Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Bacillus anthracis by using monoclonal antibody to cell wall galactose-N-acetylglucosamine polysaccharide

Guanidine extracts of crude Bacillus anthracis cell wall were used to vaccinate BALB/c mice and to develop monoclonal antibody (MAb) to vegetative cell surface antigens. Two hybridomas selected during this study produced immunoglobulin M immunoglobulins, which appear to be directed to an epitope associated with the galactose-N-acetyl-D-glucosamine polysaccharide. Both demonstrated specificity in their binding to purified B. anthracis cell wall, o-stearoyl-polysaccharide conjugates, and intact, nonencapsulated vegetative cells. The interaction of the MAbs with purified polysaccharide was inhibited by 0.5 M galactose and lactose but not by N-acetylglucosamine, glutamate, glycine, or glycerol. Inhibition by glucose or sucrose was approximately 75% of that seen with galactose. Electron microscopy showed that both MAbs interacted with the cell wall of vegetative cells as well as with the cortex of spores. Neither MAb reacted with encapsulated vegetative cells, such as those from infected guinea pigs, nor did they react with intact spores. After conjugation to fluorescein isothiocyanate, the MAbs stained intensely all B. anthracis strains tested, whereas with two exceptions, none of the strains of 20 other Bacillus spp. was stained. The exceptions, strains of Bacillus cereus, could be differentiated from B. anthracis by being beta-hemolytic on blood agar.
Calcium binding protein 1 of the protozoan parasite Entamoeba histolytica interacts with actin and is involved in cytoskeleton dynamics

Blocking expression of EhCaBP1, a calmodulin-like, four EF-hand protein from the protozoan parasite Entamoeba histolytica, resulted in inhibition of cellular proliferation. In this paper we report that EhCaBP1 is involved in dynamic changes of the actin cytoskeleton. Both endocytosis and phagocytosis were severely impaired in cells where EhCaBP1 expression was blocked by inducible expression of the antisense RNA. In wild-type cells both actin and EhCaBP1 were found to co-localize in phagocytic cups and in pseudopods. However, in antisense-blocked cells the phagocytic cup formation is affected. Analysis of the staining patterns in the presence and absence of actin dynamics inhibitors, jasplakinolide and cytochalasin D suggested that EhCaBP1 and polymerized F-actin co-localize on membrane protrusions. Direct interaction between soluble EhCaBP1 and F-actin was further demonstrated by a co-sedimentation assay. A variant of EhCaBP1 did not bind F-actin showing the specificity of the interaction between EhCaBP1 and actin. There is no significant change in the kinetics of in vitro polymerization of actin in presence of EhCaBP1, indicating that EhCaBP1 does not affect filament treadmilling. In addition, using atomic force microscopy; it was found that filaments of F-actin, polymerized in presence of EhCaBP1, were thinner. These results indicate that EhCaBP1 may be involved in dynamic membrane restructuring at the time of cell pseudopod formation, phagocytosis and endocytosis in a process mediated by direct binding of EhCaBP1 to actin, affecting the bundling of actin filaments.
SREBP-1c Transcription Factor and Lipid Homeostasis: Clinical Perspective

Insulin has long-term effects on glucose and lipid metabolism through its control on the expression of specific genes. In insulin sensitive tissues and particularly in the liver, the transcription factor sterol regulatory element binding protein-1c (SREBP-1c) transduces the insulin signal. SREBP-1c is a transcription factor which is synthetized as a precursor in the membranes of the endoplasmic reticulum and which requires post-translational modification to yield its transcriptionally active nuclear form. Insulin activates the transcription and the proteolytic maturation of SREBP-1c. SREBP-1c induces the expression of a family of genes involved in glucose utilization and fatty acid synthesis and can be considered as a thrifty gene. Since a high lipid availability is deleterious for insulin sensitivity and secretion, a role for SREBP-1c in dyslipidaemia and type 2 diabetes has been considered in genetic studies and some association demonstrated. Finally, SREBP-1c could also participate to the hepatic steatosis observed in humans and related to alcohol consumption and hyperhomocysteinaemia, two pathologies which are concomitant with a stress of the endoplasmic reticulum and an insulin-independent SREBP-1c activation.
Enhancing Binary Classification by Modeling Uncertain Boundary in Three-Way Decisions

Text classification is a process of classifying documents into predefined categories through different classifiers learned from labelled or unlabelled training samples. Many researchers who work on binary text classification attempt to find a more effective way to separate relevant texts from a large data set. However, current text classifiers cannot unambiguously describe the decision boundary between positive and negative objects because of uncertainties caused by text feature selection and the knowledge learning process. This paper proposes a three-way decision model for dealing with the uncertain boundary to improve the binary text classification performance based on the <italic> rough set</italic> techniques and centroid solution. It aims to understand the uncertain boundary through partitioning the training samples into three regions (the positive, boundary, and negative regions) by two main boundary vectors <inline-formula><tex-math notation="LaTeX">$\vec{C_{P}}$</tex-math><alternatives> <inline-graphic xlink:href="li-ieq1-2681671.gif"/></alternatives></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\vec{C_{N}}$</tex-math><alternatives> <inline-graphic xlink:href="li-ieq2-2681671.gif"/></alternatives></inline-formula>, created from the labeled positive and negative training subsets, respectively, and further resolve the objects in the boundary region by two derived boundary vectors <inline-formula><tex-math notation="LaTeX">$\vec{B_{P}}$</tex-math><alternatives> <inline-graphic xlink:href="li-ieq3-2681671.gif"/></alternatives></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\vec{B_{N}}$</tex-math><alternatives> <inline-graphic xlink:href="li-ieq4-2681671.gif"/></alternatives></inline-formula>, produced according to the structure of the boundary region. It involves an indirect strategy which is composed of two successive steps in the whole classification process: ‘two-way to three-way’ and ‘three-way to two-way’. Four decision rules are proposed from the training process and applied to the incoming documents for more precise classification. A large number of experiments have been conducted based on the standard data sets RCV1 and Reuters-21578. The experimental results show that the usage of boundary vectors is very effective and efficient for dealing with uncertainties of the decision boundary, and the proposed model has significantly improved the performance of binary text classification in terms of <inline-formula><tex-math notation="LaTeX">$F_{1}$</tex-math><alternatives> <inline-graphic xlink:href="li-ieq5-2681671.gif"/></alternatives></inline-formula> measure and <inline-formula> <tex-math notation="LaTeX">$AUC$</tex-math><alternatives><inline-graphic xlink:href="li-ieq6-2681671.gif"/> </alternatives></inline-formula> area compared with six other popular baseline models.
Loose Plant Architecture 1, an INDETERMINATE Domain Protein Involved in Shoot Gravitropism, Regulates Plant Architecture in Rice

Tiller angle and leaf angle are two important components of rice plant architecture that play a crucial role in determining grain yield. Here, we report the cloning and characterization of the Loose Plant Architecture 1 ( LPA1 ) gene in rice, the functional ortholog of AtIDD15 / SHOOT GRAVITROPISM 5 ( SGR5 ) gene. LPA1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint. LPA1 was also found to affect shoot gravitropism. Expression pattern analysis suggested that LPA1 influences plant architecture by affecting the gravitropism of leaf sheath pulvinus and lamina joint. However, LPA1 only influences gravity perception or signal transduction in coleoptile gravitropism by regulating the sedimentation rate of amyloplasts, distinct from the actions of LAZY1 . LPA1 encodes a plant-specific INDETERMINATE domain (IDD) protein and defines a novel subfamily of 28 IDD proteins with several unique conserved features. LPA1 is localized in the nucleus and functions as an active transcriptional repressor, an activity mainly conferred by a conserved ERF-associated amphiphilic repression (EAR)-like motif. Further analysis suggests that LPA1 participates in a complicated transcriptional and protein interaction network, and has evolved novel functions distinct from SGR5. This study not only facilitates to the understanding of gravitropism mechanisms, but also generates a useful genetic material for rice breeding.
Proinflammatory Mediators Enhance the Osteogenesis of Human Mesenchymal Stem Cells after Lineage Commitment

Several inflammatory processes underlie excessive bone formation, including chronic inflammation of the spine, acute infections, or periarticular ossifications after trauma. This suggests that local factors in these conditions have osteogenic properties. Mesenchymal stem cells (MSCs) and their differentiated progeny contribute to bone healing by synthesizing extracellular matrix and inducing mineralization. Due to the variation in experimental designs used in vitro, there is controversy about the osteogenic potential of proinflammatory factors on MSCs. Our goal was to determine the specific conditions allowing the pro-osteogenic effects of distinct inflammatory stimuli. Human bone marrow MSCs were exposed to tumor necrosis factor alpha (TNF-α) and lipopolysaccharide (LPS). Cells were cultured in growth medium or osteogenic differentiation medium. Alternatively, bone morphogenetic protein 2 (BMP-2) was used as osteogenic supplement to simulate the conditions in vivo. Alkaline phosphatase activity and calcium deposition were indicators of osteogenicity. To elucidate lineage commitment-dependent effects, MSCs were pre-differentiated prior treatment. Our results show that TNF-α and LPS do not affect the expression of osteogenic markers by MSCs in the absence of an osteogenic supplement. In osteogenic differentiation medium or together with BMP-2 however, these mediators highly stimulated their alkaline phosphatase activity and subsequent matrix mineralization. In pre-osteoblasts, matrix mineralization was significantly increased by these mediators, but irrespective of the culture conditions. Our study shows that inflammatory factors potently enhance the osteogenic capacity of MSCs. These properties may be harnessed in bone regenerative strategies. Importantly, the commitment of MSCs to the osteogenic lineage greatly enhances their responsiveness to inflammatory signals.
FAM29A promotes microtubule amplification via recruitment of the NEDD1–γ-tubulin complex to the mitotic spindle

Microtubules (MTs) are nucleated from centrosomes and chromatin. In addition, MTs can be generated from preexiting MTs in a γ-tubulin–dependent manner in yeast, plant, and Drosophila cells, although the underlying mechanism remains unknown. Here we show the spindle-associated protein FAM29A promotes MT-dependent MT amplification and is required for efficient chromosome congression and segregation in mammalian cells. Depletion of FAM29A reduces spindle MT density. FAM29A is not involved in the nucleation of MTs from centrosomes and chromatin, but is required for a subsequent increase in MT mass in cells released from nocodazole. FAM29A interacts with the NEDD1–γ-tubulin complex and recruits this complex to the spindle, which, in turn, promotes MT polymerization. FAM29A preferentially associates with kinetochore MTs and knockdown of FAM29A reduces the number of MTs in a kinetochore fiber, activates the spindle checkpoint, and delays the mitotic progression. Our study provides a biochemical mechanism for MT-dependent MT amplification and for the maturation of kinetochore fibers in mammalian cells.
Conditional Diagnosability of $(n,k)$-Star Networks Under the Comparison Diagnosis Model

The (n,k)-star graph, denoted by Sn,k, is an enhanced version of n-dimensional star graphs Sn, that has better scalability than Sn, and possesses several good properties, compared with hypercubes. Diagnosis has been one of the most important issues for maintaining multiprocessor-system reliability. Conditional diagnosability, which is more general than classical diagnosability, measures the multiprocessor-system diagnosability under the assumption that all neighbors of any processor in the system cannot fail simultaneously. In this paper, we investigate the conditional diagnosability of Sn,k for ( n ≥ 3 and k=1) and ( n ≥ 4 and 2 ≤ k ≤ n) under the comparison diagnosis model.
Sexual Disturbances, Rorschach Sexual Responses, and Mediating Factors

The researchers developed and demonstrated reliability for a list of Rorschach sexual responses. Sexual offenders (n = 40) and child abusers (« = 40) took the Rorschach to investigate differences in these responses. These adult male subjects were randomly assigned to either a permissive or neutral instructional set, and hypothesized differences between groups were found to exist only within the sexually permissive instruction set. Post hoc analysis suggests that subtle and gender-confusion Rorschach responses, rather than those that are obviously sexual, discriminate best between groups. Results support a 2-step model of sexual responses on the test. Gender of the examiner was not related to the results. There have been few systematic empirical studies of Rorschach sexual responses (Bergmann, 1945; Due & Wright, 1945; Gottfried, 1975; Keltikanbas, 1984; Murray, 1985; Tuber & Coates, 1985; Wheeler, 1949), and most of the research is flawed in one way or another (Exner, 1991; Weiner, 1966). Until now, the Comprehensive System (Exner, 1986) has provided most of the reliable normative data, and its sex response score reflects only those overt sex responses involving percepts of sex organs or activities related to sex function. Exner's normative data reveal that only about 4% of nonpatient adults give the narrowly denned Comprehensive System sex response. Despite this limited empirical grounding, it appears that Rorschach practitioners routinely use the test to address many aspects of sexual adjustment and management of sexual impulses. This study is an attempt to provide a systematic empirical base to the theories regarding sexual responses on the Rorschach. Most authors agree that the preoccupation with sexuality on the Rorschach suggests sexual disturbance (Exner, 1986; Holt & Havel, 1960; Rappaport, Gill, & Schafer, 1968; Schafer, 1954). According to psychoanalytic theorists, crude or primitive sexual themes should not break into consciousness under normal circumstances. Exner (1986) has demonstrated that concerns for social approval filter out sexual references and that subjects can manipulate content more easily than structure on the Rorschach. External social taboos also inhibit the verbalization of sexual material. Implicit in these previous accounts of Rorschach sexual responses is a two-step model. The first step is defensive and intrapsychic, keeping sexual responses out of awareness; the second is social and external, preventing the verbalization of sexual responses that are in one's awareness. On the basis of a review of the literature, we formulated four interrelated research questions regarding sexual disturbance and Rorschach sexual responses. Schafer's (1954) writings con
Dynamics of the Streptococcus gordonii Transcriptome in Response to Medium, Salivary α-Amylase, and Starch

ABSTRACT Streptococcus gordonii, a primary colonizer of the tooth surface, interacts with salivary α-amylase via amylase-binding protein A (AbpA). This enzyme hydrolyzes starch to glucose, maltose, and maltodextrins that can be utilized by various oral bacteria for nutrition. Microarray studies demonstrated that AbpA modulates gene expression in response to amylase, suggesting that the amylase-streptococcal interaction may function in ways other than nutrition. The goal of this study was to explore the role of AbpA in gene regulation through comparative transcriptional profiling of wild-type KS1 and AbpA− mutant KS1ΩabpA under various environmental conditions. A portion of the total RNA isolated from mid-log-phase cells grown in 5% CO2 in (i) complex medium with or without amylase, (ii) defined medium (DM) containing 0.8% glucose with/without amylase, and (iii) DM containing 0.2% glucose and amylase with or without starch was reverse transcribed to cDNA and the rest used for RNA sequencing. Changes in the expression of selected genes were validated by quantitative reverse transcription-PCR. Maltodextrin-associated genes, fatty acid synthesis genes and competence genes were differentially expressed in a medium-dependent manner. Genes in another cluster containing a putative histidine kinase/response regulator, peptide methionine sulfoxide reductase, thioredoxin protein, lipoprotein, and cytochrome c-type protein were downregulated in KS1ΩabpA under all of the environmental conditions tested. Thus, AbpA appears to modulate genes associated with maltodextrin utilization/transport and fatty acid synthesis. Importantly, in all growth conditions AbpA was associated with increased expression of a potential two-component signaling system associated with genes involved in reducing oxidative stress, suggesting a role in signal transduction and stress tolerance.
Effects of Sexually Objectifying Media on Self-Objectification and Body Surveillance in Undergraduates: Results of a 2-Year Panel Study

This study used objectification theory (B. L. Fredrickson & T.-A. Roberts, 1997) to predict that the media’s insidious practice of objectifying bodies socializes individuals to take an outsider’s perspective on the physical self (i.e., self-objectify) and to habitually monitor their appearance (i.e., engage in body surveillance). To test these hypotheses, a 2-year panel study using an undergraduate sample was conducted. Cross-lagged path models showed that exposure to sexually objectifying television measured during Year 1 increased trait self-objectification (trait SO) during Year 2 for both women and men. At the same time, trait SO during Year 1 decreased exposure to sexually objectifying television during Year 2, suggesting that both male and female participants selectively avoided sexually objectifying television based on antecedent trait SO. Moreover, exposure to sexually objectifying television and magazines increased body surveillance for men only. The discussion focuses on the process by which the media create body-focused perceptions.
Isolation and characterization of a conserved porin protein from Helicobacter pylori

Helicobacter pylori is a causative agent of gastritis in humans and is correlated with gastric ulcer formation. Infections with this bacterium have proven difficult to treat with antimicrobial agents. To better understand how this bacterium transports compounds such as antimicrobial agents across its outer membrane, identification of porin proteins is important. We have recently identified a family of H. pylori porins (HopA to HopD) (M. M. Exner, P. Doig, T. J. Trust, and R. E. W. Hancock, Infect. Immun. 63:1567-1572, 1995). Here, we report on an unrelated porin species (HopE) from this bacterium. This protein had a apparent molecular mass of 31 kDa and was seen to form 50- and 90-kDa aggregates that were designated putative dimeric and trimeric forms, respectively. The protein was purified to homogeneity and, with a model planar lipid membrane system, was shown to act as a nonselective pore with a single channel conductance in 1.0 M KCl of 1.5 nS, similarly to other bacterial nonspecific porins. An internal peptide sequence of HopE shared homology with the P2 porin of Haemophilus influenzae. HopE was also shown to be antigenic in vivo as assessed by sera taken from H. pylori-infected individuals and was immunologically conserved with both patient sera and specific monoclonal antibodies. From these data, it appears that HopE is a major nonselective porin of H. pylori. The implications of these findings are discussed.
The Clinical Significance of IDH Mutations in Essential Thrombocythemia and Primary Myelofibrosis

Background Limited data exist regarding impact of IDH mutations in Philadelphia-negative myeloproliferative neoplasms (Ph-negative MPNs). Prognostic significance of IDH mutations was asessed in 184 Ph-negative MPN patients - 107 essential thrombocythemia (ET) and 77 primary myelofibrosis (PMF). Methods High-resolution melting (HRM) analysis was used to detect IDH1 and IDH2 mutations. Results PMF and ET patients showed no significant difference for prevalence of IDH mutations. Mutant IDH (IDH1 or IDH2) was documented in five of PMF (6.5%) and two of ET patients (1.9%). IDH mutations in ET patients included one IDH1 R132C and one IDH2 R140Q. Of the five IDH-mutated PMF patients, four (80%) displayed IDH1 (three IDH1 R132C and one IDH1 R132S) and one (20%) carried IDH2 (IDH2 R140Q) mutation. Sixty percent (three in five) of IDH-mutated PMF patients carried JAK2V617F with following allele burdens: 31-50%, 5-12.5% and 31-50%, respectively. Three of 77 PMF patients (3.9%) simultaneously harbored IDH and JAK2V617F mutations. IDH mutations in PMF showed a trend towards higher rate in females (100% and 52.8%, respectively). Bleeding complications were significantly higher in IDH-mutated PMF patients compared to IDH wild-type counterparts. Trend towards a lower prevalance of acetylsalicylic acid (ASA) use was present in IDH mutant PMF patients compared to wild-type counterparts (20% and 63.9%, respectively). Death rate was higher in IDH-mutated PMF patients compared to IDH wild-type PMF patients (60% and 15.3%). In univariate analysis, a significantly shorter leukemia-free survival (LFS) was observed in IDH-mutated PMF patients. Conclusions We conclude that IDH mutations indicate a risk for leukemic transformation in PMF.
Modelling of XCO2 Surfaces Based on Flight Tests of TanSat Instruments

The TanSat carbon satellite is to be launched at the end of 2016. In order to verify the performance of its instruments, a flight test of TanSat instruments was conducted in Jilin Province in September, 2015. The flight test area covered a total area of about 11,000 km2 and the underlying surface cover included several lakes, forest land, grassland, wetland, farmland, a thermal power plant and numerous cities and villages. We modeled the column-average dry-air mole fraction of atmospheric carbon dioxide (XCO2) surface based on flight test data which measured the near- and short-wave infrared (NIR) reflected solar radiation in the absorption bands at around 760 and 1610 nm. However, it is difficult to directly analyze the spatial distribution of XCO2 in the flight area using the limited flight test data and the approximate surface of XCO2, which was obtained by regression modeling, which is not very accurate either. We therefore used the high accuracy surface modeling (HASM) platform to fill the gaps where there is no information on XCO2 in the flight test area, which takes the approximate surface of XCO2 as its driving field and the XCO2 observations retrieved from the flight test as its optimum control constraints. High accuracy surfaces of XCO2 were constructed with HASM based on the flight’s observations. The results showed that the mean XCO2 in the flight test area is about 400 ppm and that XCO2 over urban areas is much higher than in other places. Compared with OCO-2’s XCO2, the mean difference is 0.7 ppm and the standard deviation is 0.95 ppm. Therefore, the modelling of the XCO2 surface based on the flight test of the TanSat instruments fell within an expected and acceptable range.