Miracle-dz/UniFAR-FTUs huggingface dataset:
eFESTA: Ensemble Feature Exploration with Surface Density Estimates

We propose <italic>surface density estimate</italic> (SDE) to model the spatial distribution of surface features—isosurfaces, ridge surfaces, and streamsurfaces—in 3D ensemble simulation data. The inputs of SDE computation are surface features represented as polygon meshes, and no field datasets are required (e.g., scalar fields or vector fields). The SDE is defined as the kernel density estimate of the infinite set of points on the input surfaces and is approximated by accumulating the surface densities of triangular patches. We also propose an algorithm to guide the selection of a proper kernel bandwidth for SDE computation. An <underline>e</underline>nsemble <underline>F</underline>eature <underline>E</underline>xploration method based on <underline>S</underline>urface densi<underline>T</underline>y Estim<underline>A</underline>tes (<italic>e</italic>FESTA) is then proposed to extract and visualize the major trends of ensemble surface features. For an ensemble of surface features, each surface is first transformed into a density field based on its contribution to the SDE, and the resulting density fields are organized into a hierarchical representation based on the pairwise distances between them. The hierarchical representation is then used to guide visual exploration of the density fields as well as the underlying surface features. We demonstrate the application of our method using isosurface in ensemble scalar fields, Lagrangian coherent structures in uncertain unsteady flows, and streamsurfaces in ensemble fluid flows.
Machine‐learning‐derived sleep–wake staging from around‐the‐ear electroencephalogram outperforms manual scoring and actigraphy

Quantification of sleep is important for the diagnosis of sleep disorders and sleep research. However, the only widely accepted method to obtain sleep staging is by visual analysis of polysomnography (PSG), which is expensive and time consuming. Here, we investigate automated sleep scoring based on a low‐cost, mobile electroencephalogram (EEG) platform consisting of a lightweight EEG amplifier combined with flex‐printed cEEGrid electrodes placed around the ear, which can be implemented as a fully self‐applicable sleep system. However, cEEGrid signals have different amplitude characteristics to normal scalp PSG signals, which might be challenging for visual scoring. Therefore, this study evaluates the potential of automatic scoring of cEEGrid signals using a machine learning classifier (“random forests”) and compares its performance with manual scoring of standard PSG. In addition, the automatic scoring of cEEGrid signals is compared with manual annotation of the cEEGrid recording and with simultaneous actigraphy. Acceptable recordings were obtained in 15 healthy volunteers (aged 35 ± 14.3 years) during an extended nocturnal sleep opportunity, which induced disrupted sleep with a large inter‐individual variation in sleep parameters. The results demonstrate that machine‐learning‐based scoring of around‐the‐ear EEG outperforms actigraphy with respect to sleep onset and total sleep time assessments. The automated scoring outperforms human scoring of cEEGrid by standard criteria. The accuracy of machine‐learning‐based automated scoring of cEEGrid sleep recordings compared with manual scoring of standard PSG was satisfactory. The findings show that cEEGrid recordings combined with machine‐learning‐based scoring holds promise for large‐scale sleep studies.
Comment on ‘Orthogonal lipid sensors identify transbilayer asymmetry of plasma membrane cholesterol’

The plasma membrane in mammalian cells is rich in cholesterol, but how the cholesterol is partitioned between the two leaflets of the plasma membrane remains a matter of debate. Recently, Liu et al. used domain 4 (D4) of perfringolysin O as a cholesterol sensor to argue that cholesterol is mostly in the exofacial leaflet (Liu et al., 2017). This conclusion was made by interpreting D4 binding in live cells using in vitro calibrations with liposomes. However, liposomes may be unfaithful in mimicking the plasma membrane, as we demonstrate here. Also, D4 binding is highly sensitive to the presence of cytosolic proteins. In addition, we find that a D4 variant, which requires >35 mol% cholesterol to bind to liposomes in vitro, does in fact bind to the cytoplasmic leaflet of the plasma membrane in a cholesterol-dependent manner. Thus, we believe, based on the current evidence, that it is unlikely that there is a significantly higher proportion of cholesterol in the exofacial leaflet of the plasma membrane compared to the cytosolic leaflet.
Structure-based design of a quadrivalent fusion glycoprotein vaccine for human parainfluenza virus types 1–4

Significance In the United States alone, over 20,000 children are hospitalized each year from parainfluenza virus (PIV)-related illness. By age 10, most children are seropositive to several PIVs, including PIV1 and PIV2, which cause croup, and PIV3, which causes severe lower-respiratory infections. Here we assess whether the prefusion conformation of the F glycoproteins from PIV types 1–4 could induce potent neutralizing responses. We engineered mutations in the F glycoprotein that stabilized its prefusion conformation and immunized mice and nonhuman primates. The prefusion-stabilized PIV F immunogens elicited significantly higher neutralizing titers than the same F immunogens in the postfusion state, both individually and as a quadrivalent PIV1–4 F vaccine, indicating these prefusion-stabilized PIV F glycoproteins to be promising vaccine candidates. Parainfluenza virus types 1–4 (PIV1–4) are highly infectious human pathogens, of which PIV3 is most commonly responsible for severe respiratory illness in newborns, elderly, and immunocompromised individuals. To obtain a vaccine effective against all four PIV types, we engineered mutations in each of the four PIV fusion (F) glycoproteins to stabilize their metastable prefusion states, as such stabilization had previously enabled the elicitation of high-titer neutralizing antibodies against the related respiratory syncytial virus. A cryoelectron microscopy structure of an engineered PIV3 F prefusion-stabilized trimer, bound to the prefusion-specific antibody PIA174, revealed atomic-level details for how introduced mutations improved stability as well as how a single PIA174 antibody recognized the trimeric apex of prefusion PIV3 F. Nine combinations of six newly identified disulfides and two cavity-filling mutations stabilized the prefusion PIV3 F immunogens and induced 200- to 500-fold higher neutralizing titers in mice than were elicited by PIV3 F in the postfusion conformation. For PIV1, PIV2, and PIV4, we also obtained stabilized prefusion Fs, for which prefusion versus postfusion titers were 2- to 20-fold higher. Elicited murine responses were PIV type-specific, with little cross-neutralization of other PIVs. In nonhuman primates (NHPs), quadrivalent immunization with prefusion-stabilized Fs from PIV1–4 consistently induced potent neutralizing responses against all four PIVs. For PIV3, the average elicited NHP titer from the quadrivalent immunization was more than fivefold higher than any titer observed in a cohort of over 100 human adults, highlighting the ability of a prefusion-stabilized immunogen to elicit especially potent neutralization.
Entrectinib and other ALK/TRK inhibitors for the treatment of neuroblastoma

RTK plays important roles in many cellular signaling processes involved in cancer growth and development. ALK, TRKA, TRKB, TRKC, and ROS1 are RTKs involved in several canonical pathways related to oncogenesis. These proteins can be genetically altered in malignancies, leading to receptor activation and constitutive signaling through their respective downstream pathways. Neuroblastoma (NB) is the most common extracranial solid tumor in childhood, and despite intensive therapy, there is a high mortality rate in cases with a high-risk disease. Alterations of ALK and differential expression of TRK proteins are reported in a proportion of NB. Several inhibitors of ALK or TRKA/B/C have been evaluated both preclinically and clinically in the treatment of NB. These agents have had variable success and are not routinely used in the treatment of NB. Entrectinib (RXDX-101) is a pan-ALK, TRKA, TRKB, TRKC, and ROS1 inhibitor with activity against tumors with ALK, NTRK1, NTRK2, NTRK3, and ROS1 alterations in Phase I clinical trials in adults. Entrectinib’s activity against both ALK and TRK proteins suggests a possible role in NB treatment, and it is currently under investigation in both pediatric and adult oncology patients.
Modeling and Performance of Uplink Cache-Enabled Massive MIMO Heterogeneous Networks

A significant burden on wireless networks is brought by the uploading of user-generated contents to the Internet by means of applications such as social media. To cope with this mobile data tsunami, we develop a novel multiple-input multiple-output (MIMO) network architecture with randomly located base stations (BSs) a large number of antennas employing cache-enabled uplink transmission. In particular, we formulate a scenario, where the users upload their content to their strongest BSs, which are Poisson point process distributed. In addition, the BSs, exploiting the benefits of massive MIMO, upload their contents to the core network by means of a finite-rate backhaul. After proposing the caching policies, where we propose the modified von Mises distribution as the popularity distribution function, we derive the outage probability and the average delivery rate by taking advantage of tools from the deterministic equivalent and stochastic geometry analyses. Numerical results investigate the realistic performance gains of the proposed heterogeneous cache-enabled uplink on the network in terms of cardinal operating parameters. For example, insights regarding the BSs storage size are exposed. Moreover, the impacts of the key parameters such as the file popularity distribution and the target bitrate are investigated. Specifically, the outage probability decreases if the storage size is increased, while the average delivery rate increases. In addition, the concentration parameter, defining the number of files stored at the intermediate nodes (popularity), affects the proposed metrics directly. Furthermore, a higher target rate results in higher outage because fewer users obey this constraint. Also, we demonstrate that a denser network decreases the outage and increases the delivery rate. Hence, the introduction of caching at the uplink of the system design ameliorates the network performance.
Muscular strength and function after total hip arthroplasty performed with three different surgical approaches: one-year follow-up study

Background: Surgical approach influences short-term muscular strength, and leg-strength asymmetry has been demonstrated after total hip arthroplasty (THA). We evaluated muscular strength, physical function and patient-reported outcome measures (PROMs) up to 12 months postoperatively, in patients operated on using 3 different surgical approaches. Methods: 60 patients scheduled for primary THA were allocated to the direct lateral (DLA), posterior (PA) or anterior (AA) approach. The following parameters were evaluated: leg press and abduction strength, pain, 6-minute walking test, Harris Hip Score and Hip disability and Osteoarthritis Outcome Score - Physical Function Shortform (HOOS-PS). Results: Abduction strength in the DLA group was significantly more reduced than the PA and AA groups 12 months postoperatively (p < 0.001). A significant interleg difference in abduction (p < 0.01) and leg press (p < 0.03) persisted in all groups up to 6 months, and up to 12 months in the DLA (p < 0.05). In the AA group, interleg difference in leg press was present up to 12 months (p = 0.01). Pain scores were higher in the DLA than the AA group at 6 months (p = 0.01). Patients in the PA group had better HOOS-PS score than those in the DLA group 3 months postoperatively (p = 0.02). No intergroup differences in pain or PROMs were found 12 months postoperatively. Conclusion: Patients operated via the DLA had reduced muscular strength, HOOS-PS scores and higher pain scores than those who underwent PA and AA type surgery. The non-operated leg was significantly stronger than the operated leg in all groups 6 months postoperatively and this persisted up to 12 months postoperatively for the DLA and AA groups. Clinical Trial Protocol number: ClinicalTrials.gov (NCT01506024).
The Norwegian Occupational Balance Questionnaire (OBQ11-N) – development and pilot study

Abstract Background: The concept occupational balance has been linked with health and well-being, and it is therefore viewed as an important concept for occupational therapy practice, theory and research. To operationalize and measure occupational balance, the Occupational Balance Questionnaire (OBQ) was developed in Sweden. To date, no Norwegian translations of the OBQ exists. Aim: To describe the process of developing a Norwegian version of the 11-items Occupational Balance Questionnaire (OBQ11-N) and to evaluate its feasibility and face validity. Methods: The development process followed a predetermined series of steps, including forward and back translation and cognitive interviews with a pilot sample. Results: The pilot study sample (n = 8) varied with respect to age, gender and education level. There was high level of agreement between the participants with regard to their understanding of the content of the items. Three of the items were slightly modified in terms of words and phrasing. Conclusion: The OBQ11-N was developed according to established translation guidelines and appears to be feasible and have good face validity. Significance: The OBQ11-N may prove useful for assessing occupational balance and associated factors in Norwegian population groups. However, more research is needed to establish the Norwegian version of the questionnaire as psychometrically valid.
Upregulation of Helicoverpa armigera core RNA interference genes by bacterial infections and its effect on the insect–bacteria interaction

RNA interference (RNAi) is an extremely conserved defence mechanism. The antiviral role of the RNAi pathway in insects is well documented; however, the relevance of this pathway in other aspects of insect immunity is largely unknown. In this study, we questioned whether RNAi has any function during insect–bacteria interactions. For this, we assessed induction of the RNAi pathway in response to bacterial infections by monitoring the expression of dicer1/argonaute1 and dicer2/argonaute2, which are important genes in the microRNA and short interfering RNA sub‐pathways respectively. Bacterial cells of Bacillus thuringiensis and Serratia marcescens were injected into the haemocoel of fifth‐instar larvae of Helicoverpa armigera, whereas double‐distilled water was injected into control insects. Expression levels of the RNAi‐related genes increased in the bacteria‐injected larvae compared with controls. Transcript knockdown of dicer1 reduced the replication of B. thuringiensis; as a consequence, larval mortality decreased compared with the control. However, replication of S. marcescens increased following dicer1 silencing, which led to higher rates of larval mortality when compared with the control. RNAi of dicer2 promoted replication of both bacteria in the larvae and also enhanced larval mortality. Therefore, dicer1 and dicer2 affected larval survival and the replication rates of the pathogenic bacteria, suggesting their roles in the interactions.
Household overcrowding and psychological distress among Nunavik Inuit adolescents: a longitudinal study

ABSTRACT About half of Nunavik Inuit live in overcrowded households compared to very few Canadians from the general population. Living in overcrowded households is associated with greater risks of suffering from mental health problems for Canadian adolescents. The present work aims at studying prospectively the hypothesised relationship between household overcrowding at childhood and psychological distress during adolescence among Nunavik Inuit, as well as the hypothesised relationship between these phenomena when they are both measure at adolescence. Recruited as part of the Nunavik Child Development Study, 220 participants were met at 11 years old in average and then when they were 18 years old in average. Household overcrowding was assessed using the people per room ratio. Psychological distress symptoms were operationalised at adolescence using depressive symptoms and suicidal thoughts. The results did not show that childhood household crowding had a long-term effect on psychological distress. An absence of moderation by sex of the association was also found in the present study. Despite those results, household crowding could be a risk factor only when in interaction with other elements related with poverty or housing or could be experienced as a difficulty for adolescents on other aspects than depressive symptoms and suicidal thoughts.
The Effect Size Criterion in School Improvement Research

Moving beyond technical definitions and elaborate descriptions, it is safe to say that meaningful educational re­ forms seek to identify new and in­ novative ways to improve schools. With this common purpose in mind, educa­ tional reformers often focus their search efforts on one or more specific shared goals such as improving teach­ ing and learning, increasing the high school graduation rates, reducing school discipline problems, and ex­ tending parent involvement in school decision making. It is important to note that there is no one best way to structure all of the spe­ cific activities reformers can use to conduct a school improvement search. However, most \\Uuld agree that a pro­ ductive search requires a reform group to complete three general tasks. Put briefly, these tasks are (1) locating an alternative strategy that is likely to be more effective than the cur­ rent practice, (2) conducting a fair test that compares the effectiveness of both strategies, and (3) using the compara­ tive test results to reevaluate the belief regarding the increased effectiveness of the alternative strategy. When the outcome measure used in a school improvement search is a con­ tinuous variable (means or percents and their standard deviations can be determined) , the traditional method used to compare the effectiveness of two different strategies is the t test for two independent samples. In this test model, the criterion used to recognize a differential effect is the presence or absence of a statistically significant difference. This article introduces an alternative method that reformers can use to com­ pare the effectiveness of two different strategies. The alternative method uses an effect size rather than a statistical significance criterion to guide deci­ sions regarding the detection of dif­ ferential effects. The intent of this article is to elab­ orate several advantages for using the effect size criterion approach . Theoretically speaking, the effect size approach is advocated by many mod­ ern behavioral science statisticians (Cohen, 1988 and Shavelson, 1988) and research design specialists (Borg, 1988 ; Borg and Gall , 1989 ; and Shaver, 1991) . Practically speaking, the effect size approach has three distinct advantages. First, it provides a straightforward way for practitioners to accurately define meaningful differences in their own terms without reference to statistical significance. Second, this alternative approach uses exactly the same basic data used in t test models. Thus, no new data are required . Third, neither analysis of data nor reporting of results depends on having an in-depth knowl­ edge of inferential statistics. Accord­ ingly, effect size findings can be understood and easily communicated by policy makers and practitioners responsible for implementing school improvement decisions. Using a single school improvement case study to focus the discussion, these advantages are elaborated in the responses to these four specific ques­ tions :
Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis

Degradome sequencing (degradome-seq) was widely used for cleavage site mapping on the microRNA (miRNA) targets. Here, the application value of degradome-seq data in tracking the miRNA processing intermediates was reported. By adopting the parameter “signal/noise” ratio, prominent degradome signals on the miRNA precursors were extracted. For the 15 species analyzed, the processing of many miRNA precursors were supported by the degradome-seq data. We found that the supporting ratio of the “high-confidence” miRNAs annotated in miRBase was much higher than that of the “low-confidence. ” For a specific species, the percentage of the miRNAs with degradome-supported processing signals was elevated by the increment of degradome sampling diversity. More interestingly, the tissue- or cell line-specific processing patterns of the miRNA precursors partially contributed to the accumulation patterns of the mature miRNAs. In this study, we also provided examples to show the value of the degradome-seq data in miRNA annotation. Based on the distribution of the processing signals, a renewed model was proposed that the stems of the miRNA precursors were diced through a “single-stranded cropping” mode, and “loop-to-base” processing was much more prevalent than previously thought. Together, our results revealed the remarkable capacity of degradome-seq in tracking miRNA processing signals.
Multi-unit Bilateral Trade

We characterise the set of dominant strategy incentive compatible (DSIC), strongly budget balanced (SBB), and ex-post individually rational (IR) mechanisms for the multi-unit bilateral trade setting. In such a setting there is a single buyer and a single seller who holds a finite number k of identical items. The mechanism has to decide how many units of the item are transferred from the seller to the buyer and how much money is transferred from the buyer to the seller. We consider two classes of valuation functions for the buyer and seller: Valuations that are increasing in the number of units in possession, and the more specific class of valuations that are increasing and submodular.Furthermore, we present some approximation results about the performance of certain such mechanisms, in terms of social welfare: For increasing submodular valuation functions, we show the existence of a deterministic 2-approximation mechanism and a randomised e/(1 − e) approximation mechanism, matching the best known bounds for the single-item setting.