Miracle-dz/UniFAR-FTUs huggingface dataset:
Hypocapnia and Other Ventilation-Related Risk Factors for Cerebral Palsy in Low Birth Weight Infants

Ventilatory management patterns in very low birth weight newborns, particularly iatrogenic hypocapnia, have occasionally been implicated in perinatal brain damage. However, such relationships have not been explored in large representative populations. To examine the risk of disabling cerebral palsy in mechanically ventilated very low birth weight infants in relation to hypocapnia and other ventilation-related variables, we conducted a population-based prospective cohort study of 1105 newborns with birth weights of 500–2000 g born in New Jersey from mid-1984 through 1987, among whom 777 of 902 survivors (86%) had at least one neurodevelopmental assessment at age 2 y or older. Six hundred fifty-seven of 777 assessed survivors (85%), of whom 400 had been mechanically ventilated, had blood gases obtained during the neonatal period. Hypocapnia was defined as the highest quintile of cumulative exposure to arterial Pco2 levels <35 mm Hg during the neonatal period. Disabling cerebral palsy was diagnosed in six of 257 unventilated newborns (2.3%), 30 of 320 ventilated newborns without hypocapnia (9.4%), and 22 of 80 ventilated newborns with hypocapnia (27.5%). Two additional ventilatory risk factors for disabling cerebral palsy were found—hyperoxia and prolonged duration of ventilation. In a multivariate analysis, each of the three ventilatory variables independently contributed a 2- to 3-fold increase in risk of disabling cerebral palsy. These risks were additive. Although duration of mechanical ventilation in very low birth weight newborns likely represents severity of illness, both hypocapnia and hyperoxia are largely controlled by ventilatory practice. Avoidance of arterial Pco2 levels <35 mm Hg and arterial Po2 levels >60 mm Hg in mechanically ventilated very low birth weight infants would seem prudent.
Retained intravitreal lens fragments after phacoemulsification: a clinicopathological correlation

AIMS To explore the relation between clinical course and timing of vitrectomy with the nature and intensity of intraocular inflammatory response in eyes with retained intravitreal lens fragments following complicated phacoemulsification. METHODS Prospective evaluation of 22 eyes with retained lens fragments with emphasis on corneal clarity, uveitis, intraocular pressure (IOP), timing of vitrectomy, and visual outcome. Numbers of different types of inflammatory cells in vitreous washings were counted, masked to clinical details, in three non-overlapping adjacent high power fields. Relations between clinical and pathological findings were assessed. RESULTS The IOP was raised in 19 eyes before vitrectomy and remained high in nine postoperatively. The latter had higher median total cell count (104 cells/mm2) than those with normal postoperative IOP (37 cells/mm2) but this difference was not statistically significantly different (p=0.17). Nine of 22 eyes underwent vitrectomy within 1 week of cataract surgery. Median total cell count in these eyes was 20 cells/mm2 compared with 140 cells/mm2 in eyes vitrectomised later—this difference was statistically significant (p <0.001). Final visual acuity was 6/12 or better in 13 eyes, these had fewer intravitreal inflammatory cells than the remaining six with poor visual outcome and no pre-existing cause for this (three patients excluded) (p=0.02). Macrophages were the predominant inflammatory cell type. CONCLUSION There was significantly less inflammatory cell activity in eyes which had retained lens fragments removed early (within 1 week). Later removal was associated with persistently elevated IOP and poorer visual outcome.
Inter-operator spectrum sharing in future cellular systems

Inter-operator spectrum sharing has been proposed to exploit spectrum efficiency in future communication system. By using game theory and learning algorithm, we design a partially distributed implementation method. Such a method is proven to reach the system equilibrium which improves spectrum efficiency between operators. Furthermore, by queueing analysis and robust potential game, we show that the convergence rate can be accelerated by incorporating more asynchronous operator systems. This distributed implementation method creates a low complexity solution for operators to realize inter-operator spectrum sharing for 3GPP LTE-A systems or similar.
Indoor Air Quality Factors in Designing a Healthy Building

▪ Abstract Current guidelines for green buildings are cursory and inadequate for specifying materials and designing ventilation systems to ensure a healthful indoor environment, i.e. a “healthy building,” by design. Public perception, cultural preferences, litigation trends, current codes and regulations, and rapid introduction of new building materials and commercial products, as well as the prevailing design-build practices, pose challenges to systems integration in the design, construction and operation phases of modern buildings. We are on the verge of a paradigm shift in ventilation design thinking. In the past, thermal properties of air within a zone determined heating, ventilating, and air-conditioning specifications. In the future, occupant-specific and highly responsive systems will become the norm. Natural ventilation, displacement ventilation, and microzoning with subfloor plenums, along with the use of point-of-source heat control and point-of-use sensors, will evolve to create a “smart,” resp.
Three-year maintenance of improved diet and physical activity: the CATCH cohort. Child and Adolescent Trial for Cardiovascular Health.

OBJECTIVE To assess differences through grade 8 in diet, physical activity, and related health indicators of students who participated in the Child and Adolescent Trial for Cardiovascular Health (CATCH) school and family intervention from grades 3 through 5. DESIGN Follow-up of the 4-center, randomized, controlled field trial with 56 intervention and 40 control elementary schools. PARTICIPANTS We studied 3714 (73%) of the initial CATCH cohort of 5106 students from ethnically diverse backgrounds in California, Louisiana, Minnesota, and Texas at grades 6, 7, and 8. RESULTS Self-reported daily energy intake from fat at baseline was virtually identical in the control (32.7%) and intervention (32.6%) groups. At grade 5, the intake for controls remained at 32.2%, while the intake for the intervention group declined to 30.3% (P<.001). At grade 8, the between-group differential was maintained (31.6% vs 30.6%, P = .01). Intervention students maintained significantly higher self-reported daily vigorous activity than control students (P = .001), although the difference declined from 13.6 minutes in grade 5 to 11.2, 10.8, and 8.8 minutes in grades 6, 7, and 8, respectively. Significant differences in favor of the intervention students also persisted at grade 8 for dietary knowledge and dietary intentions, but not for social support for physical activity. No impact on smoking behavior or stages of contemplating smoking was detected at grade 8. No significant differences were noted among physiologic indicators of body mass index, blood pressure, or serum lipid and cholesterol levels. CONCLUSION The original CATCH results demonstrated that school-level interventions could modify school lunch and school physical education programs as well as influence student behaviors. This 3-year follow-up without further intervention suggests that the behavioral changes initiated during the elementary school years persisted to early adolescence for self-reported dietary and physical activity behaviors.
Hard X-ray In-situ Full-field Microscopy for Material Science Applications.

Hard X-ray transmission microscopy (HXTM) based on refractive X-ray optics was employed as an instrument in material science to investigate buried-in microstructures in two or three dimensions with spatial resolution approaching 100 nm [1-4]. In this microscope, the incoming beam goes through the condenser, and illuminates the sample. The objective lens magnifies the image of the sample on the highresolution CCD camera (pixel size 0.65 m). The X-ray magnification typically lies in the 5-100 range but is not strictly limited. With the extra magnification from X-ray optics, the maximum spatial resolution is no longer limited by the detector pixel size, but by the X-ray optics. The main factors influencing the spatial resolution are the numerical aperture and aberrations of objective lens.
Grey relational effort analysis technique using regression methods for software estimation

Software project planning and estimation is the most important confront for software developers and researchers. It incorporates estimating the size of the software project to be produced, estimating the effort required, developing initial project schedules, and ultimately, estimating on the whole cost of the project. Numerous empirical explorations have been performed on the existing methods, but they lack convergence in choosing the best prediction methodology. Analogy based estimation is still one of the most extensively used method in industry which is based on finding effort from similar projects from the project repository. Two alternative approaches using analogy for estimation have been proposed in this study. Firstly, a precise and comprehensible predictive model based on the integration of Grey Relational Analysis (GRA) and regression has been discussed. Second approach deals with the uncertainty in the software projects, and how fuzzy set theory in fusion with grey relational analysis can minimize this uncertainty. Empirical results attained are remarkable indicating that the methodologies have a great potential and can be used as a candidate approaches for software effort estimation. The results obtained using both the methods are subjected to rigorous statistical testing using Wilcoxon signed rank test.
Trade-offs in overhead vs effectiveness of causality inconsistency tracking for preemptive rollback in optimistic simulation

We discuss and compare three different causality inconsistency tracking mechanisms in support of preemptive rollback in optimistic parallel simulation on myrinet clusters. These mechanisms exhibit different communication/processing overhead and also different effectiveness in revealing causality inconsistency of the currently executed simulation event. By the results of an empirical study on a classical simulation benchmark we have found some trade-offs between these mechanisms, pointing out indications of application contexts for which each mechanism is expected to be well tailored.
Truncation of type IV pilin induces mucoidy in Pseudomonas aeruginosa strain PAO579

Pseudomonas aeruginosa is a Gram negative, opportunistic pathogen that uses the overproduction of alginate, a surface polysaccharide, to form biofilms in vivo. Overproduction of alginate, also known as mucoidy, affords the bacterium protection from the host's defenses and facilitates the establishment of chronic lung infections in individuals with cystic fibrosis. Expression of the alginate biosynthetic operon is primarily controlled by the alternative sigma factor AlgU (AlgT/σ22). In a nonmucoid strain, AlgU is sequestered by the transmembrane antisigma factor MucA to the cytoplasmic membrane. AlgU can be released from MucA via regulated intramembrane proteolysis by proteases AlgW and MucP causing the conversion to mucoidy. Pseudomonas aeruginosa strain PAO579, a derivative of the nonmucoid strain PAO1, is mucoid due to an unidentified mutation (muc‐23). Using whole genome sequencing, we identified 16 nonsynonymous and 15 synonymous single nucleotide polymorphisms (SNP). We then identified three tandem single point mutations in the pilA gene (PA4525), as the cause of mucoidy in PAO579. These tandem mutations generate a premature stop codon resulting in a truncated version of PilA (PilA108), with a C‐terminal motif of phenylalanine‐threonine‐phenylalanine (FTF). Inactivation of pilA108 confirmed it was required for mucoidy. Additionally, algW and algU were also required for mucoidy of PAO579. Western blot analysis indicated that MucA was less stable in PAO579 than nonmucoid PAO1 or PAO381. The mucoid phenotype and high PalgU and PalgD promoter activities of PAO579 require pilA108, algW, algU, and rpoN encoding the alternative sigma factor σ54. We also observed that RpoN regulates expression of algW and pilA in PAO579. Together, these results suggest that truncation in type IV pilin in P. aeruginosa strain PAO579 can induce mucoidy through an AlgW/AlgU‐dependent pathway.
A bioinformatics analysis of the arabidopsis thaliana epigenome. (Une analyse bioinformatique de l'Epigénome d'Arabidopsis thaliana)

Eukaryotic genomes are packed into the confines of the nucleus through a nucleoproteic structure called chromatin. Chromatin is a dynamic structure that can respond to developmental or environmental cues to regulate and orchestrate the functions of the genome. The fundamental unit of chromatin, the nucleosome, consists of a protein octamer, which contains two molecules of each of the core histone proteins (H2A, H2B, H3, H4), around which 147 bp of DNA is wrapped. The post-translational modifications (PTMs) of histones and methylation of the cytosine residues in DNA (DNA methylation) constitute primary epigenomic markers that dynamically alter the interaction of DNA with nucleosomes and participate in the regulation and control access to the underlying DNA. The main objective of my thesis was to understand the spatial and temporal dynamics of chromatin states in Arabidopsis by investigating on a genome-wide scale, patterns of DNA methylation and a set of well-characterized histone post-translational modifications. DNA methylation, a hallmark of epigenetic inactivation and heterochromatin in both plants and mammals, is largely confined to transposable elements and other repeat sequences. I show in this thesis that in Arabidopsis, methylated TE sequences having no or few matching siRNAs, and therefore unlikely to be targeted by the RNA-directed DNA methylation (RdDM) machinery, acquire DNA methylation through spreading from adjacent siRNA-targeted regions. Further, I propose that this spreading of DNA methylation through promoter regions can explain, at least in part, the negative impact of siRNA-targeted TE sequences on neighbouring gene expression. In a second part, I have contributed to integrative analysis of DNA methylation and eleven histone PTMs. I have shown through combinatorial and cluster analysis that the Arabidopsis epigenome shows simple principles of organisation and can be distinguished into four primary types of chromatin that preferentially index active genes, repressed genes, TEs, and intergenic regions. Finally, in a third part, I integrated epigenomics with transcriptome data at three different time points in a developmental window to investigate the temporal dynamics of chromatin states in response to an external stimulus. This used the light-induced transcriptional response as a paradigm to assess the impact of histone H2B monoubiquitination (H2Bub), and showed that this PTM is associated with active transcription and implicated in the selective fine-tuning of gene expression. Taken together, the work presented here contributes significantly to our understanding of the spatial organisation of chromatin states in plants, its dynamic nature and how it can contribute to allow plants to respond to a signal from the environment.
ESTHETE: a news browsing system to visualize the context and evolution of news stories

Providing the history and context(s) of a news article that emerges in the middle of an evolving news story--sometimes multiple news stories--is a complex task. The complexity of the task is compounded by the fact that different users are interested in different contexts of the article, and it is impossible to guess what a particular user is most interested in. In this paper, we introduce ESTHETE, a system that provides rich context(s) (through what we call personalized flexible context extraction), by preprocessing and storing articles in a structured representation (directed graphs) that makes it easy for the user to explore different contexts. The advantage of this approach is that the incremental computational expense in incorporating new articles as they are published is minimal. Our system is available at: http://konfrap.com/esthete.
Lifted Domain Coloring

Complex‐valued functions are fundamental objects in complex analysis, algebra, differential geometry and in many other areas such as numerical mathematics and physics. Visualizing complex functions is a non‐trivial task since maps between two‐dimensional spaces are involved whose graph would be an unhandy submanifold in four‐dimensional space. The present paper improves the technique of “domain coloring” in several aspects: First, we lift domain coloring from the complex plane to branched Riemann surfaces, which are essentially the correct domain for most complex functions. Second, we extend domain coloring to the visualization of general 2‐valued maps on surfaces. As an application of such general maps we visualize the Gauss map of surfaces as domain colored plots and establish a link to current surface parametrization techniques and texture maps. Third, we adjust the color pattern in domain and in image space to produce higher quality domain colorings. The new color schemes specifically enhance the display of singularities, symmetries and path integrals, and give better qualitative measures of the complex map.
Prion Protein Misfolding Affects Calcium Homeostasis and Sensitizes Cells to Endoplasmic Reticulum Stress

Prion-related disorders (PrDs) are fatal neurodegenerative disorders characterized by progressive neuronal impairment as well as the accumulation of an abnormally folded and protease resistant form of the cellular prion protein, termed PrPRES. Altered endoplasmic reticulum (ER) homeostasis is associated with the occurrence of neurodegeneration in sporadic, infectious and familial forms of PrDs. The ER operates as a major intracellular calcium store, playing a crucial role in pathological events related to neuronal dysfunction and death. Here we investigated the possible impact of PrP misfolding on ER calcium homeostasis in infectious and familial models of PrDs. Neuro2A cells chronically infected with scrapie prions showed decreased ER-calcium content that correlated with a stronger upregulation of UPR-inducible chaperones, and a higher sensitivity to ER stress-induced cell death. Overexpression of the calcium pump SERCA stimulated calcium release and increased the neurotoxicity observed after exposure of cells to brain-derived infectious PrPRES. Furthermore, expression of PrP mutants that cause hereditary Creutzfeldt-Jakob disease or fatal familial insomnia led to accumulation of PrPRES and their partial retention at the ER, associated with a drastic decrease of ER calcium content and higher susceptibility to ER stress. Finally, similar results were observed when a transmembrane form of PrP was expressed, which is proposed as a neurotoxic intermediate. Our results suggest that alterations in calcium homeostasis and increased susceptibility to ER stress are common pathological features of both infectious and familial PrD models.
Analysis of the gene coding for the BRCA2‐Interacting protein PALB2 in hereditary prostate cancer

The genetic basis of susceptibility to prostate cancer (PRCA) remains elusive. Mutations in BRCA2 have been associated with increased prostate cancer risk and account for around 2% of young onset (<56 years) prostate cancer cases. PALB2 is a recently identified breast cancer susceptibility gene whose protein is closely associated with BRCA2 and is essential for BRCA2 anchorage to nuclear structures. This functional relationship made PALB2 a candidate PRCA susceptibility gene.
Brief announcement: a lower bound for depth-restricted work stealing

Work stealing is a common technique used in the runtime schedulers of parallel languages such as Cilk and parallel libraries such as Intel Threading Building Blocks (TBB). Depth-restricted work stealing is a restriction of Cilk-like work stealing in which a processor blocked on a task at depth d can only steal tasks from other processors at depth greater than d. To support programs coded in a blocking style, i.e., code without explicit continuations, TBB imposes a depth restriction on work stealing to limit the stack space used by a computation. We present a lower bound on the completion time of a computation executed using a depth-restricted work-stealing scheduler. In particular, we construct a computation which on P processors runs a factor of Ω(P) slower with depth-restricted work stealing as compared to unrestricted work stealing. On this pessimal computation, depth-restricted work stealing asymptotically serializes execution while unrestricted work stealing achieves linear speedup.
Balsa: An Asynchronous Hardware Synthesis Language

The dominant hardware design paradigm is a synchronous (clocked) design style. Recent research has made asynchronous or self-timed systems attractive again. This paper introduces Balsa, a language and framework for synthesizing circuits using a technique of syntax direct translation. Balsa has been used to generate the DMA controller used in AMULET3i, an integrated asynchronous microprocessor design for embedded systems. This paper introduces the key features of the language.
Holocene history of the Great Kobuk Sand Dunes , Northwestern Alaska

Located just north of the Arctic Circle, the Great Kobuk Sand Dunes (GKSD) are an inland dune field that is closely surrounded by boreal forest. The history of the GKSD tells us about changes in aridity, a climatic parameter whose history is poorly understood at high latitudes. Vegetated dunes in several states of geomorphic preservation surround the active dune field today, evidencing a complex history of Holocene activity. Small lakes in the forest bordering the dunes accumulate wind-blown sand. We use C-dated, lake-sediment cores to reconstruct a continuous history of sand influx over the last 8000 yr. The validity of this record is supported by limiting ages obtained from stratigraphic sections within the dune field. The extent of the GKSD underwent a fluctuating shrinkage coincident with Neoglaciation. This downsizing trend was interrupted by periods of increased sand deposition into lakes occurring 4800–4200, 3300–2600, 1300–700, and 300–100 calendar years ago. Aridity in the Kobuk valley during the Holocene probably was controlled by the frequency of North Pacific storms entering the region in late summer. Our results describe the first continuous history of changing moisture balance for central Beringia during the Holocene and comprise a baseline against which future records of climatic and ecological change in this region can be compared. r 2002 Elsevier Science Ltd. All rights reserved.
Estimating Directional Statistics Using Wavefield Modeling and Mixtures of von-Mises Distributions

This letter considers the problem of estimating the directional probability distribution of wavefields observed by sensor arrays. In particular, the angular distributions of wavefields are assumed to be mixtures of von-Mises distributions. Mixture models facilitate estimating multimodal and skewed angular distributions. The von-Mises distribution is fully defined with two parameters, namely the mean direction (circular mean) and the concentration parameter. The widely-employed Gaussian distribution is not appropriate in directional statistics since its support is the entire real-line instead of the [- π,π) angular domain. A covariance-matching based estimator is proposed for the parameters of a mixture of von-Mises distributions and the corresponding Cramér-Rao lower bound is derived. A closed-form expression for the covariance matrix of the array response due to scattering is also derived based on the wavefield modeling principle. These results remain valid even for real-world conformal arrays with nonidealities including mutual coupling, mounting platform reflections, and array elements with individual directional beampatterns.