Miracle-dz/UniFAR-FTUs huggingface dataset:
Parasite specialization in a unique habitat: hummingbirds as reservoirs of generalist blood parasites of Andean birds.

Understanding how parasites fill their ecological niches requires information on the processes involved in the colonization and exploitation of unique host species. Switching to hosts with atypical attributes may favour generalists broadening their niches or may promote specialization and parasite diversification as the consequence. We analysed which blood parasites have successfully colonized hummingbirds, and how they have evolved to exploit such a unique habitat. We specifically asked (i) whether the assemblage of Haemoproteus parasites of hummingbirds is the result of single or multiple colonization events, (ii) to what extent these parasites are specialized in hummingbirds or shared with other birds and (iii) how hummingbirds contribute to sustain the populations of these parasites, in terms of both prevalence and infection intensity. We sampled 169 hummingbirds of 19 species along an elevation gradient in Southern Ecuador to analyse the host specificity, diversity and infection intensity of Haemoproteus by molecular and microscopy techniques. In addition, 736 birds of 112 species were analysed to explore whether hummingbird parasites are shared with other birds. Hummingbirds hosted a phylogenetically diverse assemblage of generalist Haemoproteus lineages shared with other host orders. Among these parasites, Haemoproteus witti stood out as the most generalized. Interestingly, we found that infection intensities of this parasite were extremely low in passerines (with no detectable gametocytes), but very high in hummingbirds, with many gametocytes seen. Moreover, infection intensities of H. witti were positively correlated with the prevalence across host species. Our results show that hummingbirds have been colonized by generalist Haemoproteus lineages on multiple occasions. However, one of these generalist parasites (H. witti) seems to be highly dependent on hummingbirds, which arise as the most relevant reservoirs in terms of both prevalence and gametocytaemia. From this perspective, this generalist parasite may be viewed as a hummingbird specialist. This challenges the current paradigm of how to measure host specialization in these parasites, which has important implications to understand disease ecology.
Evidence for tight junction protein disruption in intestinal mucosa of malignant obstructive jaundice patients

Abstract Objective. Experimental and clinical studies have shown that obstructive jaundice results in increased intestinal permeability. The mechanisms implicated in this phenomenon remain obscure. Integrated tight junctions (TJs) are essential for normal gut barrier function. TJ proteins, such as zonula occludens (ZO)-1, claudins and occludin, are indispensable to maintain the function of TJs. This study was undertaken to investigate whether TJ protein disruption occurs in the intestinal mucosa of malignant obstructive jaundice (MOJ) patients. Material and methods. Three groups were involved: Group A, MOJ patients whose bilirubin level was ≥ 43 μM; Group B, MOJ patients without jaundice; and Group C, patients who underwent gastroscopy with negative findings (controls). Biopsy was done in all participants at the second part of the duodenum, distal to the ampulla of Vater. The morphological and ultrastructural changes of intestinal mucosa were observed. The distributions and expressions of the TJ proteins occludin, ZO-1, claudin-1 and claudin-4 in intestinal mucosa were evaluated by immunohistochemistry and Western blotting. Results. Histological examination showed a mild infiltration of the lamina propria by chronic inflammatory cells in Group A compared with Groups B and C. Duodenal architecture showed that the microvillus of Group A patients was loose, the structures of junctional complexes were disrupted and the gaps between cell junctions were wider. As shown by immunohistochemical staining and Western blotting, greatly reduced expressions of occludin, ZO-1 and claudin-1 protein were detected in Group A, whereas claudin-4 expression was significantly increased. Conclusions. TJs in MOJ patients with jaundice were disrupted in the intestinal epithelium, which may have resulted from the alterations in TJ-related protein expression. TJ interruption may be a key factor contributing to intestinal mucosal barrier injury and increased intestinal permeability.
Caveolin-1 promotes Ewing sarcoma metastasis regulating MMP-9 expression through MAPK/ERK pathway

Ewing sarcoma (ES) is a bone and soft tissue sarcoma affecting mostly children and young adults. Caveolin-1 (CAV1) is a well-known target of EWS/FLI1, the main driver of ES, with an oncogenic role in ES. We have previously described how CAV1 is able to induce metastasis in ES via matrix metalloproteinase-9 (MMP-9). In the present study we showed how CAV1 silencing in ES reduced MEK1/2 and ERK1/2 phosphorylation. Accordingly, chemical inhibition of MEK1/2 resulted in reduction in MMP-9 expression and activity that correlated with reduced migration and invasion. IQ Motif Containing GTPase Activating Protein 1 (IQGAP1) silencing reduced MEK1/2 and ERK1/2 phosphorylation and MMP-9 expression. Furthermore, IQGAP1 silenced cells showed a marked decrease in their migratory and invasive capacity. We demonstrated that CAV1 and IQGAP1 localize in close proximity at the cellular edge, thus IQGAP1 could be the connecting node between CAV1 and MEK/ERK in ES metastatic phenotype. Analysis of the phosphorylation profile of CAV1-silenced cells showed a decrease of p-ribosomal protein S6 (RPS6). RPS6 can be phosphorylated by p90 ribosomal S6 kinases (RSK) proteins. CAV1-silenced cells showed reduced levels of p-RSK1 and treatment with U0126 provoked the same effect. Despite not affecting ERK1/2 and RPS6 phosphorylation status neither MMP-9 expression nor activity, RSK1 silencing resulted in a reduced migratory and invasive capacity in vitro and reduced incidence of metastases in vivo in a novel orthotopic model. The present work provides new insights into CAV1-driven metastatic process in ES unveiling novel key nodes.
ATR-Vis

The worldwide adoption of Twitter turned it into one of the most popular platforms for content analysis as it serves as a gauge of the public’s feeling and opinion on a variety of topics. This is particularly true of political discussions and lawmakers’ actions and initiatives. Yet, one common but unrealistic assumption is that the data of interest for analysis is readily available in a comprehensive and accurate form. Data need to be retrieved, but due to the brevity and noisy nature of Twitter content, it is difficult to formulate user queries that match relevant posts that use different terminology without introducing a considerable volume of unwanted content. This problem is aggravated when the analysis must contemplate multiple and related topics of interest, for which comments are being concurrently posted. This article presents Active Tweet Retrieval Visualization (ATR-Vis), a user-driven visual approach for the retrieval of Twitter content applicable to this scenario. The method proposes a set of active retrieval strategies to involve an analyst in such a way that a major improvement in retrieval coverage and precision is attained with minimal user effort. ATR-Vis enables non-technical users to benefit from the aforementioned active learning strategies by providing visual aids to facilitate the requested supervision. This supports the exploration of the space of potentially relevant tweets, and affords a better understanding of the retrieval results. We evaluate our approach in scenarios in which the task is to retrieve tweets related to multiple parliamentary debates within a specific time span. We collected two Twitter datasets, one associated with debates in the Canadian House of Commons during a particular week in May 2014, and another associated with debates in the Brazilian Federal Senate during a selected week in May 2015. The two use cases illustrate the effectiveness of ATR-Vis for the retrieval of relevant tweets, while quantitative results show that our approach achieves high retrieval quality with a modest amount of supervision. Finally, we evaluated our tool with three external users who perform searching in social media as part of their professional work.
The Novel PAPR Reduction Schemes for O‐OFDM‐Based Visible Light Communications

In this chapter, we propose two novel peak-to-average power ratio (PAPR) reduction schemes for the asymmetrically clipped optical orthogonal frequency division multiplexing (ACO-OFDM) scheme used in the visible light communications (VLC) system. In the first scheme, we implement the Toeplitz matrix based Gaussian blur method to reduce the high PAPR of ACO-OFDM at the transmitter and use the orthogonal matching pursuit algorithm to recover the original ACO-OFDM frame at the receiver. Simulation results show that for the 256-subcarrier ACO-OFDM system a ~6 dB improvement in PAPR is achieved compared with the original ACO-OFDM in terms of the complementary cumulative distribution function (CCDF), while maintaining a com- petitive bit-error rate performance compared with the ideal ACO-OFDM lower bound. In the second scheme, we propose an improved hybrid optical orthogonal frequency division multiplexing (O-OFDM) and pulse-width modulation (PWM) scheme to reduce the PAPR for ACO-OFDM. The bipolar O-OFDM signal without negative clipping is converted into a PWM format where the leading and trailing edges carry the frame synchronization and modulated information, respectively. The simulation and experi- mental results demonstrate that the proposed OFDM-PWM scheme offers a significant PAPR reduction compared to the ACO-OFDM with an improved bit error rate.
RETRACTED ARTICLE: The effect of safranal loaded mucoadhesive nanoemulsion on oxidative stress markers in cerebral ischemia

Abstract We, the Editors and Publishers of Artificial Cells, Nanomedicine, and Biotechnology, have retracted the following article: Niyaz Ahmad, Rizwan Ahmad, Atta Abbas Naqvi, Mohammad Ashafaq, Md Aftab Alam, Farhan Jalees Ahmad & Mastour Safer Al-Ghamdi. (2017). The effect of safranal loaded mucoadhesive nanoemulsion on oxidative stress markers in cerebral ischaemia. Artificial Cells, Nanomedicine, and Biotechnology, 45:4, 775–787. DOI: 10.1080/21691401.2016. 1228659 This article is retracted due to reuse of images from other articles by the same authors, representing results of different experiments. This includes Figure 1, which can also be found in: Ahmad et al. (2018). Intranasal delivery of quercetin-loaded mucoadhesive nanoemulsion for treatment of cerebral ischaemia. Artificial Cells, Nanomedicine, and Biotechnology. https://doi.org/10.1080/21691401.2017. 1337024 In addition, concerns were raised regarding the integrity of other Figures in the article, including Figures 3, 7(a), 8 and 9. When asked for an explanation, the authors were unable to provide raw data that would support the integrity of their research. As the authors were unable to provide the original images, the Editors agreed the findings of the study are no longer valid and advised for the article to be retracted. The authors do not agree with the retraction. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as “Retracted”.
Significance of Cell Cycle Regulatory Proteins as Malignant and Prognostic Biomarkers in Ovarian Epithelial Tumors

The principal objective of this study was to comprehensively assess the clinicopathologic and prognostic impacts of the expression of various cell cycle regulatory proteins in patients with ovarian epithelial tumors. The tissue microarrays were constructed from formalin-fixed, paraffin-embedded tissues of 205 ovarian epithelial tumors. We investigated 55 benign (20 serous cystadenomas, 17 mucinous cystadenomas, and 18 endometriotic cysts), 72 borderline (26 serous borderline tumors and 46 mucinous borderline tumors), and 78 malignant tumors (45 serous carcinomas, 10 mucinous adenocarcinomas, 15 endometrioid adenocarcinomas, and 8 clear cell carcinomas). Immunohistochemical staining was performed using antibodies to p16Ink4a, p53, p21Waf1/Cip1, p27Kip1, Cyclin D1, Cyclin E, Cyclin A, Cyclin B1, and Cyclin-dependent Kinase2. We noted significantly different levels of p53 and Cyclin B1 expressions between malignant and borderline tumors and between borderline and benign tumors excepting the mucinous type. The p21Waf1/Cip1 and Cyclin A were significantly overexpressed in malignant tumors compared with borderline tumors. Cyclin A, Cyclin E, and p16Ink4a were more pronounced proteins, showing differential expression patterns among the histologic types of ovarian carcinomas. We determined that the overexpression of p16Ink4a (P=0.031), Cyclin E (P=0.009), and Cyclin-dependent Kinase2 (P=0.004) were significantly associated with higher tumor grades. Overexpression of p16Ink4a was correlated with both lymph node metastasis (P=0.030) and distant metastasis (P=0.034). Overexpression of Cyclin E was associated with advanced stage (P=0.004). Higher tumor grade (P=0.008), advanced stage (P=0.001), mucinous histologic type (P=0.012), low expression levels of p16Ink4a (P=0.032), and overexpression of p53 (P=0.032) were associated with poor overall survival on multivariate analysis in patients with ovarian cancer. In serous carcinomas, old age (P=0.005), distant metastasis (P=0.020), low expression of p16Ink4a (P=0.047), and overexpression of cytoplasmic p27Kip1 (P=0.007) and Cyclin A (P=0.031) were all independent predictors of worse overall survival. Our data indicate that the overexpression of p16Ink4a and Cyclin E are valuable factors predicting disease progression and metastatic potential. Low p16Ink4a expression, overexpression of p53, cytoplasmic p27Kip1, and Cyclin A are predictive markers for shorter overall survival in ovarian carcinomas.
The Influence of Feedback on Task-Switching Performance: A Drift Diffusion Modeling Account

Task-switching is an important cognitive skill that facilitates our ability to choose appropriate behavior in a varied and changing environment. Task-switching training studies have sought to improve this ability by practicing switching between multiple tasks. However, an efficacious training paradigm has been difficult to develop in part due to findings that small differences in task parameters influence switching behavior in a non-trivial manner. Here, for the first time we employ the Drift Diffusion Model (DDM) to understand the influence of feedback on task-switching and investigate how drift diffusion parameters change over the course of task switch training. We trained 316 participants on a simple task where they alternated sorting stimuli by color or by shape. Feedback differed in six different ways between subjects groups, ranging from No Feedback (NFB) to a variety of manipulations addressing trial-wise vs. Block Feedback (BFB), rewards vs. punishments, payment bonuses and different payouts depending upon the trial type (switch/non-switch). While overall performance was found to be affected by feedback, no effect of feedback was found on task-switching learning. Drift Diffusion Modeling revealed that the reductions in reaction time (RT) switch cost over the course of training were driven by a continually decreasing decision boundary. Furthermore, feedback effects on RT switch cost were also driven by differences in decision boundary, but not in drift rate. These results reveal that participants systematically modified their task-switching performance without yielding an overall gain in performance.
Assessment of Fatigue in End Stage Renal Disease Patients Undergoing Hemodialysis: Prevalence and Associated Factors

Background: Fatigue is a common symptom referred by many patients undergoing hemodialysis. Fatigue is associated with poor health-related quality of life (HRQoL) and is an important predictor for survival of hemodialysis patients. Aim: To assess the levels of fatigue and demographic factors affecting it among patients with End Stage Renal Disease undergoing hemodialysis. Methods: This quantitative study was carried out in two Dialysis Units of Hospitals in Athens Region. Between January 2015 and June 2015, 129 hemodialysis patients completed the Greek Version of the Fatigue Assessment Scale (FAS). Demographic data of patients was recorded. For the statistical analysis IBM SPSS Statistics version 20 was used. Results: The mean FAS score was 24.99. 49 patients (38.0%) were non fatigued, 61 patients (47.3%) were fatigued, and 19 patients (13.7%) were extremely fatigued. Higher levels of fatigue were reported among hemodialysis patients residing in urban areas, in those with low educational level and unemployed. Conclusion: The findings of this study can be used in the assessment of fatigue and early identification of high-risk patients (especially of the unemployed, those who occupy with domestic works, those with low educational level and of urban citizens). Use of this knowledge by hemodialysis nurses may lead to a better understanding of the factors of fatigue in ESRD, which in turn may lead to a more effective treatment.
Assessing Vowel Centralization in Dysarthria: A Comparison of Methods.

Purpose The strength of the relationship between vowel centralization measures and perceptual ratings of dysarthria severity has varied considerably across reports. This article evaluates methods of acoustic-perceptual analysis to determine whether procedural changes can strengthen the association between these measures. Method Sixty-one speakers (17 healthy individuals and 44 speakers with dysarthria) read a standard passage. To obtain acoustic data, 2 points of formant extraction (midpoint and articulatory point) and 2 frequency measures (Hz and Bark) were trialed. Both vowel space area and an adapted formant centralization ratio were calculated using first and second formants of speakers' corner vowels. Twenty-eight listeners rated speech samples using different prompts: one with a focus on intelligibility, the other on speech precision. Results Perceptually, listener ratings of speech precision provided the best index of acoustic change. Acoustically, the combined use of an articulatory-based formant extraction point, Bark frequency units, and the formant centralization ratio was most effective in explaining perceptual ratings. This combination of procedures resulted in an increase of 17% to 27% explained variance between measures. Conclusions The procedures researchers use to assess articulatory impairment can significantly alter the strength of relationship between acoustic and perceptual measures. Procedures that maximize this relationship are recommended.
Alternatives to Autologous Bone Graft in Alveolar Cleft Reconstruction: The State of Alveolar Tissue Engineering

Abstract Alveolar cleft reconstruction has historically relied on autologous iliac crest bone grafting (ICBG), but donor site morbidity, pain, and prolonged hospitalization have prompted the search for bone graft substitutes. The authors evaluated bone graft substitutes with the highest levels of evidence, and highlight the products that show promise in alveolar cleft repair and in maxillary augmentation. This comprehensive review guides the craniofacial surgeon toward safe and informed utilization of biomaterials in the alveolar cleft. A literature search was performed to identify in vitro human studies that fulfilled the following criteria: Level I or Level II of evidence, ≥30 subjects, and a direct comparison between a autologous bone graft and a bone graft substitute. A second literature search was performed that captured all studies, regardless of level of evidence, which evaluated bone graft substitutes for alveolar cleft repair or alveolar augmentation for dental implants. Adverse events for each of these products were tabulated as well. Sixteen studies featuring 6 bone graft substitutes: hydroxyapatite, demineralized bone matrix (DBM), &bgr;-tricalcium phosphate (TCP), calcium phosphate, recombinant human bone morphogenic protein-2 (rhBMP-2), and rhBMP7 fit the inclusion criteria for the first search. Through our second search, the authors found that DBM, TCP, rhBMP-2, and rhBMP7 have been studied most extensively in the alveolar cleft literature, though frequently in studies using less rigorous methodology (Level III evidence or below). rhBMP-2 was the best studied and showed comparable efficacy to ICBG in terms of volume of bone regeneration, bone density, and capacity to accommodate tooth eruption within the graft site. Pricing for products ranged from $290 to $3110 per 5 mL. The balance between innovation and safety is a complex process requiring constant vigilance and evaluation. Here, the authors profile several bone graft substitutes that demonstrate the most promise in alveolar cleft reconstruction.
Evidence of change blindness in subjective image fidelity assessment

Change blindness is a striking phenomenon which basically means that we can look without seeing. It originates from a faulty communication between early vision (the eye) and visual working memory (the brain). In this paper, we present evidence that this faulty communication needs to be accounted for in image fidelity assessment (also known as full-reference image quality assessment). We designed a user study to analyse participants opinions based on how much they have to rely on their visual working memory in order to give fidelity score. Results demonstrate that significantly more severe judgments were made when reliance on visual short-term memory was minimal, suggesting limitations in the observers' ability to notice image differences in the typical pairwise comparison setup. Furthermore, a comparison of the efficiency of six state-of-the-art image fidelity assessment models (so-called metrics) reveals that five of them perform significantly better at predicting results obtained when reliance on memory is minimal.
A Comparison of Note Writers and No Note Writers in Homicide-Suicide Cases in Germany

The aim of this study is to investigate potential differences between homicide-suicide cases in which the perpetrator does or does not write a suicide note. As homicide-suicides are complex types of lethal violence for which the aggressor cannot be held accountable, suicide notes may be a valuable source of information about the background of these cases and the perpetrators’ motives. We use a national sample of N = 288 homicide-suicide cases in Germany applying group comparisons and chi-square tests for relevant variables. Perpetrators killing their own children and perpetrators leaving children behind before killing themselves write significantly more suicide notes than other perpetrators. Even though note writers and no note writers are similar regarding most sociodemographic characteristics, other differences question the generalizability between these 2 groups.