bluuebunny/crossref_metadata_2025 huggingface dataset:
Recovery in the melting pot: complex origins and restored genetic diversity in newly established Eurasian beaver (Rodentia: Castoridae) populations
Authors: Munclinger Pavel , Syrůčková Alena , Náhlovský Jan , Durka Walter , Saveljev Alexander P , Rosell Frank , Stubbe Annegret , Stubbe Michael , Ulevičius Alius , Samiya Ravchig , Yanuta Grigori , Vorel Aleš
Published: January 2022

Several larger vertebrate species have recovered from dramatic bottlenecks caused by overhunting and habitat destruction. One of the most notable comebacks concerns the Eurasian beaver (Castor fiber L.), which has increased its range by natural dispersal from both relict populations and populations established through translocations. Genetic methods have recently been used to study beavers at several locations. However, owing to a lack of reference samples from relict populations and alternative names of mitochondrial DNA haplotypes, the ancestry of re-established beaver populations remains obscure. Here, we focus on the genetic characterization of several newly established populations. Unlike previous studies, we also used microsatellite genotypes of reference samples from all relict populations. Our analysis was fully capable of tracing the origin of the nuclear and mitochondrial genome to relict populations. Although we confirmed an extraordinarily low genetic diversity in relict populations, our analysis showed restored diversity in newly established populations resulting from translocations. Recent expansions and stochastic effects have created a strong but complicated population structure, with neighbouring populations differing significantly in genetic composition. We conclude that this restored genetic diversity very likely contributes to the viability and ongoing expansion of the newly established populations.
Cellular and evolutionary perspectives on organismal cognition: from unicellular to multicellular organisms
Authors: Baluška František , Miller William B , Reber Arthur S
Published: January 2022

In this paper, we follow the evolutionary origins of cells as unicellular organisms and their evolution towards multicellularity, with a focus on plants and animals, both of which have two basic types of organismal self-identities: the immunological and the neuronal. Most cells of the animal immune system and its mesenchymal tissues are amoeba-like without flagella or cilia and form only loose cell–cell contacts. On the other hand, neuronal and epithelial cells are typically ciliated and assemble epithelial or neuronal synapses. In contrast, walled cells of higher plants lack flagella or cilia. However, lower plants up to the gymnosperm tree Ginkgo biloba have flagellated sperm cells. In our symbiotic concept of eukaryogenesis, the first ancient eukaryotic cells emerged from the merger of a large amoeba-like host cell with a small flagellated guest cell which later transformed into the eukaryotic nucleus. This duality at the origin of the eukaryotic cell matches with the duality of sexual gametes. It also corresponds to the immune system/neural dualities of organismal self-identities in both animals and plants.
Diversification of tiny toads (Bufonidae:Amazophrynella) sheds light on ancient landscape dynamism in Amazonia
Authors: Moraes Leandro J C L , Werneck Fernanda P , Réjaud Alexandre , Rodrigues Miguel T , Prates Ivan , Glaw Frank , Kok Philippe J R , Ron Santiago R , Chaparro Juan C , Osorno-Muñoz Mariela , Dal Vechio Francisco , Recoder Renato S , Marques-Souza Sérgio , Rojas Rommel R , Demay Léa , Hrbek Tomas , Fouquet Antoine
Published: January 2022

Major historical landscape changes have left significant signatures on species diversification. However, how these changes have affected the build-up and maintenance of Amazonia’s megadiversity continues to be debated. Here, we addressed this issue by focusing on the evolutionary history of a pan-Amazonian toad genus that has diversified throughout the Neogene (Amazophrynella). Based on a comprehensive spatial and taxonomic sampling (286 samples, all nominal species), we delimited operational taxonomic units (OTUs) from mitochondrial DNA sequences. We delimited 35 OTUs, among which 13 correspond to nominal species, suggesting a vast underestimation of species richness. Next, we inferred time-calibrated phylogenetic relationships among OTUs based on complete mitogenomic data, which confirmed an ancient divergence between two major clades distributed in eastern and western Amazonia, respectively. Ancestral area reconstruction analyses suggest that the Andean foothills and the Brazilian Shield region represent the ancient core areas for their diversification. These two clades, probably isolated from one other by lacustrine ecosystems in western Amazonia during the Miocene, display a pattern of northward and eastward dispersals throughout the Miocene‒Pliocene. Given the ecological association of Amazophrynella with non-flooded forests, our results reinforce the perception that ancient Amazonian landscape changes had a major impact on the diversification of terrestrial vertebrates.
Mass Drug Administration for the Control of Scabies: A Systematic Review and Meta-analysis
Authors: Lake Susanna J , Kaldor John M , Hardy Myra , Engelman Daniel , Steer Andrew C , Romani Lucia
Published: January 2022

Background

Scabies is a neglected tropical disease of the skin that can lead to impetigo, serious secondary bacterial infections and immune-mediated diseases. Mass drug administration (MDA) has been reported in several studies to reduce the prevalence of scabies and impetigo. We aimed to assess the efficacy of MDA for scabies on scabies and impetigo.

Methods

We conducted a systematic review and meta-analysis of reports on the impact of MDA on scabies and impetigo. We included randomized control trials and observational evaluations reported from January 1970 to April 2021 and involving human participants. We searched PubMed, Ovid Medline, Embase, and Cochrane. We considered MDA as treatment intended for the whole population, regardless of individual infection status or symptoms. The main outcome assessed was the change in scabies and impetigo prevalence following MDA. This review is registered with PROSPERO (CRD42020169839).

Results

We identified 1110 records, of which 11 met inclusion criteria for the review and 9 were deemed suitable for meta-analysis for scabies and 4 for impetigo. Most studies were in small populations. There was a high degree of heterogeneity between studies (I2 value 96.19%). The overall relative reduction of the impact of MDA on scabies prevalence was 79%. The effect size was comparable for MDA based on ivermectin and permethrin. MDA for scabies also led to a reduction in impetigo prevalence with a relative reduction of 66%.

Conclusions

MDA for scabies is highly effective in reducing the prevalence of scabies and impetigo. Further research is needed to determine the durability of impact, and the effectiveness of MDA regimens in larger populations.
Population Mobility and Aging Accelerate the Transmission of Coronavirus Disease 2019 in the Deep South: A County-Level Longitudinal Analysis
Authors: Zeng Chengbo , Zhang Jiajia , Li Zhenlong , Sun Xiaowen , Yang Xueying , Olatosi Bankole , Weissman Sharon , Li Xiaoming
Published: January 2022

Population mobility and aging at local areas contributed to the geospatial disparities in the coronavirus disease 2019 (COVID-19) transmission among 418 counties in the Deep South. In predicting the incidence of COVID-19, a significant interaction was found between mobility and the proportion of older adults. Effective disease control measures should be tailored to vulnerable communities.
Characteristics of Reported Deaths Among Fully Vaccinated Persons With Coronavirus Disease 2019—United States, January–April 2021
Authors: François Watkins Louise K , Mitruka Kiren , Dorough Layne , Bressler Sara S , Kugeler Kiersten J , Sadigh Katrin S , Birhane Meseret G , Nolen Leisha D , Fischer Marc
Published: January 2022

Background

Vaccines against coronavirus disease 2019 (COVID-19) are highly efficacious, but severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections do occur after vaccination. We characterized COVID-19 cases among fully vaccinated persons with an outcome of death.

Methods

We analyzed COVID-19 cases voluntarily reported to the Centers for Disease Control and Prevention by US health departments from 1 January to 30 April 2021. We included cases among US residents with a positive SARS-CoV-2 test result ≥14 days after completion of an authorized primary vaccine series and who had a known outcome (alive or dead) as of 31 May 2021. When available, specimens were sequenced for viral lineage and death certificates were reviewed for cause(s) of death.

Results

Of 8084 fully vaccinated persons with reported COVID-19 during the surveillance period, 245 (3.0%) died. Compared with patients who remained alive, those who died were older (median age, 82 vs 57 years;), more likely to reside in a long-term care facility (51% vs 18%), and more likely to have ≥1 underlying health condition associated with risk for severe disease (64% vs 24%) (all P < .01). Among 245 deaths, 191 (78%) were classified as COVID-19 related. Of 106 deaths with available death certificates, COVID-19 was listed for 81 deaths (77%). There were no differences in the type of vaccine administered or the most common viral lineage (B.1.1.7).

Conclusions

COVID-19 deaths are rare in fully vaccinated persons, occurring most commonly in those with risk factors for severe disease, including older age and underlying health conditions. All eligible persons should be fully vaccinated against COVID-19 and follow other prevention measures to mitigate exposure risk.
Visit-to-visit blood pressure variability and risk of dementia in chronic kidney disease patients: why are blood pressure changes so important in cognitive functions?
Authors: Yavuz Furkan , Kanbay Mehmet
Published: January 2022

Chronic kidney disease (CKD) is associated with cognitive functional impairment or dementia in addition to cardiovascular diseases. Aging of the population and the increasing prevalence of CKD in elderly patients are making dementia more prevalent. Blood pressure (BP) variability is an important risk factor for dementia. Although ample data link high BP variability with the risk of dementia in the general population, data on CKD patients are scarce. An observational cohort study conducted by Park et al., including 103 139 patients, demonstrated a strong association between higher visit-to-visit BP variability and increased risk of dementia in CKD patients. Both higher systolic and diastolic BP variabilities were associated with any type of dementia, including Alzheimer's and vascular dementia. Physicians must be aware of BP variability when evaluating CKD patients with hypertension.
Real-World Treatment Patterns and Physician Preferences for Biologics in Moderate-to-Severe Inflammatory Bowel Disease: Retrospective Chart Review in Europe
Authors: Huynh Lynn , Hass Steve , Peyrin-Biroulet Laurent , Duh Mei Sheng , Sipsma Heather , Cheng Mu , Lax Angie , Nag Arpita
Published: January 2022

Background

With many options available for treating inflammatory bowel disease (IBD) in Europe, this study sought to characterize physician treatment preferences and real-world treatment patterns in patients with moderate-to-severe ulcerative colitis (UC) and Crohn’s disease (CD).

Methods

This was a retrospective, noninterventional, physician-administered study. Gastroenterologists and general practitioners (n = 348) in France, Germany, and the United Kingdom provided information on treatment preferences and extracted information from records of patients with moderate-to-severe UC (n = 587) or CD (n = 417) who had received biologic, biosimilar or Janus kinase inhibitor therapies (2014–2019) and had IBD-related medical history available 6 months before and after treatment initiation.

Results

Physicians largely preferred infliximab and adalimumab or their biosimilars as first-line therapy for UC (originators, 65.8%; biosimilars, 26.1%) and CD (originators, 61.8%; biosimilars, 30.5%). Effectiveness was the most cited reason for treatment preference (92%–93% of physicians). Three-quarters of patients (UC, 75.8%; CD, 73.6%) received infliximab or adalimumab originators in the first line, with more patients receiving infliximab biosimilars than adalimumab biosimilars (12.4%–12.5% and 0.5%–4.1%, respectively, across UC and CD). Persistence was longer for first-line infliximab than adalimumab (UC, 26.6 vs 21.2 months; CD, 31.2 vs 26.7 months) and was generally shorter for their respective biosimilars. Nonbiologic treatments were used in combination with biologics in 14.1% (UC) and 11.5% (CD) of patients. Most patients received 1 biologic therapy (UC, 90.6%; CD, 83.2%); only 9.4% (UC) and 16.8% (CD) received a second biologic.

Conclusions

Infliximab and adalimumab originators dominated first-line biologic therapy for moderate-to-severe UC and CD. Understanding real-world treatment patterns can help assess new treatment uptake and suggest opportunities for improving treatment.
A chromosome-level genome assembly of an alpine plant Crucihimalaya lasiocarpa provides insights into high-altitude adaptation
Authors: Feng Landi , Lin Hao , Kang Minghui , Ren Yumeng , Yu Xi , Xu Zhanpeng , Wang Shuo , Li Ting , Yang Wenjie , Hu Quanjun
Published: January 2022

It remains largely unknown how plants adapt to high-altitude habitats. Crucihimalaya (Brassicaceae) is an alpine genus occurring in the Qinghai–Tibet Plateau characterized by cold temperatures and strong ultraviolet radiation. Here, we generated a chromosome-level genome for C. lasiocarpa with a total size of 255.8 Mb and a scaffold N50 size of 31.9 Mb. We first examined the karyotype origin of this species and found that the karyotype of five chromosomes resembled the ancestral karyotype of the Brassicaceae family, while the other three showed strong chromosomal structural variations. In combination with the rough genome sequence of another congener (C. himalaica), we found that the significantly expanded gene families and positively selected genes involved in alpine adaptation have occurred since the origin of this genus. Our new findings provide valuable information for the chromosomal karyotype evolution of Brassicaceae and investigations of high-altitude environment adaptation of the genus.
A 0/1h-algorithm using cardiac myosin-binding protein C for early diagnosis of myocardial infarction
Authors: Kaier Thomas E , Twerenbold Raphael , Lopez-Ayala Pedro , Nestelberger Thomas , Boeddinghaus Jasper , Alaour Bashir , Huber Iris-Martina , Zhi Yuan , Koechlin Luca , Wussler Desiree , Wildi Karin , Shrestha Samyut , Strebel Ivo , Miro Oscar , Martín-Sánchez Javier F , Christ Michael , Kawecki Damien , Keller Dagmar I , Rubini Gimenez Maria , Marber Michael , Mueller Christian ,   APACE Investigators, Freese Michael , Ratmann Paul David , Prepoudis Alexandra , Gualandro Danielle M , Geigy Nicolas , Reichlin Tobias , Rentsch Katharina , Maier Mario , Troester Valentina , Gehrke Juliane , Coscia Tania , Glarner Noemi , Schoepfer Hadrien , Buechi Michael , Walter Joan , Sanchez Ana Yufera , Puelacher Christian , du Fay de Lavallaz Jeanne , Sanzione Alessandra , Schäfer Ibrahim , Hillinger Petra , López Beatriz , Adrada Esther Rodriguez , Muzyk Piotr , Morawiec Beata , Parenica Jiri , Ganovská Eva , Lohrmann Jens , Buser Andreas , von Eckardstein Arnold , Bingisser Roland , Nickel Christian
Published: January 2022

Aims

Cardiac myosin-binding protein C (cMyC) demonstrated high diagnostic accuracy for the early detection of non-ST-elevation myocardial infarction (NSTEMI). Its dynamic release kinetics may enable a 0/1h-decision algorithm that is even more effective than the ESC hs-cTnT/I 0/1 h rule-in/rule-out algorithm.

Methods and results

In a prospective international diagnostic study enrolling patients presenting with suspected NSTEMI to the emergency department, cMyC was measured at presentation and after 1 h in a blinded fashion. Modelled on the ESC hs-cTnT/I 0/1h-algorithms, we derived a 0/1h-cMyC-algorithm. Final diagnosis of NSTEMI was centrally adjudicated according to the 4th Universal Definition of Myocardial Infarction. Among 1495 patients, the prevalence of NSTEMI was 17%. The optimal derived 0/1h-algorithm ruled-out NSTEMI with cMyC 0 h concentration below 10 ng/L (irrespective of chest pain onset) or 0 h cMyC concentrations below 18 ng/L and 0/1 h increase <4 ng/L. Rule-in occurred with 0 h cMyC concentrations of at least 140 ng/L or 0/1 h increase ≥15 ng/L. In the validation cohort (n = 663), the 0/1h-cMyC-algorithm classified 347 patients (52.3%) as ‘rule-out’, 122 (18.4%) as ‘rule-in’, and 194 (29.3%) as ‘observe’. Negative predictive value for NSTEMI was 99.6% [95% confidence interval (CI) 98.9–100%]; positive predictive value 71.1% (95% CI 63.1–79%). Direct comparison with the ESC hs-cTnT/I 0/1h-algorithms demonstrated comparable safety and even higher triage efficacy using the 0h-sample alone (48.1% vs. 21.2% for ESC hs-cTnT-0/1 h and 29.9% for ESC hs-cTnI-0/1 h; P < 0.001).

Conclusion

The cMyC 0/1h-algorithm provided excellent safety and identified a greater proportion of patients suitable for direct rule-out or rule-in based on a single measurement than the ESC 0/1h-algorithm using hs-cTnT/I.

Trial registration

ClinicalTrials.gov number, NCT00470587.
Case report: Mechanical mitral prosthetic valve thrombosis in the context of COVID-19 despite effective anticoagulation
Authors: Jeckelmann Clarisse , Djokic Bojan , Duchatelle Valérie , Girod Grégoire
Published: January 2022

Background

The SARS-CoV2 virus has been an emerging virus since December 2019 and is the cause of a global pandemic whose clinical manifestations extend far beyond respiratory disease.

Case summary

A patient with severe coronavirus disease 2019 respiratory infection, carrying a mechanical mitral valve and under anticoagulation, was admitted to our cardiology department because of a new atrial fibrillation, which turned out to be related to thrombosis of the mitral mechanical valve.

Conclusion

The pro-coagulant effect of the SARS-CoV2 virus does not spare patients at risk of thrombosis, even under effective anticoagulation. In patients with mechanical valves under vitamin K antagonist treatment, there is a high risk of thrombus formation. The treatment is based on thrombolysis by therapeutic anticoagulation, fibrinolysis, or surgery depending on the size, composition of thrombus, and clinical manifestation.
Prognostic factors of 10-year mortality after coronary artery bypass graft surgery: a secondary analysis of the arterial revascularization trial
Authors: Talukder Suprateeka , Dimagli Arnaldo , Benedetto Umberto , Gray Alastair , Gerry Stephen , Lees Belinda , Krzych Łukasz , Gaudino Mario , Taggart David P , Flather Marcus
Published: January 2022

OBJECTIVES

The objective of this investigation was to determine the preoperative prognostic factors of long-term (10-year) mortality in patients treated with isolated coronary artery bypass graft surgery in the arterial revascularization trial (ART).

METHODS

A post hoc analysis of the ART was conducted. Cumulative 10-year mortality was estimated using the Kaplan–Meier method. Prospectively collected preoperative data were used to determine the prognostic factors of 10-year all-cause mortality in patients who participated in the ART (Cox proportional hazards model).

RESULTS

A total of 3102 patients who participated in the ART were included in the analysis. Ten-year follow-up was completed in 3040 patients (98%). A total of 644 patients (20.8%) had died by 10 years. Preoperative factors that were identified as statistically significant predictors of 10-year mortality in the multivariable analysis (all P ≤ 0.01) were: left ventricular ejection fraction, atrial fibrillation, age, diabetes, prior cerebrovascular event (stroke or transient ischaemic attack), serum creatinine and smoking status. The following variables were significantly associated in univariable models but did not retain significance in the multivariable model for mortality: non-Caucasian ethnicity, hypertension, peripheral vascular disease, chronic obstructive pulmonary disease and prior myocardial infarction.

CONCLUSIONS

Independent predictors of 10-year mortality in the ART were multifactorial. Several key independent predictors of 10-year mortality in the ART were identified including: heart function, renal function, cerebrovascular disease, age, atrial fibrillation, smoking status and diabetes. Understanding which preoperative variables influence long-term outcome after coronary artery bypass grafting may help to target treatments to those at higher risk to reduce mortality.
Effects of the harvesting technique and external stenting on progression of vein graft disease 2 years after coronary artery bypass
Authors: Sandner Sigrid E , Donovan Terrence John , Edelstein Stav , Puskas John D , Angleitner Philipp , Krasopoulos George , Channon Keith , Gehrig Thomas , Rajakaruna Cha , Ladyshenskij Leonid , De Silva Ravi , Bonaros Nikolaos , Bolotin Gil , Jacobs Stephan , Thielmann Matthias , Choi Yeong-Hoon , Ohri Sunil , Lipey Alexander , Friedrich Ivar , Taggart David P
Published: January 2022

OBJECTIVES

In a post hoc analysis of the VEST III trial, we investigated the effect of the harvesting technique on saphenous vein graft (SVG) patency and disease progression after coronary artery bypass grafting.

METHODS

Angiographic outcomes were assessed in 183 patients undergoing open (126 patients, 252 SVG) or endoscopic harvesting (57 patients, 114 SVG). Overall SVG patency was assessed by computed tomography angiography at 6 months and by coronary angiography at 2 years. Fitzgibbon patency (FP I, II and III) and intimal hyperplasia (IH) in a patient subset were assessed by coronary angiography and intravascular ultrasound, respectively, at 2 years.

RESULTS

Baseline characteristics were similar between patients who underwent open and those who underwent endoscopic harvesting. Open compared with endoscopic harvesting was associated with higher overall SVG patency rates at 6 months (92.9% vs 80.4%, P = 0.04) and 2 years (90.8% vs 73.9%, P = 0.01), improved FP I, II and III rates (65.2% vs 49.2%; 25.3% vs 45.9%, and 9.5% vs 4.9%, respectively; odds ratio 2.81, P = 0.09) and reduced IH area (-31.8%; P = 0.04) and thickness (-28.9%; P = 0.04). External stenting was associated with improved FP I, II and III rates (odds ratio 2.84, P = 0.01), reduced IH area (-19.5%; P < 0.001) and thickness (-25.0%; P < 0.001) in the open-harvest group and reduced IH area (-12.7%; P = 0.01) and thickness (-9.5%; P = 0.21) in the endoscopic-harvest group.

CONCLUSIONS

A post-hoc analysis of the VEST III trial showed that open harvesting is associated with improved overall SVG patency and reduced IH. External stenting reduces SVG disease progression, particularly with open harvesting.
Strength of EU-level food environment policies and priority recommendations to create healthy food environments
Authors: Djojosoeparto Sanne K , Kamphuis Carlijn B M , Vandevijvere Stefanie , Murrin Celine , Stanley Isobel , Romaniuk Piotr , Harrington Janas M , Poelman Maartje P ,   the PEN Consortium
Published: January 2022

Background

Food environments impact on diets, obesity and non-communicable diseases (NCDs). Government policies are essential to create healthy food environments. This study aimed to assess the strength of European Union (EU)-level policies, and identify and prioritize actions for the EU to create healthy food environments.

Methods

The Healthy Food Environment Policy Index (Food-EPI) was applied. The Food-EPI included 26 policy and 24 infrastructure support indicators. Independent experts (n = 31) rated the strength of EU-level policies and infrastructure support for each of these indicators (on a 5-point scale, from very weak to very strong) and identified and prioritized actions to improve food environments.

Results

For 65% of the 26 policy indicators, EU-level policies were rated as weak and for 23% as very weak. For 63% of the 24 infrastructure support indicators, EU-level policies were rated as moderate and for 33% as weak. The experts recommended 18 policy and 19 infrastructure support actions to the EU. The Top 5 prioritized policy actions included three actions in the food composition domain (e.g. setting mandatory food composition targets), one action in the food prices domain and one action in the food promotion domain. The Top 5 prioritized infrastructure support actions included three actions in the leadership domain (e.g. developing a high-level NCDs Prevention Strategy) and two actions in the monitoring domain.

Conclusions

There is large potential for the EU to strengthen its policies and infrastructure support in order to improve food environments. This study specifies priority actions for the EU to create healthy food environments.
16S rRNA gene sequence diversity in Faecalibacterium prausnitzii-complex taxa has marked impacts on quantitative analysis
Authors: Tanno Hiroki , Maeno Shintaro , Salminen Seppo , Gueimonde Miguel , Endo Akihito
Published: January 2022

Faecalibacterium prausnitzii has been suggested as a biomarker of a healthy microbiota in human adults. Here, we report a taxonomic study of F. prausnitzii using genomic information and evaluation of the quantitative real-time PCR (qPCR) assay by focusing on specific primers to quantify its population. Average nucleotide identity values revealed that strains deposited as F. prausnitzii in a public database were separated into eight genomogroups with significant differences at the species level. A total of six of the 10 primer pairs used in the previous studies for qPCR of F. prausnitzii contained sequence mismatches to 16S rRNA gene sequences of the tested strains with markedly different levels by in silico analysis. In vitro primer evaluation by qPCR generally agreed with the in silico analysis, and markedly reduced amount of DNA was recorded by qPCR in combination with the primer pairs containing sequence mismatches. The present study demonstrated that a part of the accumulated knowledge on F. prausnitzii is maybe based on biased results.
A deep learning framework for characterization of genotype data
Authors: Ausmees Kristiina , Nettelblad Carl
Published: January 2022

Dimensionality reduction is a data transformation technique widely used in various fields of genomics research. The application of dimensionality reduction to genotype data is known to capture genetic similarity between individuals, and is used for visualization of genetic variation, identification of population structure as well as ancestry mapping. Among frequently used methods are principal component analysis, which is a linear transform that often misses more fine-scale structures, and neighbor-graph based methods which focus on local relationships rather than large-scale patterns. Deep learning models are a type of nonlinear machine learning method in which the features used in data transformation are decided by the model in a data-driven manner, rather than by the researcher, and have been shown to present a promising alternative to traditional statistical methods for various applications in omics research. In this study, we propose a deep learning model based on a convolutional autoencoder architecture for dimensionality reduction of genotype data. Using a highly diverse cohort of human samples, we demonstrate that the model can identify population clusters and provide richer visual information in comparison to principal component analysis, while preserving global geometry to a higher extent than t-SNE and UMAP, yielding results that are comparable to an alternative deep learning approach based on variational autoencoders. We also discuss the use of the methodology for more general characterization of genotype data, showing that it preserves spatial properties in the form of decay of linkage disequilibrium with distance along the genome and demonstrating its use as a genetic clustering method, comparing results to the ADMIXTURE software frequently used in population genetic studies.
The Sounds of Memory: Extending the Age–Prospective Memory Paradox to Everyday Behavior and Conversations
Authors: Haas Maximilian , Mehl Matthias R , Ballhausen Nicola , Zuber Sascha , Kliegel Matthias , Hering Alexandra
Published: January 2022

Objectives

Around the turn of the millennium, the “age–prospective memory (PM) paradox” challenged the classical assumption that older adults necessarily evidence a marked decline in PM functioning. As previous investigations highlighted ecological validity to be a potential explanation, the present study sought to extend established approaches by using novel real-world assessment technologies to examine PM unobtrusively in everyday-life conversations.

Method

Next to laboratory PM tasks, real-life PM performance of 53 younger adults (19–32 years) and 38 older adults (60–81 years) was assessed from three sources: Over 9 days, participants completed an experimenter-given naturalistic task, a diary-based approach assessing self-assigned intentions, as well as an ambulatory assessment with the Electronically Activated Recorder (EAR), a device that unobtrusively samples ambient sounds to detect spontaneous speech production related to (lapses in) everyday PM.

Results

Older adults showed lower performance in laboratory PM only for the time-based task and performed either equally well as or even better than younger adults in everyday PM. With regard to PM performance as captured in real-life ambient audio data, younger adults talked more frequently about PM than older adults, but no significant difference between younger and older adults was found for speech related to PM errors.

Discussion

Findings confirmed older adults’ preserved PM performance in everyday life across different indicators with increasing ecological validity. Furthermore, as a novel method to assess conversational PM in everyday life, the EAR opens new insights about the awareness of PM lapses and the communication of intentions in real life.
Does Retirement Change What Individuals Value in Life? Results From a 3-Year Panel Study
Authors: Grünwald Olga , Damman Marleen , Henkens Kène
Published: January 2022

Objectives

In previous research on retirement, what individuals value in life is often assumed to remain stable after the transition into retirement. However, retirement exposes individuals to new social settings and might thus prompt them to reevaluate their life orientations. Quantitative empirical knowledge about this process is limited, though. This study examines the impact of retirement on changes in the perceived importance of self-development, social status, societal contribution, and generativity in older adults’ lives. We draw on the life-course framework to develop hypotheses about which life orientations are more likely to change after retirement and how.

Methods

We analyzed data collected in 2015 and 2018 among 5,034 Dutch individuals aged 60–65 and employed at baseline. Around half had fully retired at follow-up (either voluntarily or involuntarily), and 10% worked after retirement.

Results

Conditional change models reveal that voluntary full retirement was linked to statistically significant—but (very) small—decreases in the importance of self-development, social status, societal contribution, and generativity compared to continuous career work. Differences in changes of life orientations between retirement processes (i.e., postretirement work, involuntary full retirement) were also small.

Discussion

The findings point to relatively high levels of continuity during the transition from career employment to retirement, given the small effect sizes observed. The notion that after retirement, individuals will reevaluate what they value in life—as expected in light of the exposure-based mechanism from the life-course literature—seems to be less pronounced than initially expected.
Subjective Aging and Objectively Assessed Hearing Function: A Prospective Study of Older Adults
Authors: Stephan Yannick , Sutin Angelina R , Terracciano Antonio
Published: January 2022

Objectives

Subjective aging is consistently related to a range of health-related outcomes, but little is known about its relationship with sensory functioning. The present prospective study tested whether subjective age and self-perceptions of aging (SPA) are associated with objective hearing function.

Methods

Participants were 7,085 individuals aged 50–93 years (60% women, mean = 65.15, standard deviation [SD] = 8.71) from the Health and Retirement Study. Measures of subjective age, SPA, and information on demographic factors were obtained in 2008/2010. Objective hearing function was assessed 8 years later in 2016/2018. Furthermore, potential mediating variables (C-reactive protein, body mass index, physical inactivity, and chronic conditions) were assessed in 2012/2014.

Results

In regression analyses that accounted for demographic factors, older subjective age and negative SPA were associated with lower hearing acuity 8 years later. In addition, 1 SD older subjective age and negative SPA were related to a 9% and 7% higher likelihood of hearing impairment. Mediation analyses revealed that physical inactivity and chronic conditions partially mediated subjective age and SPA associations with hearing acuity. There was little evidence that the link between subjective aging and hearing was moderated by hearing aids and partial support for a moderating role of age.

Discussion

This study provides new evidence that subjective aging is prospectively related to hearing function. Individuals with older subjective age or negative SPA have unfavorable behavioral and clinical profiles that explain part of their lower hearing function. Individuals’ experience with their aging process is a marker of risk for impaired hearing.
Resilience in Interracial–Interethnic Relationships in the United States: Assessing Relationship Maintenance and Communal Orientation as Protection Against Network Stigma
Authors: Haughton Chantel , Afifi Tamara D
Published: January 2022

Using the theory of resilience and relational load as a framework, this study examined whether a stress reduction or a stress-buffering model best explained risk and resilience in interracial–interethnic relationships in the United States when managing stigma from one’s social network. Eight hundred and sixteen Black and Latinx individuals in heterosexual relationships with a white, non-Latinx partner completed the survey. The stress reduction model was a better representation of individuals’ experiences in Latinx–white relationships and the stress-buffering model was a better representation of individuals’ experiences in Black–white relationships. For Latinx individuals, greater relationship maintenance received from one’s white partner and stronger levels of communal orientation were associated with reductions in stigma-related stress and conflict, which in turn, were associated with better relationship satisfaction and less relational load. For Black individuals, relationship maintenance and communal orientation moderated the associations between stress/conflict and the relational outcomes, but in unexpected ways.
A Prospective Trial with Long Term Follow-up of Patients With Severe, Steroid-Resistant Ulcerative Colitis Who Received Induction Therapy With Cyclosporine and Were Maintained With Vedolizumab
Authors: Tarabar Dino , El Jurdi Katia , Traboulsi Cindy , Yvellez Olivia , Milenkovic Zoran , Petrovic Stanko , Subotic Bojana , Gils Ann , Brocic Tanja , Brcerevic Irina , Latinovic Olgica , Jocic Tanja , Rubin David T
Published: January 2022

Background

Combining vedolizumab with a rapid-onset drug such as cyclosporine is a novel combination treatment for severe steroid-resistant ulcerative colitis (UC). This prospective study describes the efficacy and safety of cyclosporine in conjunction with vedolizumab in patients with severe, steroid-resistant UC with 1 year of follow-up.

Methods

Seventeen steroid-resistant UC patients were treated with cyclosporine in combination with vedolizumab, with a follow up of 52 weeks. Clinical and endoscopic response, remission rates, and colectomy-free survival were the primary endpoints. Secondary endpoints included biochemical response and remission with C-reactive protein, erythrocyte sedimentation rate, and fecal calprotectin.

Results

Fifteen (88%) of 17 patients initially responded to cyclosporine and were started on vedolizumab. By week 10, 11 (73%) of 15 patients had achieved endoscopic remission with a Mayo score of ≤1. At week 26, 14 (93%) of 15 of the patients were in clinical remission and 11 (73%) were in endoscopic remission. At week 52 of follow-up, 10 (71%) of 14 of these patients continued to be in endoscopic remission and 11 (79%) of 14 were in clinical remission. Among the 10 patients in endoscopic remission, 8 (80%) reached histological remission. Colectomy-free survival rate was 82% (n = 14 of 17) at 1 year and mean C-reactive protein, erythrocyte sedimentation rate, and fecal calprotectin levels were 3.2 mg/L, 16.1 mm/h, and 168.3 µg/g, respectively. No serious adverse events were reported.

Conclusions

Bridging cyclosporine to vedolizumab in severe, steroid-refractory UC patients is effective and safe at inducing and maintaining clinical, endoscopic, and biochemical response and remission up to 52 weeks of follow-up. Larger prospective studies are warranted.
Underrepresentation of Minorities and Lack of Race Reporting in Ulcerative Colitis Drug Development Clinical Trials
Authors: Sedano Rocio , Hogan Malcolm , McDonald Cassandra , Aswani-Omprakash Tina , Ma Christopher , Jairath Vipul
Published: January 2022

Lay Summary

Historically, inflammatory bowel disease trials report high rates of White patients enrollment. To promote initiatives toward diversifying the enrolled population, we assessed the reporting of race and ethnicity of patients enrolled in pharmaceutical clinical trials for ulcerative colitis.
The expression and role of tenascin C in abdominal aortic aneurysm formation and progression
Authors: Nagel Felix , Schaefer Anne-Kristin , Gonçalves Inês Fonseca , Acar Eylem , Oszwald Andre , Kaiser Philipp , Kain Renate , Trescher Karola , Eilenberg Wolf H , Brostjan Christine , Santer David , Kiss Attila , Podesser Bruno K
Published: January 2022

OBJECTIVES

Up-regulation of tenascin C (TNC), a matricellular protein, produced mainly by vascular smooth muscle cells (VSMC), is associated with the progression and dilation of abdominal aortic aneurysms (AAA). The aims of this study were (i) to evaluate whether serum levels of TNC in patients with AAA patients correlate with aortic diameter and (ii) to clarify the role of TNC in formation and progression of AAA in a murine model.

METHODS

In 15 patients with AAA serum levels of TNC were measured and correlated with aortic diameters. Moreover, in a murine calcium chloride AAA model, the impact of TNC deficiency on AAA diameter was evaluated. Finally, human VSMC were incubated with TNC to clarify its regulating potential.

RESULTS

In the clinical cohort, there was a trend of correlation between serum TNC levels and AAA diameter (P = 0.055). TNC knock out mice with AAA showed significantly lower diameter ratios compared to the wild-type group (WT) 3 weeks (P < 0.05) and 10 weeks (P < 0.05) after AAA induction. Immunohistochemistry revealed increased TNC expression in aortic tissue from WT with AAA as compared sham-operated mice. Furthermore, WT with AAA showed a more disrupted Elastin structure than TNC knock out mice 10 weeks after AAA induction. In human aortic VSMC, TNC incubation induced expression of remodelling associated proteins.

CONCLUSIONS

TNC might play a causative role in the formation, dilation and progression of AAA. Our results indicate that TNC might be a biomarker as well as a potential therapeutic target in the treatment of AAA.
Rapid evaporative ionization mass spectrometry (intelligent knife) for point-of-care testing in acute aortic dissection surgery
Authors: Davies Hannah A , Caamano-Gutierrez Eva , Sarsby Joscelyn , Chim Ya Hua , Barrett Steve , Nawaytou Omar , Harky Amer , Field Mark , Akhtar Riaz , Madine Jillian
Published: January 2022

OBJECTIVES

Rapid evaporative ionization mass spectrometry (REIMS) can discriminate aneurysmal from normal aortic tissue. Our objective in this work was to probe the integrity of acute dissection tissue using biomechanical, biochemical and histological techniques and demonstrate that REIMS can be used to discriminate identified differences.

METHODS

Human aortic tissue was obtained from patients undergoing surgery for acute aortic dissection. Biomechanical, biochemical and histological assessment was carried out to probe mechanical properties and elastin, collagen and glycosaminoglycan composition of the tissue. Monopolar electrocautery was applied to samples and surgical aerosol aspirated and analysed by REIMS to produce mass spectral data.

RESULTS

Tissue was obtained from 10 patients giving rise to 26 tissue pieces: 10 false lumen (FL), 10 dissection flap and 6 true lumen samples. Models generated from biomechanical and biochemical data showed that FL tissue was distinct from true lumen and dissection flap tissue. REIMS identified the same pattern being able to classify tissue types with 72.4% accuracy and 69.3% precision. Further analysis of REIMS data for FL tissue suggested patients formed 3 distinct clusters. Histological and biochemical assessment revealed patterns of extracellular matrix degradation within the clusters that are associated with altered tissue integrity identified using biomechanical testing.

CONCLUSIONS

Structural integrity of the FL in acute Type A dissection could dictate future clinical distal disease progression. REIMS can detect differences in tissue integrity, supporting its development as a point-of-care test to guide surgical intraoperative decision-making.
A communication procedure between community pharmacists and primary care professionals resolves medication errors and other administrative issues
Authors: Oñatibia-Astibia Ainhoa , Larrañaga Belen , Iribar Josune , Etxeberria Arritxu , Odriozola Nekane , Montero-Muñoz Almudena , Gastelurrutia Miguel Ángel , Bustinduy Ana , Goyenechea Estibaliz
Published: January 2022

Objectives

The aim of this study was to implement a communication procedure, with agreed-upon protocols, to resolve daily medication errors and other administrative issues that require communication between community pharmacists (CPs) and primary healthcare professionals (PHCPs).

Methods

A 6-month pilot study followed by a year-length principal study was carried out in the Donostialdea Integrated Healthcare Organisation (IHO). Afterwards, the project was extended to other IHOs. The CPs identified medication errors or other administrative issues that required communication with PHCPs, contacting the customer service staff by telephone for urgent problems and by email for non-urgent problems.

Key findings

In total, 49 community pharmacies participated in the study. A total of 1179 medication errors and other administrative issues were detected, and over 90% of problems were solved in less than 24 h (n = 1079, 91.5%). Email was the more frequently used communication method (n = 874, 74.1%), and the most prevalent problems were due to absent (n = 766, 65.0%) and expired (n = 226, 19.2%) electronic prescriptions. Most of the participants were satisfied with the programme.

Conclusion

The present communication procedure between CPs and PHCPs is an efficient tool to resolve a variety of challenges that occur in community pharmacies.
Automorphic Lie Algebras and Modular Forms
Authors: Knibbeler Vincent , Lombardo Sara , Veselov Alexander P
Published: January 2022

We introduce and study certain hyperbolic versions of automorphic Lie algebras related to the modular group. Let $\Gamma $ be a finite index subgroup of $\textrm {SL}(2,\mathbb Z)$ with an action on a complex simple Lie algebra $\mathfrak g$, which can be extended to $\textrm {SL}(2,{\mathbb {C}})$. We show that the Lie algebra of the corresponding $\mathfrak {g}$-valued modular forms is isomorphic to the extension of $\mathfrak {g}$ over the usual modular forms. This establishes a modular analogue of a well-known result by Kac on twisted loop algebras. The case of principal congruence subgroups $\Gamma (N), \, N\leq 6$, is considered in more detail in relation to the classical results of Klein and Fricke and the celebrated Markov Diophantine equation. We finish with a brief discussion of the extensions and representations of these Lie algebras.
Deformed Polynuclear Growth in (1+1) Dimensions
Authors: Aggarwal Amol , Borodin Alexei , Wheeler Michael
Published: January 2022

We introduce and study a one parameter deformation of the polynuclear growth (PNG) in (1+1)-dimensions, which we call the $t$-PNG model. It is defined by requiring that, when two expanding islands merge, with probability $t$ they sprout another island on top of the merging location. At $t=0$, this becomes the standard (non-deformed) PNG model that, in the droplet geometry, can be reformulated through longest increasing subsequences of uniformly random permutations or through an algorithm known as patience sorting. In terms of the latter, the $t$-PNG model allows errors to occur in the sorting algorithm with probability $t$. We prove that the $t$-PNG model exhibits one-point Tracy–Widom Gaussian Unitary Ensemble asymptotics at large times for any fixed $t\in [0,1)$, and one-point convergence to the narrow wedge solution of the Kardar–Parisi–Zhang equation as $t$ tends to $1$. We further construct distributions for an external source that are likely to induce Baik–Ben Arous–Péché-type phase transitions. The proofs are based on solvable stochastic vertex models and their connection to the determinantal point processes arising from Schur measures on partitions.
Phylogenomics of Severe Acute Respiratory Syndrome Coronavirus 2 in Emergency Shelters for People Experiencing Homelessness
Authors: Casto Amanda M , Rogers Julia H , Link Amy C , Boeckh Michael , Jackson Michael L , Uyeki Timothy M , Englund Janet A , Starita Lea M , Chu Helen Y
Published: January 2022

Background

Residents and staff of emergency shelters for people experiencing homelessness (PEH) are at high risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The importance of shelter-related transmission of SARS-CoV-2 in this population remains unclear. It is also unknown whether there is significant spread of shelter-related viruses into surrounding communities.

Methods

We analyzed genome sequence data for 28 SARS-CoV-2-positive specimens collected from 8 shelters in King County, Washington between March and October, 2020.

Results

We identified at least 12 separate SARS-CoV-2 introduction events into these 8 shelters and estimated that 57% (16 of 28) of the examined cases of SARS-CoV-2 infection were the result of intrashelter transmission. However, we identified just a few SARS-CoV-2 specimens from Washington that were possible descendants of shelter viruses.

Conclusions

Our data suggest that SARS-CoV-2 spread in shelters is common, but we did not observe evidence of widespread transmission of shelter-related viruses into the general population.