Miracle-dz/UniFAR-FTUs huggingface dataset:
Long non-coding RNA, LINC01614 as a potential biomarker for prognostic prediction in breast cancer

Background Dysregulated long non-coding RNAs (lncRNAs) may serve as potential biomarkers of cancers including breast cancer (BRCA). This study aimed to identify lncRNAs with strong prognostic value for BRCA. Methods LncRNA expression profiles of 929 tissue samples were downloaded from TANRIC database. We performed differential expression analysis between paired BRCA and adjacent normal tissues. Survival analysis was used to identify lncRNAs with prognostic value. Univariate and multivariate Cox regression analyses were performed to confirm the independent prognostic value of potential lncRNAs. Dysregulated signaling pathways associated with lncRNA expression were evaluated using gene set enrichment analysis. Results We found that a total of 398 lncRNAs were significantly differentially expressed between BRCA and adjacent normal tissues (adjusted P value <= 0.0001 and |logFC| >= 1). Additionally, 381 potential lncRNAs were correlated Overall Survival (OS) (P value < 0.05). A total of 48 lncRNAs remained when differentially expressed lncRNAs overlapped with lncRNAs that had prognostic value. Among the 48 lncRNAs, one lncRNA (LINC01614) had stronger prognostic value and was highly expressed in BRCA tissues. LINC01614 expression was validated as an independent prognostic factor using univariate and multivariate analyses. Higher LINC01614 expression was observed in several molecular subgroups including estrogen receptors+, progesterone receptors+ and human epidermal growth factor receptor 2 (HER2)+ subgroup, respectively. Also, BRCA carrying one of four gene mutations had higher expression of LINC01614 including AOAH, CIT, HER2 and ODZ1. Higher expression of LINC01614 was positively correlated with several gene sets including TGF-β1 response, CDH1 signals and cell adhesion pathways. Conclusions A novel lncRNA LINC01614 was identified as a potential biomarker for prognosis prediction of BRCA. This study emphasized the importance of LINC01614 and further research should be focused on it.
Multi-strain Tn-Seq reveals common daptomycin resistance determinants in Staphylococcus aureus

Antibiotic-resistant Staphylococcus aureus remains a leading cause of antibiotic resistance-associated mortality in the United States. Given the reality of multi-drug resistant infections, it is imperative that we establish and maintain a pipeline of new compounds to replace or supplement our current antibiotics. A first step towards this goal is to prioritize targets by identifying the genes most consistently required for survival across the S. aureus phylogeny. Here we report the first direct comparison of multiple strains of S. aureus via transposon sequencing. We show that mutant fitness varies by strain in key pathways, underscoring the importance of using more than one strain to differentiate between core and strain-dependent essential genes. We treated the libraries with daptomycin to assess whether the strain-dependent differences impact pathways important for survival. Despite baseline differences in gene importance, several pathways, including the lipoteichoic acid pathway, consistently promote survival under daptomycin exposure, suggesting core vulnerabilities that can be exploited to resensitize daptomycin-nonsusceptible isolates. We also demonstrate the merit of using transposons with outward-facing promoters capable of overexpressing nearby genes for identifying clinically-relevant gain-of-function resistance mechanisms. Together, the daptomycin vulnerabilities and resistance mechanisms support a mode of action with wide-ranging effects on the cell envelope and cell division. This work adds to a growing body of literature demonstrating the nuanced insights gained by comparing Tn-Seq results across multiple bacterial strains.
Perceived Accessibility, Satisfaction with Daily Travel, and Life Satisfaction among the Elderly

People are living longer than they did previously, and the proportion of older people is increasing worldwide. This rapid development will have implications for the transport system, in general, and for travel behavior and accessibility to daily activities, in particular. In recent years, both research and politics have drawn the attention of the public to issues affecting the opportunities of the elderly to participate in everyday life. The debate has so far mostly focused on health issues, with limited work having been done on the ability of the elderly to live the lives they want to considering how they travel. With this view, a theoretical model, grounded in a model of travel and subjective wellbeing was developed to explore the role of perceived accessibility in satisfaction with travel and life satisfaction. Empirical data were collected from a sample of 2950 respondents (aged 60–92) from five cities in Northern Europe (Stockholm, Helsinki, Oslo, Copenhagen, Bergen) and analyzed using partial least square structural equation modeling (PLS-SEM). The findings confirmed the link between perceived accessibility, travel satisfaction, and life satisfaction. The findings also showed the role of sociodemographic and travel attributes in perceived accessibility and satisfaction with travel, as well as the moderating effects of different age groups. We conclude that this moderating role played by age clearly indicates that we should not treat the elderly as a homogenous group in research and transport planning.
RECOVERING TISSUE DEFORMATION

Recent advances in surgical robotics have provided a platform for extending the current capabilities of minimally invasive surgery by incorporating both pre-operative and intra-operative imaging data. In this tutorial paper, we introduce techniques for in vivo 3D tissue deformation recovery and tracking, based on laparoscopic or endoscopic images. These optically based techniques provide a unique opportunity for recovering surface deformation of the softtissue without the need of additional instrumentation. They can therefore be easily incorporated into the existing surgical workflow. Technically, the problem formulation is challenging due to non-rigid deformation of the tissue and instrument interaction. Current approaches and future research directions in terms of intra-operative planning and adaptive surgical navigation are explained in detail.
Treatment of pastirma with pulsed UV light: Modeling of Staphylococcus aureus inactivation and assessment of quality changes

The efficacy of pulsed UV (PUV) light treatment carried out in a wide range of fluence was investigated on pastirma slices by characterizing Staphylococcus aureus inactivation using mathematical models and by assessing the treatment effects on quality attributes. Pastirma slices inoculated on top surface with S. aureus were subjected to pulsed UV light for 5, 15, 25, 35, and 45 s at 5, 8, and 13 cm from the quartz window. Although the 5 cm/45 s treatment (72.3 J/cm2) yielded a maximum reduction of 2.99 log cfu/cm2 for S. aureus, this treatment changed the color, moisture, and thiobarbituric acid-reactive substances (TBARS) values of pastirma significantly (p < 0.05). The quality of pastirma tended to change above 20 J/cm2, below which the highest log reduction of S. aureus was ∼1.3 log cfu/cm2 obtained after the 8 cm/15 s treatment (18 J/cm2). Kamau’s model provided better fit to inactivation data (root mean square error: 0.049–0.116, Af: 1.013–1.046, R2: 0.991–0.999) than Cerf’s and Weibull models.
Ankle Bracing Decreases Vertical Jump Height and Alters Lower Extremity Kinematics

The purpose of this study was to determine the effects of ankle bracing on vertical jump performance and lower extremity kinematics and electromyography (EMG) activity. Twenty healthy college athletes participated in two sessions, separated by a minimum of 24 hr. They performed five jumps with no brace on the first day, and five jumps with both ankles braced on the second day. An average of the three highest jumps each day was used for analysis. Braced vertical jump performance significantly decreased (p = .002) as compared with the unbraced condition. In addition, hip flexion (p = .043) and ankle plantar flexion (p = .001) angles were significantly smaller during the braced vertical jump. There was also a significant reduction in soleus muscle EMG (p = .002) during the braced condition.
Topic Clustering of E-Cigarette Submissions Among Reddit Communities: A Network Perspective

E-cigarette use in the United States has significantly grown in recent years. Widespread diffusion of e-cigarette content across social media communities may be contributing to this growth. In this study, we (1) explored topics related to e-cigarettes and vaping on Reddit and (2) examined the extent to which these topics clustered across distinct communities. We analyzed a total of N = 79,783 Reddit submissions posted between March 2017 and February 2018 that mentioned at least one e-cigarette or vaping keyword. We created a dictionary to classify submissions into seven different topics related to e-cigarettes and vaping. Submissions were also categorized into one of six mutually exclusive communities identified using subreddit meta-data. Our results indicate that e-cigarette and vaping content on Reddit is primarily about the buying and selling of e-cigarette products. Other common topics included how to build vaping devices, e-juice, and e-cigarette advice. Network correlation analyses found that the distribution of our seven identified topics varied significantly among general e-cigarette, drugs, and research/news subreddit communities. Findings from this study add to a growing literature investigating e-cigarettes and vaping on social media and also contribute to network-level theories by linking communities on Reddit to the diffusion of various depictions of e-cigarettes and vaping.
Sustainability in Mega-Events: Beyond Qatar 2022

Hosting a mega-event such as the 2022 FIFA Men’s World Cup is a defining moment for Qatar, a country that is in transition, small in size and population, and rich in natural gas reserves. It is a unique opportunity to host a universal event and leave a sustainable positive legacy for the country. However, the preparation, execution, and after-effects of such events are challenging initiatives with significant long-term impacts on the economy, society, and environment in the hosting country and nearby region. This study addresses the intersection between mega sports events and sustainability, to systematically compare and learn from past mega-events and apply that to the case of the Qatar 2022 World Cup. The Qatari bid proposed a new FIFA Men’s World Cup (WC) spatial compact model around just one city area and the goal of achieving the first carbon-neutral WC. Herein, the challenges, opportunities, and progress in this scenario are evaluated accordingly, showing that local organizers are applying green technologies, urban development concepts, and strongly upholding the idea of legacies based on the Qatar National Vision 2030, which envisions sustainable development of the country. However, additional work is still needed to reduce environmental impacts and on several reported social issues.
Correlation between biofilm formation and carbapenem resistance among clinical isolates of Klebsiella pneumoniae

Background Klebsiella pneumoniae is a Gram-negative enteric bacterium that causes nosocomial infections; this bacterium has survived from harsh condition using biofilm formation in hospital equipment and cause severe infection. In the other hand, the emergence and extension of carbapenem resistance burden among K. pneumonia producing biofilm is the current concern of public health services. There are controversial findings about this subject. The aim of this study was to evaluate the correlation between biofilm formation and resistance to carbapenem among clinical isolates of K. pneumoniae. Methods A total of 160 K. pneumoniae isolates were collected from various infections of hospitalized patients. The Carba NP test and molecular methods were used for detection of carbapenem resistance isolates of K. pneumonia. Subsequently, the ability for biofilm production was performed from all isolates. Finally, Correlation of biofilm formation among carbapenem resistant isolates was calculated using χ2 and Fisher's exact tests. Results Among K. pneumoniae isolates 42.5% have carbapenemase activity by Carba NP test, while carbapenemase genes were detected in 35.6% of isolates in amplification assay. Moreover, there are 52.5% (n= 84) of all isolates were formed a strong biofilm, while 38.1% (n= 61) and 9.3% (n= 15) of isolates were middle and weak biofilm producer, respectively. Among carbapenem resistant cases (n= 68), there are 77.9% (n= 53) and 22% (n= 15) of isolates were reported as strong and middle biofilm producer, respectively. We see a significant correlation was seen between biofilm formation ability and carbapenem resistant isolates (p-value < 0.00001). Conclusion The increase of carbapenem resistance burden in biofilm producing isolates of K. pneumoniae is considered as serious alert and the basic measures to combat this phenomenon is imperative.
Neuropilin-1 Expression on CD4 T Cells Is Atherogenic and Facilitates T Cell Migration to the Aorta in Atherosclerosis

Key Points Western diet feeding increases Nrp1 on Foxp3− CD4 T cells in ApoE−/− mice. Nrp1+Foxp3− CD4 T cells are highly proliferative and atherogenic. Nrp1+Foxp3− CD4 T cells preferentially migrate to the aorta and PaLN. Neuropilin 1 (Nrp1) is a type I transmembrane protein that plays important roles in axonal guidance, neuronal development, and angiogenesis. Nrp1 also helps migrate thymus-derived regulatory T cells to vascular endothelial growth factor (VEGF)-producing tumors. However, little is known about the role of Nrp1 on CD4 T cells in atherosclerosis. In ApoE−/− mice fed a Western diet for 15 wk, we found a 2-fold increase in Nrp1+Foxp3− CD4 T cells in their spleens, periaortic lymph nodes, and aortas, compared with chow-fed mice. Nrp1+Foxp3− CD4 T cells had higher proliferation potential, expressed higher levels of the memory marker CD44, and produced more IFN-γ when compared with Nrp1− CD4 T cells. Treatment of CD4 T cells with oxLDL increased Nrp1 expression. Furthermore, atherosclerosis-susceptible mice selectively deficient for Nrp1 expression on T cells developed less atherosclerosis than their Nrp1-sufficient counterparts. Mechanistically, we found that CD4 T cells that express Nrp1 have an increased capacity to migrate to the aorta and periaortic lymph nodes compared to Nrp1− T cells, suggesting that the expression of Nrp1 facilitates the recruitment of CD4 T cells into the aorta where they can be pathogenic. Thus, we have identified a novel role of Nrp1 on CD4 T cells in atherosclerosis. These results suggest that manipulation of Nrp1 expression on T cells can affect the outcome of atherosclerosis and lower disease incidence.
Dehydrodiconiferyl alcohol from Silybum marianum (L.) Gaertn accelerates wound healing via inactivating NF‐κB pathways in macrophages

The aim of this study was to investigate the molecular mechanisms of the efficacy of lignin compound dehydrodiconiferyl alcohol (DHCA) isolated from Silybum marianum (L.) Gaertn in improving wound healing. These findings preliminarily brought to light the promising therapeutic potential of DHCA in skin wound healing.
Web-Based and mHealth Interventions for Intimate Partner Violence Victimization Prevention: A Systematic Review

Mobile health (mHealth) technologies are increasingly used across health programming including intimate partner violence (IPV) prevention to optimize screening, educational outreach, and linkages to care via telehealth. We systematically evaluated current web-based and mHealth interventions, which include web- or mobile-based delivery methods for primary, secondary, and tertiary IPV victimization prevention. We searched MEDLINE/PubMed, Embase, CINAHL, PsycINFO, Open Grey, and Google Scholar for empirical studies published 1998–2019. Studies were included if they considered empirical data, participants in adult romantic relationships, IPV as a primary or secondary outcome, and an mHealth component. The Mixed Methods Appraisal Tool was used to record critical ratings of quality among studies selected for inclusion. We assessed variation in targeted populations, types of IPV addressed, and mHealth approaches used. Of 133 studies identified for full-text review, 31 were included. Computer-based screening with or without integrated education was the most common mHealth approach (n = 8, 26%), followed by safety decision aids (n = 7, 23%). Feasibility and acceptability were found to be generally high where assessed (23% of studies, n = 7). There was limited evidence around whether mHealth interventions better addressed population needs compared to conventional interventions. mHealth tools for IPV prevention are especially acceptable in health-care settings, on mobile phone platforms, or when connecting victims to health care. Despite enthusiasm in pilot projects, evidence for efficacy compared to conventional IPV prevention approaches is limited. A major strength of mHealth IPV prevention programming is the ability to tailor interventions to individual victim needs without extensive human resource expenditure by providers.
Benefit of Practice of the Stroop Test in Young and Older Adults: Pattern of Gain and Impact of Educational Level

ABSTRACT Back-Ground/Study Context: The goal of this study was to examine how repeated practice of an inhibition test could improve performance in the test in young and older adults. In particular, we wished to explore whether the gains made during a practice program varied between age groups, and how educational level influenced practice-related gains in older adults. Thus, we tried to disentangle two hypotheses explaining the benefits of practice, namely compensation (greater gain by the lowest performers) and magnification (greater gain by the highest performers). Method: Thirty-three younger adults and 60 older adults were divided into two groups each: (1) Groups in the Practice condition had 10 sessions practicing different versions of Card C of the Stroop Test, (2) groups in the Control condition completed only the pretest and posttest. Results: Overall, results showed that the performance of both young and older adults improved more in the practice condition than in the control condition. The older adults benefited more from practice than the young adults, with earlier and more regular improvement over the 10 sessions. Moreover, the older adults with a higher educational level benefited most. Discussion: These findings seem to support both the compensation and the magnification hypotheses, depending on the variable (age or educational level).
Percutaneous 60-day peripheral nerve stimulation implant provides sustained relief of chronic pain following amputation: 12-month follow-up of a randomized, double-blind, placebo-controlled trial

Introduction Peripheral nerve stimulation (PNS) has historically been used to treat chronic pain, but generally requires implantation of a permanent system for sustained relief. A recent study found that a 60-day PNS treatment decreases post-amputation pain, and the current work investigates longer-term outcomes out to 12 months in the same cohort. Methods As previously reported, 28 traumatic lower extremity amputees with residual and/or phantom limb pain were randomized to receive 8 weeks of PNS (group 1) or 4 weeks of placebo followed by a crossover 4 weeks of PNS (group 2). Percutaneous leads were implanted under ultrasound guidance targeting the femoral and sciatic nerves. During follow-up, changes in average pain and pain interference were assessed using the Brief Pain Inventory–Short Form and comparing with baseline. Results Significantly more participants in group 1 reported ≥50% reductions in average weekly pain at 12 months (67%, 6/9) compared with group 2 at the end of the placebo period (0%, 0/14, p=0.001). Similarly, 56% (5/9) of participants in group 1 reported ≥50% reductions in pain interference at 12 months, compared with 2/13 (15%, p=0.074) in group 2 at crossover. Reductions in depression were also statistically significantly greater at 12 months in group 1 compared with group 2 at crossover. Conclusions This work suggests that percutaneous PNS delivered over a 60-day period may provide significant carry-over effects including pain relief, potentially avoiding the need for a permanently implanted system while enabling improved function in patients with chronic pain. Trial registration number NCT01996254.
FCG-ASpredictor: An Approach for the Prediction of Average Speed of Road Segments with Floating Car GPS Data

The average speed (AS) of a road segment is an important factor for predicting traffic congestion, because the accuracy of AS can directly affect the implementation of traffic management. The traffic environment, spatiotemporal information, and the dynamic interaction between these two factors impact the predictive accuracy of AS in the existing literature, and floating car data comprehensively reflect the operation of urban road vehicles. In this paper, we proposed a novel road segment AS predictive model, which is based on floating car data. First, the impact of historical AS, weather, and date attributes on AS prediction has been analyzed. Then, through spatiotemporal correlations calculation based on the data from Global Positioning System (GPS), the predictive method utilizes the recursive least squares method to fuse the historical AS with other factors (such as weather, date attributes, etc.) and adopts an extended Kalman filter algorithm to accurately predict the AS of the target segment. Finally, we applied our approach on the traffic congestion prediction on four road segments in Chengdu, China. The results showed that the proposed predictive model is highly feasible and accurate.
Context based number normalization using skip-chain conditional random fields

Verbalizing numeric text tokens is a required task for various speech-related applications, including automatic speech recognition and text-to-speech synthesis. In morphologically rich languages, such conversion involves predicting implicit morphological properties of a corresponding numeral. In this paper, we propose first-order skip-chain Conditional Random Field (CRF) models and various prepossessing techniques to leverage different contextual information. We show that our best skip-chain CRF models achieve over 80% accuracy on the set of 2000 Lithuanian sentences. Keywords—Number normalization, text normalization, conditional random field, natural language processing
The cognitive mechanisms of the power–space associations: an individual differences approach

Abstract A power–space interaction, which denotes the phenomenon that people responded faster to powerful words with up cursor keys and faster to powerless words with down cursor keys, has been repeatedly found. In the present study, we took an individual differences approach to investigate how the power–space interaction is modulated by the spatial cognition. First, we found that the amplitude of power–space interaction was relatively stable within individuals across different stimuli. And, this individual difference in power–space interaction was correlated with the individual’s spatial cognition, in such a way that participants with faster speed of mental rotation showed stronger power–space interactions. Our results shed new light on the cognitive mechanisms of the power–space associations by suggesting that spatial codes play an important role in the expression of such effect.