Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure-Based Virtual Screening Allows the Identification of Efficient Modulators of E-Cadherin-Mediated Cell–Cell Adhesion

Cadherins are a large family of transmembrane calcium-dependent cell adhesion proteins that orchestrate adherens junction formation and are crucially involved in tissue morphogenesis. Due to their important role in cancer development and metastasis, cadherins can be considered attractive targets for drug discovery. A recent crystal structure of the complex of a cadherin extracellular portion and a small molecule inhibitor allowed the identification of a druggable interface, thus providing a viable strategy for the design of cadherin dimerization modulators. Here, we report on a structure-based virtual screening approach that led to the identification of efficient and selective modulators of E-cadherin-mediated cell–cell adhesion. Of all the putative inhibitors that were identified and experimentally tested by cell adhesion assays using human pancreatic tumor BxPC-3 cells expressing both E-cadherin and P-cadherin, two compounds turned out to be effective in inhibiting stable cell–cell adhesion at micromolar concentrations. Moreover, at the same concentrations, one of them also showed anti-invasive properties in cell invasion assays. These results will allow further development of novel and selective cadherin-mediated cell–cell adhesion modulators for the treatment of a variety of cadherin-expressing solid tumors and for improving the efficiency of drug delivery across biological barriers.
Sparse Representation-Based Video Quality Assessment for Synthesized 3D Videos

The temporal flicker distortion is one of the most annoying noises in synthesized virtual view videos when they are rendered by compressed multi-view video plus depth in Three Dimensional (3D) video system. To assess the synthesized view video quality and further optimize the compression techniques in 3D video system, objective video quality assessment which can accurately measure the flicker distortion is highly needed. In this paper, we propose a full reference sparse representation-based video quality assessment method toward synthesized 3D videos. First, a synthesized video, treated as a 3D volume data with spatial (X-Y) and temporal (T) domains, is reformed and decomposed as a number of spatially neighboring temporal layers, i.e., X-T or Y-T planes. Gradient features in temporal layers of the synthesized video and strong edges of depth maps are used as key features in detecting the location of flicker distortions. Second, the dictionary learning and sparse representation for the temporal layers are then derived and applied to effectively represent the temporal flicker distortion. Third, a rank pooling method is used to pool all the temporal layer scores and obtain the score for the flicker distortion. Finally, the temporal flicker distortion measurement is combined with the conventional spatial distortion measurement to assess the quality of synthesized 3D videos. Experimental results on synthesized video quality database demonstrate our proposed method is significantly superior to the other state-of-the-art methods, especially on the view synthesis distortions induced from depth videos.
CHAPTER 13 STABLE ISOTOPE ANALYSIS : A TOOL FOR STUDYING PAST DIET , DEMOGRAPHY , AND LIFE HISTORY

This chapter is about chemical variation in the various components that make up bones and teeth and its application to studies of diet, demography, and life history. Bones and teeth provide direct evidence of past diets, including infant diets. Knowledge gained from bone chemistry relates to other sources of evidence for diet and, in turn, the interaction of diet, nutrition, and disease. Understanding infant diets and the duration of nursing relates to demographic variables such as birth spacing and population growth. Chemical variation in bones and teeth can also be linked to chemical variation in the environment and, thus, reveals information about place of residence and migration. Although stable isotope analysis may be viewed as a fairly technical research specialty, the results of such analyses make a significant contribution to the reconstruction of past human life.
Model evaluation of high-resolution urban climate simulations: using the WRF/Noah LSM/SLUCM model (Version 3.7.1) as a case study

Abstract. The veracity of urban climate simulation models should be systematically evaluated to demonstrate the trustworthiness of these models against possible model uncertainties. However, existing studies paid insufficient attention to model evaluation; most studies only provided some simple comparison lines between modelled variables and their corresponding observed ones on the temporal dimension. Challenges remain since such simple comparisons cannot concretely prove that the simulation of urban climate behaviours is reliable. Studies without systematic model evaluations, being ambiguous or arbitrary to some extent, may lead to some seemingly new but scientifically misleading findings. To tackle these challenges, this article proposes a methodological framework for the model evaluation of high-resolution urban climate simulations and demonstrates its effectiveness with a case study in the area of Shenzhen and Hong Kong SAR, China. It is intended to (again) remind urban climate modellers of the necessity of conducting systematic model evaluations with urban-scale climatology modelling and reduce these ambiguous or arbitrary modelling practices.
Computer-aided dictionary making : An efficient dictionary construction technique for content analysis

Dictionary-based content analysis has long been popular in social sciences, but manual construction of dictionaries is costly. Latent Semantic Scaling (LSS) is a computeraided technique for dictionary construction, with which users can produce valid content analysis dictionaries with either 10 to 20 exemplary ‘seed words’ or about 10 manually scored documents. In this paper, political science examples show that the accuracy of computerized content analysis with LSS dictionaries is comparable to manually compiled dictionaries. R implementation of LSS is also publicly available.
DETECTION OF POLLEN FLOW IN THE SEEDLING SEED ORCHARD OF USING DNA MARKER Acacia

Pollen pattern dispersal in seedling seed orchard (SSO) is an essential part of a tree-improvement program. Two SSOs of in South Kalimantan and South Sumatra that represent similar resources in different environments were used in this study. Genotypes of all trees and seeds from a subset of 10 mother trees in each orchard were determined for 12 microsatellite loci, and parentage analysis was carried out. The results shows that the pollen dispersal pattern in both SSOs decrease with distance from mother tree. Patterns of pollen dispersal, dispersal distance and cumulative frequency of pollen dispersal distance were similar in both SSOs. Random pollen dispersal were found in both SSOs. About 80% of all crosses were found within a 40-m distance range with the most frequent pollination distance between mother tree and male male parents was 0-10 m. No self-pollinated seed was detected. Application of all these aspects found in this study such as random pollen dispersal and the effective pollen dispersal distance can be useful for establishing seedling seed orchard, clonal seed orchard and in other tree improvement activities of .
Algorithmic Specifications in Linear Logic with Subexponentials Vivek Nigam

The linear logic exponentials ! , ? are not canonical: one can add to linear logic other such operators, say ! , ? , which may or may not allow contraction and weakening, and where l is from some pre-ordered set of labels. We shall call these additional operators subexponentials and use them to assign locations to multisets of formulas within a linear logic programming setting. Treating locations as subexponentials greatly increases the algorithmic expressiveness of logic. To illustrate this new expressiveness, we show that focused proof search can be precisely linked to a simple algorithmic specification language that contains while-loops, conditionals, and insertion into and deletion from multisets. We also give some general conditions for when a focused proof step can be executed in constant time. In addition, we propose a new logical connective that allows for the creation of new subexponentials, thereby further augmenting the algorithmic expressiveness of logic.
MACROECONOMIC FACTORS AFFECTING THE IMPORT IN TURKEY

In this study tried to determine the macro economic factors affecting the import for the period between 1998 and 2012 in Turkey, and to develop policy proposal for the future. Export, Gross Domestic Product and the Reel Effective Exchange Rate were independent variables of the model. And tried to determine the effects of these variables on Turkey’s import. Engle-Granger Two Steps Forecast Method was used in estimation of the model.
Mesenchymal stem cells versus their conditioned medium in the treatment of cisplatin-induced acute kidney injury : evaluation of efficacy and cellular side effects

Mesenchymal stem cells (MSCs) and their conditioned medium (CM) have been shown to ameliorate acute kidney injury (AKI). Potential risks of using stem cells are their participation in fibrosis and their differentiation to unwanted cells. The development of such adverse effects after therapy with CM is unknown. This study compares both the efficacy and safety of using MSCs or their CM in AKI model. Cisplatin was used to induce AKI in Sprague-Dawley rats. Rats were treated with either sub capsular injection of MSCs; or intraperitoneal injection of CM. Appropriate control was included and rats were sacrificed 5, 10, 30, and 60 days later. Kidney function parameters, urinary kidney injury molecule-1 (Kim-1), renal tissue damage, apoptosis, and proliferation were all determined. Special stains to detect adipocytes, osteoblasts, and fibrosis were also used. MSCs and their CM equally ameliorate kidney function deterioration, Kim-1 shedding in urine, renal tissue damage and tubular cell apoptosis. Even after 2 months, both equally reduced interstitial fibrosis. The MSC-treated group showed more enhancement of proliferation. However, adipocytes and osteoblast-like cells were detected where the stem cells were injected but not in the CM group. These results indicate that the use of CM might be an acceptable alternative to MSC therapy as it can attain comparable efficacy without the development of unwanted cells.
Production of isoflavones, daidzein and genistein in callus cultures of Pueraria candollei Wall. ex Benth. var. mirifica

Thanonkeo, S. and Panichajakul, S. Production of isoflavones, daidzein and genistein in callus cultures of Pueraria candollei Wall. ex Benth. var. mirifica Songklanakarin J. Sci. Technol. , 2006, 28(Suppl. 1) : 45-53 Callus cultures of Pueraria candollei var. mirifica were first established from various parts of explants with the objective of isoflavones, daidzein and genistein production. The cultures were studied on their growth and isoflavone production by various combinations of growth regulators, auxins and cytokinins at 25±2oC. Daidzein and genistein accumulated in the cells were determined. The results revealed that callus of P. candollei var. mirifica was capable of producing high level of both isoflavones consistently. The culture temperature played an important role in the growth and isoflavone production. Over twofold of growth and threefold of isoflavone production were demonstrated at 32±2oC. The callus established from the stems in MS medium supplemented with 4.5 μM 2,4-D and 0.46 μM kinetin produced the highest yield of daidzein (5.12 mg/g, DW) and genistein (2.77 mg/g, DW), which was remarkably higher than the intact plants.
TOTAL O3 COLUMNS FROM SCIAMACHY OL3.0 TO SCIAMACHY WEIGHTING FUNCTION DOAS (WFDOAS), OMI-TOMS AND GOME WFDOAS

Global stratospheric ozone columns from satellite instrument SCIAMACHY (SCanning Imaging Absorption SpectroMeter for Atmospheric CHartographY) on ENVISAT derived from the newest operational data product OL3.0 are compared to data products of the SCIAMACHY Weighting Function DOAS Algorithm (WFD), GOME WFD and OMI TOMS algorithm. The comparisons are also analysed for dependencies to total ozone, solar zenith angle and latitude. Due to the limited data set of SCIAMACHY OL3.0 with only 5 nearly complete days and 4 days with 4 orbits each the validation results are quite preliminary. There is an indication that OL3.0 data products show a major improvement compared to previous operational data versions with an agreement within 1% (RMS < 2.5%) to GOME WFD and OMI TOMS. No clear dependencies to total ozone and latitude are observed. In two cases there might be a dependency to SZA, which should be investigated further with a larger data set. The comparisons to SCIA WFD V2 showed the negative bias of 1-2% with SCIA OL3.0, which has been previously described in comparisons to GOME WFD and OMI TOMS and has been interpreted as a calibration error in SCIA lv-1, which has been accounted for in the OL3.0 processing. Despite this offset, SCIA WFD shows no dependencies to SZA, latitude and total ozone. Results help to understand how these different global total ozone data sets can be linked together for ozone trend studies.
Isolation and characterisation of seven alien monosomic addition lines of Gossypium australe

The hexaploid 2(Gossypium hirsutum L. x G. australe F. Muell.) was backcrossed to G. hirsutum to produce the pentaploid G. hirsutum x G. australe and seven alien monosomic addition lines of Gossypium australe on G. hirsutum. The different hybrids produced were characterized morphologically, cytogenetically and using genomic in situ hybridization and eighty-six Simple Sequence Repeat (SSR) markers. The analysis of their progenies allowed to quantify the frequency of genetic material exchanges between the supernumerary alien chromosome and G . hirsutum. The seven monosomic addition lines obtained constitute valuable genetic stocks to carry out fundamental and applied investigations.
Potential use of 68 Ga-apo-transferrin as a PET imaging agent for detecting Staphylococcus aureus infection

Introduction: Ga citrate has been extensively used to detect infection and inflammation since 1971. However, its clinical utility is compromised due to several limitations. The present project explored whether Ga-apo-transferrin (Ga-TF), when prepared in vitro, is a useful agent for positron emission tomography (PET) imaging of bacterial infection. Methods: An infection was induced in male Wistar rats by injecting 5×10 CFU units of Staphyococcus aureus in the right thigh muscle. Ga-TF was synthesized by mixing GaCl3 with apo-transferrin (TF, 2 mg) in sodium carbonate (0.1 M, pH 7.0) and incubating at 40°C for 1 h. Animals were injected with 10–15 MBq of Ga-TF containing approximately 0.2 mg TF and imaged at different time intervals using Siemens Biograph PET-CT. Results: When Ga-TF were injected in the infected rats, the infection lesion was detectable within 20 min post injection. The biodistribution showed the uptake at the lesion increased with time as shown by significantly increased standard uptake values for up to 4 h post injection. There was a considerable decrease in the background activity during the same period of study, giving higher target-to-muscle ratios. Blood pool activity at 3 h post injection was insignificant. GaCl3 (when not conjugated to TF) did not localize at the infection lesion up to 120 min post injection. Conclusion: The preliminary results suggest that Ga-TF is capable of detecting S. aureus infection in the rat model, within an hour after intravenous injection. Crown Copyright © 2011 Published by Elsevier Inc. All rights reserved.
Convolutional Neural Networks Accelerators on FPGA Integrated With Hybrid Memory Cube

Convolutional Neural Networks (CNN) have been widely used for non-trivial tasks such as image classification or speech recognition. As the CNNs become deeper (more and more layers), the accuracy increases, but also the computational cost and the model size. Due to the numerous application of CNNs, numerous accelerators have been proposed to handle computation and memory access pattern. Accelerators use the high parallelism of FPGAs, GPUs or custom ASICs to compute CNNs efficiently. Whereas the GPU throughput is very high, the power consumption can be, in some environment, a concern. FPGA accelerators provide a good balance between time to market and power consumption but face several challenges. FPGA resources must carefully be chosen to match network topologies. The hardware constraints, to carefully choose, are the number of DSPs/BRAMs and the external memory bandwidth. In this thesis, we present two new FPGA designs using the HMC as external memory to accelerate efficiently CNN. The first design is a 32-bit fixed point design named Memory Conscious CNN Accelerator. This design use one Convolution Layer Processor (CLP) per layer and use the parallelism of the HMC to supply data. To maximize the HMC bandwidth, a new data layout is proposed. This new layout makes data request sequential. With this new layout, the frequency of the accelerator can reach 300MHz and a throughput of 232 Images/sec on AlexNet. The second design is a low power DNN accelerator, where data layout is done before the Pipeline Execution (PE). During the layout process, Deep Compression techniques can be applied to improve performances. The PE design achieves a 66 GOPs for only 1.3 Watt of power consumption.
Exploiting Symmetries in Sequential Decision Making under Uncertainty

ions for Offline MDP Algorithms In many MDP domains, several states behave identically, and hence, can be abstracted out. Existing literature defines abstractions via an equivalence relation E ⊆ S × S, such that if (s, s′) ∈ E , then their state transitions are equivalent (for all actions). All states in an equivalence class can be collapsed into a single aggregate state in an abstract MDP, leading to significant reductions in computation. Various definitions for computing abstractions exist. Givan et al. (2003)’s conditions deduce two states to have an equivalence relation if they have the same applicable actions, local transitions lead to equivalent states and immediate costs are the same. Ravindran and Barto (2004) refine this by allowing the applicable actions to be different as long as they can be mapped to each other for this state pair. This can find more state abstractions than Givan’s conditions. We call these settings AS (Abstractions of States) and ASAM (Abstractions of States with Action Mappings), respectively. Our framework ASAP unifies and extends these previous notions of abstractions – we go beyond just an equivalence relation E over states, and compute equivalences of stateaction pairs. This additional notion of abstractions leads to a discovery of many more symmetries and obtains significant computational savings when applied to online algorithms. Monte-Carlo Tree Search (MCTS) Traditional offline MDP algorithms store the whole state space in memory and scale poorly with number of domain features. Sampling-based MCTS algorithms offer an attractive alternative. They solve finite-horizon MDPs in an online manner by interleaving planning and execution steps. A popular variant is UCT (Kocsis and Szepesvári 2006), in which during the planning phase, starting from the root state, an expectimin tree is constructed based on sampled trajectories. At each iteration, the tree is expanded by adding a leaf node. Since these MDPs are finite horizon a node is (state,depth) pair. UCT chooses an action a in a state s at depth d based on the UCB rule, argmina∈A ( Q(s, d, a)−K × √
Assignment of ICD-10 Codes to Diagnoses in Hospital Patient Records in Bulgarian

This paper briefly presents a system called EVTIMA which extracts structured data from hospital patient records in Bu lgarian language. Within this context, the article considers in more detail an im portant extraction task: the recognition of ICD diagnose codes in the free text o f patient records and their automatic assignment to text fragments. The paper s ummarises achievements in ICD codes recognition and presents the evaluation of current EVTIMA results.
A Novel Approach for Diabetic Retinopthy Classification

Sustainable Diabetic Mellitus may lead to several complications towards patients. One of the complications is diabetic retinopathy. Diabetic retinopathy is the type of complication towards the retinal and interferes with patient’s sight. Medical examination toward patients with diabetic retinopathy is observed directly through retinal images using fundus camera. Diabetic retinopathy is classified into four classes based on severity, which are: normal, non-proliferative diabetic retinopathy (NPDR), proliferative diabetic retinopathy (PDR), and macular edema (ME). The aim of this research is to develop a method which can be used to classify the level of severity of diabetic retinopathy based on patient’s retinal images. Seven texture features were extracted from retinal images using gray level co-occurence matrix three dimensional method (3D-GLCM). These features are maximum probability, correlation, contrast, energy, homogeneity, and entropy; subsequently trained using Levenberg-Marquardt Backpropagation Neural Network (LMBP). This study used 600 data of patient’s retinal images, consist of 450 data retinal images for training and 150 data retinal images for testing. Based on the result of this test, the method can classify the severity of diabetic retinopathy with sensitivity of 97.37%, specificity of 75% and accuracy of 91.67%
Interpretation of the infrared spectra of the lizardite-nepouite series in the near and middle 2 infrared range 3 4

9 A series of 1:1 silicate clays of the lizardite-nepouite series (Si2Mg3-xNixO5(OH4) with x = 10 0, 0.5, 1, 1.5, 2, 2.5, and 3) was synthesized at 220°C during 7 days from coprecipitated gels in 11 hydrothermal conditions. A clear relationship was evidenced between the d(06-33) and the Ni/Mg 12 ratio of the synthesized samples following a Vegard’s law and suggested a rather random 13 distribution of octahedral cations. For the first time, infrared spectra of this series were given in 14 both near and mid infrared spectral regions (250 7500 cm). Notably, the bands due to the OH 15 stretching vibrations and those of their first overtones in the lizardite-nepouite series were 16 attributed. The combination bands observed in the near infrared region for both end-members 17 could be attributed thanks to combinations of two or three mid infrared features. Some of the 18 observed combination bands are clearly linked to combination of different vibrational groups. 19 Infrared spectroscopy is simple to use and is a powerful tool to study the crystal-chemistry 20 of garnierites. More broadly, the improvement of band attributions especially in near infrared 21 contributes to develop the infrared analyses in field geology and remote sensing. 22