bluuebunny/crossref_metadata_2025_split huggingface dataset:
Super-enhancer-driven TOX2 mediates oncogenesis in Natural Killer/T Cell Lymphoma
Authors: Zhou Jianbiao , Toh Sabrina Hui-Min , Tan Tze King , Balan Kalpnaa , Lim Jing Quan , Tan Tuan Zea , Xiong Sinan , Jia Yunlu , Ng Siok-Bian , Peng Yanfen , Jeyasekharan Anand D. , Fan Shuangyi , Lim Soon Thye , Ong Chin-Ann Johnny , Ong Choon Kiat , Sanda Takaomi , Chng Wee-Joo 
Published: April 2023

Abstract
Background
Extranodal natural killer/T-cell lymphoma (NKTL) is an aggressive type of non-Hodgkin lymphoma with dismal outcome. A better understanding of disease biology and key oncogenic process is necessary for the development of targeted therapy. Super-enhancers (SEs) have been shown to drive pivotal oncogenes in various malignancies. However, the landscape of SEs and SE-associated oncogenes remain elusive in NKTL.

Methods
We used Nano-ChIP-seq of the active enhancer marker histone H3 lysine 27 acetylation (H3K27ac) to profile unique SEs NKTL primary tumor samples. Integrative analysis of RNA-seq and survival data further pinned down high value, novel SE oncogenes. We utilized shRNA knockdown, CRISPR-dCas9, luciferase reporter assay, ChIP-PCR to investigate the regulation of transcription factor (TF) on SE oncogenes. Multi-color immunofluorescence (mIF) staining was performed on an independent cohort of clinical samples. Various function experiments were performed to evaluate the effects of TOX2 on the malignancy of NKTL in vitro and in vivo.

Results
SE landscape was substantially different in NKTL samples in comparison with normal tonsils. Several SEs at key transcriptional factor (TF) genes, including TOX2, TBX21(T-bet), EOMES, RUNX2, and ID2, were identified. We confirmed that TOX2 was aberrantly overexpressed in NKTL relative to normal NK cells and high expression of TOX2 was associated with worse survival. Modulation of TOX2 expression by shRNA, CRISPR-dCas9 interference of SE function impacted on cell proliferation, survival and colony formation ability of NKTL cells. Mechanistically, we found that RUNX3 regulates TOX2 transcription by binding to the active elements of its SE. Silencing TOX2 also impaired tumor formation of NKTL cells in vivo. Metastasis-associated phosphatase PRL-3 has been identified and validated as a key downstream effector of TOX2-mediated oncogenesis.

Conclusions
Our integrative SE profiling strategy revealed the landscape of SEs, novel targets and insights into molecular pathogenesis of NKTL. The RUNX3-TOX2-SE-TOX2-PRL-3 regulatory pathway may represent a hallmark of NKTL biology. Targeting TOX2 could be a valuable therapeutic intervene for NKTL patients and warrants further study in clinic.
The cervical lymph node contributes to peripheral inflammation related to Parkinson’s disease
Authors: Liu Zongran , Huang Yang , Wang Xuejing , Li Jia-Yi , Zhang Can , Yang Ying , Zhang Jing 
Published: April 2023

Abstract
Background
Peripheral inflammation is an important feature of Parkinson’s disease (PD). However, if and how CNS pathology is involved in the peripheral inflammation in PD remains to be fully investigated. Recently, the existence of meningeal lymphatics and its involvement in draining cerebral spinal fluid (CSF) to the cervical lymph node has been discovered. It is known that meningeal lymphatic dysfunction exists in idiopathic PD. The deep cervical lymph node (dCLN) substantially contributes to the drainage of the meningeal lymphatics. In addition, one of the lymphatics draining components, CSF, contains abundant α-synuclein (α-syn), a protein critically involved in PD pathogenesis and neuroinflammation. Thus, we began with exploring the possible structural and functional alterations of the dCLN in a PD mouse model (A53T mice) and investigated the role of pathological α-syn in peripheral inflammation and its potential underlying molecular mechanisms.

Methods
In this study, the transgenic mice (prnp-SNCA*A53T) which specifically overexpressed A53T mutant α-syn in CNS were employed as the PD animal model. Immunofluorescent and Hematoxylin and eosin staining were used to evaluate structure of dCLN. Inflammation in dCLNs as well as in bone-marrow-derived macrophages (BMDMs) was assessed quantitatively by measuring the mRNA and protein levels of typical inflammatory cytokines (including IL-1β, IL-6 and TNF-α). Intra-cisterna magna injection, flow cytometric sorting and electrochemiluminescence immunoassays were applied to investigate the lymphatic drainage of α-syn from the CNS. RNA-seq and Western blot were used to explore how pathological α-syn mediated the inflammation in PD mice.

Results
The results unequivocally revealed substantially enlarged dCLNs, along with slow lymphatic flow, and increased inflammation in the dCLNs of A53T mice. Oligomeric α-syn drained from CSF potently activated macrophages in the dCLN via endoplasmic reticulum (ER) stress. Notably, inhibition of ER stress effectively suppressed peripheral inflammation in PD mice.

Conclusions
Our findings indicate that lymph node enlargement is closely related to macrophage activation, induced by meningeal lymphatics draining oligomeric α-syn, and contributes to the peripheral inflammation in PD. In addition, ER stress is a potential therapeutic target to ameliorate PD pathogenesis.
Offspring thermal demands and parental brooding efficiency differ for precocial birds living in contrasting climates
Authors: Kolešková Veronika , Šálek Miroslav E. , Brynychová Kateřina , Chajma Petr , Pešková Lucie , Elhassan Esmat , Petrusová Vozabulová Eva , Janatová Veronika , Almuhery Aisha , Sládeček Martin 
Published: April 2023

AbstractBackgroundChicks of precocial birds hatch well-developed and can search actively for food but their homeothermy develops gradually during growth. This makes them dependent on heat provided by parents (“brooding”), which is then traded off against other activities, mainly foraging. Although brooding has been documented in many precocial birds, little is known about the differences in the amount and efficiency of brooding care, brooding diel rhythmicity, and impact on the chick’s growth, particularly between species living in different climatic conditions.ResultsWe used multisensory dataloggers to evaluate brooding patterns in two congeneric species inhabiting contrasting climate zones: temperate Northern lapwing (Vanellus vanellus) and desert Red-wattled lapwing (Vanellus indicus). In accordance with our expectation, the adult desert lapwings brooded the chicks slightly less compared to the adult temperate lapwings. However, the desert lapwings brooded their chicks in higher ambient temperatures and less efficiently (i.e. they could not reach the same brooding temperature as the temperate lapwings), which are new and hitherto unknown brooding patterns in precocial birds. In both species, night brooding prevailed even during warm nights, suggesting a general brooding rule among birds. Although the high rates of brooding can reduce the time spent by foraging, we found no negative effect of the high brooding rate on the growth rate in either species.ConclusionsOur data suggest that the chicks of species breeding in colder climates may reduce their thermal demands, while their parents may increase the efficiency of parental brooding care. More research is however needed to confirm this as a rule across species.
The effect of temperature and invasive alien predator on genetic and phenotypic variation in the damselfly Ischnura elegans: cross-latitude comparison
Authors: Wos Guillaume , Palomar Gemma , Marszałek Marzena , Babik Wiesław , Sniegula Szymon 
Published: April 2023

AbstractBackgroundUnderstanding and predicting how organisms respond to human-caused environmental changes has become a major concern in conservation biology. Here, we linked gene expression and phenotypic data to identify candidate genes underlying existing phenotypic trait differentiation under individual and combined environmental variables. For this purpose, we used the damselflyIschnura elegans. Egg clutches from replicated high- (southern Sweden) and central-latitude (southern Poland) populations facing different degrees of seasonal time constraints were collected. Damselfly larvae were exposed to experimental treatments: current and mild warming temperatures crossed with the presence or absence of an invasive alien predator cue released by the spiny-cheek crayfish,Faxonius limosus, which is only present in Poland to date. We measured the following traits: larval development time, body size, mass and growth rate, and used the larvae for gene expression analysis by RNA-seq. Data were analysed using a multivariate approach.ResultsWe showed latitudinal differences in coping with mild warming and predator cues. When exposed to an increased temperature and a predator cue, central-latitude individuals had the shortest development and the fastest growth compared to high-latitude individuals. There was a general effect of predator cues regarding mass and growth rate reduction independent of latitude. Transcriptome analysis revealed that metabolic pathways related to larval anatomy and development tended to be upregulated in response to mild warming but only in fast-growing central-latitude individuals. Metabolic pathways linked to oxidative stress tended to be downregulated in response to a predator cue, especially in central-latitude individuals.ConclusionDifferent phenotypic and transcriptomic responses to environmental factors might be attributed to the variability inI. eleganslife history strategies between the two latitudes caused by seasonal time constraints and to its coexistence with the invasive alien predator in nature. By providing insights into how organisms may respond to future anthropogenic changes, our results may be of particular interest in conservation biology.
Modifiable factors associated with a consistently high acute pain trajectory after surgical treatment of traumatic fractures in Ethiopia: a multi-center prospective cohort study
Authors: Getachew Mestawet , Lerdal Anners , Småstuen Milada Cvancarova , Eshete Million Tesfaye , Desta Tilahun , Lindberg Maren Falch 
Published: April 2023

AbstractBackgroundIn Ethiopia, little is known about postoperative pain trajectories and possible predictive factors associated with them in patients undergoing surgery following traumatic fractures.MethodsThis multi-center prospective observational cohort study included surgical candidates for traumatic fractures (n = 218). Worst pain intensity was measured with an 11-point numeric rating scale on the first 4 postoperative days and day of hospital discharge. Growth mixture modeling was used to identify subgroups of patients based on their pain trajectories, and logistic regression models to quantify associations between pain trajectories and demographic, clinical, psychological, and life style factors.ResultsTwo postoperative pain trajectory subgroups were identified: rapid pain relief (48% of included individuals) and consistently high pain (52% of included individuals). Sub-analysis stratified by cause of injury demonstrated that higher preoperative pain was an independent risk factor for consistently high postoperative pain regardless of the patient’s injury type: traffic accident (OR = 1.48, 95% CI 1.23–1.79), machine/tool injury or conflict (OR = 1.58, 95% CI 1.11–2.26), or fall (OR = 1.47, 95% CI 1.08–1.99). Moreover, longer surgical time was a risk factor for consistently high postoperative pain among patients who had a fall-related injury (OR = 1.02, 95% CI 1.00–1.03). In contrast, among patients with a traffic-related injury, receiving a nerve block was a protective factor (OR = 0.19, 95% CI 0.04–0.87) compared with general anesthesia.ConclusionHigher preoperative pain and longer surgical time were associated with a consistently high acute postoperative pain trajectory. Clinicians may use these potentially modifiable factors to identify patients at risk for consistently high pain during the early postoperative period.
Adverse effects associated with acupuncture therapies: An evidence mapping from 535 systematic reviews
Authors: Xu Meng , Yang Chaoqun , Nian Tao , Tian Chen , Zhou Liying , Wu Yanan , Li Yanfei , Deng Xinxin , Li Xiuxia , Yang Kehu 
Published: April 2023

Abstract
Background and Objective
Considering that physicians and patients widely use acupuncture, it is necessary to explore its adverse effects during treatment. Herein, an evidence map was generated based on published studies to identify acupuncture-induced adverse effects and assess their severity, with the overarching goal of providing references for safe and effective implementation.

Methods
A comprehensive literature search was performed in four public databases (PubMed, Embase, Web of science, and the Cochrane Library) to identify relevant studies published up to 15th June 2022. In addition, relevant studies were explored in the Epistemonikos database and reference lists were retrieved as a supplement. A MeaSurement Tool to Assess systematic Reviews, Version 2 (AMSTAR-2) quality assessment tool was applied to determine the methodological quality of included systematic reviews (SRs) and/or meta-analysis (MAs), whereas Microsoft Excel 2019 tool was used for data extraction and coding. Heatmaps were generated to display disease type, countries of origin for the first authors, and the sample sizes of original studies. Moreover, bubble charts comprehensively presented intervention categories, adverse reaction types, and evidence levels.

Results
A total of 535 SRs involving 33 adverse reactions were included. Among them, 22 studies were rated as high quality, 28 as moderate, 106 as low, and the rest were of critically-low quality. Numerous adverse effects were described in the studies, including syncope (86 SRs), organ or tissue injury (233 SRs), systemic reactions (113 SRs), infection (19 SRs), and other adverse events (373 SRs). Importantly, these adverse reactions were mainly associated with 19 acupuncture techniques, including electroacupuncture (n = 67), manual acupuncture (n = 47) and acupoint catgut embedding (n = 41). Furthermore, the 535 SRs described 23 diseases, among which symptoms, signs or clinical findings (83 SRs), mental, behavioral or neurodevelopmental disorders (67 SRs), and diseases of the nervous system (66 SRs) had the highest incidence.

Conclusion
This evidence mapping explores the adverse effects of acupuncture, showing that there are multiple types of adverse reactions to acupuncture, with milder symptoms. The methodological assessment revealed that most of the included studies were of low- or critically low-quality. Therefore, there is a need for future randomized controlled trials and SRs to comprehensively analyze acupuncture-related adverse events in order to provide reliable and credible evidence.
The intracranial compartmental syndrome: a proposed model for acute brain injury monitoring and management
Authors: Godoy Daniel Agustín , Brasil Sérgio , Iaccarino Corrado , Paiva Wellingson , Rubiano Andres M. 
Published: April 2023

AbstractFor decades, one of the main targets in the management of severe acute brain injury (ABI) has been intracranial hypertension (IH) control. However, the determination of IH has suffered variations in its thresholds over time without clear evidence for it. Meanwhile, progress in the understanding of intracranial content (brain, blood and cerebrospinal fluid) dynamics and recent development in monitoring techniques suggest that targeting intracranial compliance (ICC) could be a more reliable approach rather than guiding actions by predetermined intracranial pressure values. It is known that ICC impairment forecasts IH, as intracranial volume may rapidly increase inside the skull, a closed bony box with derisory expansibility. Therefore, an intracranial compartmental syndrome (ICCS) can occur with deleterious brain effects, precipitating a reduction in brain perfusion, thereby inducing brain ischemia. The present perspective review aims to discuss the ICCS concept and suggest an integrative model for the combination of modern invasive and noninvasive techniques for IH and ICC assessment. The theory and logic suggest that the combination of multiple ancillary methods may enhance ICC impairment prediction, pointing proactive actions and improving patient outcomes.
Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock
Authors: Escamez Sacha , Robinson Kathryn M. , Luomaranta Mikko , Gandla Madhavi Latha , Mähler Niklas , Yassin Zakiya , Grahn Thomas , Scheepers Gerhard , Stener Lars-Göran , Jansson Stefan , Jönsson Leif J. , Street Nathaniel R. , Tuominen Hannele 
Published: April 2023

Abstract
Background
Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.

Results
We recorded 65 wood-related and growth traits in a population of 113 natural aspen genotypes from Sweden (https://doi.org/10.5061/dryad.gtht76hrd). These traits included three growth and field performance traits, 20 traits for wood chemical composition, 17 traits for wood anatomy and structure, and 25 wood saccharification traits as indicators of bioconversion potential. Glucose release after saccharification with acidic pretreatment correlated positively with tree stem height and diameter and the carbohydrate content of the wood, and negatively with the content of lignin and the hemicellulose sugar units. Most of these traits displayed extensive natural variation within the aspen population and high broad-sense heritability, supporting their potential in genetic improvement of feedstocks towards improved bioconversion. Finally, a genome-wide association study (GWAS) revealed 13 genetic loci for saccharification yield (on a whole-tree-biomass basis), with six of them intersecting with associations for either height or stem diameter of the trees.

Conclusions
The simple growth traits of stem height and diameter were identified as good predictors of wood saccharification yield in aspen trees. GWAS elucidated the underlying genetics, revealing putative genetic markers for bioconversion of bioenergy tree feedstocks.
Distinct CSF biomarker-associated DNA methylation in Alzheimer’s disease and cognitively normal subjects
Authors: Zhang Wei , Young Juan I. , Gomez Lissette , Schmidt Michael A. , Lukacsovich David , Varma Achintya , Chen X. Steven , Martin Eden R. , Wang Lily 
Published: April 2023

Abstract
Background
Growing evidence has demonstrated that DNA methylation (DNAm) plays an important role in Alzheimer’s disease (AD) and that DNAm differences can be detected in the blood of AD subjects. Most studies have correlated blood DNAm with the clinical diagnosis of AD in living individuals. However, as the pathophysiological process of AD can begin many years before the onset of clinical symptoms, there is often disagreement between neuropathology in the brain and clinical phenotypes. Therefore, blood DNAm associated with AD neuropathology, rather than with clinical data, would provide more relevant information on AD pathogenesis.

Methods
We performed a comprehensive analysis to identify blood DNAm associated with cerebrospinal fluid (CSF) pathological biomarkers for AD. Our study included matched samples of whole blood DNA methylation, CSF Aβ42, phosphorylated tau181 (pTau181), and total tau (tTau) biomarkers data, measured on the same subjects and at the same clinical visits from a total of 202 subjects (123 CN or cognitively normal, 79 AD) in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. To validate our findings, we also examined the association between premortem blood DNAm and postmortem brain neuropathology measured on a group of 69 subjects in the London dataset.

Results
We identified a number of novel associations between blood DNAm and CSF biomarkers, demonstrating that changes in pathological processes in the CSF are reflected in the blood epigenome. Overall, the CSF biomarker-associated DNAm is relatively distinct in CN and AD subjects, highlighting the importance of analyzing omics data measured on cognitively normal subjects (which includes preclinical AD subjects) to identify diagnostic biomarkers, and considering disease stages in the development and testing of AD treatment strategies. Moreover, our analysis revealed biological processes associated with early brain impairment relevant to AD are marked by DNAm in the blood, and blood DNAm at several CpGs in the DMR on HOXA5 gene are associated with pTau181 in the CSF, as well as tau-pathology and DNAm in the brain, nominating DNAm at this locus as a promising candidate AD biomarker.

Conclusions
Our study provides a valuable resource for future mechanistic and biomarker studies of DNAm in AD.
Plasma NfL is associated with the APOE ε4 allele, brain imaging measurements of neurodegeneration, and lower recall memory scores in cognitively unimpaired late-middle-aged and older adults
Authors: Malek-Ahmadi Michael , Su Yi , Ghisays Valentina , Luo Ji , Devadas Vivek , Chen Yinghua , Lee Wendy , Protas Hillary , Chen Kewei , Zetterberg Henrik , Blennow Kaj , Caselli Richard J. , Reiman Eric M. 
Published: April 2023

Abstract
Background
Plasma neurofilament light (NfL) is an indicator of neurodegeneration and/or neuroaxonal injury in persons with Alzheimer’s disease (AD) and a wide range of other neurological disorders. Here, we characterized and compared plasma NfL concentrations in cognitively unimpaired (CU) late-middle-aged and older adults with two, one, or no copies of the APOE ε4 allele, the major genetic risk factor for AD. We then assessed plasma NfL associations with brain imaging measurements of AD-related neurodegeneration (hippocampal atrophy and a hypometabolic convergence index [HCI]), brain imaging measurements of amyloid-β plaque burden, tau tangle burden and white matter hyperintensity volume (WMHV), and delayed and total recall memory scores.

Methods
Plasma NfL concentrations were measured in 543 CU 69 ± 9 year-old participants in the Arizona APOE Cohort Study, including 66 APOE ε4 homozygotes (HM), 165 heterozygotes (HT), and 312 non-carriers (NC). Robust regression models were used to characterize plasma NfL associations with APOE ε4 allelic dose before and after adjustment for age, sex, and education. They were also used to characterize plasma NfL associations with MRI-based hippocampal volume and WMHV measurements, an FDG PET-based HCI, mean cortical PiB PET measurements of amyloid-β plaque burden and meta-region-of-interest (meta-ROI) flortaucipir PET measurements of tau tangle burden, and Auditory Verbal Learning Test (AVLT) Delayed and Total Recall Memory scores.

Results
After the adjustments noted above, plasma NfL levels were significantly greater in APOE ε4 homozygotes and heterozygotes than non-carriers and significantly associated with smaller hippocampal volumes (r =  − 0.43), greater tangle burden in the entorhinal cortex and inferior temporal lobes (r = 0.49, r = 0.52, respectively), and lower delayed (r =  − 0.27), and total (r =  − 0.27) recall memory scores (p < 0.001). NfL levels were not significantly associated with PET measurements of amyloid-β plaque or total tangle burden.

Conclusions
Plasma NfL concentrations are associated with the APOE ε4 allele, brain imaging biomarkers of neurodegeneration, and less good recall memory in CU late-middle-aged and older adults, supporting its value as an indicator of neurodegeneration in the preclinical study of AD.