Miracle-dz/UniFAR-FTUs huggingface dataset:
The surgical anxiety questionnaire (SAQ): development and validation

Abstract Objective: Preoperative anxiety is often assessed using general anxiety measures; existing specific measures might lack content coverage and/or are not psychometrically validated. This study aimed to develop a new self-report measure of surgery-specific anxiety and test its psychometric properties. Design: The surgical anxiety questionnaire (SAQ) was developed from themes identified in qualitative research and reviewed by an interdisciplinary expert team. It was administered preoperatively to 135 patients (56% female, mean age 51) on the day of surgery alongside additional measures of preoperative anxiety, state anxiety, perceived stress, depression and social desirability. Follow-up assessment was conducted immediately post-surgery and two weeks post-surgery (n = 114) to examine recovery and predictive validity of the scale. Results: Factor analysis revealed a three component structure, including: concerns about health (six items), concerns about recovery (four items) and concerns about procedures (four items). Three additional items of relatively high concern were retained in the total score (17 items). The SAQ displayed good reliability, validity (content, construct and predictive) and adequate overall psychometric properties. Conclusions: Preliminary results suggest that the SAQ is a promising tool for measuring preoperative anxiety and predicting recovery. Recommendations for future research include employing a confirmatory factor analysis and examining test-retest reliability.
Program comprehension through reverse‐engineered sequence diagrams: A systematic review

Reverse engineering of sequence diagrams refers to the process of extracting meaningful information about the behavior of software systems in the form of appropriately generated sequence diagrams. This process has become a practical method for retrieving the behavior of software systems, primarily those with inadequate documentation. Various approaches have been proposed in the literature to produce from a given system a series of interactions that can be used for different purposes. The reason for such diversity of approaches is the need to offer sequence diagrams that can cater for the users' specific goals and needs, which can vary widely depending on the users' perception and understandability of visual representations and the target application domains. In this paper, we systematically review existing techniques in this context while focusing on their distinct purposes and potentials of providing more understandable sequence diagrams. In addition, a qualitative evaluation of such techniques is conducted to expose their adequacy and applicability for effective program comprehension. Finally, we list a set of possible extensions to the unified modeling language sequence diagram standard that we anticipate will enhance its versatility and understandability of program control flow, followed by a number of concluding remarks.
Transgenerational Effects and Epigenetic Memory in the Clonal Plant Trifolium repens

Transgenerational effects (TGE) can modify phenotypes of offspring generations playing thus a potentially important role in ecology and evolution of many plant species. These effects have been studied mostly across generations of sexually reproducing species. A substantial proportion of plant species are however reproducing asexually, for instance via clonal growth. TGE are thought to be enabled by heritable epigenetic modification of DNA, although unambiguous evidence is still scarce. On the clonal herb white clover (Trifolium repens), we tested the generality of clonal TGE across five genotypes and five parental environments including soil contamination and above-ground competition. Moreover, by genome wide-methylation variation analysis we explored the role of drought, one of the parental environments that triggered the strongest TGE. We tested the induction of epigenetic changes in offspring generations using several intensities and durations of drought stress. We found that TGE of different environments were highly genotype specific and all tested environments triggered TGE at least in some genotypes. In addition, parental drought stresses triggered epigenetic change in T. repens and most of the induced epigenetic change was maintained across several clonal offspring generations. We conclude that TGE are common and genotype specific in clonal plant T. repens and potentially under epigenetic control.
Investigations on the mechanism of progesterone in inhibiting endometrial cancer cell cycle and viability via regulation of long noncoding RNA NEAT1/microRNA‐146b‐5p mediated Wnt/β‐catenin signaling

Progesterone is often used to protect the endometrium and prevent endometrial cancer. An intensive study on its molecular mechanism in endometrial cancer would contribute to the development of more promising therapies. Relevant lncRNAs and mRNAs expression data in endometrial cancer cell line Ishikawa pretreated and post‐treated with progesterone were derived from Gene Expression Omnibus (accession no. GSE29435), and then we analyzed long noncoding RNAs and mRNAs with differential expressions in two different conditions. The Cytoscape software, TargetScan, miRanda, and Human microRNA Disease Database (HMDD) websites were employed. Gene set enrichment analysis (GSEA) was used to determine related Kyoto Encyclopedia of Genes and Genomes pathways alteration in Ishikawa cells treated with progesterone. In addition to bioinformatics analysis, Reverse Transcription‐Polymerase Chain Reaction (RT‐PCR), Western blot, and dual‐luciferase reporter assays were performed. The impact of progesterone on cell propagation and cell cycle was testified by colony formation and flow cytometry analysis. LncRNA nuclear enriched abundant transcript 1 (NEAT1) was the most significantly downregulated lncRNA in endometrial cancer cells treated with progesterone. Lymphoid enhancing factor 1 (LEF1) was positively associated with NEAT1, and eventually hsa_miR‐146b‐5p was validated to target both LEF1 and NEAT1. Wnt/β‐catenin signaling pathway was identified to involve in endometrial cancer. NEAT1 or LEF1 was overexpressed in endometrial cancer cells while downregulated following post‐treatment with progesterone. Conversely, miR‐146b‐5p was notably decreased in Ishikawa cells while upregulated after treatment with progesterone. Downstream gene c‐myc or MMP9 regulated by upstream gene LEF1 in Wnt/β‐catenin signaling pathway was remarkably increased in Ishikawa cells and positively related with NEAT1. Progesterone inhibited cell cycle and viability through regulating NEAT1/miR‐146b‐5p axis via Wnt/β‐catenin signaling pathway. Progesterone exerted suppressive influence on endometrial cancer progression via regulation of lncRNA NEAT1/miR‐146b‐5p‐mediated Wnt/β‐catenin signaling pathway, which might reveal new strategies for developing more effective therapeutics. © 2018 IUBMB Life, 71(1):223–234, 2019
Discriminating Alzheimer's disease progression using a new hippocampal marker from T1‐weighted MRI: The local surface roughness

Hippocampal atrophy is one of the main hallmarks of Alzheimer's disease (AD). However, there is still controversy about whether this sign is a robust finding during the early stages of the disease, such as in mild cognitive impairment (MCI) and subjective cognitive decline (SCD). Considering this background, we proposed a new marker for assessing hippocampal atrophy: the local surface roughness (LSR). We tested this marker in a sample of 307 subjects (normal control (NC) = 70, SCD = 87, MCI = 137, AD = 13). In addition, 97 patients with MCI were followed‐up over a 3‐year period and classified as stable MCI (sMCI) (n = 61) or progressive MCI (pMCI) (n = 36). We did not find significant differences using traditional markers, such as normalized hippocampal volumes (NHV), between the NC and SCD groups or between the sMCI and pMCI groups. However, with LSR we found significant differences between the sMCI and pMCI groups and a better ability to discriminate between NC and SCD. The classification accuracy of the LSR for NC and SCD was 68.2%, while NHV had a 57.2% accuracy. In addition, the classification accuracy of the LSR for sMCI and pMCI was 74.3%, and NHV had a 68.3% accuracy. Cox proportional hazards models adjusted for age, sex, and education were used to estimate the relative hazard of progression from MCI to AD based on hippocampal markers and conversion times. The LSR marker showed better prediction of conversion to AD than NHV. These results suggest the relevance of considering the LSR as a new hippocampal marker for the AD continuum.
Synergistic co-delivery of doxorubicin and melittin using functionalized magnetic nanoparticles for cancer treatment: loading and in vitro release study by LC–MS/MS

Abstract In this study, citric acid-functionalized Fe3O4 magnetic nanoparticles (CA-MNPs) were prepared via a coprecipitation method and were fully characterized. Doxorubicin (DOX) and melittin (MEL), as anticancer agents, were loaded onto CA-MNPs surface through electrostatic interactions with the aim to achieve an effective co-delivery system for cancer therapy. The loading efficiency and in vitro release profiles of DOX and MEL were investigated by liquid chromatography–tandem mass spectrometry (LC–MS/MS). The MS/MS step was performed in the selected reaction monitoring (SRM) mode which enabled simultaneous quantification of the analytes with high specificity and sensitivity. An excellent loading efficiency of about 100% was achieved for DOX and MEL in a drug to nanocarrier ratio of 1:10. The in vitro release of the drugs from CA-MNPs was evaluated for 8 h at pH 7.4, 5.5 and 4.5. The experimental results revealed that the release behaviour of both of the anticancer agents was strongly pH-dependent and significantly enhanced at pH 4.5. The in vitro MTT assay on MCF-7 breast cancer cell line exhibited a synergistic effect between DOX and MEL which led to substantially greater antitumor efficacy, compared to single administration of these anticancer agents at equivalent doses. The results indicated that the co-delivery system of (DOX/MEL)-loaded CA-MNPs is highly capable to be used in magnetically targeted cancer therapy. Graphical Abstract
Immunometabolism features of metabolic deregulation and cancer

Immunometabolism is a branch dealing at the interface of immune functionalities and metabolic regulations. Considered as a bidirectional trafficking, metabolic contents and their precursors bring a considerable change in immune cells signal transductions which as a result affect the metabolic organs and states as an implication. Lipid metabolic ingredients form a major chunk of daily diet and have a proven contribution in immune cells induction, which then undergo metabolic pathway shuffling inside their ownself. Lipid metabolic states activate relevant metabolic pathways inside immune cells that in turn prime appropriate responses to outside environment in various states including lipid metabolic disorders itself and cancers as an extension. Although data on Immunometabolism are still growing, but scientific community need to adjust and readjust according to recent data on given subject. This review attempts to provide current important data on Immunometabolism and consequently its metabolic ramifications. Incumbent data on various lipid metabolic deregulations like obesity, metabolic syndrome, obese asthma and atherosclerosis are analysed. Further, metabolic repercussions on cancers and its immune modalities are also analysed.
Environment patterns and mental health of older adults in long-term care facilities: the role of activity profiles

Abstract Objectives: This study adopts the International Classification of Functioning, Disability and Health (ICF) model to determine extent to which the clustered patterns of long-term care (LTC) environment and activity participation are associated with older residents’ mental health. Method: This study enrolled a stratified equal probability sample of 634 older residents in 155 LTC institutions in Taiwan. Latent profile analysis and latent class analysis were conducted to explore the profiles for environment and activity participation. Multilevel modeling was performed to elucidate the hypothesized relationships. Results: Three environment profiles (Low-, Moderate-, and High-Support Environment) based on physical, social, and attitudinal environment domains and two activity profiles (Low- and High-Activity Participation) across seven activity domains were identified. Compared to the Low-Support class, older adults in the Moderate- and High-Support Environment classes had better mental health. Older residents in those two classes were more likely to be in the “High Activity Participation” class, which in turn, exhibited better mental health. Conclusion: Environment and activity participation directly relate to older residents’ mental health. Activity participation also mediates the link between environment and mental health. A combination of enhanced physical, social, and attitudinal environments, and continual engagement in various activities may optimize older LTC residents’ mental health.
Impact of lithiated cobalt oxide and phosphate nanoparticles on rainbow trout gill epithelial cells

Abstract Metal oxide and phosphate nanoparticles (NPs) are ubiquitous in emerging applications, ranging from energy storage to catalysis. Cobalt-containing NPs are particularly important, where their widespread use raises questions about the relationship between composition, structure, and potential for environmental impacts. To address this gap, we investigated the effects of lithiated metal oxide and phosphate NPs on rainbow trout gill epithelial cells, a model for environmental exposure. Lithium cobalt oxide (LCO) NPs significantly reduced cell viability at10 µg/mL, while a 10-fold higher concentration of lithiated cobalt hydroxyphosphate (LCP) NPs was required to significantly reduce viability. Exposure to Li+ and Co2+ alone, at concentrations relevant to ion released from the NPs, did not reduce cell viability and minimally impacted reactive oxygen species (ROS) levels. Both LCO- and LCP-NPs were found within membrane-bound organelles. However, only LCP-NPs underwent rapid and complete dissolution in artificial lysosomal fluid. Unlike LCP-NPs, LCO-NPs significantly increased intracellular ROS, could be found within abnormal multilamellar bodies, and induced formation of intracellular vacuoles. Increased p53 gene expression, measured in individual cells, was observed at sub-toxic concentrations of both LCO- and LCP-NPs, implicating both in inductions of cellular damage and stress at concentrations approaching predicted environmental levels. Our results implicate the intact NP, not the dissolved ions, in the observed adverse effects and show that LCO-NPs significantly impact cell viability accompanied by increase in intracellular ROS and formation of organelles indicative of cell stress, while LCP-NPs have minimal adverse effects, possibly due to their rapid dissolution in acidic organelles.
Reports of perceived racial discrimination among African American children predict negative affect and smoking behavior in adulthood: A sensitive period hypothesis

Abstract We examined the prospective relations between a cultural risk factor, perceived racial discrimination (PRD), and subsequent negative affect and health behavior (smoking) in a panel of 889 African American children (part of the Family and Community Health Study). Cultural moderators (protective factors) of these relations were also examined. PRD was assessed six times from ages 10.5 (Wave 1) to 24.5 (Wave 6), and negative affect (anger and depressive symptoms) was assessed at Wave 2 (age 12.5) and Wave 6 (age 24.5). Results indicated that Wave 1 PRD predicted Wave 6 smoking, controlling for multiple factors related to smoking and/or PRD, including smoking at age 15.5. Structural equation models indicated that these relations between Wave 1 PRD and smoking were mediated by both early and later negative affect. The models also indicated that Wave 1 PRD had a direct impact on Wave 6 anger (assessed 14 years later), controlling for the effects of PRD on early affect. Cultural socialization was associated with lower rates of adolescent smoking, and it buffered the relation between PRD and Wave 6 anger. The impact of early PRD experiences along with suggestions for culturally informed interventions and preventive interventions that might buffer against early PRD effects are discussed.
A Long Interval from a Spinal Cord Lesion to a Subsequent Brain Lesion in Primary Central Nervous System Vasculitis

Primary central nervous system vasculitis (PCNSV) is an uncommon vasculitis restricted to the small- and medium-sized vessels in the brain and spinal cord. Previously, only 9 cases have been reported that initially manifested as an isolated spinal cord lesion with subsequent brain involvement, where the longest interval from the onset to brain involvement was 1 year and 11 months. We herein report the case of an isolated spinal cord lesion with subsequent brain involvement appearing seven years and five months later. This case shows that brain lesions can develop after an extended interval from spinal onset in PCNSV.
SMARCA4-deficient Thoracic Sarcomas: Clinicopathologic Study of 30 Cases With an Emphasis on Their Nosology and Differential Diagnoses

SMARCA4-deficient thoracic sarcoma (SMARCA4-DTS) is a recently described entity with an aggressive clinical course and specific genetic alterations of the BAF chromatin remodeling complex. In the present study, we reviewed the clinical and pathologic features of 30 cases of SMARCA4-DTS, discussed its main differential diagnoses and the challenging diagnostic scenarios that the average pathologist may face. In addition, we tested the specificity of the “SMARCA4-DTS immunohistochemical signature” (co-loss of SMARCA4 and SMARCA2 with overexpression of SOX2) in a large cohort of intrathoracic malignancies. Patients ranged from 28 to 90 years of age (median: 48 y), with a marked male predominance (male:female=9:1) and they were usually smokers. Tumors were generally large compressive masses located in the mediastinum (n=13), pleura (n=5), lung (n=2) or in 2 or more of these topographies (n=10). Treatment strategies were varied, including 1 case treated with EZH2 inhibitors. Median overall survival was 6 months. Histologically, tumors were poorly differentiated frequently showing rhabdoid features. A subset of cases showed a focal myxoid stroma (7%, n=2/30) and rare cases displayed a previously unreported pattern simulating desmoplastic small round cell tumors (7%, n=2/30). Making a diagnosis was challenging when dealing with biopsy material from massively necrotic tumors and in this setting the expression of SOX2, CD34, and SALL4 proved useful. All tested cases displayed concomitant loss of SMARCA4 and SMARCA2 and most tumors expressed epithelial markers (Pan-keratin or EMA) (n=29/30), SOX2 (n=26/27), and CD34 (n=17/27). SMARCB1 expression was retained in all cases (23/23). SALL4 and Claudin-4 were expressed in a subset of cases (n=7/21 and 2/19, respectively). TTF-1 and P63 were focally expressed in 1 case each. P40 and NUT were not expressed (0/23 and 0/20, respectively) The SMARCA4-DTS immunohistochemical signature was both sensitive and specific, with only a subset of small cell carcinoma of the ovary hypercalcemic type showing overlapping phenotypes. Our study confirms and expands the specific features of SMARCA4-DTS, emphasizing the fact that they can be straightforwardly identified by pathologists.
LoRa LPWAN Propagation Channel Modelling in IIUM Campus

LoRa, one of the most outstanding low power wide area network (LPWAN) technology has unique and remarkable features. Because of its long-range coverage, low power consumption and low cost system architecture, Lora WAN has becoming a favorable option for performing communication in most of IoT wireless applications. This project aimed at quantifying the foliage effect in terms of attenuation and its overall contribution to the path-loss and link budget calculations. Specifically, five tree types were studied and their contribution to the path loss were quantified for different path crossings (e.g., trunk, tree-top and branches). The trees are Licuala Grandis, Mimusops Elengi, Mangifera Indica, Cyrtostachys Renda and Livistona Chinensis. Mimusops Elengi tree, characterized by its big size and crown density, gave the strongest mean foliage attenuation accumulating up to 20 dB. Trunks contribute even higher attenuation in comparison to tree-tops and branches. The Okumura/Hata, Log-normal shadowing and foliage models are used as references for this propagation models development. Our study showed that Okumura fails to capture the effect of foliage in International Islamic University Malaysia, Gombak campus that is rich in trees. This goes to illustrate the necessity for considering the tropical environment where the characterization of foliage attenuation plays an important role in determining the propagation model path-loss and link budget needed for LoRa network design and planning.
Constraints of Metabolic Energy on the Number of Synaptic Connections of Neurons and the Density of Neuronal Networks

Neuronal networks in the brain are the structural basis of human cognitive function, and the plasticity of neuronal networks is thought to be the principal neural mechanism underlying learning and memory. Dominated by the Hebbian theory, researchers have devoted extensive effort to studying the changes in synaptic connections between neurons. However, understanding the network topology of all synaptic connections has been neglected over the past decades. Furthermore, increasing studies indicate that synaptic activities are tightly coupled with metabolic energy, and metabolic energy is a unifying principle governing neuronal activities. Therefore, the network topology of all synaptic connections may also be governed by metabolic energy. Here, by implementing a computational model, we investigate the general synaptic organization rules for neurons and neuronal networks from the perspective of energy metabolism. We find that to maintain the energy balance of individual neurons in the proposed model, the number of synaptic connections is inversely proportional to the average of the synaptic weights. This strategy may be adopted by neurons to ensure that the ability of neurons to transmit signals matches their own energy metabolism. In addition, we find that the density of neuronal networks is also an important factor in the energy balance of neuronal networks. An abnormal increase or decrease in the network density could lead to failure of energy metabolism in the neuronal network. These rules may change our view of neuronal networks in the brain and have guiding significance for the design of neuronal network models.