Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene expression profiles relate to SS18/SSX fusion type in synovial sarcoma

We applied 27k spotted cDNA microarray slides to assess gene expression profiles in 26 samples from 24 patients with synovial sarcomas (SS). The data were analyzed in relation to histopathologic type, cytogenetic aberrations, gene fusion type and development of distant metastases. Supervised analysis based on gene fusion type in 12 SS with SS18/SSX1 and 9 with SS18/SSX2 revealed significant differences in gene expression profiles. Among the discriminators were several genes that have previously been found to be upregulated in SS, including AXL, ZIC2, SPAG7, AGRN, FOXC1, NCAM1 and multiple metallothioneins. Histopathology and degree of cytogenetic complexity did not significantly influence expression, whereas a genetic signature that related to development of metastases could be discerned, albeit with a high false‐positive rate. In conclusion, our findings demonstrate differentially expressed genes for the 2 major gene fusion variants in SS, SS18/SSX1 and SS18/SSX2, and thereby suggest that these result in different downstream effects. © 2005 Wiley‐Liss, Inc.
Nuclear lamina assembly, synthesis and disaggregation during the cell cycle in synchronized HeLa cells.

The pattern of assembly, synthesis and disaggregation of the nuclear envelope-associated lamina in synchronized HeLa cells has been examined by means of immunofluorescence microscopy of cell preparations treated with antibody to lamina polypeptide LP67 or lamin B, using the nomenclature of Gerace and Blobel. During the cell cycle the distribution of lamina polypeptide varies dramatically. Three distinct stages can be detected with respect to its location and synthesis: (1) Lamina polypeptide is cytoplasmically distributed during cell division particularly at the time of complete nuclear envelope breakdown. At telophase it is reassembled and becomes associated with regions of the chromosome surface. This process continues into early Glt lamina polypeptide associating progressively with the outer surface of the chromosomes; simultaneously its cytoplasmic concentration is reduced. The traffic of antigen from cytoplasm to the chromosomes is highest between telophase and Gt but continues at a reduced rate during G1. Inhibition of protein synthesis during division and G^ does not inhibit G1 lamina reformation, suggesting that the Gj lamina is constructed from depolymerized cytoplasmically-stored polypeptide derived from the previous cell cycle. (2) Lamin B is synthesized in S-phase. The protein is rapidly accumulated at the nuclear periphery during the doubling of the nuclear surface. There is very little if any cytoplasmic location of lamina polypeptide in <S-phase cells. The 5-phase pattern of lamina distribution persists through early and mid G,. (3) Towards the end of G, and particularly with the onset of prophase, the nuclear membrane-bound lamina is released into the cytoplasm over approximately 30 min. (Fusion between metaphase and either Gx or .S-phase cells also results in the depolymerization of lamin B within 30 min.) Lamina polypeptides appear in the cytoplasm before the nuclear envelope has disappeared, and protein synthesis in Gt is required for complete lamina disaggregation. Lamina reformation in late mitosis and the polarity of its appearance in the telophase cell can be perturbed by treatment with colcemid or low temperature so that lamina is induced to associate with metaphase and anaphase chromosomes. In the absence of spindle microtubules lamina reformation may proceed around the surface of whole chromosomes, leading to the formation of micronuclei in Gl cells. We propose that in the normal cell nuclear envelope formation at telophase is related to the terminal distribution of cytoskeleton structures such that lamina is laid down only on the outer surface of the telophase genome beginning at the telomeric chromosome ends adjacent to the remaining mitotic fibres of the cleavage furrow.
Photoplethysmography detection by smartphone's videocamera

Smartphone's video cameras become more and more powerful while the devices itself become used by many people. That allows utilizing them for many every-day tasks. One of such suitable application of the widely used smartphones is monitoring the state of the health. In this paper we propose an approach to detect the photoplethysmograph signal from the fingertip using a smartphone's camera and built-in LED. The proposed solution allows detecting the proper heart rate and is robust to different situations of wrong-usage of the system.
Abridging source code

In this paper, we consider the problem of source code abridgment, where the goal is to remove statements from a source code in order to display the source code in a small space, while at the same time leaving the ``important'' parts of the source code intact, so that an engineer can read the code and quickly understand purpose of the code. To this end, we develop an algorithm that looks at a number of examples, human-created source code abridgments, and learns how to remove lines from the code in order to mimic the human abridger. The learning algorithm takes into account syntactic features of the code, as well as semantic features such as control flow and data dependencies. Through a comprehensive user study, we show that the abridgments that our system produces can decrease the time that a user must look at code in order to understand its functionality, as well as increase the accuracy of the assessment, while displaying the code in a greatly reduced area.
Extracting ontology concept hierarchies from text using Markov logic

Ontologies have proven to be a powerful tool for many tasks such as natural language processing and information filtering and retrieval. However their development is an error prone and expensive task. One approach for this problem is to provide automatic or semi-automatic support for ontology construction. This work presents the Probabilistic Relational Hierarchy Extraction (PREHE) technique, an approach for extracting concept hierarchies from text that uses statistical relational learning and natural language processing for combining cues from many state-of-the-art techniques. A Markov Logic Network has been developed for this task and is described here. A preliminary evaluation of the proposed approach is also outlined.
The Chinese International Student Experience in a Time of Increased Enrolment at the University of California, Santa Barbara

From 2010 to 2013, the number of degree-seeking Chinese international students at the University of California, Santa Barbara (UCSB) increased from 82 to 596. This number includes both undergraduate and graduate students. With such a controversial and much discussed topic of international student enrolment at US universities, this was the perfect time for me to interview Chinese international students in order to determine what their overall university experience is like and what challenges arise. The interviews revealed that Chinese students had highly educated parents whose intention had been to send their children abroad from an early age. In combination with the collectivist conservative culture and the concept of filial piety (Deutsch, 2004) this creates hard-working students with a drive to attend prestigious universities for academic, cultural and social reasons. My study and previous research have shown that Chinese international students focus on academic study first and leisure second (Li & Stodolska, 2006) and that they face both academic and social challenges. Academically, challenges arose with completing academic papers on time and learning how to interact with American students in the classroom. Half of the students recommended more social activities to help build relationships with American students.
Fiber-needle Swept-source Optical Coherence Tomography System for the Identification of the Epidural Space in Piglets

Background:Epidural needle insertion is traditionally a blind technique whose success depends on the experience of the operator. The authors describe a novel method using a fiber-needle–based swept-source optical coherence tomography (SSOCT) to identify epidural space. Methods:An optical fiber probe was placed into a hollow 18-gauge Tuohy needle. It was then inserted by an experienced anesthesiologist to continuously construct a series of two-dimensional SSOCT images by mechanically rotating the optical probe. To quantify this observation, both the average SSOCT signal intensities and their diagnostic potentials were assessed. The insertions were performed three times into both the lumbar and thoracic regions of five pigs using a paramedian approach. Results:A side-looking SSOCT is constructed to create a visual image of the underlying structures. The image criteria for the identification of the epidural space from the outside region were generated by the analysis of a training set (n = 100) of ex vivo data. The SSOCT image criteria for in vivo epidural space identification are high sensitivity (0.867 to 0.965) and high specificity (0.838 to 0.935). The mean value of the average signal intensities exhibits statistically significant differences (P < 0.01) and a high discriminatory capacity (area under curve = 0.88) between the epidural space and the outside tissues. Conclusions:This is the first study to introduce a SSOCT fiber probe embedded in a standard epidural needle. The authors anticipate that this technique will reduce the occurrence of failed epidural blocks and other complications such as dural punctures.
Forst: Question Answering System for Second-stage Examinations at NTCIR-12 QA Lab-2 Task

Japanese university entrance exams have two stages: The National Center Test (multiple choice-type questions) and second-stage examinations (complex questions including terms and essays). We participated in all phases of NTCIR-11 QA Lab-1 and NTCIR-12 QA Lab-2 task’s Japanese subtask and our system answered all of the questions. At QA Lab-2 task, we focused on term and essay questions in the second-stage exams and we improved the term type answering and the essay type answering.
Applications of data assimilation to forecasting indoor environment

Data assimilation (DA) is a technique to combine numerical predictions and experimental measurements, which has been commonly used by the community of numerical weather forecasting but is relatively new to the field of indoor environment. Among all data assimilation methods, Ensemble Kalman Filter (EnKF) is especially suitable to solve large-scale nonlinear problems due to its low computation requirement. In this paper, two new applications of EnKF to forecasting indoor environment are presented. The first study is to forecast the contaminant transport in a residential house based on a multi-room tracer gas decay experiment. The forecast model avoids calculating source term in the given problem by rapid updating model states with EnKF while still providing significant forecast lead time. The second study is to predict the fire smoke dispersion in a multi-room compartment fire without giving actual heat release rates (HRRs) as model inputs. Compared to conventional deterministic models, the EnKF models improve the predictions significantly.
Coordinated control of an underwater glider fleet in an adaptive ocean sampling field experiment in Monterey Bay

A full‐scale adaptive ocean sampling network was deployed throughout the month‐long 2006 Adaptive Sampling and Prediction (ASAP) field experiment in Monterey Bay, California. One of the central goals of the field experiment was to test and demonstrate newly developed techniques for coordinated motion control of autonomous vehicles carrying environmental sensors to efficiently sample the ocean. We describe the field results for the heterogeneous fleet of autonomous underwater gliders that collected data continuously throughout the month‐long experiment. Six of these gliders were coordinated autonomously for 24 days straight using feedback laws that scale with the number of vehicles. These feedback laws were systematically computed using recently developed methodology to produce desired collective motion patterns, tuned to the spatial and temporal scales in the sampled fields for the purpose of reducing statistical uncertainty in field estimates. The implementation was designed to allow for adaptation of coordinated sampling patterns using human‐in‐the‐loop decision making, guided by optimization and prediction tools. The results demonstrate an innovative tool for ocean sampling and provide a proof of concept for an important field robotics endeavor that integrates coordinated motion control with adaptive sampling. © 2010 Wiley Periodicals, Inc.
Accumulation of Checkpoint Protein 53BP1 at DNA Breaks Involves Its Binding to Phosphorylated Histone H2AX*

53BP1 participates in the cellular response to DNA damage. Like many proteins involved in the DNA damage response, 53BP1 becomes hyperphosphorylated after radiation and colocalizes with phosphorylated H2AX in megabase regions surrounding the sites of DNA strand breaks. However, it is not yet clear whether the phosphorylation status of 53BP1 determines its localization or vice versa. In this study we mapped a region upstream of the 53BP1 C terminus that is required and sufficient for the recruitment of 53BP1 to these DNA break areas. In vitro assays revealed that this region binds to phosphorylated but not unphosphorylated H2AX. Moreover, using H2AX-deficient cells reconstituted with wild-type or a phosphorylation-deficient mutant of H2AX, we have shown that phosphorylation of H2AX at serine 140 is critical for efficient 53BP1 foci formation, implying that a direct interaction between 53BP1 and phosphorylated H2AX is required for the accumulation of 53BP1 at DNA break sites. On the other hand, radiation-induced phosphorylation of the 53BP1 N terminus by the ATM (ataxia-telangiectasia mutated) kinase is not essential for 53BP1 foci formation and takes place independently of 53BP1 redistribution. Thus, these two damage-induced events, hyperphosphorylation and relocalization of 53BP1, occur independently in the cell.
The Criminal 'Edgework' Alternative Hypothesis: Is the Advancement of Entertainment and Communications Media Reducing Crime?

In an unexpected turn, the Western world is experiencing a steady reduction in crime, which began in the mid – 1990’s. In an attempt to make sense of this 15 year crime drop, Criminologists have been proposing many different explanations, all of which suffer from a lack of evidence to provide validity and reliability. The idea is that this 15 year crime drop is partly due to the unintended consequences of some form of relatively new human activity or invention. The proposition put forward within this dissertation is whether the advancement in entertainment and communications media has played a part in this crime recession. The argument is that this advancement in media technology has provided a substitute and a distraction from committing real life crime. The new emerging trend in Criminology has been to cite Routine Activities Theory as an explanation for the crime drop, and given that the advancement in entertainment and communications media has been an obvious change in society, the theory has been incorporated into this study. The notion of ‘edgework’ is also a focus, as it is an original and interesting concept that humans craving for the exhilaration of risk can cause crime, and that modern day media technologies may provide an alterative avenue to feed this craving. We may call this hypothesis: The ‘Edgework’ Alternative Hypothesis. Ultimately, however, it is clear that the study suffers from the same lack of evidence and support that other explanations suffer, and that further research is needed in order to validate the research. At present, the research is very much down to individual opinion.
On the Geometry of Rectifiable Sets with Carleson and Poincar\'e-type Conditions

A central question in geometric measure theory is whether geometric properties of a set translate into analytical ones. In 1960, E. R. Reifenberg proved that if an $n$-dimensional subset $M$ of $\mathbb{R}^{n+k}$ is well approximated by $n$-planes at every point and at every scale, then $M$ is a locally bi-H\"older image of an $n$-plane. Since then, Reifenberg's theorem has been refined in several ways in order to ensure that $M$ is a bi-Lipschitz image of an $n$-plane. In this paper, we show that a Carleson condition on the oscillation of the unit normal of an $n$-Ahlfors regular rectifiable subset $M$ of $\mathbb{R}^{n+1}$ satisfying a Poincar\'e-type inequality is sufficient to prove that $M$ is contained inside a bi-Lipschitz image of an $n$-dimensional affine subspace of $\mathbb{R}^{n+1}$. We also show that this Poincar\'e-type inequality encodes geometrical information about $M$, namely it implies that $M$ is quasiconvex.
Quarterly Assessment of Short-Acting β2-Adrenergic Agonist Use as a Predictor of Subsequent Health Care Use for Asthmatic Patients in the United States

Purpose. An annual time frame for risk assessment may not account for the variable course of asthma. The purpose of this study was to determine whether excessive short-acting β2-adrenergic agonist (SABA) dispensed quarterly was associated with asthma exacerbations in the subsequent quarter. Patients and Methods. This retrospective cohort analysis included 93,604 health plan members aged 6–56 years with ≥2 years of continuous enrollment (2003–2007), an asthma diagnosis, and asthma prescription claims. The amount of SABA dispensed in claims (metered-dose inhaler and nebulized) was converted to canister equivalents (CEs) in the first observation quarter and categorized as 0, 0.5–3, and ≥3 (excessive SABA use). Asthma exacerbation risk (hospitalization, emergency department [ED] visit, or oral corticosteroid [OCS] claim in the subsequent quarter) was assessed using logistic regression. Covariates used in the regression models were age, sex, geographic region, comorbidities, specialist consultation, asthma controller medication use, and asthma severity. Results. The cohort included 33,951 patients aged 6–17 years (36%) and 59,653 aged 18–56 years (64%); 64% had 0 SABA CE, and 5% had >3 SABA CEs. Compared with 0 CE, excessive SABA use (>3 CEs) was associated with an increased likelihood of hospitalization (adjusted odds ratio [OR]: 3.15, 95% confidence interval [CI]: 1.89–5.27) and an ED/urgent care (UC) visit (adjusted OR: 3.14, 95% CI: 2.32–4.28). Conclusion: The risk of an asthma exacerbation was associated with excessive SABA use in the previous quarter. Assessment of excessive SABA dispensed during a calendar quarter can be used to identify patients at increased exacerbation risk in the subsequent quarter.
Utilization of different nitrogen sources by the marine cyanobacteria Prochlorococcus and Synechococcus

Prochlorococcus is the most abundant phytoplankter throughout the photic zone in stratified marine waters and experiences distinct gradients of light and nitrogen nutrition. Physiologically and genetically distinct Prochlorococcus ecotypes partition the water column: high‐B/A (low‐light adapted) ecotypes are generally restricted to the deep euphotic zone near or at the nitracline. Low‐B/A (high‐light adapted) ecotypes predominate in, but are not limited to, NO3-‐depleted surface waters, where they outnumber coexisting Synechococcus populations. The niche partitioning by different Prochlorococcus ecotypes begs the question of whether they also differ in their nitrogen (N) utilization physiology, especially with respect to NO3- utilization. To explore this possibility, we studied the capabilities of different Prochlorococcus and Synechococcus strains to grow on a variety of N sources. We found that all the isolates grew well on NH4+ and all were capable of urea utilization, occasionally at a lower growth rate. None of the Prochlorococcus isolates were able to grow with NO3-. Four high‐B/A Prochlorococcus isolates grew on NO3-, but all others did not. Whole genome analysis of the low‐B/A Prochlorococcus MED4 revealed that the genes required for NO uptake and reduction were absent. The genome of the high‐B/A Prochlorococcus MIT 9313 also lacked the NO3- utilization genes but has homologs of genes required for NO3- utilization consistent with its physiology and ecology. Thus, the utilization of different N sources in the marine environment is partitioned among closely related ecotypes, each with adaptations optimized for the environment where these sources are available.
Detecting the Moment of Completion: Temporal Models for Localising Action Completion

Action completion detection is the problem of modelling the action's progression towards localising the moment of completion - when the action's goal is confidently considered achieved. In this work, we assess the ability of two temporal models, namely Hidden Markov Models (HMM) and Long-Short Term Memory (LSTM), to localise completion for six object interactions: switch, plug, open, pull, pick and drink. We use a supervised approach, where annotations of pre-completion and post-completion frames are available per action, and fine-tuned CNN features are used to train temporal models. Tested on the Action-Completion-2016 dataset, we detect completion within 10 frames of annotations for ~75% of completed action sequences using both temporal models. Results show that fine-tuned CNN features outperform hand-crafted features for localisation, and that observing incomplete instances is necessary when incomplete sequences are also present in the test set.
Gunshot acoustic component localization with distributed circular microphone arrays

Gunshot acoustic localization for military and urban security systems has long been an important topic of research. In recent years the development of independent Unmanned Ground Sensors (UGS), interconnected through Wireless Sensor Networks (WSN), performing distributed cooperative localization, has grown in popularity. This paper considers a 2D Direction of Arrival (DOA) estimation method for compact circular array UGS, establishing gunshot direction at close range, and discusses problems, situated with gunshot acoustic component analysis. The proposed method is aimed at reducing the computational cost of DOA calculation for implementation on embedded hardware of WSN smart sensors. It is compared with the SRP-PHAT localization algorithm and is proven to provide adequate DOA estimates, while being more computationally effective.
Social capital and burnout among mental healthcare providers

Abstract Background: Provider burnout is a critical problem in mental health services. Contributing factors have been explicated across three domains: personal, job and organizational characteristics. Of these, organizational characteristics, including workplace environment, appear to be particularly important given that most interventions addressing burnout via the other domains (e.g. bolstering personal coping skills) have been modestly effective at best. Aims: This study builds on previous research by using social capital as a framework for the experience of work social milieu, and aims to provide a richer understanding of how workplace social environment might impact burnout and help create more effective ways to reduce burnout. Methods: Providers (n = 40) taking part in a larger burnout intervention study were randomly selected to take part in interviews regarding their workplace environment and burnout. Participant responses were analyzed thematically. Results: Workplace social milieu revolved around two primary themes: workplace social capital in provider burnout and the protective qualities of social capital in cohesive work teams that appear to mitigate burnout. Conclusions: These results imply that work environments where managers support collaboration and social interaction among work teams may reduce burnout.