Miracle-dz/UniFAR-FTUs huggingface dataset:
The Krakow receptor modelling inter-comparison exercise

Second to oil, coal is globally the biggest energy source. Coal combustion is utilized mainly for power generation in industry, but in many metropolitan areas in East Europe and Asia also for residential heating in small stoves and boilers. The present investigation, carried out as a case study in a typical major city situated in a European coal combustion region (Krakow, Poland), aims at quantifying the impact on the urban air quality of residential heating by coal combustion in comparison with other potential pollution sources such as power plants, industry and traffic. For that purpose, gaseous emissions (NOx, SO2) were measured for 20 major sources, including small stoves and boilers, and the emissions of particulate matter (PM) was chemically analyzed for 52 individual compounds together with outdoor and indoor PM10 collected during typical winter pollution episodes. The data was analyzed using multivariate receptor modelling yielding source apportionments for PM10, B(a)P and other regulated air pollutants associated with PM10, namely Cd, Ni, As, and Pb. The source apportionment was accomplished using the chemical mass balance modelling (CMB) and constrained positive matrix factorization (CMF) and compared to five other multivariate receptor models (PMF, PCA-MLRA, UNMIX, SOM, CA). The results are potentially very useful for planning abatement strategies in all areas of the world, where coal combustion in small appliances is significant. During the pollution episodes under investigation the PM10 and B(a)P concentrations were up to 8-200 times higher than the European limit values. The major culprit for these extreme pollution levels was shown to be residential heating by coal combustion in small stoves and boilers (>50% for PM10 and >90% B(a)P), whereas road transport ( PM10 and much lower than the outdoor concentrations and were found to have the same sources as outdoor PM10 and B(a)P The inorganic secondary aerosol component of PM10 amounted to around 30%, which may be attributed for a large part to the industrial emission of the precursors SO2 and NOX.
Occurrence and Concentrations of Toxic VOCs in the Ambient Air of Gumi, an Electronics-Industrial City in Korea

This study was carried out to characterize the occurrence and concentrations of a variety of volatile organic compounds (VOCs) including aliphatic, aromatic, halogenated, nitrogenous, and carbonyl compounds, in the ambient air of Gumi City, where a large number of electronics industries are found. Two field monitoring campaigns were conducted for a one year period in 2003/2004 and 2010/2011 at several sampling sites in the city, representing industrial, residential and commercial areas. More than 80 individual compounds were determined in this study, and important compounds were then identified according to their abundance, ubiquity and toxicity. The monitoring data revealed toluene, trichloroethylene and acetaldehyde to be the most significant air toxics in the city, and their major sources were mainly industrial activities. On the other hand, there was no clear evidence of an industrial impact on the concentrations of benzene and formaldehyde in the ambient air of the city. Overall, seasonal variations were not as distinct as locational variations in the VOCs concentrations, whereas the within-day variations showed a typical pattern of urban air pollution, i.e., increase in the morning, decrease in the afternoon, and an increase again in the evening. Considerable decreases in the concentrations of VOCs from 2003 to 2011 were observed. The reductions in the ambient concentrations were confirmed further by the Korean PRTR data in industrial emissions within the city. Significant decreases in the concentrations of benzene and acetaldehyde were also noted, whereas formaldehyde appeared to be almost constant between the both campaigns. The decreased trends in the ambient levels were attributed not only to the stricter regulations for VOCs in Korea, but also to the voluntary agreement of major companies to reduce the use of organic solvents. In addition, a site planning project for an eco-friendly industrial complex is believed to play a contributory role in improving the air quality of the city.
Density-based clustering of data streams at multiple resolutions

In data stream clustering, it is desirable to have algorithms that are able to detect clusters of arbitrary shape, clusters that evolve over time, and clusters with noise. Existing stream data clustering algorithms are generally based on an online-offline approach: The online component captures synopsis information from the data stream (thus, overcoming real-time and memory constraints) and the offline component generates clusters using the stored synopsis. The online-offline approach affects the overall performance of stream data clustering in various ways: the ease of deriving synopsis from streaming data; the complexity of data structure for storing and managing synopsis; and the frequency at which the offline component is used to generate clusters. In this article, we propose an algorithm that (1) computes and updates synopsis information in constant time; (2) allows users to discover clusters at multiple resolutions; (3) determines the right time for users to generate clusters from the synopsis information; (4) generates clusters of higher purity than existing algorithms; and (5) determines the right threshold function for density-based clustering based on the fading model of stream data. To the best of our knowledge, no existing data stream algorithms has all of these features. Experimental results show that our algorithm is able to detect arbitrarily shaped, evolving clusters with high quality.
Identifying Signatures of Natural Climate Variability in Time Series of Global-Mean Surface Temperature: Methodology and Insights

Abstract Global-mean surface temperature is affected by both natural variability and anthropogenic forcing. This study is concerned with identifying and removing from global-mean temperatures the signatures of natural climate variability over the period January 1900–March 2009. A series of simple, physically based methodologies are developed and applied to isolate the climate impacts of three known sources of natural variability: the El Nino–Southern Oscillation (ENSO), variations in the advection of marine air masses over the high-latitude continents during winter, and aerosols injected into the stratosphere by explosive volcanic eruptions. After the effects of ENSO and high-latitude temperature advection are removed from the global-mean temperature record, the signatures of volcanic eruptions and changes in instrumentation become more clearly apparent. After the volcanic eruptions are subsequently filtered from the record, the residual time series reveals a nearly monotonic global warming pattern since .
Work in progress: Application of unsupervised learning method toward student's metacognition assessment

There has been awareness of the importance of metacognitive skill in learning processes, especially for university students, who are required to be more self-regulated. Therefore, monitoring the development of such skill is needed to ensure student's achievements. Currently, in classroom learning environments, student's metacognition can be observed conventionally by using interview or think-aloud procedures, however, the tasks are tedious and impractical for big number of students. Therefore, an automatic student's metacognition assessment/modeling is in progress. This paper proposes a partly automatic metacognition assessment, which is an implementation of unsupervised learning method. This proposed method is proven using a case study in which the dataset was gathered by administering Metacognitive Awareness Inventory (MAI) questionnaire to undergraduate students in our department. Experiment shows that the proposed method could be utilized for automatic assessment of student's metacognition. Two groups of students are identified, one that does well in their metacognitive awareness and the other one that needs further guidance and advisory to help them achieve better results and avoid failures.
Hybrid Models Identified a 12-Gene Signature for Lung Cancer Prognosis and Chemoresponse Prediction

Background Lung cancer remains the leading cause of cancer-related deaths worldwide. The recurrence rate ranges from 35–50% among early stage non-small cell lung cancer patients. To date, there is no fully-validated and clinically applied prognostic gene signature for personalized treatment. Methodology/Principal Findings From genome-wide mRNA expression profiles generated on 256 lung adenocarcinoma patients, a 12-gene signature was identified using combinatorial gene selection methods, and a risk score algorithm was developed with Naïve Bayes. The 12-gene model generates significant patient stratification in the training cohort HLM & UM (n = 256; log-rank P = 6.96e-7) and two independent validation sets, MSK (n = 104; log-rank P = 9.88e-4) and DFCI (n = 82; log-rank P = 2.57e-4), using Kaplan-Meier analyses. This gene signature also stratifies stage I and IB lung adenocarcinoma patients into two distinct survival groups (log-rank P<0.04). The 12-gene risk score is more significant (hazard ratio = 4.19, 95% CI: [2.08, 8.46]) than other commonly used clinical factors except tumor stage (III vs. I) in multivariate Cox analyses. The 12-gene model is more accurate than previously published lung cancer gene signatures on the same datasets. Furthermore, this signature accurately predicts chemoresistance/chemosensitivity to Cisplatin, Carboplatin, Paclitaxel, Etoposide, Erlotinib, and Gefitinib in NCI-60 cancer cell lines (P<0.017). The identified 12 genes exhibit curated interactions with major lung cancer signaling hallmarks in functional pathway analysis. The expression patterns of the signature genes have been confirmed in RT-PCR analyses of independent tumor samples. Conclusions/Significance The results demonstrate the clinical utility of the identified gene signature in prognostic categorization. With this 12-gene risk score algorithm, early stage patients at high risk for tumor recurrence could be identified for adjuvant chemotherapy; whereas stage I and II patients at low risk could be spared the toxic side effects of chemotherapeutic drugs.
Laparoscopic living donor hepatectomy: a review of current status

Over the last two decades, laparoscopic surgery has been adopted in various surgical fields. Its advantages of reduced blood loss, reduced postoperative morbidity, shorter hospital stay, and excellent cosmetic outcome compared with conventional open surgery are well validated. In comparison with other abdominal organs, laparoscopic hepatectomy has developed relatively slowly due to the potential for massive bleeding, technical difficulties and a protracted learning curve. Furthermore, applications to liver graft procurement in living donor liver transplantation (LDLT) have been delayed significantly due to concerns about donor safety, graft outcome and the need for expertise in both laparoscopic liver surgery and LDLT. Now, laparoscopic left lateral sectionectomy in adult‐to‐pediatric LDLT is considered the standard of care in some experienced centers. Currently, the shift in application has been towards left lobe and right lobe graft procurement in adult LDLT from left lateral section in pediatric LDLT. However, the number of cases is too small to validate the safety and reproducibility. The most important concern in LDLT is donor safety. Even though a few studies reported the technical feasibility and comparable outcomes to conventional open surgery, careful validating through larger sample sized studies is needed to achieve standardization and wide application.
Exon‐skipped dystrophins for treatment of Duchenne muscular dystrophy: Mass spectrometry mapping of most exons and cooperative domain designs based on single molecule mechanics

Force‐bearing linkages between the cytoskeleton and extracellular matrix are clearly important to normal cell viability—as is evident in a disease such as Duchenne muscular dystrophy (DMD) which arises in the absence of the linkage protein dystrophin. Therapeutic approaches to DMD include antisense‐mediated skipping of exons to delete nonsense mutations while maintaining reading frame, but the structure and stability of the resulting proteins are generally unclear. Here we use mass spectrometry to detect most dystrophin exons, and we express and physically characterize dystrophin “nano”‐constructs based on multiexon deletions that might find use in a large percentage of DMD patients. The primary structure challenge is addressed first with liquid chromatography tandem mass spectrometry (LC‐MS/MS) which can detect tryptic peptides from 53 of dystrophin's 79 exons; equivalent information from immunodetection would require 53 different high‐specificity antibodies. Folding predictions for the nano‐constructs reveal novel helical bundle domains that arise out of exon‐deleted “linkers,” while secondary structure studies confirm high helicity and also melting temperatures well above physiological. Extensional forces with an atomic force microscope nonetheless unfold the constructs, and the ensemble of unfolding trajectories reveal the number of folded domains, proving consistent with structure predictions. A mechanical cooperativity parameter for unfolding of tandem domains is also introduced as the best predictor of a multiexon deletion that is asymptomatic in humans. The results thereby provide insight and confidence in exon‐skipped designs. © 2010 Wiley‐Liss, Inc.
The lysosomal enzyme receptor protein (LERP) is not essential, but is implicated in lysosomal function in Drosophila melanogaster

ABSTRACT The lysosomal enzyme receptor protein (LERP) of Drosophila melanogaster is the ortholog of the mammalian cation-independent mannose 6-phosphate (Man 6-P) receptor, which mediates trafficking of newly synthesized lysosomal acid hydrolases to lysosomes. However, flies lack the enzymes necessary to make the Man 6-P mark, and the amino acids implicated in Man 6-P binding by the mammalian receptor are not conserved in LERP. Thus, the function of LERP in sorting of lysosomal enzymes to lysosomes in Drosophila is unclear. Here, we analyze the consequence of LERP depletion in S2 cells and intact flies. RNAi-mediated knockdown of LERP in S2 cells had little or no effect on the cellular content or secretion of several lysosomal hydrolases. We generated a novel Lerp null mutation, LerpF6, which abolishes LERP protein expression. Lerp mutants have normal viability and fertility and display no overt phenotypes other than reduced body weight. Lerp mutant flies exhibit a 30–40% decrease in the level of several lysosomal hydrolases, and are hypersensitive to dietary chloroquine and starvation, consistent with impaired lysosome function. Loss of LERP also enhances an eye phenotype associated with defective autophagy. Our findings implicate Lerp in lysosome function and autophagy.
The APC I1307K allele conveys a significant increased risk for cancer

This study is the first attempt to evaluate the association between the APC I1307K variant and overall cancer risk. It is unique in both its large sample size and in the reliability of data in the control group. The findings described in this article have major implications in terms of identifying asymptomatic individuals who are at increased risk to harbor cancer and therefore targeted to be enrolled in specific early detection and prevention programs. The prevalence of the APC I1307K missense mutation among Ashkenazi Jews is ∼6%. Carriers are at an increased risk for colorectal neoplasia. In this study, we examined the association of this variant with non‐colorectal cancers. Consecutive 13,013 healthy subjects who underwent screening at the Integrated Cancer Prevention Center between 2006 and 2014 were enrolled. This population was supplemented with 1,611 cancer patients from the same institution. Demographics, medical history, and pathological data were recorded. Mortality data were obtained from the Ministry of Health's registry. The prevalence of APC I1307K in cancer patients and healthy subjects was compared. The APC I1307K variant was detected in 189 (11.8%) cancer patients compared to 614 (4.7%) healthy subjects, reflecting an adjusted age and sex odds ratio (OR) of 2.53 (p < 0.0001). History of two or more cancer types was associated with a positive carrier prevalence (OR = 4.38 p < 0.0001). Males had significantly increased carrier prevalence in lung, urologic, pancreatic, and skin cancers. The carrier prevalence among females was significantly higher only in breast and skin cancers. Female carriers developed cancer at a significantly older age compared to non‐carriers (average 62.7 years vs. 57.8, respectively, p = 0.027), had better survival rates (HR = 0.58, p = 0.022) and overall increased longevity (average age of death 78.8 vs. 70.4 years, respectively, p = 0.003). In conclusion, the APC I1307K variant is a reliable marker for overall cancer risk (OR 2.53). Further studies are needed to evaluate its use for specific cancer types—particularly in males. Female carriers have better prognosis and increased lifespan.
An Investigation Into the Choral Singer's Experience of Music Performance Anxiety

The purpose of this study was to examine the performance experiences of choral singers with respect to music performance anxiety. Members of seven semiprofessional choirs ( N = 201) completed questionnaires pertaining to their experience of performance anxiety in the context of their performance history, their experience with conductors, and their use of coping mechanisms. Results indicated that performance anxiety was a common experience for these choral singers. Solo performances were reported to be more anxiety inducing than ensemble experiences, but performing in instrumental ensembles induced greater anxiety than choral ensembles. Participants with college music training reported less frequent, although not less severe, episodes of performance anxiety than those without. The conductor emerged as one of the primary factors in choral singers' experience of performance anxiety.
ACTIN‐RELATED PROTEIN (ARP2) INSERTS INTO ARTIFICIAL LIPID MEMBRANES

Arp2 is localized in the cytoplasm of eukaryotic cells where it controls actin dynamics. Computer analyses have suggested one possible lipid binding site, residues 185–202 of the primary amino acid sequence on Arp2, that could allow for membrane attachment/insertion. We expressed this region as a fusion protein with schistosomal glutathione S‐transferase (GST) and investigated the interaction of this fragment with mixtures of dioleoylphosphatidylserine (DOPS) and dioleoylphosphatidylglycerol (DOPG) phospholipids in reconstituted lipid bilayers using differential scanning calorimetry (DSC). Calorimetric measurements showed that as the fusion protein increased, the main chain transition enthalpy decreased and the chain‐melting temperature shifted, which is indicative of partial protein insertion into the hydrophobic region of the lipid membrane. This was confirmed using the Langmuir Blodgett technique (film balance) on lipid monolayers. The dissociation constant (Kd) determined by the temperature jump method was approximately 1. 1μM.
SLP-76 Is a Direct Substrate of SHP-1 Recruited to Killer Cell Inhibitory Receptors*

Activation of immune system cells via antigen-, Fc-, or natural killer cell-triggering-receptor stimulation is aborted by co-engagement of inhibitory receptors. Negative signaling by killer cell inhibitory receptors and related receptors depends on the Src homology 2 (SH2)-containing protein tyrosine phosphatase SHP-1. Using a combination of direct binding and functional assays, we demonstrated that the SH2 domain-containing leukocyte protein 76 (SLP-76) is a specific target for dephosphorylation by SHP-1 in T cells and natural killer cells. Furthermore, we showed that tyrosine-phosphorylated SLP-76 is required for optimal activation of cytotoxic lymphocytes, suggesting that the targeted dephosphorylation of SLP-76 by SHP-1 is an important mechanism for the negative regulation of immune cell activation by inhibitory receptors.
DISFLUENT SPEECH AND THE VISUAL WORLD: AN APPLICATION OF THE VISUAL WORLD PARADIGM TO THE STUDY OF SPOKEN LANGUAGE COMPREHENSION By

DISFLUENT SPEECH AND THE VISUAL WORLD: AN APPLICATION OF THE VISUAL WORLD PARADIGM TO THE STUDY OF SPOKEN LANGUAGE COMPREHENSION By Karl Gregory David Bailey Input to the language comprehension system frequently deviates from ideal delivery. One major type of deviation is speech disfluency: the pauses, ums, uhs, repeated words and false starts that occur throughout spontaneous speech. While a few studies have examined the effects of disfluent speech on the language comprehension system, there is relatively little understanding of the online effects of disfluent speech. In this dissertation, I use a newly rediscovered methodology known as the visual world paradigm to examine some effects of disfluent speech on syntactic parsing and reanalysis which were initially described in studies using offline tasks. This methodology takes advantage of a link between eye movements within a constrained visual world and the processing of spoken language. An initial study intended to demonstrate the value of this paradigm for the study of the online effects of disfluency on syntactic parsing found mixed results. Some measures showed evidence of the effects of disfluencies on parsing, but other measures showed no such effects. In addition, previously reported effects from the particular visual world used in this initial study failed to replicate. As a result, several experiments were used to examine the visual world task in greater depth with the goal of better adapting the task to the study of disfluency. A modified version of the original disfluency study indicated that this paradigm is more suited to the study of lexical processing and referent resolution, rather than syntactic processing. A final experiment using a new visual world task, however, provided online information about the relative difficulty of various kinds of disfluency. In addition to these experiments, I also describe plans to examine current procedures for analyzing data in the visual world paradigm and develop a suite of analyses for use in visual world experiments.
Isolation of a circular plasmid region sufficient for autonomous replication and transformation of infectious Borrelia burgdorferi

Borrelia burgdorferi contains abundant circular and linear plasmids, but the mechanism of replication of these extrachromosomal elements is unknown. A B. burgdorferi 9 kb circular plasmid (cp9) was amplified in its entirety by the polymerase chain reaction and used to construct a shuttle vector that replicates in Escherichia coli and B. burgdorferi. A 3.3 kb region of cp9 containing three open reading frames was used to construct a smaller shuttle vector, designated pBSV2. This vector was stably maintained in B. burgdorferi, indicating that all elements necessary for autonomous replication are probably located on this 3.3 kb fragment. A non‐infectious B. burgdorferi strain was efficiently transformed by pBSV2. Additionally, infectious B. burgdorferi was also successfully transformed by pBSV2, indicating that infectious strains of this important human pathogen can now be genetically manipulated.