Miracle-dz/UniFAR-FTUs huggingface dataset:
Insulator dynamics and the setting of chromatin domains

The early discovery of cis‐regulatory elements able to promote transcription of genes over large distances led to the postulate that elements, termed insulators, should also exist that would limit the action of enhancers, LCRs and silencers to defined domains. Such insulators were indeed found during the past fifteen years in a wide range of organisms, from yeast to humans. Recent advances point to an important role of transcription factors in insulator activity and demonstrate that the operational observation of an insulator effect relies on a delicate balance between the “efficiency” of the insulator and that of the element to be counteracted. In addition, genuine insulator elements now appear less common than initially envisaged, and they are only found at loci displaying a high density of coding or regulatory information. Where this is not the case, chromatin domains of opposing properties are thought to confront each other at “fuzzy” boundaries. In this article, we propose models for both fixed and fuzzy boundaries that incorporate probabilistic and dynamic parameters. BioEssays 26:523–532, 2004. © 2004 Wiley Periodicals, Inc.
Plant Growth Promotion by Volatile Organic Compounds Produced by Bacillus subtilis SYST2

Bacterial volatiles play a significant role in promoting plant growth by regulating the synthesis or metabolism of phytohormones. In vitro and growth chamber experiments were conducted to investigate the effect of volatile organic compounds (VOCs) produced by the plant growth promoting rhizobacterium Bacillus subtilis strain SYST2 on hormone regulation and growth promotion in tomato plants. We observed a significant increase in plant biomass under both experimental conditions; we observed an increase in photosynthesis and in the endogenous contents of gibberellin, auxin, and cytokinin, while a decrease in ethylene levels was noted. VOCs emitted by SYST2 were identified through gas chromatography-mass spectrometry analysis. Of 11 VOCs tested in glass jars containing plants in test tubes, only two, albuterol and 1,3-propanediole, were found to promote plant growth. Furthermore, tomato plants showed differential expression of genes involved in auxin (SlIAA1. SlIAA3), gibberellin (GA20ox-1), cytokinin (SlCKX1), expansin (Exp2, Exp9. Exp 18), and ethylene (ACO1) biosynthesis or metabolism in roots and leaves in response to B. subtilis SYST2 VOCs. Our findings suggest that SYST2-derived VOCs promote plant growth by triggering growth hormone activity, and provide new insights into the mechanism of plant growth promotion by bacterial VOCs.
Effect of gingival and dental plaque antiseptic decontamination on nosocomial infections acquired in the intensive care unit: A double-blind placebo-controlled multicenter study*

Objective:To document the effect of gingival and dental plaque antiseptic decontamination on the rate of nosocomial bacteremias and respiratory infections acquired in the intensive care unit (ICU). Design:Prospective, multicenter, double-blind, placebo-controlled efficacy study. Setting:Six ICUs: three in university hospitals and three in general hospitals. Patients:A total of 228 nonedentulous patients requiring endotracheal intubation and mechanical ventilation, with an anticipated length of stay ≥5 days. Interventions:Antiseptic decontamination of gingival and dental plaque with a 0.2% chlorhexidine gel or a placebo gel, three times a day, during the entire ICU stay. Measurements and Main Results:Demographic and clinical characteristics, organ function data (Logistic Organ Dysfunction score), severity of condition (Simplified Acute Physiologic Score), and dental plaque status were assessed at baseline and until 28 days. Bacteriologic sampling of dental plaque and saliva was done every 5 days, and blood, tracheal aspirate, and bronchoalveolar lavage cultures were performed when appropriate. The primary efficacy end point was the incidence of bacteremia, bronchitis, and ventilator-associated pneumonia, expressed as a percentage and per 1000 ICU days. All baseline characteristics were similar between the treated and the placebo groups. The incidence of nosocomial infections was 17.5% (13.2 per 1000 ICU days) in the placebo group and 18.4% (13.3 per 1000 ICU days) in the plaque antiseptic decontamination group (not significant). No difference was observed in the incidence of ventilator-associated pneumonia per ventilator or intubation days, mortality, length of stay, and care loads (secondary end points). On day 10, the number of positive dental plaque cultures was significantly lower in the treated group (29% vs. 66%; p < .05). Highly resistant Pseudomonas, Acinetobacter, and Enterobacter species identified in late-onset ventilator-associated pneumonia and previously cultured from dental plaque were not eradicated by the antiseptic decontamination. No side effect was reported. Conclusions:Gingival and dental plaque antiseptic decontamination significantly decreased the oropharyngeal colonization by aerobic pathogens in ventilated patients. However, its efficacy was insufficient to reduce the incidence of respiratory infections due to multiresistant bacteria.
Layered mafic-ultramafic intrusions of Fennoscandia: Europe’s treasure chest for magmatic metal deposits

Northeastern Fennoscandia hosts a rich diversity of mafic-ultramafic intrusions of variable shape and size, emplaced in different tectonic regimes over a period spanning ca. 600 million years (from 1.88 – 2.5 Ga). Several of the bodies contain world-class ore deposits, notably the Kemi Cr deposit and the Pechenga Ni deposits. Other deposits include Ni and Cu at Kevitsa, Kotalahti and Sakatti, V at Koillismaa, and platinum-group elements at Portimo and Penikat. These deposits constitute important resources to shield Europe from potential future supply shortages of key industrial metals.
Reliability Analysis of ZFS

The reliability of a ﬁle system considerably depends upon how it deals with on-disk data corruption. A ﬁle sys-tem should ideally be able to detect and recover from all kinds of data corruptions on disk. ZFS is a new ﬁlesys-tem that arrives almost a generation after the introduction of other desktop ﬁlesystems like ext and NTFS and makes strong claims about its reliability mechanisms.In this paper we examine how ZFS deals with on disk data corrup-tions. We use the knowledge of on disk structures of ZFS to perform corruptions on different types of ZFS objects. This “type aware” corruption enables us to perform a systematic exploration of the data protection mechanism of ZFS from various types of data corruptions. This paper performs 90 experiments on ten different ZFS disk objects. The results of these corruption experiments give us information about the classes of on disk faults handled by ZFS. We also get a measure of the robustness of ZFS and gain valuable lessons on building a reliable and robust ﬁle system.
Widowhood and Mortality: A Meta-Analysis

Background While the "widowhood effect" is well known, there is substantial heterogeneity in the magnitude of effects reported in different studies. We conducted a meta-analysis of widowhood and mortality, focusing on longitudinal studies with follow-up from the time of bereavement. Methods and Findings A random-effects meta-analysis was conducted to calculate the overall relative risk (RR) for subsequent mortality among 2,263,888 subjects from 15 prospective cohort studies. We found a statistically significant positive association between widowhood and mortality, but the widowhood effect was stronger in the period earlier than six months since bereavement (overall RR = 1.41, 95% CI: 1.26, 1.57) compared to the effect after six months (overall RR = 1.14, 95% CI: 1.10, 1.18). Meta-regression showed that the widowhood effect was not different for those aged younger than 65 years compared to those older than 65 (P = 0.25). There was, however, a difference in the magnitude of the widowhood effect by gender; for women the RR was not statistically significantly different from the null (overall RR = 1.04, 95% CI: 1.00, 1.08), while it was for men (overall RR = 1.23, 95% CI: 1.18, 1.28). Conclusions The results suggest that further studies should focus more on the mechanisms that generate this association especially among men.
Radiocarbon Dating of a Speleothem Record of Paleoclimate for Angkor, Cambodia

Abstract We report the chronological construction for the top portion of a speleothem, PC1, from southern Cambodia with the aim of reconstructing a continuous high-resolution climate record covering the fluorescence and decline of the medieval Khmer kingdom and its capital at Angkor (~9th–15th centuries AD). Earlier attempts to date PC1 by the standard U-Th method proved unsuccessful. We have therefore dated this speleothem using radiocarbon. Fifty carbonate samples along the growth axis of PC1 were collected for accelerator mass spectrometry (AMS) analysis. Chronological reconstruction for PC1 was achieved using two different approaches described by Hua et al. (2012a) and Lechleitner et al. (2016a). Excellent concordance between the two age-depth models indicates that the top ~47 mm of PC1 grew during the last millennium with a growth hiatus during ~1250–1650 AD, resulting from a large change in measured 14C values at 34.4–35.2 mm depth. The timing of the growth hiatus covers the period of decades-long droughts during the 14th–16th centuries AD indicated in regional climate records.
Eddy-Induced Particle Dispersion in the Near-Surface North Atlantic

AbstractThis study investigates the anisotropic properties of the eddy-induced material transport in the near-surface North Atlantic from two independent datasets, one simulated from the sea surface height altimetry and one derived from real-ocean surface drifters, and systematically examines the interactions between the mean- and eddy-induced material transport in the region. The Lagrangian particle dispersion, which is widely used to characterize the eddy-induced tracer fluxes, is quantified by constructing the “spreading ellipses. ” The analysis consistently demonstrates that this dispersion is spatially inhomogeneous and strongly anisotropic. The spreading is larger and more anisotropic in the subtropical than in the subpolar gyre, and the largest ellipses occur in the Gulf Stream vicinity. Even at times longer than half a year, the spreading exhibits significant nondiffusive behavior in some parts of the domain. The eddies in this study are defined as deviations from the long-term time-mean. The contr.
Reproducibility of the 6-Minute Walk Test for Ambulatory Oxygen Prescription

Background: Ambulatory oxygen is frequently prescribed for patients with chronic obstructive pulmonary disease (COPD) who have oxygen desaturation ≤88% during exercise. The 6-min walk test (6MWT) with continuous pulse oximetry monitoring is a common method to document this oxygen desaturation, but the reproducibility of this test in determining the need for ambulatory oxygen in patients with COPD is not well documented. Objective:The aim of this study was to establish the reproducibility of the 6MWT in determining the need for ambulatory oxygen prescription in stable COPD patients using the Centers for Medicare and Medicaid (CMS) criteria for ambulatory oxygen prescription. Methods:The study was designed as a prospective observational study in an academic health center and associated pulmonary rehabilitation program. Eighty-eight COPD patients referred to pulmonary rehabilitation underwent continuous pulse oximetry while performing standard 6MWT on 3 separate days. Results: Fifty-one (58%) of these patients desaturated by continuous pulse oximetry to an SpO2 ≤88% on a least one of the 6MWTs. Only 26 patients (30%) demonstrated consistency in meeting the criteria for ambulatory oxygen set forth by the CMS on all three 6MWT with a κ statistic of 0.62. The percent agreement between 6MWTs for ambulatory oxygen prescription was 72% and the paired observation was 51%. Conclusions: The 6MWT distance is simple and widely used as a consistent measure of functional capacity in patients with COPD; however, the 6MWT oxygen saturation has only modest reproducibility in determining the need for ambulatory oxygen in stable COPD patients undergoing pulmonary rehabilitation.
Breeding Biology of the Three-Striped Warbler in Venezuela: a Contrast between Tropical and Temperate Parulids

Abstract We document reproductive life history traits of the Three-striped Warbler (Basileuterus tristriatus) from 146 nests in Venezuela and compare our results to data from the literature for other tropical and temperate parulid species. Mean (± SE) clutch size was 1.96 ± 0.03 eggs (n = 96) and fresh egg mass was 2.09 ± 0.02 g. The incubation period was 15.8 ± 0.2 days (n = 23) and the nestling period was 10.5 ± 0.3 days (n = 12). Males did not incubate and rarely provided food for females during incubation. Females had 57 ± 2% (n = 49) nest attentiveness (% of time on the nest incubating), which caused egg temperature to commonly become cold relative to development. Both adults fed nestlings and feeding rates increased with nestling age. The growth rate constant for nestlings based on mass was K = 0.490, which is slower than for north temperate warblers. Predation was the primary source of nest failure and only 22% of nests were successful based on a Mayfield daily predation rate of 0.048 ± 0.006. Our literature review indicates parulids differ strongly in life histories between temperate and tropical/subtropical sites with species in the tropics having, on average, smaller clutches, longer incubation periods, lower nest attentiveness, longer off-bouts, and longer nestling periods.
Psychotic symptoms in normal‐pressure hydrocephalus

Two patients with a psychiatric history of about 20 years, and clinical and neuroradiological signs of normal‐pressure hydrocephalus (NPH) are reported. One had a periodic psychosis subsequent to a tuberculous meningitis, and this overshadowed the slight classical symptoms of NPH. She had received at least 120 treatments with electro‐convulsive therapy. The second patient suffered from a paranoid psychosis; other signs of NPH were moderate though progressive. Both patients showed definite improvement of their NPH symptoms after ventriculo‐atrial shunting, and psychotic symptoms ceased totally. Follow‐up was 5 years for the patient with periodic psychoais. The other patient died from septicaemia 2.5 years after shunting.
Normative Scores for the NIH Toolbox Dynamic Visual Acuity Test from 3 to 85 Years

As part of the National Institutes of Health Toolbox initiative, a computerized test of dynamic visual acuity (cDVA) was developed and validated as an easy-to-administer, cost- and time-efficient test of vestibular and visual function. To establish normative reference values, 3,992 individuals, aged 3–85 years, without vestibular pathology underwent cDVA testing at multiple clinical research testing facilities across the United States. Test scores were stratified by sociodemographic characteristics. cDVA was worse in males (p < 0.001) and those subjects 50 years or older, while there was no difference in dynamic visual acuity across age groups binned from 3 to 49 years. Furthermore, we used these normative cDVA data as a criterion reference to compare both the long (validated) and short versions of the test. Both versions can distinguish between those with and without vestibular pathology (p = 0.0002 long; p = 0.0025 short). The intraclass correlation coefficient between long- and short-cDVA tests was 0.86.
Using machine learning for non-intrusive modeling and prediction of software aging

The wide-spread phenomenon of software (running image) aging is known to cause performance degradation, transient failures or even crashes of applications. In this work we describe first a method for monitoring and modeling of performance degradation in SOA applications, particularly application servers. This method works for a large class of the aging processes caused by resource depletion (e.g. memory leaks). It can be deployed non-intrusively in a production environment, under arbitrary service request distributions. Based on this schema we investigate in the second part of the paper how machine learning (classification) algorithms can be used for proactive detection of performance degradation or sudden drops caused by aging. We leverage the predictive power of these algorithms with several techniques to make the measurement-based aging models more adaptive and more robust against transient failures. We evaluate several state-of-the-art classification methods for their accuracy and computational efficiency in this scenario. The studies are performed on a data set generated by a TPC-W benchmark instrumented with a memory leak injector. The results show that the probing method yields accurate aging models with low overhead and the machine learning approach gives statistically significant short-term predictions of degrading application performance. Both approaches can be used directly to fight aging via adaptive software rejuvenation (restart of the application), for operator alerting, or for short-term capacity planning.
Acculturation, sociodemographic and lifestyle factors associated with compliance with physical activity recommendations in the Mexican-American Mano A Mano cohort

Objectives Being physically active is important for health, and few Mexican-Americans meet national US physical activity recommendations. The aim of this study was to investigate sociodemographic, acculturation and lifestyle factors that were associated with meeting physical activity recommendations in this group. Design and setting A cross-sectional analysis of a large population-based cohort study in southern Texas, USA. Participants Between 2001 and 2011, 21 551 adult members of the Mexican-American Mano A Mano cohort completed baseline questionnaires on physical activity and other lifestyle factors. Outcomes Meeting US physical activity recommendations was defined as participating in 150 min of moderate, or 75 min of vigorous, activity per week. Factors contributing to the likelihood of meeting physical activity recommendations were examined by sex and country of birth in multivariate logistic regression models. Results Less than half of all men and less than a quarter of all women met US physical activity recommendations. Having some college education, greater acculturation and current alcohol use were each associated with greater odds of meeting physical activity recommendations in all groups except US-born men. Higher body mass index was associated with lower odds of meeting recommendations in US-born and Mexico-born women. Conclusions Results demonstrate that factors associated with meeting physical activity recommendations differ by sex and country of birth. Tailored interventions to increase Mexican-Americans’ activity levels to achieve health benefits should consider education, acculturation and alcohol use.
An Application of the Theory of Planned Behavior to the Proximal and Distal Etiology of Sexual Offending

Emerging from social psychology, the theory of planned behavior offers a potentially useful theoretical framework for research into the etiology of sexual offending in adults and adolescents. The theory of planned behavior-a cognitive-affective theory about the role of attitudes, subjective norms, and perceived behavioral control on behaviors-may provide a means by which to link distal etiological factors into proximal ones involved in the offense process, providing greater specificity to the ‘‘abused- abuser’’ hypothesis. The theory of planned behavior also provides a theoretical framework with which to specify mechanisms involved in the proximal offense cycle. Important new directions for research resulting from this conceptual advance are presented, along with limitations of the theory in its application to the etiology of sexual offending. This theoretical framework directs practitioners to classify sexual offenders’ cognitive distortions by whether they involve behavioral beliefs, normative beliefs, and/or control beliefs and to modify treatment activities accordingly.
Vascular Effects of Advanced Glycation End-Products: Content of Immunohistochemically Detected AGEs in Radial Artery Samples as a Predictor for Arterial Calcification and Cardiovascular Risk in Asymptomatic Patients with Chronic Kidney Disease

Objectives. Our aim was to determine whether vascular deposition of advanced glycation end-products (AGEs) is associated with arterial calcification and cardiovascular mortality in chronic kidney disease (CKD) patients and to assess the relationships between vascular content of AGEs and selected clinical and biochemical parameters. Materials and Methods. The study comprised 54 CKD patients (33 hemodialyzed, 21 predialyzed). Examined parameters included BMI, incidence of diabetes, plasma fasting glucose, AGEs, soluble receptor for AGEs and 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging, serum C-reactive protein (hsCRP), plasminogen activator inhibitor-1 (PAI-1), and fetuin-A. Fragments of radial artery obtained during creation of hemodialysis access were stained for calcifications using alizarin red. AGEs deposits were identified immunohistochemically and their relative content was quantified. Results. Vascular content of AGEs was positively correlated with BMI, hsCRP, fetuin-A, PAI-1, and DPPH scavenging in simple regression; only fetuin-A was an independent predictor in multiple regression. There was a significant positive trend in the intensity of AGEs immunostaining among patients with grades 1, 2, and 3 calcifications. AGEs immunostaining intensity predicted 3-year cardiovascular mortality irrespective of patient's age. Conclusions. The present study demonstrates an involvement of AGEs in the development of medial arterial calcification and the impact of arterial AGE deposition on cardiovascular mortality in CKD patients.
Here, there and everywhere: emotion and mental state talk in different social contexts predicts empathic helping in toddlers

A growing body of literature suggests that parents socialize early-emerging prosocial behavior across varied contexts and in subtle yet powerful ways. We focus on discourse about emotions and mental states as one potential socialization mechanism given its conceptual relevance to prosocial behavior and its known positive relations with emotion understanding and social-cognitive development, as well as parents' frequent use of such discourse beginning in infancy. Specifically, we ask how parents' emotion and mental state talk (EMST) with their toddlers relates to toddlers' helping and how these associations vary by context. Children aged 18- to 30-months (n = 38) interacted with a parent during book reading and joint play with toys, two everyday contexts that afford parental discussion of emotions and mental states. Children also participated in instrumental and empathic helping tasks. Results revealed that although parents discuss mental states with their children in both contexts, the nature of their talk differs: during book reading parents labeled emotions and mental states significantly more often than during joint play, especially simple affect words (e.g., happy, sad) and explanations or elaborations of emotions; whereas they used more desire talk and mental state words (e.g., think, know) in joint play. Parents' emotion and mental state discourse related to children's empathic, emotion-based helping behavior; however, it did not relate to instrumental, action-based helping. Moreover, relations between parent talk and empathic helping varied by context: children who helped more quickly had parents who labeled emotion and mental states more often during joint play and who elicited this talk more often during book reading. As EMST both varies between contexts and exhibits context-specific associations with empathic prosocial behavior early in development, we conclude that such discourse may be a key form of socialization in emerging prosociality.