bluuebunny/crossref_metadata_2025 huggingface dataset:
Abundant and Rare Bacterial Taxa Structuring Differently in Sediment and Water in Thermokarst Lakes in the Yellow River Source Area, Qinghai-Tibet Plateau
Authors: Ren Ze , Zhang Cheng , Li Xia , Ma Kang , Cui Baoshan
Published: March 2022

Thermokarst lakes are forming from permafrost thaw and are severely affected by accelerating climate change. Sediment and water in these lakes are distinct habitats but closely connected. However, our understanding of the differences and linkages between sediment and water in thermokarst lakes remains largely unknown, especially from the perspective of community assembly mechanisms. Here, we examined bacterial communities in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau. Bacterial taxa were divided into abundant and rare according to their relative abundance, and the Sorensen dissimilarity (βsor) was partitioned into turnover (βturn) and nestedness (βnest). The whole bacterial communities and the abundant and rare subcommunities differed substantially between sediment and water in taxonomical composition, α-diversity, and β-diversity. Sediment had significantly lower α-diversity indexes but higher β-diversity than water. In general, bacterial communities are predominantly governed by strong turnover processes (βturn/βsor ratio of 0.925). Bacterial communities in sediment had a significantly higher βturn/βsor ratio than in water. Abundant subcommunities were significantly lower in the βturn/βsor ratio compared with rare subcommunities. The results suggest that the bacterial communities of thermokarst lakes, especially rare subcommunities or particularly in sediment, might be strongly structured by heterogeneity in the source material, environmental filtering, and geographical isolation, leading to compositionally distinct communities. This integral study increased our current knowledge of thermokarst lakes, enhancing our understanding of the community assembly rules and ecosystem structures and processes of these rapidly changing and vulnerable ecosystems.
Phylogeny and Ecology of Trebouxia Photobionts From Bolivian Lichens
Authors: Kosecka Magdalena , Kukwa Martin , Jabłońska Agnieszka , Flakus Adam , Rodriguez-Flakus Pamela , Ptach Łucja , Guzow-Krzemińska Beata
Published: March 2022

In the past few years, new phylogenetic lineages inTrebouxiawere detected as a result of molecular approaches. These studies included symbiont selectivity in lichen communities, transects along altitudinal gradients at local and global scales and the photobiont diversity in local populations of lichen-forming fungal species. In most of these studies, phylogenetic and haplotype analyses based on the internal transcribed spacer (ITS) locus have continuously allowed the recognition of new monophyletic lineages, which suggests that still numerous undiscoveredTrebouxialineages can be hidden in lichens from unexplored areas, especially in the tropics. Here, we estimated the biodiversity of photobionts in Bolivian Andean vegetation and assessed their specificity. About 403 lichen samples representing 42 genera, e.g.,Haematomma,Heterodermia,Hypotrachyna,Lecanora,Lepra,Leucodermia,Parmotrema,Pertusaria,Polyblastidium, andUsnea, containingTrebouxiaphotobionts, were analyzed. ITS ribosomal DNA (rDNA) andrbcL markers were used. We obtainedTrebouxiasequences from Bolivian samples belonging to already described clades A, C, I, and S. Thirty-nineTrebouxialineages were distinguished within these clades, while 16 were new. To reveal the structure of the community of Bolivian photobionts and their relationships with mycobionts, the comparative effects of climate, altitude, geographical distances, substrate, and habitat type, as well as functional traits of lichens such as growth forms, propagation mode and secondary metabolites, were analyzed. Furthermore, new Bolivian records were included in analysis on a global scale. In our study, the mycobiont genus or even species are the most important factors correlated with photobiont identity. Moreover, we revealed that the community of Bolivian photobionts is shaped by altitude.
A Visualized Isothermal Amplification Method for Rapid and Specific Detection of Emetic and Non-emetic Bacillus cereus in Dairy Products
Authors: Wang Lei , Yang Huansen , Wang Kun , Yang Haitao , Zhao Mengdi , Shang Yuping , Wang Fang , Dong Jingquan , Zhao Weiguo , Li Li , Liang Wei , Wang Yan
Published: March 2022

Bacillus cereus is widely distributed in foods, especially dairy products, and can lead to diarrhea (non-emetic B. cereus) and emesis (emetic B. cereus). Although diarrhea due to B. cereus is usually mild, emesis can lead to acute encephalopathy and even death. To develop rapid and sensitive detection methods for B. cereus in foods, specific primers targeting the gyrase B (gyrB) and cereulide synthetase (ces) genes were designed and screened using recombinase polymerase amplification (RPA). Probes and base substitutions were introduced to improve specificity and eliminate primer-dependent artifacts. The 5′ ends of the reverse primers and probes were modified with biotin and fluorescein isothiocyanate for detection of RPA products on a lateral flow strip (LFS). The developed RPA-LFS assay allows detection within 20 min at 37°C with no cross-reactivity with other foodborne pathogens. The limit of detection was 104 copies/ml and 102 CFU/ml in pure cultures and milk, respectively. Comparisons with established methods using cream obtained similar results. A specific, rapid, and sensitive RPA-LFS assay was successfully developed for on-site detection of B. cereus in dairy products to distinguish emetic from non-emetic strains.
Photobiont Diversity in Lichen Symbioses From Extreme Environments
Authors: De Carolis Roberto , Cometto Agnese , Moya Patricia , Barreno Eva , Grube Martin , Tretiach Mauro , Leavitt Steven D. , Muggia Lucia
Published: March 2022

Fungal–algal relationships—both across evolutionary and ecological scales—are finely modulated by the presence of the symbionts in the environments and by the degree of selectivity and specificity that either symbiont develop reciprocally. In lichens, the green algal genus Trebouxia Puymaly is one of the most frequently recovered chlorobionts. Trebouxia species-level lineages have been recognized on the basis of their morphological and phylogenetic diversity, while their ecological preferences and distribution are still only partially unknown. We selected two cosmopolitan species complexes of lichen-forming fungi as reference models, i.e., Rhizoplaca melanophthalma and Tephromela atra, to investigate the diversity of their associated Trebouxia spp. in montane habitats across their distributional range worldwide. The greatest diversity of Trebouxia species-level lineages was recovered in the altitudinal range 1,000–2,500 m a.s.l. A total of 10 distinct Trebouxia species-level lineages were found to associate with either mycobiont, for which new photobionts are reported. One previously unrecognized Trebouxia species-level lineage was identified and is here provisionally named Trebouxia “A52.” Analyses of cell morphology and ultrastructure were performed on axenically isolated strains to fully characterize the new Trebouxia “A52” and three other previously recognized lineages, i.e., Trebouxia “A02,” T. vagua “A04,” and T. vagua “A10,” which were successfully isolated in culture during this study. The species-level diversity of Trebouxia associating with the two lichen-forming fungi in extreme habitats helps elucidate the evolutionary pathways that this lichen photobiont genus traversed to occupy varied climatic and vegetative regimes.
Diagnostic Performance of a Novel CXCL10 mRNA Release Assay for Mycobacterium tuberculosis Infection
Authors: Pan Liping , Huang Mailing , Jia Hongyan , Deng Guofang , Chen Yu , Wei Rongrong , Zhang Mingxia , Li Xin , Sun Qi , Fang Mutong , Ren Pengfei , Xing Aiying , Chen Qi , Li Xinxin , Du Boping , Chen Tao , Gao Mengqiu , Zhang Zongde
Published: March 2022

One-fourth of the world’s population has been infected with Mycobacterium tuberculosis (M.tb). Although interferon-gamma release assays (IGRAs) have been shown to be valid methods for identifying M.tb infection and auxiliary methods for diagnosis of active tuberculosis (TB), lower sensitivity and higher indeterminate rate were often detected among immunosuppressed patients. IP-10 was an alternative biomarker due to the higher expression level after M.tb antigen stimulation, but whether CXCL10 mRNA (the gene that transcribes for the IP-10 protein) can be used as a target for M.tb infection diagnosis was limited. Therefore, we aimed to evaluate the performance of a novel M.tb-specific CXCL10 mRNA release assay in diagnosis of M.tb infection. Suspected TB patients and healthy controls were prospectively recruited between March 2018 and November 2019 from three hospitals in China. CXCL10 mRNA release assay and traditional interferon-gamma release assay (T-SPOT.TB) were simultaneously performed on peripheral blood. Of the 1,479 participants enrolled in the study, 352 patients with definite TB and 153 healthy controls were analyzed. CXCL10 mRNA release assay provided a sensitivity of 93.9% (95% CI = 90.8–96.2%) and a specificity of 98.0% (95% CI = 94.3–99.6%) in the diagnosis of M.tb infection, respectively, while T-SPOT.TB gave a sensitivity of 94.5% (95% CI = 91.5–96.6%) and a specificity of 100% (95% CI = 97.6–100.0%) in the diagnosis of M.tb infection, respectively. The diagnostic performance of CXCL10 mRNA release assay was consistent with T-SPOT.TB, with a total coincidence rate of 95.0% (95% CI = 93.0–96.9%) and a Cohen’s kappa value of 0.89 (0.84–0.93, p < 0.001). However, among TB patients with HIV co-infection (n = 14), CXCL10 mRNA release assay presented significantly higher positive rate [92.9% (66.1–99.8%) vs. 61.5% (31.6–86.1%), p = 0.029] than those of T-SPOT.TB. These results suggested that M.tb-specific CXCL10 mRNA was a novel and useful target in the diagnosis of M.tb infection.
Genome Sequencing of Rahnella victoriana JZ-GX1 Provides New Insights Into Molecular and Genetic Mechanisms of Plant Growth Promotion
Authors: Kong Wei-Liang , Wang Wei-Yu , Zuo Sheng-Han , Wu Xiao-Qin
Published: March 2022

Genomic information for bacteria within the genus Rahnella remains limited. Rahnella sp. JZ-GX1 was previously isolated from the Pinus massoniana rhizosphere in China and shows potential as a plant growth-promoting (PGP) bacterium. In the present work, we combined the GridION Nanopore ONT and Illumina sequencing platforms to obtain the complete genome sequence of strain JZ-GX1, and the application effects of the strain in natural field environment was assessed. The whole genome of Rahnella sp. JZ-GX1 comprised a single circular chromosome (5,472,828 bp, G + C content of 53.53%) with 4,483 protein-coding sequences, 22 rRNAs, and 77 tRNAs. Based on whole genome phylogenetic and average nucleotide identity (ANI) analysis, the JZ-GX1 strain was reidentified as R. victoriana. Genes related to indole-3-acetic acid (IAA), phosphorus solubilization, nitrogen fixation, siderophores, acetoin, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, gamma-aminobutyric acid (GABA) production, spermidine and volatile organic compounds (VOCs) biosynthesis were present in the genome of strain JZ-GX1. In addition, these functions were also confirmed by in vitro experiments. Importantly, compared to uninoculated control plants, Pyrus serotina, Malus spectabilis, Populus euramericana (Dode) Guinier cv. “San Martino” (I-72 poplar) and Pinus elliottii plants inoculated with strain JZ-GX1 showed increased heights and ground diameters. These findings improve our understanding of R. victoriana JZ-GX1 as a potential biofertilizer in agriculture.
Re-vegetation Improves Soil Quality by Decreasing Soil Conductivity and Altering Soil Microbial Communities: A Case Study of an Opencast Coal Mine in the Helan Mountains
Authors: Li Zihao , Liu Bingru , Chen Zifeng , Mao Dachuan , Jiang Xingsheng
Published: March 2022

Microbial communities constitute a diverse genetic resource pool in the soil and are key indicators of soil health and quality. How re-vegetation affects soil microbial diversity and community composition at the dump of an opencast coal mine is largely unknown. Using high-throughput sequencing, we performed a comparative study of the bacterial and fungal communities from non-vegetated (bare land) soil and from areas re-vegetated by Astragalus laxmannii, Halogeton arachnoideus, and Artemisia desertorum at an opencast coal mine in the Helan Mountains in western China. These results indicated that re-vegetation significantly reduced soil conductivity. The soils re-vegetated by all three plant species showed greater richness of bacterial species than the bare land, and soils re-vegetated with A. desertorum and A. laxmannii showed significantly greater richness of fungal species than bare land. The bacterial and fungal β-diversity values differed significantly between vegetated and non-vegetated soil, and these differences were more pronounced for bacterial communities than for fungal communities. Re-vegetation significantly increased the relative abundances of Proteobacteria and Bacteroidota and decreased the relative abundance of Chloroflexi. The decreasing soil conductivity that occurred with re-vegetation was found to be an important environmental determinant of the soil microbial community. This study provides evidence that re-vegetation may enhance soil quality via decreasing soil conductivity and altering the soil microbial community, and A. laxmannii was found to be a more effective species than H. arachnoideus or A. desertorum with respect to decreasing soil conductivity and altering the soil microbial communities in the Opencast Coal Mine arid region. This work may provide a helpful guideline for selection of plant species for re-vegetation projects.
Adaptation to Varying Salinity in Halomonas elongata: Much More Than Ectoine Accumulation
Authors: Hobmeier Karina , Cantone Martina , Nguyen Quynh Anh , Pflüger-Grau Katharina , Kremling Andreas , Kunte Hans Jörg , Pfeiffer Friedhelm , Marin-Sanguino Alberto
Published: March 2022

The halophilic γ-proteobacterium Halomonas elongata DSM 2581T thrives at salt concentrations well above 10 % NaCl (1.7 M NaCl). A well-known osmoregulatory mechanism is the accumulation of the compatible solute ectoine within the cell in response to osmotic stress. While ectoine accumulation is central to osmoregulation and promotes resistance to high salinity in halophilic bacteria, ectoine has this effect only to a much lesser extent in non-halophiles. We carried out transcriptome analysis of H. elongata grown on two different carbon sources (acetate or glucose), and low (0.17 M NaCl), medium (1 M), and high salinity (2 M) to identify additional mechanisms for adaptation to high saline environments. To avoid a methodological bias, the transcripts were evaluated by applying two methods, DESeq2 and Transcripts Per Million (TPM). The differentially transcribed genes in response to the available carbon sources and salt stress were then compared to the transcriptome profile of Chromohalobacter salexigens, a closely related moderate halophilic bacterium. Transcriptome profiling supports the notion that glucose is degraded via the cytoplasmic Entner-Doudoroff pathway, whereas the Embden-Meyerhoff-Parnas pathway is employed for gluconeogenesis. The machinery of oxidative phosphorylation in H. elongata and C. salexigens differs greatly from that of non-halophilic organisms, and electron flow can occur from quinone to oxygen along four alternative routes. Two of these pathways via cytochrome bo' and cytochrome bd quinol oxidases seem to be upregulated in salt stressed cells. Among the most highly regulated genes in H. elongata and C. salexigens are those encoding chemotaxis and motility proteins, with genes for chemotaxis and flagellar assembly severely downregulated at low salt concentrations. We also compared transcripts at low and high-salt stress (low growth rate) with transcripts at optimal salt concentration and found that the majority of regulated genes were down-regulated in stressed cells, including many genes involved in carbohydrate metabolism, while ribosome synthesis was up-regulated, which is in contrast to what is known from non-halophiles at slow growth. Finally, comparing the acidity of the cytoplasmic proteomes of non-halophiles, extreme halophiles and moderate halophiles suggests adaptation to an increased cytoplasmic ion concentration of H. elongata. Taken together, these results lead us to propose a model for salt tolerance in H. elongata where ion accumulation plays a greater role in salt tolerance than previously assumed.
Gut Microbiome Succession in Chinese Mitten Crab Eriocheir sinensis During Seawater–Freshwater Migration
Authors: Shao Chenxi , Zhao Wenqian , Li Nannan , Li Yinkang , Zhang Huiming , Li Jingjing , Xu Zhiqiang , Wang Jianjun , Gao Tianheng
Published: March 2022

Biological migration is usually associated with disturbances and environmental changes that are key drivers in determining the diversity, community compositions, and function of gut microbiome. However, little is known about how gut microbiome is affected by disturbance such as salinity changes during migration from seawater to freshwater. Here, we tracked the gut microbiome succession of Chinese mitten crabs (Eriocheir sinensis) during their migrations from seawater to freshwater and afterward using 16S rDNA sequencing for 127 days, and explored the temporal patterns in microbial diversity and the underlying environmental factors. The species richness of gut microbiome showed a hump-shaped trend over time during seawater–freshwater migration. The community dissimilarities of gut microbiome increased significantly with day change. The turnover rate of gut microbiome community was higher during seawater–freshwater transition (1–5 days) than that in later freshwater conditions. Salinity was the major factor leading to the alpha diversity and community dissimilarity of gut microbiome during seawater–freshwater transition, while the host selection showed dominant effects during freshwater stage. The transitivity, connectivity, and average clustering coefficient of gut microbial co-occurrence networks showed decreased trends, while modularity increased during seawater–freshwater migration. For metabolic pathways, “Amino Acid Metabolism” and “Lipid Metabolism” were higher during seawater–freshwater transition than in freshwater. This study advances our mechanistic understanding of the assembly and succession of gut microbiota, which provides new insights into the gut ecology of other aquatic animals.
Probiotics, Their Extracellular Vesicles and Infectious Diseases
Authors: Domínguez Rubio A. Paula , D’Antoni Cecilia L. , Piuri Mariana , Pérez Oscar E.
Published: March 2022

Probiotics have been shown to be effective against infectious diseases in clinical trials, with either intestinal or extraintestinal health benefits. Even though probiotic effects are strain-specific, some “widespread effects” include: pathogen inhibition, enhancement of barrier integrity and regulation of immune responses. The mechanisms involved in the health benefits of probiotics are not completely understood, but these effects can be mediated, at least in part, by probiotic-derived extracellular vesicles (EVs). However, to date, there are no clinical trials examining probiotic-derived EVs health benefits against infectious diseases. There is still a long way to go to bridge the gap between basic research and clinical practice. This review attempts to summarize the current knowledge about EVs released by probiotic bacteria to understand their possible role in the prevention and/or treatment of infectious diseases. A better understanding of the mechanisms whereby EVs package their cargo and the process involved in communication with host cells (inter-kingdom communication), would allow further advances in this field. In addition, we comment on the potential use and missing knowledge of EVs as therapeutic agents (postbiotics) against infectious diseases. Future research on probiotic-derived EVs is needed to open new avenues for the encapsulation of bioactives inside EVs from GRAS (Generally Regarded as Safe) bacteria. This could be a scientific novelty with applications in functional foods and pharmaceutical industries.
Efficacy of Povidone Iodine Against Microbial Biofilms in Breast Implants With Different Textures: Results From an in vitro Study
Authors: Fernández-Ibarburu Borja , Díaz-Navarro Marta , Ibarra Gorka , Rivera Andrés , Hafian Rama , Irigoyen Ãlvaro , Carrillo Raquel , Pérez-Cano Rosa , Muñoz Patricia , García-Ruano Ángela , Lasso José M. , Guembe María
Published: March 2022

Background

In the practice of breast augmentation and reconstruction, implant irrigation with various solutions has been widely used to prevent infection and capsular contracture, but to date, there is no consensus on the optimal protocol to use. Recently, application of povidone iodine (PI) for 30 min has shown in vitro to be the most effective irrigating formula in reducing contamination in smooth breast implants. However, as 30 min is not feasible intraoperatively, it is necessary to determine whether shorter times could be equally effective as well as to test it in both smooth and textured implants.

Methods

We tested the efficacy of 10% PI at 1′, 3′, and 5′ against biofilms of 8 strains (2 ATCC and 6 clinical) of Staphylococcus spp. on silicone disks obtained from Mentor® and Polytech® implants of different textures. We analyzed the percentage reduction of cfu counts, cell viability and bacterial density between treatment (PI) and control (sterile saline, SS) groups for each time of application. We consider clinical significance when > 25% reduction was observed in cell viability or bacterial density.

Results

All textured implants treated with PI at any of the 3 exposure times reduced 100% bacterial load by culture. However, none of the implants reached enough clinical significance in percentage reduction of living cells. Regarding bacterial density, only 25–50 μm Polytxt® Polytech® implants showed significant reduction at the three PI exposure times.

Conclusion

PI is able to inhibit bacterial growth applied on the surface of breast implants regardless of the exposure time. However, no significant reduction on living cells or bacterial density was observed. This lack of correlation may be caused by differences in texture that directly affect PI absorption.
Development and Co-design of NeuroOrb: A Novel “Serious Gaming” System Targeting Cognitive Impairment in Parkinson’s Disease
Authors: Guglietti Bianca , Hobbs David A. , Wesson Bradley , Ellul Benjamin , McNamara Angus , Drum Simon , Collins-Praino Lyndsey E.
Published: March 2022

Whilst Parkinson’s disease (PD) is typically thought of as a motor disease, a significant number of individuals also experience cognitive impairment (CI), ranging from mild-CI to dementia. One technique that may prove effective in delaying the onset of CI in PD is cognitive training (CT); however, evidence to date is variable. This may be due to the implementation of CT in this population, with the motor impairments of PD potentially hampering the ability to use standard equipment, such as pen-and-paper or a computer mouse. This may, in turn, promote negative attitudes toward the CT paradigm, which may correlate with poorer outcomes. Consequently, optimizing a system for the delivery of CT in the PD population may improve the accessibility of and engagement with the CT paradigm, subsequently leading to better outcomes. To achieve this, the NeuroOrb Gaming System was designed, coupling a novel accessible controller, specifically developed for use with people with motor impairments, with a “Serious Games” software suite, custom-designed to target the cognitive domains typically affected in PD. The aim of the current study was to evaluate the usability of the NeuroOrb through a reiterative co-design process, in order to optimize the system for future use in clinical trials of CT in individuals with PD. Individuals with PD (n = 13; mean age = 68.15 years; mean disease duration = 8 years) were recruited from the community and participated in three co-design loops. After implementation of key stakeholder feedback to make significant modifications to the system, system usability was improved and participant attitudes toward the NeuroOrb were very positive. Taken together, this provides rationale for moving forward with a future clinical trial investigating the utility of the NeuroOrb as a tool to deliver CT in PD.
Association Between Copper and Global Cognition and the Moderating Effect of Iron
Authors: Choe Young Min , Suh Guk-Hee , Lee Boung Chul , Choi Ihn-Geun , Lee Jun Ho , Kim Hyun Soo , Kim Jee Wook
Published: March 2022

Background

Despite the known association between abnormal serum copper levels and Alzheimer’s disease (AD) or cognitive decline, the association between copper, iron, and cognition remains poorly investigated. We examined the association between serum copper levels and global cognition measured using the Mini-Mental State Examination (MMSE) in older adults with normal copper levels. We also explored the moderating effect of iron on this association.

Methods

The study enrolled 99 non-demented adults between 65 and 90 years of age. All the participants underwent comprehensive clinical assessments and serum copper measurements. Global cognitive performance was measured by the MMSE. All copper levels were within the normal range and were stratified into three categories: < 87 (low), 87–98 (medium), and > 98 (high: used as a reference category) μg/dL.

Results

Serum copper level (as a continuous variable) was significantly associated with MMSE score (B = 0.065, 95% confidence interval = 0.023–0.108, p = 0.003). Low serum copper group showed significantly decreased MMSE score compared to high copper one (B = −2.643, 95% confidence interval = −4.169 to -1.117, p < 0.001), while middle copper category had no difference (B = −1.211, 95% confidence interval = −2.689 to 0.268, p = 0.107). There was a significant low serum copper ×iron interaction effect on the MMSE score (B = 0.065, 95% confidence interval = 0.016–0.114, p = 0.010). Subgroup analyses showed that low serum copper was significantly associated with a low MMSE score in the low-iron (B = −4.174, 95% confidence interval = −6.607 to −1.741, p = 0.001) but not high-iron subgroup (B = −0.721, 95% confidence interval = −2.852 to 1.409, p = 0.495).

Conclusion

Our findings from non-demented older adults suggest that a low serum copper level within the normal range was associated with AD or cognitive decline and this is moderated by iron. To prevent AD or cognitive decline, clinicians need to pay attention to avoiding low serum copper and iron levels, even within the clinical normal range.
A Markerless Pose Estimator Applicable to Limbless Animals
Authors: Garg Vranda , André Selina , Giraldo Diego , Heyer Luisa , Göpfert Martin C. , Dosch Roland , Geurten Bart R. H.
Published: March 2022

The analysis of kinematics, locomotion, and spatial tasks relies on the accurate detection of animal positions and pose. Pose and position can be assessed with video analysis programs, the “trackers.” Most available trackers represent animals as single points in space (no pose information available) or use markers to build a skeletal representation of pose. Markers are either physical objects attached to the body (white balls, stickers, or paint) or they are defined in silico using recognizable body structures (e.g., joints, limbs, color patterns). Physical markers often cannot be used if the animals are small, lack prominent body structures on which the markers can be placed, or live in environments such as aquatic ones that might detach the marker. Here, we introduce a marker-free pose-estimator (LACE Limbless Animal traCkEr) that builds the pose of the animal de novo from its contour. LACE detects the contour of the animal and derives the body mid-line, building a pseudo-skeleton by defining vertices and edges. By applying LACE to analyse the pose of larval Drosophila melanogaster and adult zebrafish, we illustrate that LACE allows to quantify, for example, genetic alterations of peristaltic movements and gender-specific locomotion patterns that are associated with different body shapes. As illustrated by these examples, LACE provides a versatile method for assessing position, pose and movement patterns, even in animals without limbs.
Effect of Torso Kinematics on Gait Phase Estimation at Different Walking Speeds
Authors: Hong Woolim , Lee Jinwon , Hur Pilwon
Published: March 2022

Human gait phase estimation has been studied in the field of robotics due to its importance for controlling wearable devices (e.g., prostheses or exoskeletons) in a synchronized manner with the user. As data-driven approaches have recently risen in the field, researchers have attempted to estimate the user gait phase using a learning-based method. Thigh and torso information have been widely utilized in estimating the human gait phase for wearable devices. Torso information, however, is known to have high variability, specifically in slow walking, and its effect on gait phase estimation has not been studied. In this study, we quantified torso variability and investigated how the torso information affects the gait phase estimation result at various walking speeds. We obtained three different trained models (i.e., general, slow, and normal-fast models) using long short-term memory (LSTM). These models were compared to identify the effect of torso information at different walking speeds. In addition, the ablation study was performed to identify the isolated effect of the torso on the gait phase estimation. As a result, when the torso segment's angular velocity was used with thigh information, the accuracy of gait phase estimation was increased, while the torso segment's angular position had no apparent effect on the accuracy. This study suggests that the torso segment's angular velocity enhances human gait phase estimation when used together with the thigh information despite its known variability.
Deep Learning-Enabled Clinically Applicable CT Planbox for Stroke With High Accuracy and Repeatability
Authors: Wang Yang , Zhu Junkai , Zhao Jinli , Li Wenyi , Zhang Xin , Meng Xiaolin , Chen Taige , Li Ming , Ye Meiping , Hu Renfang , Dou Shidan , Hao Huayin , Zhao Xiaofen , Wu Xiaoming , Hu Wei , Li Cheng , Fan Xiaole , Jiang Liyun , Lu Xiaofan , Yan Fangrong
Published: March 2022

Background

Computed tomography (CT) plays an essential role in classifying stroke, quantifying penumbra size and supporting stroke-relevant radiomics studies. However, it is difficult to acquire standard, accurate and repeatable images during follow-up. Therefore, we invented an intelligent CT to evaluate stroke during the entire follow-up.

Methods

We deployed a region proposal network (RPN) and V-Net to endow traditional CT with intelligence. Specifically, facial detection was accomplished by identifying adjacent jaw positions through training and testing an RPN on 76,382 human faces using a preinstalled 2-dimensional camera; two regions of interest (ROIs) were segmented by V-Net on another training set with 295 subjects, and the moving distance of scanning couch was calculated based on a pre-generated calibration table. Multiple cohorts including 1,124 patients were used for performance validation under three clinical scenarios.

Results

Cranial Automatic Planbox Imaging Towards AmeLiorating neuroscience (CAPITAL)-CT was invented. RPN model had an error distance of 4.46 ± 0.02 pixels with a success rate of 98.7% in the training set and 100% with 2.23 ± 0.10 pixels in the testing set. V-Net-derived segmentation maintained a clinically tolerable distance error, within 3 mm on average, and all lines presented with a tolerable angle error, within 3° on average in all boundaries. Real-time, accurate, and repeatable automatic scanning was accomplished with and a lower radiation exposure dose (all P < 0.001).

Conclusions

CAPITAL-CT generated standard and reproducible images that could simplify the work of radiologists, which would be of great help in the follow-up of stroke patients and in multifield research in neuroscience.
Corticospinal Tract Hypoperfusion Associated With Unexplained Early Neurological Deterioration After Intravenous Thrombolysis
Authors: Zhang Danfeng , Zhong Wansi , Chen Luowei , Xu Chao , Yan Shenqiang , Zhou Ying , Ma Xiaodong , Lou Min
Published: March 2022

Background and Purpose

Early neurological deterioration (END) occurs in 10% among patients with acute ischemic stroke (AIS) who are receiving intravenous thrombolysis (IVT). Over half of them have no straightforward causes, which is referred to as unexplained END. We aimed to explore whether the presence of baseline corticospinal tract (CST) hypoperfusion could predict the development of unexplained END at 24 h in patients with AIS after receiving IVT.

Methods

We retrospectively analyzed the clinical and imaging data from patients with AIS who received IVT. Unexplained END was defined as ≥ 2-point increase of National Institutes of Health Stroke Scale (NIHSS) from baseline to 24 h without straightforward causes. Hypoperfusion lesions involving CST and other cerebral areas were identified on perfusion maps.

Results

Among 807 patients, CST hypoperfusion and non-CST hypoperfusion occurred in 488 (60.5%) and 319 (39.5%) patients, respectively. Patients with CST hypoperfusion were more likely to have unexplained END compared with patients with non-CST hypoperfusion (16.6 vs. 2.8%, P < 0.001). Binary logistics regression analysis showed that CST hypoperfusion was independently associated with unexplained END after IVT (OR = 5.64; 95% CI: 2.699–11.785; P < 0.001) after adjusting for baseline NIHSS, onset to needle time, baseline hypoperfusion volume, atrial fibrillation, and hypertension.

Conclusions

Patients with CST hypoperfusion were more likely to suffer from unexplained END after IVT, implying potential mechanisms and potential prevention of unexplained END.
Postural Sway in Parkinson's Disease and Multiple Sclerosis Patients During Tasks With Different Complexity
Authors: Warmerdam Elke , Schumacher Maike , Beyer Thorben , Nerdal Patrik Theodor , Schebesta Linda , Stürner Klarissa H. , Zeuner Kirsten E. , Hansen Clint , Maetzler Walter
Published: March 2022

Neurological diseases are associated with static postural instability. Differences in postural sway between neurological diseases could include “conceptual” information about how certain symptoms affect static postural stability. This information might have the potential to become a helpful aid during the process of finding the most appropriate treatment and training program. Therefore, this study investigated static postural sway performance of Parkinson's disease (PD) and multiple sclerosis (MS) patients, as well as of a cohort of healthy adults. Three increasingly difficult static postural tasks were performed, in order to determine whether the postural strategies of the two disease groups differ in response to the increased complexity of the balance task. Participants had to perform three stance tasks (side-by-side, semi-tandem and tandem stance) and maintain these positions for 10 s. Seven static sway parameters were extracted from an inertial measurement unit that participants wore on the lower back. Data of 47 healthy adults, 14 PD patients and 8 MS patients were analyzed. Both healthy adults and MS patients showed a substantial increase in several static sway parameters with increasingly complex stance tasks, whereas PD patients did not. In the MS patients, the observed substantial change was driven by large increases from semi-tandem and tandem stance. This study revealed differences in static sway adaptations between PD and MS patients to increasingly complex stance tasks. Therefore, PD and MS patients might require different training programs to improve their static postural stability. Moreover, this study indicates, at least indirectly, that rigidity/bradykinesia and spasticity lead to different adaptive processes in static sway.
Insights Into the Role of Heat Shock Protein 27 in the Development of Neurodegeneration
Authors: Holguin Bianka A. , Hildenbrand Zacariah L. , Bernal Ricardo A.
Published: March 2022

Small heat shock protein 27 is a critically important chaperone, that plays a key role in several essential and varied physiological processes. These include thermotolerance, apoptosis, cytoskeletal dynamics, cell differentiation, protein folding, among others. Despite its relatively small size and intrinsically disordered termini, it forms large and polydisperse oligomers that are in equilibrium with dimers. This equilibrium is driven by transient interactions between the N-terminal region, the α-crystallin domain, and the C-terminal region. The continuous redistribution of binding partners results in a conformationally dynamic protein that allows it to adapt to different functions where substrate capture is required. However, the intrinsic disorder of the amino and carboxy terminal regions and subsequent conformational variability has made structural investigations challenging. Because heat shock protein 27 is critical for so many key cellular functions, it is not surprising that it also has been linked to human disease. Charcot-Marie-Tooth and distal hereditary motor neuropathy are examples of neurodegenerative disorders that arise from single point mutations in heat shock protein 27. The development of possible treatments, however, depends on our understanding of its normal function at the molecular level so we might be able to understand how mutations manifest as disease. This review will summarize recent reports describing investigations into the structurally elusive regions of Hsp27. Recent insights begin to provide the required context to explain the relationship between a mutation and the resulting loss or gain of function that leads to Charcot-Marie Tooth disease and distal hereditary motor neuropathy.
Changes in Quinoa Seed Fatty Acid Profile Under Heat Stress Field Conditions
Authors: Matías Javier , Rodríguez María José , Granado-Rodríguez Sara , Cruz Verónica , Calvo Patricia , Reguera María
Published: March 2022

The nutritional quality of quinoa is often related to the high protein content of their seeds. However, and despite not being an oilseed crop, the oil composition of quinoa seeds is remarkable due to its profile, which shows a high proportion of polyunsaturated fatty acids (PUFAs), particularly in essential fatty acids such as linoleic (ω-6) and α-linolenic (ω-3). In line with this, this study aimed at evaluating the effect of elevated temperatures on the oil composition of different quinoa cultivars grown in the field in two consecutive years (i.e., 2017 and 2018). In 2017, heat stress episodes resulted in a reduced oil content and lower quality linked to decreased ratios of oleic acid:linoleic acid, larger omega-6 (ω-6) to omega-3 (ω-3) ratios, and lower monounsaturated fatty acid (MUFA) and higher PUFA contents. Furthermore, the correlations found between mineral nutrients such as phosphorous (P) and the contents of oleic and linoleic acids emphasize the possibility of optimizing oil quality by controlling fertilization. Overall, the results presented in this study show how the environmental and genetic factors and their interaction may impact oil quality in quinoa seeds.
Empirically-Derived Dietary Patterns in Relation to Non-Alcoholic Fatty Liver Diseases Among Adult Participants in Amol, Northern Iran: A Structural Equation Modeling Approach
Authors: Doustmohammadian Azam , Pishgar Elham , Clark Cain C. T. , Sobhrakhshankhah Elham , Nikkhah Mehdi , Faraji Amir Hossein , Motamed Nima , Mansourian Mohsen Reza , Amirkalali Bahareh , Maadi Mansooreh , Kasaii Maryam Sadat , Ebrahimi Hamidreza , Zamani Farhad
Published: March 2022

Dietary modifications remain the mainstay in managing nonalcoholic fatty liver disease (NAFLD). Published data on the effect of overall dietary patterns on NAFLD is scarce. The present study aims to extract the dietary patterns and investigate their association to NAFLD by gender, using structural equation modeling, among adult participants in Amol, northern Iran. In this cross-sectional study, data from 3,149 participants in the Amol cohort study (55.3% men, n = 1,741) were analyzed. Usual dietary intake was assessed by a validated 168-items semiquantitative food frequency questionnaire. We classified major dietary patterns by explanatory factor analysis (EFA) and confirmatory factor analysis (CFA). NAFLD diagnosis was based on ultrasound scanning, including increased hepatic echogenicity, abnormal appearance of hepatic arteries, and diaphragm in the absence of excessive alcohol consumption. Multivariable logistic regression and structural equation modeling (SEM) were used to explore the relationship between dietary patterns and NAFLD. Three distinct dietary patterns, including western, healthy, and traditional/mixed dietary patterns, were identified. Adult male who adhere to the western dietary pattern were more affected with NAFLD risk [Q1, Q2, Q3, Q4, odds ratio (OR) = 1, 1.16, 1.34, 1.39; 95% confidence interval (CI) = 0.83–1.61, 0.96–1.85, 0.98–1.96, ptrend = 0.04, respectively]. A full mediating effect of healthy dietary pattern, western dietary pattern, and traditional dietary pattern via dietary acid load (DAL) proxy (of dietary patterns to DAL: βstd = −0.35, p < 0.006, βstd = 0.15, p = 0.009, and βstd = 0.08, p = 0.001, respectively), on NAFLD was found through mediation analysis using SEM. A western dietary pattern comprising frequent intake of salty and sweet snacks, soft drinks, refined grains, processed meats, cooked and fried potatoes, eggs, and coffee was associated with a higher odds of NAFLD in an Iranian male population. Additionally, our findings might provide a mechanistic explanation for the association between dietary patterns and NAFLD via DAL proxy. However, further prospective studies, including assessing acid-base biomarkers, are needed.
Adherence to the Mediterranean Diet in Relation to Gastric Cancer in Afghanistan
Authors: Amiry Freshta , Mousavi Seyed Mohammad , Barekzai Ahmad Mujtaba , Esmaillzadeh Ahmad
Published: March 2022

Background

Despite the adherence to the Mediterranean dietary pattern (MD) being associated with a reduced risk of several cancers, there is no report about the highly prevalent diet-disease associations in Afghanistan, particularly about gastric cancer (GC).

Objective

The aim of this study was to investigate the association between MD and GC in Afghanistan.

Methods

This hospital-based case-control study was carried out on a total number of 270 subjects (90 cases and 180 controls) aged between 20 and 75 years. Using the convenience-sampling method, cases and controls were selected. Cases were patients with GC whose condition was pathologically confirmed. The controls were apparently healthy people who were matched with cases in terms of age (±5 years) and sex. Assessment of dietary intake was done using a pre-tested food frequency questionnaire, designed specifically for Afghanistan. Adherence to the MD pattern was done based on the scores suggested in earlier studies.

Results

Out of 270 studied subjects, 73% were men. We found that subjects in the highest tertile of MD score had 52% decreased odds of GC (OR: 0.48; 95% CI: 0.24–0.98, P-trend = 0.05) compared with those in the lowest tertile. After considering potential environmental factors, age, and sex, the observed association disappeared (OR: 0.43; 95% CI: 0.13–1.38, P-trend = 0.41). After further adjustment for BMI in the last model, we found that participants with the highest MD score were 83% less likely to have GC than those in the lowest tertile (OR: 0.17; 95% CI: 0.03–0.80, P-trend = 0.14).

Conclusion

We found that greater adherence to MD might be associated with a lower odds of GC.
Food Protein-Induced Allergic Proctocolitis: The Effect of Maternal Diet During Pregnancy and Breastfeeding in a Mediterranean Population
Authors: Vassilopoulou Emilia , Feketea Gavriela , Konstantinou George N. , Zekakos Xypolias Dimitris , Valianatou Mina , Petrodimopoulou Maria , Vourga Vasiliki , Tasios Ioannis , Papadopoulos Nikolaos G.
Published: March 2022

Background

The aim of the current investigation was to explore the association of food protein-induced allergic proctocolitis (FPIAP) with the maternal diet during pregnancy and breastfeeding in Greek infants.

Methods

A multicenter retrospective case-control study was conducted in 6 regions in Greece, with 96 mothers of infants with and 141 mothers of infants without a history of FPIAP. Maternal dietary habits during pregnancy and breastfeeding were evaluated with the following validated questionnaires: (a) The Mediterranean Diet Score and (b) The Mediterranean Oriented Culture-Specific Semi-Quantitative Food Frequency Questionnaire.

Results

FPIAP was associated with cow's milk (83.6%), egg (7.3%), wheat (6.4%), and beef (6.4%) in the maternal diet. Adherence to Mediterranean Diet was similar among the mothers. Mothers of FPIAP infants consumed more vegetables. Elastic net prediction models showed that, in this Mediterranean population, increased consumption during pregnancy and lactation of common allergens, whole grain products, homemade food, fish and shellfish, and fruits was associated with a decreased risk of FPIAP. Conversely, a high intake of vegetables, sugar and total fat, and non-stick/grilled cooking, were associated with increased risk of FPIAP, as was a high intake of salt and white flour during lactation only.

Conclusions

Components of a maternal Mediterranean Diet may protect against FPIAP when traditional cooking methods are adopted and fish, fruit, and whole wheat products are consumed frequently during pregnancy and breastfeeding.
Evolving Food Choices Among the Urban Indian Middle-Class: A Qualitative Study
Authors: Kumar Gargi S. , Kulkarni Mrinmoyi , Rathi Neha
Published: March 2022

One of the leading risk factors for an escalating obesity burden in India is non-nutritious choices. Underpinned by the nutrition transition theory, this qualitative inquiry was designed to understand the urban middle-class Indian consumers’ views about processed foods and rapidly changing food choices. The study consisted of two phases, the first phase consisted of focus group discussions pertaining to the definition and conception of processed foods and the second phase consisted of interviews regarding the changing food environment. A convenience sample of Indian consumers aged 40–65 years were recruited from Mumbai and Kochi to participate in focus group discussions (FGD1 – nine participants and FGD2 – seven participants) and semi-structured face-to-face interviews (N = 22). Both discussions and interviews were audio-recorded and transcribed verbatim. Thematic analysis was used to analyze the transcribed data. Features of processed foods mentioned were chemical and physical processing, prolonged shelf life and poor nutritional quality. Factors influencing food choices and consumption of processed foods reported by participants could be categorized into changes in the socio-cultural environment and changes in the food environment. Changes in the socio-cultural environment included globalization and urbanization, long work days and sedentary living, rise in income levels and decrease in household cooking. Changes in the food environment included increased availability and accessibility of processed foods, replacement of traditional Indian diet with Western food, food as indicators of status, food advertisements and convenience. These results are consistent with nutrition transition theory and provide useful direction for public health policies aimed at promoting healthy diets.