Miracle-dz/UniFAR-FTUs huggingface dataset:
Protter: interactive protein feature visualization and integration with experimental proteomic data

SUMMARY The ability to integrate and visualize experimental proteomic evidence in the context of rich protein feature annotations represents an unmet need of the proteomics community. Here we present Protter, a web-based tool that supports interactive protein data analysis and hypothesis generation by visualizing both annotated sequence features and experimental proteomic data in the context of protein topology. Protter supports numerous proteomic file formats and automatically integrates a variety of reference protein annotation sources, which can be readily extended via modular plug-ins. A built-in export function produces publication-quality customized protein illustrations, also for large datasets. Visualizations of surfaceome datasets show the specific utility of Protter for the integrated visual analysis of membrane proteins and peptide selection for targeted proteomics. AVAILABILITY AND IMPLEMENTATION The Protter web application is available at http://wlab.ethz.ch/protter. Source code and installation instructions are available at http://ulo.github. io/Protter/. CONTACT wbernd@ethz.ch SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Evidence of Combat in Triceratops

Background The horns and frill of Triceratops and other ceratopsids (horned dinosaurs) are interpreted variously as display structures or as weapons against conspecifics and predators. Lesions (in the form of periosteal reactive bone, healing fractures, and alleged punctures) on Triceratops skulls have been used as anecdotal support of intraspecific combat similar to that in modern horned and antlered animals. If ceratopsids with different cranial morphologies used their horns in such combat, this should be reflected in the rates of lesion occurrence across the skull. Methodology/Principal Findings We used a G-test of independence to compare incidence rates of lesions in Triceratops (which possesses two large brow horns and a smaller nasal horn) and the related ceratopsid Centrosaurus (with a large nasal horn and small brow horns), for the nasal, jugal, squamosal, and parietal bones of the skull. The two taxa differ significantly in the occurrence of lesions on the squamosal bone of the frill (P = 0.002), but not in other cranial bones (P>0.20). Conclusions/Significance This pattern is consistent with Triceratops using its horns in combat and the frill being adapted as a protective structure for this taxon. Lower pathology rates in Centrosaurus may indicate visual rather than physical use of cranial ornamentation in this genus, or a form of combat focused on the body rather than the head.
A Review of Fine-Scale Land Use and Land Cover Classification in Open-Pit Mining Areas by Remote Sensing Techniques

Over recent decades, fine-scale land use and land cover classification in open-pit mine areas (LCCMA) has become very important for understanding the influence of mining activities on the regional geo-environment, and for environmental impact assessment procedure. This research reviews advances in fine-scale LCCMA from the following aspects. Firstly, it analyzes and proposes classification thematic resolution for LCCMA. Secondly, remote sensing data sources, features, feature selection methods, and classification algorithms for LCCMA are summarized. Thirdly, three major factors that affect LCCMA are discussed: significant three-dimensional terrain features, strong LCCMA feature variability, and homogeneity of spectral-spatial features. Correspondingly, three key scientific issues that limit the accuracy of LCCMA are presented. Finally, several future research directions are discussed: (1) unitization of new sensors, particularly those with stereo survey ability; (2) procurement of sensitive features by new sensors and combinations of sensitive features using novel feature selection methods; (3) development of robust and self-adjusted classification algorithms, such as ensemble learning and deep learning for LCCMA; and (4) application of fine-scale mining information for regularity and management of mines.
Multidecadal accumulation of anthropogenic and remineralized dissolved inorganic carbon along the Extended Ellett Line in the northeast Atlantic Ocean

Marine carbonate chemistry measurements have been carried out annually since 2009 during UK research cruises along the Extended Ellett Line (EEL), a hydrographic transect in the northeast Atlantic Ocean. The EEL intersects several water masses that are key to the global thermohaline circulation, and therefore the cruises sample a region in which it is critical to monitor secular physical and biogeochemical changes. We have combined results from these EEL cruises with existing quality‐controlled observational data syntheses to produce a hydrographic time series for the EEL from 1981 to 2013. This reveals multidecadal increases in dissolved inorganic carbon (DIC) throughout the water column, with a near‐surface maximum rate of 1.80 ± 0.45 µmol kg−1 yr−1. Anthropogenic CO2 accumulation was assessed, using simultaneous changes in apparent oxygen utilization (AOU) and total alkalinity (TA) as proxies for the biogeochemical processes that influence DIC. The stable carbon isotope composition of DIC (δ13CDIC) was also determined and used as an independent test of our method. We calculated a volume‐integrated anthropogenic CO2 accumulation rate of 2.8 ± 0.4 mg C m−3 yr−1 along the EEL, which is about double the global mean. The anthropogenic CO2 component accounts for only 31 ± 6% of the total DIC increase. The remainder is derived from increased organic matter remineralization, which we attribute to the lateral redistribution of water masses that accompanies subpolar gyre contraction. Output from a general circulation ecosystem model demonstrates that spatiotemporal heterogeneity in the observations has not significantly biased our multidecadal rate of change calculations and indicates that the EEL observations have been tracking distal changes in the surrounding North Atlantic and Nordic Seas.
Feasibility of Ecological Momentary Assessment of Daily Sexting and Substance Use Among Young Adult African American Gay and Bisexual Men: A Pilot Study

Background Recent evidence suggests that sexualized text communication (“sexting”) is associated with substance use and sexual risk behaviors among young adults, yet little is known about this relationship among young adult African American gay and bisexual men, a population disproportionately impacted by HIV in the United States. Rapid advances in mobile phone technology indicate a clear need for research using mobile health (mHealth) methods such as ecological momentary assessment (EMA) to serve as a viable counterpart to retrospective evaluation methods by using real-time data collection to assess sexting and substance use among this population. Objective The objective of this pilot study was to (1) describe the EMA study design and protocol, (2) characterize the study population, and (3) assess the feasibility of a random prompt text message-based thrice-daily EMA over 14 days, as a means of prospectively studying sexting, marijuana, and alcohol use among a sample of young adult African American gay and bisexual men ages 21 to 25. Methods Participants were recruited through flyers and snowball sampling during spring and summer 2015 at a community-based HIV/AIDS prevention, care, and support organization in Washington, DC. Eligible participants were enrolled in a one-time in-person study visit that consisted of informed written consent to participate in the study, a self-administered survey, a semi-structured interview, and enrollment and training in EMA data collection. Commencing the day after the study visit, a random prompt survey was texted to participants on their personal mobile phones 3 times a day over a 14-day data collection period assessing mood, texts sent, texts received, sexts sent, sexts received, marijuana want, marijuana use, and alcohol use. Results EMA feasibility was tested with 25 self-identified African American gay (n=16) and bisexual (n=9) men (mean age of 23.48 years, SD 1.5). Each random prompt survey had 8 questions with responses including yes/no and Likert scale options. There were 104 total days of EMA observation, and the retention rate was 72% (18 out of 25 participants). Participants responded to the random prompt surveys with a 57.3% compliance rate providing a total of 544 completed surveys out of 949 surveys. The overall mean response time to complete a survey was 6.1 minutes. There were significant positive associations between EMA texts sent and received questions (ρ 0.84, P<.001) as well as sexts sent and received queries (ρ 0.72, P<.001). Conclusions The use of an EMA protocol has the potential to be a very useful research tool for understanding episodic behaviors such as sexting and substance use in this relatively understudied and underserved population, and has implications for practice. Additional research is needed on how to maximize survey compliance.
Effectiveness of school‐based humanistic counselling for psychological distress in young people: Pilot randomized controlled trial with follow‐up in an ethnically diverse sample

OBJECTIVES The aim of this study was to pilot a test of the effectiveness of school-based humanistic counselling (SBHC) in an ethnically diverse group of young people (aged 11-18 years old), with follow-up assessments at 6 and 9 months. DESIGN Pilot randomized controlled trial, using linear-mixed effect modelling and intention-to-treat analysis to compare changes in levels of psychological distress for participants in SBHC against usual care (UC). TRIAL REGISTRATION ISRCTN44253140. METHODS In total, 64 young people were randomized to either SBHC or UC. Participants were aged between 11 and 18 (M = 14.2, SD = 1.8), with 78.1% of a non-white ethnicity. The primary outcome was psychological distress at 6 weeks (mid-therapy), 12 weeks (end of therapy), 6-month follow-up and 9-month follow-up. Secondary measures included emotional symptoms, self-esteem and attainment of personal goals. RESULTS Recruitment and retention rates for the study were acceptable. Participants in the SBHC condition, as compared with participants in the UC condition, showed greater reductions in psychological distress and emotional symptoms, and greater improvements in self-esteem, over time. However, at follow-up, only emotional symptoms showed significant differences across groups. CONCLUSIONS The study adds to the pool of evidence suggesting that SBHC can be tested and that it brings about short-term reductions in psychological and emotional distress in young people, across ethnicities. However, there is no evidence of longer-term effects. PRACTITIONER POINTS School-based humanistic counselling can be an effective means of reducing the psychological distress experienced by young people with emotional symptoms in the short term. The short-term effectiveness of school-based humanistic counselling is not limited to young people of a White ethnicity. There is no evidence that school-based humanistic counselling has effects beyond the end of therapy.
A cationic, C-terminal patch and structural rearrangements in Ebola virus matrix VP40 protein control its interactions with phosphatidylserine

Ebola virus (EBOV) is a filamentous lipid-enveloped virus that causes hemorrhagic fever with a high fatality rate. Viral protein 40 (VP40) is the major EBOV matrix protein and regulates viral budding from the plasma membrane. VP40 is a transformer/morpheein that can structurally rearrange its native homodimer into either a hexameric filament that facilitates viral budding or an RNA-binding octameric ring that regulates viral transcription. VP40 associates with plasma-membrane lipids such as phosphatidylserine (PS), and this association is critical to budding from the host cell. However, it is poorly understood how different VP40 structures interact with PS, what essential residues are involved in this association, and whether VP40 has true selectivity for PS among different glycerophospholipid headgroups. In this study, we used lipid-binding assays, MD simulations, and cellular imaging to investigate the molecular basis of VP40–PS interactions and to determine whether different VP40 structures (i.e. monomer, dimer, and octamer) can interact with PS-containing membranes. Results from quantitative analysis indicated that VP40 associates with PS vesicles via a cationic patch in the C-terminal domain (Lys224, 225 and Lys274, 275). Substitutions of these residues with alanine reduced PS-vesicle binding by >40-fold and abrogated VP40 localization to the plasma membrane. Dimeric VP40 had 2-fold greater affinity for PS-containing membranes than the monomer, whereas binding of the VP40 octameric ring was reduced by nearly 10-fold. Taken together, these results suggest the different VP40 structures known to form in the viral life cycle harbor different affinities for PS-containing membranes.
A Robust Oscillator for Embedded System without External Crystal

The robust voltage-controlled oscillator is presented by u sing the constant current reference and the ring oscillator for the embedded system application. The constant current reference generates the constant current for the succeeding ring oscillator to produce a stable 4MHz oscillation frequency. The proposed VCO circuit was fabricated in a 0.35 μm CMOS technology and worked with a supply voltage of 3.3 V. The chip area of the VCO was 150 μm� 130 μm. According to measured results, the oscillation frequency drift of the proposed VCO was 986 ppm/ � C over a temperature range of -25 � C to 100 � C. The phase noise of -62.29 dBc/Hz was obtained at 1 MHz offset from the carrier. Moreover, total current consumption of the entire VCO was 234.72 μA. Therefore, the proposed VCO is suitable for integration into the embedded system.
A Meta-Analysis of the Effects of Abdominoplasty Modifications on the Incidence of Postoperative Seroma.

Background Seroma is the most common complication of abdominoplasty. Certain modifications to abdominoplasty may reduce the risk of seroma. Objectives The authors evaluated the incidence of seroma for 3 abdominoplasty techniques: preservation of Scarpa's fascia, placement of progressive tension (or quilting) sutures, and application of fibrin glue. Methods In this systematic review and meta-analysis, the Cochrane Library, MEDLINE, Embase, and the International Clinical Trials Registry Platform (World Health Organization) were searched to identify studies of patients who underwent abdominoplasty with seroma as a potential "outcome. " RevMan 5.3 was utilized for data management, statistical analyses, and graph preparation. Results Fifteen studies (1824 total patients) met the criteria for inclusion in this review. The overall risk of bias was high, mainly owing to the nonrandomized nature of most studies. Abdominoplasty with preservation of Scarpa's fascia or placement of progressive tension sutures was associated with a significantly reduced incidence of seroma compared with that of standard abdominoplasty (P < 0.0001 and P < 0.0002, respectively). Abdominoplasty with application of fibrin glue was similar to standard abdominoplasty in terms of seroma development. Conclusions Placement of progressive tension sutures or preservation of Scarpa's fascia during abdominoplasty may reduce the likelihood of postoperative seroma. Application of fibrin glue has no impact on seroma formation. Level of Evidence 2.
Screening for frailty in older emergency department patients: the utility of the Survey of Health, Ageing and Retirement in Europe Frailty Instrument

Background Greater numbers of older patients are accessing hospital services. Specialist geriatric input at presentation may improve outcomes for at-risk patients. The Survey of Health, Ageing and Retirement in Europe Frailty Instrument (SHARE-FI) frailty measure, developed for use in the community, has also been used in the emergency department (ED). Aim To measure frailty, review its prevalence in older patients presenting to ED and compare characteristics and outcomes of frail patients with their non-frail counterparts. Design Patient characteristics were recorded using symphony® electronic data systems. SHARE-FI assessed frailty. Cognition, delirium and 6 and 12 months outcomes were reviewed. Methods A prospective cohort study was completed of those aged ≥70 presenting to ED over 24 h, 7 days a week. Results Almost half of 198 participants (46.7%, 93/198) were classified as frail, but this was not associated with a significant difference in mortality rates (OR 0.89, 95% CI 0.58-1.38, P = 0.614) or being alive at home at 12 months (OR 1.07, 95% CI 0.72-1.57, P = 0.745). Older patients were more likely to die (OR 2.34, 95% CI 1.30-4.21, P = 0.004) and less likely to be alive at home at 12 months (OR 0.49, 95% CI 0.23-0.83, P = 0.009). Patients with dementia (OR 0.24, P = 0.005) and on ≥5 medications (OR 0.37, 95% CI 0.16-0.87, P = 0.022) had a lower likelihood of being alive at home at 12 months. Conclusions Almost half of the sample cohort was frail. Older age was a better predictor of adverse outcomes than frailty as categorized by the SHARE-FI. SHARE-FI has limited predictability when used as a frailty screening instrument in the ED.
A Closed-Loop Model of Operator Visual Attention, Situation Awareness, and Performance Across Automation Mode Transitions

Objective: This article describes a closed-loop, integrated human–vehicle model designed to help understand the underlying cognitive processes that influenced changes in subject visual attention, mental workload, and situation awareness across control mode transitions in a simulated human-in-the-loop lunar landing experiment. Background: Control mode transitions from autopilot to manual flight may cause total attentional demands to exceed operator capacity. Attentional resources must be reallocated and reprioritized, which can increase the average uncertainty in the operator’s estimates of low-priority system states. We define this increase in uncertainty as a reduction in situation awareness. Method: We present a model built upon the optimal control model for state estimation, the crossover model for manual control, and the SEEV (salience, effort, expectancy, value) model for visual attention. We modify the SEEV attention executive to direct visual attention based, in part, on the uncertainty in the operator’s estimates of system states. Results: The model was validated using the simulated lunar landing experimental data, demonstrating an average difference in the percentage of attention ≤3.6% for all simulator instruments. The model’s predictions of mental workload and situation awareness, measured by task performance and system state uncertainty, also mimicked the experimental data. Conclusion: Our model supports the hypothesis that visual attention is influenced by the uncertainty in system state estimates. Application: Conceptualizing situation awareness around the metric of system state uncertainty is a valuable way for system designers to understand and predict how reallocations in the operator’s visual attention during control mode transitions can produce reallocations in situation awareness of certain states.
Racial and Ethnic Disparities in the Incidence of Pediatric Extracranial Embryonal Tumors

Background Few studies have comparatively assessed differences in the incidence of childhood cancer by race and ethnicity that could inform etiologic research. We aimed to identify disparities in the incidence of pediatric extracranial embryonal tumors by race and ethnicity in the United States using a population-based cancer registry. Methods Cases of extracranial embryonal tumors among children age 0 to 19 years diagnosed between 2000 and 2010 were retrieved from the Surveillance, Epidemiology, and End Results Program 18 (n = 8188). Age-standardized incidence rates and incidence rate ratios (IRRs) were obtained by race/ethnicity. Whites were the reference group. The percentage of families living below the poverty line by county was used to stratify by socioeconomic status (SES). Results All minority groups had a lower incidence of neuroblastoma (Hispanics: IRR = 0.53, 95% confidence interval [CI] = 0.47 to 0.59; blacks: IRR = 0.70, 95% CI = 0.61 to 0.81; Native-Hawaiian/Asian-Pacific-Islander (API): IRR = 0.56, 95% CI = 0.46 to 0.67; and American Indian/Alaska Native (AI/AN): IRR = 0.28, 95% CI = 0.15 to 0.48) while Hispanics had a higher incidence of retinoblastoma (IRR = 1.26, 95% CI = 1.07 to 1.48). Incidence of nephroblastoma was lower among Hispanics (IRR = 0.80, 95% CI = 0.71 to 0.91) and API (IRR = 0.43, 95% CI = 0.33 to 0.56) while equivalent for blacks. Similarly, incidence of rhabdomyosarcoma was low among Hispanics (IRR = 0.85, 95% CI = 0.74 to 0.98) and API (IRR = 0.61, 95% CI = 0.47 to 0.79) while equivalent for blacks. However, incidence of hepatoblastoma was low among blacks (IRR = 0.44, 95% CI = 0.28 to 0.68) while equivalent for Hispanics and API. Incidence of germ cell tumors was higher among Hispanics (IRR = 1.30, 95% CI = 1.19 to 1.42) and lower among blacks (IRR = 0.52, 95% CI = 0.44 to 0.61) and API (IRR = 0.79, 95% CI = 0.67 to 0.93). No effect modification by SES was observed. Conclusions Unique incidence patterns of childhood extracranial embryonal tumors exist by race and ethnicity in the United States. The interplay between race/ethnicity and genetics, epigenetics, and gene-environment interactions in the causation of these cancers deserves further investigation.
Effect of early and intensive rehabilitation in acute stroke patients: retrospective pre-/post-comparison in Japanese hospital

Abstract Purpose: There is little high-quality or large-scale clinical research focusing on the effect of early and intensive rehabilitation in Eastern countries. This study aimed to determine whether an early and intensive rehabilitation program in a Japanese hospital affects functional outcomes of acute stroke patients. Methods: In total, 1588 stroke patients were investigated. A maintained database of all hospitalized acute stroke patients admitted to our facility over two consecutive 2-year periods was reviewed. We relaunched of a new rehabilitation program to be earlier and more intensive at the midpoint of this two periods. The functional outcomes of the patients in the first 2-year period and the subsequent 2-year period were compared. Results: The total time of rehabilitation exercises per day was significantly increased from the first period to the second period. The number of patients who started rehabilitation within 24 h after admission was significantly increased in the patients admitted during the second period compared with those admitted during the first period. The Functional Independence Measure (FIM) efficiency was significantly higher in the patients admitted during the second period than in those admitted during the first period. Conclusions: An early and intensive rehabilitation program in a Japanese hospital affects functional outcomes of acute stroke patients. Implications for Rehabilitation Early and intensive rehabilitation for the stroke patients is an effective means of improving FIM score. Early and intensive rehabilitation affects the improvement of FIM efficiency without increasing adverse events.