Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge and Perceptions of Open Science among Researchers - A Case Study for Colombia

Open science can provide researchers diverse opportunities to collaborate, disseminate their research results, generate important impacts in the scientific community, and engage in effective and efficient science for the benefit of society. This study seeks to analyse and evaluate researchers’ knowledge of open science in Colombia using a survey to determine adequate instruments with which to improve research in the framework of open science. The aim of the study is to determine researchers’ current awareness of open science by considering demographic characteristics to analyse their attitudes, values, and information habits as well as the levels of institutionalism and social appropriation of open science. A representative sample of Colombian researchers was selected from the National Research System. An anonymous online survey consisting of 34 questions was sent to all professors and researchers at Colombian universities and research institutes. Sampling was random and stratified, which allowed for a representative sample of different categories of researchers, and principal component analysis (PCA) was used for the sample design. A total of 1042 responses were received, with a 95% confidence level and a margin of error of 3%. The majority of respondents knew about open science, especially in relation to open science tools (software, repositories, and networks) and open data. Researchers consider open science to be positively impacted by factors such as the rise of digital technologies, the search for new forms of collaboration, the greater availability of open data and information, and public demand for better and more effective science. In contrast, a lack of resources to develop research activities within the open science approach and the limited integration between traditional and open science are identified as the most important barriers to its use in research. These results are important for building adequate open science policy in Colombia.
Fully Convolutional Networks for Text Classification

In this work I propose a new way of using fully convolutional networks for classification while allowing for input of any size. I additionally propose two modifications on the idea of attention and the benefits and detriments of using the modifications. Finally, I show suboptimal results on the ITAmoji 2018 tweet to emoji task and provide a discussion about why that might be the case as well as a proposed fix to further improve results.
Sequential Dual Attention: Coarse-to-Fine-Grained Hierarchical Generation for Image Captioning

Image caption generation is a fundamental task to build a bridge between image and its description in text, which is drawing increasing interest in artificial intelligence. Images and textual sentences are viewed as two different carriers of information, which are symmetric and unified in the same content of visual scene. The existing image captioning methods rarely consider generating a final description sentence in a coarse-grained to fine-grained way, which is how humans understand the surrounding scenes; and the generated sentence sometimes only describes coarse-grained image content. Therefore, we propose a coarse-to-fine-grained hierarchical generation method for image captioning, named SDA-CFGHG, to address the two problems above. The core of our SDA-CFGHG method is a sequential dual attention that is used to fuse different grained visual information with sequential means. The advantage of our SDA-CFGHG method is that it can achieve image captioning in a coarse-to-fine-grained way and the generated textual sentence can capture details of the raw image to some degree. Moreover, we validate the impressive performance of our method on benchmark datasets—MS COCO, Flickr—with several popular evaluation metrics—CIDEr, SPICE, METEOR, ROUGE-L, and BLEU.
Influence of a Sustained Release Deslorelin Acetate Implant on Reproductive Physiology and Associated Traits in Laying Hens

The aim of this study was to develop an animal model with non-laying hens which would allow for investigation of the relationship between egg production and common diseases in hens. A total of 40 Lohmann Selected Leghorn hens were kept for 20 weeks in a floor housing system in two groups: group “Adult” (21 weeks of age) and group “Juvenile” (14 weeks of age). In each group, 10 hens were administered a 4.7 mg sustained release deslorelin acetate implant subcutaneously; in group “Adult” after, in group “Juvenile” before the onset of lay. In both groups, the remaining hens served as control hens. An examination of each hen was performed weekly, including ultrasonography to check for ovarian follicles, analysis of estradiol-17ß plasma concentration, and assessment of comb size. Digital radiographs of the keel bone were taken in experimental weeks 7 and 15. No follicles were detected on the ovary of treated hens for a certain time period which varied between individuals (between 8 weeks and until the end of the experiment). Estradiol-17ß concentrations were significantly higher in control hens. The comb was significantly smaller in treated hens. A lower prevalence of keel bone damage (group “Adult”) and foot pad dermatitis (FPD) (both groups) was found in treated compared to control hens. These results show that a model with laying and non-laying hens can be achieved by administering a deslorelin acetate implant. Furthermore, they indicate a relationship between egg production and keel bone damage as well as FPD.
Heme Drives Susceptibility of Glomerular Endothelium to Complement Overactivation Due to Inefficient Upregulation of Heme Oxygenase-1

Atypical hemolytic uremic syndrome (aHUS) is a severe disease characterized by microvascular endothelial cell (EC) lesions leading to thrombi formation, mechanical hemolysis and organ failure, predominantly renal. Complement system overactivation is a hallmark of aHUS. To investigate this selective susceptibility of the microvascular renal endothelium to complement attack and thrombotic microangiopathic lesions, we compared complement and cyto-protection markers on EC, from different vascular beds, in in vitro and in vivo models as well as in patients. No difference was observed for complement deposits or expression of complement and coagulation regulators between macrovascular and microvascular EC, either at resting state or after inflammatory challenge. After prolonged exposure to hemolysis-derived heme, higher C3 deposits were found on glomerular EC, in vitro and in vivo, compared with other EC in culture and in mice organs (liver, skin, brain, lungs and heart). This could be explained by a reduced complement regulation capacity due to weaker binding of Factor H and inefficient upregulation of thrombomodulin (TM). Microvascular EC also failed to upregulate the cytoprotective heme-degrading enzyme heme-oxygenase 1 (HO-1), normally induced by hemolysis products. Only HUVEC (Human Umbilical Vein EC) developed adaptation to heme, which was lost after inhibition of HO-1 activity. Interestingly, the expression of KLF2 and KLF4—known transcription factors of TM, also described as possible transcription modulators of HO-1- was weaker in micro than macrovascular EC under hemolytic conditions. Our results show that the microvascular EC, and especially glomerular EC, fail to adapt to the stress imposed by hemolysis and acquire a pro-coagulant and complement-activating phenotype. Together, these findings indicate that the vulnerability of glomerular EC to hemolysis is a key factor in aHUS, amplifying complement overactivation and thrombotic microangiopathic lesions.
A 4-Day Mindfulness-Based Cognitive Behavioral Intervention Program for CFS/ME. An Open Study, With 1-Year Follow-Up

Background: Chronic Fatigue Syndrome/Myalgic Encephalopathy (CFS/ME) is an incapacitating illness in which single treatment interventions seem to have variable effects. Based on an earlier study we have conducted a new study with a concentrated intervention program. The aims of this study were to: (1) explore the clinical course for patients with CFS/ME who participated in a treatment program delivered during four consecutive days, and (2) evaluate their satisfaction with this program. Methods: 305 patients diagnosed with CFS/ME (Oxford criteria), recruited from a clinical population referred to a specialist outpatient clinic, participated in an open uncontrolled study of the clinical course through 1 year. The study group participated in a 4-day group intervention program, comprised by education, cognitive group therapy sessions, mindfulness sessions, physical activity and writing sessions, within a context of cognitive behavioral therapy, mindfulness, acceptance and commitment model. Assessments were done by self-reports prior to the first consultation, 1 week before and 1 week after the intervention program, and at 3 months and 1 year after the intervention. SPSS 23 and R 3.3 were used for statistical analyses. The associations between case definitions and the outcome measures (Chalder Fatigue Scale (FS), Short Form 36 (SF-36) physical functioning scale) were assessed by a linear mixed effects model (LME). Results: Results showed statistically significant clinical changes for 80% of the patients after the intervention, changes being sustained through 1 year after the program. For both Fatigue Scale (FS) and the SF-36 there were statistically significant effects of time from baseline to all time points with a statistically significant drop in scores, applying the linear mixed effects model. A subgroup fulfilling the inclusion criteria from the PACE study (Chalder Fatigue Scale >6/11, SF-36 Physical functioning <65/100) showed clinically significant improvement through 1 year, changes in outcome measures were statistically significant (p < 0.001). None of the patients included in the program dropped out, and a great majority of patients expressed high satisfaction with the content, focus and amount of treatment. Conclusion: Clinical changes observed from pre-treatment to 1 year follow-up could represent effects of the 4-day concentrated intervention program, and should be further explored in a controlled study.
Exposing the Causal Effect of C-Reactive Protein on the Risk of Type 2 Diabetes Mellitus: A Mendelian Randomization Study

As a biomarker of inflammation, C-reactive protein (CRP) has attracted much attention due to its role in the incidence of type 2 diabetes mellitus (T2DM). Prospective studies have observed a positive correlation between the level of serum CRP and the incidence of T2DM. Recently, studies have reported that drugs for curing T2DM can also decrease the level of serum CRP. However, it is not yet clear whether high CRP levels cause T2DM. To evaluate this, we conducted a Mendelian randomization (MR) analysis using genetic variations as instrumental variables (IVs). Significantly associated single nucleotide polymorphisms (SNPs) of CRP were obtained from a genome-wide study and a replication study. Therein, 17,967 participants were utilized for the genome-wide association study (GWAS), and another 14,747 participants were utilized for the replication of identifying SNPs associated with CRP levels. The associations between SNPs and T2DM were from the DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) consortium. After removing SNPs in linkage disequilibrium (LD) and T2DM-related SNPs, the four remaining CRP-related SNPs were deemed as IVs. To evaluate the pooled influence of these IVs on the risk of developing T2DM through CRP, the penalized robust inverse-variance weighted (IVW) method was carried out. The combined result (OR 1.114048; 95% CI 1.058656 to 1.172338; P = 0.024) showed that high levels of CRP significantly increase the risk of T2DM. In the subsequent analysis of the relationship between CRP and type 1 diabetes mellitus (T1DM), the pooled result (OR 1.017145; 95% CI 0.9066489 to 1.14225; P = 0.909) supported that CRP levels cannot determine the risk of developing T1DM.
Topological Properties of Brain Structural Networks Represent Early Predictive Characteristics for the Occurrence of Bipolar Disorder in Patients With Major Depressive Disorder: A 7-Year Prospective Longitudinal Study

Bipolar disorder (BD) and major depressive disorder (MDD) are associated with different brain functional and structural abnormalities, but BD is hard to distinguish from MDD until the first manic or hypomanic episode. The aim of this study was to examine whether the topological properties of the brain structural network could be used to differentiate BD from MDD patients before their first manic/hypomanic episode. Diffusion tensor images were collected from 80 MDD patients and 53 healthy controls (HCs); 78 patients completed the follow-up study lasting 7 years. Among them, 12 patients were converted to BD and 64 patients remained MDD. Topological properties of the brain structural networks at baseline were compared among patients who converted to BD, patients who did not develop BD, and HCs. Patients who converted to BD displayed reduced nodal local efficiency in the left inferior frontal gyrus(IFG) compared with HCs and patients who did not convert to BD. There was no significant difference in the nodal global efficiency among the three groups. The findings suggest that the nodal local efficiency in the left IFG could serve as a potential biomarker to predict the conversion of MDD to BD before the occurrence of the first manic or hypomanic episode.
SMR Neurofeedback Training Facilitates Working Memory Performance in Healthy Older Adults: A Behavioral and EEG Study

Cognitive aging has become a major concern because life expectancy has increased and elderly populations are socially and economically active. Neurofeedback is a technique of neuromodulation through operant conditioning paradigm that uses a computer interface to provide real-time information about brain activity to increase individual self-perception and assist in modulation. The sensorimotor rhythm (SMR) training protocol is known to enhance attention and has been applied to improve cognitive performance, primarily for attention and memory gains. The aim of this study is to test if the SMR protocol can improve working memory performance in an aging population and consequently favor cognitive reserve. Seventeen older adults (12 females) took part in a randomized placebo-controlled study. They completed a visual working memory test, Delayed Matching to Sample Task (DMTS), before and after the SMR neurofeedback protocol in order to compare their visual working memory performance. Moreover, a 19-channels EEG was collected while they perform the DMTS pre- and post-training. The experimental group showed an improvement in their working memory performance after the training with similar activation power, mainly in theta and beta frequency band at frontal and alpha at temporal regions. The sham group showed some variations in the score of working memory after the training, but were not statistically significant and their power spectrum demonstrate enhancement in alpha and beta band frontal and temporal. The group that did not receive neurofeedback training did not show a change in their working memory performance, neither in their EEG spectrum. The results suggest that neurofeedback can benefit brain reserve in an aging population because individuals enhanced their working memory performance after training and have their EEG activation changed according to expected in working memory tasks.
Direct Bypass Surgery Vs. Combined Bypass Surgery for Hemorrhagic Moyamoya Disease: A Comparison of Angiographic Outcomes

Objective: Extracranial-intracranial bypass is currently recognized as the optimal treatment for hemorrhagic-type moyamoya disease (MMD) which reduces incidence of rebleeding. Recent studies have reported the advantage of combined bypass over direct bypass for the general MMD patients. However, the effect of direct bypass and combined bypass surgery specifically for hemorrhagic-type MMD had not been investigated yet. Methods: Hemorrhagic-type MMD patients who underwent direct and combined bypass surgery with complete clinical and radiological documentation from a multicenter cohort between 2009 and 2017 were retrospectively included. Surgical methods included superficial temporal artery-middle cerebral artery (STA-MCA) anastomosis (direct bypass), combined STA-MCA bypass with encephalodurosynangiosis (EDS), and combined STA-MCA bypass with encephaloduroarteriosynangiosis (EDAS). Matsushima standard on follow-up catheter angiography was used to assess surgical outcome. Modified Rankin Scale, incidence of rebleeding and ischemia during follow-up were recorded. Rebleeding-free survival rates between direct and combined bypass were compared by Kaplan-Meier analysis. Results: Sixty eight hemorrhagic-onset MMD patients were included in this study, among which 71 hemispheres were treated with surgery (direct bypass: 17; bypass+EDS: 24; bypass+EDAS: 30). Forty six (64.8%) hemispheres had satisfactory revascularization (Matsushima level 2–3) and 26 (36.6%) had poor neoangiogenesis. Matsushima level was not significantly different between surgical groups (P = 0.258). Good neoangiogenesis from dural grafts was achieved in 26 (36.6%) hemispheres, and good neoangiogenesis from STA grafts was only seen in 4 (out of 30, 12.5%) hemispheres. Multivariate analysis showed bypass patency [P < 0.001, OR (95%CI): 13.41 (3.28–54.80)] and dural neoangiogenesis [P < 0.001, OR (95%CI): 13.18 (3.26–53.36)] both independently contributed to good angiographic outcome. During follow-up, incidences of rebleeding or ischemic events, and re-bleeding free survival rate were not significantly different between surgical groups (P = 0.433, P = 0.559, and P = 0.997). However, patients who underwent combined bypass surgery had significantly lower mRS at follow-up comparing to patients who underwent direct bypass (P = 0.006). Conclusion: Combined bypass surgery and direct bypass surgery offered similar revascularization for hemorrhagic MMD. Bypass patency and dural angiogenesis both contributed to revascularization independently. The potential of indirect bypass to grow new vessels in hemorrhagic-MMD patients was generally limited, but dural leaflets offered better neoangiogenesis than STA grafts and was therefore recommended for surgical revascularization of hemorrhagic MMD.
Negative Energy Balance Does Not Alter Fat-Free Mass During the Yukon Arctic Ultra—The Longest and the Coldest Ultramarathon

Purpose: The objective of this study was to determine alterations in caloric balance, body composition, metabolites, and cytokines in athletes participating in the Yukon Arctic Ultra. Methods: Ten participants traveling on foot in the 2017 692-km event were recruited for the study. Measurements and samples were obtained at pre-event, 278 km (C1), 384 km (C2), and post-event. Body composition measurements were obtained using bioelectrical impedance analysis. Accelerometer devices were utilized to provide an estimation of caloric expenditure and dietary recalls provided assessments of caloric intake. Blood serum samples were collected, processed, and analyzed using enzyme-linked immunosorbent assays or nuclear magnetic resonance. Results were analyzed using linear mixed model, presented as means ± SD, and considered significant at p < 0.05. Results: Participants (8 males, 2 females; age: 37 ± 10 years; body mass index: 24.4 ± 2.5 kg/m2) were recruited. Four males and one female completed the entire event in 260 ± 19 h. Caloric intake/expenditure was 4,126 ± 1,115 kcal/day and 6,387 ± 781 kcal/day, respectively, indicating a caloric deficit of 2,261 ± 1,543 kcal/day. Total mass, body mass index, and fat mass were reduced at each time point of the event. Fat-free mass (FFM) was unchanged throughout the event. Follistatin was increased at C1 (1,715 ± 876 pg/ml) in comparison to baseline. Acetoacetate increased significantly at post-event (6.1 ± 1.5 mg/ml). Conclusions: Despite a pronounced caloric deficit and sustained activity under extreme cold conditions, FFM was preserved with an increase in serum follistatin and acetoacetate. Future studies should be directed at the role of nutrient strategies and/or training methods on the retention of FFM under these conditions.
Language Network Function in Young Children Born Very Preterm

Language deficits are reported in preterm born children across development. Recent neuroimaging studies have found functional alterations in large-scale brain networks underlying these language deficits, but the early childhood development of the language network has not been investigated. Here, we compared intrinsic language network connectivity in 4-year-old children born VPT and term-born controls, using defined language regions (Broca’s area, Wernicke’s areas, and their homologues in the right hemisphere). Resting-state functional magnetic resonance imaging (fMRI) was obtained, and the group differences in whole-brain connectivity were examined from each seed as well as correlations with language outcomes. We found significantly decreased functional connectivity in almost all language regions in children born VPT compared to their term controls. Notably, Broca’s area homologue in the right hemisphere emerged as a functional hub of decreased connectivity in VPT group, specifically to bilateral inferior frontal and supramarginal gyri; connectivity strength between Broca’s area homologue with the right supramarginal and the left inferior frontal gyri was associated with better language outcomes at 4 years of age. Wernicke’s area and its homologue also showed decreased inter-hemispheric connections to bilateral supramarginal gyri in the VPT group. Decreased intra- and inter-hemispheric connectivity among primary language regions suggests immature and altered function in the language network in children born VPT.