Immunological and histopathological changes in Penaeus semisulcatus challenged with Vibrio harveyi

Two-hundred and sixty five green tiger shrimp juveniles (Penaeus semisulcatus) with the average weight of 7-12g were collected from Helleh farms in Bushehr province and transported to Iran Shrimp Research Center of Bushehr in October, 2009. The juveniles were acclimated for two weeks. The experiment was designed in three treatments (named 3, 4 and 5) and two controls (named 1 and 2) in triplicate with 15 shrimp in each repetition prepared of glass aquarium. All the treatments and repetitions were exposed to Vibrio harveyi (NCBI: GU974342.1). The concentrations of the treatments were 10^8,10^6 and 10^4 CFU ml^-1 in individual containers dedicated for each mentioned treatment (3, 4 and 5, respectively). The controls prepared with no any bacteria and fully filled with chlorinated and UV treated sea water were named 1 and 2 respectively. The hemolymph were withdrawn from abdominal segments of samples for measuring THC and TPC evaluation at designed hours (2, 6, 12, 24, 48, 96, 144, 192 and 240). The shrimp samples were also fixed in Davidson fixative for histopathological studies. The results showed that the difference of THC value between controls and group 3 during 12 till 96 hours of experiment was significant (P 0.05) between group 5 and control groups of THC. The data showed that differences of TPC value between control groups during 24 to 96 hours were significant (P< 0.05), whereas the differences between controls with groups 4 and 5 during 48 to 144 hours and 192 hours, were significant (P< 0.05) respectively. TPC and THC were observed with an increase in the concentration of bacteria and passing the time as inverse bell shape procedure. In histopathology, gills showed melanization and color changed to brown and black. The hepatopancreas cells revealed necrosis and vacuolization of B, E, R and F cells. The bolitas ball and bacterial colonization was observed in the intestine. Our results showed that Vibrio harveyi with 10^8 and 10^6 cell/ml decreased immunity factors such as THC and TPC. The histopathological changes increased with increasing the concentration of bacterial level. This finding can be used for assessing the health of shrimp culture and prevention of vibriosis

Spin-glass state and reversed magnetic anisotropy induced by Cr doping in the Kitaev magnet α-RuCl3

Magnetic properties of the substitution series Ru1-xCrxCl3 were investigated to determine the evolution from the anisotropic Kitaev magnet α-RuCl3 with Jeff=1/2 magnetic Ru3+ ions to the isotropic Heisenberg magnet CrCl3 with S=3/2 magnetic Cr3+ ions. Magnetization measurements on single crystals revealed a reversal of the magnetic anisotropy under doping, which we argue to arise from the competition between anisotropic Kitaev and off-diagonal interactions on the Ru-Ru links and approximately isotropic Cr-Ru and isotropic Cr-Cr interactions. In addition, combined magnetization, ac susceptibility, and specific-heat measurements clearly show the destabilization of the long-range magnetic order of α-RuCl3 in favor of a spin-glass state of Ru1-xCrxCl3 for a low doping of x≤0.1. The corresponding freezing temperature as a function of Cr content shows a broad maximum around x ≤ 0.45

Data Summarization with Social Contexts

While social data is being widely used in various applications such as sentiment analysis and trend prediction, its sheer size also presents great challenges for storing, sharing and processing such data. These challenges can be addressed by data summarization which transforms the original dataset into a smaller, yet still useful, subset. Existing methods find such subsets with objective functions based on data properties such as representativeness or informativeness but do not exploit social contexts, which are distinct characteristics of social data. Further, till date very little work has focused on topic preserving data summarization, despite the abundant work on topic modeling. This is a challenging task for two reasons. First, since topic model is based on latent variables, existing methods are not well-suited to capture latent topics. Second, it is difficult to find such social contexts that provide valuable information for building effective topic-preserving summarization model. To tackle these challenges, in this paper, we focus on exploiting social contexts to summarize social data while preserving topics in the original dataset. We take Twitter data as a case study. Through analyzing Twitter data, we discover two social contexts which are important for topic generation and dissemination, namely (i) CrowdExp topic score that captures the influence of both the crowd and the expert users in Twitter and (ii) Retweet topic score that captures the influence of Twitter users' actions. We conduct extensive experiments on two real-world Twitter datasets using two applications. The experimental results show that, by leveraging social contexts, our proposed solution can enhance topic-preserving data summarization and improve application performance by up to 18%

Ab initio Pseudopotential Plane-wave Calculations of the Electronic Structure of YBa_2Cu_3O_7

We present an ab initio pseudopotential local density functional calculation for stoichiometric high-Tc cuprate YBa_2Cu_3O_7 using the plane-wave basis set. We have overcome well-known difficulties in applying pseudopotential methods to first-row elements, transition metals, and rare-earth materials by carefully generating norm-conserving pseudopotentials with excellent transferability and employing an extremely efficient iterative diagonalization scheme optimized for our purpose. The self-consistent band structures, the total and site-projected densities of states, the partial charges and their symmetry-decompositions, and some characteristic charge densities near E_f are presented. We compare our results with various existing (F)LAPW and (F)LMTO calculations and establish that the ab initio pseudopotential method is competitive with other methods in studying the electronic structure of such complicated materials as high-Tc cuprates. [8 postscript files in uuencoded compressed form]Comment: 14 pages, RevTeX v3.0, 8 figures (appended in postscript file), SNUTP 94-8

An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery.

Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs

Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer

The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (PNA) with the O6-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA directed assembly of homo- and hetero-dimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template directed assembly of PNA modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels which may find use in the study of assembly processes in cells

Land subsidence hazard in iran revealed by country-scale analysis of sentinel-1 insar

Many areas across Iran are subject to land subsidence, a sign of exceeding stress due to the over-extraction of groundwater during the past decades. This paper uses a huge dataset of Sentinel-1, acquired since 2014 in 66 image frames of 250×250km, to identify and monitor land subsidence across Iran. Using a two-step time series analysis, we first identify subsidence zones at a medium scale of 100m across the country. For the first time, our results provide a comprehensive nationwide map of subsidence in Iran and recognize its spatial distribution and magnitude. Then, in the second step of analysis, we quantify the deformation time series at the highest possible resolution to study its impact on civil infrastructure. The results spots the hazard posed by land subsidence to different infrastructure. Examples of road and railways affected by land subsidence hazard in Tehran and Mashhad, two of the most populated cities in Iran, are presented in this study