Miracle-dz/UniFAR-FTUs huggingface dataset:
A Type III Secretion System Is Required for Aeromonas hydrophila AH-1 Pathogenesis

ABSTRACT Aeromonas hydrophila is a gram-negative opportunistic pathogen in fish and humans. Many bacterial pathogens of animals and plants have been shown to inject anti-host virulence determinants into the hosts via a type III secretion system (TTSS). Degenerate primers based on lcrD family genes that are present in every known TTSS allowed us to locate the TTSS gene cluster in A. hydrophila AH-1. A series of genome walking steps helped in the identification of 25 open reading frames that encode proteins homologous to those in TTSSs in other bacteria. PCR-based analysis showed the presence of lcrD homologs (ascV) in all of the 33 strains of A. hydrophila isolated from various sources. Insertional inactivation of two of the TTSS genes (aopB and aopD) led to decreased cytotoxicity in carp epithelial cells, increased phagocytosis, and reduced virulence in blue gourami. These results show that a TTSS is required for A. hydrophila pathogenesis. This is the first report of sequencing and characterization of TTSS gene clusters from A. hydrophila. The TTSS identified here may help in developing suitable vaccines as well as in further understanding of the pathogenesis of A. hydrophila.
Role of Proinflammatory CD68+ Mannose Receptor− Macrophages in Peroxiredoxin-1 Expression and in Abdominal Aortic Aneurysms in Humans

Objective—Abdominal aortic aneurysms (AAAs), dilations of the infrarenal aorta, are characterized by inflammation and oxidative stress. We previously showed increased levels of peroxiredoxin-1 (PRDX-1) in macrophages cultured from AAA patients. The purpose of the study was to determine which subpopulation of macrophages is present in AAAs and is involved in upregulation of PRDX-1 in aneurysmal disease. Methods and Results—This study used immunohistochemistry with antibodies against CD68 and mannose receptor (MR) to determine the subtype of macrophages in AAA tissue samples (n=33); laser capture microdissection to isolate each subtype; and quantitative–reverse transcriptase-polymerase chain reaction, Western blot, and ELISA to assess PRDX-1 mRNA and PRDX-1protein levels in both types. Proinflammatory CD68+MR− macrophages predominated in adventitial tissue, whereas the intraluminal thrombus contained CD68+MR+ macrophages. The presence of lipids and iron-containing deposits confirmed their phagocytic phenotype. Laser capture microdissection-isolated CD68+MR− and CD68+MR+ macrophages, characterized by quantitative–reverse transcriptase-polymerase chain reaction (TNF, IL1B, MRC1, and CCL18) and Western blot (stabilin and hemoglobin), validated the microdissected subtypes. PRDX-1 expression was colocalized with CD68+MR− macrophages. PRDX-1 mRNA and PRDX-1 protein were both more abundant in CD68+MR− than CD68+MR+ macrophages in AAA. Conclusion—These findings suggest that the proteins or mRNAs expressed by the proinflammatory CD68+MR− macrophages may contribute to aneurysmal pathology.
Distinct Neurophysiological Mechanisms Support the Online Formation of Individual and Across-Episode Memory Representations

Individual experiences often overlap in their content, presenting opportunities for rapid generalization across them. In this study, we show in 2 independent experiments that integrative encoding-the ability to form individual and across memory representations during online encoding-is supported by 2 distinct neurophysiological responses. Brain potential is increased gradually during encoding and fit to a trial level memory measure for individual episodes, whereas neural oscillations in the theta range (4-6 Hz) emerge later during learning and predict participants' generalization performance in a subsequent test. These results suggest that integrative encoding requires the recruitment of 2 separate neural mechanisms that, despite their co-occurrence in time, differ in their underlying neural dynamics, reflect different brain learning rates and are supportive of the formation of opposed memory representations, individual versus across-event episodes.
Sleep Homeostasis and Models of Sleep Regulation

According to the two-process model of sleep regulation, the timing and structure of sleep are determined by the interaction of a homeostatic and a circadian process. The original qualitative model was elaborated to quantitative versions that included the ultradian dynamics of sleep in relation to the non-REM-REM sleep cycle. The time course of EEG slow-wave activity, the major marker of non-REM sleep homeostasis, as well as daytime alertness were simulated successfully for a considerable number of experimental protocols. They include sleep after partial sleep deprivation and daytime napping, sleep in habitual short and long sleepers, and alertness in a forced desynchrony protocol or during an extended photoperiod. Simulations revealed that internal desynchronization can be obtained for different shapes of the thresholds. New developments include the analysis of the waking EEG to delineate homeostatic and circadian processes, studies of REM sleep homeostasis, and recent evidence for local, use-dependent sleep processes. Moreover, nonlinear interactions between homeostatic and circadian processes were identified. In the past two decades, models have contributed considerably to conceptualizing and analyzing the major processes underlying sleep regulation, and they are likely to play an important role in future advances in the field.
Posttraumatic Growth Following the Terrorist Attacks of September 11, 2001: Cognitive, Coping, and Trauma Symptom Predictors in an Internet Convenience Sample

Cognitive, coping, and trauma symptom predictors of posttraumatic growth (PTG; measured with the Posttraumatic Growth Inventory) were examined in a large convenience sample (n =1505) participating in a longitudinal Internet-based study following the terrorist attacks of 9/11/01. Results indicate that initial PTG levels (mean 9 weeks post-attacks) were generally associated with higher trauma symptoms (measured with the PTSD Checklist - Specific), positive changes in worldview (measured with the Changes in Outlook Questionnaire), more denial, and less behavioral disengagement (measured with the Brief COPE). Additionally, PTG had a curvilinear association with level of trauma symptoms, such that those reporting symptoms at intermediate levels reported the highest levels of growth. Levels of PTG declined somewhat over time with the exception of Spiritual Change. As expected, PTG levels at follow-up (mean 6.5 months post-attacks) were primarily predicted by initial PTG levels; however, decreases from baseline .
Minor physical anomalies in patients with first-episode psychosis: their frequency and diagnostic specificity

Background An increased prevalence of minor physical anomalies (MPAs) has been extensively documented in schizophrenia but their specificity for the disorder remains unclear. We investigated the prevalence and the predictive power of MPAs in a large sample of first-episode psychotic patients across a range of diagnoses. Method MPAs were examined in 242 subjects with first-episode psychosis (50% schizophrenia, 45% affective psychosis and 5% substance-induced psychosis) and 158 healthy controls. Categorical principal components analysis and analysis of variance were undertaken, and individual items with the highest loading were tested using the χ2 test. Results Overall facial asymmetry, assymetry of the orbital landmarks, and frankfurt horizontal significantly differentiated patients with schizophrenia and affective psychosis from controls, as did a ‘V-shaped’ palate, reduced palatal ridges, abnormality of the left ear surface and the shape of the left and right ears. Patients with affective psychosis had significantly lowered eye fissures compared with control subjects. Conclusions MPAs are not specific to schizophrenia, suggesting a common developmental pathway for non-affective and affective psychoses. The topographical distribution of MPAs in this study is suggestive of an insult occurring during organogenesis in the first trimester of pregnancy.
Switching of membrane organelles between cytoskeletal transport systems is determined by regulation of the microtubule-based transport

Intracellular transport of membrane organelles occurs along microtubules (MTs) and actin filaments (AFs). Although transport along each type of the cytoskeletal tracks is well characterized, the switching between the two types of transport is poorly understood because it cannot be observed directly in living cells. To gain insight into the regulation of the switching of membrane organelles between the two major transport systems, we developed a novel approach that combines live cell imaging with computational modeling. Using this approach, we measured the parameters that determine how fast membrane organelles switch back and forth between MTs and AFs (the switching rate constants) and compared these parameters during different signaling states. We show that regulation involves a major change in a single parameter: the transferring rate from AFs onto MTs. This result suggests that MT transport is the defining factor whose regulation determines the choice of the cytoskeletal tracks during the transport of membrane organelles.
Image registration for image-based rendering

Image-based rendering (IBR) has received much attention in recent years for its ability to synthesize photo-realistic novel views. To support translational motion, existing IBR methods either require a large amount of reference images or assume that some geometric information is available. However, rendering with a large amount of images is very expensive in terms of image acquisition, data storage, and memory costs. As IBR accepts various kinds of geometric proxy, we may use image registration techniques, such as stereo matching and structure and motion recognition, to obtain geometric information to help reduce the number of images required. Unfortunately, existing image registration techniques only support a small search range and require closely sampled reference images. This results in a high spatial sampling rate, making IBR impractical for use in scalable walkthrough environments. Our primary objective of this project is to develop an image registration technique that would recover the geometric proxy for IBR while, at the same time, reducing the number of reference images required. In this paper, we analyze the roles and requirements of an image registration technique for reducing the spatial sampling rate. Based on these requirements, we present a novel image registration technique to automatically recover the geometric proxy from reference images. With the distinguishing feature of supporting a large search range, the new method can accurately identify correspondences even though the reference images may only be sparsely sampled. This can significantly reduce the acquisition effort, the model size, and the memory cost.
SSI Properties Revisited

The static single information (SSI) form is an extension of the static single assignment (SSA) form, a well-established compiler intermediate representation that has been successfully used for numerous compiler analysis and optimizations. Several interesting results have also been shown for SSI form concerning liveness analysis and the representation of live-ranges of variables, which could make SSI form appealing for just-in-time compilation. Unfortunately, we have uncovered several mistakes in the previous literature on SSI form, which, admittedly, is already quite sparse. This article corrects the mistakes that are most germane to SSI form. We first explain why the two definitions of SSI form proposed in past literature, first by C. S. Ananian, then by J. Singer, are not equivalent. Our main result is then to prove that basic blocks, and thus program points, can be totally ordered so that live-ranges of variables correspond to intervals on a line, a result that holds for both variants of SSI form. In other words, in SSI form, the intersection graph defined by live-ranges is an interval graph, a stronger structural property than for SSA form for which the intersection graph of live-ranges is chordal. Finally, we show how this structure of live-ranges can be used to simplify liveness analysis.
Mesothelin Expression in Human Lung Cancer

Purpose: To investigate mesothelin as a new target for immunotherapy in lung cancer. Experimental Design: Mesothelin mRNA and protein expression were assessed by reverse transcription-PCR, immunoblotting, and immunohistochemistry in human lung cancer specimens. Expression was also characterized in human lung cancer cell lines by flow cytometry and immunoblotting. The SS1P immunotoxin specific for mesothelin was assessed for its cytotoxic activity against lung cancer cells. Results: We found that mesothelin mRNA was expressed in 83% of lung adenocarcinomas (10 of 12 patients). The mesothelin precursor protein was detected in 82% of lung adenocarcinoma (9 of 11 patients), and its mature form was detected in 55% (6 of 11 patients). Immunohistochemistry showed strong and diffuse mesothelin staining in human lung adenocarcinomas and weak or modest staining in squamous cell carcinomas. We detected mesothelin mRNA in 78% of lung cancer cell lines (7 of 9) of the NCI-60 cell line panel. Mesothelin mRNA and proteins were expressed at a high level in non–small cell lung cancer lines EKVX, NCI-H460, NCI-H322M, and NCI-H522. Flow cytometric analysis showed high surface expression of mesothelin in NCI-H322M and EKVX cell lines. Immunotoxin SS1P showed high cytotoxic activity on NCI-H322M and EKVX cells with IC50 values ranging from 2 to 5 ng/mL. Conclusions: Mesothelin is expressed on the surface of most lung adenocarcinoma cells. Immunotoxin SS1P is cytotoxic against mesothelin-expressing lung cancer cell lines and merits evaluation as a new therapeutic agent in treating non–small cell lung cancer.
The Effectiveness of Receipt-Based Attacks on ThreeBallot

The ThreeBallot voting system is an end-to-end voter-verifiable voting system. Each voter fills out three ballots according to a few simple rules and takes a copy of one of them home as a receipt for verification purposes. All ballots are posted on a public bulletin board so that any voter may verify the result. In this paper, we provide the first steps toward investigating the effectiveness of attacks using the voter's receipt and the bulletin board, using a theoretical rather than simulation-based approach. Focusing on two-candidate races, we determine thresholds for when a voter's vote can be reconstructed from their receipt, and when a coercer can effectively verify if a voter followed instructions by looking for prespecified patterns on the bulletin board. Combining these two results allows us to determine safe ballot sizes that resist known attacks. We also generalize a previous observation that an individual receipt can leak information about a voter's choices.
The GSTM1 Null Genotype Increased Risk of Gastric Cancer: A Meta-Analysis Based on 46 Studies

Background Glutathione S-transferases M1 (GSTM1) is an important phase II metabolizing enzyme. The null genotype of GSTM1 causes total loss of GSTM1 enzyme activity and numerous studies have investigated the association between GSTM1 null genotype and gastric cancer risk. Methods This meta-analysis was designed to investigate the relationship between GSTM1 null genotype and susceptibility to gastric cancer and assess the influence of Helicobacter pylori infection, smoking, Lauren’s classification, and other factors. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the association strength. Results A total of 46 eligible studies were indentified and analyzed in this meta-analysis, including 8138 cases of gastric cancer and 13867 controls. Pooled results showed that the GSTM1 null genotype was associated with a significantly increased risk of gastric cancer (OR=1.217, 95% CI: 1.113-1.331, Pheterogeneity<0.001). Sub-group analysis suggested that the significant association was only observed in Asians (OR=1.273, 95%: 1.137-1.426, Pheterogeneity = 0.002), but not in Caucasians. The increased risk was found among H. pylori positive population (OR=1.928, 95% CI: 1.028-3.615, Pheterogeneity=0.065), while no association was found among H. pylori negative population (OR=0.969, 95% CI: 0.618-1.521, Pheterogeneity=0.168). For smoking status, the GSTM1 null genotype increased risk of gastric cancer in both ever-smokers and non-smokers. Source of control, sample size, location of tumor and Lauren’s classification did not modify the association. Conclusions In this meta-analysis based on 46 epidemiological studies, we show that the GSTM1 null genotype is associated with an increased risk of gastric cancer among Asians but not among Caucasians. H. pylori infection but not smoking status could modify the association.
NEW IMPLICIT PRIMITIVES USED IN RECONCUSTRUCTION BY SKELET ONS

Implicit surfaces defined by density functions allow an easy modell ing for different objects with a property of soft blending. So they can be used in reconstruction of objects which are defined by their skeletons. The discrete skeleton of an object can be break down in several primitives. In this article we present new implicit primitives which allow us to build a corresponding element for each skeleton’s type.
Effective SAR sea ice image segmentation and touch floe separation using a combined multi-stage approach

Accurate sea-ice segmentation from satellite synthetic aperture radar (SAR) images plays an important role for understanding the interactions between sea-ice, ocean and atmosphere in the Arctic. Processing sea-ice SAR images are challenging due to poor spatial resolution and severe speckle noise. In this paper, we present a multi-stage method for the sea-ice SAR image segmentation, which includes edge-preserved filtering for preprocessing, k-means clustering for segmentation and conditional morphology filtering for post-processing. As such, the effect of noise has been suppressed and the under-segmented regions are successfully corrected.
Geometric encoding: forging the high performance context sensitive points-to analysis for Java

Context sensitive points-to analysis suffers from the scalability problem. We present the geometric encoding to capture the redundancy in the points-to analysis. Compared to BDD and EPA, the state of the art, the geometric encoding is much more efficient in processing the encoded facts, especially for the high-order context sensitivity with the heap cloning. We also developed two precision preserving techniques, constraints distillation and 1-CFA SCC modeling, to further improve the efficiency, in addition to the precision performance trade-off scheme. We evaluate our points-to algorithm with two variants of the geometric encoding, Geom and HeapIns, on 15 widely cited Java benchmarks. The evaluation shows that the Geom based algorithm is 11x and 68x faster than the worklist/BDD based 1-object-sensitive analysis in Paddle, and the speedup steeply goes up to 24x and 111x, if the HeapIns algorithm is used. Meanwhile, being very efficient in time, the precision is still equal to and sometime better than the 1-object-sensitive analysis.
hsp72 Inhibits Focal Adhesion Kinase Degradation in ATP-depleted Renal Epithelial Cells*

Prior heat stress (HS) or the selective overexpression of hsp72 prevents apoptosis caused by exposure to metabolic inhibitors by protecting the mitochondrial membrane and partially reducing caspase-3 activation. Focal adhesion kinase (FAK), a tyrosine kinase, exhibits anti-apoptotic properties and is a potential target for degradation by caspase-3. This study tested the hypothesis that hsp72 interacts with FAK, preventing caspase-3-mediated degradation during ATP depletion. ATP depletion (5 mmNaCN and 5 mm 2-deoxy-d-glucose in the absence of medium glucose) caused FAK degradation within 15 min. FAK degradation was completely prevented by a caspase-3-specific inhibitor. HS induced the accumulation of hsp72, increased the interaction between hsp72 and FAK, and significantly inhibited FAK degradation during ATP depletion. Selective overexpression of wild-type hsp72 (but not hsp72ΔEEVD) reproduced the protective effects of HS on FAK cleavage. Purified hsp72 prevented the degradation of FAK by caspase-3 in vitro in a dose-dependent manner without affecting caspase-3 activity. Interaction between hsp72 and FAK is critical because both exogenous ATP and deletion of the substrate-binding site decreased protection of FAK by hsp72. These data indicate that FAK is an early target of injury in cells exposed to metabolic inhibitors and demonstrate that hsp72 reduces caspase-3-mediated proteolysis of FAK, an anti-apoptotic protein.
A small, thermostable, and monofunctional chorismate mutase from the archaeon Methanococcus jannaschii.

The gene for chorismate mutase (CM) from the archaeon Methanococcus jannaschii, an extreme thermophile, was subcloned and expressed in Escherichia coli. This gene, which belongs to the aroQ class of CMs, encodes a monofunctional enzyme (AroQf) able to complement the CM deficiency of an E. coli mutant strain. The purified protein follows Michaelis-Menten kinetics (kcat = 5.7 s-1 and Km = 41 microM at 30 degreesC) and displays pH-independent activity in the range of pH 5-9. Its activation parameters [Delta H = 16.2 kcal/mol, Delta S = -1. 7 cal/(mol.K)] are similar to those of another well characterized AroQ class CM, the mesophilic AroQp domain from E. coli. Like AroQp, the thermophilic CM is an alpha-helical dimer, but approximately 5 kcal/mol more stable than its mesophilic counterpart as judged from equilibrium denaturation studies. The possible origins of the thermostability of M. jannaschii AroQf, the smallest natural CM characterized to date, are discussed in light of available sequence and tertiary structural information.
AIDS Knowledge, Self-Esteem, Perceived AIDS Risk, and Condom Use Among Female Commercial Sex Workers1

This paper reports on research to identify previously unidentified psychosocial factors associated with condom use among female prostitutes plying their trade on the streets of a large midwestern city in the US. The report opens with a review of the literature on condom use among such a population on the risk of HIV/AIDS to heterosexual women and on psychological barriers to condom use. Next the report 1) describes the "enabling resources" model applied to the study as focusing on HIV/AIDS knowledge level of self-esteem and perception of personal risk and 2) reviews the literature on these topics. The research method is presented as involving 60-minute interviews with 141 female "streetwalkers" that gathered information on the enabling resources condom use sociodemographic factors reproductive health history history of injecting drug use and sex behavior. Statistical analysis of the data revealed that these high-risk women rarely use condoms but are more likely to use them during commercial sex than during relational sex. Individuals with more knowledge about safer sex are more likely to practice it as are those with higher self-esteem and a personal awareness of risk. These findings point to the necessity of strengthening programs that urge use of condoms during relational sex and about the importance of programs that seek to improve population-specific AIDS education as well as those that seek to improve self-esteem and coping skills.