Miracle-dz/UniFAR-FTUs huggingface dataset:
On the impact of layout quality to understanding UML diagrams

Practical experience suggests that use and understanding of UML diagrams is greatly affected by the quality of their layout. However, existing experimental evidence for this effect is been weak and inconclusive. In this paper, we explore two explanations. Firstly, we observe that the visual qualities of diagrams are more prominent in earlier life cycle phases so that the impact of layout quality should be more apparent in models and diagram types used there, an aspect not studied in previous research. Secondly, in practice, good layouts use many different heuristics simultaneously whereas previous research considered them in isolation only. In this paper, we report the results of a series of controlled experiments using compound layouts on requirements analysis models. With very high significance, we find a notable impact of the layout quality measured by different aspects of cognitive load.
Unsupervised Placental Gene Expression Profiling Identifies Clinically Relevant Subclasses of Human Preeclampsia

Preeclampsia (PE) is a complex, hypertensive disorder of pregnancy, demonstrating considerable variability in maternal symptoms and fetal outcomes. Unfortunately, prior research has not accounted for this variability, resulting in a lack of robust biomarkers and effective treatments for PE. Here, we created a large (N=330) clinically relevant human placental microarray data set, consisting of 7 previously published studies and 157 highly annotated new samples from a single BioBank. Applying unsupervised clustering to this combined data set identified 3 clinically significant probable etiologies of PE: “maternal”, with healthy placentas and term deliveries; “canonical”, exhibiting expected clinical, ontological, and histopathologic features of PE; and “immunologic” with severe fetal growth restriction and evidence of maternal antifetal rejection. Moreover, these groups could be distinguished using a small quantitative polymerase chain reaction panel and demonstrated varying influence of maternal factors on PE development. An additional subclass of PE placentas was also revealed to form because of chromosomal abnormalities in these samples, supported by array-based comparative genomic hybridization analysis. Overall, our findings represent a new paradigm in our understanding of the origins and maternal–placental contributions to the pathology of PE. The study of PE represents a unique opportunity to access human tissue associated with a complex hypertensive disorder, and our novel approach could be applied to other hypertensive and heterogeneous human diseases.
Inhibition of Cytochromes P450: Existing and New Promising Therapeutic Targets

Mammalian cytochromes P450 have been shown to play highly important roles in the metabolism of drugs and xenobiotics as well as in the biosynthesis of a variety of endogenous compounds, many of them displaying hormonal function. The role of P450s as therapeutic targets is still inadequately recognized although several P450 inhibitors became efficient drugs that even reached blockbuster status. Here, we try to give a comprehensive overview on cytochromes P450s, which are already well-established targets – particularly focussing on the treatment of infectious diseases, metabolic disorders and cancer – and on those, which have a high potential to become successful targets. In addition, the design of inhibitors of cytochromes P450 will be discussed.
Incidence and Consequences of Neonatal Alloimmune Thrombocytopenia: A Systematic Review

BACKGROUND: Neonatal alloimmune thrombocytopenia (NAIT) is a potentially devastating disease that may lead to intracranial hemorrhage in the fetus or neonate, often with death or major neurologic damage. There are no routine screening programs for NAIT, preventive measures are taken only in a subsequent pregnancy. To estimate the population incidence of NAIT and its consequences, we conducted a review of the literature. Our results may aid in the design of a screening program. METHODS: An electronic literature search included Medline, Embase, Cochrane database and references of retrieved articles. Eligible for inclusion were all prospective studies aimed at diagnosing NAIT in a general, nonselected newborn population, with sufficient information on platelet count at birth, bleeding complications, and treatment. Titles and abstracts were reviewed, followed by review of full text publications. Studies were independently assessed by 2 reviewers for methodologic quality. Disagreements were resolved by consensus, including a third reviewer. RESULTS: From the initial 768 studies, 21 remained for full text analysis, 6 of which met the inclusion criteria. In total, 59 425 newborns were screened, with severe thrombocytopenia in 89 cases (0.15%). NAIT was diagnosed in 24 of these 89 newborns (27%). In 6 (25%) of these cases, an intracranial hemorrhage was found, all likely of antenatal origin. CONCLUSIONS: NAIT is among the most important causes of neonatal thrombocytopenia. Intracranial hemorrhage due to NAIT occurs in 10 per 100 000 neonates, commonly before birth. Screening for NAIT might be effective but should be done antenatally.
Fitting Models of Multiple Hypotheses to Partial Population Data: Investigating the Causes of Cycles in Red Grouse

There are two postulated causes for the observed periodic fluctuations (cycles) in red grouse (Lagopus lagopus scoticus). The first involves interaction with the parasitic nematode Trichostrongylus tenuis. The second invokes delayed regulation through the effect of male aggressiveness on territoriality. Empirical evidence exists to support both hypotheses, and each hypothesis has been modeled deterministically. However, little effort has gone into looking at the combined effects of the two mechanisms or formally fitting the corresponding models to field data. Here we present a model for red grouse dynamics that includes both parasites and territoriality. To explore the single and combined hypotheses, we specify three versions of this model and fit them to data using Bayesian state‐space modeling, a method that allows statistical inference to be performed on mechanistic models such as ours. Output from the three models is then examined to determine their goodness of fit and the biological plausibility of the parameter values required by each to fit the population data. While all three models are capable of emulating the observed cyclic dynamics, only the model including both aggression and parasites does so under consistently realistic parameter values, providing theoretical support for the idea that both mechanisms shape red grouse cycles.
Early online identification of attention gathering items in social media

Activity in social media such as blogs, micro-blogs, social networks, etc is manifested via interaction that involves text, images, links and other information items. Naturally, some items attract more attention than others, expressed with large volumes of linking, commenting or tagging activity, to name a few examples. Moreover, high attention can be indicative of emerging events, breaking news or generally indicate information items of interest to a vast set of people. The numbers associated with digital social activity are astonishing: in excess of millions of blog posts, tweets and forums updates per day, millions of tags in photos, news articles or blogs. Being able to identify information items that gather much attention in such a real time information collective is a challenging task. In this paper, we consider the problem of early online identification of items that gather a lot of attention in social media. We model social media activity using ISIS, a stochastic model for Interacting Streaming Information Sources, that intuitively captures the concept of attention gathering information items. Given the challenge of the information overload characterizing digital social activity, we present sequential statistical tests that enable early identification of attention gathering items. This effectively reduces the set of items one has to monitor in real time in order to identify pieces of information attracting a lot of attention. Experiments on real data demonstrate the utility of our model, as well as the efficiency and effectiveness of the proposed sequential statistical tests.
Thoracic Manifestations of Sickle Cell Disease

Sickle cell disease is the most common inherited disease in the African American population. Multiorgan pathologic features with a predilection for thoracic organs predominate. Acute cardiopulmonary diseases include acute chest syndrome, pneumonia, and left ventricular failure. Cardiomegaly, pleural effusions, pulmonary consolidation, pulmonary edema on chest radiographs, and ground-glass opacities on computed tomographs are characteristic. Chronic changes include sickle cell lung disease with lung fibrosis, pulmonary arterial hypertension, hyperkinetic circulation related to severe anemia, and thoracic skeletal abnormalities; the latter are H-shaped vertebrae, rib infarction, and extramedullary hematopoesis.
Polly: "being there" through the parrot and a guide

Telepresence systems usually lack mobility. Polly, a wearable telepresence device, allows users to explore remote locations or experience events remotely by means of a person that serves as a mobile "guide". We built a series of hardware prototypes and our current, most promising embodiment consists of a smartphone mounted on a stabilized gimbal that is wearable. The gimbal enables remote control of the viewing angle as well as providing active image stabilization while the guide is walking. We present qualitative findings from a series of 8 field tests using either Polly or only a mobile phone. We found that guides felt more physical comfort when using Polly vs. a phone and that Polly was accepted by other persons at the remote location. Remote participants appreciated the stabilized video and ability to control camera view. Connection and bandwidth issues appear to be the most challenging issues for Polly-like systems.
Ant Colony Optimization for mapping, scheduling and placing in reconfigurable systems

Modern heterogeneous embedded platforms, composed of several digital signal, application specific and general purpose processors, also include reconfigurable devices supporting partial dynamic reconfiguration. These devices can change the behavior of some of their parts during execution, allowing hardware acceleration of more sections of the applications. Nevertheless, partial dynamic reconfiguration imposes severe overheads in terms of latency. For such systems, a critical part of the design phase is deciding on which processing elements (mapping) and when (scheduling) executing a task, but also how to place them on the reconfigurable device to guarantee the most efficient reuse of the programmable logic. In this paper we propose an algorithm based on Ant Colony Optimization (ACO) that simultaneously executes the scheduling, the mapping and the linear placing of tasks, hiding reconfiguration overheads through pre-fetching. Our heuristic gradually constructs solutions and then searches around the best ones, cutting out non-promising areas of the design space. We show how to consider the partial dynamic reconfiguration constraints in the scheduling, placing and mapping problems and compare our formulation to other heuristics that address the same problems. We demonstrate that our proposal is more general and robust, and finds better solutions (16.5% in average) with respect to competing solutions.
MONIC: modeling and monitoring cluster transitions

There is much recent work on detecting and tracking change in clusters, often based on the study of the spatiotemporal properties of a cluster. For the many applications where cluster change is relevant, among them customer relationship management, fraud detection and marketing, it is also necessary to provide insights about the nature of cluster change: Is a cluster corresponding to a group of customers simply disappearing or are its members migrating to other clusters? Is a new emerging cluster reflecting a new target group of customers or does it rather consist of existing customers whose preferences shift? To answer such questions, we propose the framework MONIC for modeling and tracking of cluster transitions. Our cluster transition model encompasses changes that involve more than one cluster, thus allowing for insights on cluster change in the whole clustering. Our transition tracking mechanism is not based on the topological properties of clusters, which are only available for some types of clustering, but on the contents of the underlying data stream. We present our first results on monitoring cluster transitions over the ACM digital library.
Algorithm Performance and Problem Structure for Flow-shop Scheduling

Test suites for many domains often fail to model features present in real-world problems. For the permutation flow-shop sequencing problem (PFSP), the most popular test suite consists of problems whose features are generated from a single uniform random distribution. Synthetic generation of problems with characteristics present in real-world problems is a viable alternative. We compare the performance of several competitive algorithms on problems produced with such a generator. We find that, as more realistic characteristics are introduced, the performance of a state-of-the-art algorithm degrades rapidly: faster and less complex stochastic algorithms provide superior performance. Our empirical results show that small changes in problem structure or problem size can influence algorithm performance. We hypothesize that these performance differences may be partially due to differences in search space topologies; we show that structured problems produce topologies with performance plateaus. Algorithm sensitivity to problem charaeteristics suggests the need to construct test suites more representative of real-world applications.
Identification of cancer stem cells and a strategy for their elimination

It has been established previously that up to 40% of mouse CD34+ hematopoietic stem cells are capable of internalizing exogenous dsDNA fragments both in vivo and ex vivo. Importantly, when mice are treated with a combination of cyclophosphamide and dsDNA, the repair of interstrand crosslinks in hematopoietic progenitors is attenuated, and their pluripotency is altered. Here we show for the first time that among various actively proliferating mammalian cell populations there are subpopulations capable of internalizing dsDNA fragments. In the context of cancer, such dsDNA-internalizing cell subpopulations display cancer stem cell-like phenotype. Furthermore, using Krebs-2 ascites cells as a model, we found that upon combined treatment with cyclophosphamide and dsDNA, engrafted material loses its tumor-initiating properties which we attribute to the elimination of tumor-initiating stem cell subpopulation or loss of its tumorigenic potential.
Space–Time Covariation of Mortality with Temperature: A Systematic Study of Deaths in France, 1968–2009

Background The temperature–mortality relationship has repeatedly been found, mostly in large cities, to be U/J-shaped, with higher minimum mortality temperature (MMT) at low latitudes being interpreted as indicating human adaptation to climate. Objectives Our aim was to partition space with a high-resolution grid to assess the temperature–mortality relationship in a territory with wide climate diversity, over a period with notable climate warming. Methods The 16,487,668 death certificates of persons > 65 years of age who died of natural causes in continental France (1968–2009) were analyzed. A 30-km × 30-km grid was placed over the map of France. Generalized additive model regression was used to assess the temperature–mortality relationship for each grid square, and extract the MMT and the RM25 and RM25/18 (respectively, the ratios of mortality at 25°C/MMT and 25°C/18°C). Three periods were considered: 1968–1981 (P1), 1982–1995 (P2), and 1996–2009 (P3). Results All temperature–mortality curves computed over the 42-year period were U/J-shaped. MMT and mean summer temperature were strongly correlated. Mean MMT increased from 17.5°C for P1 to 17.8°C for P2 and to 18.2°C for P3 and paralleled the summer temperature increase observed between P1 and P3. The temporal MMT rise was below that expected from the geographic analysis. The RM25/18 ratio of mortality at 25°C versus that at 18°C declined significantly (p = 5 × 10–5) as warming increased: 18% for P1, 16% for P2, and 15% for P3. Conclusions Results of this spatiotemporal analysis indicated some human adaptation to climate change, even in rural areas. Citation: Todd N, Valleron AJ. 2015. Space–time covariation of mortality with temperature: a systematic study of deaths in France, 1968–2009. Environ Health Perspect 123:659–664; http://dx.doi. org/10.1289/ehp.1307771
HMGA1 Levels Influence Mitochondrial Function and Mitochondrial DNA Repair Efficiency

ABSTRACT HMGA chromatin proteins, a family of gene regulatory factors found at only low concentrations in normal cells, are almost universally overexpressed in cancer cells. HMGA proteins are located in the nuclei of normal cells except during the late S/G2 phases of the cell cycle, when HMGA1, one of the members of the family, reversibly migrates to the mitochondria, where it binds to mitochondrial DNA (mtDNA). In many cancer cells, this controlled shuttling is lost and HMGA1 is found in mitochondria throughout the cell cycle. To investigate the effects of HMGA1 on mitochondria, we employed a genetically engineered line of human MCF-7 cells in which the levels of transgenic HMGA1 protein could be reversibly controlled. “Turn-ON” and “turn-OFF” time course experiments were performed with these cells to either increase or decrease intracellular HMGA1 levels, and various mitochondrial changes were monitored. Results demonstrated that changes in both mtDNA levels and mitochondrial mass inversely paralleled changes in HMGA1 concentrations, strongly implicating HMGA1 in the regulation of these parameters. Additionally, the level of cellular reactive oxygen species (ROS) increased and the efficiency of repair of oxidatively damaged mtDNA decreased as consequences of elevated HMGA1 expression. Increased ROS levels and reduced repair efficiency in HMGA1-overexpressing cells likely contribute to the increased occurrence of mutations in mtDNA frequently observed in cancer cells.
Ngram2vec: Learning Improved Word Representations from Ngram Co-occurrence Statistics

The existing word representation methods mostly limit their information source to word co-occurrence statistics. In this paper, we introduce ngrams into four representation methods: SGNS, GloVe, PPMI matrix, and its SVD factorization. Comprehensive experiments are conducted on word analogy and similarity tasks. The results show that improved word representations are learned from ngram co-occurrence statistics. We also demonstrate that the trained ngram representations are useful in many aspects such as finding antonyms and collocations. Besides, a novel approach of building co-occurrence matrix is proposed to alleviate the hardware burdens brought by ngrams.
Aspectual Support for Specifying Requirements in Software Product Lines

We present an aspect-oriented requirements specification system for software product lines. We encapsulate nonfunctional concerns as a set of advices for transforming parameterized requirements to product-specific requirements. We apply our system to the Health Watcher case study to demonstrate our approach. We sort out system requirements, exception handling requirements (alternate flows) and non-functional requirements and represent them as aspects in our framework. We have implemented a prototype transformation tool which takes these aspects along with the basic functional requirements as input and produces a requirements document with all applicable aspects woven in.
A Time-Variant Processing Approach for the Analysis of Alpha and Gamma MEG Oscillations During Flicker Stimulus Generated Entrainment

Repetitive flicker stimulation (photic driving) offers the possibility to study the properties and coupling characteristics of stimulation-sensitive neuronal oscillators by means of the MEG/EEG analysis. With flicker frequencies in the region of the individual alpha band frequency, the dynamics of the entrainment process of the alpha oscillation, as well as the dynamics of the accompanying gamma oscillations and the coupling between the oscillations, are investigated by means of an appropriate combination of time-variant analysis methods. The Hilbert and the Gabor transformation reveal time-variant properties (frequency entrainment, phase locking, and n:m synchronization) of the entrainment process in the whole frequency range. Additionally, time-variant partial directed coherence is applied to identify ocular saccadic interferences and to study the directed information transfer between the recording sites of the simultaneously derived MEG/EEG data during the entrainment. The MEG data is the focus of this methodological study as the entrainment effects of the alpha oscillation are stronger in MEG than in the EEG. The occipital brain region (visual cortex) was mainly investigated and the dynamics of the alpha entrainment quantified. It can be shown that at the beginning of this entrainment, a transient, strongly phase-locked “40-Hz” gamma oscillation occurs.
How much choice is too much?

Providing a learner-centered perspective is in keeping with modern constructivist approaches to learning, and this means that courses must be designed with learner attributes and choice in mind. Concerns over accreditation and the need for accountability at the post-secondary level seem to contradict freedom of choice and flexibility of term work, but this need not be the case. This paper outlines numerous strategies for offering choice and flexibility to students in a freshman programming course. Approaches include flexible deadlines, the ability to re-submit work that has already been assessed, writing tasks, contributing to course content, bonuses for embellishments and extra work, and choices about which problems to solve. All of the strategies have been employed in classes, and students' reactions as well as effects on student engagement and quality of work are described.