Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Structure Similarity-Based Methods for Identifying Drug-Like Compounds

The prediction of biologically active compounds is of great importance for high-throughput screening (HTS) approaches in drug discovery and chemical genomics. Many computational methods in this area focus on measuring the structural similarities between chemical structures. However, traditional similarity measures are often too rigid or they consider only global similarities between structures. This study introduces two new alternative search approaches that overcome most of these limitations. First, the maximum common substructure (MCS) approach provides a more promising and flexible alternative for predicting bioactive compounds. A new backtracking algorithm for MCS is proposed here and compared to global similarity measurements. Our algorithm provides high flexibility in the matching process and is very efficient in identifying local structural similarities. To apply the MCS-based similarity measure in predictive models of biological activity of compounds, the concept of basis compounds is introduced to enable researchers to easily combine the MCS-based and traditional similarity measures with modern machine learning techniques. Our experiments on real compound datasets demonstrate that MCS complements the wellknown atom pair descriptor-based similarity measure. By combining these two measures, we propose an SVM-based algorithm for predicting the biological activities of chemical compounds with high specificity and sensitivity.In similarity search and clustering applications of very large compound sets, most methods are limited in efficiency and scalability and cannot handle today's large compound datasets with several million entries. This is particularly true for MCS-based methods and the computation complexity renders MCS infeasible for large compound dataset. The second main topic of this study addresses this time performance issue by introducing a new method for greatly accelerating similarity search and clustering of very large compound sets using embedding and indexing techniques. The method, which can be used with MCS-based as well as traditional similarity measures, embeds compounds in a high-dimensional Euclidean space and searches this space using an efficient index-aware nearest neighbor search method based on Locality Sensitive Hashing. The method can also be used to accelerate cluster analysis of large compound sets. When applied to similarity search in compound datasets as large as PubChem, we found that the method was 40-200 times faster than sequential search methods, while maintaining comparable recall rates. It also made MCS-based similarity search tractable for large compound datasets. When applied to the clustering of such compound datasets, it helped to reduce the computation time from several months to only a few days.
Food consumption and nutrient intake in Italian school children: results of the ZOOM8 study

Abstract The food consumption and food habits of Italian third-class-primary-school children were assessed and their energy and nutrient intakes were compared with requirements. The study involved 1740 subjects (900 males and 840 females) aged 8–9 years, from the north, centre and south of Italy. Body weight and height were measured. Parents filled in a semi-quantitative Food Frequency Questionnaire for their child. The results showed that the diet of Italian children is unbalanced in terms of macronutrients and deficient in fiber. The average daily intakes of fruit (234 g/d), vegetables (134 g/d) and legumes (17 g/d), were lower than the nationally recommended ones. The percentages of energy intake from fats (41%) and from carbohydrates (45%) were higher and lower respectively than recommended. Low intakes of fiber (13.5 g/d) were reported. A national nutrition policy in Italy should focus on nutrition education programs in schools and for parents.
Cerebrospinal Fluid Research Cerebrospinal Fluid Supports Viability and Proliferation of Cortical Cells in Vitro, Mirroring in Vivo Development

Background: The central nervous system develops around a fluid filled compartment. Recently, attention has turned to the potential role of the fluid (cerebrospinal fluid, CSF) in the developmental process. In particular, the cerebral cortex develops from the germinal epithelium adjacent to the CSF with regulation of cell proliferation and differentiation provided by cells adjacent to the fluid-filled subarachnoid space.
Learning the Determinants of Satisfaction and Usage Intention of Instant Messaging

This study proposes a model for evaluating usage intention toward interactive information technology. The test results reveal that usage intention is influenced directly by satisfaction, perceived ease of use, perceived personalization, and perceived social interaction, while being also influenced indirectly by perceived reliability, perceived instantaneity, perceived ease of use, perceived social image, and perceived social interaction via the mediation of satisfaction.
A survey of pre–operative fear *

Fear is an emotion. It cannot be measured objectively but only subjectively and by observing the physiological response to it. It is a long appreciated concept that emotion has a profound effect on the action of the heart. Fifteen hundred years before the birth of Christ, the description ‘the trembling heart of fear’ was used in the Old Testament1. It was reported thirty-two years ago that reaction to fear can produce transitory electro-cardiographic changes in the T waves2. Nine years later, it was demonstrated that premature cardiac contractions could be produced experimentally during the discussion of sensitive topics 3. More recently, the emotional interaction with cardiac states has again been investigated. In one study the interpersonal conflict in a closed group of men was observed4, and in another, the cardiac response in Scuba divers was noted and co-related with psychological factors5. The arrhythmias commonly noted in patients whose cardiac rhythm has been influenced by emotional over-reaction are, paroxysmal tachycardia, premature contractions, atrial fibrillation and flutter and, occasionally, ventricular tachycardias. The precipitation of ectopic rhythms by psychogenic factors may result from many causes. Stimuli from the central nervous system may affect both the sympathetic and parasympathetic systems and the endocrine system and especially the thyroid and adrenal glands. These factors actjng alone or in combination, result in increased cardiac excitability7. Fear activates the sympathetic nervous system causing constriction of the blood vessels innervated by a-receptors, dilatation of blood vessels innervated by preceptors, increase in heart rate and blood pressure. The constrictions of digital vessels have been measured with a digital plethysmograph and these results used as an objective measurement of anxietys. A case in which terror may have led to adrenergic hyperactivity and the collapse of the patient was reported in 19529 and more recently the occurrence of ventricular fibrillation in a terrified patient during the use of drugs which sensitise the heart to adrenaline was described 10.
Larval and adult fish assemblages along the Northwest Passage: the shallow Kitikmeot and the ice-covered Parry Channel as potential barriers to dispersal

Climate warming and sea ice decline are expected to increase fish population movements in the circumpolar Arctic, including across the Canadian Arctic Archipelago (CAA). Knowledge gaps on present distribution, habitat uses, barriers to dispersal, and population connectivity along the Northwest Passage (NWP) limit science-based management of fish in the North American Arctic. Pelagic trawl, bottom trawl, and ichthyoplankton net collections from the US Beaufort Sea to Baffin Bay between 2005 and 2017 are used to map fish distribution along the NWP and identify potential zoogeographic barriers. In the Kitikmeot (southern CAA), the combination of shallow depths, sub-zero temperatures and slow water circulation may represent a physical barrier reducing the dispersal of marine fish between western and eastern regions. In contrast, the Parry Channel (northern CAA) may exemplify a disappearing sea ice barrier as climate warming unfolds and allow new genetic exchanges.
Correlation of Cardiac Markers and Biomarkers With Blood Pressure of Middle‐Aged Marathon Runners

Runners with exercise‐induced high blood pressure have recently been reported to exhibit higher levels of cardiac markers, vasoconstrictors, and inflammation. The authors attempted to identify correlations between exercise‐related personal characteristics and the levels of biochemical/cardiac markers in marathon runners in this study. Forty healthy runners were enrolled. Blood samples were taken both before and after finishing a full marathon. The change in each cardiac/biochemical marker over the course of the marathon was determined. All markers were significantly (P<.001) increased immediately after the marathon (creatine kinase‐MB [CK‐MB]: 7.9±2.7 ng/mL, cardiac troponin I (cTnI): 0.06±0.10ng/mL, N‐terminal pro–B‐type natriuretic peptide (NT‐proBNP): 95.7±76.4, endothelin‐1: 2.7±1.16, high‐sensitivity C‐reactive protein [hs‐CRP]: 0.1±0.09, creatine kinase [CK]: 315.7±94.0, lactate dehydrogenase [LDH]: 552.8±130.3) compared with their premarathon values (CK‐MB: 4.3±1.3, cTnI: 0.01±0.003, NT‐proBNP: 27.6±31.1, endothelin‐1: 1.11±0.5, hs‐CRP: 0.06±0.07, CK: 149.2±66.0, LDH: 399±75.1). In middle‐aged marathon runners, factors related to increased blood pressure were correlated with marathon‐induced increases in cTnI, NT‐proBNP, endothelin‐1, and hs‐CRP. These correlations were observed independent of running history, records of finishing, and peak oxygen uptake.
Compositional Signatures in Acoustic Backscatter Over Vegetated and Unvegetated Mixed Sand‐Gravel Riverbeds

Multibeam acoustic backscatter has considerable utility for remote characterization of spatially heterogeneous bed sediment composition over vegetated and unvegetated riverbeds of mixed sand and gravel. However, the use of high‐frequency, decimeter‐resolution acoustic backscatter for sediment classification in shallow water is hampered by significant topographic contamination of the signal. In mixed sand‐gravel riverbeds, changes in the abiotic composition of sediment (such as homogeneous sand to homogeneous gravel) tend to occur over larger spatial scales than is characteristic of small‐scale bedform topography (ripples, dunes, and bars) or biota (such as vascular plants and periphyton). A two‐stage method is proposed to filter out the morphological contributions to acoustic backscatter. First, the residual supragrain‐scale topographic effects in acoustic backscatter with small instantaneous insonified areas, caused by ambiguity in the local (beam‐to‐beam) bed‐sonar geometry, are removed. Then, coherent scales between high‐resolution topography and backscatter are identified using cospectra, which are used to design a frequency domain filter that decomposes backscatter into the (unwanted) high‐pass component associated with bedform topography (ripples, dunes, and sand waves) and vegetation, and the (desired) low‐frequency component associated with the composition of sediment patches superimposed on the topography. This process strengthens relationships between backscatter and sediment composition. A probabilistic framework is presented for classifying vegetated and unvegetated substrates based on acoustic backscatter at decimeter resolution. This capability is demonstrated using data collected from diverse settings within a 386 km reach of a canyon river whose bed varies among sand, gravel, cobbles, boulders, and submerged vegetation.
The Cardiovascular Comorbidity in Children with Chronic Kidney Disease (4C) study: objectives, design, and methodology.

BACKGROUND AND OBJECTIVES Children and adolescents with chronic kidney disease (CKD) are at high risk for cardiovascular morbidity and mortality. A systemic arteriopathy and cardiomyopathy has been characterized in pediatric dialysis patients by the presence of morphologic and functional abnormalities. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS The Cardiovascular Comorbidity in Children with CKD (4C) Study is a multicenter, prospective, observational study aiming to recruit more than 600 children, aged 6 to 17 years, with initial GFR of 10 to 45 ml/min per 1.73 m(2). The prevalence, degree, and progression of cardiovascular comorbidity as well as its association with CKD progression will be explored through longitudinal follow-up. The morphology and function of the heart and large arteries will be monitored by sensitive noninvasive methods and compared with aged-matched healthy controls. Multiple clinical, anthropometric, biochemical, and pharmacologic risk factors will be monitored prospectively and related to the cardiovascular status. A whole-genome association study will be performed to identify common genetic variants associated with progression of cardiovascular alterations and/or renal failure. Monitoring will be continued as patients reach end-stage renal disease and undergo different renal replacement therapies. RESULTS While cardiovascular morbidity in adults is related to older age and additional risk factor load (e.g., diabetes), the role of CKD-specific factors in the initiation and progression of cardiac and vascular disease are likely to be characterized with greater sensitivity in the pediatric age group. CONCLUSIONS The 4C study is expected to provide innovative insight into cardiovascular and renal disease progression in CKD.
NeXtCrowd: Lightweight And Efficient Network Design for Dense Crowd Counting

Dense crowd counting remains a challenging task due to complex backgrounds, large-scale scenes, diversity of human features, and computational performance requirements. Unlike past solutions with additional designs or complex architectures, we argue that the counting task only needs to give an approximate number or density distribution of people in the scene, without exact location and classification, suggesting that a relatively lightweight architecture is sufficient for this task. Motivated by this line of thought, we explore whether a simple convolutional architecture can maintain counting performance in dense crowd counting. We propose an efficient CNN framework for crowd counting, namely NeXtCrowd. Specifically, we eliminate some unnecessary architectures to reduce the complexity and number of parameters of the backbone architecture, thus improving its computational efficiency and generalization capability. We then improve the performance and stability of the network by choosing the corresponding loss function and optimization method based on the task characteristics. Last we adopt a regression layer with Global Response Normalization to generate the density map, which can make better use of the information of each channel in the deep image features, and aggregate a more accurate density map of dense crowd. Without using additional architectures, NeXtCrowd can still achieve state-of-the-art performance on several dense crowd datasets. On the UCF-QNRF and ShanghaiTech Part A datasets, our model reduces the root mean squared error by 16.87 (131.4) and 7.9 (86.29), respectively” over the baseline methods.
p53 Codon 72 polymorphism and gastric cancer risk in a Chinese Han population.

BACKGROUND studies investigating the association between p53 codon 72 polymorphism and gastric cancer risk report conflicting results. Our recent meta-analysis suggests that the p53 codon 72 polymorphism may be associated with gastric cancer among Asians. AIM the objective of this study was to investigate the association between p53 codon 72 polymorphism and gastric cancer risk in Chinese Han patients. METHODS we extracted the peripheral blood samples from 150 patients with gastric cancer and 150 control subjects. Polymerase chain reaction-restriction fragment length polymorphism analysis was performed to detect p53 codon 72 polymorphism in these patients. RESULTS patients with gastric cancer had a significantly lower frequency of Arg/Arg (odds ratio [OR] = 0.48, 95% confidence interval [95% CI] = 0.28, 0.80; p = 0.005) than control subjects. Patients with cardia gastric cancer had a significantly higher frequency of Pro/Pro (OR = 2.26, 95% CI = 1.12, 4.55; p = 0.02) than those with noncardia gastric cancer. Patients with advanced gastric cancer had a significantly higher frequency of Arg/Arg (OR = 2.66, 95% CI = 1.06, 6.65; p = 0.03) than those with early gastric cancer. When stratified by the Lauren's classification, histological differentiation of gastric cancer, no statistically significant result was observed. CONCLUSION this study suggests that the p53 codon 72 polymorphism may be associated with gastric cancer in Chinese Han patients, and that difference in genotype distribution may be associated with the location and stage of gastric cancer.
Effect Size Discovery Learning Model on Students Critical Thinking Skills

This study aims to determine the effect size of the discovery model on students' critical thinking skills. This type of research is meta-analysis research. The research sample comes from the analysis of 10 national and international journals indexed by SINTA, Scopus and Web of Science. The data source search process comes from Google Scholar, ScienceDirect, Eric and Wiley. The keywords for searching data sources are discovery learning model and critical thinking skills. Data collection techniques were direct observation and documentation. Data analysis is statistical analysis by calculating the effect size of each study with the help of JSAP. The results showed that the average effect size was 0.90 with very high criteria, the average value of the experimental class was 85. 90 and the control class was 72.10 and the N-gain value was 0.52. These findings indicate a positive effect of the discovery learning model on students' critical thinking skills. The discovery model helps students be more active and have higher-level thinking skills in learning
Soluble amyloid-&bgr; precursor protein binds its cell surface receptor in a cooperative fashion with glypican and syndecan proteoglycans

Summary Proteolytic processing of amyloid-&bgr; precursor protein (APP) generates the amyloid-&bgr; peptide, which plays a central role in Alzheimer disease. The physiological function of APP and its proteolytic fragments, however, remains barely understood. Here we show that, on the basis of its binding characteristics, the secreted ectodomain of APP (sAPP) is a new member of the heparin-binding growth factor superfamily. Like other of its members, sAPP binds in a bivalent manner to the plasma membrane with two different subdomains. The N-terminal growth-factor-like domain (GFLD) is necessary and sufficient for protein-receptor binding, whereas the E2-domain mediates interaction with membrane-anchored heparan sulfate proteoglycans (HSPGs). The membrane-anchored HSPGs function as low-affinity co-receptors for sAPP and enhance the affinity to the sAPP receptor. Our findings provide a solid basis for the further identification of this receptor.
BREAKING THE COHERENCE BARRIER: A NEW THEORY FOR COMPRESSED SENSING

This paper presents a framework for compressed sensing that bridges a gap between existing theory and the current use of compressed sensing in many real-world applications. In doing so, it also introduces a new sampling method that yields substantially improved recovery over existing techniques. In many applications of compressed sensing, including medical imaging, the standard principles of incoherence and sparsity are lacking. Whilst compressed sensing is often used successfully in such applications, it is done largely without mathematical explanation. The framework introduced in this paper provides such a justification. It does so by replacing these standard principles with three more general concepts: asymptotic sparsity, asymptotic incoherence and multilevel random subsampling. Moreover, not only does this work provide such a theoretical justification, it explains several key phenomena witnessed in practice. In particular, and unlike the standard theory, this work demonstrates the dependence of optimal sampling strategies on both the incoherence structure of the sampling operator and on the structure of the signal to be recovered. Another key consequence of this framework is the introduction of a new structured sampling method that exploits these phenomena to achieve significant improvements over current state-of-the-art techniques.
Downstaging of hepatocellular cancer before liver transplant: Long‐term outcome compared to tumors within Milan criteria

We report on the long‐term intention‐to‐treat (ITT) outcome of 118 patients with hepatocellular carcinoma (HCC) undergoing downstaging to within Milan/United Network for Organ Sharing T2 criteria before liver transplantation (LT) since 2002 and compare the results with 488 patients listed for LT with HCC meeting T2 criteria at listing in the same period. The downstaging subgroups include 1 lesion >5 and ≤8 cm (n = 43), 2 or 3 lesions at least one >3 and ≤5 cm with total tumor diameter ≤8 cm (n = 61), or 4‐5 lesions each ≤3 cm with total tumor diameter ≤8 cm (n = 14). In the downstaging group, 64 patients (54.2%) had received LT and 5 (7.5%) developed HCC recurrence. Two of the five patients with HCC recurrence had 4‐5 tumors at presentation. The 1‐ and 2‐year cumulative probabilities for dropout (competing risk) were 24.1% and 34.2% in the downstaging group versus 20.3% and 25.6% in the T2 group (P = 0.04). Kaplan‐Meier's 5‐year post‐transplant survival and recurrence‐free probabilities were 77.8% and 90.8%, respectively, in the downstaging group versus 81% and 88%, respectively, in the T2 group (P = 0.69 and P = 0.66, respectively). The 5‐year ITT survival was 56.1% in the downstaging group versus 63.3% in the T2 group (P = 0.29). Factors predicting dropout in the downstaging group included pretreatment alpha‐fetoprotein ≥1,000 ng/mL (multivariate hazard ratio [HR]: 2.42; P = 0.02) and Child's B versus Child's A cirrhosis (multivariate HR: 2.19; P = 0.04). Conclusion: Successful downstaging of HCC to within T2 criteria was associated with a low rate of HCC recurrence and excellent post‐transplant survival, comparable to those meeting T2 criteria without downstaging. Owing to the small number of patients with 4‐5 tumors, further investigations are needed to confirm the efficacy of downstaging in this subgroup. (Hepatology 2015;61:1968–1977)
Efficacy of Chemotherapy for Advanced Non-Small Cell Lung Cancer with Idiopathic Pulmonary Fibrosis

Background: Idiopathic pulmonary fibrosis (IPF) is the most common type of idiopathic interstitial pneumonia and is associated with an independent increased risk of lung carcinogenesis. The benefit of chemotherapy for lung cancer in cases of IPF remains unknown. Objectives: This study was conducted to elucidate the efficacy of chemotherapy for advanced non-small cell lung cancer (NSCLC) in patients with IPF. Methods: Advanced (i.e. stage IIIB and IV) NSCLC patients with IPF who received systemic chemotherapy were studied. Response rate, toxicity, overall survival and progression-free survival were investigated. Results: Between January 2000 and December 2009, 21 patients were enrolled in this study and treated with chemotherapy. The overall response rate with the 1st regimen was 42.9%. The median overall survival was 11.4 months, the 1-year survival rate was 28.6% and the median PFS was 5.4 months. Conclusions: This study showed that advanced NSCLC patients with IPF may benefit from chemotherapy; well-controlled studies are still needed to clarify the efficacy.