these vast data sets, we explore the use of a self-supervised, physics-aware neural network capable of Bayesian kinematic modelling of galaxies. We demonstrate the network’s ability to model the kinematics of cold gas in galaxies with an emphasis on recovering physical parameters and accompanying modelling errors. The model is able to recover rotation curves, inclinations and disc scale lengths for both CO and H i data which match well with those found in the literature. The model is also able to provide modelling errors over learned parameters, thanks to the application of quasi-Bayesian Monte Carlo dropout. This work shows the promising use of machine learning, and in particular, self-supervised neural networks, in the context of kinematically modelling galaxies. This work represents the first steps in applying such models for kinematic fitting and we propose that variants of our model would seem especially suitable for enabling emission-line science from upcoming surveys with e.g. the SKA, allowing fast exploitation of these large data sets.
RNA thermoswitches modulateStaphylococcus aureusadaptation to ambient temperatures
Authors: Catalan-Moreno Arancha , Cela Marta , Menendez-Gil Pilar , Irurzun Naiara , Caballero Carlos J , Caldelari Isabelle , Toledo-Arana Alejandro
Published: February 2021

Thermoregulation of virulence genes in bacterial pathogens is essential for environment-to-host transition. However, the mechanisms governing cold adaptation when outside the host remain poorly understood. Here, we found that the production of cold shock proteins CspB and CspC from Staphylococcus aureus is controlled by two paralogous RNA thermoswitches. Through in silico prediction, enzymatic probing and site-directed mutagenesis, we demonstrated that cspB and cspC 5′UTRs adopt alternative RNA structures that shift from one another upon temperature shifts. The open (O) conformation that facilitates mRNA translation is favoured at ambient temperatures (22°C). Conversely, the alternative locked (L) conformation, where the ribosome binding site (RBS) is sequestered in a double-stranded RNA structure, is folded at host-related temperatures (37°C). These structural rearrangements depend on a long RNA hairpin found in the O conformation that sequesters the anti-RBS sequence. Notably, the remaining S. aureus CSP, CspA, may interact with a UUUGUUU motif located in the loop of this long hairpin and favour the folding of the L conformation. This folding represses CspB and CspC production at 37°C. Simultaneous deletion of the cspB/cspC genes or their RNA thermoswitches significantly decreases S. aureus growth rate at ambient temperatures, highlighting the importance of CspB/CspC thermoregulation when S. aureus transitions from the host to the environment.
E pluribus unum? Political fractionalization and deviations from the law of one price in the USA
Authors: Antonini Massimo , Fielding David , Pires Jacinta
Published: February 2021

The magnitude of deviations from the Law of One Price (LOP) across cities depends on a number of characteristics, including language differences, distance, and other correlates of trade costs. We show that in the USA, political differences between cities are an equally important determinant of LOP deviations. LOP deviations are smaller if the cities are both strongly Democrat or both strongly Republican. These effects are of a similar order of magnitude to those of distance, and suggest that political differences represent a substantial barrier to competition.
Combined Endoscopic Endonasal and Contralateral Transmaxillary Approach for Petrous Cholesteatoma: 2-Dimensional Operative Video
Authors: Wang Wei-Hsin , Lan Ming-Ying , Snyderman Carl H , Gardner Paul A
Published: February 2021

This 59-yr-old man presented with headache, dizziness, diplopia, and right-side hearing impairment for years. The objective degree of hearing impairment was not available. Magnetic resonance imaging (MRI) showed a right petrous apex lesion centered behind the right petrous internal carotid artery and extending lateral to the medial aspect of the right internal auditory canal. A combined endoscopic endonasal and left contralateral transmaxillary (CTM) approach was performed, and gross-total resection was achieved. Peeling the cyst wall from the dura resulted in minor weeping. It was covered with a left-sided, vascularized nasoseptal flap. His dizziness and diplopia improved immediately after the surgery. Histopathology revealed an epidermoid cyst. In this surgical video, we demonstrate the key steps of the CTM approach for access to the petrous apex posterior to the petrous internal carotid artery (ICA).

The patient gave informed consent for surgery and video recording.
The Narrative Enjoyment and Appreciation Rationale
Authors: Tamborini Ron , Grady Sara M. , Baldwin Joshua , McClaran Nikki , Lewis Robert
Published: February 2021

The narrative enjoyment and appreciation rationale (NEAR) builds on dual-process logic to distinguish these two forms of audience response to media entertainment shaped by either an intuitive or deliberative processing system. Three message features are critical in determining how these systems govern response: (1) the absence or presence of intuition conflict in the narrative, (2) the extent to which different intuitions are made salient (i.e., emphasized in the plot), and (3) the satisfaction/thwarting of those salient intuitions, where satisfaction refers to reward for acts that conform to intuitions, and thwarting refers to the inverse of this. When all salient intuitive needs are satisfied by entertainment experience, positive affect produced by intuitive processes is labeled enjoyment. By comparison, when the entertainment experience satisfies the most salient intuitive needs, but not all salient intuitive needs, positive affect produced by deliberative processing is labeled appreciation.
Musical Congruity in Advertising
Authors: Oakes Steve , Abolhasani Morteza
Published: February 2021

This chapter provides a review of the empirical literature on music in advertising and uses the overarching concept of musical congruity (or musical fit) to identify underlying patterns and enable more meaningful analysis of frequently disparate studies. Established and emerging research themes in music and advertising are examined in depth. Although the chapter focuses mainly on the findings of quantitative studies, it concludes with a section examining the more recent phenomenon of netnographic research into music in advertising. Ways in which netnography builds upon ethnography for the digital age are examined. The chapter concludes with a discussion of future research themes in music and advertising.
EIN3-Mediated Ethylene Signaling Attenuates Auxin Response during Hypocotyl Thermomorphogenesis
Authors: Kim Jae Young , Park Young-Joon , Lee June-Hee , Kim Zee Hwan , Park Chung-Mo
Published: February 2021

The gaseous phytohormone ethylene plays vital roles in diverse developmental and environmental adaptation processes, such as fruit ripening, seedling establishment, mechanical stress tolerance and submergence escape. It is also known that in the light, ethylene promotes hypocotyl growth by stimulating the expression of PHYTOCHROME INTERACTING FACTOR3 (PIF3) transcription factor, which triggers microtubule reorganization during hypocotyl cell elongation. In particular, ethylene has been implicated in plant responses to warm temperatures in recent years. However, it is currently unclear how ethylene signals are functionally associated with hypocotyl thermomorphogenesis at the molecular level. Here, we show that ETHYLENE-INSENSITIVE3 (EIN3)-mediated ethylene signals attenuate hypocotyl thermomorphogenesis by suppressing auxin response. At warm temperatures, when the activity of the PIF4 thermomorphogenesis promoter is prominently high, the ethylene-activated EIN3 transcription factor directly induces the transcription of ARABIDOPSIS PP2C CLADE D7 (APD7) gene encoding a protein phosphatase that inactivates the plasma membrane (PM) H+-ATPase proton pumps. In conjunction with the promotive role of the PM H+-ATPases in hypocotyl cell elongation, our observations strongly support that the EIN3-directed induction of APD7 gene is linked with the suppression of auxin-induced cell expansion, leading to the reduction in thermomorphogenic hypocotyl growth. Our data demonstrate that APD7 acts as a molecular hub that integrates ethylene and auxin signals into hypocotyl thermomorphogenesis. We propose that the ethylene–auxin signaling crosstalks via the EIN3-APD7 module facilitate the fine-tuning of hypocotyl thermomorphogenesis under natural environments, which often fluctuate in a complex manner.
Epidemiology of Early and Late Onset Neonatal Sepsis in Very Low Birthweight Infants
Authors: Köstlin-Gille Natascha , Härtel Christoph , Haug Clara , Göpel Wolfgang , Zemlin Michael , Müller Andreas , Poets Christian F. , Herting Egbert , Gille Christian
Published: February 2021

Background:

Sepsis is a major cause of death in neonates. Knowledge about epidemiology, risk factors, causative pathogens and outcome of neonatal sepsis is important to improve neonatal care. For Germany, only few data on neonatal sepsis in very low birth weight (VLBW) infants exist.

Methods:

Data from 14,926 preterm infants with birth weight <1500 g and gestational age between 22 0/7 weeks and 31 6/7 collected between January 2009 and December 2017 were analyzed for frequency of early-onset sepsis (EOS) and late-onset sepsis (LOS) and for causative pathogens. Risk factors for the development of EOS and LOS and outcomes after EOS and LOS were analyzed by multivariate logistic regression models.

Results:

EOS occurred in 1.1% of infants and LOS in 11.9%. Escherichia coli was the most common pathogen in EOS, coagulase-negative staphylococci in LOS. Multidrug-resistant organisms were detected in 8.4% of EOS and 3.9% of LOS cases. Risk factors for EOS were lower gestational age, intra-amniotic infection and spontaneous delivery. Risk factors for LOS were lower gestational age, small for gestational age, central lines, endotracheal ventilation and history of EOS. Both EOS and LOS were independently associated with adverse neonatal outcome.

Conclusions:

These data from a large German neonatal cohort confirm neonatal sepsis as the most common cause of morbidity and mortality in VLBW infants, as well as E. coli and coagulase-negative staphylococci as the most prevalent pathogens. Multidisciplinary approaches such as antibiotic stewardship, hygiene and feeding strategies are necessary to further reduce the burden of sepsis in VLBW infants.
Clinical Manifestations of Gastrointestinal Symptoms in COVID-19 Patients
Authors: Abbasinia Mohammad , Hormati Ahmad , Eshagh Hossaini Seyed Kamal , Foroghi Ghomi Seyed Yaser , Zamani Farhad , Afifian Mahboubeh , Ahmadpour Sajjad
Published: February 2021

After the outbreak of novel coronavirus disease 2019 (COVID-19) in Wuhan, China, its spread to other countries is rapidly increasing. In this integrative review, we report the prevalence of gastrointestinal symptoms in patients with COVID-19. For this purpose, available articles on gastrointestinal manifestations in patients with COVID-19, which were reported from China, were reviewed. All reviewed articles were searched from December 11, 2019, to June 20, 2020, based on specific key words. Related findings in these articles show that the main target of COVID-19 is lung tissue, as after the virus enters the body, it mainly causes respiratory symptoms in affected patients. But in addition to respiratory symptoms, it is possible that, over time, these patients present with other symptoms, the most obvious of which are gastrointestinal symptoms. It is well documented that diarrhea and vomiting are the most common gastrointestinal symptoms in COVID-19 patients. As part of this report, we also look at the incidence and frequency of gastrointestinal symptoms in COVID-19 patients in Iran. The results can be used by providers as a guideline for better management of gastrointestinal symptoms in these patients.
Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report
Authors: Hernandez Matthew M. , Gonzalez-Reiche Ana S. , Alshammary Hala , Fabre Shelcie , Khan Zenab , van De Guchte Adriana , Obla Ajay , Ellis Ethan , Sullivan Mitchell J. , Tan Jessica , Alburquerque Bremy , Soto Juan , Wang Ching-Yi , Sridhar Shwetha Hara , Wang Ying-Chih , Smith Melissa , Sebra Robert , Paniz-Mondolfi Alberto E. , Gitman Melissa R. , Nowak Michael D. , Cordon-Cardo Carlos , Luksza Marta , Krammer Florian , van Bakel Harm , Simon Viviana , Sordillo Emilia Mia
Published: February 2021

New York City (NYC) emerged as a coronavirus disease 2019 (COVID-19) epicenter in March 2020, but there is limited information regarding potentially unrecognized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections before the first reported case. We utilized a sample pooling strategy to screen for SARS-CoV-2 RNA in de-identified, respiratory pathogen-negative nasopharyngeal specimens from 3,040 patients across our NYC health system who were evaluated for respiratory symptoms or influenza-like illness during the first 10 weeks of 2020. We obtained complete SARS-CoV-2 genome sequences from samples collected between late February and early March. Additionally, we detected SARS-CoV-2 RNA in pooled specimens collected in the week ending 25 January 2020, indicating that SARS-CoV-2 caused sporadic infections in NYC a full month before the first officially documented case.

ONE SENTENCE SUMMARY

Molecular surveillance demonstrates that SARS-CoV-2 caused influenza-like illness in NYC before the first reported case.
Categorizing ultra-processed food intake in large-scale cohort studies: evidence from the Nurses’ Health Studies, the Health Professionals Follow-up Study, and the Growing Up Today Study
Authors: Khandpur Neha , Rossato Sinara , Drouin-Chartier Jean-Philippe , Du Mengxi , Martinez Euridice , Sampson Laura , Monteiro Carlos , Zhang Fang Fang , Willett Walter , Fung Teresa T. , Sun Qi
Published: February 2021

Objective

There is limited description and documentation of the methods used for the categorization of dietary intake according to the NOVA classification, in large-scale cohort studies. This manuscript details the strategy employed for categorizing the food intake, assessed using food frequency questionnaires (FFQs), of participants in the Nurses’ Health Studies (NHS) I and II, the Health Professionals Follow-up Study (HPFS), and the Growing Up Today Studies (GUTS) I and II into the four NOVA groups to identify the ultra-processed portion of their diets.

Methods

A four-stage approach was employed: (1) compilation of all food items from the FFQs used at different waves of data collection; (2) assignment of food items to a NOVA group by three researchers working independently; (3) checking for consensus in categorization and shortlisting food items for which there was disagreement; (4) discussions with experts and use of additional resources (research dieticians, cohort-specific documents, online grocery store scans) to guide the final categorization of the short-listed items.

Results

At stage 1, 205 and 315 food items were compiled from the adult and GUTS FFQ food lists, respectively. Over 70% of food items from all cohorts were assigned to a NOVA group after stage 2 and the remainder were shortlisted for further discussion (stage 3). Two rounds of reviews at stage 4 helped with the categorization of 96.5% of items from the adult cohorts and 90.7% items from the youth cohort. The remaining products were assigned to a non-ultra-processed food group and ear-marked for sensitivity analyses. Of all items in the food lists, 36.1% in the adult cohorts and 43.5% in the GUTS cohorts were identified as ultra-processed.

Conclusion

An iterative, conservative approach was used to categorize food items from the NHS, HPFS and GUTS FFQ food lists according to their grade of processing. The approach relied on discussions with experts and was informed by insights from the research dieticians, information provided by cohort-specific documents, and scans of online supermarkets. Future work is needed to validate this approach.
Emerging SARS-CoV-2 Lineages in Middle Eastern Jordan with Increasing Mutations Near Antibody Recognition Sites
Authors: Hajjo Rima , Sabbah Dima A. , Bardaweel Sanaa K.
Published: February 2021

The genomic analysis of the 556 viral sequences from Jordan uncovered three dominant genetic SARS-CoV-2 lineages that are currently circulating in Jordan: B.1.1.312 (76%), B.1.36.10 (11%), and B.1.1.7 (6%), replacing the genetic strains that were dominant before sustained community transmission in Jordan. This raises speculations about these new genetic lineages and their relationship to the severity of disease symptoms in Jordan.
A new variant of ASIC2 mediates sodium retention in nephrotic syndrome
Authors: Fila Marc , Sassi Ali , Brideau Gaëlle , Cheval Lydie , Morla Luciana , Houillier Pascal , Walter Christine , Gennaoui Michel , Collignon L Laure , Keck Mathilde , Planelles Gabrielle , Bakouh Naziha , Peuchmaur Michel , Deschênes Georges , Anegon Ignacio , Remy Séverine , Vogt Bruno , Crambert Gilles , Doucet Alain
Published: February 2021

Idiopathic nephrotic syndrome (INS) is characterized by proteinuria and renal Na retention leading to oedema. This Na retention is usually attributed to epithelial sodium channel (ENaC) activation following plasma aldosterone increase. However, most nephrotic patients show normal aldosterone levels. Using a corticosteroid-clamped rat model of INS (CC-PAN), we showed that the observed electrogenic and amiloride-sensitive Na retention could not be attributed to ENaC. We, then, identified a truncated variant of acid sensing ion channel 2b (ASIC2b) that induced sustained acid-stimulated sodium currents when co-expressed with ASIC2a. Interestingly, CC-PAN nephrotic ASIC2b-null rats did not develop sodium retention. We finally showed that expression of the truncated ASIC2b in kidney was dependent on the presence of albumin in the tubule lumen and activation of ERK in renal cells. Finally, the presence of ASIC2 mRNA was also detected in kidney biopsies from patients with INS but in any of the patients with other renal diseases. We have, therefore, identified a novel variant of ASIC2b responsible for the renal Na retention in the pathological context of INS.
Accommodating site variation in neuroimaging data using normative and hierarchical Bayesian models
Authors: Bayer Johanna M. M. , Dinga Richard , Kia Seyed Mostafa , Kottaram Akhil R. , Wolfers Thomas , Lv Jinglei , Zalesky Andrew , Schmaal Lianne , Marquand Andre
Published: February 2021

Abstract

The potential of normative modeling to make individualized predictions from neuroimaging data has enabled inferences that go beyond the case-control approach. However, site effects are often confounded with variables of interest in a complex manner and can bias estimates of normative models, which has impeded the application of normative models to large multi-site neuroimaging data sets. In this study, we suggest accommodating for these site effects by including them as random effects in a hierarchical Bayesian model. We compared the performance of a linear and a non-linear hierarchical Bayesian model in modeling the effect of age on cortical thickness. We used data of 570 healthy individuals from the ABIDE (autism brain imaging data exchange) data set in our experiments. In addition, we used data from individuals with autism to test whether our models are able to retain clinically useful information while removing site effects. We compared the proposed single stage hierarchical Bayesian method to several harmonization techniques commonly used to deal with additive and multiplicative site effects using a two stage regression, including regressing out site and harmonizing for site with ComBat, both with and without explicitly preserving variance related to age and sex as biological variation of interest. In addition, we made predictions from raw data, in which site has not been accommodated for. The proposed hierarchical Bayesian method showed the best predictive performance according to multiple metrics. Beyond that, the resulting z-scores showed little to no residual site effects, yet still retained clinically useful information. In contrast, performance was particularly poor for the regression model and the ComBat model in which age and sex were not explicitly modeled. In all two stage harmonization models, predictions were poorly scaled, suffering from a loss of more than 90 % of the original variance. Our results show the value of hierarchical Bayesian regression methods for accommodating site variation in neuroimaging data, which provides an alternative to harmonization techniques. While the approach we propose may have broad utility, our approach is particularly well suited to normative modelling where the primary interest is in accurate modelling of inter-subject variation and statistical quantification of deviations from a reference model.

1

Highlights

Development and presentation of normative modeling approach based on hierarchical Bayesian modeling that can be applied to large multi-site neuroimaging data sets.

Comparison of performance of Hierarchical Bayesian model including site as predictor to several common ways to harmonize for multi-site effects.

Presentation of normative modeling as site correction tool.
Shadow ORFs illuminated: long overlapping genes inPseudomonas aeruginosaare translated and under purifying selection
Authors: Kreitmeier Michaela , Ardern Zachary , Abele Miriam , Ludwig Christina , Scherer Siegfried , Neuhaus Klaus
Published: February 2021

The existence of overlapping genes (OLGs) with significant coding overlaps revolutionises our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in the medically important Gram-negative bacteriumPseudomonas aeruginosa. Both OLG pairs show sequence features consistent with being genes and transcriptional signals in RNA sequencing data. Translation of both OLGs was confirmed by ribosome profiling and mass spectrometry. Quantitative proteomics of samples taken during different phases of growth revealed regulation of protein abundances, implying biological functionality. Both OLGs are taxonomically highly restricted, and likely arose by overprinting within the genus. Evidence for purifying selection further supports functionality. The OLGs reported here are the longest yet proposed in prokaryotes and are among the best attested in terms of translation and evolutionary constraint. These results highlight a potentially large unexplored dimension of prokaryotic genomes.
Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle,Leptinotarsa decemlineata
Authors: Pélissié Benjamin , Chen Yolanda H. , Cohen Zachary P. , Crossley Michael S. , Hawthorne David J. , Izzo Victor , Schoville Sean D.
Published: February 2021

Background

Insecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices. An improved understanding of the evolutionary mechanisms that allow pests to rapidly adapt to novel control tactics will help prevent economically damaging outbreaks. The Colorado potato beetle (CPB),Leptinotarsa decemlineata,is a global super-pest that rapidly evolves resistance to insecticides. Using whole genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, non-mutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation.

Results

Population genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit only modest reductions in nucleotide diversity, relative to non-pest ancestral populations, and show evidence of recent demographic expansion. Genome scans of selection provide clear signatures of repeated adaptation across different CPB populations, with especially strong evidence that insecticide resistance involves selection of different genes in different populations. Similarly, analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns.

Conclusion

CPB evolves insecticide resistance repeatedly across agricultural regions, and oftentimes at the same loci, supporting a prominent role of polygenic evolution from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. An important future goal will be to understand how polygenic resistance phenotypes spread among local pest populations, in order to refine integrated pest management practices to maintain the efficacy and sustainability of novel control techniques.
Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum inC. elegans
Authors: Rajaei Moein , Shekhar Saxena Ayush , Johnson Lindsay M. , Snyder Michael C. , Crombie Timothy A. , Tanny Robyn E. , Andersen Erik C. , Joyner-Matos Joanna , Baer Charles F.
Published: February 2021

Important clues about natural selection can be gleaned from discrepancies between the properties of segregating genetic variants and of mutations accumulated experimentally under minimal selection, provided the mutational process is the same in the lab as in nature. The ratio of transitions to transversions (Ts/Tv) is consistently lower inC. elegansmutation accumulation (MA) experiments than in nature, which has been argued to be in part due to increased oxidative stress in the lab environment. Using whole-genome sequence data from a set ofC. elegansMA lines carrying a mutation (mev-1) that increases the cellular titer of reactive oxygen species (ROS), leading to increased endogenous oxidative stress, we find that the base-substitution spectrum is similar betweenmev-1lines, its wild-type progenitor (N2), and another set of MA lines derived from a different wild strain (PB306). By contrast, the rate of short insertions is greater in themev-1lines, consistent with studies in other organisms in which environmental stress led to an increase in the rate of insertion-deletion mutations. Further, the mutational properties of mononucleotide repeats in all strains are qualitatively different from those of non-mononucleotide sequence, both for indels and base-substitutions, and whereas the non-mononucleotide spectra are fairly similar between MA lines and wild isolates, the mononucleotide spectra are very different. The discrepancy in mutational spectra between lab MA experiments and natural variation is likely due to a consistent (but unknown) effect of the lab environment that manifests itself via different modes of mutability and/or repair at mononucleotide loci.
Testing potential mechanisms of conspecific sperm precedence inDrosophila pseudoobscura
Authors: Peckenpaugh Brooke , Castillo Dean M. , Moyle Leonie C.
Published: February 2021

Drosophila pseudoobscurafemales that co-occur with sister speciesD. persimilisshow elevated fertilization by conspecific sperm when they mate with both a heterospecific and a conspecific male. This phenomenon, known as conspecific sperm precedence (CSP), has evolved as a mechanism to avoid maladaptive hybridization withD. persimilis. In this study, we assessed pericopulatory (during mating) and postcopulatory (after mating) traits in crosses with sympatric or allopatricD. pseudoobscurafemales and conspecific or heterospecific males to evaluate potential mechanisms of CSP in this system. We observed shorter copulation duration in crosses with sympatric females, but found no difference in quantity of sperm transferred or female reproductive tract toxicity between sympatry and allopatry. Our data also support the hypothesis that parasperm, a short, sterile sperm morph, can protect fertile eusperm from theD. pseudoobscurafemale reproductive tract, though it is unclear how this might affect patterns of sperm use in sympatry vs. allopatry. Overall, these results suggest that copulation duration could potentially contribute to the elevated CSP observed in sympatry.
Correcting excess mortality for pandemic-associated population decreases
Authors: Faust Jeremy Samuel , Du Chengan , Li Shu-Xia , Lin Zhenqiu , Krumholz Harlan M.
Published: February 2021

Objectives

We identify a correction for excess mortality that takes the sudden unexpected changes in the size of the United States population into account.

Design

This is a weekly cross-sectional analysis of all-cause mortality since week 5, 2020. We describe and apply a simple correction that takes population changes into account in order to provide corrected weekly estimates of expected deaths for 2020 and 2021.

Setting

The United States.

Participants

All United States residents.

Interventions

The covid-19 pandemic.

Main outcome measures

Expected and excess mortality for the United States during the covid-19 period.

Results

As of week 53, 2020 (ending January 2, 2021), approximately >10,200 more excess deaths have occurred in the United States than could be detected if expected deaths projections were not amended to reflect population decreases during 2020. The figure is projected to rise to >12,600 (>600 weekly) by week 5, 2021. Assuming recent excess mortality and pandemic-associated visa reductions continue until the earliest time herd immunity could be approached resulting from a combination of infections and vaccinations (week 17, 2021), if point estimates of expected deaths are not corrected, expected deaths will be overestimated (and therefore potential excess mortality underestimated) by ∼43,000 during 2021, or >53,300 since the outbreak of the pandemic measurement period (beginning week 5, 2020). By late December 2021, weekly expected death differences are projected to approach 1,000 per week.

Conclusions

Current models measuring excess mortality should be revised immediately so that public health officials do not lose the ability to detect ongoing excess mortality as the population changes continue to compound, lowering the number of weekly expected deaths. A similar approach should be used in the middle and late phases of all future pandemics.
How has the COVID-19 pandemic impacted on smoking and nicotine dependence among people with severe mental ill health? Analysis of linked data from a UK Closing the Gap Cohort
Authors: Peckham Emily , Allgar Victoria , Crosland Suzanne , Heron Paul , Johnston Gordon , Newbronner Elizabeth , Ratschen Elena , Spanakis Panagiotis , Wadman Ruth , Walker Lauren , Gilbody Simon
Published: February 2021

Smoking rates are higher for people who use mental health services which contributes substantially to health inequalities. Smoking can lead to worse COVID-19 outcomes, yet it remains unclear whether smoking has changed for people who use mental health services. We examined smoking patterns in a large clinical cohort of people with SMI before and during the pandemic. We found high levels of nicotine dependence and heavier patterns of smoking. Whilst some people had reported quitting, it is likely that smoking inequalities have become further entrenched. Mental health services should seek to mitigate this modifiable risk and source of poor health.
A Bayesian hierarchical model with integrated covariate selection and misclassification matrices to estimate neonatal and child causes of death
Authors: Mulick Amy R. , Oza Shefali , Prieto-Merino David , Villavicencio Francisco , Cousens Simon , Perin Jamie
Published: February 2021

Reducing neonatal and child mortality is a global priority. In countries without comprehensive vital registration data to inform policy and planning, statistical modelling is used to estimate the distribution of key causes of death. This modelling presents challenges given that the input data are few, noisy, often not nationally representative of the country from which they are derived, and often do not report separately on all of the key causes. As more nationally representative data come to be available, it becomes possible to produce country estimates that go beyond fixed-effects models with national-level covariates by incorporating country-specific random effects. However, the existing frequentist multinomial model is limited by convergence problems when adding random effects, and had not incorporated a covariate selection procedure simultaneously over all causes. We report here on the translation of a fixed effects, frequentist model into a Bayesian framework to address these problems, incorporating a misclassification matrix with the potential to correct for mis-reported as well as unreported causes. We apply the new method and compare the model parameters and predicted distributions of eight key causes of death with those based on the previous, frequentist model.