Miracle-dz/UniFAR-FTUs huggingface dataset:
Petroleum dynamics in the sea and influence of subsea dispersant injection during Deepwater Horizon

Significance Environmental risks posed by deep-sea petroleum releases are difficult to predict and assess. We developed a physical model of the buoyant jet of petroleum liquid droplets and gas bubbles gushing into the deep sea, coupled with simulated liquid–gas equilibria and aqueous dissolution kinetics of petroleum compounds, for the 2010 Deepwater Horizon disaster. Simulation results are validated by comparisons with extensive observation data collected in the sea and atmosphere near the release site. Simulations predict that chemical dispersant, injected at the wellhead to mitigate environmental harm, increased the entrapment of volatile compounds in the deep sea and thereby improved air quality at the sea surface. Subsea dispersant injection thus lowered human health risks and accelerated response during the intervention. During the Deepwater Horizon disaster, a substantial fraction of the 600,000–900,000 tons of released petroleum liquid and natural gas became entrapped below the sea surface, but the quantity entrapped and the sequestration mechanisms have remained unclear. We modeled the buoyant jet of petroleum liquid droplets, gas bubbles, and entrained seawater, using 279 simulated chemical components, for a representative day (June 8, 2010) of the period after the sunken platform’s riser pipe was pared at the wellhead (June 4–July 15). The model predicts that 27% of the released mass of petroleum fluids dissolved into the sea during ascent from the pared wellhead (1,505 m depth) to the sea surface, thereby matching observed volatile organic compound (VOC) emissions to the atmosphere. Based on combined results from model simulation and water column measurements, 24% of released petroleum fluid mass became channeled into a stable deep-water intrusion at 900- to 1,300-m depth, as aqueously dissolved compounds (∼23%) and suspended petroleum liquid microdroplets (∼0.8%). Dispersant injection at the wellhead decreased the median initial diameters of simulated petroleum liquid droplets and gas bubbles by 3.2-fold and 3.4-fold, respectively, which increased dissolution of ascending petroleum fluids by 25%. Faster dissolution increased the simulated flows of water-soluble compounds into biologically sparse deep water by 55%, while decreasing the flows of several harmful compounds into biologically rich surface water. Dispersant injection also decreased the simulated emissions of VOCs to the atmosphere by 28%, including a 2,000-fold decrease in emissions of benzene, which lowered health risks for response workers.
Detection of exhaled carbon dioxide following intubation during resuscitation at delivery

Objectives End tidal carbon dioxide (ETCO2) monitoring can facilitate identification of successful intubation. The aims of this study were to determine the time to detect ETCO2 following intubation during resuscitation of infants born prematurely and whether it differed according to maturity at birth or the Apgar scores (as a measure of the infant’s condition after birth). Design Analysis of recordings of respiratory function monitoring. Setting Two tertiary perinatal centres. Patients Sixty-four infants, with median gestational age of 27 (range 23–34)weeks. Interventions Respiratory function monitoring during resuscitation in the delivery suite. Main outcome measures The time following intubation for ETCO2 levels to be initially detected and to reach 4 mm Hg and 15 mm Hg. Results The median time for initial detection of ETCO2 following intubation was 3.7 (range 0–44) s, which was significantly shorter than the median time for ETCO2 to reach 4 mm Hg (5.3 (range 0–727) s) and to reach 15 mm Hg (8.1 (range 0–827) s) (both P<0.001). There were significant correlations between the time for ETCO2 to reach 4 mm Hg (r=−0.44, P>0.001) and 15 mm Hg (r=−0.48, P<0.001) and gestational age but not with the Apgar scores. Conclusions The time for ETCO2 to be detected following intubation in the delivery suite is variable emphasising the importance of using clinical indicators to assess correct endotracheal tube position in addition to ETCO2 monitoring. Capnography is likely to detect ETCO2 faster than colorimetric devices.
Large Osteochondral Allografts of the Knee: Surgical Technique and Indications

Abstract Large osteochondral allograft (OCA) transplant has become a valid alternative to restore articular surface in challenging articular lesions in young and active patients, either in primary or in revision procedures. Several studies support the effectiveness and safety of OCA, but costs and graft availability limit their use. The indications are the treatment of symptomatic full-thickness cartilage lesions greater than 3 cm2, deep lesions with subchondral damage, or revision procedures when a previous treatment has failed. The goal of the transplant is to restore the articular surface with a biological implant, allow return to daily/sports activities, relieve symptoms, and delay knee arthroplasty. Grafts can be fresh, fresh-frozen, or cryopreserved; these different storage procedures significantly affect cell viability, immunogenicity, and duration of the storage. Dowel and shell technique are the two most commonly used procedures for OCA transplantation. While most cartilage lesions can be treated with the dowel technique, large and/or geometrically irregular lesions should be treated with the shell technique. OCA transplantation for the knee has demonstrated reliable mid- to long-term results in terms of graft survival and patient satisfaction. Best results are reported: in unipolar lesions, in patients younger than 30 years, in traumatic lesions and when the treatment is performed within 12 months from the onset of symptoms.
Current and Future Disease Progression of the Chronic HCV Population in the United States

Chronic hepatitis C virus (HCV) infection can lead to advanced liver disease (AdvLD), including cirrhosis, decompensated cirrhosis, and liver cancer. The aim of this study was to determine recent historical rates of HCV patient progression to AdvLD and to project AdvLD prevalence through 2015. We first determined total 2008 US chronic HCV prevalence from the National Health and Nutrition Evaluation Surveys. Next, we examined disease progression and associated non-pharmacological costs of diagnosed chronic HCV-infected patients between 2007–2009 in the IMS LifeLink and CMS Medicare claims databases. A projection model was developed to estimate AdvLD population growth through 2015 in patients diagnosed and undiagnosed as of 2008, using the 2007–2009 progression rates to generate a “worst case” projection of the HCV-related AdvLD population (i.e., scenario where HCV treatment is the same in the forecasted period as it was before 2009). We found that the total diagnosed chronic HCV population grew from 983,000 to 1.19 million in 2007–2009, with patients born from 1945–1964 accounting for 75.0% of all patients, 83.7% of AdvLD patients, and 79.2% of costs in 2009, indicating that HCV is primarily a disease of the “baby boomer” population. Non-pharmacological costs grew from $7.22 billion to $8.63 billion, with the majority of growth derived from the 60,000 new patients that developed AdvLD in 2007–2009, 91.5% of whom were born between 1945 and 1964. The projection model estimated the total AdvLD population would grow from 195,000 in 2008 to 601,000 in 2015, with 73.5% of new AdvLD cases from patients undiagnosed as of 2008. AdvLD prevalence in patients diagnosed as of 2008 was projected to grow 6.5% annually to 303,000 patients in 2015. These findings suggest that strategies to diagnose and treat HCV-infected patients are urgently needed to increase the likelihood that progression is interrupted, particularly for patients born from 1945–1964.
Barcoding Beetles: A Regional Survey of 1872 Species Reveals High Identification Success and Unusually Deep Interspecific Divergences

With 400 K described species, beetles (Insecta: Coleoptera) represent the most diverse order in the animal kingdom. Although the study of their diversity currently represents a major challenge, DNA barcodes may provide a functional, standardized tool for their identification. To evaluate this possibility, we performed the first comprehensive test of the effectiveness of DNA barcodes as a tool for beetle identification by sequencing the COI barcode region from 1872 North European species. We examined intraspecific divergences, identification success and the effects of sample size on variation observed within and between species. A high proportion (98.3%) of these species possessed distinctive barcode sequence arrays. Moreover, the sequence divergences between nearest neighbor species were considerably higher than those reported for the only other insect order, Lepidoptera, which has seen intensive analysis (11.99% vs up to 5.80% mean NN divergence). Although maximum intraspecific divergence increased and average divergence between nearest neighbors decreased with increasing sampling effort, these trends rarely hampered identification by DNA barcodes due to deep sequence divergences between most species. The Barcode Index Number system in BOLD coincided strongly with known species boundaries with perfect matches between species and BINs in 92.1% of all cases. In addition, DNA barcode analysis revealed the likely occurrence of about 20 overlooked species. The current results indicate that DNA barcodes distinguish species of beetles remarkably well, establishing their potential to provide an effective identification tool for this order and to accelerate the discovery of new beetle species.
When do we have the power to detect biological interactions in spatial point patterns?

Uncovering the roles of biotic interactions in assembling and maintaining species‐rich communities remains a major challenge in ecology. In plant communities, interactions between individuals of different species are expected to generate positive or negative spatial interspecific associations over short distances. Recent studies using individual‐based point pattern datasets have concluded that (a) detectable interspecific interactions are generally rare, but (b) are most common in communities with fewer species; and (c) the most abundant species tend to have the highest frequency of interactions. However, it is unclear how the detection of spatial interactions may change with the abundances of each species, or the scale and intensity of interactions. We ask if statistical power is sufficient to explain all three key results. We use a simple two‐species model, assuming no habitat associations, and where the abundances, scale and intensity of interactions are controlled to simulate point pattern data. In combination with an approximation to the variance of the spatial summary statistics that we sample, we investigate the power of current spatial point pattern methods to correctly reject the null model of pairwise species independence. We show the power to detect interactions is positively related to both the abundances of the species tested, and the intensity and scale of interactions, but negatively related to imbalance in abundances. Differences in detection power in combination with the abundance distributions found in natural communities are sufficient to explain all the three key empirical results, even if all pairwise interactions are identical. Critically, many hundreds of individuals of both species may be required to detect even intense interactions, implying current abundance thresholds for including species in the analyses are too low. Synthesis. The widespread failure to reject the null model of spatial interspecific independence could be due to low power of the tests rather than any key biological process. Since we do not model habitat associations, our results represent a first step in quantifying sample sizes required to make strong statements about the role of biotic interactions in diverse plant communities. However, power should be factored into analyses and considered when designing empirical studies.
Distilling a Neural Network Into a Soft Decision Tree

Deep neural networks have proved to be a very effective way to perform classification tasks. They excel when the input data is high dimensional, the relationship between the input and the output is complicated, and the number of labeled training examples is large. But it is hard to explain why a learned network makes a particular classification decision on a particular test case. This is due to their reliance on distributed hierarchical representations. If we could take the knowledge acquired by the neural net and express the same knowledge in a model that relies on hierarchical decisions instead, explaining a particular decision would be much easier. We describe a way of using a trained neural net to create a type of soft decision tree that generalizes better than one learned directly from the training data.
Telomere Length Dynamics and the Evolution of Cancer Genome Architecture

Telomeres are progressively eroded during repeated rounds of cell division due to the end replication problem but also undergo additional more substantial stochastic shortening events. In most cases, shortened telomeres induce a cell-cycle arrest or trigger apoptosis, although for those cells that bypass such signals during tumour progression, a critical length threshold is reached at which telomere dysfunction may ensue. Dysfunction of the telomere nucleoprotein complex can expose free chromosome ends to the DNA double-strand break (DSB) repair machinery, leading to telomere fusion with both telomeric and non-telomeric loci. The consequences of telomere fusions in promoting genome instability have long been appreciated through the breakage–fusion–bridge (BFB) cycle mechanism, although recent studies using high-throughput sequencing technologies have uncovered evidence of involvement in a wider spectrum of genomic rearrangements including chromothripsis. A critical step in cancer progression is the transition of a clone to immortality, through the stabilisation of the telomere repeat array. This can be achieved via the reactivation of telomerase, or the induction of the alternative lengthening of telomeres (ALT) pathway. Whilst telomere dysfunction may promote genome instability and tumour progression, by limiting the replicative potential of a cell and enforcing senescence, telomere shortening can act as a tumour suppressor mechanism. However, the burden of senescent cells has also been implicated as a driver of ageing and age-related pathology, and in the promotion of cancer through inflammatory signalling. Considering the critical role of telomere length in governing cancer biology, we review questions related to the prognostic value of studying the dynamics of telomere shortening and fusion, and discuss mechanisms and consequences of telomere-induced genome rearrangements.
A Simple Method to Reduce both Lactic Acid and Ammonium Production in Industrial Animal Cell Culture

Fed-batch animal cell culture is the most common method for commercial production of recombinant proteins. However, higher cell densities in these platforms are still limited due to factors such as excessive ammonium production, lactic acid production, nutrient limitation, and/or hyperosmotic stress related to nutrient feeds and base additions to control pH. To partly overcome these factors, we investigated a simple method to reduce both ammonium and lactic acid production—termed Lactate Supplementation and Adaptation (LSA) technology—through the use of CHO cells adapted to a lactate-supplemented medium. Using this simple method, we achieved a reduction of nearly 100% in lactic acid production with a simultaneous 50% reduction in ammonium production in batch shaker flasks cultures. In subsequent fed-batch bioreactor cultures, lactic acid production and base addition were both reduced eight-fold. Viable cell densities of 35 million cells per mL and integral viable cell days of 273 million cell-days per mL were achieved, both among the highest currently reported for a fed-batch animal cell culture. Investigating the benefits of LSA technology in animal cell culture is worthy of further consideration and may lead to process conditions more favorable for advanced industrial applications.
The effects of a double blind, placebo controlled, artificial food colourings and benzoate preservative challenge on hyperactivity in a general population sample of preschool children

Aims: To determine whether artificial food colourings and a preservative in the diet of 3 year old children in the general population influence hyperactive behaviour. Methods: A sample of 1873 children were screened in their fourth year for the presence of hyperactivity at baseline (HA), of whom 1246 had skin prick tests to identify atopy (AT). Children were selected to form the following groups: HA/AT, not-HA/AT, HA/not-AT, and not-HA/not-AT (n = 277). After baseline assessment, children were subjected to a diet eliminating artificial colourings and benzoate preservatives for one week; in the subsequent three week within subject double blind crossover study they received, in random order, periods of dietary challenge with a drink containing artificial colourings (20 mg daily) and sodium benzoate (45 mg daily) (active period), or a placebo mixture, supplementary to their diet. Behaviour was assessed by a tester blind to dietary status and by parents’ ratings. Results: There were significant reductions in hyperactive behaviour during the withdrawal phase. Furthermore, there were significantly greater increases in hyperactive behaviour during the active than the placebo period based on parental reports. These effects were not influenced by the presence or absence of hyperactivity, nor by the presence or absence of atopy. There were no significant differences detected based on objective testing in the clinic. Conclusions: There is a general adverse effect of artificial food colouring and benzoate preservatives on the behaviour of 3 year old children which is detectable by parents but not by a simple clinic assessment. Subgroups are not made more vulnerable to this effect by their prior levels of hyperactivity or by atopy.
DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin

The regulation of chromatin structure in eukaryotic cells involves abundant architectural factors such as high mobility group B (HMGB) proteins. It is not understood how these factors control the interplay between genome accessibility and compaction. In vivo, HMO1 binds the promoter and coding regions of most ribosomal RNA genes, facilitating transcription and possibly stabilizing chromatin in the absence of histones. To understand how HMO1 performs these functions, we combine single molecule stretching and atomic force microscopy (AFM). By stretching HMO1-bound DNA, we demonstrate a hierarchical organization of interactions, in which HMO1 initially compacts DNA on a timescale of seconds, followed by bridge formation and stabilization of DNA loops on a timescale of minutes. AFM experiments demonstrate DNA bridging between strands as well as looping by HMO1. Our results support a model in which HMO1 maintains the stability of nucleosome-free chromatin regions by forming complex and dynamic DNA structures mediated by protein–protein interactions.
An Experimental Exploration of the Effects of Exposure to Images of Nature on Rumination

Exposure to natural environments has been shown to have beneficial effects on mood. Rumination is a thinking style associated with negative mood, and sometimes depression, and is characterized by repetitive, intrusive thoughts, often with a negative emotional element. This study investigated whether exposure to nature, operationalized using photographs presented as a slideshow, could aid reduction in levels of state rumination. An experimental, within-between (Time x Condition) participant design was used; participants (n = 58) undertook a presentation task designed to induce rumination and influence mood. Participants were then randomly allocated to either: watch a slideshow of a natural environment, watch a slideshow of an urban environment, or wait patiently with no distractions. Data were collected at baseline, after the presentation, and after the slideshow. Environmental exposure had no effect on levels of rumination or negative mood, but did have a significant effect on levels of positive mood, ‘being away’, and ‘fascination’. Positive mood declined in those who saw the urban slideshow, but remained the same in those who saw the nature slideshow, whilst levels of being away and fascination were highest in those who saw the nature slideshow. This study extends previous restorative environment research by exploring the effects of nature on rumination.
Examining the Relation Between the Number and Location of Tuck Stitches and Bursting Strength in Circular Knitted Fabrics

*University of Gaziantep, Department of Textile Engineering, Gaziantep, Turkey Abstract Single jersey fabrics are the most common type among knitted fabrics. Their patterns are designed by loops, tuck and float stitches and their combinations. The tuck stitch has important influences on fabric properties as it increases the fabric weight, thickness and width, and makes the fabric more porous than others . In this research 12 different circular knitted fabrics were produced with different numbers of tuck stitches and were also dyed. As the most important performance property for knitted fabrics, their bursting strength properties were investigated. The aim of the study was to examine the relation between the tuck stitches and bursting strength in circular knitted fabrics according to the number and location of tuck stitches in the pattern. To achieve the most correct result, graphics and statistical analyses were used.
Intentions to drop-out of youth soccer: A test of the basic needs theory among European youth from five countries

Research arising from self-determination theory (SDT; Deci, E. L., & Ryan, R. M. (2000). The “what” and “why” of goal pursuits: Human needs and the self-determination of behavior. Psychological Inquiry, 11(4), 227–268) indicates that the quality of the social interactions between athletes and coaches, and athletes' ensuing psychological responses, are critical determinants of intentions to drop out of youth sport. Little is known regarding whether these processes hold across countries. Grounded in SDT, this study tested the invariance of a model predicting youth sport dropout across five European countries. Seven thousand seven hundred and sixty-nine grassroots players (6641 males, 1020 females (M age = 11.56, SD = 1.40) from youth soccer teams in five countries (England, France, Greece, Norway, and Spain) completed a questionnaire tapping perceptions of coach-provided autonomy support, basic psychological need satisfaction (i.e. autonomy, competence and relatedness), soccer enjoyment, and intentions to drop out of soccer in the next season. Data were analysed using structural equation modelling. The hypothesised model (autonomy support → basic needs → enjoyment → intentions to drop out of soccer) showed an acceptable fit to the data and provided evidence of configural factor loading and structural path invariance across the five countries. This study supports the applicability of the basic needs theory model as a framework to understand the determinants of drop out intentions in sport among European youth across national boundaries. Findings highlight a potential avenue for intervention that could impact children's enjoyment of, and intentions to continue, playing soccer; namely, interventions that specifically target autonomy supportive coaching.