bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractHuman 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

ABSTRACTBackgroundAlthough 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.MethodsWe 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.ResultsThe 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.ConclusionsThe 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

SUMMARYAdaptive 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

AbstractQuantitative 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.ImportanceOne 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

SummaryBackgroundAs 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.MethodsFrom 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.FindingsThe 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).ConclusionNo 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.FundingThis 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

AbstractStrictly 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

AbstractOld-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

PurposeThe 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/approachA 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.FindingsThis 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/valueThis 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

PurposeThe purpose of this paper to provide a discussion of the empirical evidence and contributing factors of the synchronization of house prices globally.Design/methodology/approachThe 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.FindingsHousing 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 implicationsThe conclusions are important for investors seeking to diversify their housing holdings internationally. The discussion should also benefit policy-makers.Originality/valueTo 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.
Impact of direct traffic effect on online sales
Authors: Kakalejčík Lukáš , Bucko Jozef , Danko Jakub 
Published: February 2020

Purpose
This study aims to analyze the impact of newly created brand awareness on customer’s buying behavior in online environment.

Design/methodology/approach
The authors analyzed more than 280,000 online customer journeys from four e-commerce stores based in Slovakia. Within the results of the interaction analysis of individual customer journeys, the authors determined three criteria based on the level of theoretical brand awareness. The purpose was to determine their occurrence in real-world data.

Findings
It was found that each of the specified criteria accounts for the significant share of the company’s revenues. Based on these criteria and the level of their occurrence, the authors introduced the term direct traffic effect.

Research limitations/implications
Because of the available Web analytics tools, the data might be imprecise because of data collection issues. There is also ambiguity in the interpretation of the customer journey.

Practical implications
The company can build awareness among prospective customers by offering them a positive customer experience during the first interactions online. Data proved that customer will not only repeatedly visit the website from the direct traffic source but also his customer journey will end with the purchase of the company’s products.

Originality/value
This paper fulfills the need for further research on the impact of multi-channel marketing on brand awareness and consumer behavior, respectively.
Optical evaluation of dithizone solution as a new radiochromic dosimeter
Authors: Rabaeh Khalid , Basfar Ahmed 
Published: February 2020

Purpose
The purpose of this paper is to propose a new dithizone solution dosimeter for high radiation applications such as polymers applications and food irradiation.

Design/methodology/approach
Gamma-rays cell of Co-60 source with 8.4 kGy/h dose rate was used to irradiate the dithizone solutions at different irradiation temperatures. The optical measurements of unirradiated and irradiated dithizone dye solution dosimeters were performed using a UV/VIS spectrophotometer at absorption peaks of 421 and 515 nm.

Findings
The new dosimeter improved significantly with the increase of dithizone dye concentrations from 0.025 to 0.1 mM. The dosimeter shows a perfect pre- and post-irradiation stability after irradiation for five days. Because of irradiation temperature dependence, the dithizone solution dosimeter should be corrected under actual processing conditions.

Practical implications
Dosimetry is a key point in quality control of radiation processing to assure that uniform and correct radiation doses are delivered to a region of interest. Therefore, this study introduces a dithizone solution dosimeter for high-dose radiation applications such as food irradiation, polymers applications and agriculture.

Originality/value
Ionizing radiation interacted with the ethanol solvent, resulting in the formation of free radicals, then these free radicals interacted with the dithizone molecule and changed the dye color from yellow to orange.