Miracle-dz/UniFAR-FTUs huggingface dataset:
Label‐Free Quantitative Proteomic Analysis of Differentially Expressed Membrane Proteins of Pulmonary Alveolar Macrophages Infected with Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus and Its Attenuated Strain

Significant differences exist between the highly pathogenic (HP) porcine reproductive and respiratory syndrome virus (PRRSV) and its attenuated pathogenic (AP) strain in the ability to infect host cells. The mechanisms by which different virulent strains invade host cells remain relatively unknown. In this study, pulmonary alveolar macrophages (PAMs) are infected with HP‐PRRSV (HuN4) and AP‐PRRSV (HuN4‐F112) for 24 h, then harvested and subjected to label‐free quantitative MS. A total of 2849 proteins are identified, including 95 that are differentially expressed. Among them, 26 proteins are located on the membrane. The most differentially expressed proteins are involved in response to stimulus, metabolic process, and immune system process, which mainly have the function of binding and catalytic activity. Cluster of differentiation CD163, vimentin (VIM), and nmII as well as detected proteins are assessed together by string analysis, which elucidated a potentially different infection mechanism. According to the function annotations, PRRSV with different virulence may mainly differ in immunology, inflammation, immune evasion as well as cell apoptosis. This is the first attempt to explore the differential characteristics between HP‐PRRSV and its attenuated PRRSV infected PAMs focusing on membrane proteins which will be of great help to further understand the different infective mechanisms of HP‐PRRSV and AP‐PRRSV.
Frontoparietal cortical activity of methamphetamine‐dependent and comparison subjects performing a delay discounting task

Relative to individuals who do not have addictive disorders, drug abusers exhibit greater devaluation of rewards as a function of their delay (“delay discounting”). The present study sought to extend this finding to methamphetamine (MA) abusers and to help understand its neural basis. MA abusers (n = 12) and control subjects who did not use illicit drugs (n = 17) participated in tests of delay discounting with hypothetical money rewards. We then used a derived estimate of each individual's delay discounting to generate a functional magnetic resonance imaging probe task consisting of three conditions: “hard choices,” requiring selections between “smaller, sooner” and “larger, later” alternatives that were similarly valued given the individual's delay discounting; “easy choices,” in which alternatives differed dramatically in value; and a “no choice” control condition. MA abusers exhibited more delay discounting than control subjects (P < 0.05). Across groups, the “hard choice > no choice” contrast revealed significant effects in the ventrolateral prefrontal cortex, dorsolateral prefrontal cortex (DLPFC), dorsal anterior cingulate cortex, and areas surrounding the intraparietal sulcus (IPS). With group comparisons limited to these clusters, the “hard choice > easy choice” contrast indicated significant group differences in task‐related activity within the left DLPFC and right IPS; qualitatively similar nonsignificant effects were present in the other clusters tested. Whereas control subjects showed less recruitment associated with easy than with hard choices, MA abusers generally did not. Correlational analysis did not indicate a relationship between this anomaly in frontoparietal recruitment and greater degree of delay discounting exhibited by MA abusers. Therefore, while apparent inefficiency of cortical processing related to decision‐making in MA abusers may contribute to the neural basis of enhanced delay discounting by this population, other factors remain to be identified. Hum. Brain Mapp, 2007. © 2006 Wiley‐Liss, Inc.
The relevance of HPA‐15 antigen expression for anti‐HPA‐15 antibody detection

Introduction: The HPA‐15 antigen system is characterized by a low antigen expression on platelets. The antibodies against this antigen are implied in fetal/neonatal alloimmune thrombocytopenia (F/NAIT), post‐transfusion purpura, and refractoriness to platelet transfusions. Detection of these antibodies appears to be related to the level of HPA‐15 expression on the platelets used in the monoclonal antibody–specific immobilization of platelet antigen (MAIPA) assay.
Aquaporins of the PIP2 Class Are Required for Efficient Anther Dehiscence in Tobacco

Several processes during sexual reproduction in higher plants involve the movement of water between cells or tissues. Before flower anthesis, anther and pollen dehydration takes place before the release of mature pollen at dehiscence. Aquaporins represent a class of proteins that mediates the movement of water over cellular membranes. Aquaporins of the plasmamembrane PIP2 family are expressed in tobacco (Nicotiana tabacum) anthers and may therefore be involved in the movement of water in this organ. To gain more insight into the role these proteins may play in this process, we have analyzed their localization using immunolocalizations and generated plants displaying RNA interference of PIP2 aquaporins. Our results indicate that PIP2 protein expression is modulated during anther development. Furthermore, in tobacco PIP2 RNA interference plants, anther dehydration was slower, and dehiscence occurred later when compared with control plants. Together, our results suggest that aquaporins of the PIP2 class are required for efficient anther dehydration prior to dehiscence.
Measurement of tumor volumes improves RECIST-based response assessments in advanced lung cancer.

OBJECTIVE This study was designed to characterize the reproducibility of measurement for tumor volumes and their longest tumor diameters (LDs) and estimate the potential impact of using changes in tumor volumes instead of LDs as the basis for response assessments. METHODS We studied patients with advanced lung cancer who have been observed longitudinally with x-ray computed tomography in a multinational trial. A total of 71 time points from 10 patients with 13 morphologically complex target lesions were analyzed. A total of 6461 volume measurements and their corresponding LDs were made by seven independent teams using their own work flows and image analysis tools. Interteam agreement and overall interrater concurrence were characterized. RESULTS Interteam agreement between volume measurements was better than between LD measurements (ı = 0.945 vs 0.734, P = .005). The variability in determining the nadir was lower for volumes than for LDs (P = .005). Use of standard thresholds for the RECIST-based method and use of experimentally determined cutoffs for categorizing responses showed that volume measurements had a significantly greater sensitivity for detecting partial responses and disease progression. Earlier detection of progression would have led to earlier changes in patient management in most cases. CONCLUSIONS Our findings indicate that measurement of changes in tumor volumes is adequately reproducible. Using tumor volumes as the basis for response assessments could have a positive impact on both patient management and clinical trials. More authoritative work to qualify or discard changes in volume as the basis for response assessments should proceed.
On Partial Regularity for the 3D Nonstationary Hall Magnetohydrodynamics Equations on the Plane

We study partial regularity of weak solutions of the three-dimensional (3D) valued nonstationary Hall magnetohydrodynamics equations on $\mathbb{R}^2$. In particular, we prove the existence of a weak solution whose set of possible singularities has the space-time Hausdorff dimension at most two.
Coveringcerts: Combinatorial Methods for X.509 Certificate Testing

Correct behaviour of X.509 certificate validation code in SSL/TLS implementations is crucial to ensure secure communication channels. Recently, there have been major efforts in testing these implementations, namely frankencerts and mucerts, which provide new ways to generate test certificates which are likely to reveal errors in the implementations of X.509 validation logic. However, it remains a significant challenge to generate effective test certificates. In this paper, we explore the applicability of a prominent combinatorial method, namely combinatorial testing, for testing of X.509 certificates. We demonstrate that combinatorial testing provides the theoretical guarantees for revealing errors in the certificate validation logic of SSL/TLS implementations. Our findings indicate that the introduced combinatorial testing constructs, coveringcerts, compare favorably to existing testing methods by encapsulating the semantics of the validation logic in the input model and employing combinatorial strategies that significantly reduce the number of tests needed. Besides the foundations of our approach, we also report on experiments that indicate its practical use.
Measurement of the gadopentetate dimeglumine partition coefficient in human myocardium in vivo: normal distribution and elevation in acute and chronic infarction.

PURPOSE To establish a method for measuring the partition coefficient (lambda) of gadopentetate dimeglumine in humans in vivo, evaluate the spatial and intersubject variation in the lambda of normal myocardium, and compare these values on a regional basis with lambda values of acute and chronic infarcted myocardium. MATERIALS AND METHODS Twelve healthy subjects and patients with acute (n = 5) or chronic (n = 5) myocardial infarction underwent magnetic resonance imaging at 1.5 T. Look-Locker images were acquired at four short-axis levels to measure myocardial and blood longitudinal relaxation time at baseline and after a 30-40-minute infusion of gadopentetate dimeglumine. lambda was calculated as DeltaR1(M)/DeltaR1(B, )where M = myocardium, and B = blood. RESULTS The magnitude of the estimated lambda in normal myocardium was uniform over the entire myocardium at 0.56 mL/g +/- 0.10 (SD). The lambda values in patients with acute (0.91 mL/g +/- 0.11, P <.001) or chronic (lambda = 0.78 mL/g +/- 0.09, P <.001) infarction were significantly elevated, as compared with those in healthy subjects. A 20% elevation in lambda, as compared with the mean value of a corresponding normal circumferential segment, allowed identification of chronically (sensitivity, 88%; specificity, 96%) or acutely (sensitivity, 100%; specificity, 98%) infarcted segments. CONCLUSION Quantification of the lambda in vivo allows differentiation between normal and acutely or chronically infarcted myocardium, with high sensitivity and specificity.
Pulmonary emphysema: subjective visual grading versus objective quantification with macroscopic morphometry and thin-section CT densitometry.

PURPOSE To compare subjective visual grading of pulmonary emphysema with macroscopic morphometry and computed tomographic (CT) densitometry. MATERIALS AND METHODS In 62 consecutive patients who underwent thinsection CT before surgical lung resection, emphysema was objectively quantified with computer-assisted macroscopic morphometry and CT densitometry. The percentage of lung macroscopically occupied by emphysema was compared with the percentage occupied on CT scans by pixels with attenuation values lower than a predefined threshold (CT densitometry). Three readers with varying degrees of expertise subjectively graded emphysema with visual assessment at two reading sessions. Data from objective quantification and subjective grading were analyzed with correlation coefficients, and interobserver and intraobserver agreement were calculated. RESULTS Subjective grading of emphysema showed less agreement with the macroscopic reference standard results (r = 0.439-0.505; P < .05) than with objective CT densitometric results (r = 0.555-0.623; P < .001). The 95% CIs for the intercepts of the linear regression lines were suggestive of systematic subjective overestimation of emphysema by all three readers. Interobserver agreement was moderate (kappa = 0.431-0.589). Intraobserver agreement was good to excellent (kappa = 0.738-0.936). The expertise of individual readers did not substantially influence results. CONCLUSION Systematic overestimation and moderate interobserver agreement may compromise subjective visual grading of emphysema, which suggests that subjective visual grading should be supplemented with objective methods to achieve precise, reader-independent quantification of emphysema.
Covarying alterations in Aβ deposition, glucose metabolism, and gray matter volume in cognitively normal elderly

β‐Amyloid (Aβ), a feature of Alzheimer's disease (AD) pathology, may precede reduced glucose metabolism and gray matter (GM) volume and cognitive decline in patients with AD. Accumulation of Aβ, however, has been also reported in cognitively intact older people, although it remains unresolved whether and how Aβ deposition, glucose metabolism, and GM volume relate to one another in cognitively normal elderly. Fifty‐two cognitively normal older adults underwent Pittsburgh Compound B–positron emission tomography (PIB‐PET), [18F]fluorodeoxyglucose‐PET, and structural magnetic resonance imaging to measure whole‐brain amyloid deposition, glucose metabolism, and GM volume, respectively. Covariance patterns of these measures in association with global amyloid burden measured by PIB index were extracted using principal component analysis–based multivariate methods. Higher global amyloid burden was associated with relative increases of amyloid deposition and glucose metabolism and relative decreases of GM volume in brain regions collectively known as the default mode network including the posterior cingulate/precuneus, lateral parietal cortices, and medial frontal cortex. Relative increases of amyloid deposition and glucose metabolism were also noted in the lateral prefrontal cortices, and relative decreases of GM volume were pronounced in hippocampus. The degree of expression of the topographical patterns of the PIB data was further associated with visual memory performance when controlling for age, sex, and education. The present findings suggest that cognitively normal older adults with greater amyloid deposition are relatively hypermetabolic in frontal and parietal brain regions while undergoing GM volume loss in overlapping brain regions. Hum Brain Mapp 35:297–308, 2014. © 2012 Wiley Periodicals, Inc.
Acute rheumatic fever

Acute rheumatic fever is an immunologically mediated multisystem disease induced by recent infection with group A streptococcus. About 5% of people have the potential to develop acute rheumatic fever after infection by a strain of streptococcus with propensity to cause the condition. Most cases (97%) occur in low-income and some middle-income countries, with indigenous populations in some affluent countries also affected. Children aged 5–15 years are most commonly affected, and rheumatic heart disease remains the most common acquired heart disease of childhood in the world. Most medical practitioners in industrialized countries will rarely, if ever, see a case. However, the dramatic decline in incidence of acute rheumatic fever in industrialized countries during the second half of the 20th century was not replicated in many developing countries, or among some indigenous and other populations living in poverty in industrialized countries.
Comparison of plasma and interstitial fluid concentrations of doxycycline and meropenem following constant rate intravenous infusion in dogs.

OBJECTIVE To compare plasma (total and unbound) and interstitial fluid (ISF) concentrations of doxycycline and meropenem in dogs following constant rate IV infusion of each drug. ANIMAL 6 adult Beagles. PROCEDURE Dogs were given a loading dose of doxycycline and meropenem followed by a constant rate IV infusion of each drug to maintain an 8-hour steady state concentration. Interstitial fluid was collected with an ultrafiltration device. Plasma and ISF were analyzed by high performance liquid chromatography. Protein binding and lipophilicity were determined. Plasma data were analyzed by use of compartmental methods. RESULTS Compared with meropenem, doxycycline had higher protein binding (11.87% [previously published value] vs 91.75 +/- 0.63%) and lipophilicity (partition coefficients, 0.02 +/- 0.01 vs 0.68 +/- 0.05). A significant difference was found between ISF and plasma total doxycycline concentrations. No significant difference was found between ISF and plasma unbound doxycycline concentrations. Concentrations of meropenem in ISF and plasma (total and unbound) were similar. Plasma half-life, volume of distribution, and clearance were 4.56 +/- 0.57 hours, 0.65 +/- 0.82 L/kg, and 1.66 +/- 2.21 mL/min/kg, respectively, for doxycycline and 0.73 +/- 0.07 hours, 0.34 +/- 0.06 L/kg, and 5.65 +/- 2.76 mL/min/kg, respectively, for meropenem. The ISF half-life of doxycycline and meropenem was 4.94 +/- 0.67 and 2.31 +/- 0.36 hours, respectively. CONCLUSIONS AND CLINICAL RELEVANCE The extent of protein binding determines distribution of doxycycline and meropenem into ISF. As a result of high protein binding, ISF doxycycline concentrations are lower than plasma total doxycycline concentrations. Concentrations of meropenem in ISF can be predicted from plasma total meropenem concentrations.
Analysis of protein profiling studies of β‐thalassemia/Hb E disease

A number of studies have used global protein profiling technologies on a range of patient samples to detect proteins that are differentially expressed in β‐thalassemia/Hb E as an aid for understanding the physiopathology of this disease. Seven studies have identified a total of 111 unique, differentially expressed proteins. Seven proteins (prothrombin, alpha‐1‐antichymotrypsin, fibrinogen beta chain, hemoglobin beta, selenium‐binding protein, microtubule‐actin cross‐linking factor and adenomatous polyposis coli protein 2) have been identified in two independent studies, whereas two proteins (carbonic anhydrase 1 and peroxiredoxin‐2) have been identified in three independent studies. Both of these latter two proteins were consistently upregulated in the studies that identified them. Ontological analysis of all differentially regulated proteins identified “response to inorganic substances” as the most significant functional annotation cluster, which is consistent with iron overload being a major pathological consequence of this disease. Despite the range of samples investigated and the relatively small number of studies undertaken, a coherent picture of the mediators of the pathological consequences of β‐thalassemia/Hb E disease is starting to emerge.
Treatment of Ammonia by Catalytic Wet Oxidation Process Over Platinum‐Rhodium Bimetallic Catalyst in a Trickle‐Bed Reactor: Effect of pH

This work adopted aqueous solutions of ammonia for use in catalytic liquid‐phase reduction in a trickle‐bed reactor with a platinum‐rhodium bimetallic catalyst, prepared by the co‐precipitation of chloroplatinic acid (H2PtCl6) and rhodium nitrate [Rh(NO3)3]. The experimental results demonstrated that a minimal amount of ammonia was removed from the solution by wet oxidation in the absence of any catalyst, while approximately 97.0% of the ammonia was removed by wet oxidation over the platinum‐rhodium bimetallic catalyst at 230°C with an oxygen partial pressure of 2.0 MPa. The oxidation of ammonia has been studied as a function of pH, and the main reaction products were determined. A synergistic effect is manifest in the platinum‐rhodium bimetallic structure, in which the material has the greatest capacity to reduce ammonia. The reaction pathway linked the oxidizing ammonia to nitric oxide, nitrogen, and water.
Substitution of two histidine residues in YadA protein of Yersinia enterocolitica abrogates collagen binding, cell adherence and mouse virulence

The plasmid‐encoded surface protein YadA of Yersinia enterocolitica mediates binding to diverse extracellular matrix (ECM) proteins, adherence to epithelial cell lines, resistance to complement lysis, autoagglutination, and is required for mouse virulence. Using site‐directed mutagenesis we attempted to analyse the relationship between structural domains and functions of YadA. In a first approach we could abrogate collagen binding by chemical modification of histidyl residues of YadA protein. This result prompted us to substitute histidyl residues (His) of conserved regions of YadA protein of Y. enterocolitica 08 by tyrosine residues using site‐directed mutagenesis. Substitution of His‐156 and His‐159 (YadA‐2 mutant) resulted in abrogation of binding to ECM proteins, of cell adherence, and in reduction of mouse virulence, whereas autoagglutination, serum complement resistance and oligomer formation remained unaffected. A striking result was obtained from the orogastric mouse‐infection model: the YadA‐2 mutant retained the ability to colonize the small intestine and to invade and multiply within the Peyer's patches but was impaired in colonizing mesenteric lymph nodes and spleen in comparison to the wild‐type strain.
HL‐A Antigens in Haematological Malignant Diseases *

Abstract. The frequency of twenty‐two HL‐A antigens has been determined in a series of one hundred and seventy patients with haematological malignant diseases. One HL‐A specificity, HL‐A 11, was found to be less frequent among the patients with haematological malignant diseases than among control subjects, Other HL‐A specificities were found to be more frequent in patients with certain diseases, as HL‐A 1 in chronic myelocytic leukaemia, HL‐A 2 in acute myeloblasts leukaemia, W 28 in lymphomas, and W 15 in Hodgkin's disease. Although the statistical significance of these variations remains doubtful, because of the relatively small number of patients tested, the findings suggest there may be a correlation between HL‐A antigens and susceptibility to haematological malignant diseases.
Golgi enlargement in Arf-depleted yeast cells is due to altered dynamics of cisternal maturation

ABSTRACT Regulation of the size and abundance of membrane compartments is a fundamental cellular activity. In Saccharomyces cerevisiae, disruption of the ADP-ribosylation factor 1 (ARF1) gene yields larger and fewer Golgi cisternae by partially depleting the Arf GTPase. We observed a similar phenotype with a thermosensitive mutation in Nmt1, which myristoylates and activates Arf. Therefore, partial depletion of Arf is a convenient tool for dissecting mechanisms that regulate Golgi structure. We found that in arf1&Dgr; cells, late Golgi structure is particularly abnormal, with the number of late Golgi cisternae being severely reduced. This effect can be explained by selective changes in cisternal maturation kinetics. The arf1&Dgr; mutation causes early Golgi cisternae to mature more slowly and less frequently, but does not alter the maturation of late Golgi cisternae. These changes quantitatively explain why late Golgi cisternae are fewer in number and correspondingly larger. With a stacked Golgi, similar changes in maturation kinetics could be used by the cell to modulate the number of cisternae per stack. Thus, the rates of processes that transform a maturing compartment can determine compartmental size and copy number.
The importance of primary gastric cancer location in 5-year survival rate

especially in developed countries (1,2,5). In spite of evidence improvement in gastric cancer diagnosis and treatment controversies exist with regard to the extent of gastric resection and the role of extended lymph node dissections. Effective postoperative adjuvant therapies remain to be defined, and novel neoadjuvant approaches are currently considered investigational. Even after potentially curative gastric resections, disease recurrence develops in at least 80% of patients (6). The aim of this study was to review our experience in 5-year survival rate with potentially curative gastric resections, connected to primary gastric cancer location.