bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Epigenetic 12-gene Signature Predictive of Poor Prognosis and MSI-like Phenotype in Human Metastatic Colorectal Carcinomas
Authors: Condelli Valentina , Calice Giovanni , Cassano Alessandra , Basso Michele , Rodriquenz Maria Grazia , Zupa Angela , Maddalena Francesca , Crispo Fabiana , Pietrafesa Michele , Aieta Michele , Sgambato Alessandro , Tortora Giampaolo , Zoppoli Pietro , Landriscina Matteo 
Published: September 2020

Abstract
Background. Epigenetic remodeling is responsible for tumor progression and drug resistance in human colorectal carcinoma (CRC). A subgroup of human CRCs exhibits the CIMP status, with extensive hypermethylation events in promoter regions of several genes, even though the prognostic significance of CIMP is controversial. This study addressed the hypothesis that DNA methylation profiling may identify metastatic CRC (mCRC) subtypes with different clinical behavior. Methods. Global methylation profile was comparatively analyzed between 24 first-line primary-resistant and 12 drug-sensitive mCRCs (in-house cohort), two subgroups of tumors with significantly different outcome. Methylation and gene expression data from 33 mCRCs of the TCGA COAD dataset (TCGA COAD cohort) were used to identify, among differentially methylated genes, a prognostic signature of functionally methylated genes. Clusters of mCRCs with different methylation patterns were further characterized for DNA mutational load, gene copy number and gene expression profiles. Human CRC HT29 and HCT116 cell lines were adapted to growth in presence of oxaliplatin and irinotecan and used as in vitro model to validate gene expression data.Results. Twelve functionally methylated genes yielded a hierarchical clustering of patients in two well-defined clusters with hypermethylated tumors characterized by a significantly worse relapse-free and overall survival compared to hypomethylated cancers and this was reproduced in both the in-house and the TCGA COAD cohorts. Interestingly, the hypermethylated poor prognosis cluster was enriched of CIMP-high and MSI-like cases. Furthermore, methylation events were enriched in genes located on q-arm of chromosomes 13 and 20, two chromosomal regions with gain/loss alterations strongly associated with adenoma-to-carcinoma progression. Finally, the expression of the 12-genes signature and MSI-enriching genes was confirmed in two independent oxaliplatin- and irinotecan-resistant CRC cell lines. Conclusions. These data represent the proof of concept that the hypermethylation of specific sets of genes may provide prognostic information being able to identify a subgroup of mCRCs with poor prognosis.
Virologic Outcomes of Switching to Dolutegravir Functional Monotherapy, or Functional Dual Therapy With Dolutegravir Plus A Non-cytosine Nucleoside Analog: A Retrospective Study of Treatment-Experienced, HIV-1 Infected Patients
Authors: Rolle Charlotte-Paige , Nguyen Vu , Hinestrosa Federico , DeJesus Edwin 
Published: September 2020

Abstract
Background Dolutegravir (DTG) monotherapy results in unacceptable virologic failure rates and the development of DTG resistance. Here, we evaluated virologic outcomes of patients switched to DTG functional monotherapy, or functional dual therapy with DTG plus a non-cytosine nucleoside analog (NA).Methods This observational study included treatment-experienced patients switched to regimens containing ≥ 3 antiretrovirals later found to be on DTG functional monotherapy, or functional dual therapy with DTG plus a non-cytosine NA based on historical genotypes. Eligible patients were either suppressed or viremic at baseline and had ≥2 HIV-1 RNA measurements at least four weeks apart following switch. The primary endpoint was the proportion with HIV-1 RNA<50 copies/mL following switch. Results Thirty-nine patients were included, 19 (49%) were found to be on DTG functional monotherapy and 20 (51%) were found to be on functional dual therapy with DTG plus a non-cytosine NA. The median duration of follow-up was 50 weeks (range 12-244). Following switch, 32/39 (82%) patients achieved or maintained an HIV-1 RNA<50 copies/mL. In 7 (18%) patients with persistent HIV-1 RNA ≥50 copies/mL, there was no evidence of treatment-emergent resistance among those with post-switch genotypes.Conclusions In this real-world cohort, the majority of whom had virus with the M184V/I and ≥ 1 additional NA mutation, switching to DTG functional monotherapy, or functional dual therapy with DTG plus a non-cytosine NA resulted in persistent HIV-1 RNA≥ 50 copies/mL in 18%. None with post-switch genotypes developed treatment-emergent resistance.
Clinical Trial of HEXORR II for Robotic Hand Movement Therapy After Stroke
Authors: Chen Ji , Black Iian , Nichols Diane , Chen Tianyao , Sandison Melissa , Casas Rafael , Lum Peter 
Published: September 2020

Abstract
BackgroundImpaired use of the hand in functional tasks remains difficult to overcome in many individuals after a stroke. This often leads to compensation strategies using the less-affected limb, which allows for independence in some aspects of daily activities. However, recovery of hand function remains an important therapeutic goal of many individuals, and is often resistant to conventional therapies. In prior work, we developed HEXORR I, a robotic device that allows practice of finger and thumb movements with robotic assistance. In this study, we describe modifications to the device, now called HEXORR II, and a clinical trial in individuals with chronic stroke. MethodsFifteen individuals with a diagnosis of chronic stroke were randomized to 12 or 24 sessions of robotic therapy. The sessions involved playing several video games using thumb and finger movement. The robot applied assistance to extension movement that was adapted based on task performance. Clinical and motion capture evaluations were performed before and after training and again at a 6 month followup. ResultsFourteen individuals completed the protocol. Fugl-Meyer scores improved significantly over the 3 time points, indicating reductions in upper extremity impairment. Flexor hypertonia (Ashworth) also decreased significantly due to the intervention. Motion capture found increased finger range of motion and extension ability when the arm was supported by gravity. However, extension ability did not improve significantly during a reach and grasp task, and there was no change in a functional measure (Action Research Arm Test). At the followup, the high dose group had significant gains in hand displacement during a forward reach task. There were no other significant differences between groups. ConclusionsFuture work with HEXORR II should focus on integrating it with functional task practice and incorporating grip and squeezing tasks. Trial registration: CLINICALTRIALS.GOV, NCT04536987. Registered 3 September 2020 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/record/NCT04536987
Triplet-Triplet Upconversion in Organic Light- Emitting Diodes: Implications to Injection Lasing
Authors: Shukla Atul , Hasan Monirul , Banappanavar Gangadhar , Ahmad Viqar , Sobus Jan , Moore Evan , Kabra Dinesh , Lo Shih-Chun , Namdas Ebinazar 
Published: September 2020

Abstract
While significant progress has been made over last few years in the field of organic solid-state lasers, achieving lasing action from organic semiconductors under electrical excitation still remains a big challenge. One of the major barriers towards electrically pumped organic lasers are optical losses due to triplet excitons. In this work, we report both experimental and theoretical results that confirm positive contribution of triplet excitons for the scope of electrically driven organic laser. We studied a model fluorescence material, 9-(9-phenylcarbazole-3-yl)-10(naphthalene-1-yl) anthracene and reveals that the threshold current densities required to achieve lasing emission under electrical injection can be significantly reduced with the aid of triplet-triplet exciton upconversion processes. Furthermore, we demonstrate that, to achieve the best performance, the singlet-triplet exciton annihilation must be minimized. These results are unprecedented and provide a pathway towards development of new class of triplet-triplet upconversion materials for injection laser.
B cell-mediated immunomodulation by S-nitrosoglutathione (GSNO) in experimental autoimmune encephalomyelitis
Authors: Kim Judong , Islam S.M. Touhidul , Won Jeseong , Singh Avtar K. , Singh Inderjit 
Published: September 2020

Abstract
Background Experimental autoimmune encephalomyelitis (EAE) is the most commonly used animal model for human multiple sclerosis (MS), a demyelinating autoimmune disease mediated by T and B lymphocytes. The aim of the present study was to investigate the role of S-nitrosoglutathione (GSNO), a physiological nitric oxide carrier molecule, in regulation of effector or regulatory B cell function as IL-6 and IL-10 expressions and thus the potential role of GSNO in targeting B cell-mediated immunopathogenesis in MS using EAE model. Methods To this purpose, the in vivo EAE mouse model, generated by immunization with myelin oligodendrocyte glycoprotein (MOG) 35-55 peptide, or in vitro model of cultured B cells stimulated with lipopolysaccharide or anti-IgM antibody were treated with exogenous GSNO or N6022, an inhibitor of GSNO reductase (GSNOR; GSNO degrading enzyme) to increase endogenous GSNO, and then analyzed for B cell specific IL-6 and IL-10 expression. Results In EAE model, administration of exogenous GSNO or inhibition of endogenous GSNO catabolism by N6022 treatment ameliorated the clinical disease with decreased CNS infiltration of B cells. In addition, GSNO/N6022 treatments increased the number of IL-10+ B cells but decreased the number of IL-6+ B cells in the CNS and spleen. Accordingly, GSNO/N6022 treatments increased the expression of IL-10 while reducing the IL-6 expression in the blood. Similar observations were also made in in vitro B cell culture model where GSNO treatment increased the IL-10+ B cells but decreased the IL-6+ B cells under BCR or TLR4 stimulatory conditions and under CD40 and BAFF co-stimulatory conditions. Accordingly, GSNO treatment increased the B cell production of IL-10 but reduced the IL-6 production under both stimulatory and co-stimulatory conditions. In vitro stimulation and co-stimulation of cultured naïve B cells increased two major distinct B cell populations; CD1dlow CD5high and CD1dhigh CD5high. In both populations, GSNO treatment increased the number of IL-10+ cells but decreased the IL-6+ cells. Conclusion These data document, for the first time, that cellular GSNO homeostasis is a critical target for the regulation of IL-10+ B cells vs. IL-6+ B cells mediated immune balance under auto-immune disease conditions.
Impacts of the Marine Hatchery Built Environment on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola Lalandi
Authors: Minich Jeremiah , Nowak Barbara , Elizur Abigail , Knight Rob , Fielder Stewart , Allen Eric 
Published: September 2020

Abstract
BackgroundMicrobial succession in vertebrates has primarily focused on vertical transmission and ontogenetic development in the mammalian gut. Teleosts comprise the majority of vertebrate diversity, yet little is known about how the microbiome develops in fish, particularly when vertical transmission is limited or absent for broadcast spawners. Biological factors such as diet, age, phylogeny, and trophic level along with environmental factors such as water salinity, temperature, and depth have been shown to influence the mucosal microbiomes of fish. Here we investigate how various microbial-rich surfaces from the built environment ‘BE’ influence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine fish, yellowtail kingfish, Seriola lalandi, over time.ResultsFor the first experiment, we sampled gill and skin microbiomes from 36 fish reared in three tank conditions, and demonstrate that the gill is more influenced by the surrounding environment than the skin. In a second experiment, fish microbiomes (gill, skin, and digesta) and the BE (tank side, water, inlet pipe, airstones, and air diffusers) were sampled from indoor reared fish at three ages (43 dph, 137 dph, 430 dph; n=12 per age). At 430 dph, 20 additional fish were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased with age. Diversity was much lower in fish from the ocean net pen compared to indoor fish. We quantified the change in community dynamics driven by the BE and show that the gill and skin are most influenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut microbiome becomes increasingly differentiated from the environment over time.ConclusionsOur findings suggest that fish mucosal microbiomes are differentially influenced by the built environment with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine fish. In addition, results demonstrate how early life (larval) exposure to stressors in the rearing environment may influence fish microbiome development which is important for animal health and aquaculture production.
A population-level analysis of changes in diel rhythms and sleep and their association with negative emotions during the outbreak of COVID-19 in China
Authors: Chen Siyu , Huang Tianyu , Huang Yutao , Nie Cenxing , Liang Jingwen , Liu Xinyan , Xu Yanwen , Guo Jinhu 
Published: September 2020

Abstract
Introduction: From December 2019, COVID-19 (novel coronavirus pneumonia) began spreading in China and has significantly affected the industrial economy and peoples’ daily lifestyle. Beginning on January 23, the public was asked to constantly stay at home for quarantine and community containment.Methods: To assess the effects of the changes in diel rhythms and sleep and their association with negative emotions during the COVID-19 outbreak, a questionnaire was administered to 451 responders for analysis between January 20, 2020, and January 31, 2020, in China.Results: We found that 34.6% of the participants reported diel rhythm disturbance. Moreover, 67.2% of the participants presented negative emotions regarding the pandemic situation, including worry, fear, downheartedness, anxiety, depression, and stupefaction; among them, worry was the most prevalent. Gender and age were significant factors for changes in the diel phases and emotions. There was a correlation between diel rhythm alterations and negative emotions. Three factors, i.e., the Spring Festival holiday, quarantines and concern regarding the pandemic situation, were associated with changes in diel rhythms, sleep, and negative emotions during the pandemic period. Holiday jet lag, quarantine (or community containment), and concerns regarding the pandemic situation had significant effects on diel rhythms, sleep and negative emotion in a substantial part of the population. Conclusions: Our findings suggest that diel rhythms and sleep and their association with negative emotions in COVID-19 patients and the normal population need to be considered. Moreover, the adjustment of diel rhythms could help relieve negative effects and improve the global health during the pandemic period.
Resuscitation of inactive ammonia-oxidizing archaea and complete nitrifiers by extracellular electrons from a heterotrophic bacterium, Bacillus amyloliquefaciens
Authors: Wu Shanghua , Dong Yuzhu , Fan Haonan , Deng Ye , Zhuang Xuliang 
Published: September 2020

Abstract
Background: Nitrification in the soil is dominated by ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and the newly discovered complete nitrifiers, which are members of complex communities. Complicated relations have been found in microbial communities, but the relations between heterotrophic bacteria and autotrophic ammonia oxidizers (AOM) are unclear, and experimental models are lacking. Here, we constructed a microcosm based on DNA stable isotope probing that was established between a heterotrophic bacterium, Bacillus amyloliquefaciens (BA), and the soil autotrophic AOM. Results: The inoculation of BA changed the activities of three indigenous nitrifiers. The originally marginal AOA and complete nitrifiers were active in the nitrification process as well as the AOB, which led to mitigation of N2O and an increase in NO. The network analysis showed that the inoculated BA was indirectly and positively linked to AOA through a Microbacteriaceae that contains genes encoding proteins responsible for transporting electrons. Further, the microbial fuel cell system indirectly confirmed the potential regulation of extracellular electron transfer (EET) between these two species. Conclusions: With our findings, a useful model to investigate the relations between heterotrophic bacteria and AOM was constructed, and evidence of EET in complex regulations was provided.
Prediction of Microvascular Invasion and Recurrence Using Preoperative 18F-FDG PET/CT Metabolic Parameters in Hepatocellular Carcinoma
Authors: Jiang Chunjuan , Ma Guang , Liu Qiufang , Song Shaoli 
Published: September 2020

Abstract
Background: Microvascular invasion (MVI) is very important in the evaluation of hepatocellular carcinoma (HCC),but diagnosis is determined by postoperative pathology; thus, preoperative non-invasive methods will play an active role. The purpose of this study was to assess the performance of metabolic parameters of preoperative 18F-fluorodeoxyglucose positron emission tomography/computerized tomography (18F-FDG PET/CT) in the prediction of MVI and postoperative recurrence in primary hepatocellular carcinoma.Methods: We retrospectively collected 72 patients with HCC who have performed 18F-FDG PET/CT scan before partial hepatectomy between 2016 and 2019. We used both normal liver tissue and inferior vena cava as the reference background, and combined with clinicopathological features, 18F-FDG PET/CT metabolic and volumetric indices to predict MVI and postoperative recurrence of primary HCC before surgery.Results: Twenty-one of the 72 patients recurred, in recurrent cases showed higher maximum standard uptake value (SUVmax), TNR (ratio of tumor SUVmax to mean SUV [SUVmean] of the background tissue), metabolic tumor volume (MTV) and total lesion glycolysis (TLG) than nonrecurrence cases(p<0.001). All 18F-FDG PET metabolic and volumetric indices for predicting postoperative HCC recurrence were significant on receiver-operating-characteristic (ROC) curve analyses (p<0.05). TNRIVC, TNRNL, MTV, TLGIVC, and TLGNL were significant factors for predicting MVI in HCC (p<0.05). On multivariate analyses, MVI, SUVmax, TNRIVC, TNRNL, MTV, TLGIVC, and TLGNL(p<0.05) are independent risk factors for predicting postoperative HCC recurrence. TNRIVC is the most relevant PET/CT parameter for predicting MVI in HCC, and MTV is the most valuable for predicting postoperative HCC recurrence. Moreover, the PET/CT parameters are more accurate for prognosis with inferior vena cava as a reference background than with normal liver tissue.Conclusion: 18F-FDG PET/CT metabolic and volumetric indices are effective predictors, and could non-invasively provide more comprehensive predictive information on MVI and postoperative recurrence of primary HCC before surgery.
One-year follow-up of The Incredible Years Parents and Babies Program: A pilot randomized controlled trial
Authors: Pontoppidan Maiken , Sandoy Tróndur Møller , Klest Sihu K. 
Published: September 2020

Abstract

Background:
The foundation of a healthy life begins in pregnancy and early adversity can have detrimental long-term consequences for affected children.

Objective:
This paper examines the effects of the Incredible Years Parents and Babies program (IYPB) at one-year follow-up when offered as a universal parenting intervention to parents with newborn infants.

Method:
We conducted a pragmatic, two-arm, parallel pilot randomized controlled trial; 112 families with newborns were randomized to IYPB intervention (n = 76) or usual care (n = 36). The IYPB program is a group intervention with eight two-hour sessions. Follow-up outcomes collected a year after the intervention ended include parental stress, depression, well-being, reflective function, sense of competence, and child cognitive and socio-emotional development.

Results:
There were no intervention effects on any of the primary or secondary parent-reported outcomes at one-year follow-up when the children were 18 months old. When examining the lowest-functioning mothers in moderator analyses, we found that mothers assigned to the IYPB group reported significantly lower scores for the interest and curiosity subscale of the parent reflective function scale than control mothers (β=-1,07 [-2.09,-0.06]).

Conclusion:
We found no long-term effects of the IYPB when offered as a universal intervention for a relatively well-functioning group of parents with infants in a setting with a high standard of usual care. The intervention was developed for more vulnerable families in settings with a low level of universal care and the program may be effective for families in those circumstances.
Skew normal small area time models for the Brazilian annual service sector survey
Authors: Azevedo Neves André Felipe , Nascimento Silva Denise Britz do , Silva Moura Fernando Antônio da 
Published: September 2020

Abstract
Small domain estimation covers a set of statistical methods for estimating quantities in domains not previously considered by the sample design. In such cases, the use of a model-based approach that relates sample estimates to auxiliary variables is indicated. In this paper, we propose and evaluate skew normal small area time models for the Brazilian Annual Service Sector Survey (BASSS), carried out by the Brazilian Institute of Geography and Statistics (IBGE). The BASSS sampling plan cannot produce estimates with acceptable precision for service activities in the North, Northeast and Midwest regions of the country. Therefore, the use of small area estimation models may provide acceptable precise estimates, especially if they take into account temporal dynamics and sector similarity. Besides, skew normal models can handle business data with asymmetric distribution and the presence of outliers. We propose models with domain and time random effects on the intercept and slope. The results, based on 10-year survey data (2007-2016), show substantial improvement in the precision of the estimates, albeit with presence of some bias.
High dimensional, robust, unsupervised record linkage
Authors: Bera Sabyasachi , Chatterjee Snigdhansu 
Published: September 2020

Abstract
We develop a technique for record linkage on high dimensional data, where the two datasets may not have any common variable, and there may be no training set available. Our methodology is based on sparse, high dimensional principal components. Since large and high dimensional datasets are often prone to outliers and aberrant observations, we propose a technique for estimating robust, high dimensional principal components. We present theoretical results validating the robust, high dimensional principal component estimation steps, and justifying their use for record linkage. Some numeric results and remarks are also presented.