Miracle-dz/UniFAR-FTUs huggingface dataset:
A Holistic Approach to Scientific Reasoning Based on Hybrid Knowledge Representations and Research Objects

1 MOTIVATION AND GOALS Under the light of current developments in AI it appears the time is ripe for a shared partnership with machines, whereby humans can benefit from augmented reasoning and information management capabilities provided that machines are endowed with the necessary intelligence to assist with such tasks. This seems to be particularly the case of the scientific domain, where some envision the development of an AI that can make major scientific discoveries and that eventually becomes worthy of a Nobel Prize [9]. This vision may still be far from realization, but it is not completely new nevertheless. NLP technologies based on well-formed, logically sound structured knowledge representations (knowledge graphs, ontologies) leverage expressive and actionable descriptions of the domain of interest through logical deduction and inference, and can provide logical explanations of reasoning outcomes. Closely related to this family of approaches, project Halo [7] aimed to develop a Digital Aristotle able to answer novel questions in scientific domains with expertise equivalent to Advanced Placement competence level. Halo enabled subject matter experts (SMEs) to model complex scientific knowledge from textbooks and related questions, based on an underlying logical formalism and a knowledge modeling workbench to assist SMEs in the task. The resulting system achieved an unprecedented question answering performance level for SMEentered knowledge, but it also had a number of severe drawbacks, including brittleness (coverage, precision or granularity gaps), scalability issues, and the need for a considerable force of well trained human labor to manually encode large amounts of scientific knowledge. On the other hand, the last decade has witnessed a shift towards statistical methods due to the increasing availability of raw data and cheap computing power. These have proved to be powerful and convenient in many linguistic tasks, such as part-of-speech tagging or dependency parsing. However, they are also limited, e.g. humans seek causal explanations, which are hard to provide based on statistical induction rather than logical deduction. Recent results in the field of distributional semantics [10] have shown promising ways to learn features from text that can complement the knowledge
Quantitative PCR Evaluation of Cellular Immune Responses in Kenyan Children Vaccinated with a Candidate Malaria Vaccine

Background The T-cell mediated immune response plays a central role in the control of malaria after natural infection or vaccination. There is increasing evidence that T-cell responses are heterogeneous and that both the quality of the immune response and the balance between pro-inflammatory and regulatory T-cells determines the outcome of an infection. As Malaria parasites have been shown to induce immunosuppressive responses to the parasite and non-related antigens this study examined T-cell mediated pro-inflammatory and regulatory immune responses induced by malaria vaccination in children in an endemic area to determine if these responses were associated with vaccine immunogenicity. Methods Using real–time RT- PCR we profiled the expression of a panel of key markers of immunogenecity at different time points after vaccination with two viral vector vaccines expressing the malaria TRAP antigen (FP9-TRAP and MVA-TRAP) or following rabies vaccination as a control. Principal Findings The vaccine induced modest levels of IFN-γ mRNA one week after vaccination. There was also an increase in FoxP3 mRNA expression in both TRAP stimulated and media stimulated cells in the FFM ME-TRAP vaccine group; however, this may have been driven by natural exposure to parasite rather than by vaccination. Conclusion Quantitative PCR is a useful method for evaluating vaccine induced cell mediated immune responses in frozen PBMC from children in a malaria endemic country. Future studies should seek to use vaccine vectors that increase the magnitude and quality of the IFN-γ immune response in naturally exposed populations and should monitor the induction of a regulatory T cell response.
Phylogeny of the titi monkeys of the Callicebus moloch group (Pitheciidae, Primates)

Callicebus is a Neotropical primate genus of the family Pitheciidae, which currently comprises 34 recognized species. Based on their morphological traits and geographic distribution, these species are currently assigned to five groups: the C. moloch, C. cupreus, C. donacophilus, C. torquatus, and C. personatus groups, although in the past, alternative arrangements have been proposed based on the analysis of morphological data. The principal disagreements among these arrangements are related to the composition of the C. moloch group. In the present study, we tested the different taxonomic proposals for the C. moloch group, based on the molecular analysis of nuclear markers (Alu insertions and flanking regions) and three mitochondrial genes (16S, COI, and Cyt b), with a total of approximately 7 kb of DNA sequence data. Phylogenetic reconstructions based on maximum likelihood and Bayesian inference methods indicated that the species of the current C. cupreus group should be reintegrated into the C. moloch group. In addition, our results corroborated previous studies suggesting that the species of the current C. personatus group form a distinct species group. We also observed a relatively subtle level of divergence between C. dubius and C. caligatus. While the known diversity of Callicebus is considerable, these findings indicate that the relationships among groups and species may still not be completely understood, highlighting the need for further research into the biological, geographic, and genetic variability of these primates, which will be fundamental to the effective conservation of the genus. Am. J. Primatol. 78:904–913, 2016. © 2016 Wiley Periodicals, Inc.
Serum Surfactant Protein D as a Biomarker for Measuring Lung Involvement in Obese Patients With Type 2 Diabetes

Context: Lung impairment is a new target for late diabetic complications. Biomarkers that could help identify patients requiring functional respiratory tests have not been reported. Objective: Our aim was to examine whether serum surfactant protein D (SP‐D) and A (SP‐A) could be useful biomarkers of lung damage in obese patients with type 2 diabetes (T2D) without known lung disease. Design and Setting: A case‐control study conducted in an ambulatory obesity unit. Patients: Forty‐nine obese patients with T2D and 98 subjects without diabetes matched by age, sex, body mass index, and waist circumference were included. Interventions: Serum SP‐D and SP‐A levels were measured using enzyme‐linked immunosorbent assay. Forced spirometry and static pulmonary volume were assessed. Results: Patients with T2D exhibited higher serum SP‐D concentrations than control subjects (P = 0.006). No differences in serum SP‐A concentrations were observed. There was an inverse association between forced expiratory volume in 1 second (FEV1) and serum SP‐D (r = −0.265; P = 0.029), as well as a significant positive relationship between SP‐D concentration and residual volume (r = 0.293; P = 0.043). From receiver operating characteristic analysis, the best SP‐D cutoff to identify a FEV1 <80% of predicted was 132.3 ng/mL (area under the curve, 0.725; sensitivity, 77.7%; specificity, 69.4%). Stepwise multivariate regression analysis showed that serum SP‐D concentration ≥132.3 ng/mL was independently associated with a FEV1 <80% of predicted (R2 = 0.406). Only the existence of T2D contributed independently to serum SD‐P variance among all subjects (R2 = 0.138). Conclusions: Serum SP‐D concentration can be a useful biomarker for detecting lung impairment in obese patients with T2D.
Predictive value of XPG rs2296147T>C polymorphism on clinical outcomes of cancer patients

The Xeroderma pigmentosum complementation group G (XPG) rs2296147T>C polymorphism is suspected to associate with the clinical outcomes of cancer patients. However, the results are inconsistent. This meta-analysis aimed to evaluate the reliable predictive value of XPG rs2296147T>C polymorphism on clinical outcomes of cancer patients. A total of 11 eligible studies were enrolled in this meta-analysis. Our results indicated that the cancer patients with TT and CT genotypes were significantly associated with better respond rates when compared with the CC genotype (TT versus (vs.) CC: odds ratio (OR) = 2.05, 95% confidence intervals (CIs), 1.32-3.20, P = 0.002; TT+CT vs. CC: OR= 1.57, 95% CI, 1.14-2.17, P = 0.005). The TT genotype and/or T allele might be associated with higher survival time for cancer patients than the CC genotype and/or C allele. The cumulative meta-analyses showed an apparent beneficial objective response of TT genotype on cancer patients. In conclusion, this meta-analysis suggests that the XPG rs2296147T>C polymorphism is associated with the clinical outcomes of cancer patients. The XPG rs2296147T>C polymorphism might be a predictive factor of prognosis in cancers patients and contribute to individual treatment in the future.
Normalized Early Postoperative Cortisol and ACTH Values Predict Nonremission After Surgery for Cushing Disease

Context Perioperative increases in adrenocorticotropic hormone (ACTH) and cortisol mimic results of corticotropin-releasing hormone (CRH) stimulation testing. This phenomenon may help identify patients with residual adenoma after transsphenoidal surgery (TSS) for Cushing disease (CD). Objective To predict nonremission after TSS for CD. Design Retrospective case-control study of patients treated at a single center from December 2003 until July 2016. Early and medium-term remission were assessed at 10 days and 11 months. Patients and Setting Two hundred and ninety-one consecutive TSS cases from 257 patients with biochemical evidence of CD seen at a clinical center. Interventions Normalized early postoperative values (NEPVs) for cortisol and ACTH were calculated as immediate postoperative cortisol or ACTH levels minus preoperative post-CRH-stimulation test levels. Main Outcome Measures Prediction of early nonremission was evaluated using logistic regression. Prediction of medium-term remission was assessed using Cox regression. Predictive ability was quantified by area under the receiver operating characteristic curve (AUROC). Results NEPVs for cortisol and ACTH predicted early nonremission [adjusted odds ratio (OR): 1.1; 95% confidence interval (CI): 1.0, 1.1; P = 0.016 and adjusted OR: 1.0; 95% CI: 1.0, 1.0; P = 0.048, respectively]. AUROC for NEPV of cortisol was 0.78 (95% CI: 0.61, 0.95); for NEPV of ACTH, it was 0.80 (95% CI: 0.61, 0.98). NEPVs for cortisol and ACTH predicted medium-term nonremission [hazard ratio (HR): 1.1; 95% CI: 1.0, 1.1; P = 0.023 and HR: 1.0; 95% CI: 1.0, 1.0; P = 0.025, respectively]. Conclusions NEPVs for cortisol and ACTH predicted nonremission after TSS for CD.
Around the world, adolescence is a time of heightened sensation seeking and immature self-regulation.

The dual systems model of adolescent risk-taking portrays the period as one characterized by a combination of heightened sensation seeking and still-maturing self-regulation, but most tests of this model have been conducted in the United States or Western Europe. In the present study, these propositions are tested in an international sample of more than 5000 individuals between ages 10 and 30 years from 11 countries in Africa, Asia, Europe and the Americas, using a multi-method test battery that includes both self-report and performance-based measures of both constructs. Consistent with the dual systems model, sensation seeking increased between preadolescence and late adolescence, peaked at age 19, and declined thereafter, whereas self-regulation increased steadily from preadolescence into young adulthood, reaching a plateau between ages 23 and 26. Although there were some variations in the magnitude of the observed age trends, the developmental patterns were largely similar across countries.
Importance of Neutralizing Monoclonal Antibodies Targeting Multiple Antigenic Sites on the Middle East Respiratory Syndrome Coronavirus Spike Glycoprotein To Avoid Neutralization Escape

ABSTRACT Middle East respiratory syndrome coronavirus (MERS-CoV) causes a highly lethal pulmonary infection with ∼35% mortality. The potential for a future pandemic originating from animal reservoirs or health care-associated events is a major public health concern. There are no vaccines or therapeutic agents currently available for MERS-CoV. Using a probe-based single B cell cloning strategy, we have identified and characterized multiple neutralizing monoclonal antibodies (MAbs) specifically binding to the receptor-binding domain (RBD) or S1 (non-RBD) regions from a convalescent MERS-CoV-infected patient and from immunized rhesus macaques. RBD-specific MAbs tended to have greater neutralizing potency than non-RBD S1-specific MAbs. Six RBD-specific and five S1-specific MAbs could be sorted into four RBD and three non-RBD distinct binding patterns, based on competition assays, mapping neutralization escape variants, and structural analysis. We determined cocrystal structures for two MAbs targeting the RBD from different angles and show they can bind the RBD only in the “out” position. We then showed that selected RBD-specific, non-RBD S1-specific, and S2-specific MAbs given prophylactically prevented MERS-CoV replication in lungs and protected mice from lethal challenge. Importantly, combining RBD- and non-RBD MAbs delayed the emergence of escape mutations in a cell-based virus escape assay. These studies identify MAbs targeting different antigenic sites on S that will be useful for defining mechanisms of MERS-CoV neutralization and for developing more effective interventions to prevent or treat MERS-CoV infections. IMPORTANCE MERS-CoV causes a highly lethal respiratory infection for which no vaccines or antiviral therapeutic options are currently available. Based on continuing exposure from established reservoirs in dromedary camels and bats, transmission of MERS-CoV into humans and future outbreaks are expected. Using structurally defined probes for the MERS-CoV spike glycoprotein (S), the target for neutralizing antibodies, single B cells were sorted from a convalescent human and immunized nonhuman primates (NHPs). MAbs produced from paired immunoglobulin gene sequences were mapped to multiple epitopes within and outside the receptor-binding domain (RBD) and protected against lethal MERS infection in a murine model following passive immunization. Importantly, combining MAbs targeting distinct epitopes prevented viral neutralization escape from RBD-directed MAbs. These data suggest that antibody responses to multiple domains on CoV spike protein may improve immunity and will guide future vaccine and therapeutic development efforts.
Comparison of timolol 0.5% + brimonidine 0.2% + dorzolamide 2% versus timolol 0.5% + brimonidine 0.2% in a Mexican population with primary open-angle glaucoma or ocular hypertension

Background The purpose of this study was to evaluate the efficacy and safety of two fixed combinations, ie, timolol 0.5% + brimonidine 0.2% + dorzolamide 2% (TBD) versus timolol 0.5% + brimonidine 0.2% (TB) in patients with primary open-angle glaucoma or ocular hypertension. Methods We performed a 3-month, randomized, double-blind study in patients with primary open-angle glaucoma or ocular hypertension and an intraocular pressure of 21–30 mmHg. Patients were randomly assigned to receive one drop of TBD or TB twice a day. The primary efficacy endpoint was change in intraocular pressure after 3 months of treatment. Safety measures were assessed by the presence of adverse events. Results Mean baseline intraocular pressure was similar at 8 am and 4 pm in the treatment groups (TBD 22.3 ± 0.9 mmHg, TB 22.4 ± 1.8 mmHg, P = 0.558; TBD 19.02 ± 1.3, TB 19.08 ± 1.2, P = 0.536, respectively). At the end of the study, the mean intraocular pressure was significantly lower in the TBD group at both 8 am (16.19 ± 2.0 mmHg versus 18.35 ± 1.4 mmHg, P = 0.000) and 4 pm (14.74 ± 2.4 mmHg versus 16.77 ± 1.4 mmHg, P = 0.000). Conclusion Fixed-combination TBD was more effective than fixed-combination TB for reducing IOP in patients with primary open-angle glaucoma.
Asymmetric Coding of Multi-View Video Plus Depth Based 3-D Video for View Rendering

The recent years have witnessed three-dimensional (3-D) video technology to become increasingly popular, as it can provide high-quality and immersive experience to end users, where view rendering with depth-image-based rendering (DIBR) technique is employed to generate the virtual views. Distortions in depth map may induce geometry changes in the virtual views, and distortions in texture video may be propagated to the virtual views. Thus, effective compression of both texture videos and depth maps is important for 3-D video system. From the perspective of bit allocation, asymmetric coding of the texture videos and depth maps is an effective way to get the optimal solution of 3-D video compression and view rendering problems. In this paper, a novel asymmetric coding method of multi-view video plus depth (MVD) based 3-D video is proposed on purpose of providing high-quality view rendering. In the proposed method, two models are proposed to characterize view rendering distortion and binocular suppression in 3-D video. Then, an asymmetric coding method of MVD-based 3-D video is proposed by combining two models in encoding framework. Finally, a chrominance reconstruction algorithm is presented to achieve accurate reconstruction. Experimental results show that compared with other methods, the proposed method can obtain higher performance of view rendering under the total bitrate constraint. Moreover, the perceptual visual quality of 3-D video is almost unaffected with the proposed method.
Atrial fibrillation as a risk factor for cognitive decline and dementia

Abstract Aims To assess whether AF is a risk factor for cognitive dysfunction we used prospective data on AF, repeat cognitive scores, and dementia incidence in adults followed over 45 to 85 years. Methods and results Data are drawn from the Whitehall II study, N = 10 308 at study recruitment in 1985. A battery of cognitive tests was administered four times (1997–2013) to 7428 participants (414 cases of AF), aged 45–69 years in 1997. Compared with AF-free participants, those with longer exposure to AF (5, 10, or 15 years) experienced faster cognitive decline after adjustment for sociodemographic, behavioural, and chronic diseases (P for trend = 0.01). Incident stroke or coronary heart disease individually did not explain the excess cognitive decline; however, this relationship was impacted when considering them together (P for trend 0.09). Analysis of incident dementia (N = 274/9302 without AF; N = 50/912 with AF) showed AF was associated with higher risk of dementia in Cox regression adjusted for sociodemographic factors, health behaviours and chronic diseases [hazard ratio (HR): 1.87; 95% confidence interval (CI): 1.37, 2.55]. Multistate models showed AF to increase risk of dementia in those free of stroke (HR: 1.67; 95% CI: 1.17, 2.38) but not those free of stroke and coronary heart disease (HR: 1.29; 95% CI: 0.74, 2.24) over the follow-up. Conclusion In adults aged 45–85 years AF is associated with accelerated cognitive decline and higher risk of dementia even at ages when AF incidence is low. At least in part, this was explained by incident cardiovascular disease in patients with AF.
Envelope analysis of nonlinear electronic circuits based on harmonic balance method

We propose here a Spice‐oriented envelope analysis based on the HB (harmonic balance) method, where Fourier coefficients are assumed to be slowly varying. The Fourier expansions of nonlinear devices are executed by MATLAB in the symbolic forms. In this time, the nonlinearities need to be approximated by the polynomial functions. The determining equation of the HB method is formulated as Sine–Cosine circuit in the form of schematic diagram using ABMs (analog behavior models) of Spice. Each sub‐circuit corresponding to the higher harmonic component is almost the same circuit topology as the original one and has dynamic elements such as capacitors and inductors. The Sine–Cosine circuit can be solved by the transient analysis of Spice. Thus, our method is rather a symbolic approach in the meaning that the HB determining equation is given by the schematic diagram of Spice. Our method can be easily applied to the analysis of middle order of nonlinear communication circuits such as mixers and amplitude modulators and to the analysis of interesting phenomena in the nonlinear oscillations. After many simulation experiments, the results show that our envelope analysis is about 50 times faster than the direct transient analysis. Copyright © 2010 John Wiley & Sons, Ltd.
Congenital Aqueductal Stenosis: Findings at Fetal MRI That Accurately Predict a Postnatal Diagnosis

BACKGROUND AND PURPOSE: Congenital aqueductal stenosis is a common cause of prenatal ventriculomegaly. An accurate diagnosis provides prognostic information and may guide obstetric management. The purpose of this study was to identify specific anatomic findings on prenatal MR imaging that can be used as predictors of congenital aqueductal stenosis. MATERIALS AND METHODS: Prenatal and postnatal MRIs of fetuses referred to our institution for ventriculomegaly between June 2008 and August 2015 were reviewed. Imaging findings in postnatally confirmed congenital aqueductal stenosis (disease group) were compared with those of ventriculomegaly cases from other causes (control group). Univariate analysis was performed using the Fisher exact test and the Wilcoxon rank test, and multivariate analysis, via the random forest method. RESULTS: Forty-three cases of ventriculomegaly had a confirmed postnatal diagnosis of congenital aqueductal stenosis. Thirty-two ventriculomegaly cases negative for congenital aqueductal stenosis were included in the control group. Dominant findings associated with an accurate prenatal diagnosis of congenital aqueductal stenosis on multivariate analysis included the following: enlarged inferior third ventricular recesses, enlargement of the lateral ventricles and third ventricle, and an abnormal corpus callosum. Findings that significantly increase the probability of congenital aqueductal stenosis (high positive predictive value) included the following: enlarged third ventricular recesses, aqueduct funneling, hemorrhage in the cerebral aqueduct, ventricular diverticulum, rhombencephalosynapsis, and dystroglycanopathy-related cerebellar dysplasia. CONCLUSIONS: Our study identified specific characteristics on fetal MR imaging that can be used as predictors of the diagnosis of congenital aqueductal stenosis. Most of these findings are secondary to the obstructive nature of the resulting hydrocephalus. Common associated malformations such as rhombencephalosynapsis and dystroglycanopathies should also increase the suspicion of congenital aqueductal stenosis when present with ventriculomegaly.