bluuebunny/crossref_metadata_2025 huggingface dataset:
Lactiplantibacillus plantarum HG20 attenuates II type collagen-induced rheumatoid arthritis in rats via anti-inflammatory and inhibition of apoptosis
Authors: Liu Chunhong , Lin Li , Cui Weidong , Wang Lei , Ai Min , Zhao Zhongwei , Ma Xiaohan , Li Shengyu
Published: October 2021

Aims

This study aimed to explore the therapeutic effects of Lactiplantibacillus plantarum HG20 (HG20) on collagen-induced arthritis (CIA) rats and its mechanism.

Methods and Results

CIA rats were established by injecting bovine type II collagen for 7 days, and treated by intragastric administration HG20 for 21 days. The foot palm temperature and arthritis score were measured once a week. The pathological changes in the knee joint were observed by hematoxylin and eosin staining. The levels of cytokines were detected by enzyme linked immunosorbent assay, and the effects of HG20 on inflammatory and apoptosis pathway of spleen cells were detected by western blot analysis. The results indicated that HG20 reduced the joint swelling degree and foot palm temperature, inhibited the development of joint histopathology, decreased the levels of pro-inflammatory cytokines, down-regulate the expression of pro-inflammatory cytokines by nuclear factor kappa-B pathway, and inhibited the apoptosis of spleen cells by inhibiting phosphatidylinositol 3-kinase/protein kinase B pathway and regulating apoptosis pathways.

Conclusions

HG20 had an adjuvant therapeutic effect on arthritis in CIA rats, and its mechanism might be related to the inflammatory and apoptosis pathway.

Significance and Impact of Study

These results revealed that HG20 could be used as a functional probiotic in the field of food and medical, and which played a potential role in the prevention and treatment of arthritis.
Detection of virulence and extended spectrum β-lactamase genes in Salmonella by multiplex high-resolution melt curve real-time PCR assay
Authors: Dhital Rajiv , Shen Zhenyu , Zhang Shuping , Mustapha Azlin
Published: October 2021

Aims

Develop and standardize multiplex high-resolution melt curve (HRM) real-time PCR assays for simultaneous detection of Salmonella virulence and extended spectrum β-lactamase (ESBL) genes in food.

Methods and Results

Two sets of multiplex real-time PCR assays targeting six virulence and three ESBL genes with internal amplification control were standardized. The first assay detected hilA, fimH, sipA, blaTEM and blaSHV, and the second detected invA, fimA, stn and blaCMY. The PCR assays were validated with DNA samples from 77 different Salmonella strains. The assay specificity was tested with DNA from 47 non-Salmonella strains. Melt curve analyses showed distinct, well-separated melting peaks of each target gene detected by their respective melting temperatures (Tm). Different food samples were spiked with 10, 102 and 103 CFU/ml of Salmonella. The optimized assays were able to detect all target genes in concentrations of as low as 10 CFU/ml in 25 g foods within 10 h of enrichment.

Conclusions

Multiplex HRM real-time PCR assays can be used as rapid detection methods for detecting Salmonella in foods.

Significance and Impact of Study

The assays developed in this study will allow for accurate detection of virulence and ESBL genes in Salmonella that are present in low concentrations in food samples.
Ocular expression of cyclin‐dependent kinase 5 in patients with proliferative diabetic retinopathy
Authors: Sano Hiroki , Namekata Kazuhiko , Niki Masanori , Semba Kentaro , Murao Fumiko , Harada Takayuki , Mitamura Yoshinori
Published: October 2021

Aims/Introduction

Inhibition of peroxisome proliferator‐activated receptor gamma (PPARγ) phosphorylation mediated by cyclin‐dependent kinase 5 (Cdk5) is one of the main mechanisms of action of antidiabetic drugs. In this study, we analyzed the ocular expression and activation of Cdk5 in patients with proliferative diabetic retinopathy (PDR).

Materials and Methods

The concentrations of PPARγ, Cdk5 and its activating subunit (p35) were determined in the vitreous body of 24 PDR and 63 control eyes by enzyme‐linked immunosorbent assay. In addition, the messenger ribonucleic acid and protein expression levels of PPARγ, Cdk5 and p35 were measured in proliferative neovascular membranes from seven PDR eyes and non‐neovascular epiretinal membranes from five control eyes by quantitative real‐time polymerase chain reaction and immunohistochemical analysis.

Results

PPARγ, Cdk5 and p35 concentrations in the vitreous body were significantly higher in the PDR group compared with the control group. There was also a positive significant correlation of Cdk5 with PPARγ and p35 in the PDR group. Furthermore, the messenger ribonucleic acid expression levels of PPARγ, Cdk5 and p35 in proliferative neovascular membranes were significantly higher in the PDR group compared with the control group. Immunostaining showed increased protein expression levels of PPARγ, Cdk5 and p35 in proliferative neovascular membranes in the PDR group compared with the control group.

Conclusions

Cdk5 activation is involved in PDR pathogenesis through PPARγ expression, and inhibition of Cdk5‐mediated PPARγ phosphorylation might be a new therapeutic target for treatment of PDR.
The relation between narcissism and aggression: A meta‐analysis
Authors: Du Tianwei V. , Miller Joshua D. , Lynam Donald R.
Published: October 2021

Objective

Narcissism is a complex, hierarchical construct that can be studied at the one, two, or three factor levels with different components within each level having their own unique nomological networks. The manner in which narcissism—both broadly and narrowly construed—is linked to aggression is important to understand given longstanding clinical and empirical observations of a link between the two and the critical implications of aggression.

Methods

The current preregistered meta‐analysis (k = 118) took a novel methodological approach in exploring the association between the three levels of narcissism (i.e., global construct level, dual‐dimension level, trifurcated level) and three indices of aggression (i.e., general, proactive, reactive).

Results

Results revealed that the global construct of narcissism shows a moderate positive association with different indices of aggression. Vulnerable narcissism associated strongly and positively with reactive aggression and general aggression. At the trifurcated level, interpersonal antagonism associated positively with all indices of aggression, agentic extraversion associated negatively with all indices of aggression, and narcissistic neuroticism associates positively with general and reactive aggression.

Conclusion

The study highlighted the importance of studying narcissism, and potentially other personality profiles, at a finer‐grained level to better understand crucial psychological processes associated with the construct of interest.
A single nucleotide mutation in exon 2 produces a novel HLA‐DRB1*07 null allele, HLA‐DRB1*07:129N
Authors: Yang Kuo‐Liang , Li Chi‐Cheng , Lin Py‐Yu
Published: October 2021

A nucleotide mutation in codon 34 of HLA‐DRB1*07:01:01:01 results in a novel allele HLA‐DRB1*07:129N.
Where to cut to delay a pandemic with minimum disruption? mathematical analysis based on the SIS model
Authors: Bartesaghi Paolo , Estrada Ernesto
Published: October 2021

We consider the problem of modifying a network topology in such a way as to delay the propagation of a disease with minimal disruption of the network capacity to reroute goods/items/passengers. We find an approximate solution to the Susceptible-Infected-Susceptible (SIS) model, which constitutes an upper bound to its exact solution. This upper bound allows direct structure-epidemic dynamic relations via the total communicability function. Using this approach we propose a strategy to remove edges in a network that significantly delays the propagation of a disease across the network with minimal disruption of its capacity to deliver goods/items/passengers. We apply this strategy to the analysis of the UK airport transportation network weighted by the number of passengers transported in 2003. We find that the removal of all flights connecting four origin-destination pairs in the UK delays the propagation of a disease by more than 300%, with a minimal deterioration of the transportation capacity of this network. These time delays in the propagation of a disease represent an important non-pharmaceutical intervention to confront an epidemic, allowing for better preparations of the health systems, while keeping the economy moving with minimal disruptions.
Center of mass energy of charged particles about Reissner–Nordström black hole
Authors: Zakria Ayesha
Published: October 2021

We study the acceleration of charged particles by Reissner Nordström black hole by taking into account the term appearing in the formula of the center of mass energy due to charge of the particle. We consider that the particle is radially falling towards the black hole, i.e., [Formula: see text]. It is found that the center of mass energy is infinitely large at the outer horizon without any constraint.
Incorporating biological networks into high-dimensional Bayesian survival analysis using an ICM/M algorithm
Authors: Pungpapong Vitara
Published: October 2021

The Cox proportional hazards model has been widely used in cancer genomic research that aims to identify genes from high-dimensional gene expression space associated with the survival time of patients. With the increase in expertly curated biological pathways, it is challenging to incorporate such complex networks in fitting a high-dimensional Cox model. This paper considers a Bayesian framework that employs the Ising prior to capturing relations among genes represented by graphs. A spike-and-slab prior is also assigned to each of the coefficients for the purpose of variable selection. The iterated conditional modes/medians (ICM/M) algorithm is proposed for the implementation for Cox models. The ICM/M estimates hyperparameters using conditional modes and obtains coefficients through conditional medians. This procedure produces some coefficients that are exactly zero, making the model more interpretable. Comparisons of the ICM/M and other regularized Cox models were carried out with both simulated and real data. Compared to lasso, adaptive lasso, elastic net, and DegreeCox, the ICM/M yielded more parsimonious models with consistent variable selection. The ICM/M model also provided a smaller number of false positives than the other methods and showed promising results in terms of predictive accuracy. In terms of computing times among the network-aware methods, the ICM/M algorithm is substantially faster than DegreeCox even when incorporating a large complex network. The implementation of the ICM/M algorithm for Cox regression model is provided in R package icmm, available on the Comprehensive R Archive Network (CRAN).
Three-Dimensional Graphene Network and UiO-66 Based Composite Photocatalysts for High Visible-Light Activity
Authors: Wang Xiaobing , Feng Chen , Zhu Chenyang , Gao Ying
Published: October 2021

Three-dimensional graphene network (3DGN) and UiO-66 co-modified composite photocatalysts are prepared to decompose dye in solution. The roles of UiO-66 and 3DGN are studied based on the adsorption capacity, visible-light activity, lifetime of photo-induce electrons and electron paramagnetic resonance curves. The rates of degradation of Rhodamine-B are [Formula: see text][Formula: see text]min[Formula: see text] and [Formula: see text][Formula: see text]min[Formula: see text] under UV- and visible-light irradiation. The major function of UiO-66 is increasing the Brunner–Emmet–Teller surface area and adsorption capacity significantly, while the effect of 3DGN is playing as an electron tank and sensitizer. Moreover, the influence of mass fraction of UiO-66 on the resulting photocatalytic performances is revealed (5[Formula: see text]wt.% is found the optimized value), and the synergy is also discussed. Finally, the photocatalytic mechanisms of the resulting photocatalysts both under the UV- and visible-light irradiation are proposed.
Lithium storage properties of Li2MoO3 and its effect as a cathode additive in full cells
Authors: Zhao Taolin , Chen Shaokang , Gao Xingyue , Zhang Yuxia
Published: October 2021

High-performance lithium–ion batteries (LIBs) are the main development direction of future energy storage devices. However, most LIBs still face a problem of high first irreversible capacity loss. Pre-lithiation technology can increase the content of active lithium source and compensate the loss of active lithium during the first cycle. Adding lithium supplement additive to the cathode provides an effective way to improve the electrochemical performance of LIBs. Here, Li2MoO3 has been investigated as a cathode additive in the full cells. In order to optimize its preparation, Li2MoO3 has been prepared by three different methods, including solid-phase method, liquid-phase method and ultrasonic method. Based on material characterization and electrochemical performance tests, Li2MoO3 material prepared by liquid-phase method shows the best lithium storage properties and chosen as a cathode additive in the LiNi[Formula: see text]Co[Formula: see text]Mn[Formula: see text]O2/SiO@C full cells. The addition of Li2MoO3 has successfully improved the electrochemical performance of the full cell. The first discharge specific capacity increases from 103.9 mAh g[Formula: see text] to 130.4 mAh g[Formula: see text]. In short, Li2MoO3 material is a promising cathode additive for LIBs.
NiS nanosheets synthesized by one-step microwave for high-performance supercapacitor
Authors: Song Jun , Du Lijun , Wang Jingyi , Zhang Huaiping , Zhang Yaodong , Li Baobi , Zhang Zhuxia , Li Tianbao , Luo Jujie
Published: October 2021

The NiS nanosheets were fabricated using one-step microwave approach with the microwave radiation of 800 W for 1.5 min. Impressively, the NiS nanosheets revealed praiseworthy electrochemical performance, with a capacitance value of 1082.8 F ⋅ g[Formula: see text] at 1 A ⋅ g[Formula: see text] and 77.8% retention over 5000 cycles at 5 A ⋅ g[Formula: see text]. Moreover, an asymmetric supercapacitor was assembled with NiS as the positive electrode and activated carbon (AC) as the negative electrode. It shows 80.42% capacity retention after 8000 cycles and an energy density of 19.45 W ⋅ h ⋅ kg[Formula: see text] at a power density of 801.05 W ⋅ kg[Formula: see text].
Bank Liquidity Hoarding and the Financial Crisis: An Empirical Evaluation
Authors: Berrospide Jose M.
Published: October 2021

I test and find supporting evidence for the precautionary motive hypothesis of liquidity hoarding for U.S. commercial banks during the global financial crisis. I find that banks held more liquid assets in anticipation of future losses from securities write-downs. Exposure to securities losses in their investment portfolios and expected loan losses (measured by loan loss reserves) represent key measures of banks’ on-balance sheet risks, in addition to off-balance sheet liquidity risk stemming from unused loan commitments. Furthermore, unrealized securities losses and loan loss reserves seem to better capture the risks stemming from banks’ asset management and provide supporting evidence for the precautionary nature of liquidity hoarding. Moreover, I find that more than one-fourth of the reduction in bank lending during the crisis is due to the precautionary motive.
Identification of Hotspot Residues in Binding of SARS-CoV-2 Spike and Human ACE2 Proteins
Authors: Mendis Jenny , Kaya Ekrem , Kucukkal Tugba G.
Published: October 2021

Coronaviruses are a large family of viruses that can cause respiratory infections with varying severity from common cold to severe diseases such as novel coronavirus disease (COVID-19). COVID-19 has been declared as a global pandemic by the World Health Organization on March 11, 2020 and with the development of vaccines it slowed down as of this date. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses its spike glycoprotein (Sgp) to bind human angiotensin-converting enzyme 2 (hACE2) receptor, and mediates membrane fusion and virus entry. The recognition of Sgp to human ACE2 and its high affinity for it has been of great importance since this provides the first step in viral entry to human cells. Therefore, it is crucial to identify key residues (hotspots) in this process. In this study, computational alanine scanning has been performed for Sgp and hACE2. The residues identified with significance in binding and other residues in close proximity were studied further through molecular mechanics-based protein binding free energy change prediction methods. Moreover, the interfacial residues in both proteins were investigated for their cooperative binding. Additionally, folding free energy changes upon mutation to Ala were calculated to assess their effect on stability of Sgp and hACE2. Our results taken together with findings from previous studies revealed the residues that are most significant and are relatively significant in binding of Sgp to human ACE2 protein.
Coronavirus disease 2019 in kidney transplant recipients: a systematic review and meta-analysis
Authors: Ho Quan Yao , Sultana Rehena , Lee Tung Lin , Thangaraju Sobhana , Kee Terence , Htay Htay
Published: October 2021

Introduction:

The clinical presentation and outcomes of coronavirus disease 2019 (COVID-19) in kidney transplant recipients (KTRs) have not been well studied.

Methods:

We performed a meta-analysis to examine the presenting features, outcomes and the effect of treatment on outcomes of KTRs with COVID-19. Database search was performed up to 5 September 2020 through PubMed, Embase, Web of Science, Scopus and CENTRAL.

Results:

Overall, 23 studies (1,373 patients) were included in the review and meta-analysis. The most common presenting symptoms included fever (74.0%, 95% confidence interval [CI] 65.3–81.1), cough (63.3%, 95% CI 56.5–69.6) and dyspnoea (47.5%, 95% CI 39.6–55.6). Pooled rates of mortality and critical illness were 21.1% (95% CI 15.3–28.4) and 27.7% (95% CI 21.5–34.8), respectively. Acute kidney injury occurred in 38.9% (95% CI 30.6–48.1) and dialysis was required in 12.4% (95% CI 8.3–18.0) of the cases.

Conclusion:

Kidney transplant recipients with COVID-19 have a similar clinical presentation as the general population, but they have higher morbidity and mortality. It is uncertain whether high-dose corticosteroid or hydroxychloroquine reduces the risks of mortality in KTRs with COVID-19.
Preparation and Properties of Thrombus-Targeted Urokinase/Multi-Walled Carbon Nanotubes (MWCNTs)-Chitosan (CS)-RGD Drug Delivery System
Authors: Zhang Ru , Luo Shang , Hao Lin-Kun , Jiang Yun-Ying , Gao Ying , Zhang Ning-Ning , Zhang Xue-Cheng , Song Yi-Min
Published: October 2021

In order to improve the therapeutic effect, prolong the action time and reduce the side effects of the first generation thrombolytic drug urokinase (UK), a novel UK/multi-walled carbon nanotubes (MWCNTs)-chitosan (CS)-arginine-glycine-aspartic acid (Arg-Gly-Asp) (RGD) drug delivery
system was synthesized by chemical bonding/non covalent bond modification/ultrasonic dispersion. The results showed that the diameter of the UK/MWCNTs-CS-RGD drug delivery system was about 30–40 nm, there was a layer of UK was attached to the surface of the tube wall, and the distribution
was relatively uniform. The average encapsulation efficiency was 83.10%, and the average drug loading was 12.81%. Interestingly, it also had a certain sustained-release effect, and its release law was best fitted by first-order kinetic equation. Moreover, the accelerated and long-term stability
test results show that it had good stability. Compared with free UK, UK/MWCNTs-CS-RGD had thrombolytic effect in vitro. In addition, MTT experiment showed that the prepared MWCNTs-CS-RGD nanomaterials had good biocompatibility. A rabbit model of carotid artery thrombosis was used to
conduct targeted thrombolysis experiments in vivo. Compared with free UK, UK/MWCNTs-CS-RGD could be enriched in the thrombosis site to achieve thrombus targeting. UK/MWCNTs-CS-RGD drug delivery system was expected to become an effective thrombolytic drug for targeted therapy of thrombosis.
Preparation and Antibacterial Performances of Electrocatalytic Zinc Oxide Nanoparticles with Diverse Morphologies
Authors: Li Junlin , Li Xiangfei , Liang Dong , Zhang Xiaojuan , Lin Qing , Hao Lingyun
Published: October 2021

This study exploits the potential of zinc oxide nanoparticles (ZnO-NPs) with diverse morphologies as catalysts and antibacterial agent. Spherical ZnO-NPs, rod-shaped ZnO-NPs and flower-shaped ZnO-NPs were prepared by microemulsion method, solvent heat method and hydrothermal method,
respectively. The structural characterizations of samples were investigated by X-ray diffraction (XRD) and scanning electron microscopy (SEM) techniques. XRD results revealed the formation of spherical ZnO-NPs, rod-shaped ZnO-NPs and flower-shaped ZnO-NPs were all wurtzite crystal structure.
SEM results showed that spherical ZnO-NPs had an average particle size of 30–40 nm, rod-shaped ZnO-NPs were about 500 nm long and 100 nm wide with obvious hexagonal crystals. Flower-shaped ZnO-NPs had a three-dimensional appearance with obvious petals. Results of electrochemical HER
(Hydrogen evolution reaction) experiments revealed that spherical ZnO-NPs exhibited the highest electrocatalytic activity at the lowest potential voltage due to their largest specific surface area. The antibacterial property of ZnO-NPs samples were studied by the optical density method and
disc diffusion method. All samples had antibacterial effects against E. coli. and flower-shaped ZnO-NPs showed the best antibacterial activity due to the largest surface area in comparison with spherical ZnO-NPs and rod-shaped ZnO-NPs, which promised the maximum Zn2+ release
as bactericide mechanism that registered in the case of different ZnO-NPs morphologies.
Population Structure of Nation-Wide Rice in Thailand
Authors: Vejchasarn Phanchita , Shearman Jeremy R. , Chaiprom Usawadee , Phansenee Yotwarit , Suthanthangjai Arissara , Jairin Jirapong , Chamarerk Varapong , Tulyananda Tatpong , Amornbunchornvej Chainarong
Published: October 2021

Background

Thailand is a country with large diversity in rice varieties due to its rich and diverse ecology. In this paper, 300 rice accessions from all across Thailand were sequenced to identify SNP variants allowing for the population structure to be explored.

Results

The result of inferred population structure from admixture and clustering analysis illustrated strong evidence of substructure in each geographical region. The results of phylogenetic tree, PCA analysis, and machine learning on population identifying SNPs also supported the inferred population structure.

Conclusion

The population structure inferred in this study contains five subpopulations that tend to group individuals based on location. So, each subpopulation has unique genetic patterns, agronomic traits, as well as different environmental conditions. This study can serve as a reference point of the nation-wide population structure for supporting breeders and researchers who are interested in Thai rice.
Overexpression of OsLCT2, a Low-Affinity Cation Transporter Gene, Reduces Cadmium Accumulation in Shoots and Grains of Rice
Authors: Tang Li , Dong Jiayu , Tan Longtao , Ji Zhongying , Li Yaokui , Sun Yuantao , Chen Caiyan , Lv Qiming , Mao Bigang , Hu Yuanyi , Zhao Bingran
Published: October 2021

Cadmium (Cd)-contaminated rice is a serious issue affecting food safety. Understanding the molecular regulatory mechanisms of Cd accumulation in rice grains is crucial to minimizing Cd concentrations in grains. We identified a member of the low-affinity cation transporter family, OsLCT2 in rice. It was a membrane protein. OsLCT2 was expressed in all tissues of the elongation and maturation zones in roots, with the strongest expression in pericycle and stele cells adjacent to the xylem. When grown in Cd-contaminated paddy soils, rice plants overexpressing OsLCT2 significantly reduced Cd concentrations in the straw and grains. Hydroponic experiment demonstrated its overexpression decreased the rate of Cd translocation from roots to shoots, and reduced Cd concentrations in xylem sap and in shoots of rice. Moreover, its overexpression increased Zn concentrations in roots by up-regulating the expression of OsZIP9, a gene responsible for Zn uptake. Overexpression of OsLCT2 reduces Cd accumulation in rice shoots and grains by limiting the amounts of Cd loaded into the xylem and restricting Cd translocation from roots to shoots of rice. Thus, OsLCT2 is a promising genetic resource to be engineered to reduce Cd accumulation in rice grains.
Multi-scale Monte Carlo simulations of gold nanoparticle-induced DNA damages for kilovoltage X-ray irradiation in a xenograft mouse model using TOPAS-nBio
Authors: Klapproth Alexander P. , Schuemann Jan , Stangl Stefan , Xie Tianwu , Li Wei Bo , Multhoff Gabriele
Published: October 2021

Background

Gold nanoparticles (AuNPs) are considered as promising agents to increase the radiosensitivity of tumor cells. However, the biological mechanisms of radiation enhancement effects of AuNPs are still not well understood. We present a multi-scale Monte Carlo simulation framework within TOPAS-nBio to investigate the increase of DNA damage due to the presence of AuNPs in mouse tumor models.

Methods

A tumor was placed inside a voxel mouse model and irradiated with either 100-kVp or 200-kVp X-ray beams. Phase spaces were employed to transfer particles from the macroscopic (voxel) scale to the microscopic scale, which consists of a cell geometry including a detailed mouse DNA model. Radiosensitizing effects were calculated in the presence and absence of hybrid nanoparticles with a $$\text{Fe}_2\text{O}_3$$

Fe
2

O
3

core surrounded by a gold layer (AuFeNPs). To simulate DNA damage even for very small energy tracks, Geant4-DNA physics and chemistry models were used on microscopic scale.

Results

An AuFeNP-induced enhancement of both dose and DNA strand breaks has been established for different scenarios. Produced chemical radicals including hydroxyl molecules, which were assumed to be responsible for DNA damage through chemical reactions, were found to be significantly increased. We further observed a dependency of the results on the location of the cells within the tumor for 200-kVp X-ray beams.

Conclusion

Our multi-scale approach allows to study irradiation-induced physical and chemical effects on cells. We showed a potential increase in cell radiosensitization caused by relatively small concentrations of AuFeNPs. Our new methodology allows the individual adjustment of parameters in each simulation step and therefore can be used for other studies investigating the radiosensitizing effects of AuFeNPs or AuNPs in living cells.
TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery
Authors: Liu Yusong , Ye Xiufen , Yu Christina Y. , Shao Wei , Hou Jie , Feng Weixing , Zhang Jie , Huang Kun
Published: October 2021

Background

Gene co-expression networks are widely studied in the biomedical field, with algorithms such as WGCNA and lmQCM having been developed to detect co-expressed modules. However, these algorithms have limitations such as insufficient granularity and unbalanced module size, which prevent full acquisition of knowledge from data mining. In addition, it is difficult to incorporate prior knowledge in current co-expression module detection algorithms.

Results

In this paper, we propose a novel module detection algorithm based on topology potential and spectral clustering algorithm to detect co-expressed modules in gene co-expression networks. By testing on TCGA data, our novel method can provide more complete coverage of genes, more balanced module size and finer granularity than current methods in detecting modules with significant overall survival difference. In addition, the proposed algorithm can identify modules by incorporating prior knowledge.

Conclusion

In summary, we developed a method to obtain as much as possible information from networks with increased input coverage and the ability to detect more size-balanced and granular modules. In addition, our method can integrate data from different sources. Our proposed method performs better than current methods with complete coverage of input genes and finer granularity. Moreover, this method is designed not only for gene co-expression networks but can also be applied to any general fully connected weighted network.
ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process
Authors: Maiolo Massimo , Gatti Lorenzo , Frei Diego , Leidi Tiziano , Gil Manuel , Anisimova Maria
Published: October 2021

Background

Current alignment tools typically lack an explicit model of indel evolution, leading to artificially short inferred alignments (i.e., over-alignment) due to inconsistencies between the indel history and the phylogeny relating the input sequences.

Results

We present a new progressive multiple sequence alignment tool ProPIP. The process of insertions and deletions is described using an explicit evolutionary model—the Poisson Indel Process or PIP. The method is based on dynamic programming and is implemented in a frequentist framework. The source code can be compiled on Linux, macOS and Microsoft Windows platforms. The algorithm is implemented in C++ as standalone program. The source code is freely available on GitHub at https://github.com/acg-team/ProPIP and is distributed under the terms of the GNU GPL v3 license.

Conclusions

The use of an explicit indel evolution model allows to avoid over-alignment, to infer gaps in a phylogenetically consistent way and to make inferences about the rates of insertions and deletions. Instead of the arbitrary gap penalties, the parameters used by ProPIP are the insertion and deletion rates, which have biological interpretation and are contextualized in a probabilistic environment. As a result, indel rate settings may be optimised in order to infer phylogenetically meaningful gap patterns.
An Ensemble Deep Learning based Predictor for Simultaneously Identifying Protein Ubiquitylation and SUMOylation Sites
Authors: He Fei , Li Jingyi , Wang Rui , Zhao Xiaowei , Han Ye
Published: October 2021

Background

Several computational tools for predicting protein Ubiquitylation and SUMOylation sites have been proposed to study their regulatory roles in gene location, gene expression, and genome replication. However, existing methods generally rely on feature engineering, and ignore the natural similarity between the two types of protein translational modification. This study is the first all-in-one deep network to predict protein Ubiquitylation and SUMOylation sites from protein sequences as well as their crosstalk sites simultaneously. Our deep learning architecture integrates several meta classifiers that apply deep neural networks to protein sequence information and physico-chemical properties, which were trained on multi-label classification mode for simultaneously identifying protein Ubiquitylation and SUMOylation as well as their crosstalk sites.

Results

The promising AUCs of our method on Ubiquitylation, SUMOylation and crosstalk sites achieved 0.838, 0.888, and 0.862 respectively on tenfold cross-validation. The corresponding APs reached 0.683, 0.804 and 0.552, which also validated our effectiveness.

Conclusions

The proposed architecture managed to classify ubiquitylated and SUMOylated lysine residues along with their crosstalk sites, and outperformed other well-known Ubiquitylation and SUMOylation site prediction tools.
Demographic history and divergence of sibling grouse species inferred from whole genome sequencing reveal past effects of climate change
Authors: Song Kai , Gao Bin , Halvarsson Peter , Fang Yun , Klaus Siegfried , Jiang Ying-Xin , Swenson Jon E. , Sun Yue-Hua , Höglund Jacob
Published: October 2021

Background

The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To understand the possible effects of on-going and future climate change it would be useful to reconstruct past population size changes and relate such to climatic events in the past. We sequenced the genomes of 32 individuals from two forest inhabiting bird species, Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of two outgroup species from Europe and China.

Results

We estimated the divergence time of Chinese Grouse and Hazel Grouse to 1.76 (0.46–3.37) MYA. The demographic history of different populations in these two sibling species was reconstructed, and showed that peaks and bottlenecks of effective population size occurred at different times for the two species. The northern Qilian population of Chinese Grouse became separated from the rest of the species residing in the south approximately 250,000 years ago and have since then showed consistently lower effective population size than the southern population. The Chinese Hazel Grouse population had a higher effective population size at the peak of the Last Glacial Period (approx. 300,000 years ago) than the European population. Both species have decreased recently and now have low effective population sizes.

Conclusions

Combined with the uplift history and reconstructed climate change during the Quaternary, our results support that cold-adapted grouse species diverged in response to changes in the distribution of palaeo-boreal forest and the formation of the Loess Plateau. The combined effects of climate change and an increased human pressure impose major threats to the survival and conservation of both species.
Endoscopic ultrasound guided fine needle biopsy (EUS-FNB) from peritoneal lesions: a prospective cohort pilot study
Authors: Kongkam Pradermchai , Orprayoon Theerapat , Yooprasert Sirilak , Sirisub Nakarin , Klaikaew Naruemon , Sanpawat Anapat , Safa Shahram , Ridtitid Wiriyaporn , Kullavanijaya Pinit , Rerknimitr Rungsun
Published: October 2021

Background

Diagnostic laparoscopy is often a necessary, albeit invasive, procedure to help resolve undiagnosed peritoneal diseases. Previous retrospective studies reported that EUS-FNA is feasible on peritoneal and omental lesions, however, EUS-FNA provided a limited amount of tissue for immunohistochemistry stain (IHC).

Aim

This pilot study aims to prospectively determine the effectiveness of EUS-FNB regarding adequacy of tissue for IHC staining, diagnostic rate and the avoidance rate of diagnostic laparoscopy or percutaneous biopsy in patients with these lesions.

Methods

From March 2017 to June 2018, patients with peritoneal or omental lesions identified by CT or MRI at the King Chulalongkorn Memorial Hospital, Bangkok, Thailand were prospectively enrolled in the study. All Patients underwent EUS-FNB. For those with negative pathological results of EUS-FNB, percutaneous biopsy or diagnostic laparoscopy was planned. Analysis uses percentages only due to small sample sizes.

Results

A total of 30 EUS-FNB passes were completed, with a median of 3 passes (range 2–3 passes) per case. For EUS-FNB, the sensitivity, specificity, PPV, NPV and accuracy of EUS-FNB from peritoneal lesions were 63.6%, 100%, 100%, 20% and 66.7% respectively. Adequate tissue for IHC stain was found in 25/30 passes (80%). The tissues from EUS results were found malignant in 7/12 patients (58.3%). IHC could be done in 10/12 patients (83.3%). Among the five patients with negative EUS results, two underwent either liver biopsy of mass or abdominal paracentesis, showing gallbladder cancer and adenocarcinoma. Two patients refused laparoscopy due to advanced pancreatic cancer and worsening ovarian cancer. The fifth patient had post-surgical inflammation only with spontaneous resolution. The avoidance rate of laparoscopic diagnosis was 58.3%. No major adverse event was observed.

Conclusions

EUS-FNB from peritoneal lesions provided sufficient core tissue for diagnosis and IHC. Diagnostic laparoscopy can often be avoided in patients with peritoneal lesions.
A rare case of severe gastroenteritis caused by Aeromonas hydrophila after colectomy in a patient with anti-Hu syndrome: a case report
Authors: Greiner Michael , Anagnostopoulos Alexia , Pohl Daniel , Zbinden Reinhard , Zbinden Andrea
Published: October 2021

Background

Aeromonas hydrophila is a gram-negative facultative anaerobic coccobacillus, which is an environmental opportunistic pathogen. A. hydrophila are involved in several infectious diseases such as gastroenteritis, septicemia and wound infections. However, gastroenteritis caused by Aeromonas spp. are rare and the clinical relevance of Aeromonas species in stool specimens is still under debate.

Case presentation

Our case concerns a 32-year-old woman who presented at hospital with a worsening watery diarrhea and fever requiring intensive care. A cholera-like illness was diagnosed. The patient had a past history of an anti-Hu syndrome with a myenteric ganglionitis. A molecular multiplex RT-PCR (QIAstat-Dx Gastrointestinal Panel, QIAGEN) covering a broad spectrum of diverse gastrointestinal pathogens performed directly from the stool was negative but the stool culture revealed growth of A. hydrophila. Further investigations of the A. hydrophila strain in cell cultures revealed the presence of a cytotoxic enterotoxin.

Conclusions

Although A. hydrophila rarely causes gastroenteritis, Aeromonas spp. should be considered as a causative agent of severe gastroenteritis with a cholera-like presentation. This case highlights the need to perform culture methods from stool samples when PCR-based methods are negative and gastrointestinal infection is suspected.
A case report of community-acquired Raoultella ornithinolytica infection in a healthy, young individual
Authors: Chen Xiaonan , Zhou Xinjian , Cao Jun , Ma Ke , Xia Zhijie
Published: October 2021

Background

Raoultella ornithinolytica is a Gram-negative bacillus that resembles Klebsiella. This bacterium is present in many soil and aquatic environments and is a major causative agent of healthcare-associated infections (HAIs) in medical staff. Clinically, it has been reported to contribute to nosocomial infections in patients that include but are not limited to gastrointestinal, skin, and genitourinary tract infections. These complications are most common in hospitalized patients with underlying immunodeficiency, multiple comorbidities, or those receiving invasive surgery.

Case presentation

We present a case of a 25-year-old patient with a R. ornithinolytica infection. The patient had no history of any disease. Her main complaints were high fever, a scattered maculopapular rash, and superficial lymph node enlargement (SLNE). Peripheral blood samples were collected for high-throughput sequencing analysis to identify pathogenic microorganisms. The results confirmed a R. ornithinolytica infection, which was treated successfully using meropenem. Loratadine was also administered to treat the patient’s compromised skin condition caused by an allergic reaction.

Conclusions

To our knowledge, this is the first case of a systemic maculopapular rash and superficial lymphadenopathy caused by a R. ornithinolytica infection acquired at the community level. Based on this case, we recommend a combination of antibiotic and antiallergic drugs to treat a R. ornithinolytica infection and associated allergic reaction to the bacteria.
Intersecting systemic and personal barriers to accessing social services: qualitative interviews in northern California
Authors: Placzek Hilary , Cruz Stephanie , Chapdelaine Michelle , Carl Mary , Levin Sara , Hsu Clarissa
Published: October 2021

Background

Addressing social risks in the clinical setting can increase patient confidence in the availability of community resources and may contribute to the development of a therapeutic alliance which has been correlated with treatment adherence and improved quality of life in mental health contexts. It is not well understood what barriers patients face when trying to connect to community resources that help address social risks. This paper aims to describe patient-reported barriers to accessing and using social needs-related resources to which they are referred by a program embedded in a safety net primary care clinic.

Methods

This is a qualitative assessment of patient-reported barriers to accessing and using social needs assistance programs. We conducted over 100 in-depth interviews with individuals in Northern California who participated in a navigation and referral program to help address their social needs and describe a unique framework for understanding how policies and systems intersect with an individual’s personal life circumstances.

Results

Individuals described two distinct domains of barriers: 1) systems-level barriers that were linked to the inequitable distribution of and access to resources, and 2) personal-level barriers that focused on unique limitations experienced by each patient and impacted the way that they accessed services in their communities. While these barriers often overlapped or manifested in similar outcomes, this distinction was key because the systems barriers were not things that individuals could control or overcome through their own initiative or by increasing individual capacity.

Conclusions

Respondents describe intersecting systemic and personal barriers that compound patients’ challenges to getting their social needs met; this includes both a picture of the inequitable distribution of and access to social services and a profile of the limitations created by individual life histories. These results speak to the need for structural changes to improve adequacy, availability, and accessibility of social needs resources. These findings highlight the need for advocacy to address systems barriers, especially the stigma that is faced by people who struggle with a variety of health and social issues, and investment in incentives to strengthen relationships between health care settings and social service agencies.
A case report of rhabdomyolysis and osteofascial compartment syndrome in a patient with hypothyroidism and diabetes
Authors: Ren Lijue , Wei Cuiying , Wei Feng , Ma Ruiting , Liu Yan , Zhang Yonghong , Wang Wei , Du Jing , Bai Lin , Xue Yexia , Cui Shaohua
Published: October 2021

Background

Hypothyroidism is frequent and has various forms of muscle involvement. We report the diagnosis and treatment of a case of rhabdomyolysis, bilateral osteofascial compartment syndrome (OCS) of the lower extremities, and peroneal nerve injury causing bilateral foot drop in a diabetic patient with hypothyroidism.

Case presentation

A 66-year-old man with diabetes for 22 years was admitted because of drowsiness, tiredness, facial swelling, and limb twitching for 2 months, and red and swollen lower limb skin for 3 days. Serum creatinine kinase (CK), CK-MB, myoglobin (Mb), blood glucose, and HbA1c were elevated. TSH, thyroid peroxidase antibodies, and antithyroglobulin antibodies were elevated. FT3 and FT4 were low. Urine was dark brown. He was diagnosed with hypothyroidism, rhabdomyolysis, and OCS. CK, CK-MB, and Mb returned to normal after treatment with thyroid hormone, insulin, albumin infusion, ceftriaxone, ulinastatin, and hemofiltration, and the redness and swelling of the lower limbs were relieved, but the patient developed dropping feet. The patient recovered well but had to undergo rehabilitation.

Conclusion

Hypothyroidism may induce rhabdomyolysis, OCS, and other complications. This case reminds us of the importance of screening for hypothyroidism and strengthens the clinicians’ understanding of the disease.
A fecal-based test for the detection of advanced adenoma and colorectal cancer: a case-control and screening cohort study
Authors: Cao Lian-Jing , Peng Xiao-Lin , Xue Wen-Qiong , Zhang Rong , Zhang Jiang-Bo , Zhou Ting , Wu Zi-Yi , Li Gai-Rui , Wang Tong-Min , He Yong-Qiao , Yang Da-Wei , Liao Ying , Tong Xia-Ting , Wang Fang , Chen Ke-Xin , Zhang Shi-Hong , Zhu Li-Qing , Ding Pei-Rong , Jia Wei-Hua
Published: October 2021

Background

Colorectal cancer (CRC) is the leading cause of cancer death worldwide. Screening is a confirmed way to reduce the incidence and mortality rates of CRC. This study aimed to identify a fecal-based, noninvasive, and accurate method for detection of colorectal cancer (CRC) and advanced adenoma (AA).

Methods

Through detection in tissue (n = 96) and fecal samples (n = 88) and tested in an independent group of fecal samples (n = 294), the methylated DNA marker ITGA4 and bacterial markers Fusobacterium nucleatum (Fn) and Pepetostreptococcusanaerobius (Pa) were identified from the candidate biomarkers for CRC and AA detection. A prediction score (pd-score) was constructed using the selected markers and fecal immunochemical test (FIT) for distinguishing AA and CRC from healthy subjects by logistic regression method. The diagnostic performance of the pd-score was compared with FIT and validated in the external validation cohort (n = 117) and in a large CRC screening cohort.

Results

The pd-score accurately identified AA and CRC from healthy subjects with an area under the curve (AUC) of 0.958, at a specificity of 91.37%; the pd-score showed sensitivities of 95.38% for CRC and 70.83% for AA, respectively. In the external validation cohort, the sensitivities of the pd-score for CRC and AA detection were 94.03% and 80.00%, respectively. When applied in screening, the pd-score identified 100% (11/11) of CRC and 70.83% (17/24) of AA in participants with both colonoscopy results and qualified fecal samples, showing an improvement by 41.19% compared to FIT.

Conclusions

The current study developed a noninvasive and well-validated approach for AA and CRC detection, which could be applied widely as a diagnostic and screening test.
COVID-19 and lipids. The role of lipid disorders and statin use in the prognosis of patients with SARS-CoV-2 infection
Authors: Surma Stanisław , Banach Maciej , Lewek Joanna
Published: October 2021

The global coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 coronavirus started in March 2020. The conclusions from numerous studies indicate that people with comorbidities, such as arterial hypertension, diabetes, obesity, underlying cardiovascular disease, are particularly vulnerable to the severe course of COVID-19. The available data also suggest that patients with dyslipidemia, the most common risk factor of cardiovascular diseases, are also at greater risk of severe course of COVID-19. On the other hand, it has been shown that COVID-19 infection has an influence on lipid profile leading to dyslipidemia, which might require appropriate treatment. Owing to antiviral, anti-inflammatory, immunomodulatory, and cardioprotective activity, statin therapy has been considered as valuable tool to improve COVID-19 outcomes. Numerous observational studies have shown potential beneficial effects of lipid-lowering treatment on the course of COVID-19 with significant improved prognosis and reduced mortality.