Miracle-dz/UniFAR-FTUs huggingface dataset:
Electroretinographic responses to luminance and cone-isolating white noise stimuli in macaques

Electroretinograms (ERGs) are mass potentials with a retinal origin that can be measured non-invasively. They can provide information about the physiology of the retina. Often, ERGs are measured to flashes that are highly unnatural stimuli. To obtain more information about the physiology of the retina, we measured ERGs with temporal white noise (TWN) stimuli that are more natural and keep the retina in a normal range of operation. The stimuli can be combined with the silent substitution stimulation technique with which the responses of single photoreceptor types can be isolated. We characterized electroretinogram (ERG) responses driven by luminance activity or by the L- or the M-cones. The ERGs were measured from five anesthetized macaques (two females) to luminance, to L-cone isolating and to M-cone isolating stimuli in which luminance or cone excitation were modulated with a TWN profile. The responses from different recordings were correlated with each other to study reproducibility and inter-individual variability. Impulse response functions (IRFs) were derived by cross-correlating the response with the stimulus. Modulation transfer functions (MTFs) were the IRFs in the frequency domain. The responses to luminance and L-cone isolating stimuli showed the largest reproducibility. The M-cone driven responses showed the smallest inter-individual variability. The IRFs and MTFs showed early (high frequency) components that were dominated by L-cone driven signals. A late component was equally driven by L- and M-cone activity. The IRFs showed characteristic similarities and differences relative to flash ERGs. The responses to TWN stimuli can be used to characterize the involvement of retinal cells and pathways to the ERG response. It can also be used to identify linear and non-linear processes.
A Moss 2-Oxoglutarate/Fe(II)-Dependent Dioxygenases (2-ODD) Gene of Flavonoids Biosynthesis Positively Regulates Plants Abiotic Stress Tolerance

Flavonoids, the largest group of polyphenolic secondary metabolites present in all land plants, play essential roles in many biological processes and defense against abiotic stresses. In the flavonoid biosynthesis pathway, flavones synthase I (FNSI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), and anthocyanidin synthase (ANS) all belong to 2-oxoglutarate/Fe(II)-dependent dioxygenases (2-ODDs) family, which catalyzes the critical oxidative reactions to form different flavonoid subgroups. Here, a novel 2-ODD gene was cloned from Antarctic moss Pohlia nutans (Pn2-ODD1) and its functions were investigated both in two model plants, Physcomitrella patens and Arabidopsis thaliana. Heterologous expression of Pn2-ODD1 increased the accumulation of anthocyanins and flavonol in Arabidopsis. Meanwhile, the transgenic P. patens and Arabidopsis with expressing Pn2-ODD1 exhibited enhanced tolerance to salinity and drought stresses, with larger gametophyte sizes, better seed germination, and longer root growth. Heterologous expression of Pn2-ODD1 in Arabidopsis also conferred the tolerance to UV-B radiation and oxidative stress by increasing antioxidant capacity. Therefore, we showed that Pn2-ODD1 participated in the accumulation of anthocyanins and flavonol in transgenic plants, and regulated the tolerance to abiotic stresses in plants, contributing to the adaptation of P. nutans to the polar environment.
Transitioning to sustainable healthy diets: A model-based and conceptual system thinking approach to optimized sustainable diet concepts in the United States

Food production and consumption are essential in human existence, yet they are implicated in the high occurrences of preventable chronic diseases and environmental degradation. Although healthy food may not necessarily be sustainable and vice versa, there is an opportunity to make our food both healthy and sustainable. Attempts have been made to conceptualize how sustainable healthy food may be produced and consumed; however, available data suggest a rise in the prevalence of health-related and negative environmental consequences of our food supply. Thus, the transition from conceptual frameworks to implementing these concepts has not always been effective. This paper explores the relative environmental and health risks associated with highly consumed food groups and develops a methodological workflow for evaluating the sustainability of diet concepts in the context of different health, socio-economic and environmental indicators. In addition, we apply the multi-criteria decision-making techniques (an integrated Analytic Hierarchy Process- Technique for order preference by similarity to ideal solution (AHP-TOPSIS) model) to examine the health and environmental impact of selected sustainable healthy diet concepts implemented in the United States. The principal findings indicate that adopting plant-based diet patterns would benefit the environment and the population's health. However, the up-scale, broad adoption and implementation of these concepts are hindered by critical bottlenecks. Hence we propose potential modification strategies through a conceptual system thinking approach to deliver optimized sustainable diet concepts to aid in the realization of the anticipated benefits of adoption/implementation.
The humidity level matters during the desiccation of Norway spruce somatic embryos

In Norway spruce, as in many other conifers, the germination capacity of somatic embryos is strongly influenced by the desiccation phase inserted after maturation. The intensity of drying during desiccation eminently affected the formation of emblings (i.e., seedlings developed from somatic embryos). Compared to non-desiccated embryos, the germination capacity of embryos desiccated at 100% relative humidity was about three times higher, but the reduction of relative humidity to 95 and 90% had a negative effect on the subsequent embryo development. The water loss observed in these embryos did not lead to an increase in lipid peroxidation, as shown by malondialdehyde levels. Another metabolic pathway in plants that mediates a response to abiotic stresses is directed toward the biosynthesis of polyamines (PAs). The activities of PA biosynthetic enzymes increased steadily in embryos during desiccation at 100% relative humidity, whereas they decreased at lower humidity. The total content of free PAs in the embryos gradually decreased throughout desiccation. The increase in free putrescine (Put) and perchloric acid-insoluble Put conjugates was observed in embryos desiccated at lower humidity. These changes were accompanied to some extent by the transcription of the genes for the PA biosynthesis enzymes. Desiccation at 100% relative humidity increased the activity of the cell wall-modifying enzymes β-1,3-glucanases and chitinases; the activities of these enzymes were also significantly suppressed at reduced humidity. The same pattern was observed in the transcription of some β-1,3-glucanase and chitinase genes. Desiccation treatments triggered metabolic processes that responded to water availability, suggesting an active response of the embryo to the reduction in humidity. A positive effect was demonstrated only for desiccation at high relative humidity. Some of the physiological characteristics described can be used as markers of inappropriate relative humidity during somatic embryo desiccation.
Assisted dying requests from people in detention: Psychiatric, ethical, and legal considerations–A literature review

The principle of equivalence of care states that prisoners must have access to the same standard of health care as the general population. If, as recent court decisions suggest, assisted dying is not limited to people with a terminal physical illness or irremediable suffering, it might also be requested by people with severe mental illness in detention. Some of the countries with legal regulations on assisted dying also have recommendations on how to handle requests from prisoners. However, detention itself can lead to psychological distress and suicidality, so we must consider whether and how people in such settings can make autonomous decisions. Ethical conflicts arise with regard to an individual's free will, right to life, and physical and personal integrity and to the right of a state to inflict punishment. Furthermore, people in prison often receive insufficient mental health care. In this review, we compare different practices for dealing with requests for assisted dying from people in prison and forensic psychiatric facilities and discuss the current ethical and psychiatric issues concerning assisted dying in such settings.
WNT4 overexpression and secretion in thymic epithelial tumors drive an autocrine loop in tumor cells in vitro

Background WNT4-driven non-canonical signaling is crucial for homeostasis and age-related involution of the thymus. Abnormal WNT signaling is important in many cancers, but the role of WNT signaling in thymic tumors is largely unknown. Materials & Methods Expression and function of WNT4 and FZD6 were analyzed using qRT–PCR, Western blot, ELISA, in biopsies of non-neoplastic thymi (NT), thymoma and thymic carcinomas. ShRNA techniques and functional assays were used in primary thymic epithelial cells (pTECs) and TC cell line 1889c. Cells were conventionally (2D) grown and in three-dimensional (3D) spheroids. Results In biopsy, WHO classified B3 thymomas and TCs showed increased WNT4 expression compared with NTs. During short-term 2D culture, WNT4 expression and secretion declined in neoplastic pTECs but not in 3D spheroids or medium supplemented with recombinant WNT4 cultures. Under the latter condition, the growth of pTECs was accompanied by increased expression of non-canonical targets RAC1 and JNK. Down-regulation of WNT4 by shRNA induced cell death in pTECs derived from B3 thymomas and led to decreased RAC1, but not JNK protein phosphorylation. Pharmacological inhibition of NF-κB decreased both RAC1 and JNK phosphorylation in neoplastic pTECs. Conclusions Lack of the age-related decline of non-canonical WNT4 expression in TETs and restoration of declining WNT4 expression through exogeneous WNT4 or 3D culture of pTECs hints at an oncogenic role of WNT4 in TETs and is compatible with the WNT4 autocrine loop model. Crosstalk between WNT4 and NF-κB signaling may present a promising target for combined interventions in TETs.
Pro-inflammatory cytokines in cystic glioblastoma: A quantitative study with a comparison with bacterial brain abscesses. With an MRI investigation of displacement and destruction of the brain tissue surrounding a glioblastoma

Cystic glioblastomas are aggressive primary brain tumors that may both destroy and displace the surrounding brain tissue as they grow. The mechanisms underlying these tumors’ destructive effect could include exposure of brain tissue to tumor-derived cytokines, but quantitative cytokine data are lacking. Here, we provide quantitative data on leukocyte markers and cytokines in the cyst fluid from 21 cystic glioblastomas, which we compare to values in 13 brain abscess pus samples. The concentration of macrophage/microglia markers sCD163 and MCP-1 was higher in glioblastoma cyst fluid than in brain abscess pus; lymphocyte marker sCD25 was similar in cyst fluid and pus, whereas neutrophil marker myeloperoxidase was higher in pus. Median cytokine levels in glioblastoma cyst fluid were high (pg/mL): TNF-α: 32, IL-6: 1064, IL-8: 23585, tissue factor: 28, the chemokine CXCL1: 639. These values were not significantly different from values in pus, pointing to a highly pro-inflammatory glioblastoma environment. In contrast, levels of IFN-γ, IL-1β, IL-2, IL-4, IL-10, IL-12, and IL-13 were higher in pus than in glioblastoma cyst fluid. Based on the quantitative data, we show for the first time that the concentrations of cytokines in glioblastoma cyst fluid correlate with blood leukocyte levels, suggesting an important interaction between glioblastomas and the circulation. Preoperative MRI of the cystic glioblastomas confirmed both destruction and displacement of brain tissue, but none of the cytokine levels correlated with degree of brain tissue displacement or peri-tumoral edema, as could be assessed by MRI. We conclude that cystic glioblastomas are highly pro-inflammatory environments that interact with the circulation and that they both displace and destroy brain tissue. These observations point to the need for neuroprotective strategies in glioblastoma therapy, which could include an anti-inflammatory approach.
Extending Output Attentions in Recurrent Neural Networks for Dialog Generation

A BSTRACT In natural language processing, attention mechanism in neural networks are widely utilized. In this paper, the research team explore a new mechanism of extending output attention in recurrent neural networks for dialog systems. The new attention method was compared with the current method in generating dialog sentence using a real dataset. Our architecture exhibits several attractive properties such as better handle long sequences and, it could generate more reasonable replies in many cases
The Assessment of Social Determinants of Health in Postsepsis Mortality and Readmission: A Scoping Review

OBJECTIVE: To summarize knowledge and identify gaps in evidence about the relationship between social determinants of health (SDH) and postsepsis outcomes. DATA SOURCES: We conducted a comprehensive search of PubMed/Medical Literature Analysis and Retrieval System Online, Excerpta Medica database, and the Cochrane Library. STUDY SELECTION: We identified articles that evaluated SDH as risk factors for mortality or readmission after sepsis hospitalization. Two authors independently screened and selected articles for inclusion. DATA EXTRACTION: We dual-extracted study characteristics with specific focus on measurement, reporting, and interpretation of SDH variables. DATA SYNTHESIS: Of 2,077 articles screened, 103 articles assessed risk factors for postsepsis mortality or readmission. Of these, 28 (27%) included at least one SDH variable. Inclusion of SDH in studies assessing postsepsis adverse outcomes increased over time. The most common SDH evaluated was race/ethnicity (n = 21, 75%), followed by payer type (n = 10, 36%), and income/wealth (n = 9, 32%). Of the studies including race/ethnicity, nine (32%) evaluated no other SDH. Only one study including race/ethnicity discussed the use of this variable as a surrogate for social disadvantage, and none specifically discussed structural racism. None of the studies specifically addressed methods to validate the accuracy of SDH or handling of missing data. Eight (29%) studies included a general statement that missing data were infrequent. Several studies reported independent associations between SDH and outcomes after sepsis discharge; however, these findings were mixed across studies. CONCLUSIONS: Our review suggests that SDH data are underutilized and of uncertain quality in studies evaluating postsepsis adverse events. Transparent and explicit ontogenesis and data models for SDH data are urgently needed to support research and clinical applications with specific attention to advancing our understanding of the role racism and racial health inequities in postsepsis outcomes.
Genomics of viruses infecting green and purple sulfur bacteria in two euxinic lakes

Viral infections of marine bacteria modulate the rates of primary production and the cycling of organic and inorganic matter in the world’s oceans. Here, we investigated the hypothesis that viral infections influence the ecology of purple and green sulfur bacteria (PSB and GSB) in anoxic and sulfidic (euxinic) lakes, modern analogs of early Earth oceans. Over 200 high and medium quality viral contigs were identified in long-read metagenomes from the sediments and water column of Lime Blue and Poison Lake, respectively. We compared these sequences with 94 predicted prophages identified in the complete genomes of PSB (n = 213) and GSB (n = 33). Viral genomes carrying psbA, encoding the small subunit of photosystem II protein, were present in all three datasets (sediment, water column, and complete genomes). The ubiquity of these genes suggests that PSB and GSB viruses interfere with the light reactions of sulfur-oxidizing autotrophs in a process similar to viral modulation of photosynthesis in Cyanobacteria. Viruses predicted to infect PSB and GSB also encoded auxiliary metabolic genes involved in reductive sulfur assimilation as cysteine, a pathway not yet described in these sulfur bacteria, as well as genes involved in pigment production (crtF) and carbon fixation (CP12, zwf, PGD). These observations highlight the potential for viral modulation of metabolic markers used as proxies to interpret biogeochemical processes in early Earth oceans.
Comparative study between Urinary Neutrophil gelatinase-associated lipocalin (NGAL) and Calprotectin for Early Detection of Acute Kidney Injury among Drug Abuse Intoxicated Cases

Background: Drug addiction is major societal problem all over the world that associated with acute kidney injury (AKI). The impact of urinary neutrophil gelatinase-associated lipocalin (NGAL) and Calprotectin on the early diagnosis of AKI have been investigated, yet no earlier comprehensive studies had been conducted in their impact among drug abuse. Aim of the Work : This work aimed to evaluate the role of urinary NGAL and Calprotectin in predicting AKI among drug abuse intoxicated cases admitted to Poison control Center Ain Shams University Hospitals (PCCASUH). To compare the accuracy of urinary NGAL and calprotectin in the diagnosis of AKI. Materials and Methods: A prospective observational study was performed on 75 patients, who were presented to (PCCASUH) with acute drug abuse toxicity from September 2018 to March 2019. Blood and urine samples were collected from all patients on the 1 st , and 3 rd day of admission. Urine NGAL and Calprotectin were assessed and compared between patients who developed AKI and who didn’t. Results: 75 patients included in the study, 20 developed AKI. At 1 st day of admission, the mean urinary NGAL and urinary calprotectin were significantly elevated among AKI group. In third day of admission there were further significant elevation. ROC curve analysis revealed that NGAL developed sensitivity of 93.0% and a specificity of 83.0% whereas urinary calprotectin developed a sensitivity of 88.4% and a specificity of 96% Conclusion and recommendations: Our findings deduced that urinaryNGAL and urinarycalprotectin levels significantly elevate in acute drug abuse intoxication cases who developed AKI for up to 72 hours of hospitalization, hence it may be regarded as an early predictors of AKI and Calprotectin could be considered more accurate. It is recommended that, all acute drug abuse intoxicated patients a urinary NGAL and Calprotectin should be done for early exclusion of AKI that could be complicating.
Neural tracking of speech does not unequivocally reflect intelligibility

During listening, brain activity tracks the rhythmic structures of speech signals. Here, we directly dissociated the contribution of neural tracking in the processing of speech acoustic cues from that related to linguistic processing. We examined the neural changes associated with the comprehension of Noise-Vocoded (NV) speech using magnetoencephalography (MEG). Participants listened to NV sentences in a 3-phase training paradigm: (1) pre-training, where NV stimuli were barely comprehended, (2) training with exposure of the original clear version of speech stimulus, and (3) post-training, where the same stimuli gained intelligibility from the training phase. Using this paradigm, we tested if the neural responses of a speech signal was modulated by its intelligibility without any change in its acoustic structure. To test the influence of spectral degradation on neural tracking independently of training, participants listened to two types of NV sentences (4-band and 2-band NV speech), but were only trained to understand 4-band NV speech. Significant changes in neural tracking were observed in the delta range in relation to the acoustic degradation of speech. However, we failed to find a direct effect of intelligibility on the neural tracking of speech in both theta and delta ranges. This suggests that acoustics greatly influence the neural tracking response to speech signals, and that caution needs to be taken when choosing the control signals for speech-brain tracking analyses, considering that a slight change in acoustic parameters can have strong effects on the neural tracking response.
Light sources and diagnostic systems currently used in photodynamic therapy

The work on photodiagnosis and photodynamic therapy focuses on therapeutic light sources and diagnostic systems applicable to detection of fluorophores in an organism as well as to the monitoring of photodynamic therapy (PDT) parameters. Optoelectronic devices employed in this method are being still improved and adapted for application in clinics. The paper presents currently available light sources used for treatment of various human organs and new designs of photodiagnostic apparatus. Also, our own designs of imaging systems and fibre fluorescence analysers are shown.
A novel automated depression detection technique using text transcript

Depression is one of the most common mental illnesses, impacting billions of people worldwide. The lack of existing resources is impeding the country's economic prosperity. As a result, new approaches for detecting and treating mental diseases as well as reaching out to individuals are required so that people can overcome their daily challenges and become more productive. An automated depression detection system can greatly aid in clinical findings and early treatment of depression. Automatic detection, like in a clinical interview can be derived from various modalities that include video, audio, and text. Among these modalities, audio characteristics are the most commonly researched while text elements are seldom investigated. In the light of the above, this paper proposes a novel automated depression identification approach based on linguistic material gathered from patient interviews. The focus is to enhance both the accuracy and efficiency of detection. The proposed approach is made up of two parts: a Bidirectional Gated Recurrent Unit (BGRU) network for dealing with linguistic information and a fully coupled network that integrates the model outputs to measure the depressed state. The proposed approach is validated using Distress Analysis Interview Corpus‐Wizard‐of‐Oz interviews dataset. To evaluate the performance precision, recall, and F1 score are computed using the proposed approach and then the comparative analysis is done with the existing approaches. The proposed approach yielded an F1 score of 0.92, indicating the existence of depression as well as the projected severity level. It is realized from the generated results that the proposed approach has outperformed the previous ones. The proposed approach can not only automatically assess the severity of depression but also enhances both the accuracy and efficiency of detection. The proposed approach indicates the feasibility of BGRU over Long Short Term Memory by achieving exceptional results for recognition of depression.