Miracle-dz/UniFAR-FTUs huggingface dataset:
Human observer performance on in-plane digital breast tomosynthesis images: Effects of reconstruction filters and data acquisition angles on signal detection

For digital breast tomosynthesis (DBT) systems, we investigate the effects of the reconstruction filters for different data acquisition angles on signal detection. We simulated a breast phantom with a 30% volume glandular fraction (VGF) of breast anatomy using the power law spectrum and modeled the breast mass as a spherical object with a 1 mm diameter. Projection data were acquired using two different data acquisition angles and numbers of projection view pairs, and in-plane breast images were reconstructed using the Feldkamp-Davis-Kress (FDK) algorithm with three different reconstruction filter schemes. To measure the ability to detect a signal, we conducted the human observer study with a binary detection task and compared the signal detectability of human to that of channelized Hotelling observer (CHO) with Laguerre-Gauss (LG) channels and dense difference-of-Gaussian (D-DOG) channels. We also measured the contrast-to-noise ratio (CNR), signal power spectrum (SPS), and β values of the anatomical noise power spectrum (NPS) to show the association between human observer performance and these traditional metrics. Our results show that using a slice thickness (ST) filter degraded the signal detection performance of human observers at the same data acquisition angle. This could be predicted by D-DOG CHO with internal noise, but the correlation between the traditional metrics and signal detectability was not observed in this work.
Dentofacial mini- and microesthetics as perceived by dental students: A cross-sectional multi-site study

Background How dental education influences students’ dental and dentofacial esthetic perception has been studied for some time, given the importance of esthetics in dentistry. However, no study before has studied this question in a large sample of students from all grades of dental school. This study sought to fill that gap. The aim was to assess if students’ dentofacial esthetic autoperception and heteroperception are associated with their actual stage of studies (grade) and if autoperception has any effect on heteroperception. Methods Between October 2018 and August 2019, a questionnaire was distributed to 919 dental students of all 5 grades of dental school at all four dental schools in Hungary. The questionnaire consisted of the following parts (see also the supplementary material): 1. Demographic data (3 items), Self-Esthetics I (11 multiple- choice items regarding the respondents’ perception of their own dentofacial esthetics), Self-Esthetics II (6 Likert-type items regarding the respondents’ perception of their own dentofacial esthetics), and Image rating (10 items, 5 images each, of which the respondents have to choose the one they find the most attractive). Both the self-esthetics and the photo rating items were aimed at the assessment of mini- and microesthetic features. Results The response rate was 93.7% (861 students). The self-perception of the respondents was highly favorable, regardless of grade or gender. Grade and heteroperception were significantly associated regarding maxillary midline shift (p < 0.01) and the relative visibility of the arches behind the lips (p < 0.01). Detailed analysis showed a characteristic pattern of preference changes across grades for both esthetic aspects. The third year of studies appeared to be a dividing line in both cases, after which a real preference order was established. Association between autoperception and heteroperception could not be verified for statistical reasons. Conclusion Our findings corroborate the results of most previous studies regarding the effect of dental education on the dentofacial esthetic perception of students. We have shown that the effect can be demonstrated on the grade level, which we attribute to the specific curricular contents. We found no gender effect, which, in the light of the literature, suggests that the gender effect in dentofacial esthetic perception is highly culture dependent. The results allow no conclusion regarding the relation between autoperception and heteroperception.
Mac-2 binding protein in non-alcoholic fatty liver disease: Is it a reliable diagnostic biomarker? A pilot study

Aim of the study This study aimed to assess the level of serum Mac-2 binding protein (Mac-2BP) as a non-invasive biomarker for the diagnosis of non-alcoholic fatty liver disease (NAFLD). Material and methods Forty patients with NAFLD and 15 healthy sex- and age-matched subjects were included in this pilot study. Serum Mac-2BP level was measured using ELISA. Liver biopsy was taken from 20 patients. Results There was no statistically significant difference between patients and controls regarding the level of Mac-2BP (p = 0.209). Mac-2BP had a statistically significant correlation with the grade of lobular inflammation (r = 0.464, p = 0.039). The Mac-2BP cut-off value used for NASH prediction was 9.55 µg/ml, with sensitivity and specificity of 100% and 91.7%, respectively. Conclusions This study showed that Mac-2BP is not elevated in NAFLD patients compared to controls. It also demonstrated that the reliability of Mac-2BP as a biomarker for NAFLD diagnosis is still controversial and needs more investigation.
Construction of Fully Conjugated Covalent Organic Frameworks via Facile Linkage Conversion for Efficient Photoenzymatic Catalysis.

Covalent organic frameworks (COFs) with improved stability and extended π-conjugation structure are highly desirable. Here, two imine-linked COFs were converted into ultrastable and π-conjugated fused-aromatic thieno[3,2-c]pyridine-linked COFs (B-COF-2 and T-COF-2). The successful conversion was confirmed by infrared and solid-state 13C NMR spectroscopies. Furthermore, the structures of thieno[3,2-c]pyridine-linked COFs were evaluated by transmission electron microscopy and powder X-ray diffraction patterns. It is noted that a slight difference in the structure leads to totally different photo-activity. The fully π-conjugated T-COF-2 containing triazine as the core exhibited excellent photo-catalytic NADH regeneration yield of 74% in 10 min.
The Relation of Brain-Derived Neurotropic Factor (BDNF) Serum Level to Sub-Domain Cognitive Functions of Indonesian Schizophrenia Patients Measured by MoCA-Ina

BACKGROUND: BDNF implies to the development of abnormal nerves and neurotransmission that occurred during the changes of cognitive functions. However, in determining initial diagnosis of schizophrenia, measurements focus on the presences of positive and negative symptoms, and general psychopathological features without concerning the BDNF serum, which involves in central nervous system as the main symptom of schizophrenia. AIM: To determine the relation of BDNF serum level to cognitive functions of schizophrenia patients based on sub-domain of Montreal Cognitive Assessment Indonesia Version (MoCA-Ina) METHODS: This study was carried out based on observational analysis with cross-sectional design study. The samples were collected by non-probability sampling and consecutive sampling by recruiting 65 of male schizophrenia patients at Prof. Dr. M. Ildrem Mental Hospital, Medan, North Sumatera, Indonesia. BDNF serum levels were analysed throughout quantitative sandwich enzyme immunoassay method, while the cognitive functions were conducted by performing the MoCA-Ina, which concern to attentions and concentrations, executive function, memory, languages, visuoconstructional abilities, numerical calculation, and orientation. RESULTS: The serum level of BDNF was accounted averagely for 27161.26, with 5350.37 of standard deviation. There was positive correlation with medium strength (r = 0.4 - < 0.6) in visuospatial function, attention (r = 0.437), and memory (r = 0.413). CONCLUSION: Relation between BDNF serum level and cognitive function occurred in visuospatial, attention and memory domains based on MoCA-Ina assessment.
COMER2: GPU-accelerated sensitive and specific homology searches

Abstract Summary Searching for homology in the vast amount of sequence data has a particular emphasis on its speed. We present a completely rewritten version of the sensitive homology search method COMER based on alignment of protein sequence profiles, which is capable of searching big databases even on a lightweight laptop. By harnessing the power of CUDA-enabled graphics processing units, it is up to 20 times faster than HHsearch, a state-of-the-art method using vectorized instructions on modern CPUs. Availability and implementation COMER2 is cross-platform open-source software available at https://sourceforge.net/projects/comer2 and https://github.com/minmarg/comer2. It can be easily installed from source code or using stand-alone installers. Contact mindaugas.margelevicius@bti.vu. lt Supplementary information Supplementary data are available at Bioinformatics online.
Endothelial Dysfunction and the Effect of Arginine and Citrulline Supplementation in Children and Adolescents With Mitochondrial Diseases

Background: In addition to the reduced energy production, characteristic of mitochondrial disorders, nitric oxide (NO) deficiency can occur as well. The NO produced by vascular endothelial cells relaxes vascular smooth muscles, resulting in vasodilation that maintains the patency of small blood vessels and promotes blood flow through microvasculature. Endothelial dysfunction due to inability of vascular endothelium to generate enough NO to maintain adequate vasodilation can result in decreased perfusion in the microvasculature of various tissues, contributing to many complications seen in individuals with mitochondrial diseases. The amino acids arginine and citrulline are NO precursors: increasing their concentrations could potentially restore NO production. Methods: In this study, we assessed endothelial dysfunction in children and adolescents with mitochondrial diseases. We also investigated the effect of arginine and citrulline supplementation on endothelial dysfunction in these individuals. We used peripheral arterial tonometry to measure the reactive hyperemic index (RHI), which is low when there is endothelial dysfunction. Results: The results demonstrated low RHI in individuals with mitochondrial diseases, indicating endothelial dysfunction. RHI increased with arginine or citrulline supplementation suggesting that supplementation with NO precursors can improve endothelial dysfunction by enhancing NO production. Conclusions: This study is the first one to use peripheral arterial tonometry methodology in mitochondrial diseases. The results of this study provide evidence for endothelial dysfunction in mitochondrial diseases and demonstrate that arginine or citrulline supplementation can alleviate the endothelial dysfunction, providing more evidence for the potential therapeutic utility of these amino acids in mitochondrial diseases.
Artificial Intelligence in the Management of Intracranial Aneurysms: Current Status and Future Perspectives

SUMMARY: Intracranial aneurysms with subarachnoid hemorrhage lead to high morbidity and mortality. It is of critical importance to detect aneurysms, identify risk factors of rupture, and predict treatment response of aneurysms to guide clinical interventions. Artificial intelligence has received worldwide attention for its impressive performance in image-based tasks. Artificial intelligence serves as an adjunct to physicians in a series of clinical settings, which substantially improves diagnostic accuracy while reducing physicians’ workload. Computer-assisted diagnosis systems of aneurysms based on MRA and CTA using deep learning have been evaluated, and excellent performances have been reported. Artificial intelligence has also been used in automated morphologic calculation, rupture risk stratification, and outcomes prediction with the implementation of machine learning methods, which have exhibited incremental value. This review summarizes current advances of artificial intelligence in the management of aneurysms, including detection and prediction. The challenges and future directions of clinical implementations of artificial intelligence are briefly discussed.
Changes in the gut microbiota of mice orally exposed to methylimidazolium ionic liquids

Ionic liquids are salts used in a variety of industrial processes, and being relatively non-volatile, are proposed as environmentally-friendly replacements for existing volatile liquids. Methylimidazolium ionic liquids resist complete degradation in the environment, likely because the imidazolium moiety does not exist naturally in biological systems. However, there is limited data available regarding their mammalian effects in vivo. This study aimed to examine the effects of exposing mice separately to 2 different methylimidazolium ionic liquids (BMI and M8OI) through their addition to drinking water. Potential effects on key target organs–the liver and kidney–were examined, as well as the gut microbiome. Adult male mice were exposed to drinking water containing ionic liquids at a concentration of 440 mg/L for 18 weeks prior to examination of tissues, serum, urine and the gut microbiome. Histopathology was performed on tissues and clinical chemistry on serum for biomarkers of hepatic and renal injury. Bacterial DNA was isolated from the gut contents and subjected to targeted 16S rRNA sequencing. Mild hepatic and renal effects were limited to glycogen depletion and mild degenerative changes respectively. No hepatic or renal adverse effects were observed. In contrast, ionic liquid exposure altered gut microbial composition but not overall alpha diversity. Proportional abundance of Lachnospiraceae, Clostridia and Coriobacteriaceae spp. were significantly greater in ionic liquid-exposed mice, as were predicted KEGG functional pathways associated with xenobiotic and amino acid metabolism. Exposure to ionic liquids via drinking water therefore resulted in marked changes in the gut microbiome in mice prior to any overt pathological effects in target organs. Ionic liquids may be an emerging risk to health through their potential effects on the gut microbiome, which is implicated in the causes and/or severity of an array of chronic disease in humans.
DNA stable‐isotope probing reveals potential key players for microbial decomposition and degradation of diatom‐derived marine particulate matter

Microbially mediated decomposition of particulate organic carbon (POC) is a central component of the oceanic carbon cycle, controlling the flux of organic carbon from the surface ocean to the deep ocean. Yet, the specific microbial taxa responsible for POC decomposition and degradation in the deep ocean are still unknown. To target the active microbial lineages involved in these processes, 13C‐labeled particulate organic matter (POM) was used as a substrate to incubate particle‐attached (PAM) and free‐living microbial (FLM) assemblages from the epi‐ and bathypelagic zones of the New Britain Trench (NBT). By combining DNA stable‐isotope probing and Illumina Miseq high‐throughput sequencing of bacterial 16S rRNA gene, we identified 14 active bacterial taxonomic groups that implicated in the decomposition of 13C‐labeled POM at low and high pressures under the temperature of 15°C. Our results show that both PAM and FLM were able to decompose POC and assimilate the released DOC. However, similar bacterial taxa in both the PAM and FLM assemblages were involved in POC decomposition and DOC degradation, suggesting the decoupling between microbial lifestyles and ecological functions. Microbial decomposition of POC and degradation of DOC were accomplished primarily by particle‐attached bacteria at atmospheric pressure and by free‐living bacteria at high pressures. Overall, the POC degradation rates were higher at atmospheric pressure (0.1 MPa) than at high pressures (20 and 40 MPa) under 15°C. Our results provide direct evidence linking the specific particle‐attached and free‐living bacterial lineages to decomposition and degradation of diatomic detritus at low and high pressures and identified the potential mediators of POC fluxes in the epi‐ and bathypelagic zones.
HIV in Canada-Surveillance Report, 2018.

Background Human immunodeficiency virus (HIV) is a global public health issue, with an estimated 36.9 million people living with HIV in 2017. HIV has been reportable in Canada since 1985 and the Public Health Agency of Canada (PHAC) continues to monitor trends in new HIV diagnoses. Objective The objective of this surveillance report is to provide an overview of the epidemiology of all reported diagnoses of HIV in Canada since 1985 with a focus on 2018 overall, and by geographic location, age group, sex, and exposure category. Methods PHAC monitors HIV through the national HIV/AIDS Surveillance System, a passive, case-based system that collates nonnominal data that is voluntarily submitted by all Canadian provinces and territories. Descriptive epidemiological analyses were conducted on national data and those relating to specific populations provided by Immigration, Refugees and Citizenship Canada and the Canadian Perinatal HIV Surveillance Program. Results In 2018, a total of 2,561 HIV diagnoses were reported in Canada, an increase of 8.2% compared with 2017. The national diagnosis rate increased to 6.9 per 100,000 population in 2018 from 6.5 per 100,000 population in 2017. Saskatchewan reported the highest provincial diagnosis rate at 14.9 per 100,000 population. The 30-39 year age group continued to have the highest HIV diagnosis rate at 15.4 per 100,000 population. Overall, the diagnosis rate for males continued to be higher than that of females (9.8 versus 4.0 per 100,000 population, respectively); however, females experienced a larger increase in reported cases and diagnosis rate. The gay, bisexual and other men who have sex with men (gbMSM) exposure category continued to represent the highest proportion of all reported adult cases (41.4%), though the proportion has decreased over time. Five perinatal HIV transmissions were documented, three were related to the mother not receiving perinatal antiretroviral therapy prophylaxis. Conclusion The number and rate of reported HIV cases in Canada increased in 2018, gbMSM continued to account for the largest exposure category and the number and rate of reported HIV cases among women increased. PHAC will continue to work with its national partners to refine the collection, analysis and publication of national data to better understand the burden of HIV in Canada.
The Adoption, Implementation, and Impact of Smoke-Free Policies among Gaelic Athletic Association Clubs in Ireland: A Qualitative Study

The Gaelic Athletic Association (GAA) is a major stakeholder in promoting smoke-free policies in Ireland. Several GAA clubs have adopted smoke-free policies, and there is a growing interest among other GAA clubs to also become smoke-free. As such, the purpose of this study is to explore the process of how GAA clubs adopt, implement, and enforce smoke-free policies in order to discover best practices that other clubs could replicate. Representatives from 15 smoke-free clubs were interviewed regarding how their club became smoke-free. Interview data were analyzed, in which four major themes emerged: (1) process (planning a smoke-free policy, communicating the policy to the community, providing smoking cessation resources), (2) barriers (opinions and behaviors of club members who smoke, bars connected to club houses, policy exceptions, visitors and umpires who were unaware of the policy), (3) enforcement (community-based style of enforcement, non-confrontational approach, non-enforcement), and (4) impact (observation of policy compliance and decrease in cigarette litter). The study’s findings indicate a general ease of becoming smoke-free with minimal barriers. As such, the GAA should urge each club to become smoke-free and to use the effective methods used by current smoke-free clubs for communicating and enforcing smoke-free policies.
Extracellular Redox Regulation of α7β Integrin-Mediated Cell Migration Is Signaled via a Dominant Thiol-Switch

While adhering to extracellular matrix (ECM) proteins, such as laminin-111, cells temporarily produce hydrogen peroxide at adhesion sites. To study the redox regulation of α7β1 integrin-mediated cell adhesion to laminin-111, a conserved cysteine pair within the α-subunit hinge region was replaced for alanines. The molecular and cellular effects were analyzed by electron and atomic force microscopy, impedance-based migration assays, flow cytometry and live cell imaging. This cysteine pair constitutes a thiol-switch, which redox-dependently governs the equilibrium between an extended and a bent integrin conformation with high and low ligand binding activity, respectively. Hydrogen peroxide oxidizes the cysteines to a disulfide bond, increases ligand binding and promotes cell migration toward laminin-111. Inversely, extracellular thioredoxin-1 reduces the disulfide, thereby decreasing laminin binding. Mutation of this cysteine pair into the non-oxidizable hinge-mutant shows molecular and cellular effects similar to the reduced wild-type integrin, but lacks redox regulation. This proves the existence of a dominant thiol-switch within the α subunit hinge of α7β1 integrin, which is sufficient to implement activity regulation by extracellular redox agents in a redox-regulatory circuit. Our data reveal a novel and physiologically relevant thiol-based regulatory mechanism of integrin-mediated cell-ECM interactions, which employs short-lived hydrogen peroxide and extracellular thioredoxin-1 as signaling mediators.
X-ray structures of catalytic intermediates of cytochrome c oxidase provide insights into its O2 activation and unidirectional proton-pump mechanisms

Cytochrome c oxidase (CcO) reduces O2 to water, coupled with a proton-pumping process. The structure of the O2-reduction site of CcO contains two reducing equivalents, Fea32+ and CuB1+, and suggests that a peroxide-bound state (Fea33+–O−–O−–CuB2+) rather than an O2-bound state (Fea32+–O2) is the initial catalytic intermediate. Unexpectedly, however, resonance Raman spectroscopy results have shown that the initial intermediate is Fea32+–O2, whereas Fea33+–O−–O−–CuB2+ is undetectable. Based on X-ray structures of static noncatalytic CcO forms and mutation analyses for bovine CcO, a proton-pumping mechanism has been proposed. It involves a proton-conducting pathway (the H-pathway) comprising a tandem hydrogen-bond network and a water channel located between the N- and P-side surfaces. However, a system for unidirectional proton-transport has not been experimentally identified. Here, an essentially identical X-ray structure for the two catalytic intermediates (P and F) of bovine CcO was determined at 1.8 Å resolution. A 1.70 Å Fe–O distance of the ferryl center could best be described as Fea34+ = O2−, not as Fea34+–OH−. The distance suggests an ∼800-cm−1 Raman stretching band. We found an interstitial water molecule that could trigger a rapid proton-coupled electron transfer from tyrosine-OH to the slowly forming Fea33+–O−–O−–CuB2+ state, preventing its detection, consistent with the unexpected Raman results. The H-pathway structures of both intermediates indicated that during proton-pumping from the hydrogen-bond network to the P-side, a transmembrane helix closes the water channel connecting the N-side with the hydrogen-bond network, facilitating unidirectional proton-pumping during the P-to-F transition.