Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamical models for neonatal intensive care monitoring

The vital signs monitoring data of an infant receiving intensive care are a rich source of information about its health condition. One major concern about the state of health of such patients is the onset of neonatal sepsis, a life-threatening bloodstream infection. As early signs are subtle and current diagnosis procedures involve slow laboratory testing, sepsis detection based on the monitored physiological dynamics is a clinically significant task. This challenging problem can be thoroughly modelled as real-time inference within a machine learning framework. In this thesis, we develop probabilistic dynamical models centred around the goal of providing useful predictions about the onset of neonatal sepsis. This research is characterised by the careful incorporation of domain knowledge for the purpose of extracting the infant’s true physiology from the monitoring data. We make two main contributions. The first one is the formulation of sepsis detection as learning and inference in an Auto-Regressive Hidden Markov Model (AR-HMM). The model investigates the extent to which physiological events observed in the patient’s monitoring traces could be used for the early detection of neonatal sepsis. In addition, the proposed approach involves exact marginalisation over missing data at inference time. When applying the ARHMM on a real-world dataset, we found that it can produce effective predictions about the onset of sepsis. Second, both sepsis and clinical event detection are formulated as learning and inference in a Hierarchical Switching Linear Dynamical System (HSLDS). The HSLDS models dynamical systems where complex interactions between modes of operation can be represented as a twolevel hidden discrete hierarchical structure. For neonatal condition monitoring, the lower layer models clinical events and is controlled by upper layer variables with semantics sepsis/nonsepsis. The model parameterisation and estimation procedures are adapted to the specifics of physiological monitoring data. We demonstrate that the performance of the HSLDS for the detection of sepsis is not statistically different from the AR-HMM, despite the fact that the latter model is given “ground truth” annotations of the patient’s physiology.
Perceived low-quality communication is not associated with greater frequency of requests for ethics consultation: Null findings from an empirical study

ABSTRACT Background: Prior research has explored reasons why health care providers may or may not choose to seek an ethics consultation. Although low-quality communication is evident in many ethics consultations, it is unknown whether poor communication in clinical settings is related to health care providers' requests for ethics involvement. Objective: To assess the relationship between self-reported ratings of health care providers' inter- and intraprofessional communication and ethics consultation requests. Method: This cross-sectional survey was conducted using a self-administered questionnaire of physicians and nurses in six intensive care units at one academic medical center in the United States. The questionnaire assessed perceptions about requesting ethics consultations and how health care providers perceive communication. Results: Two hundred sixty-two participants (228 nurses and 34 physicians) responded to the survey (response rate 55%; 59% for nurses and 41% for physicians). Requests for an ethics consult were positively associated with perceived quality of interprofessional communication (r = .13, p < .05), but perceptions of the number of ethical dilemmas that occur on participants' units each month were negatively associated with the perceived quality of intra-professional communication (r = −.17, p < .01). Conclusion: The relationship that was hypothesized between perceived poor communication and increased number of ethics consultations was not borne out by these data. Indeed, we found the opposite; these finding suggests that good inter- and intraprofessional communication may promote the use of outside resources, such as ethics, when they are needed.
A two-step method for identifying photopigment opsin and rhodopsin gene sequences underlying human color vision phenotypes

Purpose To present a detailed, reliable long range-PCR and sequencing (LR-PCR-Seq) procedure to identify human opsin gene sequences for variations in the long wavelength-sensitive (OPN1LW), medium wavelength-sensitive (OPN1MW), short wavelength-sensitive (OPN1SW), and rhodopsin (RHO) genes. Methods Color vision was assessed for nine subjects using the Farnsworth-Munsell 100 hue test, Ishihara pseudoisochromatic plates, and the Rabin cone-contrast threshold procedure (ColorDX, Konan Medical). The color vision phenotypes were normal trichromacy (n = 3), potential tetrachromacy (n = 3), dichromacy (n = 2), and unexplained low color vision (n = 1). DNA was isolated from blood or saliva and LR-PCR amplified into individual products: OPN1LW (4,045 bp), OPN1MW (4,045 bp), OPN1SW (3,326 bp), and RHO (6,715 bp). Each product was sequenced using specific internal primer sets. Analysis was performed with Mutation Surveyor software. Results The LR-PCR-Seq technique identified known single nucleotide polymorphisms (SNPs) in OPN1LW and OPN1MW gene codons (180, 230, 233, 277, and 285), as well as those for lesser studied codons (174, 178, 236, 274, 279, 298 and 309) in the OPN1LW and OPN1MW genes. Additionally, six SNP variants in the OPN1MW and OPN1LW genes not previously reported in the NCBI dbSNP database were identified. An unreported poly-T region within intron 5(c.36+126) of the rhodopsin gene was also found, and analysis showed it to be highly conserved in mammalian species. Conclusions This LR-PCR-Seq procedure (single PCR reaction per gene followed by sequencing) can identify exonic and intronic SNP variants in OPN1LW, OPN1MW, OPN1SW, and rhodopsin genes. There is no need for restriction enzyme digestion or multiple PCR steps that can introduce errors. Future studies will combine the LR-PCR-Seq with perceptual behavior measures, allowing for accurate correlations between opsin genotypes, retinal photopigment phenotypes, and color perception behaviors.
A standardized method to assess the endogenous activity and the light–response of the retinal clock in mammals

Purpose The bioluminescence reporter PER2::Luciferase (PER2::Luc) provides a powerful tool to study the regulation of biological clocks in explant tissues, including the retinal clock. However, the establishment of a standardized procedure to replicate experimental conditions and to enable meaningful comparisons between findings from different studies is still lacking. In addition, different parameters may affect the retinal circadian bioluminescence signal and its dynamic in in vitro assays. In the present study, we first evaluated the effect of sex and age on the main parameters of the mouse retinal clock. We then examined the impact of medium change on PER2::Luc rhythm and compared two light stimulation protocols of the retinal clock. Methods In a first set of experiments, retinal explants from both male and female Per2Luc mice of different ages (1 to 8 months) are cultured and the period, phase, amplitude, and rhythmic power of PER2::Luc oscillations are analyzed. In a second set of experiments, we quantified the effect of a medium change done after 4, 6, 8, 9, or 10 days of culture on the phase and period of retinal explants. Finally, we compared the phase shift and the period change resulting from two methods of light stimulations of retinal explants: the first involved the transfer of the cultured tissues from the Lumicycle into a light stimulation chamber, while the second used a light delivery apparatus embedded in the Lumicycle. Results We do not observe any sex-dependent effects on the amplitude, period, phase, and rhythmic power of the in vitro retinal PER2::Luc oscillations in animals aged of 2 to 3 months. The most remarkable effect of age is on the amplitude of PER2::Luc oscillations that significantly decrease from 1 to 4–5 months, whereas the endogenous period and rhythmic power increase slightly until 2 to 3 months and then do not change until 8 months. The phase is not affected by age. We then show that a medium change occurring after 4 days of culture does not alter the phase of PER2::Luc rhythm by comparison with day 0, whereas a medium change done after 6, 8, 9, or 10 days in culture advances the phase and lengthens the period. Finally, we observe that the physical displacement of the culture dishes containing retinal explants, even in complete darkness, induces a strong phase shift of PER2::Luc oscillations. Conclusions Our work shows that the retina cultures are particularly sensitive to some aspects of the culture procedure, and it provides an accurate standard protocol to avoid biases due to artifactually induced phase shifts resulting from the medium change or physical displacement.
Accurately Estimating Alcohol Consumption: A Comparison of Self-Administrated and Interview Methods

Abstract Background: There have been two methods of gaining retrospective self-report estimates of alcohol consumption, quantity frequency (QF) and retrospective diary (RD), offering distinct advantages and disadvantages. The typical and atypical drinking diary (TADD) was developed to benefit from each method’s advantages. Objectives: To compare estimates obtained from the TADD with corresponding estimates obtained from a QF measure (Khavari alcohol test; KAT) and an RD measure, the timeline follow-back (TLFB). It was hypothesized that the TADD’s alcohol consumption estimates would correlate strongly with those obtained from the TLFB; and the strength of the TADD–TLFB correlation would be significantly stronger than the KAT–TLFB correlation. Method: One hundred and sixty-eight (168) undergraduates (73% female) estimated their alcohol consumption for the preceding 12 weeks using all three measures. Results: The TADD (r = 0.83, p < .001) and the KAT (r = 0.066, p < .001) produced estimates of total alcohol consumption that correlated very strongly and strongly, respectively, with the TLFB. Notably, the TADD–TLFB correlation was significantly stronger than the KAT–TLFB correlation (Z = 5.10, p < .001). Moreover, the TADD’s estimates of number of drinking days (r = 0.70, p < .001) and heavy drinking episodes per week (0.77, p < .001) correlated strongly with corresponding estimates from the TLFB. The TADD and KAT provided higher estimates of alcohol consumption than the TLFB. Conclusion: Clinicians and researchers should consider using the TADD to estimate alcohol consumption in time-limited situations.
Coordinated hedgehog signaling induces new hair follicles in adult skin

Hair follicle (HF) development is orchestrated by coordinated signals from adjacent epithelial and mesenchymal cells. In humans this process only occurs during embryogenesis and viable strategies to induce new HFs in adult skin are lacking. Here, we reveal that activation of Hedgehog (Hh) signaling in adjacent epithelial and stromal cells induces new HFs in adult, unwounded dorsal mouse skin. Formation of de novo HFs recapitulated embryonic HF development, and mature follicles produced hair co-occurring with epithelial tumors. In contrast, Hh-pathway activation in epithelial or stromal cells alone resulted in tumor formation or stromal cell condensation respectively, without induction of new HFs. Provocatively, adjacent epithelial-stromal Hh-pathway activation induced de novo HFs also in hairless paw skin, divorced from confounding effects of pre-existing niche signals in haired skin. Altogether, cell-type-specific modulation of a single pathway is sufficient to reactivate embryonic programs in adult tissues, thereby inducing complex epithelial structures even without wounding.
Dopaminergic Modulation of Orofacial Mechanical Hypersensitivity Induced by Infraorbital Nerve Injury

While the descending dopaminergic control system is not fully understood, it is reported that the hypothalamic A11 nucleus is its principle source. To better understand the impact of this system, particularly the A11 nucleus, on neuropathic pain, we created a chronic constriction injury model of the infraorbital nerve (ION-CCI) in rats. ION-CCI rats received intraperitoneal administrations of quinpirole (a dopamine D2 receptor agonist). ION-CCI rats received microinjections of quinpirole, muscimol [a gamma-aminobutyric acid type A (GABAA) receptor agonist], or neurotoxin 6-hydroxydopamine (6-OHDA) into the A11 nucleus. A von Frey filament was used as a mechanical stimulus on the maxillary whisker pad skin; behavioral and immunohistochemical responses to the stimulation were assessed. After intraperitoneal administration of quinpirole and microinjection of quinpirole or muscimol, ION-CCI rats showed an increase in head-withdrawal thresholds and a decrease in the number of phosphorylated extracellular signal-regulated kinase (pERK) immunoreactive (pERK-IR) cells in the superficial layers of the trigeminal spinal subnucleus caudalis (Vc). Following 6-OHDA microinjection, ION-CCI rats showed a decrease in head-withdrawal thresholds and an increase in the number of pERK-IR cells in the Vc. Our findings suggest the descending dopaminergic control system is involved in the modulation of trigeminal neuropathic pain.
Reproducibility of Subtraction Radiography in Monitoring Changes in Approximal Carious Lesions in Children: An In Vivo Study.

BACKGROUND Laboratory studies have shown that digital subtraction radiography (DSR) can be a more effective tool, than conventional radiography, in monitoring changes in carious lesions. The clinical performance of the technique, however, has not been sufficiently researched. AIM To compare the reproducibility of DSR to that of bitewing radiographs, in monitoring changes in approximal caries in the mixed dentition. A secondary aim was to determine if assessment outcomes differed as a function of the method used. DESIGN Six assessors evaluated 310 lesions first on bitewings, then with DSR. The overall reproducibility was evaluated via intra-class correlation coefficient (ICC). Intra and inter-rater reproducibility, were assessed using weighted Kappa. Paired t-test was used to assess differences in the reproducibility across methods. RESULTS The overall reproducibility for DSR was (ICC=0.47, 95% CI=0.31-0.56). Intra and Inter-rater reproducibility were (0.65, 0.44) respectively. The overall reproducibility for bitewings was (ICC=0.45, 95% CI=0.42-0.57). Intra and Inter-rater reproducibility were (0.71, 0.46) respectively. Differences in the reproducibility across methods were not statistically significant. Significantly more lesions were scored as progressed using DSR. CONCLUSIONS The reproducibility of DSR in monitoring changes in approximal caries, is comparable to that of bitewings. Additionally, DSR detected higher proportion of progression than bitewing assessments.
Effect of Heat Treatment on the Anticancer Activity of Houttuynia cordata Thunb Aerial Stem Extract in Human Gastric Cancer SGC-7901 Cells

Abstract Gastric cancer is one of the most common malignant tumors in the world, and prevention through diet is one of the ways to control. Houttuynia cordata thunb. (HCT) is a plant having medicine and food function, has many biological properties. However, the effect of food style on the anticancer activity of HCT is not clear. So, we investigate the effect of heat treatment on anticancer activity of HCT. HCT extracts (heated aerial stem, heated subterraneous stem, heated leaves defined as HAS, HSS, HL, respectively, and not heated defined as NAS, NSS, NL, respectively) were obtained, and their inhibited activity were detected by alamar blue assay. The cell apoptosis was detected by DAPI staining and flow cytometry analysis. Western blot was performed to test the expression of apoptotic related protein. HCT showed the anticancer activity in four human tumor cell lines. Interestingly, heat treatment could increase the anticancer activity. In SCG-7901 cells, heat treatment increased anticancer activity of AS by 2-14 folds and induced apoptosis through regulating the intrinsic signaling pathways. Intriguingly, the caspase nine specific inhibitor blocked AS-reduced cell viability. Heat treatment increased the anticancer activity of HCT, and can be used as a dietary style for prevention of gastric cancer.
Spatiotemporal and spectral dynamics of multi‐item working memory as revealed by the n‐back task using MEG

Multi‐item working memory (WM) is a complex cognitive function thought to arise from specific frequency band oscillations and their interactions. While some theories and consistent findings have been established, there is still a lot of unclarity about the sources, temporal dynamics, and roles of event‐related fields (ERFs) and theta, alpha, and beta oscillations during WM activity. In this study, we performed an extensive whole‐brain ERF and time‐frequency analysis on n‐back magnetoencephalography data from 38 healthy controls. We identified the previously unknown sources of the n‐back M300, the right inferior temporal and parahippocampal gyrus and left inferior temporal gyrus, and frontal theta power increase, the orbitofrontal cortex. We shed new light on the role of the precuneus during n‐back activity, based on an early ERF and theta power increase, and suggest it to be a crucial link between lower‐level and higher‐level information processing. In addition, we provide strong evidence for the central role of the hippocampus in multi‐item WM behavior through the dynamics of theta and alpha oscillatory changes. Almost simultaneous alpha power decreases observed in the hippocampus and occipital fusiform gyri, regions known to be involved in letter processing, suggest that these regions together enable letter recognition, encoding and storage in WM. In summary, this study offers an extensive investigation into the spatial, temporal, and spectral characteristics of n‐back multi‐item WM activity.
Sorghum Malt-Based Weaning Food Formulations: Preparation, Functional Properties, and Nutritive Value

The high-volume/high-viscosity character of many commercially available weaning foods is a major constraint in providing children with enough calorie density. An attempt was made to formulate low-cost, nutritive but bulk-reduced weaning foods using sorghum malt, green gram malt, and sesame flour. The formulations thus prepared were evaluated for functional properties such as particle size, water absorption, dispersibility hot-paste and cold-paste viscosities, colour, and nutritive value with respect to calories, vitamin C, minerals, and available lysine. The ingredients showed variation in particle size: green gram malt was finer than sorghum malt, and sesame flour was much coarser. The laboratory formulations had finer particle size than a commercial sample. Green gram malt had a higher water-absorption capacity and a lower percentage of dispersibility in water than sorghum malt. The experimental formulations had lower water-absorption capacities and higher percentages of dispersibility than the commercial sample. The viscosities of 10% and 15% gruel concentrations of the experimental formulations were much lower than those of the commercial sample. CSH-I sorghum malt was darker than the other ingredients. Sensory evaluation found the experimental preparations to have good acceptability. A weaning food containing 60% sorghum malt, 30% green gram malt, and 10% sesame flour was found to have satisfactory functional characteristics and nutritive value and is recommended.
Critical function of circular RNAs in lung cancer

Lung cancer is one of the main causes of cancer‐related death in the world, especially due to its frequency and ineffective therapeutically approaches in the late stages of the disease. Despite the recent advent of promising new targeted therapies, lung cancer diagnostic strategies still have difficulty in identifying the disease at an early stage. Therefore, the characterizations of more sensible and specific cancer biomarkers have become an important goal for clinicians. Circular RNAs (circRNAs), a type of RNA with covalently closed continuous loop structures that display high structural resistance and tissue specificity pointed toward a potential biomarker role. Current investigations have identified that circRNAs have a prominent function in the regulation of oncogenic pathways, by regulating gene expression both at transcriptional and post‐transcriptional level. The aim of this review is to provide novel information regarding the implications of circRNAs in lung cancer, with an emphasis on the role in disease development and progression. Initially, we explored the potential utility of circRNAs as biomarkers, focusing on function, mechanisms, and correlation with disease progression in lung cancer. Further, we will describe the interaction between circRNAs and other non‐coding species of RNA (particularly microRNA) and their biological significance in lung cancer. Describing the nature of these interactions and their therapeutic potential will provide additional insight regarding the altered molecular landscape of lung cancer and consolidate the potential clinical value of these circular transcripts.
Looking Inside a Prototype Compact X-Ray Tube Comprising CNT-Based Cold Cathode and Transmission-Type Anode

In this article, we offer a look inside our prototype compact X-ray tube by reporting on our findings when we experimentally studied it. We studied the prototype experimentally to characterize its primary components, i.e., carbon nanotube (CNT)-based cold cathode, electrostatic lens and transmission-type anode, and to validate our previous simulation studies. We characterized the CNT-based cold cathode by studying the relationship between the electron emission current and its control parameter, electron extraction voltage. This relationship, commonly known as the current-voltage characteristic, showed an exponential-like nature that is expected from the Fowler-Nordheim model for field emission. Next, we characterized the electrostatic lens by studying the effects of lens voltage on the focal spot size. Their relationship showed a “V” trend and corroborated that we can control the focal spot size by controlling the lens voltage. We then characterized the transmission-type anode of the prototype by studying its output X-ray energy spectra at different anode voltages. We could control the highest and the mean X-ray energies generated from the transmission-type anode using the anode voltage. For the same anode voltage and aluminum filtration, when we compared the Xray energy spectrum generated from the transmission-type anode with that of the conventional reflection-type anode, we observed that the two energy spectra agreed with each other.