Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunogenicity and Tolerability to Human Papillomavirus-like Particle Vaccine in Girls and Young Women with Inflammatory Bowel Disease

Background:Female patients receiving immunosuppressive therapy may be at increased risk for human papillomavirus (HPV) infection and cervical neoplasia. Methods:We administered the 3-dose HPV vaccine Gardasil to 37 females aged 9 to 26 years with inflammatory bowel disease (IBD) prescribed immunosuppressive therapy (prospective cohort). Geometric mean titers (GMT) in milli-Merck (mMu/mL) units were determined before dose 1 and 1 month after dose 3 by competitive Luminex immunoassay (cLIA) and qualitatively compared with healthy females of similar age from Merck’s database. Side effects and adverse events were evaluated. Concurrently, in 15 similar patients with inflammatory bowel disease previously vaccinated by their primary care provider, we assessed antibody titers by competitive Luminex immunoassay and total immunoglobulin G LIA after dose 3 of vaccine (range, 0.5–27 months). Results:Mean age of prospective patients was 15 years with 51% on anti–tumor necrosis factor therapy and 49% on immunomodulators: 33 of 37 completed all 3 doses. Seropositivity after dose 3 was 100% for types 6, 11 and 16 and 96% for type 18. Geometric mean titers for HPV-6, HPV-11, HPV-16 and HPV-18 was 1080, 1682, 3975 and 858, respectively and did not qualitatively differ from healthy females. No serious adverse events were attributable to the vaccine. In the previously vaccinated cohort, seropositivity was 100% for types 6, 11, and 16, and 40% for type 18 by competitive Luminex immunoassay (93% for HPV-18 by immunoglobulin G LIA). Titers decreased with time since dose 3. Conclusions:In this small study of patients with inflammatory bowel disease prescribed immunosuppressive therapy, Gardasil was immunogenic and there were no clinically significant vaccine-associated adverse events.
Scale-specific and scale-independent measures of heart rate variability as risk indicators

We study the correlation properties of heartbeat fluctuations using scale-specific variance (root-mean-square fluctuation) and scaling (correlation) exponents as measures of healthy and cardiac impaired individuals. Our results show that the variance and the scaling exponent are uncorrelated. We find that the variance measure at certain scales is well suited to separate healthy subjects from heart patients. However, for mortality prediction the scaling exponents outperform the variance measure. Our study is based on a database containing recordings from 428 individuals after myocardial infarct (MI) and on a database containing 105 healthy subjects and 11 heart patients. The results have been obtained by applying two recently developed methods (DFA -Detrended Fluctuation Analysis and WAV -Multiresolution Wavelet Analysis) which are shown to be highly correlated.
Maximum Entropy Ecological Niche Prediction of the Current Potential Geographical Distribution of Eimeria Species of Cattle, Sheep and Goats in Mexico

Coccidiosis is a gastrointestinal disease caused by parasites of the genus Eimeria. To produce the ecological niche model for the geographic distribution of Eimeria species, the maximum entropy algorithm (MaxEnt) was used and 19 bioclimatic variables with a spatial resolution of 30 arc-seconds (approximately 1 km2) were downloaded from the World Climate Database. These were reduced to BIO2, BIO3, BIO4, BIO7 and BIO15 for each species after examining cross-correlations among them to account multicollinearity. A jackknife analysis was included to assess the contribution of five bioclimatic variables and the fit of the model was evaluated with the area under receiver operating characteristic curve (AUC). Under a current climate scenario, the jackknife evaluation of the MaxEnt model showed that BIO4 (temperature seasonality) made the greatest contribution to the distribution model for 22 Eimeria species; whereas BIO7 (temperature annual range) was the most important factor that contributes to the distribution model of 10 species. The habitat suitability model based on the maximum entropy theory was supported by AUC values higher than 0.9 and predicted that the suitable habitats for different species of Eimeria are present in southern, eastern and western areas of Mexico. Our study may support future studies exploring factors that constrain the distribution of Eimeria as well as strategies aimed at reducing the disease prevalence.
Efficient Metric Learning for Real-World Face Recognition

Real-world face recognition is a large-scale task. It is large-scale in a sense that image acquisition devices are omnipresent in our daily life. Thus, more and more images are taken every day that need to be processed, where often a human face is the object of interest. As data grows several challenges and opportunities are posed to computational face recognition algorithms, additional to the recognition challenge. A main criterion for the applicability of machine learning algorithms is the scalability in terms of learning, evaluation costs and also the needed effort to obtain labels and annotations. Scanning web-scale data sets of images containing millions of faces call for sophisticated search and retrieval strategies, where efficient algorithms are clearly beneficial. Thus, in this thesis, we introduce novel Mahalanobis metric learning methods for real-world face recognition. The goal of Mahalanobis metric learning is to exploit prior information such as labels to learn a similarity measure that is better suited for a particular task like face recognition. In particular, we propose algorithms that offer scalability in terms of learning, evaluation and required annotation. Scalability in training is introduced by a formulation that allows for learning a Mahalanobis metric that does not rely on complex optimization problems requiring computationally expensive iterations. Our algorithm is flexible enough to learn form pairwise labels and is thus applicable for a wide range of large-scale problems. To speed up evaluation we first propose a metric-based hashing strategy and second bridge the gap between metric learning and prototype learning, enabling efficient retrieval. Further, by combining metric learning and multi-task learning we account the fact that faces share strong visual similarities, which can be exploited when learning discriminative models. Moreover, a face recognition pipeline heavily relies on face detection and landmark extraction as preprocessing steps, requiring large-scale data for training. Therefore, we introduce a publicly available database with suitable training data.
Discouraged by Peer Excellence

People are exposed to exemplary peer performances often (and sometimes by design in interventions). In two studies, we showed that exposure to exemplary peer performances can undermine motivation and success by causing people to perceive that they cannot attain their peers’ high levels of performance. It also causes de-identification with the relevant domain. We examined such discouragement by peer excellence by exploiting the incidental exposure to peers’ abilities that occurs when students are asked to assess each other’s work. Study 1 was a natural experiment in a massive open online course that employed peer assessment (N = 5,740). Exposure to exemplary peer performances caused a large proportion of students to quit the course. Study 2 explored underlying psychological mechanisms in an online replication (N = 361). Discouragement by peer excellence has theoretical implications for work on social judgment, social comparison, and reference bias and has practical implications for interventions that induce social comparisons.
Substrate metabolism, appetite and feeding behaviour under low and high energy turnover conditions in overweight women

The present study aimed to investigate whether substrate metabolism, appetite and feeding behaviour differed between high and low energy turnover conditions. Thirteen overweight premenopausal women completed two 1 d trials: low energy turnover (LET) and high energy turnover (HET), in a randomised, cross-over design. In LET, subjects consumed a test breakfast (49 % carbohydrate, 37 % fat, 14 % protein) calculated to maintain energy balance over a 6 h observation period, during which metabolic rate and substrate utilisation were measured and blood samples taken. Immediately following this an ad libitum buffet meal was provided. HET was identical to LET, except that subjects walked on a treadmill for 60 min at 50 % VO2max before the test breakfast, which was increased in size (by about 65 %) to replace the energy expended during the walk and maintain energy balance over the observation period. Postprandial fat balance (i.e. the difference between fat intake and oxidation) was lower and carbohydrate balance higher in HET compared with LET throughout the postprandial period (P < 0·05 for both). After the buffet meal, carbohydrate balance did not differ between trials but energy and fat balances were lower (by 0·28 MJ and 11·6 g, respectively) in HET compared with LET (P < 0·001 for both). Carbohydrate balance immediately before the buffet meal correlated negatively with buffet energy intake (r − 0·49) and postprandial acylated ghrelin responses (r − 0·48), and positively with postprandial glucose responses (r 0·49). These findings demonstrate that HET resulted in a more positive carbohydrate balance than LET, which associated with lower subsequent energy intake. This may have implications for the regulation of body weight.
Local Ecological Knowledge and Scientific Data Reveal Overexploitation by Multigear Artisanal Fisheries in the Southwestern Atlantic

In the last decades, a number of studies based on historical records revealed the diversity loss in the oceans and human-induced changes to marine ecosystems. These studies have improved our understanding of the human impacts in the oceans. They also drew attention to the shifting baseline syndrome and the importance of assessing appropriate sources of data in order to build the most reliable environmental baseline. Here we amassed information from artisanal fishermen's local ecological knowledge, fisheries landing data and underwater visual census to assess the decline of fish species in Southeastern Brazil. Interviews with 214 fishermen from line, beach seine and spearfishing revealed a sharp decline in abundance of the bluefish Pomatomus saltatrix, the groupers Epinephelus marginatus, Mycteroperca acutirostris, M. bonaci and M. microlepis, and large parrotfishes in the past six decades. Fisheries landing data from a 16-year period support the decline of bluefish as pointed by fishermen's local knowledge, while underwater visual census campaigns show reductions in groupers' abundance and a sharp population decline of the Brazilian endemic parrotfish Scarus trispinosus. Despite the marked decline of these fisheries, younger and less experienced fishermen recognized fewer species as overexploited and fishing sites as depleted than older and more experienced fishermen, indicating the occurrence of the shifting baseline syndrome. Here we show both the decline of multigear fisheries catches – combining anecdotal and scientific data – as well as changes in environmental perceptions over generations of fishermen. Managing ocean resources requires looking into the past, and into traditional knowledge, bringing historical baselines to the present and improving public awareness.
Improving distributed representation by feature selection of Wikipedia

Distributed representation plays an important role in many application of Natural Language Processing (NLP). Today, Word2Vec model has been getting an attention against the backdrop of the easy access to enormous language data from the Internet such as Wikipedia. For the effective use of Word2Vec, we have to concern not only about the improvement of the method itself but also about the process of making training data. In this paper, we demonstrate that adequate selection of training data can make a great improvement of the performance of Word2Vec compared to existing research. We also confirmed that Wikipedia dump data is not a good source of training data as is.
The avian respiratory system: a unique model for studies of respiratory toxicosis and for monitoring air quality.

There are many distinct differences (morphologic, physiologic, and mechanical) between the bird's lung-air-sac respiratory system and the mammalian bronchoalveolar lung. In this paper, we review the physiology of the avian respiratory system with attention to those mechanisms that may lead to significantly different results, relative to those in mammals, following exposure to toxic gases and airborne particulates. We suggest that these differences can be productively exploited to further our understanding of the basic mechanisms of inhalant toxicology (gases and particulates). The large mass-specific gas uptake by the avian respiratory system, at rest and especially during exercise, could be exploited as a sensitive monitor of air quality. Birds have much to offer in our understanding of respiratory toxicology, but that expectation can only be realized by investigating, in a wide variety of avian taxa, the pathophysiologic interactions of a broad range of inhaled toxicants on the bird's unique respiratory system. Imagesp188-aFigure 1.Figure 2.Figure 3.Figure 4.Figure 5. AFigure 5. BFigure 5. CFigure 6.Figure 7.Figure 8.
What Works in Professional Development?

hat do we really know about the relationship between professional development and improvements in student learning? What evidence validates that relationship, and how trustworthy is that evidence? What does that evidence tell us about the characteristics of truly effective professional development activities? These questions guided one of the largest and most inclusive syntheses of research on effective professional development conducted to date. Scholars from the American Institutes for Research analyzed findings from over 1,300 studies that potentially address the effect of professional development on student learning outcomes. The project was sponsored by the Regional Education Laboratory-Southwest (REL SW) and funded by the Institute of Education Sciences of the U.S. Department of Education. The findings from this comprehensive analysis, titled Reviewing the Evidence on How Teacher Professional Development Affects Student Achievement (Yoon et al. 2007), shed new light on the complex relationship between professional development and improvements in student learning. It is hoped that they also will lead to new and better research on this vitally important dimension of the educational improvement What Works in Professional Development?
Antitumor activity of polyphenolic extract of Ichnocarpus frutescens.

AIM Phytochemical and dietary antioxidants are known to decrease the risk of many diseases such as cancer and cardiovascular diseases. In this study polyphenolic extract (PPE) of leaves of Ichnocarpus frutescens was evaluated for antitumor activity in vivo. MATERIALS AND METHODS Murine Ehrlich ascites carcinoma (EAC) model was used to assess PPE antitumor activity in vivo. PPE cytotoxicity was determined in vitro in U-937 monocytoid leukemia and K-562 erythroleukemia cell lines. PPE also have been assessed for the free radical scavenging activity against superoxide and nitric oxide radicals. Acute oral toxicity was performed by acute toxic classic method. The total phenolics content was quantified by the Folin-Ciocalteu method. RESULTS Results of in vivo study showed a significant decrease in tumor volume, viable tumor cell count and a significant increase of life span in the PPE treated group compared to untreated one: the life span of PPE treated animals increased by 53.41% (50 mg PPE/kg) and 73.95% (100 mg PPE/kg). PPE (5, 10 and 20 microg/mL) effectively inhibits in vitro proliferation of U-937 and K-562 cell lines. PPE exhibited pronounced radical scavenging activity with an inhibitory concentration (IC(50)) value of 167.46 microg/mL and 158.52 microg/mL against superoxide and nitric oxide radicals, respectively. CONCLUSION PPE of Ichnocarpus frutescens possesses strong free radical scavenging activity and anti-tumor activity in vitro and in vivo.
Multimarker Screening of Oxidative Stress in Aging

Aging is a complex process of organism decline in physiological functions. There is no clear theory explaining this phenomenon, but the most accepted one is the oxidative stress theory of aging. Biomarkers of oxidative stress, substances, which are formed during oxidative damage of phospholipids, proteins, and nucleic acids, are present in body fluids of diseased people as well as the healthy ones (in a physiological concentration). 8-iso prostaglandin F2α is the most prominent biomarker of phospholipid oxidative damage, o-tyrosine, 3-chlorotyrosine, and 3-nitrotyrosine are biomarkers of protein oxidative damage, and 8-hydroxy-2′-deoxyguanosine and 8-hydroxyguanosine are biomarkers of oxidative damage of nucleic acids. It is thought that the concentration of biomarkers increases as the age of people increases. However, the concentration of biomarkers in body fluids is very low and, therefore, it is necessary to use a sensitive analytical method. A combination of HPLC and MS was chosen to determine biomarker concentration in three groups of healthy people of a different age (twenty, forty, and sixty years) in order to find a difference among the groups.
Imaging oxygen consumption in forepaw somatosensory stimulation in rats under isoflurane anesthesia

The cerebral metabolic rate of oxygen (CMRO2) was dynamically evaluated on a pixel‐by‐pixel basis in isoflurane‐anesthetized and spontaneously breathing rats following graded electrical somatosensory forepaw stimulations (4, 6, and 8mA). In contrast to α‐chloralose, which is the most widely used anesthetic in forepaw‐stimulation fMRI studies of rats under mechanical ventilation, isoflurane (1.1–1.2%) provided a stable anesthesia level over a prolonged period, without the need to adjust the ventilation volume/rate or sample blood gases. Combined cerebral blood flow signals (CBF) and blood oxygenation level‐dependent (BOLD) fMRI signals were simultaneously measured with the use of a multislice continuous arterial spin labeling (CASL) technique (two‐coil setup). CMRO2 was calculated using the biophysical BOLD model of Ogawa et al. (Proc Natl Acad Sci USA 1992;89:5951–5955). The stimulus‐evoked BOLD percent changes at 4, 6, and 8mA were, respectively, 0.5% ± 0.2%, 1.4% ± 0.3%, and 2.0% ± 0.3% (mean ± SD, N = 6). The CBF percent changes were 23% ± 6%, 58% ± 9%, and 87% ± 14%. The CMRO2 percent changes were 14% ± 4%, 24% ± 6%, and 43% ± 11%. BOLD, CBF, and CMRO2 activations were localized to the forepaw somatosensory cortices without evidence of plateau for oxygen consumption, indicative of partial coupling of CBF and CMRO2. This study describes a useful forepaw‐stimulation model for fMRI, and demonstrate that CMRO2 changes can be dynamically imaged on a pixel‐by‐pixel basis in a single setting with high spatiotemporal resolution. Magn Reson Med 52:277–285, 2004. © 2004 Wiley‐Liss, Inc.
Role of neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio as prognostic markers in oral cavity cancers

Abstract Background: Various studies have associated inflammation with carcinogenesis. But still, the role of inflammatory markers in oral cancer has not been evaluated extensively. Most of the existing studies have been done on patients of varied sites, and their sample size is also scarce. In this study, we have evaluated the impact of neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) on various clinicopathological factors and survival. Methodology: This was a retrospective analysis of prospectively collected data of 400 patients with oral squamous cell cancer. The pretreatment neutrophil and lymphocyte and platelet counts were recorded, and NLR and PLR were calculated for all patients. The NLR and PLR tertiles were correlated with the incidence of various clinicopathological factors and overall survival. Results: The median follow-up of the cohort was 36 months. The mean survival of the cohort was 41.7 months. PLR was associated with higher incidence of adverse clinicopathological factors. There was a trend of decreased overall survival with increasing NLR tertile. It was found to be significant only for the group which received adjuvant chemoradiotherapy (P 0.01). Patients with higher PLR values have been found to have a lower overall survival (P 0.006). Conclusion: NLR and PLR can be used to predict survival and outcomes in patients oral cavity cancer. PLR is a good predictor for adverse clinicopathological factors and survival. NLR can predict survival only in the subset of patients who have received chemotherapy.
MRI-guided wire localization open biopsy is safe and effective for suspicious cancer on breast MRI.

BACKGROUND Magnetic resonance imaging of breast, reported to be a high sensitivity of 94% to 100%, is the most sensitive method for detection of breast cancer. The purpose of this study was to investigate our clinical experience in MRI-guided breast lesion wire localization in Chinese women. MATERIALS AND METHODS A total of 44 patients with 46 lesions undergoing MRI-guided breast lesion localization were prospectively entered into this study between November 2013 and September 2014. Samples were collected using a 1.5-T magnet with a special MR biopsy positioning frame device. We evaluated clinical lesion characteristics on pre-biopsy MRI, pathologic results, and dynamic curve type baseline analysis. RESULTS Of the total of 46 wire localization excision biopsied lesions carried out in 44 female patients, pathology revealed fourteen malignancies (14/46, 30.4%) and thirty-two benign lesions (32/46, 69.6%). All lesions were successfully localized followed by excision biopsy and assessed for morphologic features highly suggestive of malignancy according to the American College of Radiology Breast Imaging Reporting and Data System (BI-RADS) category of MRI (C4a=18, C4b=17, C4c=8,C5=3). Of 46 lesions, 37 were masses and 9 were non-mass enhancement lesions. Thirty-two lesions showed a continuous kinetics curve, 11 were plateau and 3 were washout. CONCLUSIONS Our study showed success in MRI-guided breast lesion wire localization with a satisfactory cancer diagnosis rate of 30.4%. MRI-guided wire localization breast lesion open biopsy is a safe and effective tool for the workup of suspicious lesions seen on breast MRI alone without major complications. This may contribute to increasing the diagnosis rate of early breast cancer and improve the prognosis in Chinese women.