Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural Killer Cells Promote Kidney Graft Rejection Independently of Cyclosporine A Therapy

Natural Killer (NK) cells have recently been recognized as key players in antibody-mediated chronic allograft failure, thus requiring a comprehensive understanding whether NK cells can escape conventional immunosuppressive regimens. Influence of cyclosporine A (CyA) on NK cell function was studied in a mouse model of allogeneic kidney transplantation (KTX, BALB/c to C57BL/6). Recipients were treated daily with CyA (10 mg/kg) for seven or 14 days for long term survival (day 56). Administration of CyA in recipients resulted in significantly reduced frequencies of intragraft and splenic CD8+ T cells, whereas the latter illustrated reduced IFNγ production. In contrast, intragraft and splenic NK cell frequencies remained unaffected in CyA recipients and IFNγ production and degranulation of NK cells were not reduced as compared with controls. Depletion of NK cells in combination with CyA resulted in an improvement in kidney function until day 7 and prolonged graft survival until day 56 as compared to untreated controls. Surviving animals demonstrated higher intragraft frequencies of proliferating CD4+FoxP3+Ki67+ regulatory T (TREG) cells as well as higher frequencies of CD8+CD122+ TREG. We here demonstrate that NK cell depletion combined with CyA synergistically improves graft function and prolongs graft survival, suggesting that NK cell targeting constitutes a novel approach for improving KTX outcomes.
Sleep–Wake Cycle in Young and Older Mice

Sleep plays a key role in multiple cognitive functions and sleep pattern changes with aging. Human studies revealed that aging decreases sleep efficiency and reduces the total sleep time, the time spent in slow-wave sleep (SWS), and the delta power (1–4 Hz) during sleep; however, some studies of sleep and aging in mice reported opposing results. The aim of our work is to estimate how features of sleep–wake state in mice during aging could correspond to age-dependent changes observed in human. In this study, we investigated the sleep/wake cycle in young (3 months old) and older (12 months old) C57BL/6 mice using local-field potentials (LFPs). We found that older adult mice sleep more than young ones but only during the dark phase of sleep-wake cycle. Sleep fragmentation and sleep during the active phase (dark phase of cycle), homologous to naps, were higher in older mice. Older mice show a higher delta power in frontal cortex, which was accompanied with similar trend for age differences in slow wave density. We also investigated regional specificity of sleep–wake electrographic activities and found that globally posterior regions of the cortex show more rapid eye movement (REM) sleep whereas somatosensory cortex displays more often SWS patterns. Our results indicate that the effects of aging on the sleep–wake activities in mice occur mainly during the dark phase and the electrode location strongly influence the state detection. Despite some differences in sleep–wake cycle during aging between human and mice, some features of mice sleep share similarity with human sleep during aging.
Echocardiographic Measurements in a Preclinical Model of Chronic Chagasic Cardiomyopathy in Dogs: Validation and Reproducibility

Background: The failure to translate preclinical results to the clinical setting is the rule, not the exception. One reason that is frequently overlooked is whether the animal model reproduces distinctive features of human disease. Another is the reproducibility of the method used to measure treatment effects in preclinical studies. Left ventricular (LV) function improvement is the most common endpoint in preclinical cardiovascular disease studies, while echocardiography is the most frequently used method to evaluate LV function. In this work, we conducted a robust echocardiographic evaluation of LV size and function in dogs chronically infected by Trypanosoma cruzi. Methods and Results: Echocardiography was performed blindly by two distinct observers in mongrel dogs before and between 6 and 9 months post infection. Parameters analyzed included end-systolic volume (ESV), end-diastolic volume (EDV), ejection fraction (EF), and fractional shortening (FS). We observed a significant LVEF and FS reduction in infected animals compared to controls, with no significant variation in volumes. However, the effect of chronic infection in systolic function was quite variable, with EF ranging from 17 to 66%. Using the cut-off value of EF ≤ 40%, established for dilated cardiomyopathy (DCM) in dogs, only 28% of the infected dogs were affected by the chronic infection. Conclusions: The canine model of CCC mimics human disease, reproducing the percentage of individuals that develop heart failure during the chronic infection. It is thus mandatory to establish inclusion criteria in the experimental design of canine preclinical studies to account for the variable effect that chronic infection has on systolic function.
Alteration of Testosterone Levels Changes Brain Wave Activity Patterns and Induces Aggressive Behavior in Rats

Testosterone is responsible for several changes in the brain, including behavioral and emotional responses, memory, and cognition. Given this, we investigated changes in the brain wave profile caused by supplementation with exogenous testosterone in both castrated and non-castrated rats. We also investigated the serum testosterone levels, renal and hepatic function, and the lipid and behavioral profiles. We found changes in the spectral wave power in both groups (castrated and non-castrated animals) supplemented with exogenous testosterone, consistent with an aggressive/hostile profile. These changes were observed in the electrocorticographic evaluation associated with increased power in low-frequency (delta and theta) and high-frequency (beta and gamma) activity in the supplemented animals. The castrated animals presented a significant decrease of wave power in the alpha frequency. This correlated with a decrease of the performance of the animals in the elevated plus-maze evaluation, given that the alpha wave is linked to the execution and visualization of motor processes. In the behavioral evaluation, the castrated animals presented a reduced permanence time in the elevated-plus maze, although this was prevented by the supplementation of testosterone. Testosterone supplementation induced aggressive behavior in non-castrated animals, but not in castrated ones. Supplemented animals had significantly elevated serum testosterone levels, while their urea levels were significantly lower, but without clinical significance. Our data indicate that testosterone supplementation in non-castrated rats, but not in castrated ones, causes electrocorticographic changes that could be associated with more aggressive and hostile behavior, in addition to indicating a potential for personality disorder. However, further studies are required to elucidate the cellular and molecular changes caused by acute testosterone supplementation.
Gait Disorders Questionnaire–Promising Tool for Virtual Reality Designing in Patients With Parkinson's Disease

Background: Gait disorders (GD) are frequent and disabling symptoms in patients with Parkinson's disease, mostly because they significantly limit mobility and often lead to fear of falls or actual falls. Nowadays, rehabilitation is considered to be the most effective nonpharmacological approach to reduce risk of falls. Using paradigms in virtual reality (VR) is a promising tool in neurorehabilitation because of the potential improvement in motor learning and improvement in daily functioning by replicating everyday real-life scenarios. Objective: To identify the most prevalent everyday situations which impair gait in PD that could be simulated in virtual reality (VR) environment. Methods: A newly developed self-report questionnaire consisting of 15 binary response items (YES/NO) encompassing everyday walking situations was administered to 62 patients diagnosed with idiopathic PD according to MDS Clinical Diagnostic Criteria. We included patients able to walk unassisted for at least 10 min and without significant cognitive impairment. Mokken Scale Analysis was used to evaluate psychometric properties of the scale. Results: Questionnaires from 58 patients were analyzed (31 men, age = 63 ± 9.9 y, disease duration = 7.02 ± 4.03 y, LEDD = 1115 ± 549.4 mg, H&Y = 2.4 ± 0.6). Only 10 items (out of 15) were identified as scalable and these were included in Gait Disorders Questionnaire (GDQ). The most prevalent trigger of gait disorders was walking under time pressure, followed by gait in crowded places and walking while dual-tasking. The total score of GDQ significantly correlated with the disease duration (rs = 0.347, p = 0.008) and modified H&Y staging (rs = 0.288, p = 0.028). Conclusion: With the use of GDQ we identified the most prevalent everyday transition activities that provoke gait disorders in patients with PD. The results may be useful for further development and systematic application of VR paradigms for physiotherapy of PD patients.
Unfolding adsorption on metal nanoparticles: Connecting stability with catalysis

Simple and powerful physics-based adsorption model on nanoparticles is developed using statistics, DFT, and tabulated properties. Metal nanoparticles have received substantial attention in the past decades for their applications in numerous areas, including medicine, catalysis, energy, and the environment. Despite these applications, the fundamentals of adsorption on nanoparticle surfaces as a function of nanoparticle size, shape, metal composition, and type of adsorbate are yet to be found. Herein, we introduce the first universal adsorption model that accounts for detailed nanoparticle structural characteristics, metal composition, and different adsorbates by combining first principles calculations with machine learning. Our model fits a large number of data and accurately predicts adsorption trends on nanoparticles (both monometallic and alloy) that have not been previously seen. In addition to its application power, the model is simple and uses tabulated and rapidly calculated data for metals and adsorbates. We connect adsorption with stability behavior of nanoparticles, thus advancing the design of optimal nanoparticles for applications of interest, such as catalysis.
SoyCSN: Soybean context‐specific network analysis and prediction based on tissue‐specific transcriptome data

Abstract The Soybean Gene Atlas project provides a comprehensive map for understanding gene expression patterns in major soybean tissues from flower, root, leaf, nodule, seed, and shoot and stem. The RNA‐Seq data generated in the project serve as a valuable resource for discovering tissue‐specific transcriptome behavior of soybean genes in different tissues. We developed a computational pipeline for Soybean context‐specific network (SoyCSN) inference with a suite of prediction tools to analyze, annotate, retrieve, and visualize soybean context‐specific networks at both transcriptome and interactome levels. BicMix and Cross‐Conditions Cluster Detection algorithms were applied to detect modules based on co‐expression relationships across all the tissues. Soybean context‐specific interactomes were predicted by combining soybean tissue gene expression and protein–protein interaction data. Functional analyses of these predicted networks provide insights into soybean tissue specificities. For example, under symbiotic, nitrogen‐fixing conditions, the constructed soybean leaf network highlights the connection between the photosynthesis function and rhizobium–legume symbiosis. SoyCSN data and all its results are publicly available via an interactive web service within the Soybean Knowledge Base (SoyKB) at http://soykb.org/SoyCSN. SoyCSN provides a useful web‐based access for exploring context specificities systematically in gene regulatory mechanisms and gene relationships for soybean researchers and molecular breeders.
Research article Sodium channel Na v 1.7 immunoreactivity in painful human dental pulp and burning mouth syndrome

Background: Voltage gated sodium channels Nav1.7 are involved in nociceptor nerve action potentials and are known to affect pain sensitivity in clinical genetic disorders. Aims and Objectives: To study Na v 1.7 levels in dental pulpitis pain, an inflammatory condition, and burning mouth syndrome (BMS), considered a neuropathic orofacial pain disorder. Methods: Two groups of patients were recruited for this study. One group consisted of patients with dental pulpitis pain (n = 5) and controls (n = 12), and the other patients with BMS (n = 7) and controls (n = 10). BMS patients were diagnosed according to the International Association for the Study of Pain criteria; a pain history was collected, including the visual analogue scale (VAS). Immunohistochemistry with visual intensity and computer image analysis were used to evaluate levels of Nav1.7 in dental pulp tissue samples from the dental pulpitis group, and tongue biopsies from the BMS group. Results: There was a significantly increased visual intensity score for Na v 1.7 in nerve fibres in the painful dental pulp specimens, compared to controls. Image analysis showed a trend for an increase of the Nav1.7 immunoreactive % area in the painful pulp group, but this was not statistically significant. When expressed as a ratio of the neurofilament % area, there was a strong trend for an increase of Na v 1.7 in the painful pulp group. Na v 1.7 immunoreactive fibres were seen in abundance in the sub-mucosal layer of tongue biopsies, with no significant difference between BMS and controls. Conclusion: Nav1.7 sodium channel may play a significant role in inflammatory dental pain. Clinical trials with selective Na v 1.7 channel blockers should prioritise dental pulp pain rather than BMS.
Kawasaki disease among children in the United States

Kawasaki disease (KD) is a medium-sized-vessel vasculitis that affects mostly children. The 2016 Healthcare Cost and Utilization Project Kid’s Inpatient Database (HCUP KID) was used in weighted form to investigate differences in gender, month of year, race, region, total charges, and household income in the United States. 5503 weighted cases were found. It was more common in males (3345, 60.8%) than females (2158, 39.2%) (p < 0.01). Most admitted KD patients were white (1913, 38.1%). A higher prevalence of Kawasaki disease was seen among patients of Asian or Pacific Islander background (0.2%). The southern regions of the United States reported the highest rate of admission with 2036 patients (37%). The median age on admission was 2 years (interquartile range [IQR] of 1–5, p < 0.01) and the median charge was $32,170 (IQR: $20,825–$50,502.05) (p < 0.01). Most admissions of Kawasaki disease were recorded in winter with a peak in March (623, 11.3%) (p < 0.01).
Analysis of serious adverse events in a paediatric fast breathing pneumonia clinical trial in Malawi

Introduction Pneumonia is the leading infectious killer of children. We conducted a double-blind, randomised controlled non-inferiority trial comparing placebo to amoxicillin treatment for fast breathing pneumonia in HIV-negative children aged 2–59 months in Malawi. Occurrence of serious adverse events (SAEs) during the trial were examined to assess disease progression, co-morbidities, recurrence of pneumonia and side effects of amoxicillin. Methods Enrolled children with fast breathing for age and a history of cough <14 days or difficult breathing were randomised to either placebo or amoxicillin for 3 days, and followed for 14 days to track clinical characteristics and outcomes. Medical history, physical exam, laboratory results and any chest radiographs collected at screening, enrolment and during hospitalisation were evaluated. All SAE reports were reviewed for additional information regarding hospitalisation, course of treatment and outcome. Results In total, 102/1126 (9.0%) enrolled children with fast breathing pneumonia were reported to have a SAE. Seventy-five per cent (n=77) of SAEs were pneumonia-related (p<0.01). Children<2 years of age represented the greatest proportion (61/77, 79.2%) of those with a pneumonia-related SAE. In the amoxicillin group, there were 46 SAEs and 5 (10.9%) cases were identified as possibly related to study drug (4 gastroenteritis and 1 fever). There were no life-threatening pneumonia SAEs or deaths in either group, and by the time of exit from the study, all children recovered without sequelae. Discussion In this fast breathing pneumonia clinical trial, SAEs occurred infrequently in both the amoxicillin and placebo groups, and amoxicillin was well tolerated. Trial registration number NCT02760420. https://clinicaltrials.gov/ct2/show/NCT02760420? term=ginsburg&rank=9.
Cases Referred from the Turkish National Screening Program: Frequency of Congenital Hypothyroidism and Etiological Distribution

Objective: The aim of this study was to evaluate cases referred from the congenital hypothyroidism (CH) newborn screening program. Methods: Infants referred to Pediatric Endocrinology between 30.09. 2015 - 01.04. 2018 because of suspected CH identified by National Neonatal Screening Program were prospectively evaluated. Results: Of the 109 newborns referred to our clinic, 60 (55%) were diagnosed with elevated neonatal thyroid stimulating hormone (TSH). The diagnosis of elevated neonatal TSH was made in 52 (47.7%) and eight (7.3%) infants at initial evaluation and after follow up, respectively of all referrals with 86.7% (52/60) diagnosed at initial visit. The median first and second heel prick times were 1.8 (0-7) and 8.72 (4-30) days. The median age at starting treatment of the infants diagnosed as a result of initial evaluation was 22.13 (7-53) days. Clinical findings associated with CH were present in 19 (36%) of patients. Etiology in patients diagnosed with elevated neonatal TSH on admission was: agenesis in one (2.08%); ectopia in one (2.08%); hypoplasia in 14 (29.16%); normal gland in situ 16 (33.3%); and hyperplasia in 16 (33.3%). The median time to normalization of TSH and free thyroxine concentrations after treatment initiation was 11.02 (4-30) and 9.03 (3-30) days, respectively. Conclusion: The rate of diagnosis in the first month was found to be 87%. The etiological incidence of both dysgenesis and dyshormonogenesis was equal at 33.3%. The majority of cases with normal thyroid gland will be diagnosed with transient hypothyroidism but some of them may be diagnosed with thyroid dyshormonogenesis so the rate of dyshormonogenesis will increase later after final diagnosis.
Impact of In-domain Vector Representations on the Classification of Disease-related Tweets: Avian Influenza Case Study

A number of methods have been proposed for the construction of vector representations for natural language processing (NLP) tasks. These methods have been applied to various domains and each has its own pros and cons. Despite their effectiveness, the proposed approaches usually ignore the sentiment information concerning specific tasks. In this paper, we examined various types of word vectors and their impact on the performance of a sentiment classification problem in the area of infectious diseases. Vectors were used in the embedding layer of a word-based convolutional neural network (CNN) to identify tweets pertaining to avian influenza. We proposed a new approach to build effective word embeddings for the sentiment analysis task. Furthermore, the performance of the language model was compared in terms of using various corpus sizes and vector dimensions. Our experiments indicated that initializing the sentiment learning network with domain-specific word embeddings outperforms general domain embeddings. We found that the proposed method leads to a considerable improvement in the classification performance.
Aspects of Mobility of e-Marketing from Customer Perspective

The main aim of this article is to identify students’ opinions concerning the place, role and influence of electronic marketing tools on making purchases on the Internet. The authors have applied the division of e-marketing into its traditional and electronic forms, on desktop computers and mobile devices, which was significant due to diversified opinions of clients concerning its use. The studies have been carried out with the application of a CAWI method examining a convenient, partially randomly selected sample of clients (students) who are the most active in the Internet. The studies were aimed at evaluating specific e-marketing media and techniques which, in the customers’ view, influenced shopping on the Internet. In particular, the respondents commented on the advantages, disadvantages and benefits resulting from the application of e-marketing on mobile devices. The conclusions and recommendations from the study may contribute to better use of these factors in order to facilitate consumers’ purchases, not only in the Internet.
Wideband absorbance measures in neonates and young infants

ii Declaration by author. v Publications during candidature.vi Publications included in this thesis.vii Contributions by others to the thesis.x Statement of parts of the thesis submitted to qualify for the award of another degree.xi Acknowledgements.xii
Do Online Reviews Reveal Mobile Application Usability and User Experience? The Case of WhatsApp

The variety of hardware devices and the diversity of their users imposes new requirements and expectations on designers and developers of mobile applications (apps). While the Internet has enabled new forms of communication platform, online stores provide the ability to review apps. These informal online app reviews have become a viral form of electronic word-of-mouth (eWOM), covering a plethora of issues. In our study, we set ourselves the goal of investigating whether online reviews reveal usability and user experience (UUX) issues, being important quality-in-use characteristics. To address this problem, we used sentiment analysis techniques, with the aim of extracting relevant keywords from eWOM WhatsApp data. Based on the extracted keywords, we next identified the original users’ reviews, and individually assigned each attribute and dimension to them. Eventually, the reported issues were thematically synthesized into 7 attributes and 8 dimensions. If one asks whether online reviews reveal genuine UUX issues, in this case, the answer is definitely affirmative.
Counting Instances of Objects in Color Images Using U-Net Network on Example of Honey Bees

This article presents a novel approach to segmentation and counting of objects in color digital images. The objects belong to a certain class, which in this case are honey bees. The authors briefly present existing approaches which use Convolutional Neural Networks to solve the problem of image segmentation and object recognition. The focus however is on application of U-Net convolutional neural network in an environment where knowledge about the object of interest is only limited to its rough, single pixel location. The authors provide full access to the details of the code used to implement the algorithms, as well as the data sets used and results obtained. The results show an encouraging low level of counting error at 14.27% for the best experiment.