bluuebunny/crossref_metadata_2025_split huggingface dataset:
An epigenomic landscape of cervical intraepithelial neoplasia and cervical cancer using single‐base resolution methylome and hydroxymethylome
Authors: Han Yingxin , Ji Liyan , Guan Yanfang , Ma Mengya , Li Pansong , Xue Yinge , Zhang Yinxin , Huang Wanqiu , Gong Yuhua , Jiang Li , Wang Xipeng , Xie Hong , Zhou Boping , Wang Jiayin , Wang Junwen , Han Jinghua , Deng Yuliang , Yi Xin , Gao Fei , Huang Jian 
Published: July 2021

AbstractBackgroundCervical cancer (CC) is the second leading cause of cancer death among women worldwide. Epigenetic regulation of gene expression through DNA methylation and hydroxymethylation plays a pivotal role during tumorigenesis. In this study, to analyze the epigenomic landscape and identify potential biomarkers for CCs, we selected a series of samples from normal to cervical intra‐epithelial neoplasia (CINs) to CCs and performed an integrative analysis of whole‐genome bisulfite sequencing (WGBS‐seq), oxidative WGBS, RNA‐seq, and external histone modifications profiling data.ResultsIn the development and progression of CC, there were genome‐wide hypo‐methylation and hypo‐hydroxymethylation, accompanied by local hyper‐methylation and hyper‐hydroxymethylation. Hydroxymethylation prefers to distribute in the CpG islands and CpG shores, as displayed a trend of gradual decline from health to CIN2, while a trend of increase from CIN3 to CC. The differentially methylated and hydroxymethylated region‐associated genes both enriched in Hippo and other cancer‐related signaling pathways that drive cervical carcinogenesis. Furthermore, we identified eight novel differentially methylated/hydroxymethylated‐associated genes (DES, MAL, MTIF2, PIP5K1A, RPS6KA6, ANGEL2, MPP, and PAPSS2) significantly correlated with the overall survival of CC. In addition, no any correlation was observed between methylation or hydroxymethylation levels and somatic copy number variations in CINs and CCs.ConclusionOur current study systematically delineates the map of methylome and hydroxymethylome from CINs to CC, and some differentially methylated/hydroxymethylated‐associated genes can be used as the potential epigenetic biomarkers in CC prognosis.
High accuracy tracking reveals how small conservation areas can protect marine megafauna
Authors: Hays Graeme C. , Mortimer Jeanne A. , Rattray Alex , Shimada Takahiro , Esteban Nicole 
Published: July 2021

AbstractSpace use estimates can inform conservation management but relaying high‐accuracy locations is often not straightforward. We used Fastloc‐GPS Argos satellite tags with the innovation of additional data relay via a ground station (termed a “Mote”) to record high volumes (typically >20 locations per individual per day) of high accuracy tracking data. Tags were attached in the Chagos Archipelago (Indian Ocean) in 2018–2019 to 23 immature turtles of two species for which there have been long‐standing conservation concerns: 21 hawksbill turtles (Eretmochelys imbricata) and two green turtles (Chelonia mydas). Over long tracking durations (mean 227.6 d per individual), most turtles moved very little. For example, 17 of 21 hawksbill turtles remained continuously in the lagoon where they were equipped, with 95% and 50% utilization distributions (UDs) averaging only 1.03 and 0.18 km2, respectively. Many individuals, and both species, could use the same small spaces, i.e., individuals did not maintain unique home ranges. However, three hawksbill turtles travelled hundreds of kilometers from the tagging site. Our results show that, for some large marine vertebrates, even small protected areas of only a few square kilometers can encompass the movements of a large proportion of individuals over long periods. High accuracy tracking may likewise reveal the details of space use for many other animals that move little and/or use important focal areas and where previous low‐accuracy tracking techniques have tended to overestimate space use.
Detection and survival of Candida albicans in soils
Authors: Sautour Marc , Lemaître Jean‐Paul , Ranjard Lionel , Truntzer Caroline , Basmaciyan Louise , Depret Géraldine , Hartmann Alain , Dalle Frédéric 
Published: July 2021

AbstractCandida albicans is the most common human fungal pathogen. This yeast is described as a commensal of human and animal mucosa, and very few studies have focused on its isolation in natural environments. We investigated the presence of C. albicans in a large panel of French soils. Because a culture‐based method didn't allow isolation of the yeast in a panel of 70 soils, we adapted a nested‐PCR for detecting C. albicans DNA in a panel of 460 soils. Only 7 of the 460 soil samples (1.5%) were PCR‐positive for Candida albicans. To understand which parameters influence the survival of the yeast, we studied the decline of a population of C. albicans over a period of one month in a collection of 20 soils collected throughout France. C. albicans was able to survive up to 30 days in 80% of the soils tested. Using a Spearman correlation test, we showed that the short‐term survival of C. albicans in soils was correlated with some soils chemical factors such as pH and presence of some minerals (Al, Mn, and Na). Concerning survival after 30 days, Cation Exchange Capacity (CEC) and clay content were identified as beneficial determinants of the long‐term survival of C. albicans in soils.
Impact of agitation in long‐term care residents with dementia in the United States
Authors: Fillit Howard , Aigbogun Myrlene S. , Gagnon‐Sanschagrin Patrick , Cloutier Martin , Davidson Mikhaïl , Serra Elizabeth , Guérin Annie , Baker Ross A. , Houle Christy R. , Grossberg George 
Published: July 2021

AbstractObjectivesTo describe characteristics and compare clinical outcomes including falls, fractures, infections, and neuropsychiatric symptoms (NPS) among long‐term care residents with dementia with and without agitation.MethodsA cross‐sectional secondary analysis of administrative healthcare data was conducted whereby residents with dementia residing in a long‐term care facility for ≥12 months were identified from the AnalytiCare LLC database (10/2010–06/2014) and were classified into mutually exclusive cohorts (Agitation Cohort or No‐Agitation Cohort) based on available agitation‐related symptoms. Entropy balancing was used to balance demographic and clinical characteristics between the two cohorts. The impact of agitation on clinical outcomes was compared between balanced cohorts using weighted logistic regression models.ResultsThe study included 6,265 long‐term care residents with dementia among whom, 3,313 were included in the Agitation Cohort and 2,952 in the No‐Agitation Cohort. Prior to balancing, residents in the Agitation Cohort had greater dementia‐related cognitive impairment and clinical manifestations compared to the No‐Agitation Cohort. After balancing, residents with and without agitation, respectively, received a median of five and four distinct types of medications (including antipsychotics). Further, compared to residents without agitation, those with agitation were significantly more likely to have a recorded fall (OR = 1.58), fracture (OR = 1.29), infection (OR = 1.18), and other NPS (OR = 2.11).ConclusionsAgitation in long‐term care residents with dementia was associated with numerically higher medication use and an increased likelihood of experiencing falls, fractures, infections, and additional NPS compared to residents without agitation, highlighting the unmet need for effective management of agitation symptoms in this population.
Inhibitory effect of carboxylated nanodiamond on oral pathogenic bacteria Streptococcus mutans
Authors: Quan Chuntian , Lin Haiyan , Xiao Hui , Zhao Jianjiang 
Published: July 2021

AbstractBackgroundNanodiamonds (NDs) have been demonstrated to have bactericidal activity on several microorganisms and can be used in various kinds of dental materials. NDs are potential candidates for antibacterial dental materials. However, the possible inhibitory effect of NDs on oral pathogenic bacteria is largely unknown. This study was performed to investigate the inhibitory effects of carboxylated nanodiamond (cND) on Streptococcus mutans.MethodsFourier transform infrared spectroscopy was used to confirm carboxyl groups on the surface of commercial cND. The inhibitory effect of serially diluted cND on S. mutans was evaluated by spectrophotometry and plating methods. Escherichia coli was treated as a positive control in spectrophotometry. Chlorhexidine was used as a positive control in plating methods. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were employed to confirm the antibacterial activity of cND.ResultsThe results showed that cND exhibited a significant inhibitory effect on S. mutans. For S. mutans, the minimum inhibitory concentration was 4 μg/ml and the minimum bactericidal concentration was 16 μg/ml. SEM and TEM results indicated that cND functioned as an antibacterial agent, likely due to its ability to disrupt the cell membrane of S. mutans.ConclusionIn conclusion, these findings demonstrated an inhibitory effect of cND on S. mutans and suggest its use as a potential antibacterial dental material.
Autocrine regulation of airway smooth muscle contraction by diacylglycerol kinase
Authors: Yadav Santosh K. , Sharma Pawan , Shah Sushrut D. , Panettieri Reynold A. , Kambayashi Taku , Penn Raymond B. , Deshpande Deepak A. 
Published: July 2021

AbstractDiacylglycerol kinase (DGK), a lipid kinase, catalyzes the conversion of diacylglycerol (DAG) to phosphatidic acid, thereby terminating DAG‐mediated signaling by Gq‐coupled receptors that regulate contraction of airway smooth muscle (ASM). A previous study from our laboratory demonstrated that DGK inhibition or genetic ablation leads to reduced ASM contraction and provides protection for allergen‐induced airway hyperresponsiveness. However, the mechanism by which DGK regulates contractile signaling in ASM is not well established. Herein, we investigated the role of prorelaxant cAMP‐protein kinase A (PKA) signaling in DGK‐mediated regulation of ASM contraction. Pretreatment of human ASM cells with DGK inhibitor I activated PKA as demonstrated by the phosphorylation of PKA substrates, VASP, Hsp20, and CREB, which was abrogated when PKA was inhibited pharmacologically or molecularly using overexpression of the PKA inhibitor peptide, PKI. Furthermore, inhibition of DGK resulted in induction of cyclooxygenase (COX) and generation of prostaglandin E2 (PGE2) with concomitant activation of Gs‐cAMP‐PKA signaling in ASM cells in an autocrine/paracrine fashion. Inhibition of protein kinase C (PKC) or extracellular‐signal‐regulated kinase (ERK) attenuated DGK‐mediated production of PGE2 and activation of cAMP‐PKA signaling in human ASM cells, suggesting that inhibition of DGK activates the COX‐PGE2 pathway in a PKC‐ERK‐dependent manner. Finally, DGK inhibition‐mediated attenuation of contractile agonist‐induced phosphorylation of myosin light chain 20 (MLC‐20), a marker of ASM contraction, involves COX‐mediated cAMP production and PKA activation in ASM cells. Collectively these findings establish a novel mechanism by which DGK regulates ASM contraction and further advances DGK as a potential therapeutic target to provide effective bronchoprotection in asthma.
TGF‐β signaling: A recap of SMAD‐independent and SMAD‐dependent pathways
Authors: Aashaq Sabreena , Batool Asiya , Mir Shabir Ahmad , Beigh Mushtaq Ahmad , Andrabi Khurshid Iqbal , Shah Zaffar Amin 
Published: July 2021

AbstractTransforming growth factor‐β (TGF‐β) is a proinflammatory cytokine known to control a diverse array of pathological and physiological conditions during normal development and tumorigenesis. TGF‐β‐mediated physiological effects are heterogeneous and vary among different types of cells and environmental conditions. TGF‐β serves as an antiproliferative agent and inhibits tumor development during primary stages of tumor progression; however, during the later stages, it encourages tumor development and mediates metastatic progression and chemoresistance. The fundamental elements of TGF‐β signaling have been divulged more than a decade ago; however, the process by which the signals are relayed from cell surface to nucleus is very complex with additional layers added in tumor cell niches. Although the intricate understanding of TGF‐β‐mediated signaling pathways and their regulation are still evolving, we tried to make an attempt to summarize the TGF‐β‐mediated SMAD‐dependent andSMAD‐independent pathways. This manuscript emphasizes the functions of TGF‐β as a metastatic promoter and tumor suppressor during the later and initial phases of tumor progression respectively.
Genetic counseling practice for inherited eye diseases in an Israeli medical center during the COVID‐19 pandemic
Authors: Macarov Michal , Schneider Nina , Eilat Avital , Yahalom Claudia 
Published: July 2021

AbstractInherited eye diseases (IED) are among the most common causes for childhood and young adulthood blindness in developed countries. Genetic counseling and testing have become an essential part of caregiving for families affected by one of these severe ocular pathologies. The objective of our study is to describe our experience during the 2020 (COVID‐19) pandemic, following a practice protocol of safe genetic counseling for inherited ophthalmic diseases. We conducted a review of the genetic counseling practices from January until December 2020 in a multidisciplinary clinic for patients with visual impairment, in a tertiary hospital. The new protocol covered patient screening, required personal protective equipment, and the implementation of telemedicine.One hundred and eighty‐three counseling sessions were done in this period of time; 33/183 were telemedicine counseling. The results of this study indicate that the practice of genetic counseling in regard to inherited eye diseases in the era of COVID‐19 is effective and safe. Despite the high risk of infectivity that threatened healthcare professionals, safety measures adopted to reduce the risk of infection allowed us to prevent the cancelation of routine counseling, while keeping patient care our priority. The use of telemedicine was a very useful tool for providing counseling during lockdown periods in 2020.
Examining disease boundaries: Genetics of myelodysplastic/myeloproliferative neoplasms
Authors: Hochman Michael J. , Savani Bipin N. , Jain Tania 
Published: July 2021

AbstractMyelodysplastic/myeloproliferative neoplasms (MDS/MPN) are clonal myeloid malignancies that are characterized by dysplasia resulting in cytopenias as well as proliferative features such as thrombocytosis or splenomegaly. Recent studies have better defined the genetics underlying this diverse group of disorders. Trisomy 8, monosomy 7, and loss of Y chromosome are the most common cytogenetic abnormalities seen. Chronic myelomonocytic leukemia (CMML) likely develops from early clones with TET2 mutations that drive granulomonocytic differentiation. Mutations in SRSF2 are common and those in the RAS‐MAPK pathway are typically implicated in disease with a proliferative phenotype. Several prognostic systems have incorporated genetic features, with ASXL1 most consistently demonstrating worse prognosis. Atypical chronic myeloid leukemia (aCML) is most known for granulocytosis with marked dysplasia and often harbors ASXL1 mutations, but SETBP1 and ETNK1 are more specific to this disease. MDS/MPN with ring sideroblasts and thrombocytosis (MDS/MPN‐RS‐T) most commonly involves spliceosome mutations (namely SF3B1) and mutations in the JAK‐STAT pathway. Finally, MDS/MPN‐unclassifiable (MDS/MPN‐U) is least characterized but a significant fraction carries mutations in TP53. The remaining patients have clinical and/or genetic features similar to the other MDS/MPNs, suggesting there is room to better characterize this entity. Evolution from age‐related clonal hematopoiesis to MDS/MPN likely depends on the order of mutation acquisition and interactions between various biologic factors. Genetics will continue to play a critical role in our understanding of these illnesses and advancing patient care.
Cardiac involvement in Wilson disease: Review of the literature and description of three cases of sudden death
Authors: Chevalier Kevin , Benyounes Nadia , Obadia Michaël Alexandre , Van Der Vynckt Clélie , Morvan Erwan , Tibi Thierry , Poujois Aurélia 
Published: July 2021

AbstractWilson disease (WD) is a rare genetic condition that results from a build‐up of copper in the body. It requires life‐long treatment and is mainly characterized by hepatic and neurological features. Copper accumulation has been reported to be related to the occurrence of heart disease, although little is known regarding this association. We have conducted a systematic review of the literature to document the association between WD and cardiac involvement. Thirty‐two articles were retained. We also described three cases of sudden death. Cardiac manifestations in WD include cardiomyopathy (mainly left ventricular (LV) remodeling, hypertrophy, and LV diastolic dysfunction, and less frequently LV systolic dysfunction), increased levels of troponin, and/or brain natriuretic peptide, electrocardiogram (ECG) abnormalities, and rhythm or conduction abnormalities, which can be life‐threatening. Dysautonomia has also been reported. The mechanism of cardiac damage in WD has not been elucidated. It may be the result of copper accumulation in the heart, and/or it could be due to a toxic effect of copper, resulting in the release of free oxygen radicals. Patients with signs and/or symptoms of cardiac involvement or who have cardiovascular risk factors should be examined by a cardiologist in addition to being assessed by their interdisciplinary treating team. Furthermore, ECG, cardiac biomarkers, echocardiography, and 24‐hours or more of Holter monitoring at the diagnosis and/or during the follow‐up of patients with WD need to be evaluated. Cardiac magnetic resonance imaging, although not always available, could also be a useful diagnostic tool, allowing assessment of the risk of ventricular arrhythmias and further guidance of the cardiac workup.
A role for T‐cell exhaustion in Long COVID‐19 and severe outcomes for several categories of COVID‐19 patients
Authors: Roe Kevin 
Published: July 2021

AbstractUnusual mortality rate differences and symptoms have been experienced by COVID‐19 patients, and the postinfection symptoms called Long COVID‐19 have also been widely experienced. A substantial percentage of COVID‐19‐infected individuals in specific health categories have been virtually asymptomatic, several other individuals in the same health categories have exhibited several unusual symptoms, and yet other individuals in the same health categories have fatal outcomes. It is now hypothesized that these differences in mortality rates and symptoms could be caused by a SARS‐CoV‐2 virus infection acting together with one or more latent pathogen infections in certain patients, through mutually beneficial induced immune cell dysfunctions, including T‐cell exhaustion. A latent pathogen infection likely to be involved is the protozoan parasite Toxoplasma gondii, which infects approximately one third of the global human population. Furthermore, certain infections and cancers that cause T‐cell exhaustion can also explain the more severe outcomes of other COVID‐19 patients having several disease and cancer comorbidities.
Erbium‐doped: yttrium‐aluminum‐garnet (Er:YAG) versus scaling and root planing for the treatment of periodontal disease: A single‐blinded split‐mouth randomized clinical trial
Authors: Gurpegui Abud Daniela , Shariff Jaffer A. , Linden Eric , Kang Philip Y. 
Published: July 2021

AbstractBackgroundThis randomized, controlled clinical trial aimed to compare the differences in periodontal clinical outcomes, duration of the procedure, and patient's experience between conventional scaling and root planing and erbium‐doped: yttrium‐aluminum‐garnet (Er:YAG) in the treatment of generalized moderate to severe chronic periodontitis or generalized Stages II or III, and Grade B periodontitis based on the Centers for Disease Control (CDC), American Academy of Periodontology (AAP), and European Federation of Periodontology (EFP) definitions.MethodsThirty subjects were initially recruited. In a split‐mouth fashion, right and left sides were randomly allocated into two treatment arms: conventional scaling and root planing (C‐SRP) versus laser‐assisted scaling and root planing (L‐SRP). A blinded examiner recorded clinical measurements at baseline and 3 months. Duration of the procedure was also recorded for each visit, and the patient's experience was assessed with a questionnaire at baseline, 1, and 3 months.ResultsThe final sample consisted of 26 subjects. Both treatments resulted in overall improvement, but no significant differences were found between modalities for clinical attachment gain or probing depth reduction. The duration of the procedure was approximately half for L‐SRP, and postoperative sensitivity was greater in C‐SRP.ConclusionsThe low‐energy protocol with Er:YAG (50 mJ) used for the non‐surgical treatment of moderate‐severe chronic or Stage II‐III, Grade B periodontitis performed in this study population was a treatment modality that yielded similar clinical improvements when compared to conventional scaling and root planing.
The bacterial and fungal community composition in time and space in the nest mounds of the antFormicaexsecta(Hymenoptera: Formicidae)
Authors: Lindström Stafva , Timonen Sari , Sundström Liselotte 
Published: July 2021

AbstractIn a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound‐building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the antFormicaexsectaare significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.