bluuebunny/crossref_metadata_2025 huggingface dataset:
Radiation Treatment, ATM, BRCA1/2, and CHEK2*1100delC Pathogenic Variants and Risk of Contralateral Breast Cancer
Authors: Reiner Anne S , Robson Mark E , Mellemkjær Lene , Tischkowitz Marc , John Esther M , Lynch Charles F , Brooks Jennifer D , Boice John D , Knight Julia A , Teraoka Sharon N , Liang Xiaolin , Woods Meghan , Shen Ronglai , Shore Roy E , Stram Daniel O , Thomas Duncan C , Malone Kathleen E , Bernstein Leslie , Riaz Nadeem , Woodward Wendy , Powell Simon , Goldgar David , Concannon Patrick ,   The WECARE Study Collaborative Group, Bernstein Jonine L
Published: February 2020

Whether radiation therapy (RT) affects contralateral breast cancer (CBC) risk in women with pathogenic germline variants in moderate- to high-penetrance breast cancer–associated genes is unknown. In a population-based case-control study, we examined the association between RT; variants in ATM, BRCA1/2, or CHEK2*1100delC; and CBC risk. We analyzed 708 cases of women with CBC and 1399 controls with unilateral breast cancer, all diagnosed with first invasive breast cancer between 1985 and 2000 and aged younger than 55 years at diagnosis and screened for variants in breast cancer–associated genes. Rate ratios (RR) and 95% confidence intervals (CIs) were estimated using multivariable conditional logistic regression. RT did not modify the association between known pathogenic variants and CBC risk (eg, BRCA1/2 pathogenic variant carriers without RT: RR = 3.52, 95% CI = 1.76 to 7.01; BRCA1/2 pathogenic variant carriers with RT: RR = 4.46, 95% CI = 2.96 to 6.71), suggesting that modifying RT plans for young women with breast cancer is unwarranted. Rare ATM missense variants, not currently identified as pathogenic, were associated with increased risk of RT-associated CBC (carriers of ATM rare missense variants of uncertain significance without RT: RR = 0.38, 95% CI = 0.09 to 1.55; carriers of ATM rare missense variants of uncertain significance with RT: RR = 2.98, 95% CI = 1.31 to 6.80). Further mechanistic studies will aid clinical decision-making related to RT.
Low-mass planet migration in three-dimensional wind-driven inviscid discs: a negative corotation torque
Authors: McNally Colin P , Nelson Richard P , Paardekooper Sijme-Jan , Benítez-Llambay Pablo , Gressel Oliver
Published: February 2020

We present simulations of low-mass planet–disc interactions in inviscid three-dimensional discs. We show that a wind-driven laminar accretion flow through the surface layers of the disc does not significantly modify the migration torque experienced by embedded planets. More importantly, we find that 3D effects lead to a dramatic change in the behaviour of the dynamical corotation torque compared to earlier 2D theory and simulations. Although it was previously shown that the dynamical corotation torque could act to slow and essentially stall the inward migration of a low-mass planet, our results in 3D show that the dynamical corotation torque has the complete opposite effect and speeds up inward migration. Our numerical experiments implicate buoyancy resonances as the cause. These have two effects: (i) they exert a direct torque on the planet, whose magnitude relative to the Lindblad torque is measured in our simulations to be small; (ii) they torque the gas librating on horseshoe orbits in the corotation region and drive evolution of its vortensity, leading to the negative dynamical corotation torque. This indicates that at low turbulent viscosity, the detailed vertical thermal structure of the protoplanetary disc plays an important role in determining the migration behaviour of embedded planets. If this result holds up under a more refined treatment of disc thermal evolution, then it has important implications for understanding the formation and early evolution of planetary systems.
TimeMeter assesses temporal gene expression similarity and identifies differentially progressing genes
Authors: Jiang Peng , Chamberlain Connie S , Vanderby Ray , Thomson James A , Stewart Ron
Published: February 2020

Comparative time series transcriptome analysis is a powerful tool to study development, evolution, aging, disease progression and cancer prognosis. We develop TimeMeter, a statistical method and tool to assess temporal gene expression similarity, and identify differentially progressing genes where one pattern is more temporally advanced than the other. We apply TimeMeter to several datasets, and show that TimeMeter is capable of characterizing complicated temporal gene expression associations. Interestingly, we find: (i) the measurement of differential progression provides a novel feature in addition to pattern similarity that can characterize early developmental divergence between two species; (ii) genes exhibiting similar temporal patterns between human and mouse during neural differentiation are under strong negative (purifying) selection during evolution; (iii) analysis of genes with similar temporal patterns in mouse digit regeneration and axolotl blastema differentiation reveals common gene groups for appendage regeneration with potential implications in regenerative medicine.
APPLICABILITY OF PURE PROPANE GAS FOR MICRODOSIMETRY AT BRACHYTHERAPY ENERGIES: A FLUKA STUDY
Authors: Chattaraj Arghya , Selvam T Palani
Published: February 2020

Applicability of pure propane gas for microdosimetric measurements at photon energies relevant in brachytherapy is studied using the Monte Carlo-based FLUKA code. Monoenergetic photons in the energy range of 20–1250 keV and brachytherapy sources such as 103Pd, 125I, 169Yb, 192Ir, 137Cs and 60Co are considered in the study. Using the calculated values of energy deposited in the sensitive region of LET-1/2 tissue-equivalent proportional counter filled with pure propane gas and tissue-equivalent propane gas, values of density scaling factor for the site sizes of 1 and 8 μm are obtained. The study shows that density of propane gas should be lowered by a factor of about 0.93 for 169Yb, 192Ir, 137Cs and 60Co sources for the site sizes of 1–8 μm. For 125I source, the density of propane gas requires a scaling of 0.93 for 1 μm site size, whereas for site sizes 2–8 μm, density need not be altered. 103Pd source does not require density scaling for site sizes 1–8 μm.
Advances in the understanding of the intestinal micro-environment and inflammatory bowel disease
Authors: Yan Peng-Guang , Li Jing-Nan
Published: February 2020

The human gastrointestinal tract accommodates an entire micro-environment for divergent physiologic processes, the dysbiosis of this micro-ecology has a strong inter-action with the pathogenesis of inflammatory bowel disease (IBD). In the past few years, with the advances in the understanding of microbiome, its metabolites and further application of next generation sequencing, analysis of dynamic alteration of gut micro-environment was realized, which provides numerous information beyond simple microbiota structure or metabolites differences under chronic colitis status. The subsequent intervention strategies targeting the modulation of intestinal micro-environment have been explored as a potential therapy. In this review, we will summarize the recent knowledge about multi-dimensional dysbiosis, the inter-action between fungus and bacteria under inflamed mucosa, and the clinical application of probiotics and fecal microbiota transplantation as a promising therapeutic approach in IBD.
A Comparison of Dialogic Reading, Modeling, and Dialogic Reading Plus Modeling
Authors: Coogle Christan Grygas , Parsons Allison Ward , La Croix Leslie , Ottley Jennifer R.
Published: February 2020

The authors used an alternating treatment, single-case design to determine the effect of dialogic reading, modeling, and dialogic reading plus modeling on the expressive vocabulary identification of 2 preschool children identified with autism spectrum disorder. Their preschool teacher implemented each of the conditions within the daily routines of the classroom. Each condition demonstrated effectiveness; however, the dialogic reading condition had the most robust effect on both of the children's labeling of target vocabulary words.
Evaluating the Dimensionality and Psychometric Properties of a Social–Emotional Screening Instrument for Young Children
Authors: Chen Chieh-Yu , Squires Jane , Scalise Kathleen
Published: February 2020

Social–emotional competence is important for children's lifelong positive developmental outcomes. The dimensionality and psychometric properties of a widely used social–emotional assessment, the Ages & Stages Questionnaires: Social–Emotional Second Edition (ASQ:SE-2), were investigated in this study using item response theory models. A comparison was conducted between a unidimensional model, reflecting a compound construct—social–emotional competence, and a multidimensional model, based on the theoretical framework that posits that social competence and emotional competence are highly related but different constructs. The result indicated that the multidimensional structure presented a better fit for the ASQ:SE-2 sample across most intervals (i.e., 6, 12, 18, 24, 30, 36, 48, and 60 months). The psychometric properties estimated by the multidimensional model reflected congruence between the levels of item difficulty and the design of the ASQ:SE-2 and indicated a high quality of items based on the fit item statistics. However, the expected a posteriori/plausible value reliability estimates for several younger age intervals (i.e., 6, 12, 18, and 24 months) did not meet the 0.70 benchmark. The relationship between the 2 dimensions presented a moderate correlation during infancy (r = .43–.56) and a stronger relationship in older ages (r = .71–.83).
Information and communication technology used by people with lower limb loss in Slovenia
Authors: Debeljak Mojca , Vidmar Gaj , Matjačić Zlatko , Burger Helena
Published: February 2020

World demography is changing as the population ages and there are more people with disabilities having problems to stay independently at home. Innovative technologies could help extend the independence of older people living at home. As part of a collaborative project, we investigated ownership and use of information and communication technologies (ICT) among older people with lower limb loss (LLL) using questionnaires and retrospective analysis. Our aim was to analyse factors associated with ICT use among people with LLL. We identified age as the main factor that limits ownership and use of ICT among older people with LLL in Slovenia. Cause of amputation also appears to be relevant, whereby those who had amputation because of peripheral vascular disease are more likely to use a personal or tablet computer, social networks, messaging apps, email and internet than those who had amputation because of diabetes. In addition, those living in the suburbs are more likely to use a health monitoring device than those living in the countryside.
Comparing Care of the Primary and Secondary Hemochromatosis Patients
Authors: Becker Susan
Published: February 2020

Hemochromatosis is an imbalance of excessive serum iron and is a life-threatening condition if left untreated. Due to different causes, primary and secondary hemochromatosis have different patient care considerations for the infusion nurse. Understanding the pathophysiology and how the body absorbs iron is imperative for providing the highest quality care. Since primary (hereditary) hemochromatosis originates from a gene mutation, and secondary (acquired) from excessive intake, the treatment and education must be adjusted accordingly to deliver successful outcomes for both diagnoses.
Ki67 in Gleason Pattern 3 as a Marker of the Presence of Higher-Grade Prostate Cancer
Authors: Caputo Alessandro , D’Antonio Antonio , Memoli Domenico , Sabbatino Francesco , Altieri Vincenzo , Zeppa Pio
Published: February 2020

Purpose:

Prostate biopsies may undergrade up to half of all prostate cancers (PCs), delaying definitive treatment by up to 3 years. One cause of undergrading is the partial sampling inherent in the technique. Because of this, a prostate biopsy that appears to be Gleason 3+3=6 may come either from a true 3+3=6 tumor or from a higher-grade tumor that has been sampled only partially. The main goal of the present study is to identify a way to distinguish these 2 kinds of “Gleason 3+3=6” biopsies.

Mounting evidence hints at the possibility that Gleason pattern 3 associated with higher-grade PC (aG3) is biologically distinct from pure Gleason pattern 3 (pG3).

Materials and Methods:

In this study, we used immunohistochemistry and computer-aided image analysis to compare the expression of Ki67, cyclin D1, MYC, and p53 between foci of aG3 and pG3, to search for a marker that could distinguish them.

Results:

The expression of Ki67 differed significantly between pG3 and aG3. The average Ki67 labeling index was 1.63% for pG3 and 7.62% for aG3 (P<0.01); the average number of Ki67+ cells per high-power field was 17 for pG3 and 60 for aG3 (P<0.01). The other markers did not differ significantly between pG3 and aG3.

Conclusions:

When a biopsy only shows Gleason pattern 3 PC, Ki67 immunohistochemistry could be used to distinguish the nodules of true Gleason score 3+3=6 from those that only appear to be 3+3=6 because of a sampling error. This would dramatically improve the diagnostic performance of prostate biopsies and the management of early PC.
Atomoxetine Induced Skin Picking: A Case Report
Authors: Kasar Nurdan , Yurteri Nihal
Published: February 2020

“Skin picking disorder,” also known as “dermatillomania” or “psychogenic excoriation,” is classified in the “Obsessive Compulsive and Related Disorders” category in Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition and characterized by repetitive skin picking behaviors resulting in skin lesions. Atomoxetine (ATX) is a selective norepinephrine (noradrenaline) reuptake inhibitor commonly used in the management of attention-deficit/hyperactivity disorder. Atomoxetine is considered to increase levels of noradrenaline and dopamine by inhibiting norepinephrine transporters. In this case report, we present an 8-year-old male attention-deficit/hyperactivity disorder patient with skin picking behavior due to ATX treatment. We discussed possible explanations of skin picking behavior with ATX in the light of the current literature. To our knowledge, this is the first report of skin picking due to ATX in literature, and further studies are needed to investigate the frequency and mechanisms of skin picking with ATX.
The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing
Authors: Liao Minfeng , Liu Yang , Yuan Jin , Wen Yanling , Xu Gang , Zhao Juanjuan , Chen Lin , Li Jinxiu , Wang Xin , Wang Fuxiang , Liu Lei , Zhang Shuye , Zhang Zheng
Published: February 2020

The novel coronavirus SARS-CoV-2, etiological agent of recently named Coronavirus infected disease (COVID-19) by WHO, has caused more than 2, 000 deaths worldwide since its emergency in Wuhan City, Hubei province, China, in December, 2019. The symptoms of COVID-19 varied from modest, mild to acute respiratory distress syndrome (ARDS), and the latter of which is generally associated with deregulated immune cytokine production; however, we currently know little as to the interplay between the extent of clinical symptoms and the compositions of lung immune microenvironment. Here, we comprehensively characterized the lung immune microenvironment with the bronchoalveolar lavage fluid (BALF) from 3 severe and 3 mild COVID-19 patients and 8 previously reported healthy lung controls through single-cell RNA sequence (scRNA-seq) combined with TCR-seq. Our data shows that monocyte-derived FCN1+macrophages, whereas notFABP4+alveolar macrophages that represent a predominant macrophage subset in BALF from patients with mild diseases, overwhelm in the severely damaged lungs from patients with ARDS. These cells are highly inflammatory and enormous chemokine producers implicated in cytokine storm. Furthermore, the formation of tissue resident, highly expanded clonal CD8+T cells in the lung microenvironment of mild symptom patients suggests a robust adaptive immune response connected to a better control of COVID-19. This study first reported the cellular atlas of lung bronchoalveolar immune microenvironment in COVID-19 patients at the single-cell resolution, and unveiled the potential immune mechanisms underlying disease progression and protection in COVID-19.

Highlights

Immune microenvironment of SARS-CoV-2-infected lungs revealed by scRNA/TCR seq

Increased inflammatory FCN1+ macrophages are replacing FABP4+ macrophages in the BALF from severe COVID-19 patients

Highly expanded and functional competent tissue resident clonal CD8+ T cells in mild COVID-19 patients
microRNA signatures of perioperative myocardial injury after elective non-cardiac surgery: prospective observational cohort study
Authors: May Shaun M. , Abbott Tom E.F. , Del Arroyo Ana Gutierrez , Reyes Anna , Martir Gladys , Stephens Robert C.M. , Brealey David , Cuthbertson Brian H. , Wijeysundera Duminda N. , Pearse Rupert M. , Ackland Gareth L.
Published: February 2020

Background

Elevated plasma/serum troponin, indicating perioperative myocardial injury (PMI), is common after non-cardiac surgery. However, underlying mechanisms remain unclear. Acute coronary syndrome (ACS) is associated with the early appearance of circulating microRNAs, which regulate post-translational gene expression. We hypothesised that if PMI and ACS share pathophysiological mechanisms, common microRNA signatures should be evident.

Methods

Nested case-control study of samples obtained before and after non-cardiac surgery from patients enrolled in two prospective observational studies of PMI (postoperative troponin I/T>99th centile). In cohort one, serum microRNAs were compared between patients with/without PMI, matched for age, gender and comorbidity. Real-time polymerase chain reaction quantified relative microRNA expression (cycle quantification threshold <37) before and after surgery for microRNA signatures associated with ACS, blinded to PMI. In cohort two, we analysed (EdgeR) microRNA from plasma extracellular vesicles using next-generation sequencing (Illumina HiSeq500). microRNA-messenger RNA-function pathway analysis was performed (DIANA miRPath v3.0/TopGO).

Results

MicroRNA were detectable in all 59 patients (median age:67yrs (61-75); 42% male), who had similar clinical characteristics independent of developing PMI. In cohort one, PMI was not associated with increased serum microRNA expression levels after surgery (hsa-miR-1-3p mean fold-change (FC):3.99 (95%CI:1.95-8.19); hsa-miR-133-3p FC:5.67(95%CI:2.94-10.91); p<0.001). hsa-miR-208b-3p was more commonly detected after PMI (odd ratio (OR):10.0 (95%CI:1.9-52.6); p<0.01). Bioinformatic analysis of differentially expressed microRNAs from cohorts one and two identified pathways associated with adrenergic stress involving calcium dysregulation, rather than ischaemia.

Conclusions

Circulating microRNAs synonymous with cardiac ischaemia were universally elevated in patients after surgery, independent of developing myocardial injury.
Spread and control of COVID-19 in China and their associations with population movement, public health emergency measures, and medical resources
Authors: Ying Songmin , Li Fei , Geng Xinwei , Li Zhouyang , Du Xufei , Chen Haixia , Chen Sisi , Zhang Min , Shao Zhehua , Wu Yinfang , Syeda Madiha Zahra , Yan Fugui , Che Luanqing , Zhang Bin , Lou Jian , Wang Shaobin , Chen Zhengming , Li Wen , Shen Ye , Chen Zhihua , Shen Huahao
Published: February 2020

BACKGROUND

The COVID-19 epidemic, first emerged in Wuhan during December 2019, has spread globally. While the mass population movement for Chinese New Year has significantly influenced spreading the disease, little direct evidence exists about the relevance to epidemic and its control of population movement from Wuhan, local emergency response, and medical resources in China.

METHODS

Spearman’s correlation analysis was performed between official data of confirmed COVID-19 cases from Jan 20th to Feb 19th, 2020 and real-time travel data and health resources data.

RESULTS

There were 74,675 confirmed COVID-19 cases in China by Feb 19th, 2020. The overall fatality rate was 2.84%, much higher in Hubei than in other regions (3.27% vs 0.73%). The index of population inflow from Hubei was positively correlated with total (Provincial r=0.9159, p<0.001; City r=0.6311, p<0.001) and primary cases (Provincial r=0.8702, p<0.001; City r=0.6358, p<0.001). The local health emergency measures (eg, city lockdown and traffic control) were associated with reduced infections nationwide. Moreover, the number of public health employees per capita was inversely correlated with total cases (r=−0.6295, p <0.001) and infection rates (r =−0.4912, p <0.01). Similarly, cities with less medical resources had higher fatality (r =−0.4791, p<0.01) and lower cure rates (r = 0.5286, p<0.01) among the confirmed cases.

CONCLUSIONS

The spread of the COVID-19 in China in its early phase was attributed primarily to population movement from Hubei, and effective governmental health emergency measures and adequate medical resources played important roles in subsequent control of epidemic and improved prognosis of affected individuals.
Age-dependent risks of Incidence and Mortality of COVID-19 in Hubei Province and Other Parts of China
Authors: Li Hongdou , Wang Shuang , Zhong Fan , Bao Wuyin , Li Yipeng , Liu Lei , Wang Hongyan , He Yungang
Published: February 2020

New coronavirus SARS-CoV-2 poses a big challenge for global public health in early 2020. Coronavirus Disease 2019 (COVID-19) caused by the virus rapidly spreads all over the world and takes thousands of lives in just two months. It is critical to refine the incidence and mortality risks of COVID-19 for the effective management of the general public and patients in the outbreak. In this report, we investigate the incidence and mortality risks of the infection by analyzing the age composition of 5319 infected patients, 76 fatal cases, and 1,144,648 individuals of the general public in China. Our result shows a relatively low incidence risk for young people but a very high mortality risk for seniors. Notably, mortality risk could be as high as 0.48 for people older than 80 years. Furthermore, our study suggests that a good medical service can effectively reduce the mortality rate of the viral infection to 1% or less.
Anticipatory energization revealed by pupil and brain activity guides human effort-based decision making
Authors: Kurniawan Irma T. , Grueschow Marcus , Ruff Christian C.
Published: February 2020

An organism’s fitness is determined by how it chooses to adapt effort in response to challenges. Actual effort exertion correlates with activity in dorsomedial prefrontal cortex (dmPFC) and noradrenergic pupil dilation, but little is known about how these neurophysiological processes guide decisions about future efforts: They may either provide anticipatory energization helping to accept the challenge, or a cost representation weighted against expected rewards. Here we provide evidence for the former, by measuring pupil and fMRI brain responses while humans chose whether to exert efforts to obtain rewards. Pupil-dilation rate and dMPFC fMRI activity related to anticipated effort level, with stronger correlations when participants chose to accept the challenge. These choice-dependent effort representations were stronger in participants whose behavioral choices were more sensitive to effort. Our results identify a process involving the peripheral and central human nervous system that guides decisions to exert effort by simulating the required energization.
Codon usage bias in radioresistant bacteria
Authors: Dilucca Maddalena , Pavlopoulou Athanasia , Georgakilas Alexandros G. , Giansanti Andrea
Published: February 2020

The relationship between patterns of codon usage bias (CUB), the preferential usage of synonimous nucleotide triplets encoding the same amino acid, and radioresistance was investigated int he genomes of 16 taxonomically distinct radioresistant prokaryotic organisms and in a control set of 11 non-radioresistant bacteria. The radioresistant species were found to be strongly biased towards G and C in the third synonimous codon position. ENC and neutrality plots also sugest that CUB in radioresistant bacteria is mainly affected by mutational bias. Furthermore, the availability of tRNA gene copy number was analyzed and it was found that nine radioresistant species have the sam number of tRNA gene copies for each codon. This suggests that tRNA gene copies and codon bias co-evolved in a specific way in radioresistant species.
LRRK2 mutation alters behavioral, synaptic and non-synaptic adaptations to acute social stress
Authors: Guevara Christopher A. , Matikainen-Ankney Bridget A. , Kezunovic Nebojsa , LeClair Katherine , Conway Alexander P. , Menard Caroline , Flanigan Meghan E. , Pfau Madeline , Russo Scott J. , Benson Deanna L. , Huntley George W.
Published: February 2020

Parkinson’s disease (PD) risk is increased by stress and certain gene mutations, including the most prevalent PD-linked mutationLRRK2-G2019S. Both PD and stress increase risk for psychiatric symptoms, yet it is unclear how PD-risk genes alter neural circuitry in response to stress that may promote psychopathology. Here we show significant differences between adult G2019S knockin and wildtype (wt) mice in stress-induced behaviors, with an unexpected uncoupling of depression-like and hedonic-like responses in G2019S mice. Moreover, mutant spiny projection neurons in nucleus accumbens (NAc) lack an adaptive, stress-induced change in excitability displayed by wt neurons, and instead show stress-induced changes in synaptic properties that wt neurons lack. Some synaptic alterations in NAc are already evident early in postnatal life. Thus, G2019S alters the magnitude and direction of behavioral responses to stress that may reflect unique modifications of adaptive plasticity in cells and circuits implicated in psychopathology in humans.
Feasibility of axon density metrics for brain asymmetry evaluation in the UK Biobank subsample
Authors: Maximov Ivan I. , Westlye Lars T.
Published: February 2020

Standard diffusion MRI model with intra- and extra-axonal water pools offers a set of microstructural parameters describing brain white matter architecture. However, a non-linearity of the general model and diffusion data contamination by noise and imaging artefacts make estimation of diffusion metrics challenging. In order to develop reproducible and reliable diffusion approaches and to avoid computational model degeneracy, one needs to devise additional theoretical assumptions allowing a stable numerical implementation. As a result, it is possible to estimate intra-axonal water fraction (AWF) representing one of the important structural parameters. AWF can be treated as an indirect measure of axon density and has a strong potential as useful clinical biomarker. A few diffusion approaches such as white matter tract integrity, neurite orientation dispersion and density imaging, and spherical mean technique, allow one to evaluate AWF in the frame of their theoretical assumptions. In the present study, we considered the compatibility of axon density metrics obtained from different diffusion models and the influence of the diffusion metric on a brain asymmetry estimation in UK Biobank sample consisting of 182 subjects. We found AWF derived from a spherical mean technique is the most statistically representative measure. As a result, we revealed that brain asymmetry indecies derived from intra-axonal water fraction weakly decrease along the lifespan, reducing the left-right hemisphere difference within increased age.
Herpes Simplex Virus Mistyping due to HSV-1 x HSV-2 Interspecies Recombination in Viral Gene Encoding Glycoprotein B
Authors: Casto Amanda M. , Huang Meei-Li , Xie Hong , Jerome Keith R. , Wald Anna , Johnston Christine , Greninger Alexander L.
Published: February 2020

Human herpes simplex viruses (HSV) 1 and 2 are most often typed via molecular assays. Here we describe the first known case of HSV mistyping due to a previously undescribed HSV-1 x HSV-2 recombination event in UL27, the gene that encodes glycoprotein B. This is the first reported HSV interspecies recombination event impacting this gene, which is frequently used as a target for diagnostics and experimental therapeutics.
Analysis of healthy reference ranges for clinically relevant gut microbial indicators: Mykinso cohort study in Japan
Authors: Watanabe Satoshi , Kameoka Shoichiro , Shinozaki Natsuko O. , Kubo Ryuichi , Nishida Akifumi , Kuriyama Minoru , Takeda Aya K.
Published: February 2020

Background

Although several large cohort studies have focused on the human gut microbiome, large cohort study of the Japanese gut microbiome is scarce, especially that of healthy or non-diseased individuals. The purpose of this study was to establish a reference range for gut microbial indices by collecting Japanese real-world microbiome data from a Mykinso cohort.

Methods

We collected stool samples and original survey on lifestyle from 5,843 Japanese people through Mykinso gut microbiome testing service. From the obtained 16S rRNA sequence data derived from the stool sample, the ratio and distribution of each taxon were analyzed. The relationship between different epidemiological attributes and gut microbial indicators were statistically tested.

Results

The qualitative and quantitative indicators of these common gut microbiota were confirmed to be strongly correlated with age, sex, constipation/diarrhea, and history of lifestyle-related diseases. Therefore, we set up the healthy sub-cohort that controlled for these attribute factors, and defined a reference range from the distribution of gut microbial index in that population.

Conclusions

The gut microbiota of Japanese people had high beta diversity, and there was no single “typical” gut microbiota type. We believe that the reference range of the gut microbial index obtained in this study can be a new reference value for determining the balance and health of the gut microbiota of an individual. In the future, it is necessary to clarify the clinical validity of this reference value by comparing with the clinical disease cohort.
Convergent selection in antibody repertoires is revealed by deep learning
Authors: Friedensohn Simon , Neumeier Daniel , Khan Tarik A , Csepregi Lucia , Parola Cristina , de Vries Arthur R Gorter , Erlach Lena , Mason Derek M , Reddy Sai T
Published: February 2020

Adaptive immunity is driven by the ability of lymphocytes to undergo V(D)J recombination and generate a highly diverse set of immune receptors (B cell receptors/secreted antibodies and T cell receptors) and their subsequent clonal selection and expansion upon molecular recognition of foreign antigens. These principles lead to remarkable, unique and dynamic immune receptor repertoires1. Deep sequencing provides increasing evidence for the presence of commonly shared (convergent) receptors across individual organisms within one species2-4. Convergent selection of specific receptors towards various antigens offers one explanation for these findings. For example, single cases of convergence have been reported in antibody repertoires of viral infection or allergy5-8. Recent studies demonstrate that convergent selection of sequence motifs within T cell receptor (TCR) repertoires can be identified on an even wider scale9,10. Here we report that there is extensive convergent selection in antibody repertoires of mice for a range of protein antigens and immunization conditions. We employed a deep learning approach utilizing variational autoencoders (VAEs) to model the underlying process of B cell receptor (BCR) recombination and assume that the data generation follows a Gaussian mixture model (GMM) in latent space. This provides both a latent embedding and cluster labels that group similar sequences, thus enabling the discovery of a multitude of convergent, antigen-associated sequence patterns. Using a linear, one-versus-all support vector machine (SVM), we confirm that the identified sequence patterns are predictive of antigenic exposure and outperform predictions based on the occurrence of public clones. Recombinant expression of both natural andin silico-generated antibodies possessing convergent patterns confirms their binding specificity to target antigens. Our work highlights to which extent convergence in antibody repertoires can occur and shows how deep learning can be applied for immunodiagnostics and antibody discovery and engineering.
Measurement error and resolution in quantitative stable isotope probing: implications for experimental design
Authors: Sieradzki Ella T. , Koch Benjamin J. , Greenlon Alex , Sachdeva Rohan , Malmstrom Rex R. , Mau Rebecca L. , Blazewicz Steven J. , Firestone Mary K. , Hofmockel Kirsten , Schwartz Egbert , Hungate Bruce A. , Pett-Ridge Jennifer
Published: February 2020

Quantitative stable isotope probing (qSIP) estimates the degree of incorporation of an isotope tracer into nucleic acids of metabolically active organisms and can be applied to microorganisms growing in complex communities, such as the microbiomes of soil or water. As such, qSIP has the potential to link microbial biodiversity and biogeochemistry. As with any technique involving quantitative estimation, qSIP involves measurement error; a more complete understanding of error, precision and statistical power will aid in the design of qSIP experiments and interpretation of qSIP data. We used several existing qSIP datasets of microbial communities found in soil and water to evaluate how variance in the estimate of isotope incorporation depends on organism abundance and on the resolution of the density fractionation scheme. We also assessed statistical power for replicated qSIP studies, and sensitivity and specificity for unreplicated designs. We found that variance declines as taxon abundance increases. Increasing the number of density fractions reduces variance, although the benefit of added fractions declines as the number of fractions increases. Specifically, nine fractions appear to be a reasonable tradeoff between cost and precision for most qSIP applications. Increasing replication improves power and reduces the minimum detectable threshold for inferring isotope uptake to 5 atom%. Finally, we provide evidence for the importance of internal standards to calibrate the %GC to mean weighted density regression per sample. These results should benefit those designing future SIP experiments, and provide a reference for metagenomic SIP applications where financial and computational limitations constrain experimental scope.

Importance

One of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about genomic content and potential functions, but may not reflect an organism’s activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of community interactions, but fail to link the two. Quantitative stable isotope probing (qSIP) is a method that can link the identity and function of specific microbes within a naturally occurring community. Here we explore how the resolution of density-gradient fractionation affects the error and precision of qSIP results, how they may be improved via additional replication, and cost-benefit balanced scenarios for SIP experimental design.
Clinical features and sexual transmission potential of SARS-CoV-2 infected female patients: a descriptive study in Wuhan, China
Authors: Cui Pengfei , Chen Zhe , Wang Tian , Dai Jun , Zhang Jinjin , Ding Ting , Jiang Jingjing , Liu Jia , Zhang Cong , Shan Wanying , Wang Sheng , Rong Yueguang , Chang Jiang , Miao Xiaoping , Ma Xiangyi , Wang Shixuan
Published: February 2020

Background

As of March 2, 2020, SARS-CoV-2 has infected more than 80174 people and caused 2915 deaths in China. This virus rapidly spreads to 56 countries worldwide. Thus, in order to effectively block its transmission, it is urgent to uncover all the possible transmission routes of SARS-CoV-2.

Methods

From January 28 to February 18, 2020, 35 female patients diagnosed with COVID-19 in Tongji Hospital were included in this descriptive study. The gynecologic history, clinical characteristics, laboratory findings and chest computed tomography (CT) of all patients were recorded in detail. To examine whether there is sexual transmission through vaginal from female to her partner, we employed real-time polymerase chain reaction testing (RT-PCR) to detect SARS-CoV-2 in vaginal environment (including vaginal discharge, cervical or vaginal residual exfoliated cells) and anal swab samples, and inquired recent sexual behaviors from the patients.

Findings

The age range of the 35 patients with COVID-19 was 37-88 years. Over 50% patients infected with SARS-CoV-2 had chronic diseases. We tested the vaginal environment and anal swabs from the 35 female patients with COVID-19 and found that only an anal swab sample from one patient was positive for SARS-CoV-2. All the samples from vaginal environment were negative for SARS-CoV-2. The infection rate of the patients’ sexual partner was 42·9%. Additionally, two female patients admitted having sex with their partners during a possible infection incubation period, while one patient’s partner was uninfected and the other patient’s partner was diagnosed with COVID-19 (after the diagnosis of the female patient).

Conclusion

No positive RT-PCR result was found in the vaginal environment perhaps due to the lack of ACE2 expression, which is the receptor of SARS-CoV-2, in the vagina and cervix tissues (human protein atlas). The results from this study show no evidence of transmission of SARS-CoV-2 through vaginal sex from female to her partner. However, the risk of infection of non vaginal sex and other intimate contacts during vaginal sex should not be ignored.

Funding

This work was financially supported by the Clinical Research Pilot Project of Tongji hospital, Huazhong University of Science and Technology (No. 2019CR205).
No evidence for intermolecular recombination in human fibroblast and blood mtDNA from individuals with biparental mtDNA transmission
Authors: Gui Baoheng , Yang Zeyu , Luo Shiyu , Slone Jesse , Nagaraj Sushma , Sadzewicz Lisa , Tallon Luke J. , Huang Taosheng
Published: February 2020

Strictly maternal inheritance and lack of intermolecular recombination of the human mitochondrial genome (mtDNA) are the assumed preconditions for molecular evolution studies, phylogenetic reconstruction and population genetic analyses. This hypothesis, however, has been challenged by investigations providing evidence for genetic recombination of mtDNA, thus sparking controversy. Using single-molecule real-time (SMRT) sequencing technology, we sequenced the entire mtDNA from blood and fibroblast cells from five individuals with biparental mtDNA transmission in three separate, multiple-generation families. After phasing the single nucleotide polymorphism (SNP) genotypes of mtDNA, no intermolecular recombination between paternal and maternal mtDNA was found when the mtDNA was transmitted in either biparental or maternal mode. Our study provides support for the argument that intermolecular mtDNA recombination is absent or extremely rare in humans. As a consequence, these results support the feasibility of mtDNA-based molecular evolution studies and phylogenetic and population genetic analyses for humans, while also avoiding inaccurate phylogenetic inferences and incorrect rejection of the molecular clock.
Driving factors of conifer regeneration dynamics in eastern Canadian boreal old-growth forests
Authors: Martin Maxence , Girona Miguel Montoro , Morin Hubert
Published: February 2020

Old-growth forests play a major role in conserving biodiversity, protecting water resources, sequestrating carbon, and these forests are indispensable resources for indigenous societies. To preserve the ecosystem services provided by these boreal ecosystems, it becomes necessary to develop novel silvicultural practices capable of emulating the natural dynamics and structural attributes of old-growth forests. The success of these forest management strategies depends on developing an accurate understanding of natural regeneration dynamics. Our goal was therefore to identify the main patterns and the drivers involved in the regeneration dynamics of old-growth forests, placing our focus on boreal stands dominated by black spruce (Picea mariana(L.) Mill.) and balsam fir (Balsam fir(L.) Mill.) in eastern Canada. We sampled 71 stands in a 2200 km2study area located within Quebec’s boreal region. For each stand, we noted tree regeneration (seedlings and saplings), structural attributes (diameter distribution, deadwood volume, etc.), and abiotic (topography and soil) factors. We observed that secondary disturbance regimes and topographic constraints were the main drivers of balsam fir and black spruce regeneration. Furthermore, the regeneration dynamics of black spruce appeared more complex than those of balsam fir. We observed distinct phases of seedling production first developing within the understory, then seedling growth when gaps opened in the canopy, followed by progressive canopy closure. Seedling density, rather than the sapling density, had a major role in explaining the ability of black spruce to fill the canopy following a secondary disturbance. The density of balsam fir seedlings and saplings was also linked to the abundance of balsam fir trees at the stand level. This research helps explain the complexity of old-growth forest dynamics where many ecological factors interact at multiple temporal and spatial scales. This study also improves our understanding of ecological processes within native old-growth forests and identifies the key factors to consider when ensuring the sustainable management of old-growth boreal stands.
Getting innovations adopted in the housing sector
Authors: Van Oorschot Johannes A.W.H. , Halman Johannes I.M. , Hofman Erwin
Published: February 2020

Purpose

The purpose of this study is threefold. First, to provide a taxonomy of innovations in the housing sector. Second, to create a coherent framework that includes the mechanisms that stimulate and hinder the adoption of innovation in the housing sector. Third, to develop propositions for future innovation adoption research.

Design/methodology/approach

A search in Clarivate Analytics’ Web of Science, Elsevier’ Scopus and the ARCOM database, followed by ‘snowballing’ as a backward search technique, revealed 94 scientific studies about innovation adoption in the housing sector. These studies were used to conduct a systematic narrative literature review about innovation adoption in the housing sector.

Findings

This study presents the state of knowledge about the adoption of innovation in the housing sector. Based on the unit of analysis by the studies included in our review, we present a taxonomy of housing innovation and we conclude that, typical for low-tech industries, no radical, discontinuous innovations were reported in the field of housing. Based on the data set of this review, a coherent framework has been developed, which includes four categories of determinants and underlying variables. Subsequently, 21 propositions have been deduced, which reflect the key mechanisms affecting the adoption of innovation in housing.

Originality/value

This paper is the first in which the various innovation adoption mechanisms for housing projects are integrated in a coherent innovation adoption framework. This framework not only provides an explanatory overview about innovation adoption in the housing sector but also provides insight to managers how to increase the chances to get their innovations adopted in the housing sector.
An investigation of the synchronization in global house prices
Authors: Hoesli Martin
Published: February 2020

Purpose

The purpose of this paper to provide a discussion of the empirical evidence and contributing factors of the synchronization of house prices globally.

Design/methodology/approach

The author reviewed the main studies on house price synchronization and conducted an empirical analysis using OECD house price indices. A discussion of the contributing factors of synchronization, with a focus on the demand and supply dimensions is provided, and synchronization across both countries and cities is examined.

Findings

Housing markets globally have become more synchronized; this is particularly clear for cities. The sustained demand for places that are attractive for financial motives and for lifestyle and sometimes climate along with the fact that such places tend to be supply-constrained is likely to lead to more synchronization across markets.

Practical implications

The conclusions are important for investors seeking to diversify their housing holdings internationally. The discussion should also benefit policy-makers.

Originality/value

To date, very scarce evidence exists on the synchronization of house prices globally. By surveying the results contained in previous studies and providing a thorough discussion of the possible drivers of house price synchronization, this study contributes to a better understanding of this important topic.
The evolution and alignment of institutional shareholder engagement through the King and CRISA reports
Authors: Foster Richard
Published: February 2020

Purpose

The purpose of this study is to provide a high-level review of the evolution of shareholder activism and institutional investor engagement in the corporate governance ecosystem in South Africa. Furthermore, it specifically seeks to explain the incorporation of such aspects into the various key codes and reports on corporate governance in South Africa since 1994.

Design/methodology/approach

Historical narrative and analysis.

Findings

This study highlights how shareholder activism and institutional investor engagement in the corporate governance ecosystem have been considered and addressed in South Africa since the publication of the First King Report in 1994. The progress that has been made specifically with regard to the introduction of a code for institutional investors is highlighted. The study ultimately acknowledges that this evolution is a continuing journey on the road to stakeholder inclusivity and engagement, and then concludes that the specific role and impact of institutional investors, particularly given some of the recent corporate governance failures, will require further consideration going forward. This should ensure the continued alignment of all stakeholders and assist in making the necessary improvements to the overarching governance framework and attendant culture.

Originality/value

This study is a part of a special issue that looks at the contribution of the King reports to governance globally.
A comparative study of the CISG and the North Korean contract law as to formation of a contract
Authors: Kim Sang Man
Published: February 2020

Purpose

North Korea joined the United Nations Convention on Contracts for the International Sale of Goods (CISG) as a 90th member on March 27, 2019, which will necessitate the understanding of North Korean laws, in particular, the contract law for sale. This paper aims to compare the CISG and the North Korean contract law as to the formation of a contract focusing on form and writing requirement, offer and acceptance.

Design/methodology/approach

This paper analyzes the provisions of the North Korean Civil Code and the CISG and reviews the previous research studies concerning the formation of a contract.

Findings

The CISG and the North Korean Civil Code are very similar in many aspects as to the formation of a contract. However, there are some discrepancies as to the formation of a contract to which the parties need to pay attention in choosing the governing law.

Practical implications

The parties need to pay attention to the differences concerning the formation of a contract between the North Korean Civil Code and the CISG in concluding a contract for sale with North Korea.

Originality/value

This paper will be the first research work, to the best of the author’s knowledge, on the comparison of the CISG and the North Korean contract law as to the formation of a contract.