Miracle-dz/UniFAR-FTUs huggingface dataset:
Intrauterine Exposure to Maternal Atherosclerotic Risk Factors Increases the Susceptibility to Atherosclerosis in Adult Life

Objective— Maternal hypercholesterolemia is associated with a higher incidence and faster progression of atherosclerotic lesions in neonatal offspring. We aimed to determine whether an in utero environment exposing a fetus to maternal hypercholesterolemia and associated risk factors can prime the murine vessel wall to accelerated development of cardiovascular disease in adult life. Methods and Results— To investigate the epigenetic effect in utero, we generated genetically identical heterozygous apolipoprotein E–deficient progeny from mothers with a wild-type or apolipoprotein E–deficient background. A significant increase in loss of endothelial cell volume was observed in the carotid arteries of fetuses of apolipoprotein E–deficient mothers, but fatty streak formation was absent. Spontaneous atherosclerosis development was absent in the aorta and carotid arteries in adult life. We unilaterally placed a constrictive collar around the carotid artery to induce lesion formation. In offspring from apolipoprotein E–deficient mothers, collar placement resulted in severe neointima formation in 9 of 10 mice analyzed compared with only minor lesion volume (2 of 10) in the progeny of wild-type mothers. Conclusions— We conclude that the susceptibility to neointima formation of morphologically normal adult arteries is already imprinted during prenatal development and manifests itself in the presence of additional atherogenic risk factors in adult life. Future research will concentrate on the mechanisms involved in this priming process, as well as on prevention strategies.
Characterization of neuronal death induced by focally evoked limbic seizures in the C57BL/6 mouse

Research into the molecular mechanisms of epileptic brain injury is hampered by the resistance of key mouse strains to seizure‐induced neuronal death evoked by systemically administered excitotoxins such as kainic acid. Because C57BL/6 mice are extensively employed as the genetic background for transgenic/knockout modeling in cell death research but are seizure resistant, we sought to develop a seizure model in this strain characterized by injury to the hippocampal CA subfields. Adult male C57BL/6 mice underwent focally evoked seizures induced by intraamygdala microinjection of kainic acid. Kainic acid (KA) effectively elicited ipsilateral CA3 pyramidal neuronal death within a narrow dose range of 0.1–0.3 μg, with mortality <10%. With employment of the most consistent (0.3 μg) dose, seizures were terminated 15, 30, 60, or 90 min after KA by diazepam. Damage was largely restricted to the ipsilateral CA3 subfield of the hippocampus, but injury was also consistent within CA1, suggesting that this mouse model better reflects the hippocampal neuropathology of human temporal lobe epilepsy than does the rat, in which CA1 is typically spared. Confirming this CA1 injury as seizure specific and not a consequence of ischemia, we used laser‐Doppler flowmetry to determine that cerebral perfusion did not significantly change (97% to 118%) over control. Degenerating cells were >95% neuronal as determined by neuron‐specific nuclear protein (NeuN) counterstaining of terminal deoxynucleotidyl transferase‐mediated dUTP nick end‐labeled (TUNEL) brain sections. Furthermore, TUNEL‐positive cells often exhibited the morphological features of apoptosis, and small numbers were positive for cleaved caspase‐3. These data establish a mouse model of focally evoked seizures in the C57BL/6 strain associated with a restricted pattern of apoptotic neurodegeneration within the hippocampal subfields that may be applied to research into the molecular basis of neuronal death after seizures. © 2002 Wiley‐Liss, Inc.
An all-digital phase-locked loop compiler with liberty timing files

In this paper, an all-digital phase-locked loop (ADPLL) compiler with liberty timing files (.lib) is presented. The proposed digitally controlled oscillator (DCO) frequency range estimation algorithm can accurately compute the frequency range of the DCO with only liberty timing files. Therefore, the proposed ADPLL compiler can generate a wide frequency range and monotonic response DCO circuit according to the user input specifications. The generated DCO circuit is designed with standard cells. Thus, the design turnaround time for the ADPLL can be greatly reduced. The proposed ADPLL compiler is verified with SPICE circuit simulator. The maximum frequency estimation error is smaller than 5.92% in 90nm or 65nm CMOS processes.
Myoelectric Control Development Toolbox

Surface myoelectric signals (MES) can be used as effective input for the control of upper arm prostheses. The concept of myoelectric control was introduced in the 1940’s [1]. Initially, amplitude measures were used to parameterize the MES, but simple approach imposed a practical limit of a three state system for each MES control site (e.g. rest, hand open, and hand close) [2]; therefore, to implement a multifunctional prosthetic control system, additional MES control sites were required. Graupe and Cline [3] parameterized the MES using an autoregressive-moving-average model, instead of simple amplitude measures, and were successful at discerning multiple intended limb movements from a single MES control site. This result demonstrated that given the proper signal features, it was feasible to implement a multifunctional prosthetic control system.
A Semi-Supervised Method for Segmenting Multi-Modal Data

Human activity datasets collected under natural conditions are an important source of data. Since these contain multiple activities in unscripted sequence, temporal segmentation of multimodal datasets is an important precursor to recognition and analysis. Manual segmentation is prohibitively time consuming and unsupervised approaches for segmentation are unreliable since they fail to exploit the semantic context of the data. Gathering labels for supervised learning places a large workload on the human user since it is relatively easy to gather a mass of unlabeled data but expensive to annotate. This paper proposes an active learning approach for segmenting large motion capture datasets with both small training sets and working sets. Support Vector Machines (SVMs) are learned using an active learning paradigm; after the classifiers are initialized with a small set of labeled data, the users are iteratively queried for labels as needed. We propose a novel method for initializing the classifiers, based on unsupervised segmentation and clustering of the dataset. By identifying and training the SVM with points from pure clusters, we can improve upon a random sampling strategy for creating the query set. Our active learning approach improves upon the initial unsupervised segmentation used to initialize the classifier, while requiring substantially less data than a fully supervised method; the resulting segmentation is comparable to the latter while requiring significantly less effort from the user.
Patterns of relapse and associated cost burden in schizophrenia patients receiving atypical antipsychotics

Abstract Objective: To identify relapse in schizophrenia and the main cost drivers of relapse using a cost-based algorithm. Methods: Multi-state Medicaid data (1997–2010) were used to identify adults with schizophrenia receiving atypical antipsychotics (AP). The first schizophrenia diagnosis following AP initiation was defined as the index date. Relapse episodes were identified based on (1) weeks during the ≥2 years post-index associated with high cost increase from baseline (12 months before the index date) and (2) high absolute weekly cost. A compound score was then calculated based on these two metrics, where the 54% of patients associated with higher cost increase from baseline and higher absolute weekly cost were considered relapsers. Resource use and costs of relapsers during baseline and relapse episodes were compared using incidence rate ratios (IRRs) and bootstrap methods. Results: In total, 9793 relapsers were identified with a mean of nine relapse episodes per patient. Duration of relapse episodes decreased over time (mean [median]; first episode: 34 [4] weeks; remaining episodes: 8 [1] weeks). Compared with baseline, resource utilization during relapse episodes was significantly greater in pharmacy, outpatient, and institutional visits (hospitalizations, emergency department visits), with IRRs ranging from 1.9–2.4 (all p < 0.0001). Correspondingly, relapse was associated with a mean (95% CI) incremental cost increase of $2459 ($2384–$2539) per week, with institutional visits representing 53% of the increase. Limitations: Relapsers and relapse episodes were identified using a cost-based algorithm, as opposed to a more clinical definition of relapse. In addition, their identification was based on the assumption from literature that ∼54% of schizophrenia patients will experience at least one relapse episode over a 2-year period. Conclusions: Significant cost increases were observed with relapse in schizophrenia, driven mainly by institutional visits.
Test Data Generation for Web Applications: A Constraint and Knowledge-based Approach

Software testing is an important part of the software development process. Much work been has done on automating various parts of testing. In previous work, we had proposed a knowledge-based approach to generate test scenarios for Web applications. However, our previous work did not account for generation of actual test data. Thus, in order to execute the test scenarios, the user would need to (manually) create the test data. This paper proposes an approach to generate test data for our previously proposed test scenario generation tool. Our approach can generate two types of test data: constraint-based test data and database-based test data. Our tool can now automatically execute the combined test scenario and test data. We confirmed the usefulness of our approach through a case study. Keywords-test data generation; Web applications; test scenario
An Overview of Value at Risk

This article gives a broad and accessible overview o f models o f value at risk (WR), a popular measure o f the market risk of afinancialfirm’s “book,” the list ofpositions in various instruments that expose the firm to financial risk. Roughly speaking, the value at risk o f a portjolio is the loss in market value over a given time period, such as one day or two weeks, that is exceeded with a small probability, such as 1%. We focus narrowly on the market risk associated with changes in the prices or rates of underlying traded instruments. Traditionally, this would include such aspects o f credit risk as the risk o f changes in the spreads ofpublicly traded corporate and sovereign bonds. In order to maintain a narrow focus, however, I/aR does not traditionally include, and we do not review here, the risk ofdefdult on long-term derivative contracts. We begin with models o f the distribution ofunderlying market returns and ofvolatility, emphasizing the roles o f price jumps and o f stochastic volatility in determining the ‘ffatness” o f the tails o f the distributions o f returns in various markets. We then turn to methods for approximating the value at risk o f derivatives, using numerical approximations based on delta andgamma. Estimation o f the value at risk o f a portjolio ofpositions is then discussed, beginning with the choice of which risk factors to include. A n extensive numerical example illustrates the accuracy of various alternative methods, allowing for correlated jumps in the underlying market prices. Finally, we review “scenario analysis,” which treats the potential losses associated with particular scenarios, such as a given parallel shiji o f a yield curve or a given change in volatility.
Global Variation in Cleft Palate Repairs: An Analysis of 352,191 Primary Cleft Repairs in Low- to Higher-Middle-Income Countries

Objectives Resources for repair of cleft lip and palate may be lacking in low- and middle-income countries. The Smile Train is a registered charity that supports cleft repair in resource-poor settings. In the global health care challenge, it has been suggested that many babies born with cleft palates are not repaired. This study aims to determine whether any variation exists in the proportion of cleft lip and cleft palate repairs undertaken in low- and middle-income countries. Methods Data were obtained from the Smile Train database of 352,191 consecutive cleft operations performed between 2008 and 2011 in low- to higher-middle-income countries. The ratio of cleft lip to palate repair was analyzed as a function of geographic region and by country income (gross national income). Results A significant correlation exists between both the income of a country and its geographical region to the ratio of lip and palate repair procedures undertaken. Higher-income countries had a higher ratio of cleft palate repairs. Countries in sub-Saharan Africa have the lowest proportion of cleft palate repairs. Conclusion This study emphasizes that many babies born with cleft palates in resource-poor regions do not have their palates repaired. This finding may be explained by an increased neonatal mortality in cleft palate babies. Furthermore, fewer isolated palatal clefts may present to an appropriate health care facility or there may be a reluctance to treat cleft palate due to concerns regarding higher perioperative risks or the lack of available surgical and anesthetic expertise.
Translation initiation start prediction in human cDNAs with high accuracy

MOTIVATION Correct identification of the Translation Initiation Start (TIS) in cDNA sequences is an important issue for genome annotation. The aim of this work is to improve upon current methods and provide a performance guaranteed prediction. METHODS This is achieved by using two modules, one sensitive to the conserved motif and the other sensitive to the coding/non-coding potential around the start codon. Both modules are based on Artificial Neural Networks (ANNs). By applying the simplified method of the ribosome scanning model, the algorithm starts a linear search at the beginning of the coding ORF and stops once the combination of the two modules predicts a positive score. RESULTS According to the results of the test group, 94% of the TIS were correctly predicted. A confident decision is obtained through the use of the Las Vegas algorithm idea. The incorporation of this algorithm leads to a highly accurate recognition of the TIS in human cDNAs for 60% of the cases. AVAILABILITY The program is available upon request from the author.
Logic-based Methods for Reasoning About Search in Classical Planning

I am currently roughly 9 months into my PhD studies, and the final topic of my PhD thesis is not yet fully settled. My current idea is to focus on general logic-based methods for reasoning about heuristics and other kinds of knowledge exploited by today’s classical planning systems. Planning research in the last two decades has led to the development of powerful methods for deriving heuristic distance information for classical planning, based on concepts such as delete relaxation (Hoffmann and Nebel 2001), critical paths (Haslum and Geffner 2000), abstraction (Edelkamp 2001), landmarks (Richter, Helmert, and Westphal 2008) and network flows (van den Briel et al. 2007). A limitation of much of the current work on such distance heuristics is that they are “black boxes” to the planning system that conducts the overall search for a solution: a search algorithm can feed a state to a heuristic estimator and receive a distance estimate from it, but the search algorithm does not have access to information how the given estimate was derived. For example, if a distance estimator returns an infinite heuristic estimate, telling us that a solution does not exist from a given state, it might be useful to know what it is about the current state that leads to this judgment. Perhaps this information can be generalized and usefully applied to other states later encountered during a search (similar to clause learning in SAT solving algorithms). Perhaps we can understand the power and limitations of distance heuristics better if they could give us “explanations” of how they come up with our heuristic estimates. Perhaps we could trust the implementation of an optimal heuristic search algorithm more if we had a way of independently verifying that the heuristic estimates it returns are really admissible, similar to the way that many SAT solvers can emit resolution proofs showing that input formulas claimed to be unsolvable are indeed unsolvable. I want to investigate questions of this kind by making planning heuristics and other sources of knowledge about planning tasks, such as landmarks, more transparent by representing them as logical formulas that can be used in generic logical reasoning engines. The hope is that this will lead to a better understanding of current search heuristics, generic methods for combining and generalizing heuristic information, new ways of leveraging existing SAT solving technology within planning, and in the building of bridges between current state-space search planners and SAT-based planners (Kautz and Selman 1992; Rintanen 2010) In the following I describe two concrete ideas that exemplify this general research direction. The first, “A General Framework for Deriving and Exploiting Information in Classical Planning”, describes ongoing and mostly completed work which is based on my MSc thesis, “A General LTL Framework for Describing Control Knowledge in Classical Planning” (Simon 2014). The second, “A Reachability Proof System”, describes a research idea that I intend to develop further in the next months.
Creation of a Style Independent Intelligent Autonomous Citation Indexer to Support Academic Research

This paper describes the current state of RUgle, a system for classifying and indexing papers made available on the World Wide Web, in a domain-independent and universal manner. By building RUgle with the most relaxed restrictions possible on the formatting of the documents it can process, we hope to create a system that can combine the best features of currently available closed library searches that are designed to facilitate academic research with the inclusive nature of general purpose search engines that continually crawl the web and add documents to their indexed database.
Simulation of quantum interference by reactions of chemical type

A quantum unitary evolution alternated with measurements is simulated by a bubble filled with fictitious particles called amplitude quanta that move chaotically and can be transformed by the simple rules that look like chemical reactions. A basic state of simulated system is treated as a collision of the two corresponding amplitude quanta, that gives the quantum statistics of measurements. The movement of the external membrane of the bubble corresponds to the classical dynamics of the simulated system. Measurements are treated as the membrane perforations and they are completely determined by initial conditions. An identity of particles and an entanglement is simulated by the membranes touching. The required memory grows linearly where the number of particles increases, but entangled states of the big number of particles can be simulated. The method can be used for a visualization of quantum dynamics.
Identification by differential display of alpha 6 integrin as a candidate tumor suppressor gene

A new method of differential expression cloning called differential display (DD) has been used to screen for novel tumor suppressor genes involved in breast cancer. The screen is based on positive selection at the mRNA level for genes expressed in normal mammary epithelial cells but decreased or lost in corresponding tumor cells. A candidate tumor suppressor gene recovered by DD is integrin alpha‐6 (α6), a component of the heterodimeric integrin receptors α6β1 and α6β4. Loss of α6 expression was confirmed in total RNAs by Northern blot analysis and by immunostaining with α6 antibodies. Consistent with these cell culture findings, previous immunostaining of mammary tissue sections has identified decreased α6 protein expression during breast tumor progression. Southern blot analysis demonstrated that α6 gene is present in tumor cell lines, suggesting that re‐expression may be inducible by pharmacological intervention. The likelihood that α6 may have tumor suppressing activity is supported by growing evidence of a central role for integrins in transducing growth control and differentiation signals from growth factors and the extracellular matrix (ECM). —Sager, R. , Anisowicz, A. , Neveu, M. , Liang, P., Sotiropoulou, G. Identification by differential display of alpha‐6 integrin as a candidate tumor suppressor gene. FASEB J. 7: 964‐970; 1993.
Quantification of MSCs involved in wound healing: use of SIS to transfer MSCs to wound site and quantification of MSCs involved in skin wound healing

Mesenchymal stem cells (MSCs) are known to be effective in wound healing, but not much has been reported on quantitative correlations between MSCs injected into the wound site and MSCs that actually participate in wound healing. This study traced MSCs participating in wound healing by using small intestinal submucosa (SIS) as a cell carrier, identified their moving path and calculated the number of MSCs involved in wound healing. First, MSCs were isolated from the nude mouse and 1 × 106 cells were seeded onto the centre of the SIS. MSC‐seeded SIS complexes were injected onto full‐thickness skin wounds made on the dorsum of nude mice. Tracing of MSC‐seeded SIS complex transplanted to the wound site revealed that 27.6% of the MSCs were migrated to the wound site at the first attempt. Second, repeated injection of additional MSCs did not increase the number of MSCs participating in wound healing beyond a certain constant maximum amount. The number of MSCs present in the wound site remains constant in the range 2–3 × 105 from day 1 to day 10. The expression of skin regeneration‐related growth factors was confirmed by real‐time polymerase chain reaction (PCR) and enzyme‐linked immunosorbent assay (ELISA). MSCs participating in wound healing were found not only to suppress inflammation of the wound but also to increase the skin regeneration‐related growth factors that enable the recovery of the skin. An optimal number of about 3 × 105 MSCs injected into the site was found to adapt themselves to the skin wound‐healing process effectively. Copyright © 2012 John Wiley & Sons, Ltd.