Miracle-dz/UniFAR-FTUs huggingface dataset:
TCS Research at TAC 2017: Joint Extraction of Entities and Relations from Drug Labels using an Ensemble of Neural Networks

We describe our submission at TAC 2017 for extracting entities and relations of interest from drug labels. We employ an end-to-end relation extraction system which jointly extracts both entities and relations. The task of end-to-end relation extraction consists of identifying boundaries of entity mentions, entity types of these mentions and appropriate semantic relation for each pair of mentions. Based on our earlier work (Pawar et al., 2017), a single neural network model (“All Word Pairs” model i.e. AWP-NN) is trained to assign an appropriate label to each word pair in a given sentence for performing end-to-end relation extraction. Moreover, we build an ensemble of multiple AWPNN models to achieve better performance than the individual models. We achieved 73.18% and 24.79% F-measures for entity and relation extraction, respectively.
Tonantzitlolone is a nanomolar potency activator of transient receptor potential canonical 1/4/5 channels

The diterpene ester tonantzitlolone (TZL) is a natural product, which displays cytotoxicity towards certain types of cancer cell such as renal cell carcinoma cells. The effect is similar to that of (‐)‐englerin A, and so, although it is chemically distinct, we investigated whether TZL also targets transient receptor potential canonical (TRPC) channels of the 1, 4 and 5 type (TRPC1/4/5 channels).
A Radial Basis Function based Optimization Algorithm with Regular Simplex set geometry in Ellipsoidal Trust-Regions

In this paper, we investigate two ideas in the context of the interpolation-based optimization paradigm tailored to derivative-free black-box optimization problems. The proposed architecture maintains a radial basis function interpolation model of the actual objective that is managed according to a trust-region globalization scheme. We focus on two distinctive ideas. Firstly, we explore an original sampling strategy to adapt the interpolation set to the new trust region. A better-than-linear interpolation model is guaranteed by maintaining a well-poised supporting subset that pursues a near regular simplex geometry of n + 1 points plus the trust-region center. This strategy improves the geometric distribution of the interpolation points whilst also optimally exploiting the existing interpolation set. On account of the associated minimal interpolation set size, the better-than-linear interpolation model will exhibit curvature, which is a necessary condition for the second idea. Therefore, we explore the generalization of the classic spherical to an ellipsoidal trust-region geometry by matching the contour ellipses with the inverse of the local problem hessian. This strategy is enabled by the certainty of a curved interpolation model and is introduced to accounts for the local output anisotropy of the objective function when generating new interpolation points. Instead of adapting the sampling strategy to an ellipsoid, we carry out the sampling in an affine transformed space. The combination of both methods is validated on a set of multivariate benchmark problems and compared with ORBIT.
An Updated Multi-Temporal Glacier Inventory for the Patagonian Andes With Changes Between the Little Ice Age and 2016

We present a satellite-derived glacier inventory for the whole Patagonian Andes south of 45.5°S and Tierra del Fuego including recent changes. Landsat TM/ETM+ and OLI satellite scenes were used to detect changes in the glacierized area between 1986, 2005 and 2016 for all of the 11.209 inventoried glaciers using a semi-automated procedure. Additionally we used geomorphological evidence, such as moraines and trimlines to determine the glacierized area during the Little Ice Age for almost 90% of the total glacierized area. Within the last ~150 years the glacierized area was reduced from 28.091±890 km2 to 22.636±905 km2, marking an absolute area loss of 5.455±1.269 km2 (19.4%). For the whole study region, the annual area decrease was moderate until 1986 with 0.10±0.04% a-1. Afterwards the area reduction increased, reaching annual values of 0.33±0.28% a-1and 0.25±0.5% a-1 for the periods of 1986-2005 and 2005-2016, respectively. There is a high variability of change rates throughout the Patagonian Andes. Small glaciers, especially in the north of the Northern Patagonian Icefield (NPI) and between the latter and the Southern Patagonian Icefield (SPI) had over all periods the highest rates of shrinkage, exceeding 0.92±1.22% a-1 during 2005-2016. In the mountain range of the Cordillera Darwin (CD), and also accounting for small ice fields south of 52°S, highest rates of shrinkage occurred during 1986-2005, reaching values up to 5.6±4.2% a-1, but decreased during the 2005-2016 period. Across the Andean main crest, the eastern parts of the NPI, SPI and adjoined glaciers had in absolute values the highest area reduction exceeding 2.145±482 km2 since the LIA. Large calving glaciers show a smaller relative decrease rate compared to land-terminating glaciers but account for the most absolute area loss. In general, glacier shrinkage is dependent on latitude, the initial glacier area, the environment of the glacial tongue (calving or non-calving glaciers) and in parts by glacial aspect.
Possible Synergistic Effects of Glutathione and C-Reactive Protein in the Progression of Liver Cirrhosis

Liver cirrhosis is often associated with increased inflammatory responses and changes of glutathione (GSH) status. The possible interactions between these two factors in mediating damages of liver function remain unclear. Here, we measured the inflammatory responses and GSH status in liver cirrhotic patients and compared them with healthy subjects. In addition, we assessed the relationship of the GSH status and levels of inflammatory markers with the severity of the disease. This was a cross-sectional study. In total, we recruited 63 liver cirrhotic patients with Child–Turcotte–Pugh class A scores, and 12 patients with class B–C scores, together with 110 healthy subjects. Patients with class B–C scores showed the highest level of high-sensitivity C-reactive protein (hs-CRP) when compared with class A patients or healthy subjects. Patients in class A group had significantly higher GSH levels when compared with class B–C group or healthy subjects. After adjusting for potential confounders and each other, serum hs-CRP levels showed positive association with the Child–Turcotte–Pugh scores, while GSH levels showed negative association with Child–Turcotte–Pugh scores. Interactions were found between levels of plasma GSH and serum hs-CRP (β = 0.004, p = 0.016). CRP and GSH levels, which had showed interactions, were associated with the severity of liver cirrhosis.
Cardiovascular computed tomography versus transoesophageal echocardiography after cryptogenic ischaemic stroke – a pilot study of 12 patients

Objective Transoesophageal echocardiography (TEE) is the gold standard for the detection of cardiac emboli sources in ischaemic stroke patients, but new computed tomography (CT) scanners are able to visualize the heart. This pilot study aimed to compare findings on TEE with combined cardiovascular scan and cerebral CT angiography in cryptogenic ischaemic stroke patients. Methods This pilot study enrolled patients with cryptogenic ischaemic stroke who underwent a combined cardiovascular and cerebral CT angiography scan and a TEE examination, which were interpreted in a blinded manner. Results Twelve patients with cryptogenic ischaemic stroke were included (mean age 56 years). Of these, 10 patients underwent both a combined cardiovascular and cerebral CT angiography and a TEE examination. All cardiovascular CT scans were readable at sinus rhythm. None of the simultaneous cerebral angiograms were compromised. Thrombi were not detected in any patients. Patent foramen ovale was visualized in five patients by TEE, while cardiovascular CT only identified three. Cardiovascular CT revealed in addition an X-ray negative pulmonary metastasis in one patient, aortic coarctation in another and significant coronary stenosis in four patients. Conclusion The sensitivity for detecting patent foramen ovale was considerably lower for cardiovascular CT than for TEE, however the cardiovascular CT revealed several other very important clinical findings.
Comparison of ventilation effectiveness of the bag valve mask and the LMA Air-Q SP in nurses during simulated CPR.

In a case of sudden cardiac arrest (SCA) in a health facility there is a procedure to summon a resuscitation team. Nurses are obliged to begin cardiopulmonary resuscitation with chest compressions and implement ventilation using the bag valve mask of 30:2 compressionventilation ratio. Nurses are not allowed to implement methods of advanced airway management. However, the laryngeal mask airway (LMA) was designed for people inexperienced in intubation who would be able to provide advanced airway management quickly and effectively after a short training. It is advisable to check how nurses, who in case of SCA are often the first responders, deal with advanced airway management. AIM The aim of the study was to evaluate the quality of ventilation using the bag valve mask and the LMA Air-Q SP by professionally active nurses. MATERIALS AND METHODS The study was conducted on a 38-person group of professionally active nurses working or affiliated with the District Health Care Facility in Piotrków Trybunalski. After a short pre-training lecture the nurses were assigned to ventilate the manikin with the bag valve mask (BVM) using 30:2 compressionventilation ratio and then asynchronously with the use of the LMA Air-Q SP. RESULTS The average time elapsed from the beginning of CPR to the onset of ventilation was 18 ± 5,4 s. as for the BVM and 16,15 ± 4,4 s regarding the LMA. Minute ventilation achieved with the BVM was 3,47 ± 1,43 l / min, and in case of the LMA it amounted 5,54 ± 1,73 l / min. There was no case of gastric insufflation in case of the LMA, while as for the BVM it occurred in five cases. There are very few studies focused on the LMA Air-Q SP, but some research (Jagannathan, Alexandera or Gruber) devoted to the use of the LMA in nurses, demonstrate that ventilation with the use of the LMA is effective and ensure more appropriate ventilation parameters than with the use of the BVM. CONCLUSIONS The nurses achieved better ventilation results when using the LMA. Attempts to insert the LMA were shorter than in case of the BVM.
Frugivory and seed dispersal by carnivorous mammals, and associated fruit characteristics, in undisturbed Mediterranean habitatsFrugivory and seed dispersal by carnivorous mammals, and associated fruit characteristics, in undisturbed Mediterranean habitats

The role of carnivorous mammals (Order Carnivora) in seed dispersal has remained virtually unexplored, despite the well-known fact that these animals commonly ingest fleshy fruits and defecate their seeds. This paper presents data on the dispersal of seeds by carnivores in an extensive area of relatively undisturbed habitats in southeastern Spain, and is based on the examination of more than 1,500 carnivore feces collected over a 10-yr period. Seeds from 27 plant species, representing 40% of the fleshy-fruited plants occurring in the region, were recovered from carnivore feces. Carnivores actually disperse the seeds of the vast majority of eaten fruits, as only 0.89% of the seeds found were visibly damaged (broken or cracked). Fruits eaten by carnivores represent a nonrandom subset of the regional flora with regard to color, scent, persistence after ripening, size, seediness, relative pulp richness, chemical composition of the pulp (protein, fiber, minerals), and plant growth form. Carnivore eaten species are also dispersed by birds, thus displaying a dual seed dispersal system, while species not eaten by carnivores are entirely bird-dispersed. Consideration of mammalian carnivores seems essential for a complete understanding of seed dispersal processes in the broad assemblage of Mediterranean plants having mixed, birdmammal dispersal. Available evidence suggests that fruit features associated with carnivore consumption correspond to a "generalized mammalian syndrome", and that carnivore dispersal represents the vanishing remnants of a more complex preHolocene plant-mammal seed dispersal system.
A novel framework for analyzing cortical folding patterns based on sulcal baselines and gyral crestlines

One of the most important morphometric features of cerebral cortex is its convex (gyri) and concave (sulci) folding pattern. Previous studies have shown that sulci and gyri have different anatomical and connectivity patterns. However, most cortical morphometric studies do not differentiate them and few studies have focused on the convolution folding pattern of gyri and sulci separately. In this paper, we developed a novel computational framework to study the morphometric patterns of gyral crestline and sulcal baseline in autism spectrum disorder (ASD). Specifically, the crestlines of eight major gyri and the baseline of two major sulci have been measured on each hemisphere. Our results showed dominantly decreased cortical thickness and increased curvature to the tangential direction of cortical sphere in the brain regions of ASD. Moreover, by using curvature along the lines as its shape feature vector, k-means clustering was performed to cluster the lines with similar shape patterns. Both ASD dominant clusters with more curved patterns and healthy control dominant clusters with less curved patterns were identified. These results coincide with the findings in brain developmental studies that thinner cortex will be more curved and our study may add new insights to the developing mechanism of the cause of ASD.
Application of Novel Drugs for Corneal Cell Regeneration

Corneal transplantation has been the only treatment method for corneal blindness, which is the major cause of reversible blindness. However, despite the advancement of surgical techniques for corneal transplantation, demand for the surgery can never be met due to a global shortage of donor cornea. The development of bioengineering and pharmaceutical technology provided us with novel drugs and biomaterials that can be used for innovative treatment methods for corneal diseases. In this review, the authors will discuss the efficacy and safety of pharmacologic therapies, such as Rho-kinase (ROCK) inhibitors, blood-derived products, growth factors, and regenerating agent on corneal cell regeneration. The promising results of these agents suggest that these can be viable options for corneal reconstruction and visual rehabilitation.
Automated Diagnosis of Plus Disease in Retinopathy of Prematurity Using Deep Convolutional Neural Networks

Importance Retinopathy of prematurity (ROP) is a leading cause of childhood blindness worldwide. The decision to treat is primarily based on the presence of plus disease, defined as dilation and tortuosity of retinal vessels. However, clinical diagnosis of plus disease is highly subjective and variable. Objective To implement and validate an algorithm based on deep learning to automatically diagnose plus disease from retinal photographs. Design, Setting, and Participants A deep convolutional neural network was trained using a data set of 5511 retinal photographs. Each image was previously assigned a reference standard diagnosis (RSD) based on consensus of image grading by 3 experts and clinical diagnosis by 1 expert (ie, normal, pre–plus disease, or plus disease). The algorithm was evaluated by 5-fold cross-validation and tested on an independent set of 100 images. Images were collected from 8 academic institutions participating in the Imaging and Informatics in ROP (i-ROP) cohort study. The deep learning algorithm was tested against 8 ROP experts, each of whom had more than 10 years of clinical experience and more than 5 peer-reviewed publications about ROP. Data were collected from July 2011 to December 2016. Data were analyzed from December 2016 to September 2017. Exposures A deep learning algorithm trained on retinal photographs. Main Outcomes and Measures Receiver operating characteristic analysis was performed to evaluate performance of the algorithm against the RSD. Quadratic-weighted &kgr; coefficients were calculated for ternary classification (ie, normal, pre–plus disease, and plus disease) to measure agreement with the RSD and 8 independent experts. Results Of the 5511 included retinal photographs, 4535 (82.3%) were graded as normal, 805 (14.6%) as pre–plus disease, and 172 (3.1%) as plus disease, based on the RSD. Mean (SD) area under the receiver operating characteristic curve statistics were 0.94 (0.01) for the diagnosis of normal (vs pre–plus disease or plus disease) and 0.98 (0.01) for the diagnosis of plus disease (vs normal or pre–plus disease). For diagnosis of plus disease in an independent test set of 100 retinal images, the algorithm achieved a sensitivity of 93% with 94% specificity. For detection of pre–plus disease or worse, the sensitivity and specificity were 100% and 94%, respectively. On the same test set, the algorithm achieved a quadratic-weighted &kgr; coefficient of 0.92 compared with the RSD, outperforming 6 of 8 ROP experts. Conclusions and Relevance This fully automated algorithm diagnosed plus disease in ROP with comparable or better accuracy than human experts. This has potential applications in disease detection, monitoring, and prognosis in infants at risk of ROP.
Chromosome Data for Malagasy Poison Frogs (Amphibia: Ranidae: Mantella) and Their Bearing on Taxonomy and Phylogeny

Abstract We compared chromosome morphologies for 11 species of Malagasy poison frogs, genus Mantella, and three outgroup taxa (genus Mantidactylus) using conventional and fluorescence staining techniques. All species studied had a karyotype of 2n=26, with five larger and eight smaller chromosome pairs. The 11th pair was acrocentic in Mantella nigricans which represents the first such observation in the genus. The nucleolus organizer region (NOR) was located at secondary constrictions on chromosome pair 2 in all Mantella studied and in Mantidactylus grandisonae (while located on other chromosomes in all other species of Mantidactylus studied so far). Heterochromatin distribution was highly variable among Mantella species; C-bands positively staining with DAPI and CMA3 were observed. The possible structure of these bands, seemingly containing both A+T rich and C+G rich heterochromatin, is discussed. Phylogenetic reconstruction using chromosomal characters provided very little information. Evolution of the characters studied is probably either too fast (heterochromatin arrangement) or too slow (NOR location) to match the main cladogenetic events among Mantella species groups.
No wisdom in the crowd: genome annotation in the era of big data – current status and future prospects

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery‐driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader.
The Possible Impact of Antenatal Exposure to Ubiquitous Phthalates Upon Male Reproductive Function at 20 Years of Age

Phthalates are ubiquitous environmental endocrine-disrupting chemicals suspected to interfere with developmental androgen action leading to adverse effects on male reproductive function. Prenatal exposure studies in rodents show cryptorchidism, hypospadias and reduced testicular volume (TV), testosterone and anogenital distance in males. It is postulated that there is a developmental window in utero when phthalate exposure has the most potent adverse effects. Some human studies show associations between prenatal phthalate exposure and reduced calculated “free” serum testosterone in infant boys and shorter anogenital distance. However, there are no data available yet which link antenatal exposure to long-term effects in men. We aimed to correlate antenatal phthalate exposure with adult TV, semen parameters and serum reproductive hormone concentrations. 913 men from the Western Australian (Raine) Pregnancy Cohort were contacted aged 20–22 years. 423 (56%) agreed to participate; 404 underwent testicular ultrasound examination; 365 provided semen samples, and reproductive hormones were measured in 384. Maternal antenatal serum phthalate metabolite measurements were available for 185 and 111 men, who provided serum and semen, respectively. Maternal serum collected at 18 and 34 weeks gestation, stored at −80°C, was pooled and analyzed for 32 phthalate metabolites by liquid chromatography-tandem mass spectrometry. TV was calculated, semen analysis performed by WHO approved methods, and serum concentrations of gonadotrophins, inhibin B, and testosterone measured. Eleven phthalate metabolites were detected. Primary and secondary metabolites of di-(2-ethyl-hexyl) phthalate (DEHP) and di-iso-nonyl phthalate (DiNP) were positively correlated. After correction for adult height, BMI, presence of a varicocele and exposure to maternal smoking mono-iso-nonyl phthalate (MiNP) (r = −0.22) and sums of DEHP and DiNP metabolites (r = −0.24) and the sum of the metabolites of the high molecular weight phthalates (r = −0.21) were negatively correlated with TV (all p < 0.05). After adjustment for BMI adult serum total testosterone was positively associated with exposure to the following antenatal serum phthalate metabolites: mono-(2-ethylhexyl) phthalate (r = 0.26), MiNP (r = 0.18), the sum of metabolites for DEHP (r = 0.21) and DiNP (r = 0.18), and the sum of high molecular phthalates (r = 0.20) (p = 0.0005 to p = 0.02). Given sample size, storage duration and confounding through postnatal exposures, further studies are required.
YNU-HPCC at SemEval-2018 Task 1: BiLSTM with Attention based Sentiment Analysis for Affect in Tweets

We implemented the sentiment system in all five subtasks for English and Spanish. All subtasks involve emotion or sentiment intensity prediction (regression and ordinal classification) and emotions determining (multi-labels classification). The useful BiLSTM (Bidirectional Long-Short Term Memory) model with attention mechanism was mainly applied for our system. We use BiLSTM in order to get word information extracted from both directions. The attention mechanism was used to find the contribution of each word for improving the scores. Furthermore, based on BiLSTMATT (BiLSTM with attention mechanism) a few deep-learning algorithms were employed for different subtasks. For regression and ordinal classification tasks we used domain adaptation and ensemble learning methods to leverage base model. While a single base model was used for multi-labels task.