Miracle-dz/UniFAR-FTUs huggingface dataset:
Alpha-1 antitrypsin Pi*SZ genotype: estimated prevalence and number of SZ subjects worldwide

The alpha-1 antitrypsin (AAT) haplotype Pi*S, when inherited along with the Pi*Z haplotype to form a Pi*SZ genotype, can be associated with pulmonary emphysema in regular smokers, and less frequently with liver disease, panniculitis, and systemic vasculitis in a small percentage of people, but this connection is less well established. Since the detection of cases can allow the application of preventive measures in patients and relatives with this congenital disorder, the objective of this study was to update the prevalence of the SZ genotype to achieve accurate estimates of the number of Pi*SZ subjects worldwide, based on studies performed according to the following criteria: 1) samples representative of the general population, 2) AAT phenotyping characterized by adequate methods, and 3) selection of studies with reliable results assessed with a coefficient of variation calculated from the sample size and 95% confidence intervals. Studies fulfilling these criteria were used to develop tables and maps with an inverse distance-weighted (IDW) interpolation method, to provide numerical and geographical information of the Pi*SZ distribution worldwide. A total of 262 cohorts from 71 countries were included in the analysis. With the data provided by these cohorts, a total of 1,490,816 Pi*SZ were estimated: 708,792 in Europe; 582,984 in America and Caribbean; 85,925 in Africa; 77,940 in Asia; and 35,176 in Australia and New Zealand. Remarkably, the IDW interpolation maps predicted the Pi*SZ prevalence throughout the entire world even in areas lacking real data. These results may be useful to plan strategies for future research, diagnosis, and management of affected individuals.
2017 ICCV Challenge: Detecting Symmetry in the Wild

Motivated by various new applications of computational symmetry in computer vision and in an effort to advance machine perception of symmetry in the wild, we organize the third international symmetry detection challenge at ICCV 2017, after the CVPR 2011/2013 symmetry detection competitions. Our goal is to gauge the progress in computational symmetry with continuous benchmarking of both new algorithms and datasets, as well as more polished validation methodology. Different from previous years, this time we expand our training/testing data sets to include 3D data, and establish the most comprehensive and largest annotated datasets for symmetry detection to date; we also expand the types of symmetries to include densely-distributed and medial-axis-like symmetries; furthermore, we establish a challenge-and-paper dual track mechanism where both algorithms and articles on symmetry-related research are solicited. In this report, we provide a detailed summary of our evaluation methodology for each type of symmetry detection algorithm validated. We demonstrate and analyze quantified detection results in terms of precision-recall curves and F-measures for all algorithms evaluated. We also offer a short survey of the paper-track submissions accepted for our 2017 symmetry challenge.
Cardiac energetics, oxygenation, and perfusion during increased workload in patients with type 2 diabetes mellitus

Aims Patients with type 2 diabetes mellitus (T2DM) are known to have impaired resting myocardial energetics and impaired myocardial perfusion reserve, even in the absence of obstructive epicardial coronary artery disease (CAD). Whether or not the pre-existing energetic deficit is exacerbated by exercise, and whether the impaired myocardial perfusion causes deoxygenation and further energetic derangement during exercise stress, is uncertain. Methods and results Thirty-one T2DM patients, on oral antidiabetic therapies with a mean HBA1c of 7.4 ± 1.3%, and 17 matched controls underwent adenosine stress cardiovascular magnetic resonance for assessment of perfusion [myocardial perfusion reserve index (MPRI)] and oxygenation [blood-oxygen level-dependent (BOLD) signal intensity change (SIΔ)]. Cardiac phosphorus-MR spectroscopy was performed at rest and during leg exercise. Significant CAD (>50% coronary stenosis) was excluded in all patients by coronary computed tomographic angiography. Resting phosphocreatine to ATP (PCr/ATP) was reduced by 17% in patients (1.74 ± 0.26, P = 0.001), compared with controls (2.07 ± 0.35); during exercise, there was a further 12% reduction in PCr/ATP (P = 0.005) in T2DM patients, but no change in controls. Myocardial perfusion and oxygenation were decreased in T2DM (MPRI 1.61 ± 0.43 vs. 2.11 ± 0.68 in controls, P = 0.002; BOLD SIΔ 7.3 ± 7.8 vs. 17.1 ± 7.2% in controls, P < 0.001). Exercise PCr/ATP correlated with MPRI (r = 0.50, P = 0.001) and BOLD SIΔ (r = 0.32, P = 0.025), but there were no correlations between rest PCr/ATP and MPRI or BOLD SIΔ. Conclusion The pre-existing energetic deficit in diabetic cardiomyopathy is exacerbated by exercise; stress PCr/ATP correlates with impaired perfusion and oxygenation. Our findings suggest that, in diabetes, coronary microvascular dysfunction exacerbates derangement of cardiac energetics under conditions of increased workload.
MicroRNA-210 Suppresses Junction Proteins and Disrupts Blood-Brain Barrier Integrity in Neonatal Rat Hypoxic-Ischemic Brain Injury

Cerebral edema, primarily caused by disruption of the blood-brain barrier (BBB), is one of the serious complications associated with brain injury in neonatal hypoxic-ischemic encephalopathy (HIE). Our recent study demonstrated that the hypoxic-ischemic (HI) treatment significantly increased microRNA-210 (miR-210) in the neonatal rat brain and inhibition of miR-210 provided neuroprotection in neonatal HI brain injury. The present study aims to determine the role of miR-210 in the regulation of BBB integrity in the developing brain. miR-210 mimic was administered via intracerebroventricular injection (i.c.v.) into the brain of rat pups. Forty-eight hours after the injection, a modified Rice-Vannucci model was conducted to produce HI brain injury. Post-assays included cerebral edema analysis, western blotting, and immunofluorescence staining for serum immunoglobulin G (IgG) leakage. The results showed that miR-210 mimic exacerbated cerebral edema and IgG leakage into the brain parenchyma. In contrast, inhibition of miR-210 with its complementary locked nucleic acid oligonucleotides (miR-210-LNA) significantly reduced cerebral edema and IgG leakage. These findings suggest that miR-210 negatively regulates BBB integrity in the neonatal brain. Mechanistically, the seed sequences of miR-210 were identified complementary to the 3′ untranslated region (3′ UTR) of the mRNA transcripts of tight junction protein occludin and adherens junction protein β-catenin, indicating downstream targets of miR-210. This was further validated by in vivo data showing that miR-210 mimic significantly reduced the expression of these junction proteins in rat pup brains. Of importance, miR-210-LNA preserved the expression of junction proteins occludin and β-catenin from neonatal HI insult. Altogether, the present study reveals a novel mechanism of miR-210 in impairing BBB integrity that contributes to cerebral edema formation after neonatal HI insult, and provides new insights in miR-210-LNA mediated neuroprotection in neonatal HI brain injury.
Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface

ABSTRACT A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H2 as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe2O3). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe3(PO4)2] and siderite (FeCO3). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov. IMPORTANCE A novel iron-reducing species, Orenia metallireducens sp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA. Phylogenetic, physiologic, and genomic analyses of strain Z6 found it to have unique properties for iron reducers, including (i) active microbial iron-reducing capacity under broad ranges of temperatures (20 to 60°C), pHs (6 to 9.6), and salinities (0.4 to 3.5 M NaCl), (ii) lack of c-type cytochromes typically affiliated with iron reduction in Geobacter and Shewanella species, and (iii) being the only member of the Halanaerobiales capable of reducing crystalline goethite and hematite. This study expands the scope of phylogenetic affiliations, metabolic capacities, and catalytic mechanisms for iron-reducing microbes.
Awareness of and Attitudes toward Human Papillomavirus Vaccination among Adults in Korea: 9-Year Changes in Nationwide Surveys

Purpose Human papillomavirus (HPV) vaccination has been included in the National Immunization Program in Korea since 2016. We aimed to evaluate changes in the awareness of and attitudes toward HPV vaccination, among adults in Korea since the first introduction of the vaccines in 2007. Materials and Methods A nationwide population-based survey was conducted in 2016 for 1,200 nationally representative Korean men and women; the data obtained were compared with the data from the nationwide survey conducted in 2007. Results A significant increase in the awareness of HPV infection (35.8%) and vaccination (36.9%) was observed in 2016 from 13.3% and 8.6% in 2007, respectively. Willingness to be vaccinated against HPV decreased from 55.0% in 2007 to 25.8% in 2016, and the proportion of respondents expressing uncertainty increased from 28.3% in 2007 to 43.3% in 2016. Only 12.1% of men and 22.0% of women knew about the free national HPV vaccination program for girls, launched in June 2016. Younger women, with higher income level, awareness of the HPV vaccine, and perception of the seriousness of infections had a higher willingness to be vaccinated. A high education level, awareness of HPV infection and vaccination, and perception of the seriousness of infection were positively associated with the willingness of respondents to vaccinate their daughters. Conclusion Raising the awareness of HPV infection and vaccination with appropriate knowledge is necessary for the successful implementation of the national HPV vaccination program.
No increased risk of major congenital anomalies or adverse pregnancy or neonatal outcomes following letrozole use in assisted reproductive technology

STUDY QUESTION Does letrozole use increase the risk of major congenital anomalies and adverse pregnancy and neonatal outcomes in fresh, single-embryo transfer? SUMMARY ANSWER Letrozole significantly decreases the risk of miscarriage and does not increase the risk of major congenital anomalies or adverse pregnancy or neonatal outcomes compared with natural cycles in patients undergoing ART. WHAT IS KNOWN ALREADY Letrozole is the most commonly used aromatase inhibitor for mild ovarian stimulation in ART. However, its safety in terms of pregnancy and neonatal outcomes is unclear. STUDY DESIGN SIZE, DURATION This retrospective cohort study used data from the Japanese national ART registry from 2011 to 2013. PARTICIPANTS/MATERIALS, SETTING, METHODS A total of 3136 natural cycles and 792 letrozole-induced cycles associated with fresh, single-embryo transfer and resulting in a clinical pregnancy were included in the analysis. The main pregnancy outcomes were miscarriage, ectopic pregnancy and still birth, and the neonatal outcomes were preterm delivery, low birth weight, small/large for gestational age and major congenital anomalies. Terminated pregnancies were included in the analysis of major congenital anomalies. Odds ratios (ORs) and 95% CIs were calculated using multivariate logistic regression analysis adjusted for maternal age and calendar year. MAIN RESULTS AND THE ROLE OF CHANCE The risk of miscarriage was significantly lower in women administered letrozole (adjusted OR [aOR], 0.37, 95% CI, 0.30–0.47, P < 0.001). There was no significant difference in the overall risk of major congenital anomalies between the two groups (natural cycle 1.5% vs letrozole 1.9%, aOR, 1.24, 95% CI, 0.64–2.40, P = 0.52), and no increased risk for any specific organ system. Subgroup analysis demonstrated that the risk of major congenital anomalies was not increased in patients who underwent either in vitro fertilization or ICSI, or in those who received early cleavage stage or blastocyst embryo transfer. All other pregnancy and neonatal outcomes were comparable between the two groups. LIMITATIONS REASONS FOR CAUTION Despite the large sample size, we were only able to rule out the possibility that letrozole might cause large increases in birth-defect risks in ART patients. WIDER IMPLICATIONS OF THE FINDINGS The results suggest that letrozole stimulation reduces the risk of miscarriage, with no increase in the risk of major congenital anomalies or adverse pregnancy or neonatal outcomes compared with natural cycles in women undergoing ART. Letrozole may thus be a safe option for mild ovarian stimulation. STUDY FUNDING/COMPETING INTEREST(S) None. TRIAL REGISTRATION NUMBER Not applicable.
Predictive Structure and Topology of Peroxisomal ATP-Binding Cassette (ABC) Transporters

The peroxisomal ATP-binding Cassette (ABC) transporters, which are called ABCD1, ABCD2 and ABCD3, are transmembrane proteins involved in the transport of various lipids that allow their degradation inside the organelle. Defective ABCD1 leads to the accumulation of very long-chain fatty acids and is associated with a complex and severe neurodegenerative disorder called X-linked adrenoleukodystrophy (X-ALD). Although the nucleotide-binding domain is highly conserved and characterized within the ABC transporters family, solid data are missing for the transmembrane domain (TMD) of ABCD proteins. The lack of a clear consensus on the secondary and tertiary structure of the TMDs weakens any structure-function hypothesis based on the very diverse ABCD1 mutations found in X-ALD patients. Therefore, we first reinvestigated thoroughly the structure-function data available and performed refined alignments of ABCD protein sequences. Based on the 2.85 Å resolution crystal structure of the mitochondrial ABC transporter ABCB10, here we propose a structural model of peroxisomal ABCD proteins that specifies the position of the transmembrane and coupling helices, and highlight functional motifs and putative important amino acid residues.
Comparison of multiple methods for the determination of sulphite in Allium and Brassica vegetables

ABSTRACT Sulphites are a family of additives regulated for use worldwide in food products. They must be declared on the label if they are present in concentrations greater than 10 mg kg–1, determined as sulphur dioxide (SO2). The current US regulatory method for sulphites, the optimised Monier–Williams method (OMW), produces false-positive results with vegetables from the Allium (garlic) and Brassica (cabbage) genera due to extraction conditions that are thought to cause endogenous sulphur compounds to release SO2. Recently, modifications to the OMW method (2x MW) were published that reportedly reduced this false-positive in garlic. However, no other vegetables from these genera have been investigated. In addition, an LC-MS/MS method was developed for sulphite analysis, but it has not yet been tested with these problematic matrices. Ten vegetable species were analysed using these sulphite methods (OMW titration, OMW gravimetric, 2x MW and LC-MS/MS) to determine the false-positive rate. Sulphite concentrations > 10 mg kg–1 SO2 were observed with the OMW analyses. The 2x MW method reduced the measured concentration in unsulphited samples to ≤ 10 mg kg–1 SO2 for all matrices analysed. The LC-MS/MS method showed concentrations < 10 mg kg–1 for the Brassica samples, but only displayed a slight reduction in the Allium matrices. Spiked recovery studies were conducted to determine if these methods can detect added sulphite. The 2x MW had recoveries of 17% and 42% for water and fresh garlic, respectively, and the LC-MS/MS had recoveries of 108%, 125%, 116% and 107% for water, fresh garlic, roasted garlic, and hummus, respectively. The low recoveries of the 2x MW may indicate that sulphur compounds cannot be properly quantified with this method. The ability to eliminate false-positives will enable accurate determination of added sulphite to ensure compliance with sulphite labelling requirements.
Injury-stimulated and self-restrained BMP signaling dynamically regulates stem cell pool size during Drosophila midgut regeneration

Significance Adult stem cells maintain tissue integrity by producing new cells to replenish damaged cells during tissue homeostasis and in response to injury. Using Drosophila adult midgut as a model we show that midgut injury elicited by chemical feeding or bacterial infection stimulates the production of two bone morphogenetic protein (BMP) ligands (Dpp and Gbb) that are critical for the expansion of the intestinal stem cell (ISC) population and midgut regeneration. Interestingly, we find that BMP expression is inhibited by BMP signaling itself, and this autoinhibition is required for resetting ISC pool size to the homeostatic level after tissue repair. Our study suggests that transient expansion of the stem cell population through the dynamic regulation of niche signals serves as a strategy for regeneration. Many adult organs rely on resident stem cells to maintain homeostasis. Upon injury, stem cells increase proliferation, followed by lineage differentiation to replenish damaged cells. Whether stem cells also change division mode to transiently increase their population size as part of a regenerative program and, if so, what the underlying mechanism is have remained largely unexplored. Here we show that injury stimulates the production of two bone morphogenetic protein (BMP) ligands, Dpp and Gbb, which drive an expansion of intestinal stem cells (ISCs) by promoting their symmetric self-renewing division in Drosophila adult midgut. We find that BMP production in enterocytes is inhibited by BMP signaling itself, and that BMP autoinhibition is required for resetting ISC pool size to the homeostatic level after tissue repair. Our study suggests that dynamic BMP signaling controls ISC population size during midgut regeneration and reveals mechanisms that precisely control stem cell number in response to tissue needs.
Deep-learning in Mobile Robotics - from Perception to Control Systems: A Survey on Why and Why not

Deep-learning has dramatically changed the world overnight. It greatly boosted the development of visual perception, object detection, and speech recognition, etc. That was attributed to the multiple convolutional processing layers for abstraction of learning representations from massive data. The advantages of deep convolutional structures in data processing motivated the applications of artificial intelligence methods in robotic problems, especially perception and control system, the two typical and challenging problems in robotics. This paper presents a survey of the deep-learning research landscape in mobile robotics. We start with introducing the definition and development of deep-learning in related fields, especially the essential distinctions between image processing and robotic tasks. We described and discussed several typical applications and related works in this domain, followed by the benefits from deep-learning, and related existing frameworks. Besides, operation in the complex dynamic environment is regarded as a critical bottleneck for mobile robots, such as that for autonomous driving. We thus further emphasize the recent achievement on how deep-learning contributes to navigation and control systems for mobile robots. At the end, we discuss the open challenges and research frontiers.
EFFECT OF AGING TREATMENT ON THE MICROSTRUCTURES AND HARDNESS OF Fe-Ni-Cr SUPERALLOY

Aging treatment was conducted on Fe-Ni-Cr superalloy to observe its effect on the microstructures and hardness of the material. Solution treatments were carried out at 900oC, 975oC, 1050oC, and 1125oC followed by water quenching. The samples were further treated with a double aging treatment at 720oC and 650oC for 4 hours and 12 hours respectively. Materials characterization techniques such as SEM, XRD, and optical microscopy were used to analyze the heat-treated samples. The Fe-Ni-Cr superalloy formed mainly a dendritic austenitic structure with Cr23C6 precipitated along the grain boundaries. Increase in solution treatment temperature results in dissolution of chromium carbide, coarser grain, and lower hardness for non-aged samples. Double aging treatment produced more chromium carbide, higher hardness, but no apparent change in grain size. Neither quenching nor aging treatments caused any phase transformation. The highest hardness value of 220.4 Hv was recorded for the sample solution treated at 1125oC for 2 hours and water quenched, followed by 2-step aging at temperature 720oC and 650oC for 4 hours and 12 hours respectively, and air cooled.
Mitochondria‐targeted antioxidant mitoquinone deactivates human and rat hepatic stellate cells and reduces portal hypertension in cirrhotic rats

In cirrhosis, activated hepatic stellate cells (HSC) play a major role in increasing intrahepatic vascular resistance and developing portal hypertension. We have shown that cirrhotic livers have increased reactive oxygen species (ROS), and that antioxidant therapy decreases portal pressure. Considering that mitochondria produce many of these ROS, our aim was to assess the effects of the oral mitochondria‐targeted antioxidant mitoquinone on hepatic oxidative stress, HSC phenotype, liver fibrosis and portal hypertension.