bluuebunny/crossref_metadata_2025 huggingface dataset:
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants
Authors: Yin Rui , Feng Brandon Y. , Varshney Amitabh , Pierce Brian G.
Published: October 2021

High resolution experimental structural determination of protein-protein interactions has led to valuable mechanistic insights, yet due to the massive number of interactions and experimental limitations there is a need for computational methods that can accurately model their structures. Here we explore the use of the recently developed deep learning method, AlphaFold, to predict structures of protein complexes from sequence. With a benchmark of 152 diverse heterodimeric protein complexes, multiple implementations and parameters of AlphaFold were tested for accuracy. Remarkably, many cases had highly accurate models generated as top-ranked predictions, greatly surpassing the performance of unbound protein-protein docking, whereas antibody-antigen docking was largely unsuccessful. While AlphaFold-generated accuracy predictions were able to discriminate near-native models, previously developed scoring protocols improved performance. Our study demonstrates that end-to-end deep learning can accurately model transient protein complexes, and identifies areas for improvement to guide future developments to reliably model any protein-protein interaction of interest.
MRGM: a mouse reference gut microbiome reveals a large functional discrepancy for gut bacteria of the same genus between mice and humans
Authors: Kim Nayeon , Kim Chan Yeong , Yang Sunmo , Park Dongjin , Ha Sang-Jun , Lee Insuk
Published: October 2021

The gut microbiome is associated with human diseases and interacts with dietary components and drugs. In vivo mouse models may be effective for studying diet and drug effects on the gut microbiome. We constructed a mouse reference gut microbiome (MRGM, https://www.mbiomenet.org/MRGM/) that includes newly-assembled genomes from 878 metagenomes. Leveraging samples with ultra-deep metagenomic sequencing (>130 million read pairs), we demonstrated quality improvement in assembled genomes for mouse gut microbes as sequencing depth increased. MRGM provides a catalog of 46,267 non-redundant genomes with ≥70% completeness and ≤5% contamination comprising 1,689 representative bacterial species and 15.2 million non-redundant proteins. Importantly, MRGM significantly improved the taxonomic classification rate of sequencing reads from mouse fecal samples compared to previous databases. Using MRGM, we determined that reliable low-abundance taxa profiles of the mouse gut microbiome require sequencing >10 million reads. Despite the high overall functional similarity of the mouse and human gut microbiomes, only ~10% of MRGM species are shared with the human gut microbiome. Although ~80% of MRGM genera are present in the human gut microbiome, ~70% of the shared genera have <40% of core gene content for the respective genus with human counterparts. These suggest that although metabolic processes of the human gut microbiome largely occur in the mouse gut microbiome, functional translations between them according to genus-level taxonomic commonality require caution.

Key Points

MRGM provides 46,267 genomes comprising 1,689 bacterial species of mouse gut microbiome.

Despite high overlap of genera, functional discrepancy between mouse and human gut microbiota is large.

Lineage-specific markers underestimate the completeness of assembled genomes for uncharacterized taxa.
Allele and genotype frequencies of CYP3A4, CYP3A5, CYP3A7, and GSTP1 gene polymorphisms among mainland Tibetan, Mongolian, Uyghur, and Han Chinese populations
Authors: Qi Guangzhao , Han Chao , Zhou Yubing , Wang Xin
Published: October 2021

Over 50% prescribed drugs are metabolised by cytochrome P450 3A (CYP3A) and glutathione S‐transferase pi (GSTP1) adds a glutathione to the oxidative products by CYP3A, which increases the hydrophilic property of metabolites and facilitates the excretion. Single nucleotide polymorphisms (SNPs) of CYP3A and GSTP1 show a diverse allele and genotype frequencies distribution among the world populations. The present study aimed to investigate the genotype and allele frequency distribution patterns of CYP3A4, CYP3A5, CYP3A7 and GSTP1 polymorphisms among healthy participants in mainland Tibetan, Mongolian, Uyghur, and Han Chinese populations. Blood samples were collected from 842 unrelated healthy subjects (323 Tibetan, 134 Mongolian, 162 Uyghur, and 223 Han) for genotyping analysis. Variant allele frequencies of CYP3A4 rs2242480, CYP3A5 rs776746, CYP3A7 rs2257401, and GSTP1 Ile105Val were observed in Han (0.253, 0.686, 0.312 and 0.188), Tibetan (0.186, 0.819, 0.192 and 0.173), Mongolian (0.198, 0.784, 0.228 and 0.235) and Uyghur (0.179, 0.858, 0.182 and 0.250) respectively. The allele frequency of CYP3A7*1C in Uyghur (0.019) was higher than that in Tibetan (0.002, p < 0.01). There was a strong linkage disequilibrium between CYP3A4 rs2242480, CYP3A5 rs776746, and CYP3A7 rs2257401 among the four ethnic groups. The results might be useful for the precise medication in the Chinese populations.
Ultrastructural observation of filtration membrane in cell‐free and concentrated ascites reinfusion therapy for malignant ascites
Authors: Koga Kenichi , Ishihara Takeshi , Doi Yohei , Suzuki Ryota , Komatsu Masakazu , Abe Kosei , Tanaka Takahiro , Iwaki Ryuji , Hashi Hiroyuki , Sugawara Akira
Published: October 2021

Introduction

Cell‐free and concentrated ascites reinfusion therapy (CART) is used for the treatment of diuretic‐resistant ascites. An increase in circuit pressure and clogging of the filtration membrane often occur in CART for malignant ascites.

Methods

To clarify the precise mechanism of filter clogging, we performed an ultrastructural observation study of the filtration membrane after the filtration of malignant ascites.

Results

The deposition on the filtration membrane was composed of blood cells, fibrin, or both. Cellular deposition was associated with a greater number of blood cells in the original ascites fluid. In contrast, fibrin deposition was associated with higher levels of interleukin‐6, α1‐antitrypsin, haptoglobin, and fibrinogen/fibrin degradation products.

Conclusion

Our results suggest that the specific pathophysiologies of malignancy (such as inflammation or coagulation/fibrinolysis) and characteristics of malignant ascites (highly concentrated and cell‐rich) are associated with clogging of the filtration membrane during CART.
Chromosome‐scale genome assembly of Castanopsis tibetana provides a powerful comparative framework to study the evolution and adaptation of Fagaceae trees
Authors: Sun Ye , Guo Jianling , Zeng Xiaorong , Chen Risheng , Feng Yi , Chen Shuang , Yang Kai
Published: October 2021

Fagaceae species are increasingly used as models to elucidate the process and mechanism of adaptation and speciation by integrating ecology, evolution and genomics. The genus Castanopsis belongs to the family Fagaceae and is mainly distributed across subtropical and tropical Asia. In the present study, we reported the first chromosome‐scale genome assembly of Castanopsis tibetana, a common species of evergreen broadleaved forests in subtropical China. The combination of Nanopore sequencing and Hi‐C technologies enabled a high‐quality genome assembly. The final assembled genome size of C. tibetana was 878.6 Mb (97.6% of the estimated genome size), consisting of 477 contigs with an N50 length of 3.3 Mb. The benchmarking universal single‐copy orthologue (BUSCO) assessment indicated a completeness of 93.0%. Hi‐C scaffolding generated 12 pseudochromosomes, representing 98.7% of the assembled genome. Subsequently, 40,937 protein‐coding genes were predicted and 90.04% of them were functionally annotated. More than 476.9 Mb of repetitive sequences (54.3% of the genome) were identified, and the percentage of the genome covered by TE elements was 39.98%. Comparative genomics analysis revealed that C. tibetana was most closely related to Castanea mollissima and diverged at 18.48 Ma, and that C. tibetana has undergone considerable gene family expansion and contraction. Evidence of positive selection was detected in 53 genes, which showed different arrangement pattern compared to Quercus robur. The chromosome‐scale genome assembly of C. tibetana will expand Fagaceae genome resources across the family and provide a powerful comparative framework to study the adaptation and evolution of Fagaceae trees.
Successful treatment of locally advanced lung cancer using late concurrent chemoradiation therapy administered after immune checkpoint inhibitor plus platinum chemotherapy
Authors: Matsubara Taichi , Takamori Shinkichi , Fujishita Takatoshi , Toyozawa Ryo , Ito Kensaku , Yamaguchi Masafumi , Seto Takashi , Okamoto Tatsuro
Published: October 2021

Concurrent chemoradiation therapy (CRT) is the standard of care for patients with unresectable stage II/III lung cancer. However, systemic chemotherapy is required for patients who are ineligible for radical radiation therapy. There is little evidence to date for the safety and efficacy of CRT administered after treatment with immune checkpoint inhibitors (ICIs). The cases reported here had inoperable stage III lung cancer (non‐small cell lung cancer and small cell lung cancer) and were ineligible for radical radiation therapy. They were administered ICIs plus chemotherapy and subsequently underwent late concurrent CRT. Because of the remarkable tumor shrinkage achieved by the ICIs plus chemotherapy, adverse events of CRT were tolerable. They were alive without tumor progression as of this report, over 1 year after CRT was terminated. CRT is administered with curative intent, while the intent of immunochemotherapy is palliative. Late concurrent CRT after immunochemotherapy is probably effective and tolerable. After treatment with systemic chemotherapy in patients judged ineligible for radical radiation therapy, radiation therapy should be reconsidered because of its importance once tumor shrinkage has been achieved.
Salary disparities based on gender in academic emergency medicine leadership
Authors: Wiler Jennifer L. , Wendel Sarah K. , Rounds Kirsten , McGowan Becky , Baird Janette
Published: October 2021

Objective

There are significantly fewer women than men in leadership roles in health care. Previous studies have shown that, overall, male physicians earn nearly $20,000 more annually than their female physician colleagues after adjusting for confounding factors. However, there has not been a description of physician leadership compensation in relation to gender.

Methods

This was a successive cross‐sectional observation study design of 154 emergency departments in the United States from 5 years (2013, 2015–2018) using Association of Academic Chairs in Emergency Medicine and Academy of Administrators in Academic EM survey data. The primary variable of interest, leadership role, was attained by recoding the survey responses to assign primary job duty into four main categories: no leadership role, operations leadership, education leadership, and executive leadership.

Results

Overall, 8820 responses were included. Across all survey years, the mean (±SD) percentage of women in any leadership role was significantly less than men (44.5% [95% CI: 42.8, 46.2%] vs. 55.3% [95% CI: 54.1, 56.5%]). Women in leadership roles worked more clinical hours than men in the same position (female median = 1008, male median = 960). Women also had significantly lower salaries than men at each of the 5‐year time points that data are reported, with unadjusted mean salary differences of –$54,409 per year for executives, –$27,803 for operational leaders, and –$17,803 for education leaders.

Conclusions

Female physicians hold fewer leadership roles in academic emergency medicine (EM), and when they do, they work more clinical hours and are paid less than male physicians. As a specialty, EM should continue to investigate and report on gender achievement disparities as work is done to rectify the system inequalities.
Can CEO equity‐based compensation limit investment‐related agency problems?
Authors: Qu Xin , Percy Majella , Hu Fang , Stewart Jenny
Published: October 2021

Previous research suggests that investment‐cash flow sensitivity (ICS) has arisen from agency costs. This study investigates whether equity‐based compensation (EBC) reduces these costs. We find that ICS is lower when companies grant EBC to chief executive officers (CEOs). EBC with long‐term vesting periods, and especially with graded vesting conditions, is associated with a lower ICS. EBC with performance hurdles is associated with higher sensitivity. However, when the performance hurdles are set as a relative market index rather than an absolute target, the sensitivity becomes lower. Our results suggest that appropriately designed EBC plays an important role in mitigating investment‐related agency problems.
Climate and behaviour influence thermal suitability of artificial hollows for a critically endangered mammal
Authors: McComb L. B. , Lentini P. E. , Harley D. K. P. , Lumsden L. F. , Eyre A. C. , Briscoe N. J.
Published: October 2021

Artificial hollows are commonly used to mitigate the scarcity of den and nest sites that threatens fauna species globally, but there is a risk that these do not provide suitable microclimates for the populations they are intended to support. We monitored temperature, humidity and occupancy in artificial dens (nest boxes and chainsaw‐carved cavities) provided for the critically endangered Leadbeater’s possum (Gymnobelideus leadbeateri) in south‐eastern Australian forests. Monitoring occurred over both winter and summer in five habitat types spanning a broad elevational gradient (110–1580 m asl). We then used a biophysical model to explore the physiological consequences of the den temperatures recorded, and the potential effectiveness of behavioural strategies in reducing thermoregulatory costs. Monitoring revealed that nest box temperatures tracked ambient over both seasons, ranging from −5.5°C to 48.5°C, while chainsaw hollows provided more stable internal conditions. However, we found that inferences regarding the thermal suitability of artificial dens were site‐specific, and dependent upon habitat type, season and assumptions around behavioural strategies. During winter, behaviours such as the construction of large, insulative nests and huddling are likely critical in overcoming high energy costs associated with poorly insulated artificial dens. In contrast, during summer high thermoregulatory costs were predicted for the warmest (lowland) site and coincided with low nest box occupancy. Our study reinforces the importance of factoring in local climates, and behavioural and physiological strategies employed by target taxa, when implementing artificial den programs to support fauna populations.
Validity of near‐infrared light transillumination for the assessment of proximal caries in permanent teeth
Authors: Wang F , Su C , Yang C , von den Hoff JW , Bian Z , Meng L
Published: October 2021

Purpose

The aim of this study was to evaluate the performance of DIAGNOcam (DC) in diagnosing proximal caries and to compare its effectiveness with the International Caries Detection and Assessment System (ICDAS) and bitewing radiography (BWR).

Methods

118 premolars extracted for orthodontic reasons were included and examined using three detection methods and validated by histological sections as the gold standard. The sensitivity, specificity and areas under the ROC curve (Az value) at the outer half enamel (D1), inner half enamel (D2) and dentine (D3) thresholds were compared between different methods.

Results

At all categories, the specificity of DC was almost as high as ICDAS and BWR. DC showed a significantly higher sensitivity (0.68) than both visual (0.33) and radiographic examination (0.47) at the D1 threshold. DC presented the highest Az value (area under the ROC curve) at the D1 and D2 threshold (0.81, 0.86), while BWR showed the greatest Az values at D3 (0.94). Furthermore, DC had the highest association strength with the gold standard (Spearman’s ρ = 0.80).

Conclusions

It can be concluded that DC could detect proximal caries effectively and showed comparable or even better performance than ICDAS and BWR.
New observations of four waterbird species in Algerian Sahara
Authors: Chedad Abdelwahab , Bouzid Abdelhakim , Bendjoudi Djamel , Guezoul Omar
Published: October 2021

The range mapping and phenological status of four waterbird species was studied in Ghardaïa and El‐Ménéa regions between 2017 and 2021. Seasonal waterbird censuses were conducted throughout Ghardaïa and El‐Ménéa by individual counts or visual estimation. During these counts, four species were reported for the first time in this region, three passage visitors, European golden plover Pluvialis apricaria, black stork Ciconia nigra and Western Reef Heron Egretta gularis, and one winter stopover, common crane Grus grus. Observations on the species in Ghardaïa and El‐Ménéa regions are new for southern Algeria.
Transcriptome‐based identification of novel endotypes in adult atopic dermatitis
Authors: Lefèvre‐Utile Alain , Saichi Melissa , Oláh Péter , Delord Marc , Homey Bernhard , Soumelis Vassili ,   MAARS consortium
Published: October 2021

Background

Atopic dermatitis (AD) is a frequent and heterogeneous inflammatory skin disease, for which personalized medicine remains a challenge. High‐throughput approaches have improved understanding of the complex pathophysiology of AD. However, a purely data‐driven AD classification is still lacking.

Methods

To address this question, we applied an original unsupervised approach on the largest available transcriptome dataset of AD lesional (n = 82) and healthy (n = 213) skin biopsies.

Results

Taking into account pathological and physiological state, a variance‐based filtering revealed 222 AD‐specific hyper‐variable genes that efficiently classified the AD samples into 4 clusters that turned out to be clinically and biologically distinct. Comparison of gene expressions between clusters identified 3 sets of upregulated genes used to derive metagenes (MGs): MG‐I (19 genes) was associated with IL‐1 family signaling (including IL‐36A and 36G) and skin remodeling, MG‐II (23 genes) with negative immune regulation (including IL‐34 and 37) and skin architecture, and MG‐III (17 genes) with B lymphocyte immunity. Sample clusters differed in terms of disease severity (p = .02) and S. aureus (SA) colonization (p = .02). Cluster 1 contained the most severe AD, highest SA colonization, and overexpressed MG‐I. Cluster 2 was characterized by less severe AD, low SA colonization, and high MG‐II expression. Cluster 3 included mild AD, mild SA colonization, and mild expression of all MGs. Cluster 4 had the same clinical features as cluster 3 but had hyper‐expression of MG‐III. Last, we successfully validated our method and results in an independent cohort.

Conclusion

Our study revealed unrecognized AD endotypes with specific underlying biological pathways, highlighting novel pathophysiological mechanisms. These data could provide new insights into personalized treatment strategies.
QTc interval on 24‐hour holter monitor: To trust or not to trust?
Authors: Tamr Agha Mhd Khalil , Fakhri Ghina , Ahmed Mohamed , El Sedawy Omar , Abi Saleh Bernard , Bitar Fadi , Arabi Mariam
Published: October 2021

Introduction

QT interval represents the ventricular depolarization and repolarization. Its accurate measurement is critical since prolonged QT can lead to sudden cardiac death. QT is affected by heart rate and is corrected to QTc via several formulae. QTc is commonly calculated on the ECG and not the 24‐h Holter.

Methods

100 patients presenting to our institution were evaluated by an ECG followed by a 24‐h Holter. QTc measurement on both platforms using Bazett and Fridericia formulae was recorded and compared.

Results

Mean age was 14.09 years, with the majority being males. Mean heart rate was 125.87. In the ECG, the mean QTc interval via the Bazett formula was 0.40 s compared with 0.38 s using the Fridericia formula. The mean corrected QT via the Bazett formula was 0.45, 0.39, and 0.42 s for the shortest RR, the longest RR, and the average RR, respectively. In contrast to the Fridericia formula, the corrected QT interval was 0.40, 0.39, and 0.40 s for the shortest RR, the longest RR, and the average RR, respectively. Using the Bazett formula, the highest specificity was reached during the longest RR interval (92.2%), while the highest sensitivity was recorded during the shortest RR interval (40%). As for the Fridericiaformula, sensitivity always reached 0%, while the highest specificity was reached during the average RR interval.

Conclusion

QTc measured during Holter ECG reached a high specificity regardless of RR interval using the Fridericia and during the longest and the average RR interval for the Bazett formula. The consistently low sensitivity reveals that Holter ECG should not be used to rule out prolonged QT.
Decreased frequency of transplantation and lower post‐transplant survival free of re‐transplantation in LVAD patients with the new heart transplant allocation system
Authors: Jani Milena , Lee Sangjin , Acharya Deepak , Hoeksema Sarah , Boeve Theodore , Leacche Marzia , Manandhar‐Shrestha Nabin K. , Jovinge Stefan V. , Loyaga‐Rendon Renzo Y.
Published: October 2021

Purpose

To evaluate the effect of the new heart transplant (HT) allocation system in left ventricular assist device (LVAD) supported patients listed as bridge to transplantation (BTT).

Methods

Adult patients who were listed for HT between October 18, 2016 and October 17, 2019, and were supported with an LVAD, enrolled in the UNOS database were included in this study. Patients were classified in the old or new system if they were listed or transplanted before or after October 18, 2018, respectively.

Results

A total of 3261 LVAD patients were listed for transplant. Of these, 2257 were classified in the old and 1004 in the new system. The cumulative incidence of death or removal from the transplant list due to worsening clinical status at 360‐days after listing was lower in the new system (4% vs. 7%, P = .011). LVAD Patients listed in the new system had a lower frequency of transplantation within 360‐days of listing (52% vs. 61%, P < .001). A total of 1843 LVAD patients were transplanted, 1004 patients in the old system and 839 patients in the new system. The post‐transplant survival at 360 days was similar between old and new systems (92.3% vs. 90%, P = .08). However, LVAD patients transplanted in the new system had lower frequency of the combined endpoint, freedom of death or re‐transplantation at 360 days (92.2% vs. 89.6%, P = .046).

Conclusion

The new HT allocation system has affected the LVAD‐BTT population significantly. On the waitlist, LVAD patients have a decreased cumulative frequency of transplantation and a concomitant decrease in death or delisting due to worsening status. In the new system, LVAD patients have a decreased survival free of re‐transplantation at 360 days post‐transplant.
Genetic basis of growth, spring phenology, and susceptibility to biotic stressors in maritime pine
Authors: Hurel Agathe , de Miguel Marina , Dutech Cyril , Desprez‐Loustau Marie‐Laure , Plomion Christophe , Rodríguez‐Quilón Isabel , Cyrille Agathe , Guzman Thomas , Alía Ricardo , González‐Martínez Santiago C. , Budde Katharina B.
Published: October 2021

Forest ecosystems are increasingly challenged by extreme events, for example, drought, storms, pest attacks, and fungal pathogen outbreaks, causing severe ecological and economic losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e., heritability) determines its potential for human‐mediated or evolutionary change. Maritime pine (Pinus pinaster Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, spring phenology, and susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), was assessed in a range‐wide clonal common garden of maritime pine. Broad‐sense heritability was significant for height (0.219), spring phenology (0.165–0.310), and pathogen susceptibility (necrosis length caused by D. sapinea, 0.152; and by A. ostoyae, 0.021, measured on inoculated, excised branches under controlled conditions), but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae with respect to height. Taller trees showed longer necrosis length caused by D. sapinea while shorter trees were more affected by A. ostoyae. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. Finally, an association study using 4227 genome‐wide SNPs revealed several loci significantly associated with each trait (range of 3–26), including a possibly disease‐induced translation initiation factor, eIF‐5, associated with needle discoloration caused by D. sapinea. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors.
Genetic and morphological data demonstrate hybridization and backcrossing in a pair of salamanders at the far end of the speciation continuum
Authors: Arntzen Jan W. , Jehle Robert , Wielstra Ben
Published: October 2021

Deeply diverged yet hybridizing species provide a system to investigate the final stages of the speciation process. We study a hybridizing pair of salamander species—the morphologically and genetically drastically different newts Triturus cristatus and T. marmoratus—with a panel of 32 nuclear and mitochondrial genetic markers. Morphologically identified hybrids are mostly of the F1 generation and mothered by T. cristatus. The sex ratio of the F1 hybrid class is reciprocally skewed, with a preponderance of females in T. cristatus‐mothered hybrids and males in T. marmoratus‐mothered hybrids. This amounts to the Haldane effect operating in one direction of the cross. Deeper generation hybrids are occasionally produced, possibly including F1 hybrid × backcross hybrid offspring. Interspecific gene flow is low, yet skewed toward T. cristatus. This asymmetry may be caused by hybrid zone movement, with the superseding species being predisposed to introgression. The persisting gene flow between deeply differentiated species supports the notion that full genetic isolation may be selected against. Conversely, published morphological data suggest that introgressive hybridization is detrimental, with digital malformations occurring more frequently in the area of sympatry. Finally, to assist field identification, both within the area of natural range overlap and concerning anthropogenic introductions elsewhere, we document the phenotypical variation of two generations of hybrids compared with both parental species. We suggest that fluctuating range boundaries, ecological segregation, cytonuclear incompatibilities and hybrid breakdown through Bateson–Dobzhansky–Muller incompatibilities all contribute to species integrity, despite incomplete isolation during secondary contact.
Deep learning‐influenced joint vehicle‐to‐infrastructure and vehicle‐to‐vehicle communication approach for internet of vehicles
Authors: Mekala M. S. , Dhiman Gaurav , Patan Rizwan , Kallam Suresh , Ramana Kadiyala , Yadav Kusum , Alharbi Ali O.
Published: October 2021

The internet of vehicle (IoV) orchestration is an emerging technology in heterogeneous vehicles to contrivance diverse intelligent transportation applications. The roadside unit (RSU) plays a vital role during service provisioning. Vehicle‐to‐vehicle and vehicle‐to‐infrastructure communications have consistently accomplished the services in a vehicular network. However, persisting the increased vehicles' quality of experience and network vendors' utilities and which RSUs have to select for effective, reliable service are critical open research challenges to consolidate RSU services to enhance network service utility rate. In this article, we design a deep learning‐inspired RSU Service Consolidation Approach based on two‐models to enhance the service reliability by formulating the RSU coverage issue with the RSU Migration model and content delivery issue with Linear Programming‐based Multicast model. Adaptive Packet‐Error measurement system to optimize service reliability rate at the edge of cooperative vehicular network based on content correlation. The performance and efficiency are examined based on MATLAB. The simulation outcome shows RSC approach has low execution cost by 39%, service reliability rate by 71% than the state‐of‐art approaches.
A formal method for privacy‐preservation in cognitive smart cities
Authors: Khan Mohammad Ayoub
Published: October 2021

The Internet of things (IoT) and communication technologies are enabling the consumer to use the smart devices. The explosion of smart devices is shifting the IoT into a framework, which we call the cognitive IoT. The cognitive IoT can enhance many sectors such as smart cities, healthcare, industry 4.0, transportation, just to name a few. Most of the data produced in smart cities are wasted because the important information is not extracted due to lack of standard mechanism for knowledge extraction and archiving methods. This has attracted the attention of researcher to design new approaches of machine and cognitive learning that can handle vast amount of dynamic data. The cognitive smart city is the integration of IoT, smart city technology, real‐time big data analytics and artificial intelligence (AI) strategies for proactive actions. The services in smart cities relies on the collection and analysis of the data which are provided by the use themselves or accessed by the services providers. The citizen engagement is the key for success of smart city; however, the engagement may get reduced due to privacy concerns arising from data collection. Therefore, privacy‐preservation shall be achieved in a manner where valuable data is exchanged with service provider, and other third party while protecting the citizens' privacy, upholding data laws and enforcement. Therefore, there is a need to control the anonymization and mix some more techniques to preserve the quality of the data. The proposed formal method for privacy‐preservation in smart cities is based on pseudonymization, clustering, anonymization and differential privacy methods. The modified clustering algorithm selects the initial cluster based on the concept of dissimilarity between the data sequences. We have assessed the functional correctness and preformation of the proposed model for privacy‐preservation in smart cities. The proposed method has lower discriminating rate as compared to other existing methods.
The FEBS Journal: hidden gems
Authors: Breuer Manuel
Published: October 2021

Every quarter, The FEBS Journal presents some of its ‘hidden gems’—original research and review‐type articles that provide a significant advance or discuss recent developments in the molecular or cellular life sciences. These articles are of high value to the scientific community, and we like to take the opportunity to promote these contributions from previous issues of the journal, as we feel their scientific content merits a boost in exposure.
Prolonged disturbance of proteostasis induces cellular senescence via temporal mitochondrial dysfunction and subsequent mitochondrial accumulation in human fibroblasts
Authors: Takenaka Yasuhiro , Inoue Ikuo , Nakano Takanari , Ikeda Masaaki , Kakinuma Yoshihiko
Published: October 2021

Proteolytic activity declines with age, resulting in the accumulation of aggregated proteins in aged organisms. To investigate how disturbance in proteostasis causes cellular senescence, we developed a stress‐induced premature senescence (SIPS) model, in which normal human fibroblast MRC‐5 cells were treated with the proteasome inhibitor MG132 or the vacuolar‐type ATPase inhibitor bafilomycin A1 (BAFA1) for 5 days. Time‐course studies revealed a significant increase in intracellular reactive oxygen species (ROS) and mitochondrial superoxide during and after drug treatment. Mitochondrial membrane potential initially decreased, suggesting temporal mitochondrial dysfunction during drug treatment, but was restored along with mitochondrial accumulation after drug treatment. AMP‐activated protein kinase alpha was notably activated during treatment; thereafter, intracellular ATP levels significantly increased. SIPS induction by MG132 or BAFA1 was partially attenuated by co‐treatment with vitamin E or rapamycin, in which the levels of ROS, mitochondrial accumulation, and protein aggregates were suppressed, implying the critical involvement of oxidative stress and mitochondrial function in SIPS progression. Rapamycin co‐treatment also augmented the expression of HSP70 and activation of AKT, which could recover proteostasis and promote cell survival, respectively. Our study proposes a possible pathway from the disturbed proteostasis to cellular senescence via excess ROS production as well as functional and quantitative changes in mitochondria.
Understanding coralline algal responses to ocean acidification: Meta‐analysis and synthesis
Authors: Cornwall Christopher E. , Harvey Ben P. , Comeau Steeve , Cornwall Daniel L. , Hall‐Spencer Jason M. , Peña Viviana , Wada Shigeki , Porzio Lucia
Published: October 2021

Ocean acidification (OA) is a major threat to the persistence of biogenic reefs throughout the world's ocean. Coralline algae are comprised of high magnesium calcite and have long been considered one of the most susceptible taxa to the negative impacts of OA. We summarize these impacts and explore the causes of variability in coralline algal responses using a review/qualitative assessment of all relevant literature, meta‐analysis, quantitative assessment of critical responses, and a discussion of physiological mechanisms and directions for future research. We find that most coralline algae experienced reduced abundance, calcification rates, recruitment rates, and declines in pH within the site of calcification in laboratory experiments simulating OA or at naturally elevated CO2sites. There were no other consistent physiological responses of coralline algae to simulated OA (e.g., photo‐physiology, mineralogy, and survival). Calcification/growth was the most frequently measured parameters in coralline algal OA research, and our meta‐analyses revealed greater declines in seawater pH were associated with significant decreases in calcification in adults and similar but nonsignificant trends for juveniles. Adults from the family Mesophyllumaceae also tended to be more robust to OA, though there was insufficient data to test similar trends for juveniles. OA was the dominant driver in the majority of laboratory experiments where other local or global drivers were assessed. The interaction between OA and any other single driver was often additive, though factors that changed pH at the surface of coralline algae (light, water motion, epiphytes) acted antagonistically or synergistically with OA more than any other drivers. With advances in experimental design and methodological techniques, we now understand that the physiology of coralline algal calcification largely dictates their responses to OA. However, significant challenges still remain, including improving the geographic and life‐history spread of research effort and a need for holistic assessments of physiology.
Reducing model uncertainty of climate change impacts on high latitude carbon assimilation
Authors: Rogers Alistair , Serbin Shawn P. , Way Danielle A.
Published: October 2021

The Arctic–Boreal Region (ABR) has a large impact on global vegetation–atmosphere interactions and is experiencing markedly greater warming than the rest of the planet, a trend that is projected to continue with anticipated future emissions of CO2. The ABR is a significant source of uncertainty in estimates of carbon uptake in terrestrial biosphere models such that reducing this uncertainty is critical for more accurately estimating global carbon cycling and understanding the response of the region to global change. Process representation and parameterization associated with gross primary productivity (GPP) drives a large amount of this model uncertainty, particularly within the next 50 years, where the response of existing vegetation to climate change will dominate estimates of GPP for the region. Here we review our current understanding and model representation of GPP in northern latitudes, focusing on vegetation composition, phenology, and physiology, and consider how climate change alters these three components. We highlight challenges in the ABR for predicting GPP, but also focus on the unique opportunities for advancing knowledge and model representation, particularly through the combination of remote sensing and traditional boots‐on‐the‐ground science.
Effect of pyrocarbon interphase texture and thickness on tensile damage and fracture in T‐700™ carbon fiber–reinforced silicon carbide minicomposites
Authors: Duan Haozhi , Zhang Zhongwei , Li Longbiao , Li Weijie
Published: October 2021

In this paper, T‐700™ carbon fiber–reinforced silicon carbide (C/SiC) minicomposites with pyrocarbon (PyC) interphase with different textural microstructure and thickness were fabricated using the chemical vapor infiltration method. The interface properties (i.e., textural microstructure, thickness, hardness, and modulus) were obtained through multiple testing methods (i.e., Raman spectroscopy, X‐ray diffraction, scanning electron microscopy, and nanoindentation tests). Relationships between the deposition temperature and residence time with the texture type (i.e., low, medium, and high texture) were established. Uniaxial tensile experiments were conducted for C/SiC minicomposites with different PyC interphases to characterize the composite's internal damage evolution and fracture. Relationships between the composite's tensile nonlinear damage evolution, fracture strength and strain, PyC interphase texture, and thickness were established. The composite's tensile strength and fracture strain were the highest for the C/SiC minicomposite with medium‐high texture PyC interphase. For the C/SiC minicomposite with the same texture interphase, the composite's tensile strength and fracture strain were affected by the coating thickness. The higher the thickness of the coating, the lower the composite's tensile strength and fracture strain.
Effect of ethanol on astaxanthin and fatty acid production in the red yeast Xanthophyllomyces dendrorhous
Authors: Kikukawa Hiroshi , Shimizu Chisato , Hirono-Hara Yoko , Hara Kiyotaka Y.
Published: October 2021

Aim

The effects of detergent, ethanol and ethanol with plant meadowfoam oil on the growth of the red heterobasidomycete Xanthophyllomyces dendrorhous and on the production of astaxanthin (3,3′-dihydroxy-β,β-carotene-4,4′-dione) and fatty acids in this red yeast were investigated.

Methods and Results

Ethanol supplementation at a final concentration of 0.8% (v/v) caused an increase in the growth, astaxanthin production and fatty acid production of treated X. dendrorhous compared with untreated X. dendrorhous. Supplementation of meadowfoam oil with 0.8% ethanol further improved the growth and astaxanthin production of X. dendrorhous. Fatty acid compositions following supplementation with various concentrations of ethanol and oil were also analysed. With 0.8% ethanol supplementation, the ratio of linoleic acid (C18:2) and α-linolenic acid (C18:3ω3, ALA) decreased. Conversely, with 1.8% ethanol supplementation, the ALA ratio increased.

Conclusions

Ethanol can serve as a promoting factor for coproduction of astaxanthin and fatty acids in X. dendrorhous, whereas simultaneous supplementation of ethanol and meadowfoam oil can cause further astaxanthin production.

Significance and Impact of Study

Astaxanthin is widely used in various functional products because of its antioxidant activity. This study shows that X. dendrorhous can coproduce astaxanthin and functional fatty acids at high levels following supplementation with ethanol.
Intraspecific and interspecific extracellular metabolites remodel biofilms formed by thermophilic spoilage bacteria
Authors: Wang Ni , Jin Yujie , He Guoqing , Yuan Lei
Published: October 2021

Aims

Thermophilic spoilage bacteria and their biofilms formed during milk powder processing posed threats to safety and quality of dairy products. This research aims to understand more about the bacterial behaviours and their social models in biofilms.

Methods and Results

Interactional effects from both extracellular metabolites and co-culture on biofilms formation of the contaminating thermophilic bacteria were determined. The results showed that strong biofilm formers always had high AI-2 activities, including Geobacillus stearothermophilus gs1, Bacillus licheniformis bl1 and Thermoactinomyces vulgaris tv1. Metabolites from themself or other species altered their biofilm biomass detected by crystal violet staining. Dual-species cultures observed by confocal laser scanning microscope indicated either synergistic or inhibitory effects between B. circulans bc1 and G. stearothermophilus gs1, as well as B. licheniformis bl1 and G. stearothermophilus gs1. Fourier transform infrared spectrometry results revealed the significant diversities in polysaccharides of the biofilm matrix.

Conclusions

Cell communication played an important role on biofilm formation in the complex microbial community. Intraspecific and interspecific extracellular metabolites influenced collective bacterial behaviours under mixed circumstances.

Significance and impact of study

This research provided evidences on cell communication and biofilm formation of thermophilic bacteria in dairy industry.
Training direct‐care staff to implement sensory integration strategies on a psychiatric inpatient unit
Authors: Proterra Katherine , Ehrlich Shana , Romani Patrick W.
Published: October 2021

Problem

Despite the importance of sensory integration therapy on psychiatric inpatient units, there continues to be a paucity of trained providers that can delivery this service to patients.

Method

This study evaluated components of a training program to teach nurses and direct‐care staff appropriate use of sensory integration strategies. Using the research team as confederates, we collected data on how three direct‐care staff used sensory integration strategies across two conditions and with a patient admitted to the unit. Next, we implemented the didactic‐only training, which provided education for when to use different aspects of the sensory room. Finally, we transitioned to a condition in which feedback supplemented the didactic training.

Findings

Before training and following the Didactic Only Training condition, accuracy was low for all participants. All three participants' accuracy with using sensory integration strategies improved and maintained when they implemented the strategies with a patient after completing the combined intervention. We were able to use the combined intervention to improve two additional direct‐care staff's accuracy.

Conclusions

Staff training incorporating didactic training plus feedback was most effective for training appropriate use of sensory integration strategies. We also discuss the importance of having performance‐based measures to track occurrence of important skills.
Sleep habits and sleep problems associated with depressive symptoms in school‐age children
Authors: Moo‐Estrella Jesús , Arankowsky‐Sandoval Gloria , Valencia‐Flores Matilde
Published: October 2021

Problem

Sleep disturbance is a characteristic symptom of depression, but it is also a problem in itself related to the severity of this illness. Hence, the objective of this study was to examine sleep habits and sleep problems associated with increased depressive symptoms in children.

Methods

The sample included 524 children equally distributed by gender (51.1% female), with an average age of 10.29 (SD = 1.34) years. The administered instruments were the Children's Depression Inventory (CDI; Cronbach α = 0.82) and a Sleep Habits and Sleep Problems Questionnaire (α = 0.91).

Findings

The mean score for the CDI was 12.51 (SD = 6.74) and 20% presented symptoms of depression. The linear regression model showed that sleep habits associated with the increase in symptoms of depression were: little sleep, hours of sleep during the week, and wake‐up time on weekdays. In the same model, the associated sleep problems were: nocturnal awakenings, nightmares, and difficulty waking up. The presence of these sleep habits and sleep problems increased the score from 2.07 to 13.50 points on the CDI scale.

Conclusions

Depressive symptoms increase with the presence of sleep habits related to sleep deprivation and sleep problems related to parasomnias in school‐age children.
Molecular evolution and convergence of the rhodopsin gene in Gymnogobius, a goby group having diverged into coastal to freshwater habitats
Authors: Ito Ryosuke K. , Harada Shigeo , Tabata Ryoichi , Watanabe Katsutoshi
Published: October 2021

Adaptive evolution of vision‐related genes has been frequently observed in the process of invasion of new environments in a wide range of animal taxa. The typical example is that of the molecular evolution of rhodopsin associated with habitat changes in aquatic animals. However, few studies have investigated rhodopsin evolution during adaptive radiation across various habitats. In the present study, we examined the link between molecular evolutionary patterns in the rhodopsin gene and macroscopic habitat changes in Gymnogobius species (Gobiidae), which have adaptively radiated to diverse aquatic habitats including the sea, brackish waters, rivers and lakes. Analysis of amino acid substitutions in rhodopsin in the phylogenetic framework revealed convergent substitutions in 4–5 amino acids in three groups (four species), including two spectral tuning amino acid sites known to change rhodopsin's absorption wavelength. Positive selection was detected in the basal branches of each of these three groups, suggesting adaptive molecular convergence of rhodopsin. However, no significant correlation was observed between amino acid substitutions and the species’ habitat changes, suggesting molecular adaptation to some unidentified micro‐ecological environments. Taken together, these results emphasize the importance of considering not only macroscopic habitats but also micro‐ecological environments when elucidating the driving forces of adaptive evolution of the visual system.
Robotic single‐port myomectomy using the da Vinci SP surgical system: A pilot study
Authors: Lee Jung Hun , Yoo Hae Kyung , Park So Yun , Moon Hye‐Sung
Published: October 2021

Aim

To report our initial experience with robotic single‐port myomectomy (RSPM) using the da Vinci SP surgical system and to evaluate the feasibility of the procedure.

Material and Methods

This prospective observational study was performed at a university teaching hospital from January 2019 to December 2019. Sixty‐one women with symptomatic fibroids received RSPM.

Results

Based on seven resected fibroids and a maximal diameter of resected fibroids <10 cm, the women were arbitrarily divided into two groups. The mean number and maximal diameter of the removed fibroids were 3.7 ± 3.8 (2.3 ± 1.8 in Group 1 vs. 7.2 ± 5.3 in Group 2) and 7.6 ± 2.9 cm (6.8 ± 1.6 in Group 1 vs. 9.5 ± 4.3 in Group 2), respectively. The mean operation time, hemoglobin change, and hospital stay were 149.9 ± 72.9 min (123.8 ± 43.8 in Group 1 vs. 217.6 ± 89.4 in Group 2), 2.3 ± 1.0 g/dL (2.1 ± 0.9 in Group 1 vs. 2.7 ± 1.2 in Group 2), and 4.5 ± 0.8 days (4.4 ± 0.8 in Group 1 vs. 4.7 ± 0.9 in Group 2). There was no conversion to multi‐port laparoscopy or laparotomy nor were there any major complications.

Conclusions

RSPM using the da Vinci SP surgical system is feasible surgical modality for women with symptomatic fibroid and is expected to increase indications of single‐port myomectomy by solving many of the ergonomics problems inevitably accompanying single‐port laparoscopic myomectomy.