Miracle-dz/UniFAR-FTUs huggingface dataset:
Using genetics to understand the causal influence of higher BMI on depression

Abstract Background Depression is more common in obese than non-obese individuals, especially in women, but the causal relationship between obesity and depression is complex and uncertain. Previous studies have used genetic variants associated with BMI to provide evidence that higher body mass index (BMI) causes depression, but have not tested whether this relationship is driven by the metabolic consequences of BMI nor for differences between men and women. Methods We performed a Mendelian randomization study using 48 791 individuals with depression and 291 995 controls in the UK Biobank, to test for causal effects of higher BMI on depression (defined using self-report and Hospital Episode data). We used two genetic instruments, both representing higher BMI, but one with and one without its adverse metabolic consequences, in an attempt to ‘uncouple’ the psychological component of obesity from the metabolic consequences. We further tested causal relationships in men and women separately, and using subsets of BMI variants from known physiological pathways. Results Higher BMI was strongly associated with higher odds of depression, especially in women. Mendelian randomization provided evidence that higher BMI partly causes depression. Using a 73-variant BMI genetic risk score, a genetically determined one standard deviation (1 SD) higher BMI (4.9 kg/m2) was associated with higher odds of depression in all individuals [odds ratio (OR): 1.18, 95% confidence interval (CI): 1.09, 1.28, P = 0.00007) and women only (OR: 1.24, 95% CI: 1.11, 1.39, P = 0.0001). Meta-analysis with 45 591 depression cases and 97 647 controls from the Psychiatric Genomics Consortium (PGC) strengthened the statistical confidence of the findings in all individuals. Similar effect size estimates were obtained using different Mendelian randomization methods, although not all reached P < 0.05. Using a metabolically favourable adiposity genetic risk score, and meta-analysing data from the UK biobank and PGC, a genetically determined 1 SD higher BMI (4.9 kg/m2) was associated with higher odds of depression in all individuals (OR: 1.26, 95% CI: 1.06, 1.50], P = 0.010), but with weaker statistical confidence. Conclusions Higher BMI, with and without its adverse metabolic consequences, is likely to have a causal role in determining the likelihood of an individual developing depression.
Decoding hierarchical control of sequential behavior in oscillatory EEG activity

Despite strong theoretical reasons for assuming that abstract representations organize complex action sequences in terms of subplans (chunks) and sequential positions, we lack methods to directly track such content-independent, hierarchical representations in humans. We applied time-resolved, multivariate decoding analysis to the pattern of rhythmic EEG activity that was registered while participants planned and executed individual elements from pre-learned, structured sequences. Across three experiments, the theta and alpha-band activity independently coded basic elements and abstract control representations, in particular the ordinal position of basic elements, but also the identity and position of chunks. Further, a robust representation of higher-level, chunk identity information was only found in individuals with above-median working memory capacity, potentially providing a neural-level explanation for working-memory differences in sequential performance. Our results suggest that by decoding oscillations we can track how the cognitive system traverses through the states of a hierarchical control structure.
A performance evaluation of local descriptors

In this paper we compare the performance of interest point descriptors. Many different descriptors have been proposed in the literature. However, it is unclear which descriptors are more appropriate and how their performance depends on the interest point detector. The descriptors should be distinctive and at the same time robust to changes in viewing conditions as well as to errors of the point detector. Our evaluation uses as criterion detection rate with respect to false positive rate and is carried out for different image transformations. We compare SIFT descriptors (Lowe, 1999), steerable filters (Freeman and Adelson, 1991), differential invariants (Koenderink ad van Doorn, 1987), complex filters (Schaffalitzky and Zisserman, 2002), moment invariants (Van Gool et al., 1996) and cross-correlation for different types of interest points. In this evaluation, we observe that the ranking of the descriptors does not depend on the point detector and that SIFT descriptors perform best. Steerable filters come second ; they can be considered a good choice given the low dimensionality.
Three-Dimensional Probabilistic Maps of Mesial Temporal Lobe Structures in Children and Adolescents’ Brains

The hippocampus and the adjacent perirhinal, entorhinal, temporopolar, and parahippocampal cortices are interconnected in a hierarchical MTL system crucial for memory processes. A probabilistic description of the anatomical location and spatial variability of MTL cortices in the child and adolescent brain would help to assess structure-function relationships. The rhinal sulcus (RS) and the collateral sulcus (CS) that border MTL cortices and influence their morphology have never been described in these populations. In this study, we identified the aforementioned structures on magnetic resonance images of 38 healthy subjects aged 7–17 years old. Relative to sulcal morphometry in the MTL, we showed RS-CS conformation is an additional factor of variability in the MTL that is not explained by other variables such as age, sex and brain volume; with an innovative method using permutation testing of the extrema of structures of interest, we showed that RS-SC conformation was not associated with differences of location of MTL sulci. Relative to probabilistic maps, we offered for the first time a systematic mapping of MTL structures in children and adolescent, mapping all the structures of the MTL system while taking sulcal morphology into account. Our results, with the probabilistic maps described here being freely available for download, will help to understand the anatomy of this region and help functional and clinical studies to accurately test structure-function hypotheses in the MTL during development. Free access to MTL pediatric atlas: http://neurovault.org/collections/2381/.
Ethical considerations in Controlled Human Malaria Infection studies in low resource settings: Experiences and perceptions of study participants in a malaria Challenge study in Kenya

Background: The range and amount of volunteer infection studies, known as Controlled Human Infection Model (CHMI) studies, in Low-Middle Income Countries (LMICs) is increasing with rapid technological advancement, world-class laboratory facilities and increasing capacity development initiatives. However, the ethical issues these studies present in LMICs have not been empirically studied. We present findings of a descriptive social science study nested within a malaria volunteer infection study, on-going at the time of writing, at the KEMRI-Wellcome Trust Research Programme (KWTRP) on the Kenyan Coast. Methods: The study included non-participant observations, five group discussions with more than half of the CHMI study participants, two in-depth interviews with study team members, and an exit questionnaire administered to the participants. Results: Participants understood the key elements of the study, including that they would be deliberately infected with malaria parasites and may get malaria as a result, there would be regular blood draws, and they would spend up to 24 days in a residence facility away from their homes. The greatest motivation for participation was the monetary compensation of 20 USD per overnight stay given as a lump-sum at the end of their residency stay. Also appreciated were the health screening tests prior to enrolment and the positive relations with the study team. Concerns raised included the amount and regularity of blood draws experienced, and concerns that this type of research may feed into on-going rumours about research generally. Conclusion: With the increasing range and number of CHMI studies being conducted in LMICs, current ethical guidance are inadequate. This study highlights some of the ethical issues that could emerge in these settings, emphasizing the heavy responsibility placed on research review and regulatory systems, researchers and funders, as well as the importance of carefully tailored community engagement and consent processes.
Mining Supportive and Unsupportive Evidence from Facebook Using Anti-Reconstruction of the Nuclear Power Plant as an Example

The growth of online societies such as Twitter and Facebook allows people to discuss politics on the internet freely and conveniently, which has been noticed by governments recently. They would like to understand the stance of people for social agenda. In the past, researches have shown the techniques of opinion mining are able to analyze sentiment on the social media. However, the data for the debate of new political or social issues on the Web are often highly-skewed and lacking of labels, which makes the previously proposed approaches in the related work unsatisfactory. In this paper, we try to use co-training and a sentiment scoring tool to deal with this problem. Three requirements need to be fulfilled in the proposed approaches. First, they should easily start from a small set of labeled data. Second, they should be able to retrieve the minority. Third, they should report satisfactory precision. The experiment result shows the ability of these approaches to find the supportive and un-supportive evidence from very few labeled data.
Programmed cell death protein 4 deficiency suppresses foam cell formation by activating autophagy in advanced glycation end‐product low‐density lipoprotein–induced macrophages

Advanced glycation end‐product is a modified form of low‐density lipoprotein (AGE‐LDL) and accelerates atherosclerosis through undefined mechanisms. Programmed cell death protein 4 (PDCD4), a transcriptional regulator, plays an important role in the regulation of autophagy. The aim of the present study was to investigate the role of PDCD4 involved in AGE‐LDL–induced foam cell formation.
V2V radio channel properties at urban intersection and ramp on urban viaduct at 5.9 GHz

As a hotspot of wireless communication, vehicular communication is playing an important role in the smart city. This study focuses on vehicle-to-vehicle (V2V) radio channel characteristics at 5.9 GHz band based on measurement, under a ramp with soundproof wall on the urban viaduct and an urban intersection scenario, which are two similar but with slight difference propagation environments. Differences of V2V radio channel characteristics between two scenarios have been measured and analysed, in the view of best fit distribution of fades, power delay profile, delay spread, channel gain and Doppler spread. It is found that Weibull and Ricean distribution has a good match in non-line-of-sight and line-of-sight region, respectively. Transformation of different propagation mechanisms can increase or reduce the received power by 9-11 dB on average. Also, the power delay profile and root mean square delay spread are influenced by the different propagation conditions. Moreover, Ricean K-factors and Weibull shape parameters are modelled based on the least-square. The comparison of channel properties between these two classical urban scenarios is vital to the optimal design and performance of V2V communication system.
Impact of good and poor mobilizers on hematopoietic progenitor cell collection efficiency and product quality

Mobilization regimen choice is a significant contributing factor for successful hematopoietic progenitor cell (HPC) collection by leukocytapheresis and reaching the target CD34+ cell dose. How mobilization regimen affects collection efficiency and the quality of products collected using the Spectra Optia apheresis instrument is not fully known.
On the Levy-Walk Nature of Human Mobility

We report that human walks performed in outdoor settings of tens of kilometers resemble a truncated form of Levy walks commonly observed in animals such as monkeys, birds and jackals. Our study is based on about one thousand hours of GPS traces involving 44 volunteers in various outdoor settings including two different college campuses, a metropolitan area, a theme park and a state fair. This paper shows that many statistical features of human walks follow truncated power-law, showing evidence of scale-freedom and do not conform to the central limit theorem. These traits are similar to those of Levy walks. It is conjectured that the truncation, which makes the mobility deviate from pure Levy walks, comes from geographical constraints including walk boundary, physical obstructions and traffic. None of commonly used mobility models for mobile networks captures these properties. Based on these findings, we construct a simple Levy walk mobility model which is versatile enough in emulating diverse statistical patterns of human walks observed in our traces. The model is also used to recreate similar power-law inter-contact time distributions observed in previous human mobility studies. Our network simulation indicates that the Levy walk features are important in characterizing the performance of mobile network routing performance.
Assessment of haemoglobin measurement by several methods – blood gas analyser, capillary and venous HemoCue®, non‐invasive spectrophotometry and laboratory assay – in term and preterm infants

A laboratory haematology analyser is the gold standard for measuring haemoglobin concentration but has disadvantages, especially in neonates. This study compared alternative blood‐sparing and non‐invasive methods of haemoglobin concentration measurement with the gold standard. Haemoglobin concentrations were measured using a laboratory haematology analyser (reference method), blood gas analyser, HemoCue® using venous and capillary blood samples and a newly developed non‐invasive sensor for neonates < 3 kg. A total of 63 measurements were performed. Body weight (2190 (1820–2520 [967–4450]) g) and haemoglobin concentration (12.3 (10.6–15.2 [8.2–20.5]) g.dl−1) varied widely. Bias/limits of agreement between the alternative methods and reference method were −0.1/−1.2 to 1.0 g.dl−1 (blood gas analyser), −0.4/−1.8 to 1.1 g.dl−1 (HemoCue, venous blood), 0.7/−1.9 to 3.2 g.dl−1 (HemoCue, capillary blood) and −1.2/−4.3 to 2 g.dl−1 (non‐invasive haemoglobin measurement). Perfusion index, body weight and fetal haemoglobin concentration did not affect the accuracy of the alternative measurement methods, and these were successfully applied in term and preterm infants. However, the accuracies of non‐invasive haemoglobin measurement and HemoCue of capillary blood especially lacked sufficient agreement with that of the reference method to recommend these methods for clinical decision making.
De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth

Casuarina equisetifolia (C. equisetifolia), a conifer-like angiosperm with resistance to typhoon and stress tolerance, is mainly cultivated in the coastal areas of Australasia. C. equisetifolia, making it a valuable model to study secondary growth associated genes and stress-tolerance traits. However, the genome sequence is unavailable and therefore wood-associated growth rate and stress resistance at the molecular level is largely unexplored. We therefore constructed a high-quality draft genome sequence of C. equisetifolia by a combination of Illumina second-generation sequencing reads and Pacific Biosciences single-molecule real-time (SMRT) long reads to advance the investigation of this species. Here, we report the genome assembly, which contains approximately 300 megabases (Mb) and scaffold size of N50 is 1.06 Mb. Additionally, gene annotation, assisted by a combination of prediction and RNA-seq data, generated 29 827 annotated protein-coding genes and 1983 non-coding genes, respectively. Furthermore, we found that the total number of repetitive sequences account for one-third of the genome assembly. Here we also construct the genome-wide map of DNA modification, such as two novel forms N6 -adenine (6mA) and N4-methylcytosine (4mC) at the level of single-nucleotide resolution using single-molecule real-time (SMRT) sequencing. Interestingly, we found that 17% of 6mA modification genes and 15% of 4mC modification genes also included alternative splicing events. Finally, we investigated cellulose, hemicellulose, and lignin-related genes, which were associated with secondary growth and contained different DNA modifications. The high-quality genome sequence and annotation of C. equisetifolia in this study provide a valuable resource to strengthen our understanding of the diverse traits of trees.
Effect of low frequency ultrasound thawing method on the quality characteristics of Peru squid (Dosidicus gigas)

The effects of different thawing methods (air thawing, water soak thawing, refrigeration thawing, low frequency ultrasound thawing at 160, 240, 320 and 400 W) on thawing time, thawing loss, cooking loss, water-holding capacity and texture of frozen squid were investigated. The results showed that thawing loss and thawing time were reduced significantly (p < 0.05) by ultrasound thawing compared with the water soak thawing and air thawing, but the cooking loss had no significant difference (p > 0.05). Results of the ultrasound thawing especially at 160 and 240 W on microstructure showed less destructive effect on muscle. The microstructure of the muscle was destroyed significantly after air thawing and water soak thawing compared with the ultrasound thawing, which showed that more fibre structure was broken and the gap between the muscle fibres was increased significantly. Low-field NMR results showed that the ability of immobile water shifting to free water after ultrasound thawing was lower than air thawing and water soak thawing, which was consistent with the results of thawing loss and cooking loss. Ultrasound thawing might be chosen as an alternative method to enhance the quality during thawing process.
Engineering of the Filamentous Fungus Penicillium chrysogenum as Cell Factory for Natural Products

Penicillium chrysogenum (renamed P. rubens) is the most studied member of a family of more than 350 Penicillium species that constitute the genus. Since the discovery of penicillin by Alexander Fleming, this filamentous fungus is used as a commercial β-lactam antibiotic producer. For several decades, P. chrysogenum was subjected to a classical strain improvement (CSI) program to increase penicillin titers. This resulted in a massive increase in the penicillin production capacity, paralleled by the silencing of several other biosynthetic gene clusters (BGCs), causing a reduction in the production of a broad range of BGC encoded natural products (NPs). Several approaches have been used to restore the ability of the penicillin production strains to synthetize the NPs lost during the CSI. Here, we summarize various re-activation mechanisms of BGCs, and how interference with regulation can be used as a strategy to activate or silence BGCs in filamentous fungi. To further emphasize the versatility of P. chrysogenum as a fungal production platform for NPs with potential commercial value, protein engineering of biosynthetic enzymes is discussed as a tool to develop de novo BGC pathways for new NPs.
Application of Direct Immersion Solid-Phase Microextraction (DI-SPME) for Understanding Biological Changes of Mediterranean Fruit Fly (Ceratitis capitata) During Mating Procedures

Samples from three different mating stages (before, during and after mating) of the Mediterranean fruit fly Ceratitis capitata were used in this experiment. Samples obtained from whole insects were subjected to extraction with the two mixtures of solvents (acetonitrile/water (A) and methanol/acetonitrile/water (B)) and a comparative study of the extractions using the different solvents was performed. Direct immersion-solid phase microextraction (DI-SPME) was employed, followed by gas chromatographic-mass spectrometry analyses (GC/MS) for the collection, separation and identification of compounds. The method was validated by testing its sensitivity, linearity and reproducibility. The main compounds identified in the three different mating stages were ethyl glycolate, α-farnesene, decanoic acid octyl ester, 2,6,10,15-tetramethylheptadecane, 11-tricosene, 9,12-(Z,Z)-octadecadienoic acid, methyl stearate, 9-(Z)-tricosene, 9,11-didehydro-lumisterol acetate; 1,54-dibromotetrapentacontane, 9-(Z)-hexadecenoic acid hexadecyl ester, 9-(E)-octadecenoic acid and 9-(Z)-hexadecenoic acid octadecyl ester. The novel findings indicated that compound compositions were not significantly different before and during mating. However, new chemical compounds were generated after mating, such as 1-iodododecane, 9-(Z)-tricosene and 11,13-dimethyl-12-tetradecen-1-acetate which were extracted with both (A) and (B) and dodecanoic acid, (Z)-oleic acid, octadecanoic acid and hentriacontane which were extracted with (A) and ethyl glycolate, 9-hexadecenoic acid hexadecyl ester, palmitoleic acid and 9-(E)-octadecenoic acid, which were extracted with solvent (B). This study has demonstrated that DI-SPME is useful in quantitative insect metabolomics by determining changes in the metabolic compounds in response to mating periods. DI-SPME chemical extraction technology might offer analysis of metabolites that could potentially enhance our understanding on the evolution of the medfly.
Update on Medication Use Quality and Safety in Older Adults, 2017

Improving the quality of medication use and medication safety in older adults is an important public health priority and is of paramount importance for clinicians who care for them. We selected four important articles from 2017 that address these issues to annotate and critique, and we discuss the broader implications for optimizing medication use. A longer list of articles is given in an online appendix. The first study provides national data on the prevalence of central nervous system–active medication polypharmacy in older adults and how this has changed over a 9‐year period (2004–2013). The second study characterizes prevalence of and factors associated with nonadherence to antiepileptic drugs in 36,912 older adults with epilepsy, with an emphasis on minorities. The third study describes the extent of antibiotic use in residents of 381 long‐term care facilities (LTCF) in British Columbia, Canada, from 2007 to 2014. Finally, we discuss a meta‐analysis of 42 studies that evaluated the prevalence of hospital admissions caused by adverse drug reactions in older adults. This article is intended to provide a narrative review of important publications on medication use quality and safety for clinicians and researchers committed to optimizing medication use in older adults. J Am Geriatr Soc 66:2254–2258, 2018.