Miracle-dz/UniFAR-FTUs huggingface dataset:
Calculation of confidence intervals for simulation output

This article is concerned with the calculation of confidence intervals for simulation output that is dependent on two sources of variability. One, referred to as <i>simulation variability</i>, arises from the use of random numbers in the simulation itself; and the other, referred to as <i>parameter variability</i>, arises when the input parameters are unknown and have to be estimated from observed data. Three approaches to the calculation of confidence intervals are presented--the traditional asymptotic normality theory approach, a bootstrap approach and a new method which produces a conservative approximation based on performing just two simulation runs at carefully selected parameter settings. It is demonstrated that the traditional and bootstrap approaches provide similar degrees of accuracy and that whilst the new method may sometimes be very conservative, it can be calculated in a small fraction of the computational time of the exact methods.
The birthday problem and zero-error list codes

As an attempt to bridge the gap between classical information theory and the combinatorial world of zero-error information theory, this paper studies the performance of randomly generated codebooks over discrete memoryless channels under a zero-error constraint. This study allows the application of tools from one area to the other. Furthermore, it leads to an information-theoretic formulation of the birthday problem, which is concerned with the probability that in a given population, a fixed number of people have the same birthday. Due to the lack of a closed-form expression for this probability when the distribution of birthdays is not uniform, the resulting computation is not feasible in some applications; the information-theoretic formulation, however, can be analyzed for all distributions.
GRAMMATICAL MORPHEME ACQUISITION: AN ANALYSIS OF AN EFL LEARNER'S LANGUAGE SAMPLES *

This study presents an analysis of grammatical morp heme acquisition taken from a Vietnamese English learner’s speech sample. Attempting to answer what grammatical morphemes the subject has acquired and/or needs to acquire accurately, this study analyzes the learner ’s speech sample using ‘obligatory occasion’ measure. The instruments were the audio-recording of the sample and theories on grammatical morpheme studies. The finding of this study indicates that the subject has acquired some grammatical morphemes well although not yet accurately. She needs to have more extensive practice on those grammatical morphemes.
Is it Possible to Evaluate the Contribution of Visual Information to the Process of Speech Comprehension?

We report in this paper the results of a series of comprehension tests run with the aim of investigating the contribution of visual information to the process of comprehension of conversational speech. The methodology we designed was presented in a previous work [1] in which we also showed the results of a pilot test to confirm our original hypothesis that the comprehension of conversational speech decreases passing from bimodal transmission to uni-modal transmission. In order to further investigate the contribution of visual information to the process of speech comprehension, we run a new series of comprehension tests, that consisted of the following three phases: 1. submission of the multi-modal speech signal (auditory + visual); 2. submission of the sample only in the auditory modality (i.e. without the integration of visual cues); 3. submission of the sample only in the visual modality (without the integration of auditory cues). We used as sample material a short conversation held by two male speakers, edited from an Italian TV soap opera. We tested 3 groups of 12 people with no sight and hearing pathologies and also a smaller group of 5 congenitally deaf people, that served as a kind of “control” group in the third phase. It is clear from our results that the visual cues help the subjects to understand the main topic of conversation and to remember some of the details of the conversation. Moreover they seem to play an important role for the interpretation of the emotional state of the speakers. In some cases visual cues appear to be misleading.
Harms from discharge to primary care: mixed methods analysis of incident reports

Background Discharge from hospital presents significant risks to patient safety, with up to one in five patients experiencing adverse events within 3 weeks of leaving hospital. Aim To describe the frequency and types of patient safety incidents associated with discharge from secondary to primary care, and commonly described contributory factors to identify recommendations for practice. Design and setting A mixed methods analysis of 598 patient safety incident reports in England and Wales related to ‘Discharge’ from the National Reporting and Learning System. Method Detailed data coding (with 20% double-coding), data summaries generated using descriptive statistical analysis, and thematic analysis of special-case sample of reports. Incident type, contributory factors, type, and level of harm were described, informing recommendations for future practice. Results A total of 598 eligible reports were analysed. The four main themes were: errors in discharge communication (n = 151; 54% causing harm); errors in referrals to community care (n = 136; 73% causing harm); errors in medication (n = 97; 87% causing harm); and lack of provision of care adjuncts such as dressings (n = 62; 94% causing harm). Common contributory factors were staff factors (not following referral protocols); and organisational factors (lack of clear guidelines or inefficient processes). Improvement opportunities include developing and testing electronic discharge methods with agreed minimum information requirements and unified referrals systems to community care providers; and promoting a safety culture with ‘safe discharge’ checklists, discharge coordinators, and family involvement. Conclusion Significant harm was evident due to deficits in the discharge process. Interventions in this area need to be evaluated and learning shared widely.
Macquarie University at BioASQ 5b – Query-based Summarisation Techniques for Selecting the Ideal Answers

Macquarie University’s contribution to the BioASQ challenge (Task 5b Phase B) focused on the use of query-based extractive summarisation techniques for the generation of the ideal answers. Four runs were submitted, with approaches ranging from a trivial system that selected the first n snippets, to the use of deep learning approaches under a regression framework. Our experiments and the ROUGE results of the five test batches of BioASQ indicate surprisingly good results for the trivial approach. Overall, most of our runs on the first three test batches achieved the best ROUGE-SU4 results in the challenge.
Bootstrapping an Unsupervised Approach for Classifying Agreement and Disagreement

People tend to have various opinions about topics. In discussions, they can either agree or disagree with another person. The recognition of agreement and disagreement is a useful prerequisite for many applications. It could be used by political scientists to measure how controversial political issues are, or help a company to analyze how well people like their new products. In this work, we develop an approach for recognizing agreement and disagreement. However, this is a challenging task. While keyword-based approaches are only able to cover a limited set of phrases, machine learning approaches require a large amount of training data. We therefore combine advantages of both methods by using a bootstrapping approach. With our completely unsupervised technique, we achieve an accuracy of 72.85%. Besides, we investigate the limitations of a keyword based approach and a machine learning approach in addition to comparing various sets of features.
Construct validation of the English version of Readiness for Interprofessional Learning Scale (RIPLS): Are Chinese undergraduate students ready for ‘shared learning’?

ABSTRACT Interprofessional education has been receiving attention as a result of research suggesting the benefits of interpersonal collaboration in healthcare. In Hong Kong, the implementation of the Interprofessional Team-based Learning programme provides implicit call to study the psychometric properties of Readiness for Interprofessional Learning Scale (RIPLS) to clarify if this is a valid measure when used in the Chinese undergraduate healthcare context. This study examines the psychometric properties of RIPLS involving predominantly Chinese undergraduate healthcare students in Hong Kong. Using within- and between-network approaches to construct validity, we investigated the applicability of English version of RIPLS among 469 predominantly Hong Kong Chinese students who have competence in the English language. These participants were from complementary health professional programmes: biomedical sciences, chinese medicine, medicine, nursing, and pharmacy, from two universities in Hong Kong. The within-network test results indicated that RIPLS had good internal consistency reliability. Results of the confirmatory factor analysis lend support to the overall factor structure of hypothesized four-factor solution although one item obtained non-significant factor loading. The between-network test also suggests that various subscales of RIPLS correlated systematically with theoretically relevant constructs: collective efficacy, team impact on quality of learning, and team impact on clinical reasoning ability. The RIPLS is a valid measure to estimate the Chinese undergraduate healthcare students’ readiness to engage in interprofessional learning.
Tectonometamorphic history of mid-crustal rocks at Aishihik Lake, southwest Yukon

Field mapping, petrography, thermodynamic modelling, and U-Pb (monazite and zircon) and 40Ar/39Ar geochronology reveal the tectonometamorphic history of polydeformed, amphibolite-facies rocks near Aishihik Lake, Yukon. Detrital zircon U-Pb ages suggest that these rocks are correlative to the Snowcap assemblage of the Yukon Tanana terrane. A penetrative regional foliation (S1) developed during the late Paleozoic, as S1 is cross-cut by a late Permian pluton. Permian plutons also exhibit less strain than Mississippian plutons near Aishihik Lake. The main foliation (S2) reflects west-verging, ductile shear (D2) during amphibolite facies metamorphism. Dating of Low-Y metamorphic monazite constrains the timing of D2 to 200-190 Ma. Peak T and P during D2 were 640-650 °C and ~7 kbar, respectively. High-Y monazite ages date regional decompression at ca. 188 Ma. 40Ar/39Ar thermochronology results indicate regional cooling through muscovite closure at ca. 175 Ma, whereas ca. 126 Ma biotite may reflect cooling following east-verging Jura-Cretaceous deformation (D3).
Emergence of Micronuclei and Their Effects on the Fate of Cells under Replication Stress

The presence of micronuclei in mammalian cells is related to several mutagenetic stresses. In order to understand how micronuclei emerge, behave in cells, and affect cell fate, we performed extensive time-lapse microscopy of HeLa H2B-GFP cells in the presence of hydroxyurea at low concentration. Micronuclei formed after mitosis from lagging chromatids or chromatin bridges between anaphase chromosomes and were stably maintained in the cells for up to one cell cycle. Nuclear buds also formed from chromatin bridges or during interphase. If the micronuclei-bearing cells entered mitosis, they either produced daughter cells without micronuclei or, more frequently, produced cells with additional micronuclei. Low concentrations of hydroxyurea efficiently induced multipolar mitosis, which generated lagging chromatids or chromatin bridges, and also generated multinuclear cells that were tightly linked to apoptosis. We found that the presence of micronuclei is related to apoptosis but not to multipolar mitosis. Furthermore, the structural heterogeneity among micronuclei, with respect to chromatin condensation or the presence of lamin B, derived from the mechanism of micronuclei formation. Our study reinforces the notion that micronucleation has important implications in the genomic plasticity of tumor cells.
Agonist of growth hormone-releasing hormone reduces pneumolysin-induced pulmonary permeability edema

Aggressive treatment with antibiotics in patients infected with Streptococcus pneumoniae induces release of the bacterial virulence factor pneumolysin (PLY). Days after lungs are sterile, this pore-forming toxin can still induce pulmonary permeability edema in patients, characterized by alveolar/capillary barrier dysfunction and impaired alveolar liquid clearance (ALC). ALC is mainly regulated through Na+ transport by the apically expressed epithelial sodium channel (ENaC) and the basolaterally expressed Na+/K+-ATPase in type II alveolar epithelial cells. Because no standard treatment is currently available to treat permeability edema, the search for novel therapeutic candidates is of high priority. We detected mRNA expression for the active receptor splice variant SV1 of the hypothalamic polypeptide growth hormone-releasing hormone (GHRH), as well as for GHRH itself, in human lung microvascular endothelial cells (HL-MVEC). Therefore, we have evaluated the effect of the GHRH agonist JI-34 on PLY-induced barrier and ALC dysfunction. JI-34 blunts PLY-mediated endothelial hyperpermeability in monolayers of HL-MVEC, in a cAMP-dependent manner, by means of reducing the phosphorylation of myosin light chain and vascular endothelial (VE)-cadherin. In human airway epithelial H441 cells, PLY significantly impairs Na+ uptake, but JI-34 restores it to basal levels by means of increasing cAMP levels. Intratracheal instillation of PLY into C57BL6 mice causes pulmonary alveolar epithelial and endothelial hyperpermeability as well as edema formation, all of which are blunted by JI-34. These findings point toward a protective role of the GHRH signaling pathway in PLY-induced permeability edema.
Vascular structure of the earliest shark teeth

Here we use synchrotron tomography to characterise dental vasculature in the oldest known tooth-bearing sharks, Leonodus carlsi Mader, 1986 and Celtiberina maderi Wang, 1993. Three dimensional reconstruction of the vascular system and microstructure of both taxa revealed a complex and dense network of canals, including horizontal, ascending and secondary bifurcated canals, as well as histological features consistent with an osteodont histotype. However, L. carlsi and C. maderi also exhibit significant morphological differences, showing Leonodus a typical diplodont tooth morphology with a linguo-labially elongated base, that contrast with Celtiberina’s teeth that show a single conical cusp curved lingually with a week developed flat base mesio-distally extended, perhaps reflecting distant relationship. These data are compatible with a pre-Devonian diversification of the two main tooth types traditionally recognised in Palaeozoic sharks (i.e., “cladodont” vs “diplodont”). Finally, our data demonstrate that existing dental classification schemes based on styles of vascularisation are over-simplified, especially when Palaeozoic taxa are considered.
ROTATION AND OUTFLOW MOTIONS IN THE VERY LOW-MASS CLASS 0 PROTOSTELLAR SYSTEM HH 211 AT SUBARCSECOND RESOLUTION

HH 211 is a nearby young protostellar system with a highly collimated jet. We have mapped it in 352 GHz continuum, SiO (J = 8 − 7), and HCO+ (J = 4 − 3) emission at up to ∼0. ″2 resolution with the Submillimeter Array (SMA). The continuum source is now resolved into two sources, SMM1 and SMM2, with a separation of ∼ 84 AU. SMM1 is seen at the center of the jet, probably tracing a (inner) dusty disk around the protostar driving the jet. SMM2 is seen to the southwest of SMM1 and may trace an envelope-disk around a small binary companion. A flattened envelope-disk is seen in HCO+ around SMM1 with a radius of ∼ 80 AU perpendicular to the jet axis. Its velocity structure is consistent with a rotation motion and can be fitted with a Keplerian law that yields a mass of ∼50 ± 15 MJup (a mass of a brown dwarf) for the protostar. Thus, the protostar could be the lowest mass source known to have a collimated jet and a rotating flattened envelope-disk. A small-scale (∼200 AU) low-speed (∼2 km s−1) outflow is seen in HCO+ around the jet axis extending from the envelope-disk. It seems to rotate in the same direction as the envelope-disk and may carry away part of the angular momentum from the envelope-disk. The jet is seen in SiO close to ∼100 AU from SMM1. It is seen with a “C-shaped” bending. It has a transverse width of ≲ 40 AU and a velocity of ∼ 170 ± 60 km s−1. A possible velocity gradient is seen consistently across its innermost pair of knots, ∼0.5 km s−1 at ∼10 AU, consistent with the sense of rotation of the envelope-disk. If this gradient is an upper limit of the true rotational gradient of the jet, then the jet carries away a very small amount of angular momentum of ≲ 5 AU km s−1 and thus must be launched from the very inner edge of the disk near the corotation radius.
Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data

Peptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules of peptide presentation for a given MHC-I molecule is extensive, and predictors of peptide–MHC interactions constitute an attractive alternative. Recently, an increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is, in general, challenging due to the polyspecificity nature of the data. We here outline a general pipeline for dealing with this challenge and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in silico models. We illustrate the approach here in the context of MHC-I molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T-cell epitopes. The prediction model is freely available at http://www.cbs. dtu.dk/services/NetMHCpan/NetBoLApan. The approach has here been applied to the BoLA-I system, but the pipeline is readily applicable to MHC systems in other species.
The Effect of Electronic Health Record Use and Patient-Centered Communication on Cancer Screening Behavior: An Analysis of the Health Information National Trends Survey

The present study used the 2013 Health Information National Trends Survey (N = 3185) to examine the effects of patient-centered communication (PCC) and the use of electronic health records (EHRs) on the likelihood of patients receiving a recommended screening for cancer (i.e., mammogram, PSA test). Self-determination theory, a framework of self-initiated extrinsic behaviors, was applied to test mediation models of PCC and EHR use, respectively, through patient activation. The results demonstrated that PCC and EHR use predicted cancer screening (mediated through patient activation), but only for women recommended for biannual mammograms. The aforementioned relationship was not found for men who are recommended for prostate cancer screening. PCC and EHRs do appear to facilitate a patient’s ability to take care of their own health, but only under certain circumstances. It was additionally found that men were more likely to report higher degrees of physician PCC when their physicians maintained an EHR, whereas women reported no difference. Future research should examine more nuanced personality factors that affect the perception of PCC in the presence of EHRs and the relationship between men’s activation and likelihood of receiving a cancer screen.
An Information Retrieval Method Based on Sequential Access Patterns

It has become much more difficult to access relevant information from the Web With the explosive growth of information available on the World Wide Web. One of the promising approaches is web usage mining, which mines web logs for user models and recommendations. Different from most web recommender systems that are mainly based on clustering and association rule mining, this paper proposes an web personalization system that uses sequential access pattern mining. In the proposed system an efficient sequential pattern-mining algorithm is used to identify frequent sequential web access patterns. The access patterns are then stored in a compact tree structure, called Pattern-tree, which is then used for matching and generating web links for recommendations. In this paper, the proposed system is described, and its performance is evaluated.
Modulation of tumor cell growth in vivo by extracellular matrix metalloprotease inducer.

OBJECTIVE To investigate if loss of extracellular matrix metalloprotease inducer (EMMPRIN) will inhibit the growth of head and neck squamous cell carcinoma (HNSCC) tumor cell lines in vivo. Tumor cell-derived EMMPRIN is highly overexpressed in HNSCC and is thought to be induced by surrounding fibroblasts to stimulate matrix metalloproteases, which modulate tumor cell invasion, growth, and angiogenesis. DESIGN In vivo study using FaDu tumor xenografts. SETTING Academic research facility. SUBJECTS Severe combined immunodeficiency (SCID) mice. INTERVENTIONS The HNSCC cell line FaDu was transfected with EMMPRIN (FaDu/E), control vector (FaDu), or plasmid-expressing small-interfering RNA against EMMPRIN (FaDu/siE). Tumor cells combined with fibroblast cells were xenografted onto the flank of SCID mice. Tumors were measured biweekly over 4 weeks, at which time the mice were killed, and tumor samples were analyzed for proliferation (Ki-67 immunohistochemical analysis), vascularization (factor VIII staining), and apoptosis (TUNEL [terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate-biotin nick end labeling] assay). MAIN OUTCOME MEASURE Growth of head and neck cancer cell lines genetically engineered to express variable levels of EMMPRIN. RESULTS Tumor growth positively correlated and animal survival negatively correlated with increasing EMMPRIN expression. FaDu/E tumor growth was significantly larger at 4 weeks compared with FaDu tumors (P = .006). Similarly, the control vector-transfected FaDu tumors were significantly larger than FaDu/siE (P < .001). Immunohistochemical analysis demonstrated increased Ki-67 in EMMPRIN-transfected cells, without a significant change in the rate of apoptosis between groups. Vascular density and tumor formation rate also increased significantly with EMMPRIN expression. CONCLUSION This study suggests that anti-EMMPRIN-targeted therapy may prove to be a novel treatment option in HNSCC.
Classifying Non-Sentential Utterances in Dialogue: A Machine Learning Approach

In this article we use well-known machine learning methods to tackle a novel task, namely the classification of non-sentential utterances (NSUs) in dialogue. We introduce a fine-grained taxonomy of NSU classes based on corpus work, and then report on the results of several machine learning experiments. First, we present a pilot study focused on one of the NSU classes in the taxonomybare wh-phrases or sluicesand explore the task of disambiguating between the different readings that sluices can convey. We then extend the approach to classify the full range of NSU classes, obtaining results of around an 87% weighted F-score. Thus our experiments show that, for the taxonomy adopted, the task of identifying the right NSU class can be successfully learned, and hence provide a very encouraging basis for the more general enterprise of fully processing NSUs.