Miracle-dz/UniFAR-FTUs huggingface dataset:
Examining the Walking Accessibility, Willingness, and Travel Conditions of Residents in Saudi Cities

Rapid urban expansion and population growth in Saudi cities over the past four decades have increased vehicular accidents and traffic congestion and have impacted the daily walking conditions of the residents. Walking has various health and environmental benefits. In North American and European countries, three factors have been found to motivate a resident to walk within their community: their accessibility to community social and business facilities, their perception and willingness, and the safety conditions of the roads and sidewalks within their community for walking. This study examined these factors and their role in the walking habits of the residents in the neighborhoods of Doha and Dana districts in Saudi Arabia’s eastern city of Dhahran. Data were collected through field observations and by randomly sampling and interviewing 200 residents. Geographic Information Systems (GIS) and SPSS statistical software were used for data analysis. The results show that most of the community facilities are randomly placed in the districts. Mosques are the closest facility to each resident with an average accessibility distance of 242m. Almost 43% of the respondents prefer daily walking while the rest are hesitant due to hot weather during summer and narrow and poorly designed sidewalks. The sidewalks were also found to be blocked by trees, street signals, and illegally parked vehicles. Future studies should explore the accessibility to facilities, willingness, climate, and health conditions of the residents, and the road and sidewalk conditions for walking in other cities of the Kingdom.
The Time Course of Recognition Memory Impairment and Glial Pathology in the hApp-J20 Mouse Model of Alzheimer’s Disease

The role of cellular changes in the neurovascular unit is increasingly being investigated to understand the pathogenesis of Alzheimer’s disease. The aim of the current study was to determine the time course of recognition memory impairment in the J20 mouse model of AD, in relation to neuroinflammatory responses and the pathology of Aβ. Male hAPP-J20 and wild-type mice were assessed at 3, 6, 9, and 12 months of age. The spontaneous object recognition (SOR) task provided a measure of memory, with assessment of both a short delay (1 min) and a long delay (4 hrs). Immunohistochemistry was used to characterise Aβ-deposition, and quantify astrocyte and microglial responses. At all ages tested J20 mice had impaired long-term, but preserved short-term, recognition memory. Wild-types demonstrated preserved long-term memory up to 9 months of age, and preserved short-term memory at all ages tested. Plaque pathology in the J20 mice was present from 6 months onwards, with co-localisation of reactive microglia and activated astrocytes. Reactive microglia and astrocyte activation in the hippocampus were significantly greater in the J20 mice at 9 months, compared to wild-types. This study contributes to our understanding of the pathological and cognitive mechanisms at play in AD. J20 mice showed impairment in retaining information over longer periods from an early age, preceding the deposition of Aβ and glial activation. Defining early physiological changes in relation to cognitive decline could provide insight into new therapeutic targets early in the disease process, when intervention is most likely to effectively slow disease progression.
Status of Cassava Begomoviruses and Their New Natural Hosts in Nigeria.

A diagnostic survey was conducted in 2002-03 to determine the status of cassava mosaic begomoviruses in Nigeria and to ascertain if the virulent Ugandan variant of East African cassava mosaic virus (EACMV-Ug2) was present. Of the 418 farms visited, 48% had cassava with moderately severe or severe symptoms, whereas 52% had cassava with mild symptoms. These distributions were at random. Of the 1,397 cassava leaf samples examined, 1,106 had symptoms. In polymerase chain reaction tests, 74.1% of the symptom-bearing samples tested positive for African cassava mosaic virus (ACMV) alone, 0.3% for EACMV alone, 24.4% for mixed infections by the two viruses, and 1.2% did not react with any of the primers used. The two viruses also were detected in 32% of the 291 symptomless plants and in the whitefly vector samples. EACMV-Ug2, Indian cassava mosaic virus, and South African cassava mosaic virus were not detected in any of the whitefly or leaf samples. Most farms had ACMV in single infection as well as in mixed infections with EACMV. Most doubly infected plants showed severe symptoms. Two biological variants of ACMV were identified based on symptom expression on cassava in the field. ACMV and EACMV were detected in the leguminous plant Senna occidentalis (L.) Link and the weed Combretum confertum Lams. ; these are new natural hosts of the viruses. Although the virulent EACMV-Ug2 was not detected, the occurrence of variants of ACMV and a high proportion of mixed infections by ACMV and EACMV, which could result in recombination events such as the one that produced EACMV-Ug2, demands appropriate measures to safeguard cassava production in Nigeria.
Outcomes of the Baha Attract System combined with auricle reconstruction in mandarin speaking patients with bilateral microtia-atresia

Abstract Background: A transcutaneous bone-conduction hearing device (tBCHD), the Baha Attract System has been recently introduced to China, and very few studies have assessed the efficacy of this system in speakers of mandarin. Objectives: This study aims to analyze the functional and cosmetic outcomes of this system. Materials and Methods: This prospective study included 11 patients (nine males, two females), of mean age 16 years (range 9–32 years). Seven patients were conducted the implantation simultaneously with auricle reconstruction, and the other four were before it. Auditory results were compared between unaided patients and implanted patients. Subjective satisfaction was analyzed using three questionnaires. Results: The mean sound field thresholds were 65.9 ± 5.1 dB SPL unaided and 30.9 ± 4.7 dB SPL with an implanted Baha Attract System, resulting in a mean hearing gain of 35.0 ± 6.7 dB. The mean WRS scores were 47.8 ± 8.7% unaided and 92.1 ± 2.0% with the Baha Attract System, resulting in a mean improvement of 47.8 ± 8.7%. No adverse events were reported and questionnaires showed good patients satisfaction. Conclusions: The transcutaneous Baha Attract System is effective in mandarin speaking patients, and the combination of hearing rehabilitation and auricle reconstruction surgery is promising for patients with bilateral microtia-atresia.
Interplay between differentially expressed enzymes contributes to light color acclimation in marine Synechococcus

Significance Marine phytoplankton are responsible for nearly half of the primary productivity on Earth, and the picocyanobacterium Synechococcus contributes up to 16% of this total. Synechococcus strains optimize their fitness by using different chromophores for photosynthetic light-harvesting in different light color niches. Many Synechococcus strains use chromatic acclimation to adjust chromophore composition to ambient blue to green light ratios. We determined that interplay between two chromophore attachment enzymes, MpeY and MpeZ, plays a role in chromatic acclimation at the level of gene expression. The unique ability of these two enzymes to attach different chromophores to the same residue makes them potentially useful for differential labeling of that residue for fluorescence-imaging technologies. Marine Synechococcus, a globally important group of cyanobacteria, thrives in various light niches in part due to its varied photosynthetic light-harvesting pigments. Many Synechococcus strains use a process known as chromatic acclimation to optimize the ratio of two chromophores, green-light–absorbing phycoerythrobilin (PEB) and blue-light–absorbing phycourobilin (PUB), within their light-harvesting complexes. A full mechanistic understanding of how Synechococcus cells tune their PEB to PUB ratio during chromatic acclimation has not yet been obtained. Here, we show that interplay between two enzymes named MpeY and MpeZ controls differential PEB and PUB covalent attachment to the same cysteine residue. MpeY attaches PEB to the light-harvesting protein MpeA in green light, while MpeZ attaches PUB to MpeA in blue light. We demonstrate that the ratio of mpeY to mpeZ mRNA determines if PEB or PUB is attached. Additionally, strains encoding only MpeY or MpeZ do not acclimate. Examination of strains of Synechococcus isolated from across the globe indicates that the interplay between MpeY and MpeZ uncovered here is a critical feature of chromatic acclimation for marine Synechococcus worldwide.
In Vivo Characterization of Avian Influenza A (H5N1) and (H7N9) Viruses Isolated from Canadian Travelers

Highly pathogenic avian influenza (HPAI) H5N1 and low pathogenic avian influenza (LPAI) H7N9 viruses pose a severe threat to public health through zoonotic infection, causing severe respiratory disease in humans. While HPAI H5N1 human infections have typically been reported in Asian countries, avian H7N9 human infections have been reported mainly in China. However, Canada reported a case of fatal human infection by the HPAI H5N1 virus in 2014, and two cases of human illness associated with avian H7N9 virus infection in 2015. While the genomes of the causative viruses A/Alberta/01/2014 (H5N1) (AB14 (H5N1)) and A/British Columbia/1/2015 (H7N9) (BC15 (H7N9)) are reported, the isolates had not been evaluated for their pathogenicity in animal models. In this study, we characterized the pathogenicity of AB14 (H5N1) and BC15 (H7N9) and found that both strain isolates are highly lethal in mice. AB14 (H5N1) caused systemic viral infection and erratic proinflammatory cytokine gene expression in different organs. In contrast, BC15 (H7N9) replicated efficiently only in the respiratory tract, and was a potent inducer for proinflammatory cytokine genes in the lungs. Our study provides experimental evidence to complement the specific human case reports and animal models for evaluating vaccine and antiviral candidates against potential influenza pandemics.
The Precuneus – A Witness for Excessive Aβ Gathering in Alzheimer’s Disease Pathology

Evidence of cortical beta-amyloid (Aβ) load, assessed by Aβ positron emission tomography (Aβ-PET), is an established in vivo biomarker of Alzheimer’s disease (AD)-related pathophysiology. Qualitative assessment of Aβ-PET provides binary information; meanwhile semiquantitative approaches require a parcellation of PET image either manually or by placement of atlas-based volumes of interest. We supposed that a whole-brain approach with voxel-by-voxel standardized uptake value ratio (SUVr) parametric images may better elucidate the spatial trajectories of Aβ burden along the continuum of AD. Methods: We recruited 32 subjects with a diagnosis of probable AD dementia (ADD, n = 20) and mild cognitive impairment due to AD (MCI-AD, n = 12) according to the NIA-AA 2011 criteria. We also enrolled a control group of 6 cognitively healthy individuals (HCs) with preserved cognitive functions and negative Aβ-PET scan. The PET images were spatially normalized using the AV45 PET template in the MNI brain space. Subsequently, parametric SUVr images were calculated using the whole cerebellum as a reference region. A voxel-wise analysis of covariance was used to compare (between groups) the Αβ distribution pattern considering age as a nuisance covariate. Results: Both ADD and MCI-AD subjects showed a widespread increase in radiotracer uptake when compared with HC participants (p < 0.001, uncorrected). After applying a multiple comparison correction (p < 0.05, corrected), a relative large cluster of increased [18F]-florbetapir uptake was observed in the precuneus in the ADD and MCI-AD groups compared to HCs. Voxel-wise regression analysis showed a significant positive linear association between the voxel-wise SUVr values and the disease duration. Conclusions: The voxel-wise semiquantitative analysis shows that the precuneus is a region with higher vulnerability to Aβ depositions when compared to other cortical regions in both MCI-AD and ADD subjects. We think that the precuneus is a promising PET-based outcome measure for clinical trials of drugs targeting brain Aβ. We found a positive association between the overall Aβ-PET SUVr and the disease duration suggesting that the region-specific slow saturation of Aβ deposition continuously takes place as the disease progresses.
Attention promotes the neural encoding of prediction errors

The human brain is thought to optimise the encoding of incoming sensory information through two principal mechanisms: prediction uses stored information to guide the interpretation of forthcoming sensory events, and attention prioritizes these events according to their behavioural relevance. Despite the ubiquitous contributions of attention and prediction to various aspects of perception and cognition, it remains unknown how they interact to modulate information processing in the brain. A recent extension of predictive coding theory suggests that attention optimises the expected precision of predictions by modulating the synaptic gain of prediction error units. Since prediction errors code for the difference between predictions and sensory signals, this model would suggest that attention increases the selectivity for mismatch information in the neural response to a surprising stimulus. Alternative predictive coding models proposes that attention increases the activity of prediction (or ‘representation’) neurons, and would therefore suggest that attention and prediction synergistically modulate selectivity for feature information in the brain. Here we applied multivariate forward encoding techniques to neural activity recorded via electroencephalography (EEG) as human observers performed a simple visual task, to test for the effect of attention on both mismatch and feature information in the neural response to surprising stimuli. Participants attended or ignored a periodic stream of gratings, the orientations of which could be either predictable, surprising, or unpredictable. We found that surprising stimuli evoked neural responses that were encoded according to the difference between predicted and observed stimulus features, and that attention facilitated the encoding of this type of information in the brain. These findings advance our understanding of how attention and prediction modulate information processing in the brain, and support the theory that attention optimises precision expectations during hierarchical inference by increasing the gain of prediction errors.
Capture and display of antibodies secreted by hybridoma cells enables fluorescent on-cell screening

ABSTRACT Hybridoma methods for monoclonal antibody (mAb) cloning are a mainstay of biomedical research, but they are hindered by the need to maintain hybridomas in oligoclonal pools during antibody screening. Here, we describe a system in which hybridomas specifically capture and display the mAbs they secrete: On-Cell mAb Screening (OCMS™). In OCMS™, mAbs displayed on the cell surface can be rapidly assayed for expression level and binding specificity using fluorescent antigens with high-content (image-based) methods or flow cytometry. OCMS™ demonstrated specific mAb binding to poliovirus and rabies virus by forming a cell surface IgG “cap”, as a universal assay for anti-viral mAbs. We produced and characterized OCMS™-enabled hybridomas secreting mAbs that neutralize poliovirus and used fluorescence microscopy to identify and clone a human mAb specific for the human N-methyl-D-aspartate receptor. Lastly, we used OCMS™ to assess expression and antigen binding of a recombinant mAb produced in 293T cells. As a novel method to physically associate mAbs with the hybridomas that secrete them, OCMS™ overcomes a central challenge to hybridoma mAb screening and offers new paradigms for mAb discovery and production.
Parameters to Predict Progression-Free and Overall Survival After Peptide Receptor Radionuclide Therapy: A Multivariate Analysis in 782 Patients

Peptide receptor radionuclide therapy (PRRT) is an effective treatment for patients with neuroendocrine neoplasms. The aim of this study was to identify clinical and treatment parameters associated with progression-free survival (PFS) and overall survival (OS). Methods: All patients treated from October 2002 until March 2016 at the Zentralklinik Bad Berka with at least 3 administrations of PRRT (maximal interval of 6 mo between consecutive administrations) were included. Data were collected in 5 categories: general patient characteristics, tumor characteristics, prior treatments, radioisotope used for PRRT, and blood chemistry. Survival was analyzed using Kaplan–Meier curves. Univariate and multivariate Cox regression analyses were performed to identify parameters associated with PFS and OS. Results: In total, 782 patients were included, with a median follow-up of 36 mo. The median PFS and OS were 22 and 53 mo, respectively. Parameters associated with lower PFS in the multivariate analysis were a Ki-67 of more than 5%, previous treatment with interferon-α and chemotherapy, presence of diabetes, and chromogranin-A (CgA) levels higher than 336 μg/L. Parameters associated with lower OS were a Ki-67 of more than 10%, performance status of at least 1, previous chemotherapy and ablation, and CgA levels higher than 112 μg/L. Conclusion: Higher Ki-67 values, as well as higher CgA levels and previous chemotherapy, had a negative outcome on both PFS and OS. Furthermore, PFS was negatively associated with previous interferon-α treatment and diabetes, whereas lower OS was related to prior ablation and higher performance status.
Limits of Diagnosis and Molecular Markers for Early Detection of Ulcerative Colitis-Associated Colorectal Neoplasia

The incidence of colorectal neoplasia has been increasing among patients with long-standing and extensive ulcerative colitis (UC), and therefore surveillance colonoscopy has been widely recommended. However, because UC-associated neoplasia is often difficult to detect endoscopically and to discriminate from inflammatory regenerative epithelium histologically, the efficacy of current surveillance remains unsatisfactory. In order to overcome these difficulties, adjunctive modalities for diagnosing UC-associated neoplasia, chromo- and magnifying endoscopy for endoscopic diagnosis and analysis of p53 alteration for histological diagnosis have been introduced. Furthermore, if it were possible to differentiate UC patients with long-standing and extensive colitis into subgroups with a high and a low risk of neoplasia, it would enable physicians to conduct more intensive surveillance with these modalities for patients at higher risk. Several molecular alterations of nonneoplastic epithelium in UC patients with neoplasia may be promising as markers for identifying individuals with UC at increased risk of neoplasia. We evaluated estrogen receptor (ER) methylation of nonneoplastic colorectal epithelium to clarify whether this epigenetic alteration can contribute to the prediction of increased neoplasia risk in UC patients and demonstrated that the ER methylation level in nonneoplastic epithelium was higher throughout the colorectum in patients with neoplasia than in those without. These results suggest that analysis of ER gene methylation may be potentially useful for identifying individuals at increased risk of neoplasia among patients with long-standing and extensive UC.
Non-invasive assessment of liver fibrosis and prognosis: an update on serum and elastography markers

ABSTRACT Introduction: Non-invasive assessment of fibrosis is increasingly utilized in clinical practice to diagnose hepatic fibrosis. Non-invasive assessment of liver fibrosis relies on biologic and/or physical properties to assess tissue fibrosis. Serum markers estimate fibrosis by incorporating markers reflecting hepatic function (indirect markers) and/or markers measuring extracellular matrix degradation/fibrogenesis (direct markers). Radiology based techniques relay the mechanical properties and stiffness of a tissue, with increased stiffness associated with more advanced fibrosis. Areas covered: In this comprehensive review, the recent literature discussing serum markers and elastography-based techniques will be covered. These modalities are also explored in the setting of various liver diseases. Expert opinion: The etiology of liver disease and clinical context should be taken into consideration when non-invasive markers are incorporated in clinical practice. Non-invasive assessment of fibrosis has been most extensively utilized in hepatitis C, followed by hepatitis B and nonalcoholic fatty liver disease, but its role remains less developed in other etiologies of liver disease such as alcohol-associated liver disease and autoimmune liver disease. The role of non-invasive markers in predicting progression or regression of fibrosis, development of liver-related events and survival needs to be further explored.
Influence of OCT signal strength on macular, optic nerve head, and retinal nerve fiber layer parameters.

PURPOSE To examine the influence of different signal strengths on measurements made with optical coherence tomography (OCT) of macular, optic nerve head, and retinal nerve fiber layer (RNFL) parameters. METHODS From 2003 to 2005, 2092 children, mostly aged 12 years, were examined, and macular, optic nerve head, and RNFL parameters were measured by OCT. Multiple fast scans were acquired, and only right eyes were included in the analyses. Signal strength category was determined after averaging individual signal strengths from each scan and classifying scans as providing moderate (average signal strength, 5-7.49), good (average signal strength, 7.5-9.49), and excellent (average signal strength, >or=9.5) image quality. General linear models were used after adjustment for covariates. RESULTS Significant differences were observed between measurements obtained at excellent signal strengths compared with those obtained at moderate and good signal strengths for both macular and optic nerve parameters. However, although statistically significant, the magnitude of the differences in macular parameters was very small (approximately 5 microm, or a 2% difference). Differences in optic nerve head parameters were much greater (up to a 32% difference), with larger measurements recorded for most parameters with increasing signal strength category. Significant differences in RNFL parameters with increasing signal strength were not demonstrated. CONCLUSIONS Significantly larger macular and optic nerve head OCT measurements were obtained with increasing signal strength measurements, although absolute differences in macular measurements were small and are of questionable clinical importance. The results support the robustness of OCT in providing precise macular imaging.