Miracle-dz/UniFAR-FTUs huggingface dataset:
Ontogenesis of glomerular basement membrane: structural and functional properties

Protein A-gold immunocytochemistry was applied in combination with morphometrical approaches to reveal the alpha 1(IV), alpha 2(IV), and alpha 3(IV) chains of type IV collagen as well as entactin on renal basement membranes, particularly on the glomerular one, during maturation. The results have indicated that a heterogeneity between renal basement membranes appears during the maturation process. In the glomerulus at the capillary loop stage, both the epithelial and endothelial cell basement membranes were labeled for the alpha 1(IV) and alpha 2(IV) chains of type IV collagen and entactin. After fusion, both proteins were present on the entire thickness of the typical glomerular basement membrane. At later stages, the labeling for alpha 1(IV) and alpha 2(IV) chains of type IV collagen decreased and drifted towards the endothelial side, whereas the labeling for the alpha 3(IV) chain increased and remained centrally located. Entactin remained on the entire thickness of the basement membrane during maturation and in adult stage. The distribution of endogenous serum albumin in the glomerular wall was studied during maturation, as a reference for the functional properties of the glomerular basement membrane. This distribution, dispersed through the entire thickness of the basement membrane at early stages, shifted towards the endothelial side of the lamina densa with maturation, demonstrating a progressive acquisition of the permselectivity. These results demonstrate that modifications in the content and organization of the different constituents of basement membranes occur with maturation and are required for the establishment of the filtration properties of the glomerular basement membrane.
Sketch-based retrieval on flash movies via primary scenes

As a multimedia format, Flash is becoming more and more popular over the Web. The typical structure of Flash can benefit from both image retrieval and video retrieval methods. In this paper, we present an approach of sketch-based retrieval on flash movies with analysis on directional and motional relations. Via the selection of primary scenes, query result can be displayed to users in an ideal way. Experiment of the proposed approach is evaluated on a test set with different genres of flash movies, and it shows the usefulness of the approach.
Effects of Carbon Ion Irradiation via Periostin on Breast Cancer Cell Invasion of the Microenvironment

Radiation therapy is effective for pain and local control. However, it has some associated problems such as increased bone metastasis after irradiation and side effects to the surrounding normal bone. Over expression of periostin has been observed in bone metastatic cancer. Many studies have indicated that periostin plays an important role in bone metastasis. However, the role of periostin in the microenvironment of bone invaded by destructive cancer cells remains unclear. It has been reported that expression of periostin is significantly enhanced in bone tissues requiring reconstruction. High LET radiation therapy induces bone hyperplasia and calcification in the irradiated area. In this study, after exposure to gamma-ray and carbon ion irradiation, FM3A/R cells were co cultured with non-irradiated MC3T3-E1 cells. The expression of various bone maturation and metabolic factors in MC3T3-E1 cells was evaluated by RT-PCR or western blotting during a time course. Furthermore, Runx2, OSX, OPN, and OCN were evaluated in MC3T3-E1 cells. The expression levels of these calcification and bone formation cytokines in MC3T3-E1 cells were enhanced by co culture with carbon ion-irradiated FM3A/R cells in the early stage. Radiation therapy for bone metastatic cancer, especially carbon ion beam therapy, has excellent cell-killing effects, and also causes less bone resorption in the radiation field than that observed for gamma-ray irradiation. The differentiation and maturation of osteoblasts might be promoted by periostin stimulation. It can be expected that combined treatment with both carbon ion irradiation and periostin inhibitor administration might become a treatment of choice. Research Article Effects of Carbon Ion Irradiation via Periostin on Breast Cancer Cell Invasion of the Microenvironment Preeyaporn Srimawong1,4*, Masahiko Sawajiri1, Hiroaki Terato2, Kouichi Maruyama3, and Keiji Tanimoto1 1Department of Oral and Maxillofacial Radiology, Hiroshima University, Japan 2Analytical Research Center for Experimental Sciences, Saga University, Japan 3Research Center for Radiation Protection, National Institute of Radiological Sciences, Japan 4Department of Oral and Maxillofacial Radiology, Mahidol University, Thailand.
Endothelial Nitric Oxide Synthase Prevents Heparanase Induction and the Development of Proteinuria

Endothelial nitric oxide synthase (eNOS) deficiency exacerbates proteinuria and renal injury in several glomerular diseases, but the underlying mechanism is not fully understood. We recently showed that heparanase is essential for the development of experimental diabetic nephropathy and glomerulonephritis, and hypothesize that heparanase expression is regulated by eNOS. Here, we demonstrate that induction of adriamycin nephropathy (AN) in C57BL/6 eNOS-deficient mice leads to an increased glomerular heparanase expression accompanied with overt proteinuria, which was not observed in the AN-resistant wild type counterpart. In vitro, the eNOS inhibitor asymmetric dimethylarginine (ADMA) induced heparanase expression in cultured mouse glomerular endothelial cells. Moreover, ADMA enhanced transendothelial albumin passage in a heparanase-dependent manner. We conclude that eNOS prevents heparanase induction and the development of proteinuria.
Autism prevalence and precipitation rates in California, Oregon, and Washington counties.

OBJECTIVE To investigate empirically the possibility of an environmental trigger for autism among genetically vulnerable children that is positively associated with precipitation. DESIGN We used regression analysis to investigate autism prevalence rates and counts first in relation to mean annual county-level precipitation and then to the amount of precipitation a birth cohort was exposed to when younger than 3 years, controlling for time trend, population size, per capita income, and demographic characteristics. In some models, we included county fixed-effects rather than a full set of covariates. SETTING Counties in California, Oregon, and Washington. PARTICIPANTS Children born in California, Oregon, and Washington between 1987 and 1999. Main Exposure County-level precipitation. MAIN OUTCOME MEASURES County-level autism prevalence rates and counts. RESULTS County-level autism prevalence rates and counts among school-aged children were positively associated with a county's mean annual precipitation. Also, the amount of precipitation a birth cohort was exposed to when younger than 3 years was positively associated with subsequent autism prevalence rates and counts in Oregon counties and California counties with a regional developmental services center. CONCLUSIONS These results are consistent with the existence of an environmental trigger for autism among genetically vulnerable children that is positively associated with precipitation. Further studies focused on establishing whether such a trigger exists and identifying the specific trigger are warranted.
Seasonal Drivers of Carbon Dioxide Dynamics in a Hydrologically Modified Subtropical Tidal River and Estuary (Caboolture River, Australia)

Estuaries are dynamic hot spots for carbon cycling and atmospheric evasion. Here we assess the dynamics and drivers of CO2 in a hydrologically modified subtropical Australian estuary. Over 1 year, 10 high‐resolution spatial surveys of pCO2, radon, chromophoric dissolved organic matter, chlorophyll a, and physicochemical parameters were conducted from the estuary mouth to a weir located 25 km upstream. The riverine respiratory quotient revealed that processes besides water column respiration were driving high CO2 within the tidal river (salinity < 2) but not in the estuary (salinity > 2). Conservative mixing plots for pCO2 and 222Rn implied that groundwater may be a contributing source of CO2 during most surveys, but not during dry conditions. A multiple linear regression model explained 88% of the annual pCO2 variability, indicating that mixing, metabolism, temperature, and groundwater inputs were key drivers of CO2. Inputs from an upstream wastewater outfall potentially fuel observed seasonal algal blooms, resulting in the lowest daytime CO2 emissions periods. Postbloom surveys had the highest daytime CO2 emissions. The average tidal river CO2 atmospheric flux rate was 379 ± 53 mmol m−2 day−1. The average estuarine CO2 flux was 78 ± 17 mmol m−2 day−1, equating to 28 ± 6 mol m−2 yr−1. Although the tidal river surface area was ~10 times smaller than the estuary, about one third (35%) of the CO2 emissions were derived from the tidal river. Our results suggest that CO2 emissions along the tidal river‐estuary continuum are dynamic over small temporal and spatial scales and that a combination of hydrological and biological processes is a controlling factor of this variability.
The Case for Autoimmunity in the Etiology of Schizophrenia

The treatment of schizophrenia has frustrated clinicians for over 50 years. Despite advances in neurotransmitter identification and the development of drugs targeting these transmitters, total remission of the disease is not always achieved. Potential etiologies other than neurotransmitter dysfunction merit consideration. One intriguing concept is the possible contribution of autoimmunity in patients with the disease. This breakdown of self‐tolerance has been implicated in patients with other chronic diseases, such as type 1 diabetes mellitus and myasthenia gravis. The literature on autoimmunity as a possible mechanism in the pathogenesis of schizophrenia can be conflicting, but there is a substantial amount of circumstantial, although not conclusive, evidence of immune dysfunction in patients with schizophrenia.
Comparable efficacy of silk fibroin with the collagen membranes for guided bone regeneration in rat calvarial defects

PURPOSE Silk fibroin (SF) is a new degradable barrier membrane for guided bone regeneration (GBR) that can reduce the risk of pathogen transmission and the high costs associated with the use of collagen membranes. This study compared the efficacy of SF membranes on GBR with collagen membranes (Bio-Gide®) using a rat calvarial defect model. MATERIALS AND METHODS Thirty-six male Sprague Dawley rats with two 5 mm-sized circular defects in the calvarial bone were prepared (n=72). The study groups were divided into a control group (no membrane) and two experimental groups (SF membrane and Bio-Gide®). Each group of 24 samples was subdivided at 2, 4, and 8 weeks after implantation. New bone formation was evaluated using microcomputerized tomography and histological examination. RESULTS Bone regeneration was observed in the SF and Bio-Gide®-treated groups to a greater extent than in the control group (mean volume of new bone was 5.49 ± 1.48 mm3 at 8 weeks). There were different patterns of bone regeneration between the SF membrane and the Bio-Gide® samples. However, the absolute volume of new bone in the SF membrane-treated group was not significantly different from that in the collagen membrane-treated group at 8 weeks (8.75 ± 0.80 vs. 8.47 ± 0.75 mm3, respectively, P=.592). CONCLUSION SF membranes successfully enhanced comparable volumes of bone regeneration in calvarial bone defects compared with collagen membranes. Considering the lower cost and lesser risk of infectious transmission from animal tissue, SF membranes are a viable alternative to collagen membranes for GBR.
Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites

Techniques for targeted genetic disruption in Plasmodium, the causative agent of malaria, are currently intractable for those genes that are essential for blood stage development. The ability to use RNA interference (RNAi) to silence gene expression would provide a powerful means to gain valuable insight into the pathogenic blood stages but its functionality in Plasmodium remains controversial. Here we have used various RNA-based gene silencing approaches to test the utility of RNAi in malaria parasites and have undertaken an extensive comparative genomics search using profile hidden Markov models to clarify whether RNAi machinery exists in malaria. These investigative approaches revealed that Plasmodium lacks the enzymology required for RNAi-based ablation of gene expression and indeed no experimental evidence for RNAi was observed. In its absence, the most likely explanations for previously reported RNAi-mediated knockdown are either the general toxicity of introduced RNA (with global down-regulation of gene expression) or a specific antisense effect mechanistically distinct from RNAi, which will need systematic analysis if it is to be of use as a molecular genetic tool for malaria parasites.
Backtrack Programming

A widely used method of efftcient search is examined in detail. This examination provides the opportunity to formulate its scope and methods in their full generality. In addL tion to a general exposition of the basic process, some important refinemertts are indicated. Examples are given which illustrate the salient features of this searching process.
Using a novel T-lymph node ratio model to evaluate the prognosis of nonmetastatic breast cancer patients who received preoperative radiotherapy followed by mastectomy

Abstract We aimed to investigate the prognostic value of postpathological characters in nonmetastatic breast cancer (NMBC) patients who received preoperative radiotherapy (PRT) followed by mastectomy (MAST). We conducted retrospective analyses using the data collected from the Surveillance, Epidemiology, and End Results program of the National Cancer Institute. Univariate and multivariate analyses were performed to identify prognostic factors. Disease-specific survival was calculated by the Kaplan–Meier curve and validated by log rank test. The discriminations of independent risk factors and staging systems were compared by the area under receiver operating characteristic curves (AUC) and validated by Harrell concordance index (bootstrapping algorithm). Akaike information criterion (AIC) was applied to compare the difference of model. One thousand three hundred fifty NMBC patients who had received PRT followed by MAST from 1988 to 2013 were included in the study. We found the metastatic lymph node ratio (mLNR) staging was a superior indicator than pN staging. Thus, we proposed a T-lymph node ratio (T-NR) staging system with simplified-T categories (T0–3 and T4) and the mLNR staging. The novel T-NR staging system provided larger AUC (P = .024, .008, respectively) and the smaller AIC (P < .001) value than American Joint Committee on Cancer staging system. The novel T-NR staging system performed more accurate survival prediction and better model fitness for NMBC patients who receive PRT followed by MAST, it may provide a wide applicability in clinical decision-making.
Reflexivity and Dependency

The analyses of Pollard and Sag (1992, 1994) and Reinhart and Reuland (1993) answer why certain reflexive pronouns – so-called picture-NP-reflexives – behave anomalously in allowing co-reference with nonbinding antecedents. These reflexives are exempt from Binding Theory’s Principle A because Principle A only requires binding if a potential antecedent is available in a given local domain. The reflexive himself in (1) does not find a local antecedent in the domain of the predicate picture and hence becomes exempt from an application of Binding Theory. Just like the co-indexation of the pronoun him with the subject John, the co-indexation of the reflexive is not an instance of binding, but an indication of co-reference.
Acute and chronic posttraumatic stress disorder in motor vehicle accident victims.

OBJECTIVE This study reports the rates of acute and chronic posttraumatic stress disorder (PTSD) in a suburban community study group of 122 victims of serious motor vehicle accidents and a comparison group of 42 (who had been involved in minor, non-motor-vehicle accidents) followed over 12 months. METHOD Motor vehicle accident victims were systematically recruited and examined with comparison subjects at 1, 3, 6, 9, and 12 months after the accident. The authors used the Structured Clinical Interview for DSM-III-R to assess DSM-III-R axis I disorders including PTSD. RESULTS One month after the accident, 34.4% of the motor vehicle accident victims met criteria for PTSD (versus 2.4% of the comparison subjects). Similarly, at 3 and 6 months, rates of PTSD were higher (25.2% and 18.2%) in the motor vehicle accident victims than in the comparison group. Female victims were 4.64 times more likely than male victims to have PTSD at 1 month. Victims with a history of PTSD were 8.02 times more likely at 1 month and 6.81 times more likely at 3 months to have PTSD than those without a history of PTSD. Having an axis II disorder increased the risk for PTSD at 6 months. After adjustment for a history of PTSD and potentially confounding variables, women were 4.39 times more likely than men to develop PTSD at 1 month but did not have a higher risk for chronic PTSD; at 6 months, those with an axis II disorder were at greater risk of PTSD. CONCLUSIONS Rates of PTSD are high in victims of serious motor vehicle accidents and remain high 9 months later. Female victims have an increased risk of acute but not chronic PTSD. Individuals with a history of PTSD are at risk of acute and chronic PTSD. An axis II disorder increases the risk for chronic but not acute PTSD.
Emotion Analysis from Context Understanding: Poster Abstract

In this poster, we propose an emotion analysis method using context information gathered from sensor data. We observe that there are certain situations in which a specific emotion is strongly felt, i.e. dominant. We develop a "scenario-based" approach that focuses on creating such situations with dominant emotion, using a set of context information from sensor data. These "scenarios" undergo validation process through a preliminary survey. Finally, an application prototype detects these scenarios to return the analyzed emotion to the user.
GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003, update

GlycoSuiteDB is an annotated and curated relational database of glycan structures reported in the literature. It contains information on the glycan type, core type, linkages and anomeric configurations, mass, composition and the analytical methods used by the researchers to determine the glycan structure. Native and recombinant sources are detailed, including species, tissue and/or cell type, cell line, strain, life stage, disease, and if known the protein to which the glycan structures are attached. There are links to SWISS-PROT/TrEMBL and PubMed where applicable. Recent developments include the implementation of searching by 2D structure and substructure, disease and reference. The database is updated twice a year, and now contains over 7650 entries. Access to GlycoSuiteDB is available at http://www.glycosuite. com.
PolSAR image classification via multimodal sparse representation-based feature fusion

ABSTRACT It is well known that various features extraction approaches are utilized in polarimetric synthetic aperture (PolSAR) terrain classification for representing the data characteristic. It needs relevant and effective feature fusion algorithms to process complicated features. To address this issue, this article presents a multimodal sparse representation (MSR) framework based algorithm to fuse the different feature vectors from the complicated data space. Polarimetric data features, decomposition features, and the texture features from Pauli colour-coded image are selected to represent multimodal data in different observation modes. The corresponding multimodal manifold regularizations are added to MSR framework to approximate the data structure. Considering the independence and correlation of features, the intrinsic affinity matrices are calculated from this framework. They are processed via local preserve projection algorithm to project the multimodal features into a low dimensionally intrinsic feature space for subsequent classification. Three datasets are utilized in experiments, Western Xi’an, Flevoland, and San Francisco Bay datasets from the Radarsat-2 system in C-band. The effect of regularization parameters and different dimensional fused features are analysed in visualization and quantitation performance. The experiment results demonstrate that the effectiveness and validity of proposed method are superior to other state-of-art methods.
Electrocardiogram Signal Denoising Using Extreme-Point Symmetric Mode Decomposition and Nonlocal Means

Electrocardiogram (ECG) signals contain a great deal of essential information which can be utilized by physicians for the diagnosis of heart diseases. Unfortunately, ECG signals are inevitably corrupted by noise which will severely affect the accuracy of cardiovascular disease diagnosis. Existing ECG signal denoising methods based on wavelet shrinkage, empirical mode decomposition and nonlocal means (NLM) cannot provide sufficient noise reduction or well-detailed preservation, especially with high noise corruption. To address this problem, we have proposed a hybrid ECG signal denoising scheme by combining extreme-point symmetric mode decomposition (ESMD) with NLM. In the proposed method, the noisy ECG signals will first be decomposed into several intrinsic mode functions (IMFs) and adaptive global mean using ESMD. Then, the first several IMFs will be filtered by the NLM method according to the frequency of IMFs while the QRS complex detected from these IMFs as the dominant feature of the ECG signal and the remaining IMFs will be left unprocessed. The denoised IMFs and unprocessed IMFs are combined to produce the final denoised ECG signals. Experiments on both simulated ECG signals and real ECG signals from the MIT-BIH database demonstrate that the proposed method can suppress noise in ECG signals effectively while preserving the details very well, and it outperforms several state-of-the-art ECG signal denoising methods in terms of signal-to-noise ratio (SNR), root mean squared error (RMSE), percent root mean square difference (PRD) and mean opinion score (MOS) error index.
Range-Image: Incorporating Sensor Topology for Lidar Point Cloud Processing

This paper proposes a novel methodology for LiDAR point cloud processing that takes advantage of the implicit topology of various LiDAR sensors to derive 2D images from the point cloud while bringing spatial structure to each point. The interest of such a methodology is then proved by addressing the problems of segmentation and disocclusion of mobile objects in 3D LiDAR scenes acquired via street-based Mobile Mapping Systems (MMS). Most of the existing lines of research tackle those problems directly in the 3D space. This work promotes an alternative approach by using this image representation of the 3D point cloud, taking advantage of the fact that the problem of disocclusion has been intensively studied in the 2D image processing community over the past decade. Using the image derived from the sensor data by exploiting the sensor topology, a semi-automatic segmentation procedure based on depth histograms is presented. Then, a variational image inpainting technique is introduced to reconstruct the areas that are occluded by objects. Experiments and validation on real data prove the effectiveness of this methodology both in terms of accuracy and speed.