Miracle-dz/UniFAR-FTUs huggingface dataset:
Eurographics Symposium on Geometry Processing 2013 Sparse Iterative Closest Point

x x x (β) (α) p = 2 (a) p = 1 (b) p = . 5 Figure 1: Solving for optimal rigid alignment for incomplete geometry. (a) Traditional least-squares ICP does not distinguish between inliers and outliers, resulting in poor alignment. (b) The 1-ICP is more robust, but still cannot cope with the large amount of correspondence outliers. We show that p-ICP, with p ∈ [0, 1] robustly handles large amounts of noise and outliers. Bottom rows: Illustration of sparsity-inducing norms. (α) Regularization of the input vector (black-framed) with an p-norm leads to increased sparsity as we decrease the value of p. (β) The vector of complements provides an indication of how much its corresponding entry contributes in the optimization. Large outliers (red) contribute progressively less as we decrease p. Abstract Rigid registration of two geometric data sets is essential in many applications, including robot navigation, surface reconstruction, and shape matching. Most commonly, variants of the Iterative Closest Point (ICP) algorithm are employed for this task. These methods alternate between closest point computations to establish correspondences between two data sets, and solving for the optimal transformation that brings these correspondences into alignment. A major difficulty for this approach is the sensitivity to outliers and missing data often observed in 3D scans. Most practical implementations of the ICP algorithm address this issue with a number of heuristics to prune or reweight correspondences. However, these heuristics can be unreliable and difficult to tune, which often requires substantial manual assistance. We propose a new formulation of the ICP algorithm that avoids these difficulties by formulating the registration optimization using sparsity inducing norms. Our new algorithm retains the simple structure of the ICP algorithm, while achieving superior registration results when dealing with outliers and incomplete data. The complete source code of our implementation is provided at +3 +2 +1 p=2.0 p=1.0 p=0.5 p=0.1-1-2-3 0.5 1.0 2.0 2.5 3.0 0 z |z| p 0 0.1 0 0.1 0 0.1 0 0.1 original p = 2 p = 1 p = . 5 p = . 1 Figure 2: (left) A plot of the penalty functions used to induce sparsity in our optimization; for small values of p, large outliers do not incur a large penalty in the optimization; this allows the optimization to effectively discard correspondence outliers when computing the optimal rigid transformation. (right) The alignment of the " coatie " dataset from [AMCO08] with several values …
A parallel graph decomposition algorithm for DNA sequencing with nanopores

MOTIVATION With the potential availability of nanopore devices that can sense the bases of translocating single-stranded DNA (ssDNA), it is likely that 'reads' of length approximately 10(5) will be available in large numbers and at high speed. We address the problem of complete DNA sequencing using such reads. We assume that approximately 10(2) copies of a DNA sequence are split into single strands that break into randomly sized pieces as they translocate the nanopore in arbitrary orientations. The nanopore senses and reports each individual base that passes through, but all information about orientation and complementarity of the ssDNA subsequences is lost. Random errors (both biological and transduction) in the reads create further complications. RESULTS We have developed an algorithm that addresses these issues. It can be considered an extreme variation of the well-known Eulerian path approach. It searches over a space of de Bruijn graphs until it finds one in which (a) the impact of errors is eliminated and (b) both possible orientations of the two ssDNA sequences can be identified separately and unambiguously. Our algorithm is able to correctly reconstruct real DNA sequences of the order of 10(6) bases (e.g. the bacterium Mycoplasma pneumoniae) from simulated erroneous reads on a modest workstation in about 1 h. We describe, and give measured timings of, a parallel implementation of this algorithm on the Cray Multithreaded Architecture (MTA-2) supercomputer, whose architecture is ideally suited to this 'unstructured' problem. Our parallel implementation is crucial to the problem of rapidly sequencing long DNA sequences and also to the situation where multiple nanopores are used to obtain a high-bandwidth stream of reads.
A Common Pathway for Dendritic Cell and Early B Cell Development

B cells and dendritic cells (DCs) each develop from poorly described progenitor cells in the bone marrow (BM). Although a subset of DCs has been proposed to arise from lymphoid progenitors, a common developmental pathway for B cells and BM-derived DCs has not been clearly identified. To address this possibility, we performed a comprehensive analysis of DC differentiative potential among lymphoid and B lymphoid progenitor populations in adult mouse BM. We found that both the common lymphoid progenitors (CLPs), shown here and elsewhere to give rise exclusively to lymphocytes, and a down-stream early B-lineage precursor population devoid of T and NK cell precursor potential each give rise to DCs when exposed to the appropriate cytokines. This result contrasts with more mature B-lineage precursors, all of which failed to give rise to detectable numbers of DCs. Significantly, both CLP and early B-lineage-derived DCs acquired several surface markers associated with functional DCs, and CLP-derived DCs readily induced proliferation of allogeneic CD4+ T cells. Surprisingly, however, DC differentiation from both lymphoid-restricted progenitors was accompanied by up-regulation of CD11b expression, a cell surface molecule normally restricted to myeloid lineage cells including putative myeloid DCs. Together, these data demonstrate that loss of DC developmental potential is the final step in B-lineage commitment and thus reveals a previously unrecognized link between early B cell and DC ontogeny.
Life-history perspective of adaptive radiation in desmognathine salamanders

This study investigates interspecific variation in age at first reproduction, fecundity, and body size in multispecies assemblages of desmognathine salamanders. The hypotheses tested are that interspecific differences in body size among desmognathines stem proximately from variation in age at first reproduction and that variation in the latter trait is positively correlated with variation in fecundity among species. It is shown that a correlation between age at first reproduction and fecundity, combined with a uniform rate of survival, based on available estimates of these parameters, will yield equivalent values of net reproductive rate (Ro) among the species of a given assemblage. Such equivalence represents a form of life-history symmetry. Data from two assemblages are presented in support of the argument for symmetry. Such life-history symmetry may reflect uniformity in morphological specialization in desmognathines. Given the morphological adaptations to burrowing (head-wedging) in the subfamily, the relationship between adult body size and habitat preference in Desmognathus may reflect adaptation to the size of cover objects and composition of the substratum along the aquatic-terrestrial habitat gradient. I propose that these variables, in association with predation and competition, represent the selective factors responsible for body size diversification in Desmognathus.
Regulation of Colonization Density in the Bark Beetle Ips

-About equal numbers of each sex of flying lps paraconfusus Lanier (Coleoptera: Scolytidae) were caught on traps several meters downwind from a male-infested ponderosa pine log releasing pheromone while a significantly different ratio of over four times more females than males were caught at the pheromone source. Females oriented directly to higher concentrations of colonizing males in a felled tree while males tended to land on the host in adjacent uncolonized areas. The attraction response of walking males to a 1 : I : 1 mixture of the synthetic pheromone components ispenol-ipsdienol-cis-verbenol was reduced progressively at higher concentrations while female response continued to increase. These responses may function to regulate density of colonization and limit intraspecific competition. Key Words--Coleoptera, Scolytidae, Ipsparaconfusus, bark beetle, Pinus ponderosa, ipsenol, ipsdienol, cis-verbenol, pheromone, attractant, intraspecific competition.
Large deviation based upper bounds for the LCS-problem

We analyse and apply a large deviation and Montecarlo simulation based method for the computation of improved upper bounds on the Chvatal-Sankoff constant for i.i. d. random sequences over a finite alphabet. Our theoretical results show that this method converges to the exact value of when a control parameter converges to infinity. We also give upper bounds on the complexity for numerically computing the Chvatal-Sankoff constant to any given precision via this method. Our numerical experiments confirm the theory and allow us to give new upper bounds that are correct to two digits.
A Semiquantitative Image-analytical Method for the Recording of Dose-Response Curves in Immunocytochemical Preparations

Knowledge about intracellular signal transduction cascades is largely based on investigations of cultured cells whose responses to different stimuli are typically quantified via RIA, ELISA, or immunoblots. These techniques, which require relatively large amounts of biological material, are performed with homogenized cells and therefore do not allow localization of the molecules under investigation. We describe a protocol for recording dose-response curves directly from immunocytochemical preparations using rat pinealocytes as a model system. The cells were exposed to β-adrenergic stimuli inducing the phosphorylation of the transcription factor CREB (mediated by PKA), an increase in ICER protein levels, and synthesis and release of melatonin. Melatonin concentrations were determined by ELISA. cPKA, phosphorylated CREB, and ICER were demonstrated by immunocytochemistry and immunoblots. Dose-response curves were recorded by measuring the integrated density of the immunoreactive sites with an image analysis program. Dose-response curves from immunoblots and immunocytochemical preparations showed almost identical dynamics, validating the immunocytochemical approach, which minimizes the amount of biological material needed for such studies, allows combined quantification and localization of biomolecules, and may even be more sensitive than immunoblotting.
Chemotherapy- and cancer-related nausea and vomiting

Approximately one half of cancer patients will experience nausea or vomiting during the course of their disease either because of the cancer itself or because of their treatment. Emesis attributable to cancer warrants a careful investigation to determine whether a treatable underlying cause is responsible. Interventions using dexamethasone and octreotide may reduce vomiting attributable to bowel obstruction. In the absence of a bowel obstruction or a correctable cause, the usual approach is a sequential trial of antiemetics guided by considerations of cost and side effects. Major progress in managing chemotherapy-induced emesis followed from the use of a combination of a corticosteroid and 5-hydroxytryptamine3 (5-HT3) receptor antagonist for moderately to highly emetogenic chemotherapy. Nevertheless, vomiting still occurred in approximately 40% of women receiving chemotherapy containing an anthracycline plus cyclophosphamide and in approximately 50% of patients receiving high-dose cisplatin. The addition of aprepitant, a neurokinin 1 receptor antagonist, improved control of emesis by a further 15%–20%, and that agent is now recommended as part of standard antiemetic therapy for patients at high risk of emesis. Based largely on anecdotal experience, cannabinoids and olanzapine are sometimes also recommended in patients with refractory emesis. Phase iii trials are required to confirm their efficacy as add-ons to a corticosteroid, a 5-HT3 receptor antagonist, and possibly aprepitant.
Which Preferences Associate with School Performance? Lessons from a University Classroom Experiment

We attempt to link laboratory-based measures of preferences with measures of school performance. We measure in an incentivized way risk, time, social and competitive preferences and also cognitive abilities of university students and look for associations between these measures and two important academic outcome measures: exam results and GPA. We find consistently that cognitive abilities (proxied by the Cognitive Reflection Test (Frederick 2005)) are very well correlated with school performance. Regarding non-cognitive skills, we find suggestive evidence for many of our measured preferences. We use two alternative measures of time preference: patience and present bias. Present bias explains exam grades relatively better, while patience is better explaining GPA. Both measures of time preferences have a non-linear relation to school performance. Competitiveness matters, as students, who opt for a more competitive payment scheme in our experiments have a higher average GPA and better exam grades. We observe also that risk-averse students perform a little better than risk-loving students. That makes sense in case of multiple choice exams, because risk-loving students may want to try to pass the exam less prepared, as the possibility of passing as exam just by chance is not zero. Finally, we have also detected that cooperative preferences – the amount of money offered in a public good game – associates strongly with GPA, but in a non-linear way. Students who offered around half of their possible amounts had significantly higher GPAs than those, who offered none or all their money.
Pulmonary arterial hypertension in children

Pulmonary arterial hypertension is a serious progressive condition with a poor prognosis if not identified and treated early. Because the symptoms are nonspecific and the physical findings can be subtle, the disease is often diagnosed in its later stages. Remarkable progress has been made in the field of pulmonary arterial hypertension over the past several decades. The pathology is now better defined, and significant advances have occurred in understanding the pathobiologic mechanisms. Risk factors have been identified, and the genetics have been characterized. Advances in technology allow earlier diagnosis as well as better assessment of disease severity. Therapeutic modalities such as new drugs, e.g., epoprostenol, treprostinil, and bosentan, and surgical/interventional options, e.g., transplantation and atrial septostomy, which were unavailable several decades ago, have had a significant impact on prognosis and outcome. Thus, despite our inability to cure pulmonary arterial hypertension, advances in medical treatments over the past two decades have resulted in significant improvement in outcomes for children with various forms of pulmonary arterial hypertension. This report is a review the current state of the art for pulmonary arterial hypertension in 2004, with an emphasis on childhood pulmonary arterial hypertension and specific recommendations for current practice and future directions. Pediatr Pulmonol. 2004; 38:2–22. © 2004 Wiley‐Liss, Inc.
DB-Suite: Experiences with Three Intelligent, Web-Based Database Tutors.

E-learning is becoming more and more popular with the widespread use of computers and the Internet in educational institutions. Current e-learning courses are nearly always developed using course management systems (CMS), such as WebCT or Blackboard. Although CMS tools provide support for some administrative tasks and enable instructors to provide online instructional material, they offer no deep support for learning: students have access to on-line material, simple multi-choice quizzes and chat tools, but there is no ability to track student’s progress and adapt the learning material and instructional session to the individual student. In this paper we present our experiences with three Web-based intelligent tutoring systems in the area of databases. SQL-Tutor teaches the SQL query language, NORMIT is a data normalization tutor, and KERMIT teaches conceptual database modelling using the Entity-Relationship data model. All three tutors in DB-suite have been used and evaluated in the context of genuine teaching activities. We present the most important features of these systems, as well as evaluation results. The DB-suite tutors have proved to be very effective in supporting deep learning, and are well liked by students.
Evidence for mirror systems in emotions

Why do we feel tears well up when we see a loved one cry? Why do we wince when we see other people hurt themselves? This review addresses these questions from the perspective of embodied simulation: observing the actions and tactile sensations of others activates premotor, posterior parietal and somatosensory regions in the brain of the observer which are also active when performing similar movements and feeling similar sensations. We will show that seeing the emotions of others also recruits regions involved in experiencing similar emotions, although there does not seem to be a reliable mapping of particular emotions onto particular brain regions. Instead, emotion simulation seems to involve a mosaic of affective, motor and somatosensory components. The relative contributions of these components to a particular emotion and their interrelationship are largely unknown, although recent experimental evidence suggests that motor simulation may be a trigger for the simulation of associated feeling states. This mosaic of simulations may be necessary for generating the compelling insights we have into the feelings of others. Through their integration with, and modulation by, higher cognitive functions, they could be at the core of important social functions, including empathy, mind reading and social learning.
The Organizers' Ecology: An Empirical Study of Foreign Banks in Shanghai

The organizing stages that predate entry into an organizational population were studied from an ecological perspective. Based on a detailed analysis of foreign banks in Shanghai, findings are presented that suggest that the likelihood of moving from the organizing phase to the operational stages is nonmonotonically dependent on the length of the waiting time. We found that firms seeking to gain entry into a population are negatively affected by the presence of other organizers in close geographical proximity, while the number of already-established organizations has an inverted U-shaped relationship with the aspirants likelihood of entering a relationship that operates more broadly. After investigating the effect of the geographical location of other potential entrants, as well as the effect of relative sizes and countries of origin, we have drawn inferences about the strength of these competitors identities and their impact on a social actors decision to enter the population. Our findings are informative not only for those studying organizational founding patterns, but also for those interested in the early process of identity formation.
The carbon balance of tropical, temperate and boreal forests

Forest biomes are major reserves for terrestrial carbon, and major components of global primary productivity. The carbon balance of forests is determined by a number of component processes of carbon acquisition and carbon loss, and a small shift in the magnitude of these processes would have a large impact on the global carbon cycle. In this paper, we discuss the climatic influences on the carbon dynamics of boreal, temperate and tropical forests by presenting a new synthesis of micrometeorological, ecophysiological and forestry data, concentrating on three case-study sites. Historical changes in the carbon balance of each biome are also reviewed, and the evidence for a carbon sink in each forest biome and its likely behaviour under future global change are discussed. We conclude that there have been significant advances in determining the carbon balance of forests, but there are still critical uncertainties remaining, particularly in the behaviour of soil carbon stocks.
Thyroid Hormone Profile in Patients With Acute Coronary Syndrome

Background: Thyroid hormone has the a major role in the cardiovascular system function and cardiac a As well as to maintain the cardiovascular homeostasis A slightly change ind thyroid status actually affects cardiovascular mortality hemodynamic. The background of this study was to define the prevalence of thyroid dysfunction in acute coronary syndrome (ACS). Objectives: The primary objective was to define the prevalence of thyroid dysfunction in acute coronary syndrome, including Non-ST Segment Elevation Myocardial Infarction (NSTEMI), ST-segment Elevation Myocardial Infarction (STEMI), and unstable angina groups. The secondary objective was to determine any associations of thyroids function tests with cardiac catheterization and mortality. Patients and Methods: In a prospective, observational, and cross section study, we enrolled 400 patients admitted at the coronary care unit of King Abdulaziz University Hospital in Jeddah, Saudi Arabia. Venous blood samples were collected from patients for the evaluation of thyroid function (thyroids stimulating hormones, free triiodothyronine, and free thyroxin). Results: Excluding those taking thyroid hormone preparations, 76.7% of patients admitted with acute coronary heart disease (ST-segment elevation myocardial infarction and Non-ST segment elevation myocardial infarction), and unstable angina had euthyroidism. Thyroid dysfunction was reported in 23.3% of patients with coronary heart disease. Overall hypothyroidism prevalence was 7.8%, while subclinical hyperthyroidism in our study was 2.7%. Overt hyperthyroidism and subclinical hyperthyroidism was reported 2.0% and 0.5%, respectively. Euthyroid sick syndrome was noticed in 41 (10.2%) of critically ill patients. The mortality rate was 9.8%; all death patients had low triiodothyronine (T3) syndrome and were associated with statistically significant low free triiodothyronine (FT3) (P > 0.001). Conclusions: No significant variance was observed among patients underwent for cardiac catheterization, STEMI, NSTEMI, unstable angina, and atrial fibrillation with respect to FT4, FT3, and TSH levels during coronary care unit hospitalization based on their profile data.
Expanding the conceptual and empirical boundaries of family communication patterns: The development and validation of an Expanded Conformity Orientation Scale

ABSTRACT Family communication patterns theory (FCPT) explores how family members communicate to create a shared social reality via conversation and conformity orientations. Recently, scholars have noted that the current conceptualization and operationalization of conformity orientation is unnecessarily narrow in scope by representing conformity as controlling and repressive, rather than as cultivating homogenous attitudes, beliefs, and values among family members. To address these concerns, we tested the factor structure of the most common measure in FCPT research, the Revised Family Communication Patterns scale (Study One). Based on theoretical and methodological concerns that emerged from Study One, we then created and validated a new scale in Study Two – the Expanded Conformity Orientation Scale (ECOS). Findings from Study Two demonstrated concurrent and discriminant validity. Implications for the use of the ECOS in future studies are discussed.