Miracle-dz/UniFAR-FTUs huggingface dataset:
Current Practice in Bicistronic IRES Reporter Use: A Systematic Review

Bicistronic reporter assays have been instrumental for transgene expression, understanding of internal ribosomal entry site (IRES) translation, and identification of novel cap-independent translational elements (CITE). We observed a large methodological variability in the use of bicistronic reporter assays and data presentation or normalization procedures. Therefore, we systematically searched the literature for bicistronic IRES reporter studies and analyzed methodological details, data visualization, and normalization procedures. Two hundred fifty-seven publications were identified using our search strategy (published 1994–2020). Experimental studies on eukaryotic adherent cell systems and the cell-free translation assay were included for further analysis. We evaluated the following methodological details for 176 full text articles: the bicistronic reporter design, the cell line or type, transfection methods, and time point of analyses post-transfection. For the cell-free translation assay, we focused on methods of in vitro transcription, type of translation lysate, and incubation times and assay temperature. Data can be presented in multiple ways: raw data from individual cistrons, a ratio of the two, or fold changes thereof. In addition, many different control experiments have been suggested when studying IRES-mediated translation. In addition, many different normalization and control experiments have been suggested when studying IRES-mediated translation. Therefore, we also categorized and summarized their use. Our unbiased analyses provide a representative overview of bicistronic IRES reporter use. We identified parameters that were reported inconsistently or incompletely, which could hamper data reproduction and interpretation. On the basis of our analyses, we encourage adhering to a number of practices that should improve transparency of bicistronic reporter data presentation and improve methodological descriptions to facilitate data replication.
Discovery and Evaluation of Protein Biomarkers as a Signature of Wellness in Late-Stage Cancer Patients in Early Phase Clinical Trials

Simple Summary TARGET (tumour characterisation to guide experimental targeted therapy) matches patients entering early phase cancer clinical trials to the best treatment for them based on their genetics. Selecting only fit patients for these trials means less patients need to be recruited. Fit patients have a life expectancy of >three months. Performance status (PS) is used to measure life expectancy and is decided by doctors asking questions about patient’s activity levels. We created a Wellness Score using proteins in 55 patient’s blood samples. This score groups patients into those who were likely to die and those who were likely to be alive within six months of their blood sample. This score was more accurately able to predict a patient’s survival at six months than PS. We then reached the same conclusion in a further 77 patients. We hope this score can now be tested in an even larger group of patients. Abstract TARGET (tumour characterisation to guide experimental targeted therapy) is a cancer precision medicine programme focused on molecular characterisation of patients entering early phase clinical trials. Performance status (PS) measures a patient’s ability to perform a variety of activities. However, the quality of present algorithms to assess PS is limited and based on qualitative clinician assessment. Plasma samples from patients enrolled into TARGET were analysed using the mass spectrometry (MS) technique: sequential window acquisition of all theoretical fragment ion spectra (SWATH)-MS. SWATH-MS was used on a discovery cohort of 55 patients to differentiate patients into either a good or poor prognosis by creation of a Wellness Score (WS) that showed stronger prediction of overall survival (p = 0.000551) compared to PS (p = 0.001). WS was then tested against a validation cohort of 77 patients showing significant (p = 0.000451) prediction of overall survival. WS in both sets had receiver operating characteristic curve area under the curve (AUC) values of 0.76 (p = 0.002) and 0.67 (p = 0.011): AUC of PS was 0.70 (p = 0.117) and 0.55 (p = 0.548). These signatures can now be evaluated further in larger patient populations to assess their utility in a clinical setting.
Synthesis, Characterization, and In Vitro Insulin-Mimetic Activity Evaluation of Valine Schiff Base Coordination Compounds of Oxidovanadium(V)

Type 2 diabetes became an alarming global health issue since the existing drugs do not prevent its progression. Herein, we aimed to synthesize and characterize a family of oxidovanadium(V) complexes with Schiff base ligands derived from L-/D-valine (val) and salicylaldehyde (sal) or o-vanillin (van) as insulin-mimetic agents and to assess their potential anti-diabetic properties. Two new oxidovanadium(V) complexes, [{VVO(R-salval)(H2O)}(μ2-O){VVO(R-salval)}] and [{VVO(R-vanval)(CH3OH)}2(μ2-O)], and their S-enantiomers were synthesized and characterized. The compounds exhibit optical activity as shown by crystallographic and spectroscopic data. The stability, the capacity to bind bovine serum albumin (BSA), the cytotoxicity against human hepatoma cell line, as well as the potential anti-diabetic activity of the four compounds are investigated. The synthesized compounds are stable for up to three hours in physiological conditions and exhibit a high capacity of binding to BSA. Furthermore, the synthesized compounds display cytocompatibility at biologically relevant concentrations, exert anti-diabetic potential and insulin-mimetic activities by inhibiting the α-amylase and protein tyrosine phosphatase activity, and a long-term increase of insulin receptor phosphorylation compared to the insulin hormone. Thus, the in vitro anti-diabetic potential and insulin-mimetic properties of the newly synthesized oxidovanadium(V) compounds, correlated with their cytocompatibility, make them promising candidates for further investigation as anti-diabetic drugs.
Factors Associated with Regular Zumba Practice as Preliminary Results: A Population-Based Approach in Cebu Province, the Philippines

The prevalence of overweight/obesity in the adult population in the Philippines has doubled in the past 20 years. Zumba exercise has recently been implemented throughout the Philippines. However, there is scarce information on the effects of Zumba on obesity and Zumba participants’ characteristics in the Philippines. This study described the current practice of Zumba in the Philippines, along with the practitioners’ characteristics, and identified factors associated with Zumba participation. In this observational, cross-sectional study, a structured questionnaire was used to survey 10 Zumba locations in September 2019. Anthropometric measurements of participants were assessed. Respondents included 171 women (88.6%) and 22 men (11.4%), with a mean (±standard deviation [SD]) age of 44.1 (±8.9) years. All respondents answered that Zumba was enjoyable, and some answered “very enjoyable”. Determinants of frequent participation were as follows: being older than the mean age of participants, starting Zumba to enjoy dancing, starting Zumba not to lose weight, shopping mall location, and participation fee required. “To enjoy dance” being a motivation for Zumba practice was identified as a determinant of frequent participation rather than “to lose weight. ” The element of “enjoyable” may strongly influence the continuation and frequent participation of Zumba exercise in the Philippines.
Comparison of Vascular Morphometry in Jawbones and Long Bones: Micro-CT Study in a Rat Model Treated with Zoledronic Acid

The study was aimed at investigating the effect of zoledronic acid on vascular morphometry in jawbones and long bones on a rat model. Twenty-four skeletal mature Sprague-Dawley female rats were administered oncologic dose of zoledronic acid (ZA) or normal saline for 4 weeks and then subjected to tooth extraction on the mandible and maxilla and a bone defect creation on the femur. After the surgical procedures, ZA or saline treatment was continued until sacrifice at week 2, week 4, and week 8 postoperatively. Vascular perfusion with MICROFIL was performed on all the animals. Micro-CT analysis demonstrated a tendency of decreased vessel density and vessel number in ZA-treated groups but no statistical difference. In conclusion, the neovessel formation is suppressed but not significantly by ZA treatment, indicating that angiogenesis inhibition may contribute to the development of MRONJ but does not play a key role.
Benchmarking Audio Signal Representation Techniques for Classification with Convolutional Neural Networks

Audio signal classification finds various applications in detecting and monitoring health conditions in healthcare. Convolutional neural networks (CNN) have produced state-of-the-art results in image classification and are being increasingly used in other tasks, including signal classification. However, audio signal classification using CNN presents various challenges. In image classification tasks, raw images of equal dimensions can be used as a direct input to CNN. Raw time-domain signals, on the other hand, can be of varying dimensions. In addition, the temporal signal often has to be transformed to frequency-domain to reveal unique spectral characteristics, therefore requiring signal transformation. In this work, we overview and benchmark various audio signal representation techniques for classification using CNN, including approaches that deal with signals of different lengths and combine multiple representations to improve the classification accuracy. Hence, this work surfaces important empirical evidence that may guide future works deploying CNN for audio signal classification purposes.
Torque Curve Optimization of Ankle Push-Off in Walking Bipedal Robots Using Genetic Algorithm

Ankle push-off occurs when muscle–tendon units about the ankle joint generate a burst of positive power at the end of stance phase in human walking. Ankle push-off mainly contributes to both leg swing and center of mass (CoM) acceleration. Humans use the amount of ankle push-off to induce speed changes. Thus, this study focuses on determining the faster walking speed and the lowest energy efficiency of biped robots by using ankle push-off. The real-time-space trajectory method is used to provide reference positions for the hip and knee joints. The torque curve during ankle push-off, composed of three quintic polynomial curves, is applied to the ankle joint. With the walking distance and the mechanical cost of transport (MCOT) as the optimization goals, the genetic algorithm (GA) is used to obtain the optimal torque curve during ankle push-off. The results show that the biped robot achieved a maximum speed of 1.3 m/s, and the ankle push-off occurs at 41.27−48.34% of the gait cycle. The MCOT of the bipedal robot corresponding to the high economy gait is 0.70, and the walking speed is 0.54 m/s. This study may further prompt the design of the ankle joint and identify the important implications of ankle push-off for biped robots.
Validation of an Online Version of the Alcohol Use Disorders Identification Test (AUDIT) for Alcohol Screening in Spanish University Students

Online alcohol screening may be helpful in preventing alcohol use disorders. We assessed psychometric properties of an online version of the Alcohol Use Disorders Identification Test (AUDIT) among Spanish university students. We used a longitudinal online survey (the UNIVERSAL project) of first-year students (18–24 years old) in five universities, including the AUDIT, as part of the WHO World Mental Health International College Student (WMH-ICS) initiative. A reappraisal interview was carried out with the Timeline Followback (TLFB) for alcohol consumption categories and the Mini International Neuropsychiatric Interview (MINI) for alcohol use disorder. Reliability, construct validity and diagnostic accuracy were assessed. Results: 287 students (75% women) completed the MINI, of whom 242 also completed the TLFB. AUDIT’s Cronbach’s alpha was 0.82. The confirmatory factor analysis for the one-factor solution of the AUDIT showed a good fit to the data. Significant AUDIT score differences were observed by TLFB categories and by MINI disorders. Areas under the curve (AUC) were very large for dependence (AUC = 0.96) and adequate for consumption categories (AUC > 0.7). AUDIT cut-off points of 6/8 (women/men) for moderate-risk drinking and 13 for alcohol dependence showed sensitivity/specificity of 76.2%/78.9% and 56%/97.5%, respectively. The online version of the AUDIT is useful for detecting alcohol consumption categories and alcohol dependence in Spanish university students.
Sources of Resistance to Common Bacterial Blight and Charcoal Rot Disease for the Production of Mesoamerican Common Beans in the Southern United States

The gene pool of Mesoamerican common beans (Phaseolus vulgaris L.) includes genotypes in the small-to-medium-size seeded dry beans, as well as some snap beans from hotter environments adapted to the Southeastern United States. However, the warm and humid climate of the Southeastern United States is conducive to diseases such as Common Bacterial Blight (CBB) and Charcoal Rot (CR). The pathogens for these two diseases can survive long periods in infested soil or on seeds and are difficult to control through pesticides. Hence, field-level resistance would be the best management strategy for these diseases. The goals of this study were (1) to evaluate field-level resistance from the various commercial classes and subgroups represented in the Mesoamerican gene pool as sources for breeding beans for the region and (2) to evaluate genome-wide marker × trait associations (GWAS) using genetic markers for the genotypes. A total of 300 genotypes from the Mesoamerican Diversity Panel (MDP) were evaluated for CBB and CR in field experiments for three years. CBB resistance was also tested with a field isolate in controlled greenhouse conditions. The analysis of variance revealed the presence of variability in the MDP for the evaluated traits. We also identified adapted common bean genotypes that could be used directly in Southeastern production or that could be good parents in breeding programs for CBB and CR resistance. The GWAS detected 14 significant Single-Nucleotide Polymorphism (SNP) markers associated with CBB resistance distributed on five chromosomes, namely Pv02, Pv04, Pv08, Pv10, and Pv11, but no loci for resistance to CR. A total of 89 candidate genes were identified in close vicinity (±100 kb) to the significant CBB markers, some of which could be directly or indirectly involved in plant defense to diseases. These results provide a basis to further understand the complex inheritance of CBB resistance in Mesoamerican common beans and show that this biotic stress is unrelated to CR resistance, which was evident during a drought period. Genotypes with good yield potential for the Southeastern U.S. growing conditions were found with resistant to infection by the two diseases, as well as adaptation to the hot and humid conditions punctuated by droughts found in this region.
The “Healthcare Workers’ Wellbeing (Benessere Operatori)” Project: A Picture of the Mental Health Conditions of Italian Healthcare Workers during the First Wave of the COVID-19 Pandemic

During the last year, the COVID-19 outbreak put all the healthcare workers around the world at risk of physical and psychological sequelae. The general purpose of the present study was to assess the mental health of Italian healthcare workers during the COVID-19 outbreak and to identify high-risk groups. Here, we present results from the baseline assessment of the “Healthcare workers’ wellbeing (Benessere Operatori)” project on a sample of 1055 healthcare workers. Participants completed the Depression Anxiety Stress Scale-21, the Insomnia Severity Index, the Impact of Event Scale-Revised, the State-Trait Anger Expression Inventory-2, and the Maslach Burnout Inventory. Healthcare workers who worked in COVID wards reported higher levels of anxiety, insomnia, post-traumatic stress, anger, and burnout, compared to those reported by the healthcare workers who worked in non-COVID wards. Moreover, nurses, both in COVID and non-COVID wards, were at higher risk of experiencing psychological distress compared to other groups of healthcare workers. These findings highlight the importance of implementing targeted psychological interventions for healthcare workers operating in COVID wards and nurses, who seem to be the most vulnerable categories.
Evaluation of Policy Effectiveness by Mathematical Modeling for the Opioid Crisis with Spatial Study and Trend Analysis

The current opioid epidemic in the US presents a great problem which calls for policy supervision and regulation. In this work, the opioid cases of five states were used for trend analysis and modeling for the estimation of potential policy effects. An evaluation model was established to analyze the severity of the opioid abuse based on the entropy weight method (EWM) and rank sum ratio (RSR). Four indexes were defined to estimate the spatial distribution of development and spread of the opioid crisis. Thirteen counties with the most severe opioid abuse in five states were determined using the EWM-RSR model and those indexes. Additionally, a forecast of the development of opioid abuse was given based on an autoregressive (AR) model. The RSR values of the thirteen counties would increase to the range between 0.951 and 1.226. Furthermore, the least absolute shrinkage and selection operator (LASSO) method was adopted. The previous indexes were modified, incorporating the comprehensive socioeconomic effects. The optimal penalty term was found to facilitate the stability and reliability of the model. By using the comprehensive model, it was found that three factors—VC112, VC114, VC115—related to disabled people have a great influence on the development of opioid abuse. The simulated policies were performed in the model to decrease the values of the indicators by 10%–50%. The corresponding RSR values can decline to the range between 0.564 and 0.606. Adopting policies that benefit the disabled population should inhibit the trend of opioid abuse.
The rs1634330 Polymorphisms in the SOST Gene Are Associated with Body Composition in Chinese Nuclear Families with Male Offspring

Objective The purpose of this study was to explore the effect of the SOST gene polymorphisms on body composition in Chinese nuclear families with male offspring. Methods 1,016 individuals were recruited from 335 Chinese nuclear families with male offspring. The nuclear families consist of at least one male offspring aged 18 to 44. We genotyped the 10 tagged single-nucleotide polymorphisms (SNPs) in SOST gene (rs7220711, rs865429, rs851057, rs1708635, rs2023794, rs1234612, rs74252774, rs1634330, rs851058, and rs1513670) in all the above people. We used dual-energy X-ray absorptiometry to measure the composition of the human body. The quantitative transmission disequilibrium test (QTDT) was used to analyze the associations of the SNPs with the body composition. Results QTDT analysis showed that rs1634330 was significantly associated with trunk LM (P < 0.05). However, haplotypes were not found to be significantly associated with the body composition in the within-family association. The 1000 permutations were consistent with these within-family association results. Conclusions Our results showed that the genetic variation in the SOST gene may contribute to variations in the body composition of Chinese male offspring.
Prognostic Impact of Ki-67 Change in Locally Advanced and Early Breast Cancer after Neoadjuvant Chemotherapy: A Single Institution Experience

Systemic neoadjuvant chemotherapy (NCT) is a standard treatment for locally advanced breast cancer (LABC) and for selected early breast cancer (EBC). In these settings, the prognostic and predictive role of Ki-67 before and after NCT is unclear. The aim of our study was to investigate the prognostic role of Ki-67 change in patients not achieving pathological complete response (pCR). We retrospectively analyzed data of patients who did not achieve pCR assessing Ki-67 expression pre- and post-NCT. We stratified three groups: high reduction (>20%), low reduction (1–20%), and no reduction in Ki-67. These groups were correlated with clinical and pathological data by χ2 test. We estimated disease-free survival (DFS) and overall survival (OS) using Kaplan–Meier method, and we adopted univariate and multivariate Cox proportional hazard models. We selected 82 patients from a database of 143 patients, excluding those who were metastatic at diagnosis, achieved pCR, or lack data regarding Ki-67. Median age at diagnosis was 54 years (range 30–75); 51 patients were Luminal B, 10 human epidermal growth factor receptor 2 (HER-2) enriched, and 21 triple negative. A significant correlation between high Ki-67 reduction and luminal B HER-2-negative subtype was observed (p = 0,0035). The change in Ki-67 was significantly associated with DFS (p = 0,0596) and OS (p = 0,0120), also at multivariate analysis (p = 0,0256 for DFS; p = 0,0093 for OS). In particular, as compared to patients with low/no reduction of Ki-67, those with high Ki-67 reduction (>20%) after NCT showed better survival (60% vs. 56% vs. 83% after 5 years from diagnosis, respectively; p = 0.01). In conclusion, in our study, Ki-67 change showed a significant prognostic role in breast cancer patients treated with NCT who did not achieve pCR. Crucially, Ki-67 < 20% identifies a high-risk population that may be eligible for clinical trials with novel therapeutic interventions in adjuvant setting.
A Holographic Augmented Reality Guidance System for Patient Alignment: A Feasibility Study

Purpose To evaluate the accuracy of an augmented reality holographic guidance system for potential use in patient alignment in radiotherapy applications. Methods A cubic phantom was scanned on a CT simulator and a 3D mesh was extracted using the Eclipse Scripting API. An application was created for the Microsoft HoloLens to allow users to see the scanned mesh as a hologram overlaid in the treatment vault. Six therapists were equipped with the HoloLens glasses and instructed to move the real phantom to align with the perceived spatial hologram using only couch controls. The initial couch coordinates were recorded and then recorded at each step as the therapist moved the phantom to each new location. The application varied the position of the virtual phantom to 10 preprogrammed locations within a 40-cm cubic volume in a combination of vertical, longitudinal, and lateral axis shifts. The absolute position difference between the holographic world and real-world phantom was recorded at each step. Also, the relative position from one position to the next was recorded. Results Fifty shifts were collected across the six therapists. The mean difference between the physical position and instructed holographic position was 0.58 ± 0.31 cm for relative shifts and 0.51 ± 0.33 cm for absolute position. The maximum difference between the holographic position and the actual post shift position was 1.53 cm for relative and 1.58 cm for absolute. Conclusion Holographic augmented reality guidance using the Microsoft HoloLens provides adequate accuracy for initial treatment alignment but lacks the fine alignment accuracy of X-ray imaging systems.