bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel culture method to diagnose fungal infections with biopsy tissues
Authors: Zhao Jiankang , Zhang Yulin , Fan Yanyan , Xiong Zhujia , Xia Yudi , Zou Xiaohui , Han Jiajing , Li Binbin , Wang Chunlei , Liu Xinmeng , Lu Binghuai , Cao Bin 
Published: January 2020

AbstractBiopsy tissue is a difficult sample to gain for the identification of potential pathogen in the clinical laboratory. At present, there are no effective culture methods for small-sized biopsy tissue. In this study, we propose a novel tissue biopsy culture method based on Myco/F lytic liquid culture system, namely, tissue was grinded before injected into culture bottles. More types and numbers of fungi are cultivated using this culture system than sputum or BALF culture. A few of mycobacteria were also detected with ground tissues. The method may be a promising alternative to or supplement for the traditional plate culture in clinical practice.
MRCA time and epidemic dynamics of the 2019 novel coronavirus
Authors: Zhang Chi , Wang Mei 
Published: January 2020

AbstractThe 2019 novel coronavirus (2019-nCoV) have emerged from Wuhan, China. Studying the epidemic dynamics is crucial for further surveillance and control of the outbreak. We employed a Bayesian framework to infer the time-calibrated phylogeny and the epidemic dynamics represented by the effective reproductive number (Re) changing over time from 33 genomic sequences available from GISAID. The time of the most recent common ancestor (MRCA) was December 17, 2019 (95% HPD: December 7, 2019 – December 23, 2019). The median estimate ofReshifted from 1.6 to 1.1 on around January 1, 2020. This study provides an early insight of the 2019-nCoV epidemic. However, due to limited amount of data, one should be cautious when interpreting the results at this stage.
A critical role for Musashi in photoreceptor morphogenesis and Vision
Authors: Sundar Jesse , Matalkah Fatimah , Jeong Bohye , Stoilov Peter , Ramamurthy Visvanathan 
Published: January 2020

ABSTRACTMusashi family of RNA-binding proteins are known for their role in stem-cell renewal and are negative regulators of cell differentiation. Interestingly, in the retina, Musashi proteins, MSI1 and MSI2 are differentially expressed throughout the cycle of retinal development including robust expression in the adult retinal tissue. To study the role of Musashi proteins in the retina, we generated a pan-retinal and rod photoreceptor neuron specific conditional knockout mouse lacking MSI1 and MSI2. Independent of sex, photoreceptor neurons with simultaneous deletion of Msi1 and Msi2 were unable to respond to light and displayed severely disrupted OS morphology and ciliary defects. The retina lacking Musashi exhibited neuronal degeneration with complete loss of photoreceptors by six months. In concordance with our earlier studies that proposed a role for Musashi in regulating alternative splicing, the loss of Musashi prevented the use of photoreceptor-specific exons in transcripts critical for OS morphogenesis, ciliogenesis and synaptic transmission. Overall, we demonstrate a critical role for Musashi in the morphogenesis of terminally differentiated photoreceptor neurons. This role is in stark contrast with the canonical function of these two proteins in maintenance and renewal of stem cells.
GS-Preprocess: Containerized GUIDE-seq Data Analysis Tools with Diverse Sequencer Compatibility
Authors: Rodríguez Tomás C. , Pratt Henry E. , Liu PengPeng , Amrani Nadia , Zhu Lihua Julie 
Published: January 2020

AbstractRNA-guided nucleases (e.g. CRISPR-Cas) are used in a breadth of clinical and basic scientific subfields for the investigation or modification of biological processes. While these modern platforms for site-specific DNA cleavage are highly accurate, some applications (e.g. gene editing therapeutics) cannot tolerate DNA breaks at off-target sites, even at low levels. Thus, it is critically important to determine the genome-wide targeting profile of candidate RNA-guided nucleases prior to use. GUIDE-seq is a high-quality, easy-to-execute molecular method that detects and quantifies off-target cleavage. However, this method may remain costly or inaccessible to some researchers due to its library sequencing and analysis protocols, which require a MiSeq platform that must be preprogramed for non-standard output. Here, we present GS-Preprocess, an open-source containerized software that can use standard raw data output (BCL file format) from any Illumina sequencer to create input for the Bioconductor GUIDEseq off-target profiling package. Single-command GS-Preprocess performs FASTQ demultiplexing, adapter trimming, alignment, and UMI reference construction, improving the ease and accessibility of the GUIDE-seq method for a wide range of researchers.
The role of vegetative cell fusions in the lifestyle of the wheat fungal pathogenZymoseptoria tritici
Authors: Francisco Carolina Sardinha , Zwyssig Maria Manuela , Palma-Guerrero Javier 
Published: January 2020

AbstractThe ability of fungal cells to undergo cell fusion allows them to maximize their overall fitness. In this study, we characterized the role of thesogene orthologous inZymoseptoria triticiand the biological contribution of vegetative cell fusions in the lifestyle of this latent necrotrophic fungus. Firstly, we show thatZ. triticiundergoes self-fusion between distinct cellular structures and its mechanism is dependent on the initial cell density. Next, the deletion ofZtSoresulted in the loss of cell-to-cell communication affecting both hyphal and germlings fusion. We show thatZ. triticimutants for MAP kinase-encodingZtSlt2(orthologous MAK-1) andZtFus3(orthologous MAK-2) genes also fail to undergo self-stimulation and self-fusion, demonstrating the functional conservation of this signaling mechanism across species. Additionally, theΔZtSomutant was severely impaired in melanization, which leads us to identify a trade-off between fungal growth and melanization. Though it has been proposed that So is a scaffold protein for MAP kinase genes from the CWI pathway, its deletion did not affect the cell wall integrity of the fungus. Finally, we demonstrated that anastomose is dispensable for pathogenicity, but essential for the fruiting body development and its absence abolish the asexual reproduction ofZ. tritici. Taken together, our data show thatZtSois required for fungal development, while vegetative cell fusions are essential for fungal fitness.
Nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform bridges 4-D chromatin organization with molecular function
Authors: Li Yue , Eshein Adam , Virk Ranya K.A. , Eid Aya , Wu Wenli , Frederick Jane , VanDerway David , Gladstein Scott , Huang Kai , Anthony Nicholas M. , Bauer Greta M. , Zhou Xiang , Agrawal Vasundhara , Pujadas Emily M. , Esteve George , Chandler John E. , Bleher Reiner , de Pablo Juan J. , Szleifer Igal , Dravid Vinayak P , Almassalha Luay M. , Backman Vadim 
Published: January 2020

AbstractIn eukaryotic cells, chromatin structure is linked to transcription processes through the regulation of genome organization. Extending across multiple length-scales - from the nucleosome to higher-order three-dimensional structures - chromatin is a dynamic system which evolves throughout the lifetime of a cell. However, no individual technique can fully elucidate the behavior of chromatin organization and its relation to molecular function at all length- and timescales at both a single-cell and a cell population level. Herein, we present a multi-technique nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform that bridges electron tomography and optical superresolution imaging of chromatin conformation and transcriptional processes, with resolution down to the level of individual nucleosomes, with high-throughput, label-free analysis of chromatin packing and its dynamics in live cells. Utilizing nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nm, sub-Mb genomic size, and an internal fractal structure. The chromatin packing behavior of these domains is directly influenced by active gene transcription. Furthermore, we demonstrated that the chromatin packing domain structure is correlated among progenitor cells and all their progeny, indicating that the organization of chromatin into fractal packing domains is heritable across cell division. Further studies employing the nano-ChIA platform have the potential to provide a more coherent picture of chromatin structure and its relation to molecular function.
How Many Streamlines are Required for Reliable Probabilistic Tractography? Solutions for Microstructural Measurements and Neurosurgical Planning
Authors: Reid Lee B. , Cespedes Marcela I. , Pannek Kerstin 
Published: January 2020

AbstractDiffusion MRI tractography is commonly used to delineate white matter tracts. These delineations can be used for planning neurosurgery or for identifying regions of interest from which microstructural measurements can be taken. Probabilistic tractography produces different delineations each time it is run, potentially leading to microstructural measurements or anatomical delineations that are not reproducible. Generating a sufficiently large number of streamlines is required to avoid this scenario, but what constitutes “sufficient” is difficult to assess and so streamline counts are typically chosen in an arbitrary or qualitative manner. This work explores several factors influencing tractography reliability and details two methods for estimating this reliability. The first method automatically estimates the number of streamlines required to achieve reliable microstructural measurements, whilst the second estimates the number of streamlines required to achieve a reliable binarised trackmap than can be used clinically. Using these methods, we calculated the number of streamlines required to achieve a range of quantitative reproducibility criteria for three anatomical tracts in 40 Human Connectome Project datasets. Actual reproducibility was checked by repeatedly generating the tractograms with the calculated numbers of streamlines. We found that the required number of streamlines varied strongly by anatomical tract, image resolution, number of diffusion directions, the degree of reliability desired, the microstructural measurement of interest, and/or the specifics on how the tractogram was converted to a binary volume. The proposed methods consistently predicted streamline counts that achieved the target reproducibility. Implementations are made available to enable the scientific community to more-easily achieve reproducible tractography.
Purine-responsive expression of theLeishmania donovaniNT3 purine nucleobase transporter is mediated by a conserved RNA stem-loop
Authors: Licon M. Haley , Yates Phillip A. 
Published: January 2020

ABSTRACTThe ability to modulate gene expression in response to changes in the host environment is essential for survival of the kinetoplastid parasiteLeishmania. Unlike most eukaryotes, gene expression in kinetoplastids is predominately regulated post-transcriptionally. Consequently, RNA-binding proteins (RBPs) and mRNA-encoded sequence elements serve as primary determinants of gene regulation in these organisms; however, few have been ascribed roles in specific stress-response pathways.Leishmanialack the capacity forde novopurine synthesis and must scavenge these essential nutrients from the host.Leishmaniahave evolved a robust stress response to withstand sustained periods of purine scarcity during their lifecycle. The purine nucleobase transporter, LdNT3, is among the most substantially upregulated proteins in purine-starvedL. donovani.Here we report that the post-translational stability of the LdNT3 protein is unchanged in response to purine starvation. Instead, LdNT3 upregulation is primarily mediated by a 33 nucleotide (nt) sequence in theLdNT3mRNA 3’-untranslated region that is predicted to adopt a stem-loop structure. While this sequence is highly conserved within the mRNAs of orthologous transporters in multiple kinetoplastid species, putative stem-loops fromL. donovaniandTrypanosoma bruceinucleobase transporter mRNAs are not functionally interchangeable for purine-responsive regulation. Through mutational analysis of the element, we demonstrate that species specificity is attributable to just three variant bases within the predicted loop. Finally, we provide evidence that the abundance of thetrans-acting factor that binds theLdNT3stem-loopin vivois substantially higher than required for regulation of LdNT3 alone, implying a potential role in regulating other purine-responsive genes.
Immune dysregulation in SHARPIN-deficient mice is dependent on CYLD-mediated cell death
Authors: Ang Rosalind L. , Sundberg John P. , Sun Shao-Cong , Gillespie Virginia L. , Heeger Peter S. , Xiong Huabao , Lira Sergio A. , Ting Adrian T. 
Published: January 2020

AbstractSHARPIN, together with RNF31/HOIP and RBCK1/HOIL1, form the linear ubiquitin chain assembly complex (LUBAC) E3 ligase that catalyzes M1-linked poly-ubiquitination. Mutations inRNF31/HOIPandRBCK/HOIL1in humans andSharpinin mice lead to auto-inflammation and immunodeficiency but the mechanism underlying the immune dysregulation remains unclear. We now show that the phenotype of theSharpin-/-mice is dependent on CYLD, the deubiquitinase that removes K63-linked poly-ubiquitin chains. The dermatitis, disrupted splenic architecture, and loss of Peyer’s patches in theSharpin-/-mice were fully reversed inSharpin-/-Cyld-/-mice. There is enhanced association of RIPK1 with the death-inducing signaling complex (DISC) following TNF stimulation inSharpin-/-cells, and this is dependent on CYLD since it is reversed inSharpin-/-Cyld-/-cells. Enhanced RIPK1 recruitment to the DISC inSharpin-/-cells correlated with impaired phosphorylation of CYLD at serine 418, a modification reported to inhibit its enzymatic activity. The dermatitis in theSharpin-/-mice was also ameliorated by the conditional deletion ofCyldusingLysM-creorCx3cr1-creindicating that CYLD-dependent death of myeloid cells is inflammatory. Our studies reveal that under physiological conditions, TNF- and RIPK1-dependent cell death is suppressed by the linear ubiquitin-dependent inhibition of CYLD. TheSharpin-/-phenotype illustrates the pathological consequences when CYLD inhibition fails.Short SummaryIn the absence of SHARPIN, cells fail to properly regulate the deubiquitinase CYLD, leading to RIPK1-mediated cell death. Deletion ofCyldreverses the sensitivity ofSharpin-/-cells to TNF-induced cell death, as well as the multi-organ inflammation and immune dysfunction observed inSharpin-/-mice.
The most dangerous employees in the workplace
Authors: Lilly Juliana 
Published: January 2020

Purpose
This paper aims to summarize the existing literature on workplace respect and to help explain how employees who feel excluded and disrespected at work may retaliate against the organization.

Design/methodology/approach
A thorough review of the literature was conducted. This review is prepared by an independent writer who adds her own impartial comments and places the studies in context.

Findings
Based on the findings of the studies reviewed, employees who feel disrespected at work may retaliate by complaining or withdrawing from work. The emotions and hurt feelings resulting from disrespectful behavior are often hard to articulate, and managers may not realize how hurtful their actions are to the employee. The paper offers suggestions on how organizations may reduce the potential damage by reflecting on their work environment that may be fueling employee negativity.

Originality/value
This briefing saves busy executives and researchers hours of reading time by selecting only the best, most pertinent information and presenting it in a condensed and easy-to-digest format.
Nonprofit branding: a bibliometric analysis
Authors: Sepulcri Lara Mendes Christ Bonella , Mainardes Emerson Wagner , Belchior Cícero Caldeira 
Published: January 2020

PurposeThis study aims to examine articles on nonprofit branding over an 18-year time span to develop an overview and better understanding of the subject.Design/methodology/approachThis study used the Scopus database in a search for studies that deal, regardless of the approach, with branding in a nonprofit context. Subsequently, through a systematic review, a database with 84 articles was generated and 77 articles were submitted to bibliometric analysis.FindingsThis study identified six main research areas (brand and donation, brand management, brand orientation, nonprofit and for-profit partnership, communication strategies and stakeholder management), which were analyzed and discussed, seeking to identify the relationship between research in each area. In addition, this study presents the limitations of the research and thus verify that, although this body of literature is growing, the complexity of the nonprofit sector offers several opportunities for future research, which are pointed out at the end of the study.Practical implicationsThis study contributes to the academic literature on the topic by providing a systematization of knowledge about branding in the nonprofit sector and also offers insights about nonprofit branding to institutions and managers in this industry.Originality/valueThis is the first study, to the authors’ knowledge, to evaluate and quantify the progress of brand literature in the nonprofit sector.
Research into student mental health: where have we come and how can we improve?
Authors: Brown Poppy 
Published: January 2020

Purpose
There has previously been limited research into student mental health. However, recognition of the unique challenges and the scale of mental health problems within universities is increasing. A number of projects aiming to address the knowledge gap and develop appropriate interventions and toolkits have recently begun. The purpose of this paper is to present and evaluate such projects.

Design/methodology/approach
A critical appraisal of current and recent research in student mental health is presented in this paper.

Findings
These projects are likely to bring huge benefits. However, limitations include the need for increased collaboration, use of validated measures for evaluation, and consideration of the context of implementation.

Research limitations/implications
Future research should consider ways to overcome these limitations.

Originality/value
Discussion and evaluation of current research is important for dissemination and for encouraging future improvement.
Associations between white blood cells count and obesity in apparently healthy young adults
Authors: Ghannadiasl Fatemeh 
Published: January 2020

PurposeThe elevated white blood cells (WBCs) count has been reported to be a predictor of cardiovascular diseases, diabetes, hypertension and metabolic syndrome. This study aims to determine the associations between WBCs count and obesity in apparently healthy young adults.Design/methodology/approachIn this cross-sectional study, the authors evaluated the body mass index (BMI) in 392 apparently healthy young adults of both sexes. The WBCs count was measured using standard counter techniques. The inclusion criteria were the agreement to participate in the study, between 18 and 25 years of age, lack of self-reported diseases such as cardiovascular diseases, hypertension, kidney and infectious diseases.FindingsAccording to the BMI classification, underweight and overweight or obesity were observed in 14.58 and 11.48 per cent of young adults, respectively. The mean WBC was 6.5 ± 1.5 (×10³ cells/µL). Higher values of WBCs were found in women than in men (p= 0.02). The young adults with higher BMI had a higher WBCs count. There was a positive correlation between WBCs count and weight and BMI (r = 0.19 and r = 0.22,p< 0.001, respectively).Research limitations/implicationsThis research was a cross-sectional study. Future studies are suggested using longitudinal studies to examine more relationships between obesity and WBCs count in apparently healthy young adults.Practical implicationsThe results of this study provide evidence for weight management in this age group to reduce diseases associated with increased WBCs count.Originality/valueThe WBCs count was related to increasing levels of BMI per cent 2 C even in the normal range.
Consumers’ exposure to claims on pre-packed bread: the case of a developing country, Lebanon
Authors: Bou-Mitri Christelle , Khnaisser Lama , Bou Ghanem Mira , Merhi Samar , Fares Jessy El-Hayek , Doumit Jacqueline , Farhat Antoine G. 
Published: January 2020

PurposeThis study aims to assess the exposure of Lebanese consumers to nutrition and health claims (NHCs) on pre-packed bread.Design/methodology/approachBread samples (n= 354) from all the bakeries (n= 44) located in Mount Lebanon, between 2017 and 2018, were assessed. Breads with nutrition claims were analyzed using standard methods. A cross-sectional study was also conducted among 400 supermarket shoppers.FindingsResults showed that among the collected samples of bread (n= 354), 59.6 per cent carried at least one claim, 47.2 per cent had non-nutrient claims, 32.5 per cent had nutrition claims and 15.3 per cent presented health claims. Claims related to sugar, salt and fiber content were the most commonly used (28.8 , 16.4 and 14.7 per cent, respectively). NHCs were mostly present on whole wheat bread. Breads with claims were more expensive. Half of the participants (49.8 per cent) relied on NHCs whenever purchasing bread, especially females (OR = 2.35, 95 per cent CI = 1.44-3.84,p= 0.001), those following a specific diet (OR = 4.56, 95 per cent CI = 2.02-10.25,p< 0.001) and those with the lowest household income (OR = 0.795, 95 per cent CI = 0.639-0.989,p= 0.040).Originality/valueThe overall findings showed that Lebanese consumers are highly exposed to NHCs, especially those at higher risk which could lead to serious public health issues if their use is not strictly regulated and controlled. Moreover, NHCs could be used as a tool to increase consumers’ awareness and help them make healthier choices during shopping.
Effects of Kakato‐tsurutsuru socks on dry heels in healthy volunteer subjects
Authors: Kamo Atsuko , Umehara Yoshie , Negi Osamu , Iwata Makoto , Kamata Yayoi , Suga Yasushi , Ogawa Hideoki , Tominaga Mitsutoshi , Takamori Kenji 
Published: January 2020

AbstractKakato‐tsurutsuru (Kt) socks have been selling for almost 30 years in Japan. Wearers claim they improve heel dryness despite no scientific evidence. We investigated the effects of Kt socks on heel dryness by questionnaire, clinical scores and non‐invasive skin measurements. In a double‐blind, randomized cross‐over study, 10 healthy volunteers wore control or Kt socks over 2 weeks in sequence for 4 weeks. Skin hydration and evaporation of the medial and dorsal heel were measured before and every week during the trial. Clinical evaluations of desquamation and cracked skin were scored by a dermatologist. A visual analog scale (VAS) questionnaire of comfort, sock climate humidity and skin dryness was conducted. The VAS of comfort was significantly higher in Kt than controls. Average Δskin dryness in control and Kt groups was −1.63 and 2.22, respectively, showing a significant improvement. In the clinical findings of the dorsal side of the heel, Δdesquamation and Δcracked skin scores were significantly decreased and Δstratum corneum hydration significantly increased in Kt compared with controls. Kt socks may retain evaporated sweat with components of natural moisturizing factors, supporting the water‐holding ability of the heel stratum corneum. These findings suggest that Kt socks may improve heel skin dryness.