Miracle-dz/UniFAR-FTUs huggingface dataset:
A Joint Analysis of Multi-Paradigm fMRI Data With Its Application to Cognitive Study

With the development of neuroimaging techniques, a growing amount of multi-modal brain imaging data are collected, facilitating comprehensive study of the brain. In this paper, we jointly analyzed functional magnetic resonance imaging (fMRI) collected under different paradigms in order to understand cognitive behaviors of an individual. To this end, we proposed a novel multi-view learning algorithm called structure-enforced collaborative regression (SCoRe) to extract co-expressed discriminative brain regions under the guidance of anatomical structure of the brain. An advantage of SCoRe over its predecessor collaborative regression (CoRe) lies in its incorporation of group structures in the brain imaging data, which makes the model biologically more meaningful. Results from real data analysis has confirmed that by incorporating prior knowledge of brain structure, SCoRe can deliver better prediction performance and is less sensitive to hyper-parameters than CoRe. After validation with simulation experiments, we applied SCoRe to fMRI data collected from the Philadelphia Neurodevelopmental Cohort and adopted the scores from the wide range achievement test (WRAT) to evaluate an individual’s cognitive skills. We located 14 relevant brain regions that can efficiently predict WRAT scores and these brain regions were further confirmed by other independent studies.
The Heme-Regulated Inhibitor Pathway Modulates Susceptibility of Poor Prognosis B-Lineage Acute Leukemia to BH3-Mimetics

Antiapoptotic MCL1 is one of the most frequently amplified genes in human cancers and elevated expression confers resistance to many therapeutics including the BH3-mimetic agents ABT-199 and ABT-263. The antimalarial, dihydroartemisinin (DHA) translationally represses MCL-1 and synergizes with BH3-mimetics. To explore how DHA represses MCL-1, a genome-wide CRISPR screen identified that loss of genes in the heme synthesis pathway renders mouse BCR-ABL+ B-ALL cells resistant to DHA-induced death. Mechanistically, DHA disrupts the interaction between heme and the eIF2α kinase heme-regulated inhibitor (HRI) triggering the integrated stress response. Genetic ablation of Eif2ak1, which encodes HRI, blocks MCL-1 repression in response to DHA treatment and represses the synergistic killing of DHA and BH3-mimetics compared with wild-type leukemia. Furthermore, BTdCPU, a small-molecule activator of HRI, similarly triggers MCL-1 repression and synergizes with BH3-mimetics in mouse and human leukemia including both Ph+ and Ph-like B-ALL. Finally, combinatorial treatment of leukemia bearing mice with both BTdCPU and a BH3-mimetic extended survival and repressed MCL-1 in vivo. These findings reveal for the first time that the HRI-dependent cellular heme-sensing pathway can modulate apoptosis in leukemic cells by repressing MCL-1 and increasing their responsiveness to BH3-mimetics. This signaling pathway could represent a generalizable mechanism for repressing MCL-1 expression in malignant cells and sensitizing them to available therapeutics. Implications: The HRI-dependent cellular heme-sensing pathway can modulate apoptotic sensitivity in leukemic cells by repressing antiapoptotic MCL-1 and increasing their responsiveness to BH3-mimetics.
Think Aloud Protocol Applied in Naturalistic Driving for Driving Rules Generation

Understanding naturalistic driving in complex scenarios is an important step towards autonomous driving, and several approaches have been adopted for modeling driver’s behaviors. This paper presents the methodology known as “Think Aloud Protocol” to model driving. This methodology is a data-gathering technique in which drivers are asked to verbalize their thoughts as they are driving which are then recorded, and the ensuing analysis of the audios and videos permits to derive driving rules. The goal of this paper is to show how think aloud methodology is applied in the naturalistic driving area, and to demonstrate the validity of the proposed approach to derive driving rules. The paper presents, firstly, the background of the think aloud methodology and then presents the application of this methodology to driving in roundabouts. The general deployment of this methodology consists of several stages: driver preparation, data collection, audio and video processing, generation of coded transcript files, and the generation of driving rules. The main finding of this study is that think aloud protocol can be applied to naturalistic driving, and even some potential limitations as discussed in the paper, the presented methodology is a relatively easy approach to derive driving rules.
Ordered phases in rod-coil diblock copolymers

We study spatially ordered phases in a rod−coil diblock copolymer melt. In the weak segregation limit, we solve the self-consistent field equations by a partial numerical evaluation of the single chain partition function. In the strong segregation limit, we resort to a brushlike approximation. The structural asymmetry of the blocks has a pronounced influence on the phase diagram. We find that the only stable morphologies are those in which the coils are on the convex side of the rod−coil interface. The results are compared to experiment.
Genome-Wide Estrogen Receptor Activity in Breast Cancer

Abstract The largest subtype of breast cancer is characterized by the expression and activity of the estrogen receptor alpha (ERalpha/ER). Although several effective therapies have significantly improved survival, the adaptability of cancer cells means that patients frequently stop responding or develop resistance to endocrine treatment. ER does not function in isolation and multiple associating factors have been reported to play a role in regulating the estrogen-driven transcriptional program. This review focuses on the dynamic interplay between some of these factors which co-occupy ER-bound regulatory elements, their contribution to estrogen signaling, and their possible therapeutic applications. Furthermore, the review illustrates how some ER association partners can influence and reprogram the genomic distribution of the estrogen receptor. As this dynamic ER activity enables cancer cell adaptability and impacts the clinical outcome, defining how this plasticity is determined is fundamental to our understanding of the mechanisms of disease progression.
Personalized Image Classification by Semantic Embedding and Active Learning †

Currently, deep learning has shown state-of-the-art performance in image classification with pre-defined taxonomy. However, in a more real-world scenario, different users usually have different classification intents given an image collection. To satisfactorily personalize the requirement, we propose an interactive image classification system with an offline representation learning stage and an online classification stage. During the offline stage, we learn a deep model to extract the feature with higher flexibility and scalability for different users’ preferences. Instead of training the model only with the inter-class discrimination, we also encode the similarity between the semantic-embedding vectors of the category labels into the model. This makes the extracted feature adapt to multiple taxonomies with different granularities. During the online session, an annotation task iteratively alternates with a high-throughput verification task. When performing the verification task, the users are only required to indicate the incorrect prediction without giving the exact category label. For each iteration, our system chooses the images to be annotated or verified based on interactive efficiency optimization. To provide a high interactive rate, a unified active learning algorithm is used to search the optimal annotation and verification set by minimizing the expected time cost. After interactive annotation and verification, the new classified images are used to train a customized classifier online, which reflects the user-adaptive intent of categorization. The learned classifier is then used for subsequent annotation and verification tasks. Experimental results under several public image datasets show that our method outperforms existing methods.
Winter honeybee (Apis mellifera) populations show greater potential to induce immune responses than summer populations after immune stimuli

ABSTRACT In the temperate climates of central Europe and North America, two distinct honeybee (Apis mellifera) populations are found in colonies: short-living summer bees emerge in spring and survive until summer, whereas long-living winter bees emerge in late August and overwinter. Besides the difference in their life spans, each of these populations fulfils a different role in the colonies and individual bees have distinct physiological and immunological adaptations depending on their roles. For instance, winter worker bees have higher vitellogenin levels and larger reserves of nutrients in the fat body than summer bees. The differences between the immune systems of both populations are well described at the constitutive level; however, our knowledge of its inducibility is still very limited. In this study, we focus on the response of 10-day-old honeybee workers to immune challenges triggered in vivo by injecting heat-killed bacteria, with particular focus on honeybees that emerge and live under hive conditions. Responses to bacterial injections differed between summer and winter bees. Winter bees exhibited a more intense response, including higher expression of antimicrobial genes and antimicrobial activity, as well as a significant decrease in vitellogenin gene expression and its concentration in the hemolymph. The intense immune response observed in winter honeybees may contribute to our understanding of the relationships between colony fitness and infection with pathogens, as well as its association with successful overwintering. Summary: Immunity induced in 10-day-old workers that emerged and lived under hive conditions is stronger in winter bees than in summer bees. Immune stimuli decreased the production of the longevity marker vitellogenin.
Intergenerational impacts of trauma and hardship through parenting.

BACKGROUND Millions of people worldwide experience severe trauma in their lifetime. Trauma has immediate and long-term effects on emotional wellbeing. Moreover, the experiences of one generation may influence subsequent generations via social and biological pathways. Poor mental health and emotion dysregulation associated with trauma may affect parenting behaviours, which may have long-lasting effects on children's development. METHODS We use longitudinal data from a unique sample of 732 caregivers of children aged 6-36 months living in extremely poor rural households in Rwanda to examine associations of caregiver lifetime trauma, recent daily hardships, mental health, and emotion dysregulation with parenting behaviours reflecting parental acceptance and rejection of their offspring. RESULTS Cumulative trauma exposure (β = .234, p < .001) and recent daily hardships (β = .323, p < .001) are associated with higher levels of internalising symptoms. Trauma (β = .257, p < .001) and daily hardships (β = .323, p < 0.001) are also associated with post-traumatic stress disorder (PTSD) symptoms. Internalising symptoms predict more rejection (β = .177, p = .001), but show no association with acceptance. Caregiver PTSD symptoms predict more rejection (β = .277, p < .001) and less acceptance (β = -.190, p = .003). Both internalising symptoms (β = .557, p < .001) and PTSD symptoms (β = .606, p < .001) are strongly associated with poor emotion regulation. Indirect effects suggest that caregiver trauma and hardships affect parenting indirectly via elevated caregiver internalising symptoms and PTSD and that some of these effects are accounted for by emotion dysregulation. CONCLUSIONS Caregiver internalising and PTSD symptoms are important mechanisms through which caregiver trauma and hardship affect parenting behaviours. Emotion dysregulation is a shared mechanism linking caregivers' mental health problems with parenting behaviours that reflect acceptance and rejection of the child. Emotion regulation is indicated as a key target for prevention of adverse effects of caregiver trauma on mental health and child wellbeing.
Preparation of Opal Ball with Enhanced Light Diffraction Using Dry Self-Assembly Method

This article described the preparation of opal ball with enhanced structural colors by using silica microspheres droplet templates on polytetrafluoroethylene (PTFE) superhydrophobic surfaces. The structural colors of the opal ball wasgreatly enhanced by incorporating carbon black nanoparticles (CB-NPs) into the voids of silica colloidal crystals in the dry self-assembly (DSA) process.The presence of CB-NPs in the structure did not lead to a shift of the reflection band, but enhanced the diffraction color by increased reflectance and suppressed transmission.
Unmodified gold nanoparticles as a colorimetric probe for visual methamphetamine detection

ABSTRACT In recent years, in addition to the classic drugs, addiction to a series of new drug classes known as club drugs has increased significantly. Fast and low-cost bioassay for the detection of amphetamine-based drugs can be an effective strategy towards reducing their abuse. In this study, we designed a sensitive bioassay strategy using gold nanoparticles (GNPs) and the aptamers that possess high affinity toward methamphetamine (MA). It is suggested that the aptamer adopts different tertiary structures in the presence and/or absence of its specific target and GNPs can effectively differentiate between these two states by their characteristic surface plasmon resonance-based colour change. Visual detection of MA and 3,4-methylenedioxy-N-methylamphetamine (MDMA) in the low micromolar range is possible within minutes with the use of this method.
Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) Roots

Alternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with soil microorganisms is not fully understood. In this work, a comprehensive analysis of the transcriptome of garden pea (Pisum sativum L.) roots in symbiosis with arbuscular mycorrhiza was performed using RNAseq and following bioinformatic analysis. AS profiles of mycorrhizal and control roots were highly similar, intron retention accounting for a large proportion of the observed AS types (67%). Using three different tools (SUPPA2, DRIMSeq and IsoformSwitchAnalyzeR), eight genes with AS events specific for mycorrhizal roots of pea were identified, among which four were annotated as encoding an apoptosis inhibitor protein, a serine/threonine-protein kinase, a dehydrodolichyl diphosphate synthase, and a pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1. In pea mycorrhizal roots, the isoforms of these four genes with preliminary stop codons leading to a truncated ORFs were up-regulated. Interestingly, two of these four genes demonstrating mycorrhiza-specific AS are related to the process of splicing, thus forming parts of the feedback loops involved in fine-tuning of gene expression during mycorrhization.
IN VITRO BIO-MEDICAL STUDIES ON PSIDIUM GUAJAVA LEAVES

Distinctive parts of guava Psidium guajava L. (PG) are a great wellspring of strong and intense bio medications. The present investigation was intended to extract and to identify the bioactive component of PG leaves, utilizing HPLC and assessed the activity of ethanol(70%) extract against Helicobacter pyroli, tuberculosis, diabetic (Alpha-glucosidase inhibitory %), arthritic (albumin denaturation inhibition) and aging (Anti-Collagenase) factorials. The outcomes of HPLC identification phenolic compounds showed that ethanolic extract contained gallic acid, caffeic acid, ferulic acid, cinnamic acid and they have highest values (4.71, 4.37, 3.82, 3.55 and 3.49μg/mg, respectively followed by resorcinol, chlorogenic, syringic acid and resormarinic acid (3.09, 2.93, 2.85 and 2.49μg/mg, respectively), while flavonoids were quercetin, hesperetin, kaempferol, quercitrin and rutin, where they presented 8.94, 7.61, 7.55, 7.13 and 6.37 μg/mg, respectively followed by catechin (5.12μg/mg) and apigenin (4.83 μg/mg). The identified alkaloids were corilagin, kaempfertin, and isoquinoline and they have values 2.13, 1.89 and 1. 24μg/mg, respectively. Evaluation of inhibitory effect of PGL extract stated that PGL scored the highest values for effective concentrations (125 μg/mg) and MIC90 (26.6) comparing with activity of clarithromycin (C) (1.95 μg/mg and MIC90 (0.7), respectively against Helicobacter pyroli activity and 7. 81μg/mg and MIC90 11.94 comparing with isoniazid standard (IS) at concentration 0. 24μg/mg and MIC90 0.4 against tuberculosis activity. The IC50 of PGL against alpha-glucosidase activity comparing with values of Acarbose (A) showed that inhibitory percentage was lower at 1000μg/mg (79.22) than the value of acarbose (90.10) at the same concentration, while IC50 of PGL was higher (46.6) than that of acarbose (30.57). Percentage of albumin denaturation inhibition at 1000 μg/mg of both PGL extract and DSS were 71.34 and 89. 35μg/mg, respectively, while IC50 of both were 50.26 and 15.12, respectively. Collagenase inhibition percentage of PGL recorded 82.34 but EGCGrecorded 93.24 at concentration 1000 μg/mg. The IC50 of PGL was higher (105.3) than the value of EGCG (40.3).
Influence of calcium chelators on concentrated micellar casein solutions : from micellar structure to viscosity and heat stability

In practice it is challenging to prepare a concentrated medical product with high heat stability and low viscosity. Calcium chelators are often added to dairy products to improve heat stability, but this may increase viscosity through interactions with the casein proteins. The aim of this thesis was to obtain a better understanding of the influence of different calcium chelators on the physico-chemical properties of casein micelles and the resulting effect on viscosity and heat stability of concentrated micellar casein isolate (MCI) solutions. The calcium chelators disodium uridine monophosphate (Na2UMP), disodium hydrogen phosphate (Na2HPO4), trisodium citrate (TSC), sodium phytate (SP), and sodium hexametaphosphate (SHMP) were studied. Initially, the calcium-binding capacity of the phosphates was investigated and found to be directly related to the amount of charges. The resulting effects on physical changes of casein micelles were subsequently explored before and during heating. The viscosity of the MCI solutions increased upon addition of the calcium chelators, which was attributed to swelling of the caseins at decreasing calcium-ion activity. The calcium chelators induced different changes in turbidity of the MCI solutions, which could be related to the degree of dissociation of the casein micelles. Simulations of the ion equilibria indicated that the extent of casein micelle dissociation followed the calcium-binding capacity of the calcium chelators. Micelle dissociation occurred in the order of SHMP > SP > TSC > Na2HPO4 > Na2UMP. The results on heat stability indicated that the calcium-ion activity and state of the micellar structure before and during heating determined the heat stability of the MCI solutions. Na2UMP was the most effective heat stabilizer, as it bound sufficient free calcium ions to reduce protein aggregation without affecting the micellar structure. SHMP was the least effective heat stabilizer because of heat-induced changes occurring during heating. For polyphosphates, SHMP and SP, it was found that they decreased the isoint of casein by forming direct bindings with the caseins, for which calcium ions were not required. In conclusion, this thesis has provided new insights in the relationships between calcium chelators and their influence on the casein micelle structure and on the physico-chemical properties of concentrated MCI solutions. Also, the practical relevance for the dairy industry was described, demonstrating how different calcium chelators can manipulate the viscosity and heat stability of dairy products.
Transferable force field for carbon dioxide adsorption in zeolites

We have developed a complete force field that accurately reproduces the adsorption properties of carbon dioxide in a variety of zeolites with different topologies and compositions. The force field parameters were obtained by fitting to our own experimental data and validated with available data taken from the literature. The novelty of this force field is that it is fully transferable between different zeolite framework types, and therefore, it is applicable to all possible Si/Al ratios (with sodium as extra-framework cation) and for the first time affording the prediction of topology-specific and chemical composition-specific adsorption properties.
The Associations of SCFA with Anthropometric Parameters and Carbohydrate Metabolism in Pregnant Women

Short-chain fatty acids (SCFAs) mediate the transmission of signals between the microbiome and the immune system and are responsible for maintaining balance in the anti-inflammatory reaction. Pregnancy stages alter the gut microbiota community structure, which also synthesizes SCFAs. The study involved 90 pregnant women, divided into two groups: 48 overweight/obese pregnant women (OW) and 42 pregnant women with normal BMI (CG). The blood samples for glucose, insulin, and HBA1c were analyzed as well as stool samples for SCFA isolation (C2:0; C3:0; C4:0i; C4:0n; C5:0i; C5:0n; C6:0i; C6:0n) using gas chromatography. The SCFA profile in the analyzed groups differed significantly. A significant positive correlation between C2:0, C3:0, C4:0n and anthropometric measurements, and between C2:0, C3:0, C4:0n, and C5:0n and parameters of carbohydrate metabolism was found. SCFA levels fluctuate during pregnancy and the course of pregnancy and participate in the change in carbohydrate metabolism as well. The influence of C2:0 during pregnancy on anthropometric parameters was visible in both groups (normal weight and obese). Butyrate and propionate regulate glucose metabolism by stimulating the process of intestinal gluconeogenesis. The level of propionic acid decreases with the course of pregnancy, while its increase is characteristic of obese women, which is associated with many metabolic adaptations. Propionic and linear caproic acid levels can be an important critical point in maintaining lower anthropometric parameters during pregnancy.
Solution Processable Ionic p-i-n Organic Light-Emitting Diodes

Strong and efficient light emission from organic light emitting devices (OLEDs) fabricated by simple solution process is potentially useful for the manipulation of light in information display and lighting technologies. Recently, intensive research has been conducted into the development of OLEDs for realizing strong light emission from a simple OLED structure. In this chapter, highly efficient and enhanced light emission will be described for solution-processed phosphorescent OLEDs (PHOLEDs) doped with ionic salt, treated with the simultaneous electrical and thermal annealing. Because the simultaneous annealing causes the adsorption of charged salt ions at the electrode surfaces, the separated charges act as ionic doping in organic semiconductor layer and the electronic energy levels of the organic molecules are bended by the electric fields due to the adsorbed charged ions at the electrode interfaces, i.e., the simultaneous annealing can induce the proper formation of ionic p-i-n structure.