bluuebunny/crossref_metadata_2025_split huggingface dataset:
Age Trends in Actigraphy and Self-Report Sleep Across the Life Span: Findings From the Pittsburgh Lifespan Sleep Databank
Authors: Wallace Meredith L. , Kissel Nicholas , Hall Martica H. , Germain Anne , Matthews Karen A. , Troxel Wendy M. , Franzen Peter L. , Buysse Daniel J. , Reynolds Charles , Roecklein Kathryn A. , Gunn Heather E. , Hasler Brant P. , Goldstein Tina R. , McMakin Dana L. , Szigethy Eva , Soehner Adriane M. 
Published: January 2022

ABSTRACT

Objective
Sleep changes over the human life span, and it does so across multiple dimensions. We used individual-level cross-sectional data to characterize age trends and sex differences in actigraphy and self-report sleep dimensions across the healthy human life span.

Methods
The Pittsburgh Lifespan Sleep Databank consists of harmonized participant-level data from sleep-related studies conducted at the University of Pittsburgh (2003–2019). We included data from 1065 (n = 577 female; 21 studies) Pittsburgh Lifespan Sleep Databank participants aged 10 to 87 years without a major psychiatric, sleep, or medical condition. All participants completed wrist actigraphy and the self-rated Pittsburgh Sleep Quality Index. Main outcomes included actigraphy and self-report sleep duration, efficiency, and onset/offset timing, and actigraphy variability in midsleep timing.

Results
We used generalized additive models to examine potentially nonlinear relationships between age and sleep characteristics and to examine sex differences. Actigraphy and self-report sleep onset time shifted later between ages 10 and 18 years (23:03–24:10 [actigraphy]; 21:58–23:53 [self-report]) and then earlier during the 20s (00:08–23:40 [actigraphy]; 23:50–23:34 [self-report]). Actigraphy and self-report wake-up time also shifted earlier during the mid-20s through late 30s (07:48–06:52 [actigraphy]; 07:40–06:41 [self-report]). Self-report, but not actigraphy, sleep duration declined between ages 10 and 20 years (09:09–07:35). Self-report sleep efficiency decreased over the entire life span (96.12–93.28), as did actigraphy variability (01:54–01:31).

Conclusions
Awareness of age trends in multiple sleep dimensions in healthy individuals—and explicating the timing and nature of sex differences in age-related change—can suggest periods of sleep-related risk or resilience and guide intervention efforts.
The local wavenumber model for computation of turbulent mixing
Authors: Kurien Susan , Pal Nairita 
Published: January 2022

We present an overview of the current status in the development of a two-point spectral closure model for turbulent flows, known as the local wavenumber (LWN) model. The model is envisioned as a practical option for applications requiring multi-physics simulations in which statistical hydrodynamics quantities such as Reynolds stresses, turbulent kinetic energy, and measures of mixing such as density-correlations and mix-width evolution, need to be captured with relatively high fidelity. In this review, we present the capabilities of the LWN model since it was first formulated in the early 1990s, for computations of increasing levels of complexity ranging from homogeneous isotropic turbulence, inhomogeneous and anisotropic single-fluid turbulence, to two-species mixing driven by buoyancy forces. The review concludes with a discussion of some of the more theoretical considerations that remain in the development of this model.
This article is part of the theme issue ‘Scaling the turbulence edifice (part 2)’.
Helical fluid and (Hall)-MHD turbulence: a brief review
Authors: Pouquet Annick , Yokoi Nobumitsu 
Published: January 2022

Helicity, a measure of the breakage of reflectional symmetry representing the topology of turbulent flows, contributes in a crucial way to their dynamics and to their fundamental statistical properties. We review several of their main features, both new and old, such as the discovery of bi-directional cascades or the role of helical vortices in the enhancement of large-scale magnetic fields in the dynamo problem. The dynamical contribution in magnetohydrodynamic of the cross-correlation between velocity and induction is discussed as well. We consider next how turbulent transport is affected by helical constraints, in particular in the context of magnetic reconnection and fusion plasmas under one- and two-fluid approximations. Central issues on how to construct turbulence models for non-reflectionally symmetric helical flows are reviewed, including in the presence of shear, and we finally briefly mention the possible role of helicity in the development of strongly localized quasi-singular structures at small scale.
This article is part of the theme issue ‘Scaling the turbulence edifice (part 2)’.
The effectiveness of acupoint herbal patching for non-specific low back pain: A Protocol for systematic review and meta-analysis
Authors: Ma Tianshu , Liu WU , Dong Yan , Cheng Lei , Wang Ziyuan , Liu Xiaona , Li Tie , Liu Chengyu 
Published: January 2022

AbstractBackgroundNon-specific low back pain(NS-LBP) is related to disability and work absence and accounts for high economical costs of global.It is a problem that has a negative impact on physical, mental health of patients and quality of life. At present, acupoint herbal patching(AHP) as an adjuvant therapy is currently undergoing clinical trials in different medical centers. This study aimed to design a systematic review and meta-analysis to explore the effects of AHP on non-specific low back pain(NS-LBP).MethodsWe will search the Cochrane Central Register of Controlled Trials, PubMed, Embase, the Web of Science, the Chinese Biomedical Literature Database,the Chinese Scientific Journal Database, the Wan-Fang Database and the China National Knowledge Infrastructure. The primary outcome measures will be clinical effective rate, functional outcomes, and quality of life. Data that meets the inclusion criteria will be extracted and analyzed using RevMan V.5.3 software. Two reviewers will evaluate the studies using the Cochrane Collaboration risk of bias tool. We will use the GRADE approach to assess the overall quality of evidence supporting the primary outcomes. We will also use Spass software (Version19.0) for complex network analysis to explore the potential core prescription of acupoint herbal patching for functional constipation.ResultsThis systematic review protocol will analyze the effectiveness, quality of life, improvement of the symptom and safety of acupoint herbal patching therapy for non-specific low back pain.ConclusionThe findings of this systematic review will provide evidence to evaluate the effectiveness and safety of acupoint herbal patching for non-specific low back pain.
High performance liquid chromatography-based metabolomics of Psidium guajava Linn. leaf extracts
Authors: Gholkar Manasi S. , Daswani Poonam G. , Iyer Vidhya V. , Birdi Tannaz J. 
Published: January 2022

AbstractBackgroundOver the years, a number of methods have been introduced in the field of herbal medicine. Amongst these, metabolomics has rapidly emerged as a method of choice due to its wide applicability and versatility. High performance liquid chromatography (HPLC) is a preferred method for fingerprinting with advantages such as easy and wide availability, and relatively low maintenance cost. The current study used HPLC profiling and attempted to correlate it to anti-diarrhoeal activity of Psidium guajava (guava) extracts.MethodsNinety samples of guava leaves were collected from three locations in Maharashtra, India over three seasons. Hydroalcoholic extracts (50:50, ethanol:water) were prepared and the HPLC chromatogram of all 90 extracts obtained. A total of eight bioassays representing the important features of diarrhoeal pathogenesis were performed and the extracts were differentiated as ‘good’ or ‘poor’ according to cut-offs for each assay. The numerical data of the bioassays and the HPLC chromatogram was correlated using suitable mathematical models comprising Principal component analysis (PCA), orthogonal partial least squares (OPLS, regression) and orthogonal partial least squares discriminant analysis (OPLS-DA).ResultsOPLS-DA showed good seasonal and regional segregation of extracts. For most of the bioassays, PCA was unsuccessful in showing significant discrimination. Hence, OPLS plots were further developed; differentiation of good and poor extracts among the 90 extracts was successfully demonstrated for antibacterial activity against Shigella flexneri and Vibrio cholerae, inhibition of invasion of enteropathogenic Escherichia coli into HEp-2 epithelial cells, and cholera toxin (CT) production by V. cholerae. However, for other assays, namely, inhibition of adherence of E. coli, invasion of S. flexneri into HEp-2 cells, and inhibition of E. coli labile toxin (LT), subsets of 90 extracts were selected to demonstrate a significant correlation.ConclusionHPLC-based metabolomics has the potential to differentiate good and poor activities of guava leaf extracts. This approach can be extended for identifying phytoconstituents responsible for the anti-diarrhoeal activity of guava leaf and help standardization of crude extracts.
Programmable eukaryotic protein expression with RNA sensors
Authors: Jiang Kaiyi , Koob Jeremy , Chen Xi Dawn , Krajeski Rohan N. , Zhang Yifan , Villiger Lukas , Zhou Wenyuan , Abudayyeh Omar O. , Chen Fei , Gootenberg Jonathan S. 
Published: January 2022

AbstractThe diversity of cell types and states can be scalably measured and defined by expressed RNA transcripts. However, approaches to programmably sense and respond to the presence of specific RNAs within living biological systems with high sensitivity are lacking. RNA sensors that gate expression of reporter or cargo genes would have diverse applications for basic biology, diagnostics and therapeutics by enabling cell-state specific control of transgene expression. Here, we engineer a novel programmable RNA-sensing technology, Reprogrammable ADAR Sensors (RADARS), which leverages RNA editing by adenosine deaminases acting on RNA (ADAR) to gate translation of a protein payload on the presence of endogenous RNA transcripts. In mammalian cells, we engineer RADARS with diverse payloads, including luciferase and fluorescent proteins, with up to 164-fold activation and quantitative detection in the presence of target RNAs. We show RADARS are functional either expressed from DNA or as synthetic mRNA. Importantly, RADARS can function with endogenous cellular ADAR. We apply RADARS to multiple contexts, including RNA-sensing induced cell death via caspases, cell type identification, and in vivo control of synthetic mRNA translation, demonstrating RADARS as a tool with significant potential for gene and cell therapy, synthetic biology, and biomedical research.One Sentence SummaryA new technology utilizing ADAR mediated RNA-editing enables robust reprogrammable protein expression based on target RNA transcripts in mammalian cells, leading to broad applications in basic science research, cell engineering, and gene therapy.
How dangerous is omicron and how effective are vaccinations?
Authors: Nesteruk Igor , Rodionov Oleksii 
Published: January 2022

ABSTRACTThe sharp increase in the number of new COVID-19 cases in late 2021 and early 2022, which is associated with the spread of a new strain of coronavirus - omicron - is of great concern and makes it necessary to make at least approximate forecasts for the pandemic dynamics of the epidemic. As this rapid growth occurs even in countries with high levels of vaccinations, the question arises as to their effectiveness. The smoothed daily number of new cases and deaths per capita and the ratio of these characteristics were used to reveal the appearance of new coronavirus strains and to estimate the effectiveness of quarantine, testing and vaccination. The third year of the pandemic allowed us to compare the pandemic dynamics in the period from September 2020 to January 2021 with the same period one year later for Ukraine, EU, the UK, USA, India, Brazil, South Africa, Argentina, Australia, and in the whole world. Record numbers of new cases registered in late 2021 and early 2022 once again proved that existing vaccines cannot prevent new infections, and vaccinated people can spread the infection as intensively as non-vaccinated ones. Fortunately, the daily number of new cases already diminishes in EU, the UK, USA, South Africa, and Australia. In late January - early February 2022,the maximum averaged numbers of new cases are expected in Brazil, India, EU, and worldwide. “Omicron” waves can increase the numbers of deaths per capita, but in highly vaccinated countries, the deaths per case ratio significantly decreases.
Antagonistic regulation of Drosophila mitochondrial uncoupling protein UCP4b by cold and BMP signaling
Authors: Chatterjee Nirmalya , Song Wei , Dumesic Phillip A. , Spiegelman Bruce , Perrimon Norbert 
Published: January 2022

AbstractRegulation of energy metabolism and response to cold are intimately linked in mammals. Central to these two processes are the mitochondrial uncoupling proteins (UCPs), which by promoting proton leakage across the inner mitochondrial membrane lead to the generation of heat instead of ATP synthesis. In addition to heat generation, UCPs also influence energy storage and can protect against obesity and diabetes. Cold-blooded animals like flies also contain UCPs that protect from cold, however their regulations are poorly understood. We find that Drosophila UCP4b is induced by cold in a cell-intrinsic manner and protects against cold and obesity in fly models. Mechanistically, cold regulates UCP4b expression through calcium signaling and Spargel (Srl), the Drosophila ortholog of mammalian PGC1α. To the opposite, MAD, acting downstream of the BMP branch of the TGFβ signaling pathway, represses UCP4b expression independently of cold. Interestingly, the two mechanisms of UCP4b regulation are integrated as MAD binding to the UCP4b promoter is displaced by cold in a Srl-dependent manner. We discuss the similarities between the regulation of mammalian and Drosophila UCPs.SignificanceMitochondrial uncoupling proteins (UCPs) that uncouple the mitochondrial respiration from ATP synthesis regulate energy metabolism, non-shivering thermogenesis, and redox balance in vertebrates and invertebrates. However, their regulation in Drosophila is poorly understood. We found that Drosophila uncoupling protein UCP4b is induced by cold in a cell-autonomous fashion. Conversely, MAD, acting downstream of BMP signaling, inhibits UCP4b expression. MAD is displaced from the upstream regions of the UCP4b gene by cold. UCP4b protects Drosophila against cold and diet-induced obesity. The regulation of UCP4b by cold and BMP signaling is reminiscent of the regulation of mammalian uncoupling protein UCP1. Altogether, we discovered an important regulator of Drosophila energy metabolism which is controlled by regulatory processes that are similar between Drosophila and mammals.
A Complete Set of Equations and Parameters for the Computational Model of Mitochondrial Function for the Proximal Convoluted Tubule and Medullary Thick Ascending Limb Cells in the Rat Kidney
Authors: Bell T. William , Layton Anita T. 
Published: January 2022

AbstractTo investigate mitochondrial function of renal epithelial cells under different tissue oxygenation levels, we have developed and applied computational models of mitochondrial function of the proximal convoluted tubule and medullary thick ascending limb cells. The models predict several key cellular quantities, including ATP generation, P/O (phosphate/oxygen) ratio, proton motive force, electrical potential gradient, oxygen consumption, the redox state of important electron carriers, and ATP consumption. The complete set of model equations and parameters are presented here, together with local and global sensitivity analysis results.
Viral Cultures for Assessing Airborne Transmission of SARs-CoV-2: a Systematic Review Protocol (version 1)
Authors: Heneghan Carl J. , Spencer Elizabeth A. , Brassey Jon , Rosca Elena C. , Plüddemann Annette , Evans David H. , Conly John M. , Maltoni Susanna , Jefferson Tom , Onakpoya Igho J. 
Published: January 2022

AbstractThis is a protocol for a systematic review that aims to evaluate the role of viral cultures for assessing airborne transmission of SARS-CoV-2. The review will address the following research questions:Are airborne samples infectious?If so, what proportion are infectious, and what is the distance and duration of infectiousness in the air?What is the relationship between infectiousness and airborne PCR cycle threshold (Ct)?Is there evidence of a chain of transmission that establishes an actual instance of airborne transmission of SARS-CoV-2?What circumstances might facilitate infectious viruses being airborne over long distances?We will search LitCovid, medRxiv, Google Scholar, and the WHO Covid-19 database to identify relevant studies. We will include studies reporting airborne transmission attempting viral culture or serial qRT-PCR with or without genomic sequencing. Predictive or modelling studies will be excluded. We will assess the quality of included studies using previously published criteria.
A snapshot of the root phenotyping landscape in 2021
Authors: Delory Benjamin M. , Hernandez-Soriano Maria C. , Wacker Tomke S. , Dimitrova Anastazija , Ding Yiyang , Greeley Laura A. , Ng Jason Liang Pin , Mesa-Marín Jennifer , Xie Limeng , Zheng Congcong , York Larry M. 
Published: January 2022

AbstractRoot phenotyping describes methods for measuring root properties, or traits. While root phenotyping can be challenging, it is advancing quickly. In order for the field to move forward, it is essential to understand the current state and challenges of root phenotyping, as well as the pressing needs of the root biology community.In this letter, we present and discuss the results of a survey that was created and disseminated by members of the Graduate Student and Postdoc Ambassador Program at the 11th symposium of the International Society of Root Research. This survey aimed to (1) provide an overview of the objectives, biological models and methodological approaches used in root phenotyping studies, and (2) identify the main limitations currently faced by plant scientists with regard to root phenotyping.Our survey highlighted that (1) monocotyledonous crops dominate the root phenotyping landscape, (2) root phenotyping is mainly used to quantify morphological and architectural root traits, (3) 2D root scanning/imaging is the most widely used root phenotyping technique, (4) time-consuming tasks are an important barrier to root phenotyping, (5) there is a need for standardised, high-throughput methods to sample and phenotype roots, particularly under field conditions, and to improve our understanding of trait-function relationships.
Genome-wide regulation of KSHV RNA splicing by viral RNA-binding protein ORF57
Authors: Majerciak Vladimir , Lobanov Alexei , Cam Maggie , Zheng Zhi-Ming 
Published: January 2022

AbstractRNA splicing plays an essential role in the expression of eukaryotic genes. We previously showed that KSHV ORF57 is a viral splicing factor promoting viral lytic gene expression. In this report, we compared the splicing profile of viral RNAs in BCBL-1 cells carrying a wild-type (WT) versus the cells containing an ORF57 knock-out (57KO) KSHV genome during viral lytic infection. Our analyses of viral RNA splicing junctions from RNA-seq identified hundreds of novel viral RNA splicing events, including the splicing events spanning large parts of the viral genome and production of vIRF4 circRNAs. We found that the 57KO alters the viral RNA splicing efficiency of affected RNA splicing events. Two most susceptible RNAs to ORF57 splicing regulation are the K15 RNA with multiple exons and introns and the bicistronic RNA encoding both viral thymidylate synthase (ORF70) and membrane-associated E3-ubiquitin ligase (K3). ORF70-K3 RNA bears two introns, of which the first intron is positioned in the ORF70 coding region as an alternative intron and the second intron in the intergenic region as a constitutive intron. In WT cells expressing ORF57, most ORF70-K3 transcripts retain the first intron to maintain an intact ORF70 coding region. In contrast, in the 57KO cells, the first intron is substantially spliced out without affecting the splicing efficiency of the second intron. Using a minigene comprising of ORF70-K3 locus, we further confirmed ORF57 regulation of ORF70-K3 RNA splicing, independently of other viral factors. By monitoring protein expression, we showed that ORF57-mediated retention of the first intron leads to the expression of full-length ORF70 protein. The absence of ORF57 promotes the first intron splicing and expression of K3 protein. Altogether, we conclude that ORF57 regulates alternative splicing of ORF70-K3 bicistronic RNA to control K3-mediated immune evasion and ORF70 participation of viral DNA replication in viral lytic infection.Author summaryLike other herpesviruses, the expression of KSHV genes is in a tightly regulated manner during viral infection. The contribution of RNA splicing in the regulation of KSHV gene expression was extensively investigated in this report. We found that approximately one-third of all viral gene transcripts are spliced, with many undergoing RNA alternative splicing. We identified a subset of viral RNA splicing events susceptible to the regulation of viral RNA-binding protein ORF57. This led to the discovery of ORF57-mediated regulation of the bicistronic ORF70-K3 RNA splicing and production of viral thymidylate synthase ORF70 and viral E3-ubiquitin ligase K3. Such regulation allows timely but mutually exclusive expression of these two viral proteins to execute their unique roles in immune evasion and viral genome replication during the KSHV lytic cycle. Thus, these data provide new insight into KSHV biology. Finally, our study represents a blueprint for RNA splicing studies of other pathogens in infected cells.
Dynamic human liver proteome atlas reveals functional insights into disease pathways
Authors: Niu Lili , Geyer Philipp E. , Gupta Rajat , Santos Alberto , Meier Florian , Doll Sophia , Albrechtsen Nicolai J. Wewer , Klein Sabine , Ortiz Cristina , Uschner Frank E. , Schierwagen Robert , Trebicka Jonel , Mann Matthias 
Published: January 2022

AbstractDeeper understanding of liver pathophysiology would benefit from a comprehensive quantitative proteome resource at cell-type resolution to predict outcome and design therapy. Here, we quantify more than 150,000 sequence-unique peptides aggregated into 10,000 proteins across total liver, the major liver cell types, time-course of primary cell cultures and liver disease states. Bioinformatic analysis reveals that half of hepatocyte protein mass is comprised of enzymes and 23% of mitochondrial proteins, twice the proportion of other liver cell types. Using primary cell cultures, we capture dynamic proteome remodeling from tissue states to cell line states, providing useful information for biological or pharmaceutical research. Our extensive data serves as spectral library to characterize a human cohort of non-alcoholic steatohepatitis and cirrhosis. Dramatic proteome changes in liver tissue include signatures of stellate cell activation resembling liver cirrhosis and providing functional insights. We built a web-based dashboard application for the interactively exploration of our resource.HighlightsCell-type resolved liver proteome with copy numbers for 10,500 proteinsTime-course of human liver primary cells uncovers functional proteome shiftsA human cohort study reveals liver proteome changes in NASH and cirrhosisAn interactive web portal integrates the results for easy exploration