Miracle-dz/UniFAR-FTUs huggingface dataset:
Rehabilitation training combined acupuncture for limb hemiplegia caused by cerebral hemorrhage

Background: Previous studies have reported that rehabilitation training combined acupuncture (RTA) can be used for the treatment of limb hemiplegia (LH) caused by cerebral hemorrhage (CH). However, its effectiveness is still unclear. In this systematic review study, we aim to evaluate the effectiveness and safety of RTA for LH following CH. Methods: We will retrieve the databases of CENTRAL, EMBASE, MEDILINE, CINAHL, AMED, CBM, and CNKI from inception to March 1, 2019 with no language restrictions. The randomized controlled trials of RTA for evaluating effectiveness and safety in patients with LH following CH will be included. Cochrane risk of bias tool will be used to measure the methodological quality for all included studies. Two authors will independently select the studies, extract the data, and assess the methodological quality of included studies. A third author will be invited to discuss if any disagreements exist between 2 authors. If more than 2 eligible studies will be included, the outcome data will be pooled, and meta-analysis will be conducted if it is possible. Results: This systematic review will assess the effectiveness and safety of RTA for LH caused by CH. The primary outcome includes limbs function. The secondary outcomes consist of muscle strength, muscle tone, quality of life, and any adverse events. Conclusion: The findings of this study will summarize the current evidence of RTA for LH caused by CH, and may provide helpful evidence for the clinical treatment. Dissemination and ethics: The results of this study will be published in peer-reviewed journals or will be presented on conference meeting. This work does not require ethic approval, because it will be conducted based on the published studies. Systematic review registration: PROSPERO CRD42019120034.
Relations of Lipid Concentrations to Heart Failure Incidence: The Framingham Heart Study

Background— The relations of lipid concentrations to heart failure (HF) risk have not been elucidated comprehensively. Methods and Results— In 6860 Framingham Heart Study participants (mean age, 44 years; 54% women) free of baseline coronary heart disease, we related high-density lipoprotein cholesterol (HDL-C) and non–HDL-C to HF incidence during long-term follow-up, adjusting for clinical covariates and myocardial infarction at baseline and updating these at follow-up examinations. We evaluated dyslipidemia-specific population burden of HF by calculating population attributable risks. During follow-up (mean of 26 years), 680 participants (49% women) developed HF. Unadjusted HF incidence in the low (<160 mg/dL) versus high (≥190 mg/dL) non–HDL-C groups was 7.9% and 13.8%, respectively, whereas incidence in the high (≥55 [men], ≥65 [women] mg/dL) versus low (<40 [men], <50 [women] mg/dL) HDL-C groups was 6.1% and 12.8%, respectively. In multivariable models, baseline non–HDL-C and HDL-C, modeled as continuous measures, carried HF hazards (confidence intervals) of 1.19 (1.11 to 1.27) and 0.82 (0.75 to 0.90), respectively, per SD increment. In models updating lipid concentrations every 8 years, the corresponding hazards (confidence intervals) were 1.23 (1.16 to 1.31) and 0.77 (0.70 to 0.85). Participants with high baseline non–HDL-C and those with low HDL-C experienced a 29% and 40% higher HF risk, respectively, compared with those in the desirable categories; the population attributable risks for high non–HDL-C and low HDL-C were 7.5% and 15%, respectively. Hazards associated with non–HDL-C and HDL-C remained statistically significant after additional adjustment for interim myocardial infarction. Conclusions— Dyslipidemia carries HF risk independent of its association with myocardial infarction, suggesting that lipid modification may be a means for reducing HF risk.
Journey from the West: did tropical Graphidaceae (lichenized Ascomycota: Ostropales) evolve from a saxicolous ancestor along the American Pacific coast?

UNLABELLED PREMISE OF THE STUDY This study elucidates the phylogenetic position of a unique taxon of Graphidaceae occurring on rock in coastal desert areas, assessing its importance for our understanding of the evolution of the largest family of tropical lichenized fungi. • METHODS We used maximum likelihood and Bayesian approaches to reconstruct a three-gene phylogeny of Graphidaceae and a Bayesian molecular clock approach to estimate divergence dates for major clades, as well as Bayesian ancestral ecogeography state analysis. • KEY RESULTS The new genus Redonographa represents a new subfamily, Redonographoideae, sister to subfamily Graphidoideae. Redonographa is exclusively saxicolous and restricted to the American Pacific coast from California to central Chile, including Galapagos. It contains four species: Redonographa chilensis comb. nov., R. saxiseda comb. nov., R. saxorum comb. nov., and R. galapagoensis sp. nov. The genus Gymnographopsis, with a similar ecogeography but differing in excipular carbonization and chemistry, is also included in Redonographoideae, with the species G. chilena from Chile and G. latispora from South Africa. Molecular clock analysis indicates that Redonographoideae diverged from Graphidoideae about 132 million years ago (Ma) in the Early Cretaceous. • CONCLUSIONS The divergence date for subfamilies Redonographoideae and Graphidoideae coincides with the early breakup of Gondwana and ancient origin of the Atacama Desert. However, the common ancestor of Redonographoideae plus Graphidoideae was reconstructed to be tropical-epiphytic. Thus, even if Redonographoideae is subtropical-saxicolous, the hypothesis that Graphidoideae evolved from a subtropical-saxicolous ancestor is not supported.
A qualitative study of fish consumption during pregnancy.

BACKGROUND Many pregnant women in the United States do not consume enough docosahexaenoic acid (DHA)--an essential nutrient found in fish. Apparently conflicting findings that fish consumption is beneficial for the developing fetus, yet potentially toxic because of mercury contamination, have created uncertainty about the appropriate fish-consumption advice to provide to pregnant women. OBJECTIVE Our objective was to determine knowledge, behaviors, and received advice regarding fish consumption among pregnant women who are infrequent consumers of fish. DESIGN In 2009-2010 we conducted 5 focus groups with 22 pregnant women from the Boston area who ate <2 fish servings/wk. We analyzed transcripts by using immersion-crystallization. RESULTS Many women knew that fish might contain mercury, a neurotoxin, and had received advice to limit fish intake. Fewer women knew that fish contains DHA or what the function of DHA is. None of the women had received advice to eat fish, and most had not received information about which fish types contain more DHA or less mercury. Because of advice to limit fish intake, as well as a lack of information about which fish types they should be eating, many of the women said that they would rather avoid fish than possibly harm themselves or their infants. The participants thought that a physician's advice to eat fish and a readily available reference regarding which fish are safe to consume during pregnancy would likely have encouraged them to eat more fish. CONCLUSION Pregnant women might be willing to eat more fish if this were advised by their obstetricians or if they had an accessible reference regarding which types are safe.
Supporting the Development of Professional Identity in the Millennial Learner

* Abbreviations: I-CA2R2E — : individual connection, create, acknowledge and adjust, reflect and role model, and exchange PIF — : professional identity formation As teachers, we train learners to be knowledgeable and competent in the practice of medicine. No less important is the way teachers impact the development of learners’ professional identity. Social scientists in the 1950s noted medical education’s charge “to shape the novice into the effective practitioner of medicine, to give [them] the best available knowledge and skills, and to provide [the novice] with a professional identity so that [they] come to think, act, and feel like a physician. ”1 Many have stressed the importance of curricula focused on learners’ personal and professional development.2 An awareness of professional identity development helps teachers understand some of the workplace differences noted between generations, particularly with millennial learners. Continuing the Council on Medical Student Education in Pediatrics series on great clinical teachers, our article focuses on supporting professional identity formation (PIF) in millennial learners. Professional identity formation (ie, the socialization and professionalization of a physician) develops in stages over time.3 PIF consists of ordering and reordering personal and professional priorities as one progresses from student to effective practitioner.3–5 This process has been linked to one’s personal identity development.6 Characteristics of 3 important stages of physician PIF include the following5: Address correspondence to Michael A. Barone, MD, MPH, National Board of Medical Examiners, 3750 Market St, Philadelphia, PA 19104. E-mail: mbarone{at}nbme.org
Differential long noncoding RNAs expression in cancer-associated fibroblasts of non-small-cell lung cancer.

AIM The aim of this study was to investigate the role of long noncoding RNAs (lncRNAs) profiles in cancer-associated fibroblasts (CAFs) during non-small-cell lung cancer (NSCLC) progression. MATERIALS & METHODS Differentially expressed lncRNAs and mRNAs were detected by lncRNA microarray between three patient-paired CAFs and the adjacent normal fibroblasts, which were obtained from tumoral and nontumoral portions of surgically resected lung tissue from three primary NSCLCs. Bioinformatic analyses including gene ontology and pathway analysis were applied to these differentially expressed mRNAs. The qRT-PCR was conducted to identify the change of selected lncRNAs that might be involved in contribution of CAFs toward NSCLC. RESULTS A total of 766 lncRNAs and 750 mRNAs abnormally expressed in CAFs (fold-change >2, p < 0.05). Bioinformatic analyses indicated that these mRNAs are associated with immune function. The qPCR results were consistent with microarray data. CONCLUSION The lncRNAs profiles of CAFs may provide promising targets for further research on immune regulation during NSCLC process.
Exploring IoT Location Information to Perform Point of Interest Recommendation Engine: Traveling to a New Geographical Region

With the development of wireless Internet and the popularity of location sensors in mobile phones, the coupling degree between social networks and location sensor information is increasing. Many studies in the Location-Based Social Network (LBSN) domain have begun to use social media and location sensing information to implement personalized Points-of-interests (POI) recommendations. However, this approach may fall short when a user moves to a new district or city where they have little or no activity history and social network friend information. Thus, a need to reconsider how we model the factors influencing a user’s preferences in new geographical regions in order to make personalized and relevant recommendation. A POI in LBSNs is semantically enriched with annotations such as place categories, tags, tips or user reviews which implies knowledge about the nature of the place as well as a visiting person’s interests. This provides us with opportunities to better understand the patterns in users’ interests and activities by exploiting the annotations which will continue to be useful even when a user moves to unfamiliar places. In this research, we proposed a location-aware POI recommendation system that models user preferences mainly based on user reviews, which shows the nature of activities that a user finds interesting. Using this information from users’ location history, we predict user ratings by harnessing the information present in review text as well as consider social influence from similar user set formed based on matching category preferences and similar reviews. We use real data sets partitioned by city provided by Yelp, to compare the accuracy of our proposed method against some baseline POI recommendation algorithms. Experimental results show that our algorithm achieves a better accuracy.
Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

Background In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community, but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). Results Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates. Conclusions Sequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost effective, portable and universal approach for eukaryote DNA barcoding. Long rDNA amplicons scale up DNA barcoding by enabling the accurate recovery of taxonomic and phylogenetic diversity. However, bulk community analyses using long-read approaches may introduce biases and will require further exploration.
MeSHProbeNet: a self-attentive probe net for MeSH indexing

MOTIVATION MEDLINE is the primary bibliographic database maintained by National Library of Medicine (NLM). MEDLINE citations are indexed with Medical Subject Headings (MeSH), which is a controlled vocabulary curated by the NLM experts. This greatly facilitates the applications of biomedical research and knowledge discovery. Currently, MeSH indexing is manually performed by human experts. To reduce the time and monetary cost associated with manual annotation, many automatic MeSH indexing systems have been proposed to assist manual annotation, including Deep-MeSH and NLM's official model Medical Text Indexer (MTI). However, the existing models usually rely on the inter-mediate results of other models and suffer from efficiency issues. We propose an end-to-end framework, MeSHProbeNet (formerly named as xgx), which utilizes deep learning and self-attentive MeSH probes to index MeSH terms. Each MeSH probe enables the model to extract one specific aspect of biomedical knowledge from an input article, thus comprehensive biomedical information can be extracted with different MeSH probes and interpretability can be achieved at word level. MeSH terms are finally recommended with a unified classifier, making MeSHProbeNet both time efficient and space efficient. RESULTS MeSHProbeNet won the first place in the latest batch of Task A in the 2018 BioASQ challenge. The result on the last test set of the challenge is reported in this paper. Compared with other state-of-the-art models, such as MTI and DeepMeSH, MeSHProbeNet achieves the highest scores in all the F-measures, including Example Based F-Measure, Macro F-Measure, Micro F-Measure, Hierarchical F-Measure and Lowest Common Ancestor F-measure. We also intuitively show how MeSHProbeNet is able to extract comprehensive biomedical knowledge from an input article. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Cisplatin Synergistically Enhances Antitumor Potency of Conditionally Replicating Adenovirus via p53 Dependent or Independent Pathways in Human Lung Carcinoma

Cisplatin is ranked as one of the most powerful and commonly prescribed anti-tumor chemotherapeutic agents which improve survival in many solid tumors including non-small cell lung cancer. However, the treatment of advanced lung cancer is restricted due to chemotherapy resistance. Here, we developed and investigated survivin promoter regulating conditionally replicating adenovirus (CRAd) for its anti-tumor potential alone or in combination with cisplatin in two lung cancer cells, H23, H2126, and their resistant cells, H23/CPR, H2126/CPR. To measure the expression of genes which regulate resistance, adenoviral transduction, metastasis, and apoptosis in cancer cells, RT-PCR and Western blotting were performed. The anti-tumor efficacy of the treatments was evaluated through flow cytometry, MTT and transwell assays. This study demonstrated that co-treatment with cisplatin and CRAd exerts synergistic anti-tumor effects on chemotherapy sensitive lung cancer cells and monotherapy of CRAd could be a practical approach to deal with chemotherapy resistance. Combined treatment induced stronger apoptosis by suppressing the anti-apoptotic molecule Bcl-2, and reversed epithelial to mesenchymal transition. In conclusion, cisplatin synergistically increased the tumor-killing of CRAd by (1) increasing CRAd transduction via enhanced CAR expression and (2) increasing p53 dependent or independent apoptosis of lung cancer cell lines. Also, CRAd alone proved to be a very efficient anti-tumor agent in cancer cells resistant to cisplatin owing to upregulated CAR levels. In an exciting outcome, we have revealed novel therapeutic opportunities to exploit intrinsic and acquired resistance to enhance the therapeutic index of anti-tumor treatment in lung cancer.
Radiation protection biology then and now

Abstract Purpose: Radiation biology is a branch of the radiation research field which focuses on studying radiation effects in cells and organisms. Radiation can be used in biological investigations for two, mutually non-exclusive reasons: (1) to study biological processes by perturbing their functioning (qualitative approach) and (2) to assess consequences of radiation-induced damage (quantitative approach). While the former approach has a basic research character, the latter has an applied character that is driven by needs of medical applications and radiological protection. Radiation protection biology is defined in the sense of the second approach. The aim of the article is to provide a historical review of how radiation protection biology developed and how it influences radiological protection. Conclusions: While radiobiological investigations started immediately after the discovery of X-rays, the qualitative approach dominated until the end of World War II. After 1945, the nuclear weapons race and nuclear energy programs initiated quantitative radiobiological research. Radiation protection biology does not provide results from which radiation risks can be directly derived. Rather, it provides data that is necessary for understanding the nature of risks. Most recent years have seen, especially in Europe, a growing interest in coordinated studies on the effects of low radiation doses.
Hedyotis diffusa Willd inhibits proliferation and induces apoptosis of 5‑FU resistant colorectal cancer cells by regulating the PI3K/AKT signaling pathway.

Hedyotis diffusa Willd (HDW) is a major component frequently used in Traditional Chinese Medicine for the clinical treatment of colorectal cancer (CRC) and its associated drug resistance. However, the underlying mechanism of HDW circumventing drug resistance of cancer cells remains to be elucidated. Cancer cell resistance to apoptosis and activation of the phosphatidylinositol‑3‑kinase (PI3K)/protein kinase B (AKT) signaling pathway have been implicated as major factors in the acquired resistance to chemotherapeutic anti‑cancer drugs. The present study investigated the effect and mechanisms of action of ethanol extract of Hedyotis diffusa Willd (EEHDW) on the proliferation and apoptosis of CRC 5‑fluorouracil (5‑FU) resistant (HCT‑8/5‑FU) cells. CRC HCT‑8/5‑FU cell viability following treatment with EEHDW was determined using MTT and colony formation assay. In addition, Annexin V/propidium iodide staining with flow cytometry analysis and 4',6‑diamidino‑2‑phenylindole staining were used to determine the apoptosis of drug‑resistant cancer cells following treatment with EEHDW. The mRNA and protein expression levels of B cell leukemia/lymphoma (Bcl‑2), Bcl‑2 associated X (Bax), cyclin dependent kinase 4 (CDK4), cyclin D1 and p21 were evaluated using reverse transcription‑polymerase chain reaction and western blot analysis, respectively. Furthermore, activation of the PI3K/AKT signaling pathway and expression of phosphatase and tensin homolog (PTEN), PI3K, AKT and phosphorylated (p)‑AKT were determined. EEHDW significantly reduced cell viability, inhibited cell colony formation and promoted apoptosis of HCT‑8/5‑FU cells. Furthermore, EEHDW significantly downregulated the expression of Bcl‑2, cyclin D1 and CDK4 and upregulated the expression of Bax and p21. In addition, EEHDW inhibited the activation of the PI3K/AKT pathway by increasing expression of PTEN and suppressing the expression of PI3K and p‑AKT. The present study provided the first direct evidence that EEHDW may overcome drug‑resistance in human CRC cells by inhibiting PI3K/AKT signaling pathway and provides a basis for the improved therapeutic use of HDW in the clinical treatment of cancer.
Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II

Although chromatin organization and dynamics play a critical role in gene transcription, how they interplay remains unclear. To approach this issue, we investigated genome-wide chromatin behavior under various transcriptional conditions in living human cells using single-nucleosome imaging. While transcription by RNA polymerase II (RNAPII) is generally thought to need more open and dynamic chromatin, surprisingly, we found that active RNAPII globally constrains chromatin movements. RNAPII inhibition or its rapid depletion released the chromatin constraints and increased chromatin dynamics. Perturbation experiments of P-TEFb clusters, which are associated with active RNAPII, had similar results. Furthermore, chromatin mobility also increased in resting G0 cells and UV-irradiated cells, which are transcriptionally less active. Our results demonstrated that chromatin is globally stabilized by loose connections through active RNAPII, which is compatible with models of classical transcription factories or liquid droplet formation of transcription-related factors. Together with our computational modeling, we propose the existence of loose chromatin domain networks for various intra-/interchromosomal contacts via active RNAPII clusters/droplets.