Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution shapes govern the discovery of predictive models for gene regulation

Significance Systems biology seeks to combine experiments with computation to predict biological behaviors. However, despite tremendous data and knowledge, biological models make less-accurate predictions compared with other fields. By analyzing single-cell, single-molecule measurements of mRNA during yeast stress response, we explore why and how the shapes of experimental distributions control prediction accuracy. We show how asymmetric data distributions with long tails cause standard modeling approaches to yield excellent fits but make meaningless predictions. We show how these biases arise from the violation of fundamental assumptions in standard modeling approaches. We demonstrate how advanced computational tools solve this dilemma and achieve predictive understanding of spatiotemporal mechanisms of transcription control including RNA polymerase initiation and elongation and mRNA accumulation, transport, and decay. Despite substantial experimental and computational efforts, mechanistic modeling remains more predictive in engineering than in systems biology. The reason for this discrepancy is not fully understood. One might argue that the randomness and complexity of biological systems are the main barriers to predictive understanding, but these issues are not unique to biology. Instead, we hypothesize that the specific shapes of rare single-molecule event distributions produce substantial yet overlooked challenges for biological models. We demonstrate why modern statistical tools to disentangle complexity and stochasticity, which assume normally distributed fluctuations or enormous datasets, do not apply to the discrete, positive, and nonsymmetric distributions that characterize mRNA fluctuations in single cells. As an example, we integrate single-molecule measurements and advanced computational analyses to explore mitogen-activated protein kinase induction of multiple stress response genes. Through systematic analyses of different metrics to compare the same model to the same data, we elucidate why standard modeling approaches yield nonpredictive models for single-cell gene regulation. We further explain how advanced tools recover precise, reproducible, and predictive understanding of transcription regulation mechanisms, including gene activation, polymerase initiation, elongation, mRNA accumulation, spatial transport, and decay.
Reconciling Social Norms With Personal Interests: Indigenous Styles of Identity Formation Among Pakistani Youth

Research on identity formation has been conducted mostly in Western contexts. We extend and complement such research by exploring qualitatively the strategies and styles of identity formation employed by emerging adults in Pakistan. Whereas Western theories of identity formation often provide a negative view of normative orientation as “blind obedience” without exploring alternatives, our thematic analysis of semistructured interviews with 12 Pakistani emerging adults suggests a much more complex interplay between personal interests and normative influences on identity formation. Participants described various ways of reconciling normative expectations (parental, religious, and cultural) with their personal interests, preferences, and explorations, when deciding about their careers, relationships, and values. In Pakistani culture, normative influences seem to play a more positive and flexible role in identity formation than is suggested by previous Western research.
Sleep Quality and Quantity in Intensive Care Unit Patients: A Cross-sectional Study

Introduction: Lack of restorative sleep and altered sleep-wake cycle is a frequent problem among patients admitted to the Intensive Care Unit (ICU). This study was conducted to estimate the prevalence of poor sleep and patient's perspective of factors governing poor sleep in the ICU. Materials and Methods: A cross-sectional study was performed in medical ICU of a tertiary care hospital. A total of 32 patients admitted to the ICU for at least 24 h were recruited. A 72-h actigraphy was done followed by a subjective assessment of sleep quality by the Richards-Campbell Sleep Questionnaire (RCSQ). Patient's perspective of sleep quality and quantity and possible risk factors for poor sleep were recorded. Results: Poor sleep (defined as RCSQ <50, sensitivity 88% and specificity 87%) was found in 15 out of the 32 patients (47%). The prevalence of poor sleep was higher among patients on mechanical ventilation (n = 15) (66.7% vs. 33.3%, P < 0.05). Patients with poor sleep had higher age (median age [in years] 42.8 vs. 31.4, P = 0.008), acute physiology, and chronic health evaluation II score (mean 14 ± 5.15 vs. 9.3 ± 5.64, P = 0.02), SAPS 3 score (62.7 ± 8.9 vs. 45.6 ± 10.5, P ≤ 0.0001), and worse actigraphy parameters. Only 55.63% of total sleep time was in the night (2200–0600). All patients had discomfort from indwelling catheters and suctioning of endotracheal tubes. All patients suggested that there be a minimum interruption in the sleep for interventions or medications. Conclusion: There is a high prevalence of poor sleep among patients admitted to the ICU. There is a dire need to minimize untimely interventions and design nonpharmacological techniques to allow patients to sleep comfortably.
Gelidiella acerosa Exhibits Neuroprotective Effect Against Amyloid Beta 25–35 Peptide–Induced Toxicity in PC12 Cells

ABSTRACT Alzheimer's disease (AD) is a progressive neurodegenerative disorder with multiple pathological consequences such as oxidative stress, inflammation, apoptosis, cholinergic deficit, amyloid plaques, and tangles formation. Hence, development of drugs with multiple targets will be effective in the treatment of AD. The present study aims at evaluation of the neuroprotective effect of Gelidiella acerosa against amyloid beta 25–35 (Aβ 25–35) induced toxicity in PC12 cells. The antioxidative effect was evaluated by monitoring levels of antioxidant enzymes. Protection against ROS-induced damage was assessed by the measurement of lipid peroxidation, protein carbonyl content (PCC), 2′,7′–dichlorofluorescein diacetate (DCFH-DA) fluorescence, and nitric oxide (NO) production. The cholinesterase (ChE) inhibitory activity was also evaluated. The antiapoptotic activity was verified by caspase-3 activity. The results of antioxidant assays suggest that G. acerosa significantly (P < .05) restores the levels of antioxidant enzymes. Moreover, the seaweed extract was found to prevent the formation of intracellular ROS induced by Aβ 25–35 and thereby protects PC12 cells from macromolecular damage. The study demonstrated that G. acerosa inhibits ChE activity significantly (P < .05) in PC12 cells. The significant decrease (P < .05) in the level of caspase-3 activity indicates that the seaweed has anti-apoptotic activity. Hence, the outcome of this study signifies the neuroprotective effect of G. acerosa targeting multiple pathological consequences of AD.
Polypharmacy among the Elderly

Introduction: Older people are at risk for polypharmacy due to multiple chronic diseases. Considering the lack of information in this regard, the aim of this study was to investigate the state of polypharmacy among the elderly in the city of Amirkola in northern part of Iran. Materials and Methods: This descriptive/analytical cross-sectional study is a part of Amirkola Health and Aging Project that was conducted on 1616 individuals aged 60 years and over. The data about medications were gathered through interviews and observation of prescriptions and medications consumed by patients. The data were analyzed by SPSS software version 18, and P ≤ 0.05 was regarded significant. Results: In this study, 1616 individuals including 883 men (54.6%) and 733 women (45.3%) were investigated. The average age of individuals was 69.37 ± 7.42. Among the investigated individuals, 526 including 368 men (41.7%) and 158 women (21.6%) consumed no medications. The prevalence of polypharmacy in this study was 23.1%, which was 32.7% in women and 15.2% in men (odds ratio = 1.51, 95% confidence interval: 1.10–1.93). The most prevalent group of medications used in both genders was cardiovascular drugs. Conclusions: Regarding the considerable prevalence of polypharmacy among the elderly, especially in aged women, serious efforts are required to manage polypharmacy. Provision of educational programs for physicians, personnel of pharmacies, and the staff of health-care centers in order for appropriate and safe consumption of medications in aged people is absolutely necessary.
Tracking the Within-Trial, Cross-Trial, and Developmental Dynamics of Cognitive Control: Evidence From the Simon Task.

Six- to 8-year-olds, 10- to 12-year-olds, and adults (N = 108) performed the Simon task by reaching to targets on a digital display. The spatial and temporal characteristics of their movements were used to assess how two key processes underlying cognitive control-a threshold adjustment process and a controlled selection process-unfold over the course of a response (within-trial dynamics), are modulated by recent experience (cross-trial dynamics), and contribute to age-related gains in control (developmental dynamics). The results indicate that the controlled selection process undergoes a more protracted development than the threshold adjustment process. The results also shed light on a prominent debate concerning the cross-trial dynamics of control by supporting the feature integration account over the conflict adaptation account.
Bioactive Materials: A Short Review

In every field of dentistry and medicine, bioactive materials have been widely used. These materials are used for regeneration, repair, and reconstruction in the field of conservative dentistry and endodontics. These materials are used in different forms and composition and act directly on vital tissue, helping in its healing and repair. These materials directly function because of induction of various growth factors and different cells. This article summarizes the types and uses of bioactive materials.
The Arabidopsis Calcium-Dependent Protein Kinases (CDPKs) and Their Roles in Plant Growth Regulation and Abiotic Stress Responses

As a ubiquitous secondary messenger in plant signaling systems, calcium ions (Ca2+) play essential roles in plant growth and development. Within the cellular signaling network, the accurate decoding of diverse Ca2+ signal is a fundamental molecular event. Calcium-dependent protein kinases (CDPKs), identified commonly in plants, are a kind of vital regulatory protein deciphering calcium signals triggered by various developmental and environmental stimuli. This review chiefly introduces Ca2+ distribution in plant cells, the classification of Arabidopsis thaliana CDPKs (AtCDPKs), the identification of the Ca2+-AtCDPK signal transduction mechanism and AtCDPKs’ functions involved in plant growth regulation and abiotic stress responses. The review presents a comprehensive overview of AtCDPKs and may contribute to the research of CDPKs in other plants.
Relationships Amongst Aggression, Self-Theory, Loneliness, and Depression in Emerging Adults

The purpose of this study was to examine the relationships amongst aggression, self-theory, loneliness, and depression. The study group consisted of 904 student volunteers from various undergraduate programs of a university in Central Anatolia. Simple and hierarchical multiple linear regression analyses, as well as t-tests, were used to analyze the data. In the preliminary analysis performed, females’ depression levels and males’ aggression levels are higher. The study findings revealed that self-theory negatively and significantly predicted aggression, whereas loneliness and depression positively and significantly predicted aggression in emerging adulthood. Another important finding showed that both direct and indirect relationships exist between self-theory and aggression. According to these findings, loneliness and depression play partially mediating roles individually, and fully mediating roles together, with regard to the relationship between self-theory and aggression.
Lutein and Zeaxanthin Isomers Protect against Light-Induced Retinopathy via Decreasing Oxidative and Endoplasmic Reticulum Stress in BALB/cJ Mice

Oxidative stress (OS) and endoplasmic reticulum stress (ERS) are the major factors underlying photoreceptor degeneration. Lutein, RR-zeaxanthin (3R,3’R-zeaxanthin) and RS (meso)-zeaxanthin (3R,3’S-RS- zeaxanthin) (L/Zi) could protect against cell damage by ameliorating OS in retina. In this study, we examined the effect of L/Zi supplementation in a mouse model of photoreceptor degeneration and investigated whether the treatment of L/Zi ameliorated OS and ERS. BALB/cJ mice after light exposure were used as the animal model. The protective effects of L/Zi were observed by electroretinography (ERG) and terminal deoxyuridine triphosphate nick-end labeling (TUNEL) analysis. The underlying mechanisms related to OS and ERS were explored by Western blotting. After L/Zi treatment, the ERG amplitudes were significantly higher, and the number of TUNEL-positive cells was significantly reduced compared to that of the vehicle group. Western blotting results revealed that OS was ameliorated according to the significant downregulation of phosphorylated c-Jun N-terminal kinase (p-JNK), and significant upregulation of nuclear factor erythroid 2-related factor 2 (Nrf2). In addition, ERS was reduced according to the significant downregulation of 78 kDa glucose-regulated protein (GRP78), phosphorylated protein kinase RNA-like endoplasmic reticulum kinase (p-PERK), activating transcription factor 4 (ATF4) and activating transcription factor (ATF6). Our data shows that L/Zi provided functional and morphological preservation of photoreceptors against light damage, which is probably related to its mitigation of oxidative and endoplasmic reticulum stress.
Rosacea‐like demodicosis (but not primary demodicosis) and papulopustular rosacea may be two phenotypes of the same disease – a microbioma, therapeutic and diagnostic tools perspective

The scope of their research appears to be limited to the effects of Demodex spp in rosacea and thus does not consider possible confounding factors such as the effects of Bacillus oleronius, which has been isolated from Demodex folliculorum and been identified as a trigger of inflammation in rosacea(2). Other endosymbionts described as related to Demodex are:I.Bacillus simplex, which was isolated from Demodex folliculorum in a patient with primary demodicosis(3) II. Bacillus pumilus positive culture and mass spectrometry were found in a patient with rosacea and D. Folliculorum(4)III.Bacillus cereus, instead of B. oleronius was identified in a patient with secondary demodicosis associated with steroid-induced rosacea-like facial dermatitis in one positive culture. (5) Would they care to comment on this? This article is protected by copyright. All rights reserved.
Shear Elasticity of Magnetic Gels with Internal Structures

We present the results of the theoretical modeling of the elastic shear properties of a magnetic gel, consisting of soft matrix and embedded, fine magnetizable particles, which are united in linear chain-like structures. We suppose that the composite is placed in a magnetic field, perpendicular to the direction of the sample shear. Our results show that the field can significantly enhance the mechanical rigidity of the soft composite. Theoretical results are in quantitative agreement with the experiments.
A New Context-Sensitive Decision Making System for Mobile Cloud Offloading

Recently, with the rapid spread use of mobile devices, some problems have begun to emerge. The most important of these are that the mobile devices batteries’ life may be short and that these devices may be in some cases. The complex tasks that must be addressed to solve such problems on mobile devices can be transferred to the cloud environment when appropriate conditions are met. The decision to offload to the cloud environment at this stage is very important. In this thesis, a context-aware decision-making system has been developed for offloading to cloud environments. Unlike similar tasks, the processes determined for transfer to the cloud are not run randomly, but rather according to the mobile user's application usage habits. The developed system was implemented in a real environment for one month. According to the results, it was determined that processes transferred to the cloud were completed in less time and consumed less energy.
Structure Based Prediction of Asparagine Deamidation Propensity in Monoclonal Antibodies

ABSTRACT Identification of asparagine (Asn) sites that are prone to deamidation is critical for the development of therapeutic monoclonal antibodies (mAbs). Despite a common chemical degradation pathway, the rates of Asn deamidation can vary dramatically among different sites, and prediction of the sensitive deamidation sites is still challenging. In this study, characterization of Asn deamidation for five IgG1 and five IgG4 mAbs under both normal and stressed conditions revealed dramatic differences in the Asn deamidation rates. A comprehensive analysis of the deamidation sites indicated that the deamidation rate differences could be explained by differences in the local structure conformation, structure flexibility and solvent accessibility. A decision tree was developed to predict the deamidation propensity for all Asn sites in IgG mAbs based on the analysis of these three structural parameters. This decision tree will allow potential Asn deamidation hot spots to be identified early in development.
Assessment of Commercially Available Immunoassays to Measure Glucocorticoid Metabolites in African Grey Parrot (Psittacus Erithacus) Droppings: A Ready Tool for Non-Invasive Monitoring of Stress

Simple Summary The African Grey Parrot is a very popular bird commonly found in zoological collections. However, captivity can prevent it from meeting its natural needs and so become an ongoing stressor, leading sometimes to clinical and/or behavioral disorders. Non-invasive forms of stress assessment are of definite interest for monitoring welfare in captive bird populations. One notable stress outcome is the excretion of glucocorticoid metabolites (from the stress hormone corticosterone) in droppings. The aim of this study was to carefully assess methods of glucocorticoid metabolites extraction and measurement in droppings from African Grey Parrots. Several extraction and enzyme immunoassays procedures were tested, based on the evaluation of analytical quality parameters and biological relevance. The best procedure was found to be a combination of a 60% methanol extraction with the use of a commercial corticosterone enzyme immunoassay. To determine whether this method was suitable for assessing different stress levels, a significant correlation with another reliable stress marker in birds, the Heterophil: Lymphocyte Ratio, was evidenced. This method can thus be used to evaluate stress in African Gray Parrots in a non-invasive way and help to monitor their welfare in zoo populations for instance. Abstract Despite being undomesticated, African Grey Parrots (Psittacus erithacus) are commonly found in captivity, in zoos or as pets. Captivity can be an ongoing stressor. Non-invasive glucocorticoid metabolites (GCM) measurements from bird droppings are of interest for assessing stress but require careful evaluation in each newly studied species. This study describes the assessment of such methods for Psittacus erithacus to provide tools for evaluating stress and monitoring welfare. We evaluated 12 method combinations of GCM extraction and enzyme immunoassay (EIA) from a pool of African Grey Parrot droppings, through the validation of several analytical parameters. Then, Heterophil: Lymphocyte Ratios (HLR), another reliable stress marker, were determined and correlated to individual dropping GCM concentrations for 29 birds to determine whether the method is biologically relevant. We found that the best procedure to measure GCM in African Grey Parrot droppings is a combination of 60% methanol extraction measured using a Corticosterone EIA kit (Cayman Chemical Company) from fresh or dry droppings. The establishment of a significant correlation (Pearson coefficient correlation = 0.48; p = 0.0082) between HLR and GCM in the studied population confirmed the method biological relevance. This method can thus be applied to assess stress in Psittacus erithacus and support welfare monitoring in zoo populations.
Methods for the Real-World Evaluation of Fall Detection Technology: A Scoping Review

Falls in older adults present a major growing healthcare challenge and reliable detection of falls is crucial to minimise their consequences. The majority of development and testing has used laboratory simulations. As simulations do not cover the wide range of real-world scenarios performance is poor when retested using real-world data. There has been a move from the use of simulated falls towards the use of real-world data. This review aims to assess the current methods for real-world evaluation of fall detection systems, identify their limitations and propose improved robust methods of evaluation. Twenty-two articles met the inclusion criteria and were assessed with regard to the composition of the datasets, data processing methods and the measures of performance. Real-world tests of fall detection technology are inherently challenging and it is clear the field is in its infancy. Most studies used small datasets and studies differed on how to quantify the ability to avoid false alarms and how to identify non-falls, a concept which is virtually impossible to define and standardise. To increase robustness and make results comparable, larger standardised datasets are needed containing data from a range of participant groups. Measures that depend on the definition and identification of non-falls should be avoided. Sensitivity, precision and F-measure emerged as the most suitable robust measures for evaluating the real-world performance of fall detection systems.
A questionnaire-based analysis of parental perspectives on pediatric cochlear implant (CI) re/habilitation services: a pilot study from a developing CI service in India

Objective: To study parental perspectives on re/habilitation services offered for pediatric cochlear implant (CI) users at a non-profit organization in India. Methodology: A non-standardized questionnaire comprising 46 items was created to understand perspectives of parents of pediatric CI users. Questions were designed to examine re/habilitation services from the angles of service delivery, parental stress levels, reasons for delay in obtaining services, sources of emotional support, concerns, and fears during each stage starting from diagnosis of hearing loss to CI surgery, re/habilitation services and parents’ views of their children post-CI. The questionnaire was posed to 30 parents and responses were recorded and coded. Results and discussion: Qualitative and quantitative analyses based on parents’ responses identified several factors that significantly influenced parental perspectives during each stage. The major factors delaying the decision to go for CI included a fear of surgery, lack of funds for CI and the subsequent re/habilitation process, and limited knowledge. Key concerns were the child’s academic performance and social acceptance. Familial support played an important role during each stage. A significant reduction in the parental stress levels was observed following CI surgery. Parents indicated that local support for therapy, financial assistance and better guidance at each stage would substantially help in lowering stress levels. Conclusions: The parental perspectives analyzed in this study can be utilized towards improving the quality of service delivery in terms of parental satisfaction and outcomes post-CI. Efforts should be taken to improve parental awareness, funding options, and access to re/habilitation services and social networks connecting similar parents.