Miracle-dz/UniFAR-FTUs huggingface dataset:
Data-driven discovery of mid-pregnancy immune markers associated with maternal lifetime stress: results from an urban pre-birth cohort

Abstract Changes to the maternal inflammatory milieu may be a mechanism through which maternal psychosocial stress is transmitted to the fetus. Research investigating a limited number of immune markers may miss important signals. We take a proteomics approach to investigate maternal lifetime stress and 92 biomarkers of immune system status. Participants were enrolled in an urban, dual-site (Boston, n = 301 and New York City, n = 110) pregnancy cohort. We measured maternal lifetime history of stress and trauma using the validated Life Stressor Checklist-Revised (LSC-R). We measured a panel of 92 immune-related proteins in mid-pregnancy serum using proximity extension assay technology. We leveraged the dual-site study design to perform variable selection and inference within the cohort. First, we used LASSO to select immune markers related to maternal stress among Boston mothers. Then, we performed OLS regression to examine associations between maternal stress and LASSO-selected proteins among New York City mothers. LASSO regression selected 19 immune proteins with non-null coefficients (CCL11, CCL23, CD244, CST5, CXCL1, CXCL5, CXCL10, CX3CL1, FGF-23, IL-5, IL-7, IL-10, IL-17C, MCP-2, MMP-1, SLAMF1, ST1A1, TNF-β, and TWEAK). Of these, only the chemotactic cytokine CX3CL1 (i.e. fractalkine) was significantly associated with maternal stress among the validation sample (percent change in LSC-R score per 1% increase in relative fractalkine expression: 0.74, 95% confidence interval: 0.19, 1.28). Expanding research suggests fractalkine plays an important role in many aspects of pregnancy and fetal development and is stress-sensitive. We found that maternal lifetime history of stress and trauma was significantly associated with elevated serum fractalkine levels during pregnancy.
Cell generation dynamics underlying naive T-cell homeostasis in adult humans

Thymic involution and proliferation of naive T cells both contribute to shaping the naive T cell repertoire as humans age, but a clear understanding of the roles of each throughout a human lifespan has been difficult to determine. By measuring nuclear bomb test-derived 14C in genomic DNA we determined the turnover rates of CD4+ and CD8+ naïve T cell populations and defined their dynamics in healthy individuals ranging from 20-65 years of age. We demonstrate that naïve T cell generation decreases with age, and that this could be explained by a combination of declining cell loss, peripheral division and thymic production during adulthood. We investigated putative mechanisms underlying age-related changes in homeostatic regulation of naïve T cell turnover using mass cytometry to profile candidate signaling pathways involved in T cell activation and proliferation in CD4+ naive T cells relative to CD31 expression, a marker of thymic proximity. We show that basal NF-κB phosphorylation inversely correlated with CD31 expression and thus is decreased in peripherally expanded naive T cell clones. Functionally we found that NF-κB signaling was essential for naive T cell proliferation to the homeostatic growth factor IL-7, and reduced NF-κB phosphorylation in CD4+CD31− naive T cells is linked to reduced homeostatic proliferation potential. Our results reveal an age-related decline in naïve T cell turnover as a putative regulator of naïve T cell diversity and identify a molecular pathway that restricts proliferation of peripherally expanded naive T cell clones that accumulate with age.
Efficient Spatial Temporal Convolutional Features for Audiovisual Continuous Affect Recognition

Affective dimension prediction from multi-modal is becoming an increasingly attractive research field in artificial intelligence (AI) and human-computer interaction (HCI) . Previous works have shown that discriminative features from multiple modalities are of importance to accurately recognize emotional states. Recently, deep representations have proved to be effective for emotional state recognition. To investigate new deep spatial-temporal features and evaluate their effectiveness for affective dimension recognition, in this paper, we propose:~(1) combining a pre-trained 2D-CNN and a 1D-CNN for learning deep spatial-temporal features from video images and audio spectrograms; and~(2) a spatial-Temporal Graph Convolutional Networks (ST-GCN) adapted to facial landmarks graph. To evaluate the effectiveness of the proposed spatial-temporal features for affective dimension prediction, we propose Deep Bidirectional Long Short-Term Memory Networks (DBLSTM) model for single-modality prediction, early-fusion and late-fusion predictions. With respect to the liking dimension, we use the text modality for prediction. Experimental results, on the AVEC2019 CES dataset, show that our proposed spatial-temporal features and recognition model obtain promising results. On the development set, the obtained concordance correlation coefficient (CCC) is up to $0.724$ for arousal and $0.705$ for valence, and on the test set, the CCC is $0.513$ for arousal and $0.515$ for valence, which outperform the baseline system with corresponding CCC of $0.355$ and $0.468$ on arousal and valence, respectively.
Sensorimotor and pain‐related alterations of the gray matter and white matter in Type 2 diabetic patients with peripheral neuropathy

Although diabetic peripheral neuropathy (DPN) has long been considered a disease of the peripheral nervous system, recent neuroimaging studies have shown that alterations in the central nervous system may play a crucial role in its pathogenesis. Here, we used surface‐based morphometry (SBM) and tract‐based spatial statistics (TBSS) to investigate gray matter (GM) and white matter (WM) differences between patients with DPN (n = 67, 44 painless and 23 painful) and healthy controls (HCs; n = 88). Compared with HCs, patients with DPN exhibited GM abnormalities in the pre‐ and postcentral gyrus and in several deep GM nuclei (caudate, putamen, medial pallidum, thalamus, and ventral nuclear). They also exhibited altered WM tracts (corticospinal tract, spinothalamic tract, and thalamocortical projecting fibers). These findings suggest impaired motor and somatosensory pathways in DPN. Further, patients with DPN (particularly painful DPN) exhibited morphological differences in the cingulate, insula, prefrontal cortex, and thalamus, as well as impaired WM integrity in periaqueductal WM and internal and external capsules. This suggests pain‐perception/modulation pathways are altered in painful DPN. Intermodal correlation analyses found that the morphological indices of the brain regions identified by the SBM analysis were significantly correlated with the fractional anisotropy of brain regions identified by the TBSS analysis, suggesting that the GM and WM alterations were tightly coupled. Overall, our study showed sensorimotor and pain‐related GM and WM alterations in patients with DPN, which might be involved in the development of DPN.
Non-Ige Mediated Food Allergy.

Food allergies, defined as an immune response to food proteins, affect as many as 8% of young children and 2% of adults in westernized countries, and their prevalence appears to be rising like all allergic diseases. In addition to well-recognized urticaria and anaphylaxis triggered by IgE antibody-mediated immune responses, there is an increasing recognition of cell-mediated disorders such as eosinophilic esophagitis and food protein-induced enterocolitis. Non-IgE-Mediated gastrointestinal food allergies are an heterogeneous group of food allergies in which there is an immune reaction against food but the primary pathogenesis is not a production of IgE and activation of mastcells and basophils. Those diseases tend to affect mainly the gastrointestinal tract and can present as acute (FPIES) or chronic reaction such as Celiac disease, Eosinophilic Esophagitis (EoE), Food Protein Induced Allergic Proctocolitis (FPIAP). The role of food allergy in Non-EoE gastrointestinal Eosinophilc disorders (Non-EoE EGID) is poorly defined. In some diseases like Celiac Disease and possibly EoE T cell seems to play a major role in initiating the immunological reaction against food, however in FPIES and FPIAP the mechanism of sensitization is not clear. Diagnosis require food challenges and/or endoscopies in most of the patients. Celiac disease have some validated biomarkers but none of the other Non-IgE mediated food allergies have such biomarkers that can be used for monitoring or diagnosis of the diseases. Treatment of Non-IgE food allergy rely on diet (FPIES, Celiac disease and EoE) and/or use of drugs (i.e steroids, PPI) in EoE and Non-EoE EGID. Non-gE mediated food allergies are object of intense investigation.
Research of noise reduction about sEMG signal for live working based on MEEMD and DFA

In order to eliminate the noise in Surface Electromyography(sEMG) signals for live working, a sEMG signal denoising method based on MEEMD and DFA was proposed. The sEMG signals of right arm biceps after wearing insulating gloves were collected under typical working conditions, and the Detrend Fluctuation Analysis (DFA) was used as a filtering index to enhance the recognition ability of Modified Ensemble Empirical Mode Decomposition (MEEMD) on the effective information in sEMG signals, so as to improve the effect of secondary noise reduction. The results show that the MAE, MSE and SNR of DFA-MEEMD secondary denoising method are 4.40×10-3, 5.80x10−5 and 25.4dB respectively for typical sEMG signals with strong noise, which can provide a method for e1xtracting useful information from sEMG signals.
15‐LOX‐1 has diverse roles in the resensitization of resistant cancer cell lines to doxorubicin

Lipoxygenases (LOXs) are a family of enzymes that can oxygenate polyunsaturated fatty acids. As a member of the family, 15‐lipoxygenase‐1 (15‐LOX‐1) specifically metabolizes arachidonic acid and linoleic acid. 15‐LOX‐1 can affect physiological and pathophysiological events via regulation of the protein–lipid interactome, alterations in intracellular redox state and production of lipid metabolites that are involved in the induction and resolution of inflammation. Although several studies have shown that 15‐LOX‐1 has an antitumorigenic role in many different cancer models, including breast cancer, the role of the protein in cancer drug resistance has not been established yet. In this study, we, for the first time, aimed to show the potential role of 15‐LOX‐1 in acquired doxorubicin (DOX) resistance in MCF7 and HeLa cancer cell lines. Our results show that ALOX15 was transcriptionally downregulated in DOX‐resistant cells compared with their drug‐sensitive counterparts. Moreover, overexpression of ALOX15 in the drug‐resistant cells resulted in resensitization of those cells to DOX in a cell‐dependent manner. 15‐LOX‐1 expression could induce apoptosis by activating PPARγ and enhance the accumulation of DOX in drug‐resistant MCF7 cells by altering cellular motility properties, and membrane dynamics. However, HeLa DOX cells did not show any of these effects but were susceptible to cell death when treated with 13(S)‐HODE. These results underline the role and importance of 15‐LOX‐1 in cancer drug resistance, and points to novel mechanisms as a therapeutic approach to overcome cancer drug resistance.
Sustained activity of novel THIOMAB antibody-antibiotic conjugate against Staphylococcus aureus in a mouse model: Longitudinal pharmacodynamic assessment by bioluminescence imaging

Staphylococcus aureus (S. aureus) infections are a leading cause of death by an infectious agent. Survival within host phagocytic cells is one mechanism by which S. aureus evades antibiotic treatment. A novel THIOMAB™ antibody-antibiotic conjugate (TAC) strategy was developed to kill S. aureus intracellularly and mitigate the spread of infection. In this report, we used a longitudinal whole-body bioluminescence imaging method to study the antibacterial dynamics of TAC alone or in combination with vancomycin in a mouse infection model. Injections of stably luminescent S. aureus bacteria into mice resulted in exponential increases in whole body bioluminescence with a reduction in body weight and survival rate. Vancomycin, a standard-of-care antibiotic, suppressed bacterial growth in mice. However, bacterial growth rebounded in these animals once treatment was discontinued. In contrast, single dose of TAC showed rapid reduction of bioluminescence intensity, which persisted for up to 19 days. The combination of TAC and vancomycin achieved a more sustained and significantly greater reduction of bioluminescence compared with vancomycin alone. In summary, the present study showed an imaging method to longitudinally assess antibacterial drug dynamics in mice and demonstrated that TAC monotherapy or in combination with vancomycin had superior and sustained activity compared to vancomycin alone.
Lipidomics of Brain Tissues in Rats Fed Human Milk from Chinese Mothers or Commercial Infant Formula

Holistic benefits of human milk to infants, particularly brain development and cognitive behavior, have stipulated that infant formula be tailored in composition like human milk. However, the composition of human milk, especially lipids, and their effects on brain development is complex and not fully elucidated. We evaluated brain lipidome profiles in weanling rats fed human milk or infant formula using non-targeted UHPLC-MS techniques. We also compared the lipid composition of human milk and infant formula using conventional GC-FID and HPLC-ELSD techniques. The sphingomyelin class of lipids was significantly higher in brains of rats fed human milk. Lipid species mainly comprising saturated or mono-unsaturated C18 fatty acids contributed significantly higher percentages to their respective classes in human milk compared to infant formula fed samples. In contrast, PUFAs contributed significantly higher percentages in brains of formula fed samples. Differences between human milk and formula lipids included minor fatty acids such as C8:0 and C12:0, which were higher in formula, and C16:1 and C18:1 n11, which were higher in human milk. Formula also contained higher levels of low- to medium-carbon triacylglycerols, whereas human milk had higher levels of high-carbon triacylglycerols. All phospholipid classes, and ceramides, were higher in formula. We show that brain lipid composition differs in weanling rats fed human milk or infant formula, but dietary lipid compositions do not necessarily manifest in the brain lipidome.
Ultra-processed foods and excessive free sugar intake in the UK: a nationally representative cross-sectional study

Objectives To describe dietary sources of free sugars in different age groups of the UK population considering food groups classified according to the NOVA system and to estimate the proportion of excessive free sugars that could potentially be avoided by reducing consumption of their main sources. Design and setting Cross-sectional data from the UK National Diet and Nutrition Survey (2008–2014) were analysed. Food items collected using a 4-day food diary were classified according to the NOVA system. Participants 9364 individuals aged 1.5 years and above. Main outcome measures Average dietary content of free sugars and proportion of individuals consuming more than 10% of total energy from free sugars. Data analysis Poisson regression was used to estimate the associations between each of the NOVA food group and intake of free sugars. We estimated the per cent reduction in prevalence of excessive free sugar intake from eliminating ultra-processed foods and table sugar. Analyses were stratified by age group and adjusted for age, sex, ethnicity, survey year, region and equivalised household income (sterling pounds). Results Ultra-processed foods account for 56.8% of total energy intake and 64.7% of total free sugars in the UK diet. Free sugars represent 12.4% of total energy intake, and 61.3% of the sample exceeded the recommended limit of 10% energy from free sugars. This percentage was higher among children (74.9%) and adolescents (82.9%). Prevalence of excessive free sugar intake increased linearly across quintiles of ultra-processed food consumption for all age groups, except among the elderly. Eliminating ultra-processed foods could potentially reduce the prevalence of excessive free sugar intake by 47%. Conclusion Our findings suggest that actions to reduce the ultra-processed food consumption generally rich in free sugars could lead to substantial public health benefits.
First data on chigger mites (Acariformes: Trombiculidae) of Saudi Arabia, with a description of four new species

Abstract A collection of chigger mites from three species of rodents in the ‘Asir Region of Saudi Arabia resulted in the finding of 19 species. Four new species are described: Schoutedenichia asirensis sp. nov., Schoutedenichia saudi sp. nov., Microtrombicula microscuta sp. nov., and Microtrombicula muhaylensis sp. nov. Fifteen species—Gahrliepia lawrencei Jadin and Vercammen-Grandjean, 1952, Schoengastiella wansoni Wolfs and Vercammen-Grandjean, Walchia parvula Schluger, Ascoschoengastia browni Taufflieb, Mouchet and Courtois, Helenicula lukshumiae Nadchatram and Traub, Schoutedenichia thracica Kolebinova, Schoutedenichia zarudnyi Kudryashova, Ericotrombidium caucasicum (Schluger), Ericotrombidium galliardi (Vercammen-Grandjean and Taufflieb), Ericotrombidium kazeruni (Kudryashova), Microtrombicula centropi (Vercammen-Grandjean), Microtrombicula hoogstraali (Radford), Microtrombicula hyracis (Vercammen-Grandjean), Microtrombicula traubi (Muljarskaja and Verdieva), and Pentidionis agamae (André)—are for the first time recorded in Saudi Arabia and on new host species. Six of them are for the first time recorded outside their type localities and five were only known previously from the African continent.
Automatic Semantic Text Tagging on Historical Lexica by Combining OCR and Typography Classification: A Case Study on Daniel Sander's Wörterbuch der Deutschen Sprache

When converting historical lexica into electronic form the goal is not only to obtain a high quality OCR result for the text but also to perform a precise automatic recognition of typographical attributes in order to capture the logical structure. For that purpose, we present a method that enables a fine-grained typography classification by training an open source OCR engine both on traditional OCR and typography recognition and show how to map the obtained typography information to the OCR recognized text output. As a test case, we used a German dictionary (Sander's Wörterbuch der Deutschen Sprache) from the 19th century, which comprises a particularly complex semantic function of typography. Despite the very challenging material, we achieved a character error rate below 0.4% and a typography recognition that assigns the correct label to close to 99% of the words. In contrast to many existing methods, our novel approach works with real historical data and can deal with frequent typography changes even within lines.
Biomarkers in medicine: an overview.

Recently, biomarkers in medicine have gained comprehensive scientific and clinical interest. Biomarker or biological marker defined as alteration in the constituents of tissues or body fluids provide a powerful approach to understanding the spectrum of chronic diseases with application in at least 5 areas like screening, diagnosis, prognostication, prediction of disease recurrence and therapeutic monitoring. Therefore, biomarkers are biological indicators of diseases that can be measured either in vivo by biomedical imaging or in vitro by laboratory methods. Many kinds of biomarkers are available in the field of medical science with lots of positive as well as negative effect. These markers can also reflect the entire spectrum of disease from the earliest manifestations to the terminal stages and will become one of the major driving forces of pharmaceutical research and drug development in the coming years. Generally, a biomarker is potentially useful along the whole spectrum of the disease processbefore diagnosis; for screening and risk assessment, during diagnosis; for staging, grading and selecting the initial therapy and during treatment for monitoring therapy, selecting additional therapy or monitoring recurrent diseases. This brief review describes the types and major uses of biomarkers in clinical investigation. Review Article British Journal of Medicine & Medical Research, 4(8): 1701-1718, 2014 1702
Multi-modality Depression Detection via Multi-scale Temporal Dilated CNNs

Depression, a prevalent mental illness, is negatively impacting on individual and society. This paper targets the Depression Detection Challenge with AI Sub-challenge (DDS) task of Audio Visual Emotion Challenge (AVEC) 2019. Firstly, two task-specific features are proposed: 1) deep contextual text features, which incorporate global text features and sentiment scores estimated by fine-tuned Bidirectional Encoder Representations from Transformers (BERT); 2) span-wise dense temporal statistical features, in which multiple statistical functions are conducted in each continuous time span. Furthermore, we propose a multi-scale temporal dilated CNN to precisely capture the hidden temporal dependency in the data for automatic multi-modality depression detection. Our proposed framework achieves competitive performance with Concordance Correlation Coefficient (CCC) of 0.466 on development set and 0.430 on test set which is remarkably higher than the baseline result of 0.269 on development set and 0.120 on test set.
Signaling impacts of GMO labeling on fruit and vegetable demand

Food labels may have both informational and signaling influences on consumer demand. We conduct a choice experiment with over 1,300 subjects to examine the signaling effect of the food product labels on consumer demand for other competing products in the market. Specifically, we focus on the genetically modified (GM) text labeling for fresh produce (strawberries, apples, and potatoes) in the United States. Contrary to some previous studies, our results indicate that the absence-claim label (Not-GM) does not have a negative impact on the demand for related conventional products. Instead, we find that consumer demand for unlabeled products is significantly enhanced with the introduction of presence-claimed GM labels. Our results contribute to the ongoing discussion of the enactment of mandatory labeling for GM foods by the federal U.S. government. Our results suggest that, in the case of direct text disclosure labels, consumers may no longer differentiate between unlabeled products and Not-GM-labeled products after the mandatory GM labeling law is in effect.