Miracle-dz/UniFAR-FTUs huggingface dataset:
Core-dependent changes in genomic predictions using the Algorithm for Proven and Young in single-step genomic best linear unbiased prediction

Abstract Single-step genomic best linear unbiased prediction with the Algorithm for Proven and Young (APY) is a popular method for large-scale genomic evaluations. With the APY algorithm, animals are designated as core or noncore, and the computing resources to create the inverse of the genomic relationship matrix (GRM) are reduced by inverting only a portion of that matrix for core animals. However, using different core sets of the same size causes fluctuations in genomic estimated breeding values (GEBVs) up to one additive standard deviation without affecting prediction accuracy. About 2% of the variation in the GRM is noise. In the recursion formula for APY, the error term modeling the noise is different for every set of core animals, creating changes in breeding values. While average changes are small, and correlations between breeding values estimated with different core animals are close to 1.0, based on the normal distribution theory, outliers can be several times bigger than the average. Tests included commercial datasets from beef and dairy cattle and from pigs. Beyond a certain number of core animals, the prediction accuracy did not improve, but fluctuations decreased with more animals. Fluctuations were much smaller than the possible changes based on prediction error variance. GEBVs change over time even for animals with no new data as genomic relationships ties all the genotyped animals, causing reranking of top animals. In contrast, changes in nongenomic models without new data are small. Also, GEBV can change due to details in the model, such as redefinition of contemporary groups or unknown parent groups. In particular, increasing the fraction of blending of the GRM with a pedigree relationship matrix from 5% to 20% caused changes in GEBV up to 0.45 SD, with a correlation of GEBV > 0.99. Fluctuations in genomic predictions are part of genomic evaluation models and are also present without the APY algorithm when genomic evaluations are computed with updated data. The best approach to reduce the impact of fluctuations in genomic evaluations is to make selection decisions not on individual animals with limited individual accuracy but on groups of animals with high average accuracy.
Preoperative Hepatic and Regional Arterial Chemotherapy in Patients Who Underwent Curative Colorectal Cancer Resection

Supplemental Digital Content is available in the text Objective: To evaluate the effects of the addition of preoperative hepatic and regional arterial chemotherapy (PHRAC) on prognosis of stage II and III colorectal cancer (CRC) in a multicenter setting. Summary of Background Data: Our previous single-center pilot trial suggested that PHRAC in combination with surgical resection could reduce the occurrence of liver metastasis (LM) and improve survival in CRC patients. Methods: A prospective multi-center randomized controlled trial was conducted from December 2008 to December 2012 at 5 hospitals in China. Eligible patients with clinical stage II or III CRC who underwent curative resection were randomized to receive PHRAC plus adjuvant therapy (PHRAC arm) or adjuvant therapy alone (control arm). The primary endpoint was DFS. Secondary endpoints were cumulative LM rates, overall survival (OS), and safety (NCT00643877). Results: A total of 688 patients from 5 centers in China were randomly assigned (1:1) to each arm. The five-year DFS rate was 77% in the PHRAC arm and 65% in the control arm (HR = 0.61, 95% CI 0.46–0.81; P = 0.001). The 5-year LM rates were 7% and 16% in the PHRAC and control arms, respectively (HR = 0.37, 95% CI 0.22–0.63; P < 0.001). The 5-year OS rate was 84% in the PHRAC arm and 76% in the control arm (HR = 0.61, 95% CI 0.43–0.86; P = 0.005). There were no significant differences regarding treatment related morbidity or mortality between the two arms. Conclusions: The addition of PHRAC could improve DFS in patients with stage II and III CRC. It reduced the incidence of LM and improved OS without compromising patient safety. Trial Registration: ClinicalTrials.gov identifier: NCT00643877.
Prevalence and genetic variability of occult hepatitis B virus in a human immunodeficiency virus positive patient cohort in Gondar, Ethiopia

Background Occult hepatitis B (OHB) is a major concern in HIV infected patients as it associates with a high risk of HBV reactivation and disease progression. However, data on the prevalence of OHB among HIV positive patients in Ethiopia is lacking. This study aims to determine the prevalence of OHB in HBV/HIV co-infected patients from Gondar, Ethiopia. Methods A total of 308 consented HIV positive patients were recruited from the University of Gondar Teaching Hospital, Ethiopia. Clinical and demographic data of the participants were recorded. Plasma was tested for HBsAg and anti-HBc using commercial assays (Abbott Architect). In HBsAg negative anti-HBc positive patient samples, total DNA was isolated and amplified using nested PCR with primers specific to HBV polymerase, surface and pre-core/core regions, followed by Sanger sequencing and HBV mutational analysis using MEGA 7.0. Results Of the total study subjects, 62.7% were female, median age 38.4 years, interquartile range (IQR): 18–68, and 208 (67.5%) had lifestyle risk factors for HBV acquisition. Two hundred and ninety-one study subjects were HIV+/HBsAg-, out of which 115 (39.5%) were positive for anti-HBc. Occult hepatitis B was detected in 19.1% (22/115) of anti-HBc positive HIV patients. HBV genotype D was the predominant genotype (81%) among OHB positive patients. Mutations associated with HBV drug resistance, HBV reactivation, and HCC risk were detected in 23% (5/22), 14% (3/22) and 45.5% (10/22) of patients, respectively. Conclusion This study found a high rate of occult hepatitis B in HIV patients. Further, high rates of mutations associated with HBV reactivation, drug resistance, and HCC risk were detected in these patients. These data highlighted the need for integrating OHB screening for proper management of liver diseases in HIV patients.
Marek’s Disease Virus Cluster 3 miRNAs Restrict Virus’ Early Cytolytic Replication and Pathogenesis

Herpesvirus-encoded microRNAs (miRNAs) have been discovered in infected cells; however, lack of a suitable animal model has hampered functional analyses of viral miRNAs in vivo. Marek’s disease virus (MDV) (Gallid alphaherpesvirus 2, GaHV-2) genome contains 14 miRNA precursors, which encode 26 mature miRNAs, grouped into three clusters. In this study, the role of MDV-encoded cluster 3 miRNAs, also known as mdv1-miR-M8-M10, in pathogenesis was evaluated in chickens, the natural host of MDV. Our results show that deletion of cluster 3 miRNAs did not affect virus replication and plaque size in cell culture, but increased early cytolytic replication of MDV in chickens. We also observed that deletion of cluster 3 miRNAs resulted in significantly higher virus reactivation from peripheral blood lymphocytes. In addition, pathogenesis studies showed that deletion of cluster 3 miRNAs resulted in more severe atrophy of lymphoid organs and reduced mean death time, but did not affect the incidence of MDV-associated visceral tumors. We confirmed these results by generating a cluster 3 miRNA revertant virus in which the parental MDV phenotype was restored. To the best of our knowledge, our study provides the first evidence that MDV cluster 3 miRNAs play an important role in modulating MDV pathogenesis.
Recognition of Typical Locomotion Activities Based on the Sensor Data of a Smartphone in Pocket or Hand

With the ubiquity of smartphones, the interest in indoor localization as a research area grew. Methods based on radio data are predominant, but due to the susceptibility of these radio signals to a number of dynamic influences, good localization solutions usually rely on additional sources of information, which provide relative information about the current location. Part of this role is often taken by the field of activity recognition, e.g., by estimating whether a pedestrian is currently taking the stairs. This work presents different approaches for activity recognition, considering the four most basic locomotion activities used when moving around inside buildings: standing, walking, ascending stairs, and descending stairs, as well as an additional messing around class for rejections. As main contribution, we introduce a novel approach based on analytical transformations combined with artificially constructed sensor channels, and compare that to two approaches adapted from existing literature, one based on codebooks, the other using statistical features. Data is acquired using accelerometer and gyroscope only. In addition to the most widely adopted use-case of carrying the smartphone in the trouser pockets, we will equally consider the novel use-case of hand-carried smartphones. This is required as in an indoor localization scenario, the smartphone is often used to display a user interface of some navigation application and thus needs to be carried in hand. For evaluation the well known MobiAct dataset for the pocket-case as well as a novel dataset for the hand-case were used. The approach based on analytical transformations surpassed the other approaches resulting in accuracies of 98.0% for pocket-case and 81.8% for the hand-case trained on the combination of both datasets. With activity recognition in the supporting role of indoor localization, this accuracy is acceptable, but has room for further improvement.
News Media in Lebanon: Quantifying the Confidence Using Parametric and Non-parametric Testing

Providing a clear statistical analysis of news media confidence levels in a nation adds value to the integrity to the reported news as well as a basis for comparison among sources and the outcome may influence on the population‘s approach and attitude towards the current happenings. Lebanon, a Middle Eastern nation, is under continuous scrutiny by other nations due to its continuous and recurring conflicts being political, social or armed conflicts related events which may influence its surrounding geopolitical environment. Although the United States of America, in particular, has been a leading country in what relates to news media and press accuracy and fairness studies, countries like Lebanon lack such assessments and reports. This study, exploratory in nature, using both parametric and nonparametric statistical testing assessed the news media in Lebanon by relying on a previously run poll questionnaire that was administered on nine time intervals along a time frame of four years. Its purpose was to assess and quantify the Lebanese news media and press accuracy and fairness. One important implication of the research was that it showed how parametric and non-parametric tests converge to offer a common assessment of the topic in question. This paper followed a streamlined research process capitalizing on a first hand treatise of the descriptive outcomes of 4850 questionnaires. Moreover, the paper presented reliability, validity and dependence analysis specific to the existing sample data. Results obtained match their reported counterparts mainly in the USA, where the percentage of negative news media assessment in Lebanon is estimated to be 64% which matches the 63% reported in the USA. Findings of this work add new insights to the academic community, academicians and researchers, policy makers in the private as well as the public news media institutions.
Autochthonous West Nile virus infection outbreak in humans, Leipzig, Germany, August to September 2020

Following a distinct summer heat wave, nine autochthonous cases of West Nile fever and West Nile neuroinvasive disease, including one fatality, were observed in Leipzig, Germany, in August and September 2020. Phylogenetic analysis demonstrated close relationships in viruses from humans, animals and mosquitos in eastern Germany, obtained during the preceding 2 years. The described large cluster of autochthonous West Nile virus infections in Germany indicates endemic seasonal circulation of lineage 2 viruses in the area.
Encyclopedic Handbook of Emulsion Technology

Characterization of water/oil interfaces a few examples of the importance of phase diagrams for the properties and behaviour of emulsions structure and stability of emulsions coupling of coalescence and flocculation in dilute water/oil emulsions macroemulsions from the perspective of microemulsions dielectric spectroscopy on emulsions and related colloidal systems - a review electroacoustic characterization of emulsions acoustic and electroacoustic spectroscopy for characterizing emulsions and microemulsions food emulsions ultrasonic characterization of food emulsions rheology of concentrated emulsions emulsions -the NMR perspective surface forces and emulsions stability microcalorimetry video enhanced microscopy investigation of droplets and size distributions conductivity measurements multiple emulsions environmental emulsions towards the atomic-level simulations of water-in-crude oil membranes asphaltene based crude oil emulsions heavy crude oil emulsions water-in-crude oil emulsions in recovery of hydrocarbons for oil sand interfacial rheology of crude oil emulsions film properties of ashaltenes and resins chemical demulsification of stable crude oil and bitumen emulsions in petroleum recovery - a review demulsifiers in oil industry dynamic processes in surfactant stabilized emulsions three-phase wellstream gravity separation compact electrostatic coalescer technology formation of gas hydrates in stationary and flowing water/oil emulsions.
A Potential Theragnostic Regulatory Axis for Arthrofibrosis Involving Adiponectin (ADIPOQ) Receptor 1 and 2 (ADIPOR1 and ADIPOR2), TGFβ1, and Smooth Muscle α-Actin (ACTA2)

(1) Background: Arthrofibrosis is a common cause of patient debility and dissatisfaction after total knee arthroplasty (TKA). The diversity of molecular pathways involved in arthrofibrosis disease progression suggest that effective treatments for arthrofibrosis may require a multimodal approach to counter the complex cellular mechanisms that direct disease pathogenesis. In this study, we leveraged RNA-seq data to define genes that are suppressed in arthrofibrosis patients and identified adiponectin (ADIPOQ) as a potential candidate. We hypothesized that signaling pathways activated by ADIPOQ and the cognate receptors ADIPOR1 and ADIPOR2 may prevent fibrosis-related events that contribute to arthrofibrosis. (2) Methods: Therefore, ADIPOR1 and ADIPOR2 were analyzed in a TGFβ1 inducible cell model for human myofibroblastogenesis by both loss- and gain-of-function experiments. (3) Results: Treatment with AdipoRon, which is a small molecule agonist of ADIPOR1 and ADIPOR2, decreased expression of collagens (COL1A1, COL3A1, and COL6A1) and the myofibroblast marker smooth muscle α-actin (ACTA2) at both mRNA and protein levels in basal and TGFβ1-induced cells. (4) Conclusions: Thus, ADIPOR1 and ADIPOR2 represent potential drug targets that may attenuate the pathogenesis of arthrofibrosis by suppressing TGFβ-dependent induction of myofibroblasts. These findings also suggest that AdipoRon therapy may reduce the development of arthrofibrosis by mediating anti-fibrotic effects in joint capsular tissues.
Transdermal Delivery of Salmon Calcitonin Using a Dissolving Microneedle Array: Characterization, Stability, and In vivo Pharmacodynamics

Salmon calcitonin (sCT) is a polypeptide drug, possessing the ability to inhibit osteoclast-mediated bone resorption. Just like other bioactive macromolecules, sCT is generally administered to the patients by either injection for poor compliance or through nasal spray for low bioavailability, which limits its use as therapeutic drugs. In the present study, to overcome the limitations of the conventional routes, two new dissolving microneedle arrays (DMNAs) based on transdermal sCT delivery systems were developed, namely sCT-DMNA-1 (sCT/Dex/K90E) and sCT-DMNA-2 (sCT/Dex-Tre/K90E) with the same dimension, meeting the requirements of suitable mechanical properties. An accurate and reliable method was established to determine the needle drug loading proportion in sCT-DMNAs. The stability study exhibited that the addition of trehalose could improve the stability of sCT in DMNA under high temperature and humidity. Further, in vivo pharmacodynamic study revealed that DMNA patch could significantly enhanced relative bioavailability to approximately 70%, and the addition of trehalose was found to be beneficial for sCT transdermal delivery. Therefore, sCT-DMNA is expected to replace traditional dosage form, providing a secure, efficient, and low-pain therapeutic strategy for bone disorders.
Towards a Functional Approach to the Assessment of Daily Life Physical Activity in Children: Are the PAQ-C and Fitbit Flex-2 Technically Adequate?

Considering the need for functional physical activity (PA) measures in PA settings, this study sought to determine the technical adequacy of the Physical Activity Questionnaire for Older Children (PAQ-C) and the Fitbit Flex-2, two instruments with promising features for wide use, using the Actigraph GT3X+ accelerometer as the criterion reference. A total of 218 Greek children (94 boys, 124 girls; mean age = 10.99 ± 1.52 years) volunteered to join in. Participants wore the PA trackers for seven days and completed the PAQ-C. Moreover, a sub-group (n = 60) recompleted the PAQ-C after a week. Results revealed acceptable internal consistency and excellent test–retest reliability for the PAQ-C. Regarding concurrent validity, weak to moderate correlations with PA parameters recorded by the GT3X+ were revealed for the total PAQ-C and were excellent for the Flex-2, while a Bland–Altman plot indicated good agreement. Finally, in alignment with relevant literature, significant gender, but no age, differences were found in participants’ PA records in all the tools applied. The above results support the use of the PAQ-C and the Fitbit Flex-2 in children. Considering that they shed light into different parameters of children’s habitual PA, their combined utilisation, providing comprehensive information, is strongly recommended.
Arterial Spin-Labeling Perfusion for PHACE Syndrome

BACKGROUND AND PURPOSE: Arterial stroke is a rare-but-reported complication in patients with posterior fossa brain malformations, hemangiomas, arterial anomalies, coarctation of the aorta and cardiac defects, and eye abnormalities (PHACE) syndrome. Currently, stroke risk is inferred by the severity of arterial anomalies identified on MRA, though no evidenced-based data exist. The purpose of our study was to determine whether arterial spin-labeling MR imaging perfusion can detect alterations in CBF in patients with PHACE syndrome. MATERIALS AND METHODS: Records were reviewed from 3 institutions for all patients with PHACE syndrome who underwent arterial spin-labeling from 2000 to 2019. CBF was qualitatively investigated with arterial spin-labeling to determine whether there was decreased or normal perfusion. Arterial anomalies were characterized on MRA imaging, and parenchymal brain findings were evaluated on conventional MR imaging sequences. RESULTS: Forty-one patients with PHACE syndrome had arterial spin-labeling imaging. There were 30 females and 11 males (age range, 7 days to 15 years). Of the 41 patients, 10 (24%) had decreased CBF signal corresponding to a major arterial territory. Ten of 10 patients had decreased CBF signal in the anterior circulation, 2/10 had decreased anterior and posterior circulation CBF signal, 2/10 had decreased bilateral anterior circulation CBF signal, and 1/10 had globally decreased CBF signal. Forty of 41 (97.5%) patients had at least 1 arteriopathy, and in those with decreased CBF signal, the arteriopathy corresponded to the CBF signal alteration in 10/10 patients. CONCLUSIONS: Arterial spin-labeling can potentially characterize hemodynamic changes in patients with PHACE syndrome.
Therapeutic Strategies to Reduce the Toxicity of Misfolded Protein Oligomers

The aberrant aggregation of proteins is implicated in the onset and pathogenesis of a wide range of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases. Mounting evidence indicates that misfolded protein oligomers produced as intermediates in the aggregation process are potent neurotoxic agents in these diseases. Because of the transient and heterogeneous nature of these elusive aggregates, however, it has proven challenging to develop therapeutics that can effectively target them. Here, we review approaches aimed at reducing oligomer toxicity, including (1) modulating the oligomer populations (e.g., by altering the kinetics of aggregation by inhibiting, enhancing, or redirecting the process), (2) modulating the oligomer properties (e.g., through the size–hydrophobicity–toxicity relationship), (3) modulating the oligomer interactions (e.g., by protecting cell membranes by displacing oligomers), and (4) reducing oligomer toxicity by potentiating the protein homeostasis system. We analyze examples of these complementary approaches, which may lead to the development of compounds capable of preventing or treating neurodegenerative disorders associated with protein aggregation.
Quality of Life and Mental Health in Multiple Sclerorsis Patients in Bosnia and Herzegovina Measured by Generc and Disease-Specific Questionaire.

BACKGROUND Multiple sclerosis (MS) as chronic neurodegenerative disease significantly impact patients' quality of life (QoL). QoL instruments can be generic (EQ-5D, SF-36) and disease-specific like MSQoL-54. Use of disease-specific instruments is preferred since it captures broader symptoms related to MS than generic instruments. Mental health is impacted by MS and different psychiatric conditions significantly impact QoL. We have conducted prospective non-interventional study among MS patients. Aim was to measure and compare MS patients QoL by generic and disease-specific instrument at baseline and after one year and to identify potential correlation between these two types of measurements and to assess mental health scores among MS patients in Bosnia and Herzegovina (B&H) and other countries. SUBJECTS AND METHODS Study included 62 patients diagnosed with MS and treated at Neurology clinic in Sarajevo from April 2016 to May 2017. Study was approved by Ethical Committee. QoL has been measured by EQ-5D and MSQoL-54. Measurement has been performed at baseline and after 12 months. RESULTS Average utility score measured by EQ-5D at the baseline and end of the study were 0.688 and 0.639 respectively with no significant difference (p=0.850). EQ-5D utility and MSQoL-54 score showed high correlation at baseline; rho=0.873 p=0.0001 for physical health and rho=0.711 p=0.0001 for mental health. At the end of the study no significant correlations have been found (p>0.05). High negative correlation found between EDSS and scores measured by EQ-5D and MSQoL-54; at baseline (rho=-0.744 p=0.0001) and at the end of the study (rho=-0.832 p=0.0001). Similar MS impact and loss of QoL found in B&H and other countries. CONCLUSIONS Both instruments can be used in measuring QoL but disease-specific are preferred since they capture broader symptoms impacting MS patient QoL. Using QoL instruments could drive clinician decision and patient-centric care as well as reimbursement and policy decision by recording treatment outcomes.