Miracle-dz/UniFAR-FTUs huggingface dataset:
Sodium in commonly consumed fast foods in New Zealand: a public health opportunity

Abstract Objective (i) To determine the Na content of commonly consumed fast foods in New Zealand and (ii) to estimate Na intake from savoury fast foods for the New Zealand adult population. Design Commonly consumed fast foods were identified from the 2008/09 New Zealand Adult Nutrition Survey. Na values from all savoury fast foods from chain restaurants (n 471) were obtained from nutrition information on company websites, while the twelve most popular fast-food types from independent outlets (n 52) were determined using laboratory analysis. Results were compared with the UK Food Standards Agency 2012 sodium targets. Nutrient analysis was completed to estimate Na intake from savoury fast foods for the New Zealand population using the 2008/09 New Zealand Adult Nutrition Survey. Setting New Zealand. Subjects Adults aged 15 years and above. Results From chain restaurants, sauces/salad dressings and fried chicken had the highest Na content (per 100 g) and from independent outlets, sausage rolls, battered hotdogs and mince and cheese pies were highest in Na (per 100 g). The majority of fast foods exceeded the UK Food Standards Agency 2012 sodium targets. The mean daily Na intake from savoury fast foods was 283 mg/d for the total adult population and 1229 mg/d for fast-food consumers. Conclusions Taking into account the Na content and frequency of consumption, potato dishes, filled rolls, hamburgers and battered fish contributed substantially to Na intake for fast-food consumers in New Zealand. These foods should be targeted for Na reduction reformulation.
Polycyclic aromatic hydrocarbons in placenta

Concentrations of chrysene, benz [a I anthracene, benzo [a I -pyrene, benzo [h lfluoranthene, indeno [1,2,3 -c,d] pyrene, dibenz [a,h I anthracene, and benzo [g,h,i] perylene were measured in placentas from 200 women from two cities in Ukraine, Kyiv and Dniprodzerzhinsk. The participants had no special exposures and were chosen from among subjects in an ongoing study of reproductive health. All seven of the polycyclic aromatic hydrocarbons (PAHs) were found in all placentas, with the sole exception of benzo [a I pyrene in one placenta. Chrysene was present at the highest concentrations, with median 1.38 ng/g dry weight. Dibenz[a,h]anthracene and benzo[g,h,ilperylene had the lowest concentrations; each had median 0.73 ng/g dry weight. Concentrations in Kyiv were slightly higher than those in Dniprodzerzhinsk, butthe differencewas significantonlyfor dibenz [a,h I anthracene. Dibenz [a,h] anthracene and benzo[g,h,ijperylene increased significantly with maternal body mass index, but other PAHs showed no such pattern. Placentas from deliveries in autumn or winter had slightly but not significantly higher concentrations. Concentrations were not related to maternal age. There were too few smokers in the sample for meaningful evaluation. No associations were seen between any of the placental PAH concentrations and birth weight of the infant.
How to shuffle and scatter pieces of a puzzle over a metropolitan area

We propose a new architecture for broadcasting an enormous amount of information over a large population of users in a typical urban area via multiple base stations for delay tolerant applications. The core idea is that each base station partially broadcasts the information instead of transmitting the whole information. In particular, the large target file is broken into M smaller chunks and is provided to N base stations. Each base station i independently generates Mi <; M linear combinations of the chunks using random linear network coding (RLNC) techniques and broadcasts it to the users in its coverage area. Users then code and exchange packets in their possession via their short range communication links (e.g. bluetooth). Thanks to the random nature of human mobility patterns, it is expected that after a while, the placement of the users would be mixed enough so that users can obtain sufficient number of chunks to decode the entire file. The proposed architecture provides a fundamentally bandwidth efficient scheme for delay tolerant broadcast applications and has the potential to be implemented in practice. In particular, the proposed approach is completely opportunistic i.e. it does not require any routing algorithm. We evaluate the performance of the proposed architecture via extensive simulations using a well known human mobility patterns simulator.
Correction: The Rhizosphere Selects for Particular Groups of Acidobacteria and Verrucomicrobia

There is a lack in our current understanding on the putative interactions of species of the phyla of Acidobacteria and Verrucomicrobia with plants. Moreover, progress in this area is seriously hampered by the recalcitrance of members of these phyla to grow as pure cultures. The purpose of this study was to investigate whether particular members of Acidobacteria and Verrucomicrobia are avid colonizers of the rhizosphere. Based on previous work, rhizosphere competence was demonstrated for the Verrucomicrobia subdivision 1 groups of Luteolibacter and Candidatus genus Rhizospheria and it was hypothesized that the rhizosphere is a common habitat for Acidobacteria subdivision 8 (class Holophagae). We assessed the population densities of Bacteria, Verrucomicrobia subdivision 1 groups Luteolibacter and Candidatus genus Rhizospheria and Acidobacteria subdivisions 1, 3, 4, 6 and Holophagae in bulk soil and in the rhizospheres of grass, potato and leek in the same field at different points in time using real-time quantitative PCR. Primers of all seven verrucomicrobial, acidobacterial and holophagal PCR systems were based on 16S rRNA gene sequences of cultivable representatives of the different groups. Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres. In particular, the Holophaga 16S rRNA gene number were more abundant in the leek rhizosphere than in bulk soil and the rhizospheres of grass and potato. Attraction to, and colonization of, leek roots by Holophagae strain CHC25 was further shown in an experimental microcosm set-up. In the light of this remarkable capacity, we propose to coin strain CHC25 Candidatus Porrumbacterium oxyphilus (class Holophagae, Phylum Acidobacteria), the first cultured representative with rhizosphere competence.
Stationary Eddy Response to Surface Boundary Forcing: Idealized GCM Experiments*

Abstract A set of atmospheric general circulation model (AGCM) experiments under idealized conditions is performed to investigate atmospheric response to surface boundary forcing by extratropical land–sea contrast, large-scale orography, and tropical sea surface temperature (SST) distribution. Stationary eddies forced by the extratropical land–sea distribution are strongest in high latitudes, but their amplitudes are modest and comparable to internal chaotic variability. By contrast, the stationary eddy response to zonal variations in tropical SST is strong and robust in both the subtropics and midlatitudes. While these SST-forced stationary waves are trapped within the troposphere, those induced by orography show a strong vertical propagation into the stratosphere. Analysis of transient eddies indicates that orography is effective in generating a zonally localized storm track while extratropical land–sea contrast has little effect on the zonal variation of upper-level storm activity. A vorticity budget a.
GRAFT SELECTION IN ANTERIOR CRUCIATE LIGAMENT RECONSTRUCTION

Introduction Anterior cruciate ligament (ACL) reconstruction is one of the most studied surgeries performed within any surgical specialty. The focus of much of this research has been related to graft selection and its impact on clinical outocmes. Favorable characteristics of graft options for ACL reconstruction include those that have similar structural and biomechanical characteristics of the native ligament, allow for secure fixation, permit rapid biologic incorporation, and have limited donor site morbidity. 61 Ideally, the graft selected should allow for early, active rehabilitation and maintain its biomechanical properties and strength until full graft incorporation and biologic maturation. Ultimately, any graft construct should approximate or exceed the physical and mechanical properties of the native ACL. (Table 1)
Decomposition Rates and Residue-Colonizing Microbial Communities of Bacillus thuringiensis Insecticidal Protein Cry3Bb-Expressing (Bt) and Non-Bt Corn Hybrids in the Field

ABSTRACT Despite the rapid adoption of crops expressing the insecticidal Cry protein(s) from Bacillus thuringiensis (Bt), public concern continues to mount over the potential environmental impacts. Reduced residue decomposition rates and increased tissue lignin concentrations reported for some Bt corn hybrids have been highlighted recently as they may influence soil carbon dynamics. We assessed the effects of MON863 Bt corn, producing the Cry3Bb protein against the corn rootworm complex, on these aspects and associated decomposer communities by terminal restriction fragment length polymorphism (T-RFLP) analysis. Litterbags containing cobs, roots, or stalks plus leaves from Bt and unmodified corn with (non-Bt+I) or without (non-Bt) insecticide applied were placed on the soil surface and at a 10-cm depth in field plots planted with these crop treatments. The litterbags were recovered and analyzed after 3.5, 15.5, and 25 months. No significant effect of treatment (Bt, non-Bt, and non-Bt+I) was observed on initial tissue lignin concentrations, litter decomposition rate, or bacterial decomposer communities. The effect of treatment on fungal decomposer communities was minor, with only 1 of 16 comparisons yielding separation by treatment. Environmental factors (litterbag recovery year, litterbag placement, and plot history) led to significant differences for most measured variables. Combined, these results indicate that the differences detected were driven primarily by environmental factors rather than by any differences between the corn hybrids or the use of tefluthrin. We conclude that the Cry3Bb corn tested in this study is unlikely to affect carbon residence time or turnover in soils receiving these crop residues.
Lithium: Measurement of Young's Modulus and Yield Strength

The Lithium Collection Lens is used for anti-proton collection. In analyzing the structural behavior during operation, various material properties of lithium are often needed. properties such as density, coefficient of thermal expansion, thermal conductivity, specific heat, compressability, etc.; are well known. However, to the authors knowledge there is only one published source for Young's Modulus. This paper reviews the results from the testing of Young's Modulus and the yield strength of lithium at room temperature.
Does a single session of electroconvulsive therapy alter the neural response to emotional faces in depression? A randomised sham-controlled functional magnetic resonance imaging study

Negative neurocognitive bias is a core feature of major depressive disorder that is reversed by pharmacological and psychological treatments. This double-blind functional magnetic resonance imaging study investigated for the first time whether electroconvulsive therapy modulates negative neurocognitive bias in major depressive disorder. Patients with major depressive disorder were randomised to one active (n=15) or sham electroconvulsive therapy (n=12). The following day they underwent whole-brain functional magnetic resonance imaging at 3T while viewing emotional faces and performed facial expression recognition and dot-probe tasks. A single electroconvulsive therapy session had no effect on amygdala response to emotional faces. Whole-brain analysis revealed no effects of electroconvulsive therapy versus sham therapy after family-wise error correction at the cluster level, using a cluster-forming threshold of Z>3.1 (p<0.001) to secure family-wise error <5%. Groups showed no differences in behavioural measures, mood and medication. Exploratory cluster-corrected whole-brain analysis (Z>2.3; p<0.01) revealed electroconvulsive therapy-induced changes in parahippocampal and superior frontal responses to fearful versus happy faces as well as in fear-specific functional connectivity between amygdala and occipito-temporal regions. Across all patients, greater fear-specific amygdala – occipital coupling correlated with lower fear vigilance. Despite no statistically significant shift in neural response to faces after a single electroconvulsive therapy session, the observed trend changes after a single electroconvulsive therapy session point to an early shift in emotional processing that may contribute to antidepressant effects of electroconvulsive therapy.
The Power to Protect: Household Bargaining and Female Condom Use

Women may face systematically greater benefits than men from adopting certain technologies. Yet women often hold lower bargaining power, meaning that men's preferences may constrain household adoption when decisions are joint. When low female bargaining power constrains adoption of the first-best technology, introducing a version of the technology that is second-best in terms of cost or effectiveness, but more acceptable to men, may increase adoption and welfare. This paper contributes the first explicit model and test of the trade-offs when introducing a second-best technology in such a setting. We conduct a field experiment introducing female condoms (which are less effective and more expensive than male condoms, but often preferred by men) in an area with high HIV prevalence. We observe an increase in the likelihood that women have sex and find strongest adoption of female condoms among women with lower bargaining power, who were previously having unprotected sex.
Graph Signal Recovery via Primal-Dual Algorithms for Total Variation Minimization

We consider the problem of recovering a smooth graph signal from noisy samples taken on a subset of graph nodes. The smoothness of the graph signal is quantified in terms of total variation. We formulate the signal recovery task as a convex optimization problem that minimizes the total variation of the graph signal while controlling its global or node-wise empirical error. We propose a first-order primal-dual algorithm to solve these total variation minimization problems. A distributed implementation of the algorithm is devised to handle large-dimensional applications efficiently. We use synthetic and real-world data to extensively compare the performance of our approach with state-of-the-art methods.
Impact of biogas digesters on wood utilisation and self-reported back pain for women living on rural Kenyan smallholder dairy farms

Abstract Women living on rural Kenyan dairy farms spend significant amounts of time collecting wood for cooking. Biogas digesters, which generate biogas for cooking from the anaerobic decomposition of livestock manure, are an alternative fuel source. The objective of this study was to quantify the quality of life and health benefits of installing biogas digesters on rural Kenyan dairy farms with respect to wood utilisation. Women from 62 farms (31 biogas farms and 31 referent farms) participated in interviews to determine reliance on wood and the impact of biogas digesters on this reliance. Self-reported back pain, time spent collecting wood and money spent on wood were significantly lower (p<0.01) for the biogas group, compared to referent farms. Multivariable linear regression showed that wood consumption increased by 2 lbs/day for each additional family member living on a farm. For an average family of three people, the addition of one cow was associated with increased wood consumption by 1.0 lb/day on biogas farms but by 4.4 lbs/day on referent farms (significant interaction variable – likely due to additional hot water for cleaning milk collection equipment). Biogas digesters represent a potentially important technology that can reduce reliance on wood fuel and improve health for Kenyan dairy farmers.
Identification and Characterization of Human Orthologues to Saccharomyces cerevisiae Upf2 Protein and Upf3 Protein (Caenorhabditis elegans SMG-4)

ABSTRACT Nonsense-mediated mRNA decay (NMD), also called mRNA surveillance, is an important pathway used by all organisms that have been tested to degrade mRNAs that prematurely terminate translation and, as a consequence, eliminate the production of aberrant proteins that could be potentially harmful. In mammalian cells, NMD appears to involve splicing-dependent alterations to mRNA as well as ribosome-associated components of the translational apparatus. To date, human (h) Upf1 protein (p) (hUpf1p), a group 1 RNA helicase named after itsSaccharomyces cerevisiae orthologue that functions in both translation termination and NMD, has been the only factor shown to be required for NMD in mammalian cells. Here, we describe human orthologues to S. cerevisiae Upf2p and S. cerevisiae Upf3p (Caenorhabditis elegans SMG-4) based on limited amino acid similarities. The existence of these orthologues provides evidence for a higher degree of evolutionary conservation of NMD than previously appreciated. Interestingly, human orthologues toS. cerevisiae Upf3p (C. elegans SMG-4) derive from two genes, one of which is X-linked and both of which generate multiple isoforms due to alternative pre-mRNA splicing. We demonstrate using immunoprecipitations of epitope-tagged proteins transiently produced in HeLa cells that hUpf2p interacts with hUpf1p, hUpf3p-X, and hUpf3p, and we define the domains required for the interactions. Furthermore, we find by using indirect immunofluorescence that hUpf1p is detected only in the cytoplasm, hUpf2p is detected primarily in the cytoplasm, and hUpf3p-X localizes primarily to nuclei. The finding that hUpf3p-X is a shuttling protein provides additional indication that NMD has both nuclear and cytoplasmic components.
Parallel and Divergent Evolutionary Solutions for the Optimization of an Engineered Central Metabolism in Methylobacterium extorquens AM1

Bioengineering holds great promise to provide fast and efficient biocatalysts for methanol-based biotechnology, but necessitates proven methods to optimize physiology in engineered strains. Here, we highlight experimental evolution as an effective means for optimizing an engineered Methylobacterium extorquens AM1. Replacement of the native formaldehyde oxidation pathway with a functional analog substantially decreased growth in an engineered Methylobacterium, but growth rapidly recovered after six hundred generations of evolution on methanol. We used whole-genome sequencing to identify the basis of adaptation in eight replicate evolved strains, and examined genomic changes in light of other growth and physiological data. We observed great variety in the numbers and types of mutations that occurred, including instances of parallel mutations at targets that may have been “rationalized” by the bioengineer, plus other “illogical” mutations that demonstrate the ability of evolution to expose unforeseen optimization solutions. Notably, we investigated mutations to RNA polymerase, which provided a massive growth benefit but are linked to highly aberrant transcriptional profiles. Overall, we highlight the power of experimental evolution to present genetic and physiological solutions for strain optimization, particularly in systems where the challenges of engineering are too many or too difficult to overcome via traditional engineering methods.
Clinical Epidemiology of Buruli Ulcer from Benin (2005-2013): Effect of Time-Delay to Diagnosis on Clinical Forms and Severe Phenotypes

Buruli Ulcer (BU) is a neglected infectious disease caused by Mycobacterium ulcerans that is responsible for severe necrotizing cutaneous lesions that may be associated with bone involvement. Clinical presentations of BU lesions are classically classified as papules, nodules, plaques and edematous infiltration, ulcer or osteomyelitis. Within these different clinical forms, lesions can be further classified as severe forms based on focality (multiple lesions), lesions’ size (>15cm diameter) or WHO Category (WHO Category 3 lesions). There are studies reporting an association between delay in seeking medical care and the development of ulcerative forms of BU or osteomyelitis, but the effect of time-delay on the emergence of lesions classified as severe has not been addressed. To address both issues, and in a cohort of laboratory-confirmed BU cases, 476 patients from a medical center in Allada, Benin, were studied. In this laboratory-confirmed cohort, we validated previous observations, demonstrating that time-delay is statistically related to the clinical form of BU. Indeed, for non-ulcerated forms (nodule, edema, and plaque) the median time-delay was 32.5 days (IQR 30.0–67.5), while for ulcerated forms it was 60 days (IQR 20.0–120.0) (p = 0.009), and for bone lesions, 365 days (IQR 228.0–548.0). On the other hand, we show here that time-delay is not associated with the more severe phenotypes of BU, such as multi-focal lesions (median 90 days; IQR 56–217.5; p = 0.09), larger lesions (diameter >15cm) (median 60 days; IQR 30–120; p = 0.92) or category 3 WHO classification (median 60 days; IQR 30–150; p = 0.20), when compared with unifocal (median 60 days; IQR 30–90), small lesions (diameter ≤15cm) (median 60 days; IQR 30–90), or WHO category 1+2 lesions (median 60 days; IQR 30–90), respectively. Our results demonstrate that after an initial period of progression towards ulceration or bone involvement, BU lesions become stable regarding size and focal/multi-focal progression. Therefore, in future studies on BU epidemiology, severe clinical forms should be systematically considered as distinct phenotypes of the same disease and thus subjected to specific risk factor investigation.
Phone-based cepstral polynomial SVM system for speaker recognition

We have been using a phone-based cepstral system with polynomial features in NIST evaluations for the past two years. This system uses three broad phone classes, three states per class, and third-order polynomial features obtained from MFCC features. In this paper, we present a complete analysis of the system. We start from a simpler system that does not use phones or states and show that the addition of phones gives a significant improvement. We show that adding state information does not provide improvement on its own but provides a significant improvement when used with phone classes. We complete the system by applying nuisance attribute projection (NAP) and score normalization. We show that splitting features after a joint NAP over all phone classes results in a significant improvement. Overall, we obtain about 25% performance improvement with polynomial features based on phones and states, and obtain a system with performance comparable to a state-of-the-art SVM system.