bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimizing Outcomes in Neck Lift Surgery
Authors: O’Daniel Thomas Gerald
Published: February 2021

Background

In certain patients there is an imbalance between the volume of the anterior neck and the mandibular confines that requires reductional sculpting and repositioning of the hyoid to optimize neck-lifting procedures.

Objectives

A quantitative volumetric analysis of the impact of the management of supraplatysmal and subplatysmal structures of the neck by comparing surgical specimens was performed to determine the impact of reduction on cervical contouring.

Methods

In 152 patients undergoing deep cervicoplasty, the frequency of modification of each surgical maneuver and the amount of supraplatysmal and subplatysmal volume removed was measured by a volume-displacement technique.

Results

The mean total volume removed from the supraplatysmal and subplatysmal planes during deep cervicoplasty was 22.3 cm3 with subplatysmal volume representing 73% of the total. Subplatysmal volume was reduced in 152 patients. Deep fat volume was reduced in 96% of patients by a mean of 7 cm3, submandibular gland volume in 76% of patients by a mean of 6.5 cm3, anterior digastric muscle volume in 70% of patients by a mean of 1.8 cm3, perihyoid fascia volume in 32% of patients by a mean of <1 cm3, and mylohyoid volume in 14% of patients by a mean of <1 cm3. The anterior digastric muscles were plicated to reposition the hyoid in 34% of cases. Supraplatysmal fat reduction was 6.3 cm3 in 40% of patients.

Conclusions

The study provides a comprehensive analysis of the impact of volume modification of the central neck during deep cervicoplasty. This objective evaluation of neck volume may help guide clinicians in the surgical planning process and provide a foundation for optimizing cervicofacial rejuvenation techniques.

Level of Evidence: 4
Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family
Authors: Fujimoto Zui , Hong Le Thi Thu , Kishine Naomi , Suzuki Nobuhiro , Kimura Keitarou
Published: February 2021

Bacillus subtilis YabJ protein belongs to the highly conserved YjgF/YER057c/UK114 family, which has a homotrimeric quaternary structure. The dominant allele of yabJ gene that is caused by a single amino acid mutation of Ser103Phe enables poly-γ-glutamic acid (γPGA) production of B. subtilis under conditions where the cell-density signal transduction was disturbed by the loss of DegQ function. X-ray crystallography of recombinant proteins revealed that unlike the homotrimeric wild-type YabJ, the mutant YabJ(Ser103Phe) had a homotetrameric quaternary structure, and the structural change appeared to be triggered by an inversion of the fifth β-strand. The YabJ homotetramer has a hole that is highly accessible, penetrating through the tetramer, and 2 surface concaves as potential ligand-binding sites. Western blot analyses revealed that the conformational change was also induced in vivo by the Ser103Phe mutation.
Metabolomic analysis on blood of transgenic mice overexpressing PGC-1α in skeletal muscle
Authors: Sugimoto Takumi , Uchitomi Ran , Hatazawa Yukino , Miura Shinji , Kamei Yasutomi
Published: February 2021

PGC-1α expression increases in skeletal muscles during exercise and regulates the transcription of many target genes. In this study, we conducted a metabolomic analysis on the blood of transgenic mice overexpressing PGC-1α in its skeletal muscle (PGC-1α-Tg mice) using CE-TOFMS. The blood level of homovanillic acid (dopamine metabolite) and the gene expression of dopamine metabolic enzyme in the skeletal muscle of PGC-1α-Tg mice were high. The blood level of 5-methoxyindoleacetic acid was also high in PGC-1α-Tg mice. The blood levels of branched-chain α-keto acids and β-alanine were low in PGC-1α-Tg mice. These metabolites in the skeletal muscle were present in low concentration. The changes in these metabolites may reflect the skeletal muscle condition with increasing PGC-1α, such as exercise.
Brassica rapaL. activates macrophages via Toll-like receptors
Authors: Takahashi Fuka , Endo Katsunori , Matsui Rina , Yamamoto Kana , Tanaka Sachi
Published: February 2021

Macrophages can initiate innate immune responses against microbes and cancer. The aim of this study was to elucidate the effects of Brassica rapa L. on macrophages. The production of interleukin (IL)-6, tumor necrosis factor (TNF)-α, and interferon-γ induced by the insoluble fraction of B. rapa L. was decreased in macrophage-depleted spleen cells compared with controls. The insoluble fraction of B. rapa L. induced expression of H-2Kb, I-Ab, CD40, and CD86, production of cytokines and nitric oxide, and phagocytic activity in RAW264 cells. After treatment with the insoluble fraction, IL-6 and TNF-α production was significantly decreased by anti-Toll-like receptor (TLR)2 mAb or polymyxin B compared with the control. Furthermore, insoluble fraction-mediated cytokine production was significantly lower in peritoneal macrophages from TLR2−/− and TLR4−/− mice compared with wild-type mice. These results suggest that B. rapa L. is a potentially effective immunomodulator for activating macrophages to prevent infections.
Pomolic acid in persimmon peel suppresses the increase in glycerol-3 phosphate dehydrogenase activity in 3T3-L1 adipocytes
Authors: Izuchi Ryoichi , Katsuki Takahiro
Published: February 2021

Persimmon peels, though usually discarded, are useful sources of nutraceuticals. In this study, persimmon peel–derived pomolic acid was found to suppress the increase in the activity of glycerol-3 phosphate dehydrogenase, a neutral fat synthesis-related enzyme, in 3T3-L1 adipocytes, whereas oleanolic and ursolic acids did not exert this effect. Therefore, persimmon peel may be an effective functional food material.
Unexpected reversal of stereochemistry observed in the addition of methallyltrimethylsilane to a chiral α-keto imide
Authors: Ishii Sayaka , Saito Katsuya , Kuwahara Shigefumi , Enomoto Masaru
Published: February 2021

A Lewis acid–promoted nucleophilic addition of methallyltrimethylsilane to a chiral α-keto imide proceeded with stereoselectivity opposite to that predicted from Soai's report. The difference in the structure of α-keto imides between Soai's and our cases might have affected the diastereofacial selectivity.
Rapid recovery of phytic acid from rice brans using chitosan nanofiber-based porous hydrogels
Authors: Nitta Sachiko , Iwamoto Hiroyuki
Published: February 2021

Phytic acid (PA) is a new type of naturally occurring pharmaceutical for afflictions such as cancer, diabetes, and renal calculi. The efficient, low-cost extraction of PA from biowaste is much sought after. Herein, highly pure PA was obtained from rice bran by adsorption at low pH onto porous chitosan nanofiber hydrogels. Due to the large surface area of the chitosan nanofiber-based porous hydrogels, the adsorption equilibrated within 60 min. Adsorption of PA was influenced by the buffer pH, temperature, and the ratio of chitosan in the hydrogel. PA was recovered by soaking the hydrogel in alkaline solution. After concentrating the solution and washing the residue with ethanol, highly pure sodium phytate was obtained with 32.2%-38.7% yield, as confirmed by Fourier transform infrared and high-performance liquid chromatography. To our knowledge, this is the first report on the recovery of pure PA in high yield without using toxic solvents.
Sea urchin gangliosides exhibit neuritogenic effects in neuronal PC12 cells via TrkA- and TrkB-related pathways
Authors: Wang Xiaoxu , Li Yiyang , Wang Yuliu , Liu Yanjun , Xue Changhu , Cong Peixu , Xu Jie
Published: February 2021

Gangliosides (GLSs) are ubiquitously distributed in all tissues but highly enriched in nervous system. Currently, it is unclear how exogenous GLSs regulate neuritogenesis, although neural functions of endogenous GLSs are widely studied. Herein, we evaluated the neuritogenic activities and mechanism of sea urchin gangliosides (SU-GLSs) in vitro. These different glycosylated SU-GLSs, including GM4(1S), GD4(1S), GD4(2A), and GD4(2G), promoted differentiation of NGF-induced PC12 cells in a dose-dependent and structure-selective manner. Sulfate-type and disialo-type GLSs exhibited stronger neuritogenic effects than monosialoganglioside GM1. Furthermore, SU-GLSs might act as neurotrophic factors possessing neuritogenic effects, via targeting tyrosine-kinase receptors (TrkA and TrkB) and activating MEK1/2-ERK1/2-CREB and PI3K-Akt-CREB pathways. This activation resulted in increased expression and secretion of brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF). These pathways were verified by specific inhibitors. Our results confirmed the neuritogenic functions of SU-GLS in vitro and indicated their potential roles as natural nutrition for neuritogenesis.
Identification of a polyphenol and its antioxidant properties from the roasting reaction of alginic acid
Authors: Doi Sayaka , Shindo Yukino , Masuda Akiko , Oyama Yasuo , Masuda Toshiya
Published: February 2021

The radical scavenging activity of marine polysaccharides was enhanced by their high-temperature treatment (roasting reaction model). The product obtained from alginic acid exhibited maximum activity, and a radical scavenger, alginetin, was identified in the product. Its antioxidant activities were examined by chemical methods, which confirmed that it possessed a stoichiometrically greater antioxidant capacity than that of Trolox.
The influence of the R47H triggering receptor expressed on myeloid cells 2 variant on microglial exosome profiles
Authors: Mallach Anna , Gobom Johan , Zetterberg Henrik , Hardy John , Piers Thomas M , Wray Selina , Pocock Jennifer M
Published: February 2021

Variants in the triggering receptor expressed on myeloid cells 2 gene are linked with an increased risk of dementia, in particular the R47Hhet triggering receptor expressed on myeloid cells 2 variant is linked to late-onset Alzheimer’s disease. Using human induced pluripotent stem cells-derived microglia, we assessed whether variations in the dynamics of exosome secretion, including their components, from these cells might underlie some of this risk. We found exosome size was not altered between common variant controls and R47Hhet variants, but the amount and constitution of exosomes secreted were different. Exosome quantities were rescued by incubation with an ATP donor or with lipids via a phosphatidylserine triggering receptor expressed on myeloid cells 2 ligand. Following a lipopolysaccharide or phagocytic cell stimulus, exosomes from common variant and R47Hhet microglia were found to contain cytokines, chemokines, APOE and triggering receptor expressed on myeloid cells 2. Differences were observed in the expression of CCL22, IL-1β and triggering receptor expressed on myeloid cells 2 between common variant and R47Hhet derived exosomes. Furthermore unlike common variant-derived exosomes, R47Hhet exosomes contained additional proteins linked to negative regulation of transcription and metabolic processes. Subsequent addition of exosomes to stressed neurones showed R47Hhet-derived exosomes to be less protective. These data have ramifications for the responses of microglia in Alzheimer’s disease and may point to further targets for therapeutic intervention.
Mapping Specific Mental Content during Musical Imagery
Authors: Regev Mor , Halpern Andrea R , Owen Adrian M , Patel Aniruddh D , Zatorre Robert J
Published: February 2021

Humans can mentally represent auditory information without an external stimulus, but the specificity of these internal representations remains unclear. Here, we asked how similar the temporally unfolding neural representations of imagined music are compared to those during the original perceived experience. We also tested whether rhythmic motion can influence the neural representation of music during imagery as during perception. Participants first memorized six 1-min-long instrumental musical pieces with high accuracy. Functional MRI data were collected during: 1) silent imagery of melodies to the beat of a visual metronome; 2) same but while tapping to the beat; and 3) passive listening. During imagery, inter-subject correlation analysis showed that melody-specific temporal response patterns were reinstated in right associative auditory cortices. When tapping accompanied imagery, the melody-specific neural patterns were reinstated in more extensive temporal-lobe regions bilaterally. These results indicate that the specific contents of conscious experience are encoded similarly during imagery and perception in the dynamic activity of auditory cortices. Furthermore, rhythmic motion can enhance the reinstatement of neural patterns associated with the experience of complex sounds, in keeping with models of motor to sensory influences in auditory processing.
Etiology of Early-Onset Neonatal Sepsis and Antibiotic Resistance in Bukavu, Democratic Republic of the Congo
Authors: Mulinganya Guy M , Claeys Maud , Balolebwami Serge Z , Bamuleke Bertrand A , Mongane Jules I , Boelens Jerina , Delanghe Joris , De Vos Daniel , Kambale Richard M , Maheshe Ghislain B , Mateso Guy M , Bisimwa Ghislain B , Malembaka Espoir B , Vaneechoutte Mario , Cools Piet , Callens Steven
Published: February 2021

Background

The Democratic Republic of the Congo (DRC) has one of the highest neonatal death rates (between 14% and 28%) in the world. In the DRC, neonatal sepsis causes 15.6% of this mortality, but data on the bacterial etiology and associated drug susceptibility are lacking.

Methods

Hemocultures of 150 neonates with possible early-onset neonatal sepsis (pEOS) were obtained at the Hôpital Provincial Général de Référence de Bukavu (Bukavu, DRC). The newborns with pEOS received an empirical first-line antimicrobial treatment (ampicillin, cefotaxime, and gentamicin) based on the synopsis of international guidelines for the management of EOS that are in line with World Health Organization (WHO) recommendations. Isolates were identified using matrix-assisted laser desorption/ ionization time-of-flight mass spectrophotometry. Antibiotic resistance was assessed using the disk diffusion method.

Results

Fifty strains were obtained from 48 patients and identified. The 3 most prevalent species were Enterobacter cloacae complex (42%), Klebsiella pneumoniae (18%), and Serratia marcescens (12%). Enterobacter cloacae isolates were resistant to all first-line antibiotics. All K. pneumoniae and S. marcescens isolates were resistant to ampicillin, and the majority of the K. pneumoniae and half of the S. marcescens isolates were resistant to both cefotaxime and gentamicin. All E. cloacae complex strains, 89% of K. pneumoniae, and half of S. marcescens had an extended-spectrum ß-lactamase phenotype.

Conclusions

The most prevalent pathogens causing EOS in Bukavu were E. cloacae complex, K. pneumoniae, and S. marcescens. Most of these isolates were resistant to the WHO-recommended antibiotics.
Spatial dynamics of Chinese Muntjac related to past and future climate fluctuations
Authors: Sun Zhonglou , Orozco-terWengel Pablo , Chen Guotao , Sun Ruolei , Sun Lu , Wang Hui , Shi Wenbo , Zhang Baowei
Published: February 2021

Climate fluctuations in the past and in the future are likely to result in population expansions, shifts, or the contraction of the ecological niche of many species, and potentially leading to the changes in their geographical distributions. Prediction of suitable habitats has been developed as a useful tool for the assessment of habitat suitability and resource conservation to protect wildlife. Here, we model the ancestral demographic history of the extant modern Chinese Muntjac Muntiacus reevesi populations using approximate Bayesian computation (ABC) and used the maximum entropy model to simulate the past and predict the future spatial dynamics of the species under climate oscillations. Our results indicated that the suitable habitats for the M. reevesi shifted to the Southeast and contracted during the Last Glacial Maximum, whereas they covered a broader and more northern position in the Middle Holocene. The ABC analyses revealed that the modern M. reevesi populations diverged in the Middle Holocene coinciding with the significant contraction of the highly suitable habitat areas. Furthermore, our predictions suggest that the potentially suitable environment distribution for the species will expand under all future climate scenarios. These results indicated that the M. reevesi diverged in the recent time after the glacial period and simultaneously as its habitat’s expanded in the Middle Holocene. Furthermore, the past and future climate fluctuation triggered the change of Chinese muntjac spatial distribution, which has great influence on the Chinese muntjac’s population demographic history.
Back to the vinyl age: a narrative report of a total computer blackout at a large university medical centre
Authors: Lehmann Lorenz H , Meder Benjamin
Published: February 2021

We report here our experience during a total blackout of all computer systems at a large-scale medical university centre lasting for almost 2 days, affecting not only the hospital information system but also all picture archieving systems, access to laboratory data, office, and email software and even the personnel’s ability to log into their accounts. While initially threatening, staff quickly adapted to the situation and the promise of ‘digital health’ to enable more time for the patient and improve communication, was essentially fulfilled when our computer system was totally down. Based on our experience, we recommend an involvement of health professionals and their medical societies in every step of the digital transformation to accomplish this mission in a responsible, safe, and human-centred way.
Fast and inexpensive whole-genome sequencing library preparation from intact yeast cells
Authors: Vonesch Sibylle C , Li Shengdi , Szu Tu Chelsea , Hennig Bianca P , Dobrev Nikolay , Steinmetz and Lars M
Published: February 2021

Through the increase in the capacity of sequencing machines massively parallel sequencing of thousands of samples in a single run is now possible. With the improved throughput and resulting drop in the price of sequencing, the cost and time for preparation of sequencing libraries have become the major bottleneck in large-scale experiments. Methods using a hyperactive variant of the Tn5 transposase efficiently generate libraries starting from cDNA or genomic DNA in a few hours and are highly scalable. For genome sequencing, however, the time and effort spent on genomic DNA isolation limit the practicability of sequencing large numbers of samples. Here, we describe a highly scalable method for preparing high-quality whole-genome sequencing libraries directly from Saccharomyces cerevisiae cultures in less than 3 h at 34 cents per sample. We skip the rate-limiting step of genomic DNA extraction by directly tagmenting lysed yeast spheroplasts and add a nucleosome release step prior to enrichment PCR to improve the evenness of genomic coverage. Resulting libraries do not show any GC bias and are comparable in quality to libraries processed from genomic DNA with a commercially available Tn5-based kit. We use our protocol to investigate CRISPR/Cas9 on- and off-target edits and reliably detect edited variants and shared polymorphisms between strains. Our protocol enables rapid preparation of unbiased and high-quality, sequencing-ready indexed libraries for hundreds of yeast strains in a single day at a low price. By adjusting individual steps of our workflow, we expect that our protocol can be adapted to other organisms.
De novo genome assembly of the tobacco hornworm moth (Manduca sexta)
Authors: Gershman Ariel , Romer Tatiana G , Fan Yunfan , Razaghi Roham , Smith Wendy A , Timp Winston
Published: February 2021

The tobacco hornworm, Manduca sexta, is a lepidopteran insect that is used extensively as a model system for studying insect biology, development, neuroscience, and immunity. However, current studies rely on the highly fragmented reference genome Msex_1.0, which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. We present a new reference genome for M. sexta, JHU_Msex_v1.0, applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly is 470 Mb and is ∼20× more continuous than the original assembly, with scaffold N50 > 14 Mb. We annotated the assembly by lifting over existing annotations and supplementing with additional supporting RNA-based data for a total of 25,256 genes. The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of the M. sexta genome improves resequencing studies and benefits future research on M. sexta as a model organism.
MoBPSweb: A web-based framework to simulate and compare breeding programs
Authors: Pook Torsten , Büttgen Lisa , Ganesan Amudha , Ha Ngoc-Thuy , Simianer Henner
Published: February 2021

In this study, we introduce a new web-based simulation framework (“MoBPSweb”) that combines a unified language to describe breeding programs with the simulation software MoBPS, standing for “Modular Breeding Program Simulator.” Thereby, MoBPSweb provides a flexible environment to log, simulate, evaluate, and compare breeding programs. Inputs can be provided via modules ranging from a Vis.js-based environment for “drawing” the breeding program to a variety of modules to provide phenotype information, economic parameters, and other relevant information. Similarly, results of the simulation study can be extracted and compared to other scenarios via output modules (e.g., observed phenotypes, the accuracy of breeding value estimation, inbreeding rates), while all simulations and downstream analysis are executed in the highly efficient R-package MoBPS.
Heuristic hyperparameter optimization of deep learning models for genomic prediction
Authors: Han Junjie , Gondro Cedric , Reid Kenneth , Steibel Juan P
Published: February 2021

There is a growing interest among quantitative geneticists and animal breeders in the use of deep learning (DL) for genomic prediction. However, the performance of DL is affected by hyperparameters that are typically manually set by users. These hyperparameters do not simply specify the architecture of the model; they are also critical for the efficacy of the optimization and model-fitting process. To date, most DL approaches used for genomic prediction have concentrated on identifying suitable hyperparameters by exploring discrete options from a subset of the hyperparameter space. Enlarging the hyperparameter optimization search space with continuous hyperparameters is a daunting combinatorial problem. To deal with this problem, we propose using differential evolution (DE) to perform an efficient search of arbitrarily complex hyperparameter spaces in DL models, and we apply this to the specific case of genomic prediction of livestock phenotypes. This approach was evaluated on two pig and cattle datasets with real genotypes and simulated phenotypes (N = 7,539 animals and M = 48,541 markers) and one real dataset (N = 910 individuals and M = 28,916 markers). Hyperparameters were evaluated using cross-validation. We compared the predictive performance of DL models using hyperparameters optimized by DE against DL models with “best practice” hyperparameters selected from published studies and baseline DL models with randomly specified hyperparameters. Optimized models using DE showed a clear improvement in predictive performance across all three datasets. DE optimized hyperparameters also resulted in DL models with less overfitting and less variation in predictive performance over repeated retraining compared to non-optimized DL models.
Characterization of a pericentric inversion in plateau fence lizards (Sceloporus tristichus): evidence from chromosome-scale genomes
Authors: Bedoya Ana M , Leaché Adam D
Published: February 2021

Spiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n = 36 chromosomes, Sceloporus exhibits substantial karyotype variation ranging from 2n =  22 to 46 chromosomes. We present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n =  22 with six pairs of macrochromosomes and five pairs of microchromosomes and a pericentric inversion polymorphism on chromosome 7 that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84–1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in ∼15K predicted gene models. Our assemblies confirmed the presence of a 4.62-Mb pericentric inversion on chromosome 7, which contains 62 annotated coding genes with known functions. In addition, we collected population genomics data using double digest RAD-sequencing for 44 S. tristichus to estimate population structure and phylogeny across the Colorado Plateau. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone.
EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture
Authors: Costa-Neto Germano , Galli Giovanni , Carvalho Humberto Fanelli , Crossa José , Fritsche-Neto Roberto
Published: February 2021

Envirotyping is an essential technique used to unfold the nongenetic drivers associated with the phenotypic adaptation of living organisms. Here, we introduce the EnvRtype R package, a novel toolkit developed to interplay large-scale envirotyping data (enviromics) into quantitative genomics. To start a user-friendly envirotyping pipeline, this package offers: (1) remote sensing tools for collecting (get_weather and extract_GIS functions) and processing ecophysiological variables (processWTH function) from raw environmental data at single locations or worldwide; (2) environmental characterization by typing environments and profiling descriptors of environmental quality (env_typing function), in addition to gathering environmental covariables as quantitative descriptors for predictive purposes (W_matrix function); and (3) identification of environmental similarity that can be used as an enviromic-based kernel (env_typing function) in whole-genome prediction (GP), aimed at increasing ecophysiological knowledge in genomic best-unbiased predictions (GBLUP) and emulating reaction norm effects (get_kernel and kernel_model functions). We highlight literature mining concepts in fine-tuning envirotyping parameters for each plant species and target growing environments. We show that envirotyping for predictive breeding collects raw data and processes it in an eco-physiologically smart way. Examples of its use for creating global-scale envirotyping networks and integrating reaction-norm modeling in GP are also outlined. We conclude that EnvRtype provides a cost-effective envirotyping pipeline capable of providing high quality enviromic data for a diverse set of genomic-based studies, especially for increasing accuracy in GP across untested growing environments.
Why are rare variants hard to impute? Coalescent models reveal theoretical limits in existing algorithms
Authors: Si Yichen , Vanderwerff Brett , Zöllner Sebastian
Published: February 2021

Genotype imputation is an indispensable step in human genetic studies. Large reference panels with deeply sequenced genomes now allow interrogating variants with minor allele frequency < 1% without sequencing. Although it is critical to consider limits of this approach, imputation methods for rare variants have only done so empirically; the theoretical basis of their imputation accuracy has not been explored. To provide theoretical consideration of imputation accuracy under the current imputation framework, we develop a coalescent model of imputing rare variants, leveraging the joint genealogy of the sample to be imputed and reference individuals. We show that broadly used imputation algorithms include model misspecifications about this joint genealogy that limit the ability to correctly impute rare variants. We develop closed-form solutions for the probability distribution of this joint genealogy and quantify the inevitable error rate resulting from the model misspecification across a range of allele frequencies and reference sample sizes. We show that the probability of a falsely imputed minor allele decreases with reference sample size, but the proportion of falsely imputed minor alleles mostly depends on the allele count in the reference sample. We summarize the impact of this error on genotype imputation on association tests by calculating the r2 between imputed and true genotype and show that even when modeling other sources of error, the impact of the model misspecification has a significant impact on the r2 of rare variants. To evaluate these predictions in practice, we compare the imputation of the same dataset across imputation panels of different sizes. Although this empirical imputation accuracy is substantially lower than our theoretical prediction, modeling misspecification seems to further decrease imputation accuracy for variants with low allele counts in the reference. These results provide a framework for developing new imputation algorithms and for interpreting rare variant association analyses.
Maize centromeric chromatin scales with changes in genome size
Authors: Wang Na , Liu Jianing , Ricci William A , Gent Jonathan I , Dawe R Kelly
Published: February 2021

Centromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.
Delirium in Older Patients With COVID-19: Prevalence, Risk Factors, and Clinical Relevance
Authors: Mendes Aline , Herrmann François R , Périvier Samuel , Gold Gabriel , Graf Christophe E , Zekry Dina
Published: February 2021

Background

Delirium prevalence increases with age and is associated with poor outcomes. We aimed to investigate the prevalence and risk factors for delirium in older patients hospitalized with COVID-19, as well as its association with length of stay and mortality.

Method

This was a retrospective study of patients aged 65 years and older hospitalized with COVID-19. Data were collected from computerized medical records and all patients had delirium assessment at admission. Risk factors for delirium as well as the outcomes mentioned above were studied by 2-group comparison, logistic regression, and Cox proportional hazard models.

Results

Of a total of 235 Caucasian patients, 48 (20.4%) presented with delirium, which was hypoactive in 41.6% of cases, and hyperactive and mixed in 35.4% and 23.0%, respectively. Patients with cognitive impairment had a nearly 4 times higher risk of developing delirium compared to patients who were cognitively normal before SARS-CoV-2 infection (odds ratio 3.7; 95% CI: 1.7–7.9, p = .001). The presence of delirium did not modify the time from symptoms’ onset to hospitalization or the length of stay in acute care, but it was associated with an increased risk of dying (hazard ratio 2.1; 95% CI: 1.2–3.7, p = .0113).

Conclusion

Delirium was a prevalent condition in older people admitted with COVID-19 and preexisting cognitive impairment was its main risk factor. Delirium was associated with higher in-hospital mortality. These results highlight the importance of early recognition of delirium especially when premorbid cognitive comorbidities are present.
Cocomposing an Aesthetic Self Through Play: Toward a Transformative Framework for Dementia Care
Authors: Li Bing Yu
Published: February 2021

Background and Objectives

Aging and deterioration mark a new phase in many older adults’ life, highlighting the importance of creativity and imagination. This article introduces the implementation of an innovative program, Play Intervention for Dementia, at a nursing home in Hong Kong, with emphasis on its contribution to the conceptual framework for understanding the selfhood of older adults with dementia.

Research Design and Methods

As a community-based participatory action research project, this study democratized knowledge production by integrating voices of practitioners with diverse backgrounds through video-based methods.

Results

Play, as an activity replete with free expressions and impulsive interactions, is an ideal realm for exploring and establishing selfhood with older adults with dementia. It has been found that “aesthetic self,” an alternative self emerging from immediate aesthetic experience and carrying transformative power within the caring relationship, is a necessary element of self-construction in life with dementia.

Discussion and Implications

Integrating theories and practice, this framework provides a new lens for understanding and responding to selfhood, disease, and life.
NEU1 is more abundant in uveitic retina with concomitant desialylation of retinal cells
Authors: Lorenz Lea , Amann Barbara , Hirmer Sieglinde , Degroote Roxane L , Hauck Stefanie M , Deeg Cornelia A
Published: February 2021

Desialylation of cell surface glycoproteins carried out by sialidases affects various immunological processes. However, the role of neuraminidase 1 (NEU1), one of the four mammalian sialidases, in inflammation and autoimmune disease is not completely unraveled to date. In this study, we analyzed the retinal expression of NEU1 in equine recurrent uveitis (ERU), a spontaneous animal model for autoimmune uveitis. Mass spectrometry revealed significantly higher abundance of NEU1 in retinal Müller glial cells (RMG) of ERU-diseased horses compared to healthy controls. Immunohistochemistry uncovered NEU1 expression along the whole Müller cell body in healthy and uveitic states and confirmed higher abundance in inflamed retina. Müller glial cells are the principal macroglial cells of the retina and play a crucial role in uveitis pathogenesis. To determine whether higher expression levels of NEU1 in uveitic RMG correlate with the desialylation of retinal cells, we performed lectin-binding assays with sialic acid-specific lectins. Through these experiments, we could demonstrate a profound loss of both α2-3- and α2-6-linked terminal sialic acids in uveitis. Hence, we hypothesize that the higher abundance of NEU1 in uveitic RMG plays an important role in the pathogenesis of uveitis by desialylation of retinal cells. As RMG become activated in the course of uveitis and actively promote inflammation, we propose that NEU1 might represent a novel activation marker for inflammatory RMG. Our data provide novel insights in the expression and implication of NEU1 in inflammation and autoimmune disease.
Come together to promote health: case study and theoretical perspectives from a Kenyan community-based program
Authors: Goodman Michael L , Elliott Aleisha J , Gitari Stanley , Keiser Philip , Raimer-Goodman Lauren , Seidel Sarah E
Published: February 2021

Over the past four decades, group-based microfinance programs have spread rapidly throughout south Asia, sub-Saharan Africa and Latin America. Recent evaluations of the programs have identified social capital as a common byproduct of frequent association by members, increasing trust, belonging and normative influence. Concurrently, social capital is increasingly recognized as an important health determinant. We present an overview of a program intervention operating in Kenya that utilizes a microfinance approach to produce social capital, and seeks to leverage that social capital to promote health at three levels—the village, group, and individual. A theory of change is presented for each of these three levels, demonstrating conceptually and with program examples how social capital can be applied to promote health. Related social theories and approaches, further research and program directions are given for each of the three levels. We identify potential to improve a broad range of health outcomes through this innovative model, which requires engagement with health promotion researchers and planners in low- and middle-income countries for further refinement and validation.
Evaluation of soybean (Glycine max L.) adaptation to northern European regions under different agro-climatic scenarios
Authors: Boulch Guénolé , Elmerich Chloé , Djemel Amina , Lange Bastien
Published: February 2021

Soybean is a candidate crop to increase the independency of Europe in leguminous protein crops. However, its adaptation to northern European regions is not yet well defined due to the lack of long-term references. Herein, we simulated soybean yield potential in northern France and identified the main yield limiting factors under rainfed vs. irrigated conditions. Two cultivars representing maturity groups 000 and 00 were planted within three different trials. Leaf area index, shoot and pod biomass, main phenological stages and yield were recorded to evaluate CROPGRO-soybean model predictability. Adjustment of genetic coefficients was performed prior to simulate yield on 21-years weather database (1999–2018) at Beauvais (France, N 49.46°, E 2.07°) and Estrées-Mons (France, N 49.88°, E 3.01°) under different water regimes and planting dates. Predictions showed that adding irrigation at grain filling period would increase yield potential to the level of non-water limited scenarios. Although simulated yield variability is reduced with irrigation, the remaining variability suggests that water is not the only yield-limiting factor. A tentative explanation is proposed by deriving environmental covariates from the model. The analysis confirmed the importance of precipitation amount (optimum around 200 mm) and duration (optimum around 60 days) of the flowering to physiological maturity period under rainfed conditions. Under irrigated conditions, increasing evapotranspiration and average minimum temperature affected simulated yield positively while increasing the number of days below 10 °C had a negative impact. These results give insights for soybean crop management and bring indications to breeders for adapting the existing genetic material to northern Europe.
Effects of different defatted rice bran sources and processing technologies on nutrient digestibility in cannulated growing pigs
Authors: Huang Bingbing B , Sun Zhiqiang Q , Wang Li , Wang Lu , Shi Huangwei W , Hu Qile L , Lyu Zhiqian Q , Li Defa F , Zang Jianjun J , Lai Changhua H
Published: February 2021

The objective of this study was to evaluate the effects of different defatted rice bran (DFRB) sources and processing technologies on nutrient digestibility in different intestinal segments of pigs. Nine barrows with T-cannula in the distal ileum were randomly allotted to nine different sources in which oil was pressed extracted for seven sources and was solvent extracted for two sources. The experiment contained 6 periods of 12 d, including 8 d for diet adaptation, 2 d for fecal collection, and 2 d for digesta collection. The apparent ileal digestibility (AID) of dry matter (DM), ash, total dietary fiber (TDF), insoluble dietary fiber (IDF), neutral detergent fiber (NDF), acid detergent fiber (ADF), and hemicellulose in different sources of DFRB was quite variable. There were no differences in the AID of dietary gross energy (GE), organic matter (OM), ether extract (EE), crude protein (CP), and soluble dietary fiber (SDF) between different sources of DFRB. There were no differences in the AID of dietary EE, TDF, IDF, and hemicellulose between different processing technologies. Pressed DFRBs have greater (P < 0.05) average AID of dietary GE, DM, ash, OM, CP, SDF, and NDF and lower (P < 0.01) ADF compared with solvent-extracted DFRBs. The apparent total tract digestibility (ATTD) of most of the dietary nutrients, except for the ATTD of dietary EE, SDF, and hemicellulose, significantly varied in different sources of DFRB (P < 0.05). In addition, pressed DFRB had greater (P < 0.05) ATTD of dietary SDF, NDF, ADF, and hemicellulose compared with solvent-extracted DFRB. The apparent hindgut digestibility (AHD) of dietary DM, SDF, NDF, and ADF significantly varied (P <0.05) in different sources of DFRB. Exception with DM, there are no differences in the AHD of nutrients digestibility between pressed DFRB and solvent-extracted DFRB. In conclusion, DFRB in different sources and processing technologies with different physicochemical properties had different effects on nutrient digestibility in the foregut and hindgut of pigs.
Home range, habitat selection, density, and diet of golden jackals in the Eastern Plains Landscape, Cambodia
Authors: Kamler Jan F , Minge Christin , Rostro-García Susana , Gharajehdaghipour Tazarve , Crouthers Rachel , In Visattha , Pay Chen , Pin Chanratana , Sovanna Prum , Macdonald David W
Published: February 2021

We used radiocollars and GPS collars to determine the movements and habitat selection of golden jackals (Canis aureus) in a seasonally dry deciduous forest with no human settlements in eastern Cambodia. We also collected and analyzed 147 scats from jackals to determine their seasonal diet and prey selection. The mean (± SE) annual size of home-range ranges (47.1 ± 2.5 km2; n = 4), which were mutually exclusive between mated pairs, was considerably larger than that previously reported for this species, resulting in an extremely low density (0.01 jackal/km2). The unusually large home ranges and low density probably were due to the harsh dry season when most understory vegetation is burned and nearly all waterholes dry up, thereby causing a large seasonal decline in the availability of small vertebrate prey. Resident groups consisted of an alpha pair, but no betas, and were situated only in areas not occupied by leopards (Panthera pardus) and dholes (Cuon alpinus). Jackals avoided dense forests and streams, and had a strong selection for dirt roads, possibly to avoid larger predators. Overall the jackal diet was diverse, with at least 16 prey items identified, and there was no significant difference in diet composition between the cool-dry and hot-dry seasons. Scat analysis showed that the main food items consumed by jackals were processional termites (Hospitalitermes spp.; 26% biomass consumed), followed by wild pig (Sus scrofa; 20%), muntjac (Muntiacus vaginalis; 20%), and civets (17%). Compared to available biomass, jackals were not random in their consumption of ungulates because muntjac were selectively consumed over larger ungulate species. Dietary overlap with dholes and leopards was relatively low, and consumption patterns indicated jackals were preying on ungulates rather than scavenging from kills of larger carnivores. Our results showed that the jackal is an extremely adaptable and opportunistic species that exhibits unique behaviors to survive in an extreme environment near the edge of its distribution.
Post-operative abscess in inguinal hernial sac—case report of an unusual complication of perforated acute appendicitis
Authors: Chan Chin Bruno M , Aakif Muhammad , Khan Ata U
Published: February 2021

Acute appendicitis is a common condition, with a lifetime risk of 7–8%. Common complications of surgical management include bleeding, bowel injury, residual abscess formation and post-operative ileus. This is a rare case of a 50-year-old male who underwent laparoscopic converted to open appendicectomy for perforated acute appendicitis, with a complication of post-operative fluid collection that extended into the right inguinal hernia sac.
The Death of Molly Schultz: Race, Magic, and the Law in the Post-slavery Caribbean
Authors: De Barros Juanita
Published: February 2021

This article uses a singular event, the murder trial of a multiracial group of men and women accused of killing a young white girl, to examine the complex interactions between individual experiences and larger social patterns in the twentieth-century British Caribbean. It explores responses to the tragic death of a young child in British Guiana, Molly Schultz, notably its political and legal repercussions, by focusing on the Afro- and Indo-Guianese accused, the colonial prosecutors, and the multiethnic opposition politicians who became involved. Colonial officials took advantage of this death to pass two pieces of legislation. One strengthened the local anti-obeah (magic) law, a change that remained in effect until the late twentieth century. The second was a new law that effectively prevented poor, non-white Guianese from sitting on juries, part of an official attempt to help buttress white political power and a response to the racial fears of a colonial elite. I argue that the quotidian struggles of daily life shaped the lives and the stories of those accused of Molly Schultz’s murder. Their experiences helped create the context in which these men and women became involved in the case and informed their explanations of their actions; their accounts in turn influenced the official version of Molly Schultz’s death, including the role of obeah. The Indo- and Afro-creole lawyers and politicians who took up the case may not have represented themselves as believing in the magical practices purportedly at the center of these events, but they recognized their political significance. Contemporary racial tensions and political considerations influenced the legal proceedings but the everyday lives of ordinary Guianese helped shaped the outcome and the surrounding debates.
Challenging Custodialism: Families and Eugenic Institutionalization at the Pennsylvania Training School for Feeble-Minded Children at Elwyn
Authors: Chamberlain Chelsea D
Published: February 2021

Historians have described how powerful eugenic ideologies fueled the rapid expansion of custodial institutionalization of the so-called feebleminded in the early twentieth century. Using new sources from the recently opened archive of the Pennsylvania Training School for Feeble-Minded Children at Elwyn, this article argues that in practice, this transition to custodialism was difficult, uneven, and subject to constant compromise. Institutional residents and their families contested expert prognoses and disciplinary methods and maintained relationships across institutional boundaries. Their vernacular ideas about mental impairment, curability, and the purpose of institutional segregation produced a gap between eugenic discourse and institutional life. The challenges that residents and their families levied were neither absolute nor consistent: their force and success depended on their class status, community contexts, and most significantly, the perceived severity of a resident’s impairment. Residents with greater care needs were frequently relegated to the background, not only in psycho-medical professionals’ treatises and administration but in the expectations that families brought to bear on the institution. Decades before institutionalized people and their families formed political advocacy groups that struggled for deinstitutionalization and civil rights, they fought individual battles that pitted their intimate knowledge against expertise. Although their victories were small and statistically rare, they tested the bounds of psycho-medical authority and established the ideological and practical limits of eugenic mass institutionalization.