bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of personalised risk prediction models for early detection and diagnosis of primary liver cancer among the English primary care population using the QResearch® database: research protocol and statistical analysis plan
Authors: Liao Weiqi , Jepsen Peter , Coupland Carol , Innes Hamish , Matthews Philippa C. , Campbell Cori , Barnes Eleanor , Hippisley-Cox Julia ,   DeLIVER consortium
Published: January 2022

AbstractBackground and research aimThe incidence and mortality of liver cancer have been increasing in recent years in the UK. However, liver cancer is still under-studied. The Early Detection of Hepatocellular Liver Cancer (DeLIVER-QResearch) project aims to address the research gap and generate new knowledge to improve early detection and diagnosis of primary liver cancer from general practice and at the population level. There are three research objectives: (1) to understand the current epidemiology of primary liver cancer in England, (2) to identify and quantify the symptoms and comorbidities associated with liver cancer, and (3) to develop and validate prediction models for early detection of liver cancer suitable for implementation in clinical settings.MethodsThis population-based study uses the QResearch® database (version 46) and includes patients aged 25-84 years old and without a diagnosis of liver cancer at the cohort entry (study period: 1 January 2008 to 31 December 2020). The team conducted a literature review (with additional clinical input) to inform the inclusion of variables for data extraction from the QResearch database. A wide range of statistical techniques will be used for the three research objectives, including descriptive statistics, multiple imputation for missing data, conditional logistic regression to investigate the association between the clinical features (symptoms and comorbidities) and the outcome, fractional polynomial terms to explore the non-linear relationship between continuous variables and the outcome, and Cox regression for the prediction model. We have a specific focus on the 1-year, 5-year, and 10-year absolute risks of developing liver cancer, as risks at different time points have different clinical implications. The internal-external validation approach will be used, and the discrimination and calibration of the prediction model will be evaluated.DiscussionThe DeLIVER-QResearch project uses large-scale representative population-based data to address the most relevant research questions for early detection and diagnosis of primary liver cancer in England. This project has great potential to inform the national cancer strategic plan and yield substantial public and societal benefits.Medical Subject Headings (MeSH)Liver Neoplasms; Carcinoma, Hepatocellular; Cholangiocarcinoma; Clinical Decision Rules; Early Detection of Cancer; Early Diagnosis; Symptom Assessment; Comorbidity
Comprehensive analysis of Histone deacetylases genes in the prognosis and immune infiltration of glioma patients
Authors: Liu Aibin , Li Yanyan , Shen Lin , Li Na , Shen Liangfang , Li Zhanzhan 
Published: January 2022

AbstractThe occurrence and development of tumors are closely related to histone deacetylases (HDACs). However, the overall biology and prognosis are still unknown in glioma. In the present study, we comprehensively explored the biology function and prognosis of eleven HDAC genes in glioma, which may contribute the more understanding of molecular mechanisms and potential therapeutic targets for glioma patients.We systematically described the expression files, molecular subtypes, prognostic value, immune filtration and tumor microenvironment and gene alteration, function and pathways enrichment, and drug sensitivity using TCGA and CGGA datasets. We developed and validated the prognostic model based on HDACs genes in glioma using LASSO, univariate, and multivariate cox regression. Receiver operating characteristic analyses were used for model evaluating. We also validated the expressions of HDACs genes included in the model in non-tumor and glioma tissues samples. Glioma patients can be divided into two subclasses based on eleven HDAC genes, and patients from two subclasses had markedly different survival outcomes. Then, using six HDAC genes (HDAC1, HDAC3, HDAC4, HDAC5, HDAC7, and HDAC9), we established a prognostic model in glioma patients, and this prognostic model was well validated in an independent cohort population. Furthermore, the calculated risk score from six HDACA genes expression was suggested to be an independent prognostic factor, which can predict the five-year overall survival of glioma patients well. High-risk patients can be attributed to multiple complex function and molecular signaling pathways, and the genes alterations of high- and low-risk patients were significantly different. We also found that different survival outcomes of high- and low-risk patients could be involved in the differences of immune filtration level and tumor microenvironment. Subsequently, we identified several small molecular compounds that could be favorable for glioma patients’ treatment. And finally, the expression levels of HDAC genes from prognostic model were validated in glioma and non-tumor tissues samples.Our results revealed the clinical utility and potential molecular mechanisms of HDAC genes in glioma. Model based on six HDAC genes can predict the overall survival of glioma patients well, which can be served as potential therapeutic targets.
Emergence of glycogen synthase kinase-3 interaction domain enhances phosphorylation of SARS-CoV-2 nucleocapsid protein
Authors: Yun Jun Seop , Kim Nam Hee , Song Hyeeun , Cha So Young , Hwang Kyu Ho , Lee Jae Eun , Jeong Cheol-Hee , Song Sang Hyun , Kim Seonghun , Cho Eunae Sandra , Kim Hyun Sil , Yook Jong In 
Published: January 2022

ABSTRACTA structural protein of SARS-CoV-2, nucleocapsid (N) protein is abundantly expressed during viral replication. The N protein is phosphorylated by glycogen synthase kinase (GSK)-3 on the serine/arginine (SR) rich motif located in disordered regions. Although phosphorylation by GSK-3β constitutes a critical event for viral replication, the molecular mechanism underlying N phosphorylation is not well understood. In this study, we found the putative alpha-helix L/FxxxL/AxxRL motif known as the GSK-3 interacting domain (GID), commonly found in many endogenous GSK-3β binding proteins, such as Axins, FRATs, WWOX and GSKIP. Indeed, N interacts with GSK-3β similarly to Axin, and Leu to Glu substitution of the GID abolished the interaction, with loss of N phosphorylation. Unlike with endogenous GID proteins, the N interaction neither disturbs endogenous GSK-3 activity nor regulates subsequent canonical Wnt activity and the Snail-EMT program. Notably, N abundance in SARS-CoV-2 is incomparably high compared to other coronaviruses, such as 229E, OC43 and HKU1. Compared to other coronaviruses, N harbors a CDK1 primed phosphorylation site and Gly-rich linker for enhanced phosphorylation by GSK-3β. Furthermore, we found that the S202R mutant found in Delta and R203K/G204R mutant found in the Omicron variant allows increased abundance and hyper-phosphorylation of N. Our observations suggest that the emergence of GID and mutations for increased phosphorylation in N may have contributed to the emergence of SARS-CoV-2 and evolution of variants, respectively. Further study, especially in a BSL3-equipped facility, is required to elucidate the functional importance of GID and N phosphorylation in SARS-CoV-2 and variants.
P38 kinases mediate NLRP1 inflammasome activation after ribotoxic stress response and virus infection
Authors: Jenster Lea-Marie , Lange Karl-Elmar , Normann Sabine , vom Hemdt Anja , Wuerth Jennifer D. , Schiffelers Lisa D.J. , Tesfamariam Yonas M. , Gohr Florian N. , Klein Laura , Kaltheuner Ines H. , Lapp Dorothee J. , Mayer Jacob , Moecking Jonas , Ploegh Hidde L. , Latz Eicke , Geyer Matthias , Kümmerer Beate M. , Schmidt Florian I. 
Published: January 2022

SummaryInflammasomes integrate cytosolic evidence of infection or damage to mount inflammatory responses. The inflammasome sensor NLRP1 is expressed in human keratinocytes and coordinates inflammation in the skin. We found that diverse stress signals converge on the activation of p38 kinases to initiate human NLRP1 inflammasome assembly: UV irradiation and microbial molecules that initiate the ribotoxic stress response critically relied on the MAP3 kinase ZAKα to activate p38 and ultimately human NLRP1. Infection with insect-transmitted alphaviruses, including Semliki Forest, Ross River, and Chikungunya virus, also activated NLRP1 in a p38-dependent manner. In the absence on ZAKα, inflammasome assembly was maintained, although at reduced levels, indicating contribution of other upstream kinases. NLRP1 activation by direct nanobody-mediated ubiquitination was independent of p38 activity. Stimulation of p38 by overexpression of MAP2 kinases MKK3 or MKK6 is sufficient for NLRP1 activation, and NLRP1 is directly phosphorylated by p38. Taken together, we define p38 activation as a unifying signaling hub that controls NLRP1 inflammasome activation by integrating a variety of cellular stress signals relevant to the skin.
The temporal and contextual stability of activity levels in hippocampal CA1 cells
Authors: Hayashi Yuichiro , Kobayakawa Ko , Kobayakawa Reiko 
Published: January 2022

AbstractRecent long-term optical imaging studies have demonstrated that the activity levels of hippocampal neurons in a familiar environment change on a daily to weekly basis. However, it is unclear whether there is any time-invariant property in the cells’ neural representations. In this study, using miniature fluorescence microscopy, we measured the neural activity of the mouse hippocampus in four different environments every 3 days. Although the activity level of hippocampal neurons fluctuated greatly in each environment across days, we found a significant correlation between the activity levels for different days, and the correlation was higher for averaged activity levels across multiple environments. When the number of environments used for averaging was increased, a higher activity correlation was observed. Furthermore, the number of environments in which a cell showed activity was preserved. Cells that showed place cell activity in many environments had greater spatial information content, and thus carried a higher amount of information about the current position. In contrast, cells that were active only in a small number of environments provided sparse representation for the environment. These results suggest that each cell has not only an inherent activity level but also play a characteristic role in the coding of space.Significance StatementRecent studies have revealed that place cell activity in the hippocampal CA1 cells exhibit instability on a daily to weekly scale. However, it is unclear whether there is any invariant property in the activity of the cells. In this study, we found that, although the activity level of CA1 neurons fluctuated greatly in one environment, the mean activity level across multiple environments was more stable. Furthermore, the number of environments in which a cell showed activity was preserved over time. These results suggest that even though the spatial code changes dynamically, each cell has an inherent activity level and plays a characteristic role in spatial coding.
A novel neuroelectrophysiological age index implicates brain health and sleep disorders
Authors: Yook Soonhyun , Park Hea Ree , Park Claire , Park Gilsoon , Lim Diane C. , Kim Jinyoung , Joo Eun Yeon , Kim Hosung 
Published: January 2022

AbstractSleep architecture and microstructures alter with aging and sleep disorder-led accelerated aging. We proposed a sleep electroencephalogram (EEG) based brain age prediction model using convolutional neural networks. We then associated the estimated brain age index (BAI) with brain structural aging features, sleep disorders and various sleep parameters. Our model also showed a higher BAI (predicted brain age minus chronological age) is associated with cortical thinning in various functional areas. We found a higher BAI for sleep disorder groups compared to healthy sleepers, as well as significant differences in the spectral pattern of EEG among different sleep disorders (lower power in slow and ϑ waves for sleep apnea vs. higher power in β and σ for insomnia), suggesting sleep disorder-dependent pathomechanisms of aging. Our results demonstrate that the new EEG-BAI can be a biomarker reflecting brain health in normal and various sleep disorder subjects, and may be used to assess treatment efficacy.
Crystal structure of an RNA/DNA strand exchange junction
Authors: Cofsky Joshua C. , Knott Gavin J. , Gee Christine L. , Doudna Jennifer A. 
Published: January 2022

AbstractShort segments of RNA displace one strand of a DNA duplex during diverse processes including transcription and CRISPR-mediated immunity and genome editing. These strand exchange events involve the intersection of two geometrically distinct helix types—an RNA:DNA hybrid (A-form) and a DNA:DNA homoduplex (B-form). Although previous evidence suggests that these two helices can stack on each other, it is unknown what local geometric adjustments could enable A-on-B stacking. Here we report the X-ray crystal structure of an RNA-5’/DNA-3’ strand exchange junction at an anisotropic resolution of 1.6 to 2.2 Å. The structure reveals that the A-to-B helical transition involves a combination of helical axis misalignment, helical axis tilting and compression of the DNA strand within the RNA:DNA helix, where nucleotides exhibit a mixture of A- and B-form geometry. These structural principles explain previous observations of conformational stability in RNA/DNA exchange junctions, enabling a nucleic acid architecture that is repeatedly populated during biological strand exchange events.
Genome-wide analysis identifies Homothorax and Extradenticle as regulators of insulin in Drosophila Insulin-Producing cells
Authors: Winant M. , Buhler K. , Clements J. , De Groef S. , Hens K. , Vulsteke V , Callaerts P. 
Published: January 2022

AbstractDrosophila Insulin-Producing Cells (IPCs) are the main production site of the Drosophila Insulin-like peptides or Dilps which have key roles in regulating growth, development, reproduction, lifespan and metabolism. To better understand the signalling pathways and transcriptional networks that are active in the IPCs we queried publicly available transcriptome data of over 180 highly inbred fly lines for dilp expression and used this as the input for a Genome-wide association study (GWAS). This resulted in the identification of variants in 125 genes that were associated with variation in dilp expression. The function of 57 of these genes in the IPCs was tested using an RNAi-based approach. We found that IPC-specific depletion of most genes resulted in differences in expression of one or more of the dilps. We then elaborated further on homothorax, one of the candidate genes with the strongest effect on dilp expression. We found that Homothorax and its binding partner Extradenticle are involved in regulating dilp2, -3 and -5 expression and that genetic depletion of both transcription factors leads to phenotypes associated with reduced insulin signalling. Furthermore, we provide evidence that other transcription factors involved in eye development are also functional in the IPCs. In conclusion, we showed that this GWAS approach using gene expression levels as input identified genetic regulators implicated in IPC function and dilp expression.
Structural and mechanistic basis of σ-dependent transcriptional pausing
Authors: Pukhrambam Chirangini , Molodtsov Vadim , Kooshbaghi Mahdi , Tareen Ammar , Vu Hoa , Skalenko Kyle S. , Su Min , Zhou Yin , Winkelman Jared T. , Kinney Justin B. , Ebright Richard H. , Nickels Bryce E. 
Published: January 2022

AbstractIn σ-dependent transcriptional pausing, the transcription initiation factor σ, translocating with RNA polymerase (RNAP), makes sequence-specific protein-DNA interactions with a promoter-like sequence element in the transcribed region, inducing pausing. It has been proposed that, in σ-dependent pausing, the RNAP active center can access off-pathway “backtracked” states that are substrates for the transcript-cleavage factors of the Gre family, and on-pathway “scrunched” states that mediate pause escape. Here, using site-specific protein-DNA photocrosslinking to define positions of the RNAP trailing and leading edges and of σ relative to DNA at the λPR’ promoter, we show directly that σ-dependent pausing in the absence of GreB in vitro predominantly involves a state backtracked by 2-4 bp, and that σ-dependent pausing in the presence of GreB in vitro and in vivo predominantly involves a state scrunched by 2-3 bp. Analogous experiments with a library of 47 (∼16,000) transcribed-region sequences show that the state scrunched by 2-3 bp--and only that state--is associated with the consensus sequence, T-3N-2Y-1G+1, (where -1 corresponds to the position of the RNA 3’ end), which is identical to the consensus for pausing in initial transcription, and which is related to the consensus for pausing in transcription elongation. Experiments with heteroduplex templates show that sequence information at position T-3 resides in the DNA nontemplate strand. A cryo-EM structure of a complex engaged in σ-dependent pausing reveals positions of DNA scrunching on the DNA nontemplate and template strands and suggests that position T-3 of the consensus sequence exerts its effects by facilitating scrunching.
Biodiversity of the Genus Trichoderma in the Rhizosphere of Coffee (Coffea arabica) Plants in Ethiopia and their Potential Use in Biocontrol of Coffee Wilt Disease
Authors: Mulatu Afrasa , Megersa Negussie , Abena Tariku , Kanagarajan Selvaraju , Liu Qinsong , Alemu Tesfaye , Vetukuri Ramesh R. 
Published: January 2022

AbstractThe present study investigated the distribution status and biodiversity of Trichoderma species surveyed from coffee rhizosphere soil samples from Ethiopia and their potential for biocontrol of coffee wilt disease (CWD) caused by Fusarium xylarioides. Trichoderma isolates were identified based on molecular approaches and morphological characteristics followed by biodiversity analysis using different biodiversity indices. The antagonistic potential of Trichoderma isolates was evaluated against F. xylarioides using the dual confrontation technique and agar diffusion bioassays. A relatively high diversity of species was observed including 16 taxa and 11 undescribed isolates. Trichoderma asperellum, T. asperelloides and T. longibrachiatum were classified as abundant species, with dominance (Y) values of 0.062, 0.056 and 0.034, respectively. Trichoderma asperellum was the most abundant species (comprising 39.6% of all isolates) in all investigated coffee ecosystems. Shannon’s biodiversity index (H), the evenness (E), Simpson’s biodiversity index (D), and the abundance index (J) were calculated for each coffee ecosystem, revealing that species diversity and evenness were highest in the Jimma zone (H =1.97, E = 0.76, D = 0.91, J = 2.73). The average diversity values for Trichoderma species originating from the coffee ecosystem were H = 1.77, D = 0.7, E = 0.75 and J = 2.4. In vitro confrontation experiments revealed that T. asperellum AU131 and T. longibrachiatum AU158 reduced the mycelial growth of F. xylarioides by over 80%. The potential use of these Trichoderma species for disease management of F. xylarioides and to reduce its impact on coffee cultivation is discussed in relation to Ethiopia’s ongoing coffee wilt disease crisis.
Hippocampal delta oscillations entrain neuronal activity, modulate gamma amplitude and convey information about running speed on a treadmill
Authors: Furtunato Alan MB , Pedrosa Rafael , Lobão-Soares Bruno , Tort Adriano BL , Belchior Hindiael 
Published: January 2022

ABSTRACTLocomotion has long been associated with rhythmic oscillations in the rat hippocampus. Running speed and acceleration affect the spectral density at the theta (6-10 Hz) and gamma (30-150 Hz) bands and the rhythmic entrainment of neuronal activity. However, less is known about other oscillatory rhythms. Recent studies have shown that oscillatory activity in the delta (1-4 Hz) band also relates to locomotion in stationary conditions, such as running on a treadmill or in a running wheel. To further investigate the effects of stationary running on hippocampal oscillations, we recorded CA1 local field potentials and neuronal activity while rats ran at different speed protocols on a treadmill. We found a remarkable oscillatory activity at 2 Hz that was strongly modulated by running speed. Delta power and peak frequency were highest at the fastest running speed, both in constant and progressively increasing speed protocols. Delta and theta oscillations co-occurred and showed independent relationships in their instantaneous power and frequency. Moreover, the delta phase modulated the amplitude of low-gamma (20-50 Hz) oscillations and the spiking activity of putative pyramidal neurons in a speed-dependent manner. Finally, spectral components in the delta frequency range, but not theta, predicted running speed using a naive Bayes classifier. In summary, our study shows that locomotion-related delta oscillations convey information about stationary running speed and coordinate hippocampal rhythmic activity in a speed-dependent manner.Statement of significanceTheta and gamma oscillations are hallmarks of rhythmic activity in the rat hippocampus during locomotion and exploratory behaviors, but less is known about other oscillatory rhythms. This study shows the emergence of delta (∼2 Hz) oscillations in the dorsal CA1 of rats running on a treadmill. Locomotion-related delta oscillations are independent of the concomitant theta activity and convey information about running speed. Delta waves modulate low-gamma oscillations and the spiking activity of pyramidal neurons in a speed-dependent way. These results suggest that oscillatory activity in the delta band aids rhythmic coordination during stationary locomotor behaviors.
Cullin-5 regulates nuclear positioning and reveals insights on the sensing of the nuclear-to-cytoplasmic ratio in Drosophila embryogenesis
Authors: Hayden Luke , Chao Anna , Deneke Victoria E. , Puliafito Alberto , Di Talia Stefano 
Published: January 2022

SummaryIn most metazoans, early embryonic development is characterized by rapid division cycles which pause before gastrulation at the mid-blastula transition (MBT).1 These early cleavage divisions are accompanied by cytoskeletal rearrangements which ensure proper nuclear positioning. Yet, the molecular mechanisms controlling nuclear positioning are not fully elucidated. In Drosophila, early embryogenesis unfolds in a multinucleated syncytium, and nuclei rapidly move across the anterior-posterior (AP) axis at cell cycles 4-6 in a process driven by actomyosin contractility and cytoplasmic flows.2,3 Previously, shackleton (shkl) mutants were identified in which this axial spreading is impaired.4 Here, we show that shkl mutants carry mutations in the cullin-5 (cul-5) gene. Live imaging experiments show that Cul-5 is downstream of the cell cycle but required for cortical actomyosin contractility. The nuclear spreading phenotype of cul-5 mutants can be rescued by reducing Src activity genetically, suggesting that a major target of Cul-5 is Src kinase. cul-5 mutants display gradients of nuclear density across the AP axis at the MBT which we exploit to study cell cycle control as a function of the N/C ratio. We found that the N/C ratio is sensed collectively in neighborhoods of about 100μm and such collective sensing is required for a precise MBT in which all the nuclei in the embryo pause their division cycle. Moreover, we found that the response to the N/C ratio is slightly graded along the AP axis. These two features can be linked to the spatiotemporal regulation of Cdk1 activity. Collectively, our results reveal a new pathway controlling nuclear spreading and provide a quantitative dissection of how nuclear cycles respond to the N/C ratio.