Miracle-dz/UniFAR-FTUs huggingface dataset:
LncRNA MEG3 contributes to adenosine‐induced cytotoxicity in hepatoma HepG2 cells by downregulated ILF3 and autophagy inhibition via regulation PI3K‐AKT‐mTOR and beclin‐1 signaling pathway

Adenosine is a promising cytotoxic reagent for tumors, long noncoding RNA (lncRNA) maternally expressed gene 3 (MEG3) has been indicated to play critical roles in tumorigenesis, ILF3 has been recognized as a MEG3‐binding protein, however, the roles of adenosine and MEG3 on hepatoma are still ambiguous. To clarify the effects of MEG3 on the adenosine‐induced cytotoxicity in hepatoma, MEG3 and ILF3 lentivirus were transduced into human hepatoma HepG2 cells to stimulate overexpression of MEG3 (OE MEG3) and overexpression of ILF3 (OE ILF3), furthermore, ILF3 small interfering RNA (siRNA) was also applied to downregulate the expression of ILF3. In this study, autophagy was markedly inhibited by low concentration of adenosine, which present by not only inhibited transformation from LC3‐I to LC3‐II and autophagosomes formation, but also the elevation of mTOR and reduction of beclin‐1 proteins. Furthermore, low concentration of adenosine also exerted marked cytotoxicity representing induced cell apoptosis together with reductions of cell viability and migration, which were also markedly enhanced by OE MEG3. Novelly and excitingly, adenosine markedly stimulated MEG3 expression, OE MEG3 markedly decreased the ILF3 expression in HepG2 cells, and the adenosine‐induced autophagy inhibition, together with the ratio of p‐PI3K/PI3K, p‐AKT/AKT, and p‐mTOR/mTOR were also boosted by OE MEG3. More interestingly, OE ILF3 increased autophagy, whereas downregulated ILF3, especially in the case of adenosine, led to marked autophagy inhibition by decreasing beclin‐1. The present study demonstrates autophagy inhibition is involved in the adenosine‐induced cytotoxicity in HepG2 cells, the cytotoxicity can be synergized by OE MEG3 via downregulated ILF3 to activate PI3K/Akt/mTOR and inactivate the beclin‐1 signaling pathway. In conclusion, MEG3 and inhibition of autophagy might be potential targets for augmenting adenosine‐induced cytotoxicity in hepatoma.
Sensitivity of the Memory Validity Profile (MVP): Raising the bar

ABSTRACT The Memory Validity Profile (MVP) is a performance validity test (PVT) designed specifically for pediatric populations and utilizes specific cut-points for identifying noncredible performance at different ages. This study aims to evaluate the MVP using a known-groups design to determine optimal cut-off scores for detecting noncredible performance in youths with mild traumatic brain injury (mTBI) across different age-groups. Participants were 114 youths (age 5–17) with mTBI who were referred for neuropsychological evaluation in a hospital-based concussion clinic. All participants were administered the Nonverbal-Medical Symptom Validity Test (NV-MSVT) and the MVP. Participants who failed the NV-MSVT were also administered the TOMM. Participants who failed both the NV-MSVT and the TOMM comprised the criterion group (i.e., the “Failed two PVTs” group). Participants who failed only one PVT were excluded from the analysis. ROC curve analyses revealed good discriminability (AUC = .844: 95%, CI = 676–1.0, p = .001) with acceptable sensitivity (.73) and specificity (.91) for an optimal MVP Total score cut-off ≤31. There were no differences in MVP Total scores across age-groups. In conclusion, adopting stricter cut-points for non-credible performance and applying these consistently across all age groups in a mTBI population increases the clinical utility of the MVP.
The integration of information across lexical and sublexical processes in spelling

We report on a brain-injured subject, LAT, who made phonologically plausible errors in word spelling (e.g., “bouquet” spelled as BOUKET). Although many of his errors are phonologically plausible they contained low-frequency (yet lexically correct) spellings (/ei/ spelled as ET in BOUK ET). Because these errors are phonologically plausible they do not appear to have been generated by the lexical process, yet because they contain low probability, lexically correct elements they do not appear to be have been generated by the sublexical process. We present analyses that specifically support the conclusion that many of LAT's phonologically plausible responses to word stimuli consist of the integrated output of elements generated by both the lexical and sublexical processes. This evidence constitutes strong support for the notion that lexical and sublexical processes share information during the course of spelling a familiar word.
Women’s Well-Being After Relocation to Independent Living Communities

Late-life relocation to independent living communities is increasing, especially among women. This study described the impact of relocation on the health and well-being of 31 older women who moved from a private residence to an independent living community. Schumacher and Meleis’ (1994) nursing model of transition guided the study. Health status, social activity, self-esteem, depression, and quality of life were measured pre- and postmove. Post-move women reported a significant increase in engagement in social activities and higher quality of life. Participants’ levels of self-esteem, depression, and quality of life were found to correspond with three relocation transition styles: full integration, partial integration, and minimal integration. These preliminary findings suggest that nurses who identify older women with low self-esteem, high depressive symptoms, and low quality of life pre-move may be at risk for poor relocation outcomes. Interventions to ease the transition process and improve relocation adjustment are needed.
Nodular focal fat sparing of liver mimicking hepatocellular carcinoma in contrast-enhanced ultrasound

Abstract Introduction: Focal fatty sparing is a manifestation of fatty liver. Nodular focal fatty sparing of liver sometimes is a mimicker of malignant lesion, especially metastatic tumor. There are some case reports about this kind of tricks revealed by computed tomography (CT) and magnetic resonance imaging. However, few reports described nodular focal sparing of liver presenting an enhancement mode of hepatocellular carcinoma (HCC) in contrast-enhanced ultrasound (CEUS). Patient concerns: A 37-year-old male had a long history of alcohol abuse and hepatitis B virus infection. Routine blood examination showed an elevation of triglyceride, and tumor markers were unremarkable. Conventional ultrasound indicated a diffuse fatty liver with a hypoechoic nodular lesion. CEUS revealed hyperenhancement in arterial phase and washout in late phase of this hypoechoic lesion. Contrast-enhanced CT showed a similar enhancement mode of the mass with CEUS. Diagnosis: A clinical diagnosis of HCC was made. Then, liver resection was conducted. Postoperative histopathologic and immunohistochemical results of the lesion revealed no presence of tumor cells except for heterogeneous hepatic steatosis. So a final diagnosis of hepatic focal fatty sparing was determined. Interventions: Liver resection was conducted according to the clinical diagnosis of HCC. Outcomes: After general postoperative administration, the patient was told to discharge. Then, he had been undergoing regular serological tests and imaging examinations in our hospital for 39 months and found no manifestation of liver tumor. Conclusion: According to guidelines, it is typical that hepatic focal fatty change (FFC) presents a mode of persistent iso-enhancement in CEUS. However, atypical enhancement presence of FFC in imaging examinations may occur and lead to misdiagnosis, which calls for more attention.
Establishing the Japan-Store house of animal radiobiology experiments (J-SHARE), a large-scale necropsy and histopathology archive providing international access to important radiobiology data

Abstract Purpose: Projects evaluating the effects of radiation, within the National Institutes of Quantum and Radiological Science and Technology (QST), National Institute of Radiological Sciences (NIRS), have focused on risk analyses for life shortening and cancer prevalence using laboratory animals. Genetic and epigenetic alterations in radiation-induced tumors have been also analyzed with the aim of better understanding mechanisms of radiation carcinogenesis. As well as the economic and practical limitations of repeating such large-scale experiments, ethical considerations make it vital that we store and share the pathological data and samples of the animal experiments for future use. We are now constructing such an archive called the Japan-Storehouse of Animal Radiobiology Experiments (J-SHARE). Methods: J-SHARE records include information such as detailed experimental protocols, necropsy records and photographs of organs at necropsy. For each animal organs and tumor tissues are dissected, and parts are stored as frozen samples at −80 °C. Samples fixed with formalin are also embedded in paraffin blocks for histopathological analyses. Digital copies of stained tissues are being systematically saved using a virtual slide system linked to original records by barcodes. Embedded and frozen tissues are available for molecular analysis. Conclusion: Similar archive systems for radiation biology have also been under construction in the USA and Europe, the Northwestern University Radiation Archive (NURA), and STORE at the BfS, respectively. The J-SHARE will be linked with the sister-archives and made available for collaborative research to institutions and universities all over the world.
The Long-term Impacts of Birth Weight and Respiratory Complications after a Preterm Birth

Background: Infant respiratory distress syndrome (RDS) and bronchopulmonary dysplasia (BPD) remain important respiratory complications of preterm births. This study aims at establishing the incidence and impact of respiratory complications and extreme low birth weight (ELBW) on the healthcare utilization of a population of preterm infants. Methods: Retrospective cohort study using administrative healthcare databases of the province of Quebec (Canada). The main outcome measures of healthcare utilization, hospital admissions, hospital mortality and use of prescription drugs were studied in 55 033 subjects born prematurely with or without respiratory complications such as BPD or RDS between 1999 and 2009. Results: Preterm infants with BPD and RDS had significantly higher hospital readmissions per person-year. This trend persisted for the entire duration of the 10-year follow-up. Diagnoses of childhood asthma, attention deficit hyperactivity disorder and cerebral palsy were more frequent in BPD subjects, but were not influenced by birth weight. Extreme low birth weight carried odds ratio of 38.0 [33.5, 43.2] and 3.5 [3.2, 3.9] respectively for the occurrence of BPD and RDS, and was associated with greater mortality, longer hospital stay and more medical visits per person-year. Except for anxiolytics and sedatives, bronchopulmonary dysplasia subjects were not more likely to have been prescribed neurological and psychiatric medications. Conclusions: Birth weight is a major determinant in the occurrence of respiratory complications following a preterm birth. The impacts of BPD and extreme low birth weight following a preterm birth have lasting consequences on respiratory health and healthcare utilization.
Transcriptome Analyses Reveal Effects of Vitamin C-Treated Donor Cells on Cloned Bovine Embryo Development

Somatic cell nuclear transfer (SCNT) is a very powerful technique used to produce genetically identical or modified animals. However, the cloning efficiency in mammals remains low. In this study, we aimed to explore the effects of vitamin C (Vc)-treated donor cells on cloned embryos. As a result, Vc treatment relaxed the chromatin of donor cells and improved cloned embryo development. RNA sequencing was adopted to investigate the changes in the transcriptional profiles in early embryos. We found that Vc treatment increased the expression of genes involved in the cell–substrate adherens junction. Gene ontology (GO) analysis revealed that Vc treatment facilitated the activation of autophagy, which was deficient in cloned two-cell embryos. Rapamycin, an effective autophagy activator, increased the formation of cloned blastocysts (36.0% vs. 25.6%, p < 0.05). Abnormal expression of some coding genes and long non-coding RNAs in cloned embryos was restored by Vc treatment, including the zinc-finger protein 641 (ZNF641). ZNF641 compensation by means of mRNA microinjection improved the developmental potential of cloned embryos. Moreover, Vc treatment rescued some deficient RNA-editing sites in cloned two-cell embryos. Collectively, Vc-treated donor cells improved the development of the cloned embryo by affecting embryonic transcription. This study provided useful resources for future work to promote the reprogramming process in SCNT embryos.
Radioactive contraband detection: A Bayesian approach

Radionuclide emissions from nuclear contraband challenge both detection and measurement technologies to capture and record each event. The development of a sequential Bayesian processor incorporating both the physics of gamma-ray emissions and the measurement of photon energies offers a physics-based approach to attack this challenging problem. It is shown that a "physics-based" structure can be used to develop an effective detection technique, but also motivates the implementation of this approach using particle filters to enhance and extract the required information. The resulting processor is applied to feasibility data obtained from a controlled proof-of-concept experiment.
Very Bright Phycoerythrobilin Chromophore for Fluorescence Biolabeling

Biliproteins have extended the spectral range of fluorescent proteins into the far‐red (FR) and near‐infrared (NIR) regions. These FR and NIR fluorescent proteins are suitable for the bioimaging of mammalian tissues and are indispensable for multiplex labeling. Their application, however, presents considerable challenges in increasing their brightness, while maintaining emission in FR regions and oligomerization of monomers. Two fluorescent biliprotein triads, termed BDFP1.2/1.6:3.3:1.2/1.6, are reported. In mammalian cells, these triads not only have extremely high brightness in the FR region, but also have monomeric oligomerization. The BDFP1.2 and BDFP1.6 domains covalently bind to biliverdin, which is accessible in most cells. The BDFP3.3 domain noncovalently binds phycoerythrobilin that is added externally. A new method of replacing phycoerythrobilin with proteolytically digested BDFP3.3 facilitates this labeling. BDFP3.3 has a very high fluorescence quantum yield of 66 %, with maximal absorbance at λ=608 nm and fluorescence at λ=619 nm. In BDFP1.2/1.6:3.3:1.2/1.6, the excitation energy that is absorbed in the red region by phycoerythrobilin in the BDFP3.3 domain is transferred to biliverdin in the two BDFP1.2 or BDFP1.6 domains and fluoresces at λ≈670 nm. The combination of BDFP3.3 and BDFP1.2/1.6:3.3:1.2/1.6 can realize dual‐color labeling. Labeling various proteins by fusion to these new fluorescent biliproteins is demonstrated in prokaryotic and mammalian cells.
Population genomics of an outbreak of the potato late blight pathogen, Phytophthora infestans, reveals both clonality and high genotypic diversity

Summary An outbreak of the potato late blight pathogen Phytophthora infestans in Denmark was characterized in order to resolve the population structure and determine to what extent sexual reproduction was occurring. A standard set of microsatellite simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers generated using restriction site‐associated DNA sequencing (RAD‐seq) were employed in parallel. A total of 83 individuals, isolated from seven different potato fields in 2014, were analysed together with five Danish whole‐genome sequenced isolates, as well as two Mexican individuals used as an outgroup. From a filtered dataset of 55 288 SNPs, population genomics analyses revealed no sign of recombination, implying clonality. In spite of this, multilocus genotypes were unique to individual potato fields, with little evidence of gene flow between fields. Ploidy analysis performed on the SNPs dataset indicated that the majority of isolates were diploid. These contradictory results with clonality and high genotypic diversity may suggest that rare sexual events likely still contribute to the population. Comparison of the results generated by SSRs vs SNPs data indicated that large marker sets, generated by RAD‐seq, may be advised going forward, as it provides a higher level of genetic discrimination than SSRs.
Mudi, a web tool for identifying mutations by bioinformatics analysis of whole‐genome sequence

In forward genetics, identification of mutations is a time‐consuming and laborious process. Modern whole‐genome sequencing, coupled with bioinformatics analysis, has enabled fast and cost‐effective mutation identification. However, for many experimental researchers, bioinformatics analysis is still a difficult aspect of whole‐genome sequencing. To address this issue, we developed a browser‐accessible and easy‐to‐use bioinformatics tool called Mutation discovery (Mudi; http://naoii.nig.ac.jp/mudi_top.html), which enables ‘one‐click’ identification of causative mutations from whole‐genome sequence data. In this study, we optimized Mudi for pooled‐linkage analysis aimed at identifying mutants in yeast model systems. After raw sequencing data are uploaded, Mudi performs sequential analysis, including mapping, detection of variant alleles, filtering and removal of background polymorphisms, prioritization, and annotation. In an example study of suppressor mutants of ptr1‐1 in the fission yeast Schizosaccharomyces pombe, pooled‐linkage analysis with Mudi identified mip1+, a component of Target of Rapamycin Complex 1 (TORC1), as a novel component involved in RNA interference (RNAi)‐related cell‐cycle control. The accessibility of Mudi will accelerate systematic mutation analysis in forward genetics.
Cognitive self-regulation influences pain-related physiology

Cognitive self-regulation can shape pain experience, but little is known about whether it affects autonomic responses to painful events. In this study, participants (N = 41) deployed a cognitive strategy based on reappraisal and imagination to regulate pain up or down on different trials while skin conductance responses (SCR) and electrocardiogram (ECG) activity were recorded. Using a machine learning approach, we developed stimulus-locked SCR and ECG physiological markers predictive of pain ratings. The markers demonstrated high sensitivity when predicting pain ratings, r = 0.55-0.83. In an independent dataset (N = 84), they discriminated different levels of painful heat with 74-93% accuracy and showed some specificity relative to discriminating levels of vicarious pain (50-71% accuracy; chance is 50%). Cognitive self-regulation increased and decreased both pain ratings and physiology in accordance with regulatory goals. These findings suggest that self-regulation can impact autonomic nervous system responses to painful stimuli and provide pain-selective autonomic profiles for future studies. Author Summary It is well known that cognitive self-regulation can modulate pain perception in humans, yet its physiological consequences are difficult to quantify, as the pain- and task-related physiological responses are intricately intertwined. Here, we developed physiological markers predictive of pain report from skin conductance response (SCR) and electrocardiogram (ECG) data collected from 41 participants while they experienced painful thermal stimulations without regulating their pain. These markers were validated on an independent dataset, and then tested for effects of reappraisal-based cognitive self-regulation. When participants were instructed to use this strategy to increase the amount of pain they experienced, expression of the pain-predictive physiological markers increased, and when participants were instructed to reduce the amount of pain they felt, expression of the physiological markers decreased. These results demonstrate that cognitive pain regulation using a conscious, reappraisal-based strategy not only impacts the way participants report pain, but also the way their autonomic physiology responds to pain.
Regulation of Notch signaling by the chromatin-modeling protein Hat-trick

ABSTRACT Notch signaling plays a pleiotropic role in a variety of cellular processes, including cell fate determination, differentiation, proliferation and apoptosis. The increasingly complex regulatory mechanisms of Notch signaling account for the many functions of Notch during development. Using a yeast two-hybrid screen, we identiﬁed the Drosophila DNA-binding protein Hat-trick (Htk) to be an interacting partner of Notch-intracellular domain (Notch-ICD); their physical interaction was further validated by co-immunoprecipitation experiments. htk genetically interacts with Notch pathway components in trans-heterozygous combinations. Loss of htk function in htk mutant somatic clones resulted in the downregulation of Notch targets, whereas its overexpression caused ectopic expression of Notch targets, without affecting the level of the Notch protein. In the present study, immunocytochemical analyses demonstrate that Htk and overexpressed Notch-ICD colocalize in the same nuclear compartment. Here, we also show that Htk cooperates with Notch-ICD and Suppressor of Hairless to form an activation complex and binds to the regulatory sequences of Notch downstream targets such as Enhancer of Split complex genes, to direct their expression. Together, our results suggest a novel mode of regulation of Notch signaling by the chromatin-modeling protein Htk. Summary: Hat-trick, a novel interactor of Notch that genetically interacts with Notch pathway components, is a component of the Notch-Su(H) activation complex and positively regulates Notch signaling.
The formation-keeping of multiple mobile robots using chained-poles

In this paper, we propose an formation-keeping and changing methods for outdoor multiple mobile robots in chained form. The proposed method is designed to maintain the follower to its desired distance and orientation with respect to the pole using the concept of virtual force such as potential field. We use the centralized system and the client robots use the behavior-based control to perform kinematic control to keep formation. The relationship of each poles that is expressed by set of distance and angle is the description of the formation type and the type converting is performed using this set. In addition, we also examine the stability and capability in the simulation and experiments with real robots.
Deep Sequential Models for Suicidal Ideation From Multiple Source Data

This paper presents a novel method for predicting suicidal ideation from electronic health records (EHR) and ecological momentary assessment (EMA) data using deep sequential models. Both EHR longitudinal data and EMA question forms are defined by asynchronous, variable length, randomly sampled data sequences. In our method, we model each of them with a recurrent neural network, and both sequences are aligned by concatenating the hidden state of each of them using temporal marks. Furthermore, we incorporate attention schemes to improve performance in long sequences and time-independent pre-trained schemes to cope with very short sequences. Using a database of 1023 patients, our experimental results show that the addition of EMA records boosts the system recall to predict the suicidal ideation diagnosis from 48.13% obtained exclusively from EHR-based state-of-the-art methods to 67.78%. Additionally, our method provides interpretability through the t-distributed stochastic neighbor embedding (t-SNE) representation of the latent space. Furthermore, the most relevant input features are identified and interpreted medically.