Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the clinical performance of four fungus-specific immunoglobulin E detection systems in patients with Aspergillus allergy.

BACKGROUND Allergic bronchopulmonary aspergillosis (ABPA) is an airway disease caused by Aspergillus (mainly Aspergillus fumigatus). OBJECTIVE To evaluate the diagnostic performance of four fungal-related allergen-specific immunoglobulin E (sIgE) detection systems. METHODS A total of 99 patients with ABPA and 30 control patients admitted to the First Affiliated Hospital of Guangzhou Medical University from 2017 to 2019 were included in the study. Four allergen detection systems were used to detect Aspergillus-related sIgE. RESULTS The 99 patients were divided into two groups based on the total IgE. Fluorescence immunoassay for fungal mixtures detected positive rates of 100% and 81% in the Confirmed and Probable groups, respectively. For Aspergillus fumigatus, the positive rates were 90.2% and 87.9%, respectively. In the detection of sIgE of fungal mixtures in all ABPA patients, the sensitivity of System 1 was 90.9%, which was higher than for the other three systems (System 2, 38.4%; System 3, 44.4%; System 4, 52.5%), All four systems have excellent specificity ( > 90.0%) and had higher consistency in the Confirmed group than in the Probable group (P < 0.05). Consistency for the Aspergillus mixture and Aspergillus fumigatus detected by fluorescence immunoassay was 90.2% and 86.2% in the Confirmed and Probable groups, respectively. CONCLUSIONS Despite the many methods used to detect fungal-related sIgE, the ImmunoCAP system has the best clinical diagnostic performance. It is recommended that this method be used to detect fungal (mixtures or Aspergillus fumigatus) sIgE in order to reduce the missed diagnosis rate of ABPA.
Vasoplegic syndrome after cardiovascular surgery: A review of pathophysiology and outcome‐oriented therapeutic management

Background: Vasoplegic syndrome (VPS) is defined as systemic hypotension due to profound vasodilatation and loss of systemic vascular resistance (SVR), despite normal or increased cardiac index, and characterized by inadequate response to standard doses of vasopressors, and increased morbidity and mortality. It occurs in 9%–44% of cardiac surgery patients after cardiopulmonary bypass (CPB). The underlying pathophysiology following CPB consists of resistance to vasopressors (inactivation of Ca2+ voltage gated channels) on the one hand and excessive activation of vasodilators (SIRS, iNOS, and low AVP) on the other. Use of angiotensin‐converting enzyme inhibitor (ACE‐I), calcium channel blockers, amiodarone, heparin, low cardiac reserve (EF < 35%), symptomatic congestive heart failure, and diabetes mellitus are the perioperative risk factors for VPS after cardiac surgery in adults. Till date, there is no consensus about the outcome‐oriented therapeutic management of VPS. Vasopressors such as norepinephrine (NE; 0.025–0.2 µg/kg/min) and vasopressin (0.06 U/min or 6 U/h median dose) are the first choice for the treatment. The adjuvant therapy (hydrocortisone, calcium, vitamin C, and thiamine) and rescue therapy (methylene blue [MB] and hydroxocobalamin) are also considered when perfusion goals (meanarterial pressure [MAP] > 60–70 mmHg) are not achieved with nor‐epinephrine and/or vasopressin.
Tracking bacterial effector protein delivery into host cells

Bacterial Type IV secretion systems (T4SSs) are a functionally heterogeneous group of nanomachines that can deliver substrates into a wide range of target cells. The Helicobacter pylori Cag T4SS has an important role in the pathogenesis of gastric cancer. CagA, the only effector protein known to be secreted by the H. pylori Cag T4SS, enters human gastric cells and causes alterations in intracellular signaling that are linked to cancer pathogenesis. Understanding the molecular mechanisms by which CagA is delivered into gastric cells has been hindered by the lack of robust methods for monitoring this process. A publication in this issue of Molecular Microbiology describes a split luciferase assay for monitoring T4SS‐mediated translocation of CagA into host cells. The use of this translocation reporter allowed the quantification of CagA translocation in real‐time assays, thereby facilitating the analysis of the kinetics of CagA delivery. This system also allowed the tracking of several types of CagA fusion proteins and confirmed that protein unfolding is important for secretion by the Cag T4SS. This commentary discusses T4SS‐dependent delivery of H. pylori CagA into host cells and the use of the split luciferase system for monitoring bacterial protein secretion and delivery into target cells.
The influence of putrescine on the structure, enzyme activity and stability of α-chymotrypsin

Information on protein stability is essential to study protein structure, activity, and interactions with ligands. The interaction of putrescine with α-chymotrypsin (α-Chy) was investigated by using different types of spectroscopic techniques in an aqueous medium at two temperatures (25 and 35 °C), in combination with a molecular docking study and molecular dynamics simulation. Fluorescence measurements showed that the observed quenching was a dynamic one. The intrinsic fluorescence of α-chymotrypsin was decreased in the presence of putrescine due to the excited-state proton transfer. Additionally, circular dichroism results revealed that putrescine binding had no dramatic influence on the α-chymotrypsin structure. Molecular docking also indicated that the hydrogen bonds interactions were dominant in the binding site.
Intra- and inter-rater reliability for the measurement of the cross-sectional area of ankle tendons assessed by magnetic resonance imaging

Background The cross-sectional area (CSA) records make an essential measurement for determining the mechanical properties of tendons, such as stress and strength. However, there is no consensus regarding the best method to record the CSA from different tendons. Purpose To determine intra- and inter-rater reliability for CSA measures from magnetic resonance imaging (MRI) of the following tendons: tibialis anterior; tibialis posterior; fibularis longus and brevis; and Achilles. Material and Methods We designed an observational study with repeated measures taken from a convenience sample of 20 participants diagnosed with acute or chronic ankle sprain. Two independent raters took three separate records from the CSA of ankle tendon images of each MRI slice. The intra-class correlation coefficient (ICC) and 95% limits of agreement (LoA) defined the quality (associations) and magnitude (differences), respectively, of intra- and inter-rater reliability on the measures plotted by the Bland–Altman method. Results Data showed very high intra- and inter-rater correlations for measures taken from all tendons analyzed (ICC 0.952–0.999). It also revealed an excellent agreement between raters (0.12%–2.3%), with bias no higher than 2 mm2 and LoA in the range of 4.4–7.9 mm2. The differences between repeated measures recorded from the thinnest tendons (fibularis longus and brevis) revealed the lowest bias and narrowest 95% LoA. Conclusion Reliability for the CSA of ankle tendons measured from MRI taken by independent rates was very high, with the smallest differences between raters observed when the thinnest tendon was analyzed.
Male infertility: Role of vitamin D and oxidative stress markers

Spermatozoa are vulnerable to oxidative stress because of their inherent reduced antioxidant defence and DNA repair mechanisms. Polyunsaturated fatty acids in sperm plasma membrane break down to cytotoxic lipid aldehyde, 4‐Hydroxynonenal, whereas 3‐Nitrotyrosine is generated by peroxynitrite induced tyrosine nitration. Both oxidative stress markers contribute to altered sperm function and infertility. Vitamin D, a membrane antioxidant, has a potential scavenger capacity. We compared oxidative stress markers and vitamin D in male subjects with normal and altered sperm parameters and explored association of these markers: 4‐Hydroxynonenal and 3‐Nitrotyrosine with Vitamin D. Higher 4‐Hydroxynonenal levels in altered sperm parameter group and a negative correlation with sperm count, motility and morphology (p < 0.001) was observed. Vitamin D serum concentration in altered sperm parameters was less (p = 0.016) showing a significant positive correlation with sperm count and morphology. 4‐Hydroxynonenal was significantly higher in altered sperm parameters showing negative correlation with vitamin D. Highest serum concentrations of 4‐Hydroxynonenal were observed in vitamin D‐deficient subjects. Significantly higher concentration of 4‐Hydroxynonenal was estimated in altered sperm parameters of vitamin D sufficient group (p < 0.001). This suggests 4‐Hydroxynonenal as an oxidative stress marker leading to altered sperm function and infertility with some association with vitamin D; needs to be explored.
Synthesis at several length scales of zeolite A membranes using a continuous flow method

ABSTRACT Zeolite A membranes were synthesized in the inner side of porous TiO2 and α-Al2O3 tubular supports by a continuous method. The methodology was then used at several scales for preparing membranes on TiO2 and α-Al2O3 supports with lengths of 6, 12 and 25 cm. Formation of an homogeneous zeolite film was confirmed by XRD and SEM in all supports. Single-gas permeation experiments (He, H2, N2 and n-C3H8) indicated that Knudsen diffusion was the predominant mechanism in both supports. All the synthesized membranes present high flux and moderate selectivity to water in water–ethanol mixtures.
Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation.

Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.
Assessing Human Exposure To Acrylamide

Acrylamide is considered as probably carcinogenic to humans. The International Agency for Research on Cancer (IARC) rates it as a Group 2A reagent. Therefore, human exposure to acrylamide in occupational settings has been of concern for a long time. Until recently, tobacco smoke was assumed to be the only major source of acrylamide exposure in the general population. Now, it is well established that acrylamide is formed in food during processing or cooking at high temperatures. Surveys showed that acrylamide can be found in most types of food, with highest amounts measured in French fries and potato chips. The concentrations found in some foods exceed the concentrations found for other environmental contaminants, such as pesticides. The Division of Laboratory Sciences at CDC’s National Center for Environmental Health, through a biomonitoring program project, is assessing people’s exposure to this chemical. The goal is to better assess the magnitude and distribution of human exposure to acrylamide and risks associated with this exposure in the general population. Project researchers are measuring biomarkers of exposure such as hemoglobin adducts of acrylamide and its primary metabolite glycidamide. First assessments show that biomarker levels mainly range between 27 pmol/g globin and 148 pmol/g globin for acrylamide and glycidamide adducts, respectively. Biomarker values in smokers are about 3 to 4 times higher than in non-smokers. An initial study looked at the effects of acrylamide in food on biomarkers of acrylamide exposure. Results indicate that acrylamide consumed through food has a more profound effect on glycidamide adduct levels than on acrylamide adduct levels. The acrylamide biomarker concentrations determined so far are within the range reported by other investigators. Smoking appears to be an important contributor to the background exposure found in people.
THAN: task-driven hierarchical attention network for the diagnosis of mild cognitive impairment and Alzheimer's disease.

Background To assist doctors to diagnose mild cognitive impairment (MCI) and Alzheimer's disease (AD) early and accurately, convolutional neural networks based on structural magnetic resonance imaging (sMRI) images have been developed and shown excellent performance. However, they are still limited in their capacity in extracting discriminative features because of large sMRI image volumes yet small lesion regions and the small number of sMRI images. Methods We proposed a task-driven hierarchical attention network (THAN) taking advantage of the merits of patch-based and attention-based convolutional neural networks for MCI and AD diagnosis. THAN consists of an information sub-network and a hierarchical attention sub-network. In the information sub-network, an information map extractor, a patch-assistant module, and a mutual-boosting loss function are designed to generate a task-driven information map, which automatically highlights disease-related regions and their importance for final classification. In the hierarchical attention sub-network, a visual attention module and a semantic attention module are devised based on the information map to extract discriminative features for disease diagnosis. Results Extensive experiments were conducted for four classification tasks: MCI versus (vs.) normal controls (NC), AD vs. NC, AD vs. MCI, and AD vs. MCI vs. NC. Results demonstrated that THAN attained the accuracy of 81.6% for MCI vs. NC, 93.5% for AD vs. NC, 80.8% for AD vs. MCI, and 62.9% for AD vs. MCI vs. NC. It outperformed advanced attention-based and patch-based methods. Moreover, information maps generated by the information sub-network could highlight the potential biomarkers of MCI and AD, such as the hippocampus and ventricles. Furthermore, when the visual and semantic attention modules were combined, the performance of the four tasks was highly improved. Conclusions The information sub-network can automatically highlight the disease-related regions. The hierarchical attention sub-network can extract discriminative visual and semantic features. Through the two sub-networks, THAN fully exploits the visual and semantic features of disease-related regions and meanwhile considers global features of sMRI images, which finally facilitate the diagnosis of MCI and AD.
Effects of omega-7 palmitoleic acids on skeletal muscle differentiation in a hyperglycemic condition

Maternal obesity and diabetes are known to be involved in fetal myogenesis, but the later stages of myogenesis are not well understood. In this study, we investigated the influence of a hyperglycemic environment on L6 skeletal myoblast differentiation and the function of omega-7 palmitoleic acids. Exposure to a high concentration of glucose (25 mM) in high-glucose culture medium (HG) increased the expression of myogenic genes (MyoD, Myogenin, MRF4, Myhc2x, and Myhc2a) and the synthesis of myosin. HG also activated the PI3K/AKT pathway revealed muscle cell differentiation. Furthermore, the levels of reactive oxygen species (ROS) and an inflammatory cytokine (Tnfaip3; tumor necrosis factor alpha-induced protein 3), which are crucial for the growth and differentiation of skeletal muscle, were increased by HG. Palmitoleic acids suppressed the expression levels of myogenic regulatory genes and increased the expression level of a cell proliferation-related gene (Pax3). Trans-palmitoleic acid and eicosapentaenoic acid (TPA and EPA) increased the phosphorylation level of MAPK/ERK1/2 and downregulated ROS generation and Tnfaip3 expression. In contrast, cis-palmitoleic acid inactivated MAPK/ERK1/2, leading to increased ROS generation. In conclusion, a hyperglycemic environment mediated by HG induced excessive muscle differentiation. Palmitoleic acids inhibited myoblast differentiation by downregulating muscle-specific genes. Moreover, trans-palmitoleic acids may have beneficial antioxidant and/or anti-inflammatory effects in cells.
Analyzing long-term water quality of lakes in Rhode Island and the northeastern United States with an anomaly approach

Addressing anthropogenic impacts on aquatic ecosystems is a focus of lake management. Controlling phosphorus and nitrogen can mitigate these impacts, but determining management effectiveness requires long-term datasets. Recent analysis of the LAke multi-scaled GeOSpatial and temporal database for the Northeast (LAGOS-NE) United States found stable water quality in the northeastern and midwestern United States; however, sub-regional trends may be obscured. We used the University of Rhode Island’s Watershed Watch Volunteer Monitoring Program (URIWW) dataset to determine if there were sub-regional (i.e., 3000 km2) water quality trends. URIWW has collected water quality data on Rhode Island lakes and reservoirs for over 25 yr. The LAGOS-NE and URIWW datasets allowed for comparison of water quality trends at regional and sub-regional scales, respectively. We assessed regional (LAGOS-NE) and sub-regional (URIWW) trends with yearly median anomalies calculated on a per-station basis. Sub-regionally, temperature and chlorophyll a increased from 1993 to 2016. Total nitrogen, total phosphorus, and the nitrogen:phosphorus ratio (N:P) were stable. At the regional scale, the LAGOS-NE dataset showed similar trends to prior studies of the LAGOS-NE with chlorophyll a, total nitrogen, and N:P all stable over time. Total phosphorus did show a very slight increase. In short, algal biomass, as measured by chlorophyll a in Rhode Island lakes and reservoirs increased, despite stability in total nitrogen, total phosphorus, and the nitrogen to phosphorus ratio. Additionally, we demonstrated both the value of long-term monitoring programs, like URIWW, for identifying trends in environmental condition, and the utility of site-specific anomalies for analyzing for long-term water quality trends.
Validity and reliability of the Indonesian version of the Chronic Urticaria Quality of Life Questionnaire (CU-Q2oL).

BACKGROUND Assessment of quality of life is needed to assess therapeutic response. There is currently no instrument available for assessing the quality of life of chronic urticaria patients in Indonesia. CU-Q2oL is a specific questionnaire for chronic urticaria that was first developed in Italian. Validity and reliability tests are important to ensure that the language or term used are appropriate to the local culture and there is no change in the validity and reliability of the questionnaire. OBJECTIVE The aim of this study is to develop an Indonesian version of CU-Q2oL. METHODS The Italian version CU-Q2oL was translated into Indonesian and underwent cross-cultural adaptation. The translated questionnaire was completed online by 40 chronic urticaria patients of the Dermatovenereology Outpatient Clinic of the Cipto Mangunkusumo General Hospital, Jakarta, Indonesia. RESULTS Validity test resulted in correlation coefficient values for all questions of 0.467 to 0.856. Reliability test showed a Cronbach's α coefficient of all questions of 0.923 and the intraclass correlation coefficient (ICC) for all questions was 0.913. CONCLUSIONS This study demonstrates that the Indonesian CU-Q2oL questionnaire is valid, reliable, and suitable to assess the quality of life of chronic urticaria patients in Indonesia.
The importance of peripheral vision when searching 3D real-world scenes: A gaze-contingent study in virtual reality

Abstract Visual search in natural scenes is a complex task relying on peripheral vision to detect potential targets and central vision to verify them. The segregation of the visual fields has been particularly established by on-screen experiments. We conducted a gaze-contingent experiment in virtual reality in order to test how the perceived roles of central and peripheral visions translated to more natural settings. The use of everyday scenes in virtual reality allowed us to study visual attention by implementing a fairly ecological protocol that cannot be implemented in the real world. Central or peripheral vision was masked during visual search, with target objects selected according to scene semantic rules. Analyzing the resulting search behavior, we found that target objects that were not spatially constrained to a probable location within the scene impacted search measures negatively. Our results diverge from on-screen studies in that search performances were only slightly affected by central vision loss. In particular, a central mask did not impact verification times when the target was grammatically constrained to an anchor object. Our findings demonstrates that the role of central vision (up to 6 degrees of eccentricities) in identifying objects in natural scenes seems to be minor, while the role of peripheral preprocessing of targets in immersive real-world searches may have been underestimated by on-screen experiments.
CTP promotes efficient ParB-dependent DNA condensation by facilitating one-dimensional diffusion from parS

Faithful segregation of bacterial chromosomes relies on the ParABS partitioning system and the SMC complex. In this work, we used single-molecule techniques to investigate the role of cytidine triphosphate (CTP) binding and hydrolysis in the critical interaction between centromere-like parS DNA sequences and the ParB CTPase. Using a combined optical tweezers confocal microscope, we observe the specific interaction of ParB with parS directly. Binding around parS is enhanced by the presence of CTP or the non-hydrolysable analogue CTPγS. However, ParB proteins are also detected at a lower density in distal non-specific DNA. This requires the presence of a parS loading site and is prevented by protein roadblocks, consistent with one-dimensional diffusion by a sliding clamp. ParB diffusion on non-specific DNA is corroborated by direct visualization and quantification of movement of individual quantum dot labelled ParB. Magnetic tweezers experiments show that the spreading activity, which has an absolute requirement for CTP binding but not hydrolysis, results in the condensation of parS-containing DNA molecules at low nanomolar protein concentrations.