Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictors of Mild Cognitive Impairment Stability, Progression, or Reversion in the Lothian Birth Cohort 1936

Background: Mild cognitive impairment (MCI) describes a borderland between healthy cognition and dementia. Progression to and reversion from MCI is relatively common but more research is required to understand the factors affecting this fluidity and improve clinical care interventions. Objective: We explore these transitions in MCI status and their predictive factors over a six-year period in a highly-phenotyped longitudinal study, the Lothian Birth Cohort 1936. Methods: MCI status was derived in the LBC1936 at ages 76 (n = 567) and 82 years (n = 341) using NIA-AA diagnostic guidelines. Progressions and reversions between healthy cognition and MCI over the follow-up period were assessed. Multinomial logistic regression assessed the effect of various predictors on the likelihood of progressing, reverting, or maintaining cognitive status. Results: Of the 292 participants who completed both time points, 41 (14%) participants had MCI at T1 and 56 (19%) at T2. Over the follow-up period, 74%remained cognitively healthy, 12%transitioned to MCI, 7%reverted to healthy cognition, and 7%maintained their baseline MCI status. Findings indicated that membership of these transition groups was affected by age, cardiovascular disease, and number of depressive symptoms. Conclusion: Findings that higher baseline depressive symptoms increase the likelihood of reverting from MCI to healthy cognition indicate that there may be an important role for the treatment of depression for those with MCI. However, further research is required to identify prevention strategies for those at high risk of MCI and inform effective interventions that increase the likelihood of reversion to, and maintenance of healthy cognition.
An end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction

Accurately identifying potential drug-target interactions (DTIs) is a key step in drug discovery. Although many related experimental studies have been carried out for identifying DTIs in the past few decades, the biological experiment-based DTI identification is still timeconsuming and expensive. Therefore, it is of great significance to develop effective computational methods for identifying DTIs. In this paper, we develop a novel 'end-to-end' learning-based framework based on heterogeneous 'graph' convolutional networks for 'DTI' prediction called end-to-end graph (EEG)-DTI. Given a heterogeneous network containing multiple types of biological entities (i.e. drug, protein, disease, side-effect), EEG-DTI learns the low-dimensional feature representation of drugs and targets using a graph convolutional networks-based model and predicts DTIs based on the learned features. During the training process, EEG-DTI learns the feature representation of nodes in an end-to-end mode. The evaluation test shows that EEG-DTI performs better than existing state-of-art methods. The data and source code are available at: https://github.com/MedicineBiology-AI/EEG-DTI.
Mechanism of Sulfate Expansion in Hydrated Portland Cement

The origin of sulfate expansion was studied on a series of cements of different compositions and on mixes of pure compounds. The observed data support the theory that the expansion is related to a topochemical formation and/or oriented growth of ettringite. An uptake of water from the environment is not essential for the expansion to take place even though it enhances the extent of expansion. The absence of expansion in iron-rich cements appears to be due to reduced and delayed ettringite formation in these cements and to an altered morphology of the formed ettringite.
GABA from vasopressin neurons regulates the time at which suprachiasmatic nucleus molecular clocks enable circadian behavior

Significance In mammals, the suprachiasmatic nucleus (SCN) functions as the master circadian clock to orchestrate multiple circadian biological rhythms in the body. Although almost all SCN neurons contain γ-aminobutyric acid (GABA) as a neurotransmitter, the physiological roles of GABA in the SCN network are poorly understood. We show that mice lacking GABA release specifically from arginine vasopressin (AVP)-producing neurons, one of the major neuron types in the SCN, retain an SCN that progresses normally at the clock gene level but fires aberrantly with bimodal rhythm. Accordingly, the mice demonstrate locomotor activity at inappropriate times with respect to the clock gene-based SCN clock. GABAergic transmission from AVP neurons may regulate SCN firing rhythm to modulate when SCN molecular clocks enable daily behavior. The suprachiasmatic nucleus (SCN), the central circadian pacemaker in mammals, is a network structure composed of multiple types of γ-aminobutyric acid (GABA)-ergic neurons and glial cells. However, the roles of GABA-mediated signaling in the SCN network remain controversial. Here, we report noticeable impairment of the circadian rhythm in mice with a specific deletion of the vesicular GABA transporter in arginine vasopressin (AVP)-producing neurons. These mice showed disturbed diurnal rhythms of GABAA receptor-mediated synaptic transmission in SCN neurons and marked lengthening of the activity time in circadian behavioral rhythms due to the extended interval between morning and evening locomotor activities. Synchrony of molecular circadian oscillations among SCN neurons did not significantly change, whereas the phase relationships between SCN molecular clocks and circadian morning/evening locomotor activities were altered significantly, as revealed by PER2::LUC imaging of SCN explants and in vivo recording of intracellular Ca2+ in SCN AVP neurons. In contrast, daily neuronal activity in SCN neurons in vivo clearly showed a bimodal pattern that correlated with dissociated morning/evening locomotor activities. Therefore, GABAergic transmission from AVP neurons regulates the timing of SCN neuronal firing to temporally restrict circadian behavior to appropriate time windows in SCN molecular clocks.
Perceptual Connectivity Influences Toddlers’ Attention to Known Objects and Subsequent Label Processing

While recent research suggests that toddlers tend to learn word meanings with many “perceptual” features that are accessible to the toddler’s sensory perception, it is not clear whether and how building a lexicon with perceptual connectivity supports attention to and recognition of word meanings. We explore this question in 24–30-month-olds (N = 60) in relation to other individual differences, including age, vocabulary size, and tendencies to maintain focused attention. Participants’ looking to item pairs with high vs. low perceptual connectivity—defined as the number of words in a child’s lexicon sharing perceptual features with the item—was measured before and after target item labeling. Results revealed pre-labeling attention to known items is biased to both high- and low-connectivity items: first to high, and second, but more robustly, to low-connectivity items. Subsequent object–label processing was also facilitated for high-connectivity items, particularly for children with temperamental tendencies to maintain focused attention. This work provides the first empirical evidence that patterns of shared perceptual features within children’s known vocabularies influence both visual and lexical processing, highlighting the potential for a newfound set of developmental dependencies based on the perceptual/sensory structure of early vocabularies.
Connected, Respected and Contributing to Their World: The Case of Sexual Minority and Non-Minority Young People in Ireland

Outcome 5 of the Irish Better Outcomes, Brighter Futures national youth policy framework (“Connected, respected, and contributing to their world”) offers a suitable way to study psychosocial determinants of adolescent health. The present study (1) provides nationally representative data on how 15- to 17-year-olds score on these indicators; (2) compares sexual minority (same- and both-gender attracted youth) with their non-minority peers. We analyzed data from 3354 young people (aged 15.78 ± 0.78 years) participating in the Health Behaviour in School-aged Children (HBSC) study in Ireland. Age and social class were associated with the indicators only to a small extent, but girls were more likely than boys to report discrimination based on gender and age. Frequency of positive answers ranged from 67% (feeling comfortable with friends) to 12% (being involved in volunteer work). Sexual minority youth were more likely to feel discriminated based on sexual orientation, age, and gender. Both-gender attracted youth were less likely than the other groups to report positive outcomes. Same-gender attracted youth were twice as likely as non-minority youth to volunteer. The results indicate the importance of a comprehensive approach to psycho-social factors in youth health, and the need for inclusivity of sexual minority (especially bisexual) youth.
Lung Microbiome in Cystic Fibrosis

The defective mucociliary clearance due to CFTR malfunctioning causes predisposition to the colonization of pathogens responsible for the recurrent inflammation and rapid deterioration of lung function in patients with cystic fibrosis (CF). This has also a profound effect on the lung microbiome composition, causing a progressive reduction in its diversity, which has become a common characteristic of patients affected by CF. Although we know that the lung microbiome plays an essential role in maintaining lung physiology, our comprehension of how the microbial components interact with each other and the lung, as well as how these interactions change during the disease’s course, is still at an early stage. Many challenges exist and many questions still to be answered, but there is no doubt that manipulation of the lung microbiome could help to develop better therapies for people affected by CF.
Mechanistic Study of Cathodic Electrodeposition of Zinc Oxide and Zinc Hydroxychloride Films from Oxygenated Aqueous Zinc Chloride Solutions

Films of zinc oxide and related compounds [ZnO, ZnO x (OH) y , Zn(OH) x Cl y ] are electrodeposited cathodically in aqueous zinc chloride solutions using dissolved oxygen as a precursor. The influence of the precursor concentrations, pH, and deposition temperature on the growth, composition, and properties of the films are investigated by means of in situ techniques : voltammetry, electrochemical quartz-crystal microgravimetry, surface pH, and ex situ techniques: X-ray diffraction, infrared spectroscopy, scanning electron microscopy, and energy dispersive spectroscopy. The deposition mechanism is analyzed in terms of electrochemically induced surface precipitation due to an increase of local pH resulting from the oxygen reduction reaction. This approach allows us to explain the formation of either zinc hydroxychloride compounds or zinc oxide from their calculated solubility diagrams. In conditions of the formation of ZnO, a dramatic effect of temperature is observed, with a transition between amorphous insulating zinc oxyhydroxide to well-crystallized and conducting zinc oxide when the temperature increases (T transition 50 °C).
Multimodal ultrasound parameters aided carotid plaque risk stratification in patients with asymptomatic carotid stenosis

Background Risk stratification of asymptomatic carotid plaque remains an issue in stroke prevention in clinical practice. Purpose To investigate whether a multimodal ultrasound (MMU) model would help plaque risk stratification in patients with asymptomatic carotid stenosis. Material and Methods A prospective study was conducted of symptomatic and asymptomatic patients with > 50% proximal internal carotid artery (ICA) stenosis. All patients underwent MMU examination. Multivariable regression analyses were performed to identify parameters associated with ischemic vascular events (IVE). These parameters were used to develop a scoring nomogram to assess the probability of IVE. We elaborated the diagnostic performance of the MMU nomogram using receiver operating characteristic (ROC) curves. Results From December 2018 to December 2019, 98 patients (75 men, mean age 67 ± 8 years) were included; 50 were symptomatic and 48 were asymptomatic. Multivariable regression analyses revealed that plaque surface morphology (PSM) (odds ratio [OR] 2.99, 95% confidence interval [CI] 1.26–7.12, P = 0.013), intraplaque neovascularization (IPN) grades (OR 3.23, 95% CI 1.77–5.89, P<0.001), and carotid stenosis degree (CSD) (OR 4.12, 95% CI 1.47–11.55, P = 0.007) were independently associated with IVE. For the nomogram, the area under the ROC curve was 0.85 (95% CI 0.77–0.92) and the Hosmer-Lemeshow test P value was 0.822. Conclusions In patients with proximal ICA > 50%, PSM, IPN grades, and CSD were independent variables associated with IVE. The MMU nomogram provided favorable value to risk stratification of IVE. Future large-scale studies with long-term follow-up are needed to validate these findings.
Synthesis and photodynamic activities of novel silicon(IV) phthalocyanines axially substituted with water soluble groups against HeLa cancer cell line.

In this study, compounds 1 and 2, and their silicon(iv) phthalocyanine (SiPc) derivatives 3 and 4, which bear these ligands as substituents on the axial positions were synthesized. These SiPcs (3 and 4) were also converted to their water soluble derivatives (3a and 4a). All these novel compounds were fully characterized by a combination of spectroscopic data such as FT-IR, 1H-NMR, 13C-NMR and UV-vis as well as mass spectroscopy. The photophysicochemical properties (fluorescence quantum yields and lifetimes, singlet oxygen, and photodegradation quantum yields) were investigated in DMSO for all the studied SiPcs (3 and 4) and in both DMSO and aqueous solutions for the water soluble SiPcs (3a and 4a). Effects of quaternization of these phthalocyanines on photophysicochemical properties were also determined. The photodynamic therapy activities of the water soluble SiPcs (3a and 4a) were tested against to the HeLa cancer cell lines and these phthalocyanines exhibited cytotoxicity against these cell lines.
Cadmium and nickel uptake by tomato and spinach seedlings: plant or transport control?

Environmental context Uptake of metal ions by plants is often predicted with equilibrium models, which assume that the rate limiting step is trans-membrane uptake of the metal in the roots rather than the transport of the metal ion towards the site of uptake. Evidence is given that uptake of cadmium by plants is under strong transport control at environmentally relevant concentrations, whereas nickel uptake borders between transport and plant control. This explains the lack of ion competition effects for Cd uptake, whereas both proton and Mg ions were found to compete with Ni uptake. Abstract Equilibrium models for metal uptake by biota assume that the uptake is rate limited by the internalisation of the metal across the cell membrane (plant control). However, evidence has been found that Cd uptake by plants is controlled by the diffusive transport of the free ion to the root at low Cd2+ activities. In this study, the uptake of Cd and Ni by tomato and spinach in nutrient solution was compared to assess whether Ni uptake is under plant or transport control. The diffusive gradient in thin films (DGT) technique was used to measure the maximal diffusive flux. In unbuffered solutions, the uptake flux of Ni was approximately three-fold smaller than that of Cd at free ion concentrations below 1 µM. Stirring the solution increased the uptake of Cd, but not that of Ni at low free ion concentration. The presence of DGT-labile complexes increased the uptake of Cd, but not that of Ni, except at high pH (pH 7). Increasing the solution pH increased Cd uptake only when solution Cd2+ activities were strongly buffered. Overall, the results indicated that the Cd uptake was strongly diffusion limited and that uptake is likely to be under transport control in natural environments. Uptake of nickel, on the other hand, appears to be at the border between plant and transport control. This finding has practical applications, e.g. competition effects at the root have little effect on Cd uptake and chelator-assisted phytoextraction is expected to have less effect for Ni than for Cd.
Early Detection of Plant Viral Disease Using Hyperspectral Imaging and Deep Learning

Early detection of grapevine viral diseases is critical for early interventions in order to prevent the disease from spreading to the entire vineyard. Hyperspectral remote sensing can potentially detect and quantify viral diseases in a nondestructive manner. This study utilized hyperspectral imagery at the plant level to identify and classify grapevines inoculated with the newly discovered DNA virus grapevine vein-clearing virus (GVCV) at the early asymptomatic stages. An experiment was set up at a test site at South Farm Research Center, Columbia, MO, USA (38.92 N, −92.28 W), with two grapevine groups, namely healthy and GVCV-infected, while other conditions were controlled. Images of each vine were captured by a SPECIM IQ 400–1000 nm hyperspectral sensor (Oulu, Finland). Hyperspectral images were calibrated and preprocessed to retain only grapevine pixels. A statistical approach was employed to discriminate two reflectance spectra patterns between healthy and GVCV vines. Disease-centric vegetation indices (VIs) were established and explored in terms of their importance to the classification power. Pixel-wise (spectral features) classification was performed in parallel with image-wise (joint spatial–spectral features) classification within a framework involving deep learning architectures and traditional machine learning. The results showed that: (1) the discriminative wavelength regions included the 900–940 nm range in the near-infrared (NIR) region in vines 30 days after sowing (DAS) and the entire visual (VIS) region of 400–700 nm in vines 90 DAS; (2) the normalized pheophytization index (NPQI), fluorescence ratio index 1 (FRI1), plant senescence reflectance index (PSRI), anthocyanin index (AntGitelson), and water stress and canopy temperature (WSCT) measures were the most discriminative indices; (3) the support vector machine (SVM) was effective in VI-wise classification with smaller feature spaces, while the RF classifier performed better in pixel-wise and image-wise classification with larger feature spaces; and (4) the automated 3D convolutional neural network (3D-CNN) feature extractor provided promising results over the 2D convolutional neural network (2D-CNN) in learning features from hyperspectral data cubes with a limited number of samples.
Prediction and clinical utility of a liver cancer risk model in Chinese adults: A prospective cohort study of 0.5 million people

China has made rapid progress in reducing the incidence of HBV infection in the past three decades, along with a rapidly changing lifestyle and aging population. We aimed to develop and validate an up‐to‐date liver cancer risk prediction model with routinely available predictors and evaluate its applicability for screening guidance. Using data from the China Kadoorie Biobank, we included 486 285 participants in this analysis. Fifteen risk factors were included in the model. Flexible parametric survival models were used to estimate the 10‐year absolute risk of liver cancer. Decision curve analysis was performed to evaluate the net benefit of the model to quantify clinical utility. A total of 2706 participants occurred liver cancer over the 4 814 320 person‐years of follow‐up. Excellent discrimination of the model was observed in both development and validation datasets, with c‐statistics (95% CI) of 0.80 (0.79‐0.81) and 0.80 (0.78‐0.82) respectively, as well as excellent calibration of observed and predicted risks. Decision curve analysis revealed that use of the model in selecting participants for screening improved benefit at a threshold of 2% 10‐year risk, compared to current guideline of screening all HBsAg carriers. Our model was more sensitive than current guideline for cancer screening (28.17% vs 25.96%). We developed and validated a CKB‐PLR (Prediction for Liver cancer Risk Based on the China Kadoorie Biobank Study) model to predict the absolute risk of liver cancer for both HBsAg seropositive and seronegative populations. Application of the model is beneficial for precisely identifying the high‐risk groups among the general population.
The Food Poisoning Toxins of Bacillus cereus

Bacillus cereus is a ubiquitous soil bacterium responsible for two types of food-associated gastrointestinal diseases. While the emetic type, a food intoxication, manifests in nausea and vomiting, food infections with enteropathogenic strains cause diarrhea and abdominal pain. Causative toxins are the cyclic dodecadepsipeptide cereulide, and the proteinaceous enterotoxins hemolysin BL (Hbl), nonhemolytic enterotoxin (Nhe) and cytotoxin K (CytK), respectively. This review covers the current knowledge on distribution and genetic organization of the toxin genes, as well as mechanisms of enterotoxin gene regulation and toxin secretion. In this context, the exceptionally high variability of toxin production between single strains is highlighted. In addition, the mode of action of the pore-forming enterotoxins and their effect on target cells is described in detail. The main focus of this review are the two tripartite enterotoxin complexes Hbl and Nhe, but the latest findings on cereulide and CytK are also presented, as well as methods for toxin detection, and the contribution of further putative virulence factors to the diarrheal disease.
A NIST facility for resonant soft x-ray scattering measuring nano-scale soft matter structure at NSLS-II

We present the design and performance of a polarized resonant soft x-ray scattering (RSoXS) station for soft matter characterization built by the national institute of standards and technology at the national synchrotron light source-II (NSLS-II). The RSoXS station is located within the spectroscopy soft and tender beamline suite at NSLS-II located in Brookhaven national laboratory, New York. Numerous elements of the RSoXS station were designed for optimal performance for measurements on soft matter systems, where it is of critical importance to minimize beam damage and maximize collection efficiency of polarized x-rays. These elements include a novel optical design, sample manipulator and sample environments, as well as detector setups. Finally, we will report the performance of the measurement station, including energy resolution, higher harmonic content and suppression methods, the extent and mitigation of the carbon absorption dip on optics, and the range of polarizations available from the elliptically polarized undulator source.