Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased expression of mRNA for matrix metalloproteinases-1 and -3 and tissue inhibitor of metalloproteinases-1 in intestinal biopsy specimens from patients with coeliac disease

Background Extracellular matrix (ECM) degradation may play a role in villus atrophy in coeliac disease (CD). Aims To compare the cellular expression of mRNA transcripts for the two major matrix degrading proteases, matrix metalloproteinase (MMP)-1 and MMP-3, their inhibitor, tissue inhibitor of metalloproteinases (TIMP)-1, and procollagen I in the intestinal mucosa of patients with untreated and treated CD and normal controls. Patients/Methods Duodenal biopsy specimens from ten untreated CD patients, from six of these after a gluten free diet, and from ten control patients were hybridised with 35S-labelled RNA probes. The number of positive cells in the subepithelial region and lamina propria were counted microscopically. Results The numbers of cells positive for MMP-1 (p<0.005), MMP-3 (p<0.01), and TIMP-1 (p<0.05) mRNA were higher in the subepithelial region of CD mucosa than in that from controls. In the lamina propria, only cells positive for MMP-1 mRNA were increased in CD patients compared with controls (p<0.01). MMP-1 and MMP-3 mRNA expression returned to normal in CD patients after treatment with a gluten free diet (p<0.05), while TIMP-1 mRNA expression remained elevated. The number of procollagen I mRNA expressing cells did not change. Expression of MMP-1 and MMP-3 mRNA was mainly localised to subepithelial fibroblasts and macrophages. Conclusions The decreased ratio of collagen I and TIMP-1 mRNA expressing cells to MMP-1 and MMP-3 mRNA expressing cells in untreated CD suggests a shift towards ECM degradation. ECM degradation by activated subepithelial fibroblasts and macrophages may be an important mechanism driving mucosal transformation in CD.
Using G-Theory to Enhance Evidence of Reliability and Validity for Common Uses of the Paulhus Deception Scales

We applied a new approach to Generalizability theory (G-theory) involving parallel splits and repeated measures to evaluate common uses of the Paulhus Deception Scales based on polytomous and four types of dichotomous scoring. G-theory indices of reliability and validity accounting for specific-factor, transient, and random-response measurement error supported use of polytomous over dichotomous scores as contamination checks; as control, explanatory, and outcome variables; as aspects of construct validation; and as indexes of environmental effects on socially desirable responding. Polytomous scoring also provided results for flagging faking as dependable as those when using dichotomous scoring methods. These findings argue strongly against the nearly exclusive use of dichotomous scoring for the Paulhus Deception Scales in practice and underscore the value of G-theory in demonstrating this. We provide guidelines for applying our G-theory techniques to other objectively scored clinical assessments, for using G-theory to estimate how changes to a measure might improve reliability, and for obtaining software to conduct G-theory analyses free of charge.
Tomographic Left Ventricular Volumetric Emptying Analysis by Real-Time 3-Dimensional Echocardiography: Influence of Left Ventricular Dysfunction With and Without Electrical Dyssynchrony

Background—The sequence of left ventricular (LV) systolic emptying is not completely understood. Using real-time 3-dimensional echocardiography, we investigated this sequence and LV synchronicity in physiological and pathological conditions. Methods and Results—The study population consisted of 116 healthy volunteers, 20 top-level athletes, 35 patients with LV dysfunction, and 84 patients with LV dysfunction and left bundle-branch block (LBBB). We subdivided the LV into 16 volumetric segments for regional analysis and into apical, middle, and basal regions to calculate the mean of end-systolic times and the time to minimum systolic volume of each region. In healthy volunteers and in top-level athletes, the emptying systolic times increased smoothly from apex to base. These differences determined an apex-to-base time gradient in the LV emptying sequence. In patients with LV dysfunction and without LBBB, this gradient was maintained with a relatively higher LV dyssynchrony. However, in patients with LV dysfunction and LBBB, there was no clear sequence in LV emptying volumes, and this group had the highest LV dyssynchrony. Conclusions—Real-time 3-dimensional echocardiography tomographic slicing of the LV enables accurate analysis of LV emptying in physiological conditions and in conditions of LV dysfunction with and without electrical dyssynchrony. Progressive dilation of LV produces deterioration in LV synchronicity. However, it is the presence of LV dysfunction in combination with LBBB that determines the loss of the apex-to-base time gradient in LV emptying.
On the p-adic Beilinson conjecture for number fields

We formulate a conjectural p-adic analogue of Borel’s theorem relating regulators for higher K-groups of number fields to special values of the corresponding ζ-functions, using syntomic regulators and p-adic Lfunctions. We also formulate a corresponding conjecture for Artin motives, and state a conjecture about the precise relation between the p-adic and classical situations. Parts of the conjectures are proved when the number field (or Artin motive) is Abelian over the rationals, and all conjectures are verified numerically in various other cases.
Antibody to Ricin A Chain Hinders Intracellular Routing of Toxin and Protects Cells Even after Toxin Has Been Internalized

Background Mechanisms of antibody-mediated neutralization are of much interest. For plant and bacterial A-B toxins, A chain mediates toxicity and B chain binds target cells. It is generally accepted and taught that antibody (Ab) neutralizes by preventing toxin binding to cells. Yet for some toxins, ricin included, anti-A chain Abs afford greater protection than anti-B. The mechanism(s) whereby Abs to the A chain neutralize toxins are not understood. Methodology/Principal Findings We use quantitative confocal imaging, neutralization assays, and other techniques to study how anti-A chain Abs function to protect cells. Without Ab, ricin enters cells and penetrates to the endoplasmic reticulum within 15 min. Within 45–60 min, ricin entering and being expelled from cells reaches equilibrium. These results are consistent with previous observations, and support the validity of our novel methodology. The addition of neutralizing Ab causes ricin accumulation at the cell surface, delays internalization, and postpones retrograde transport of ricin. Ab binds ricin for >6hr as they traffic together through the cell. Ab protects cells even when administered hours after exposure. Conclusions/Key Findings We demonstrate the dynamic nature of the interaction between the host cell and toxin, and how Ab can alter the balance in favor of the cell. Ab blocks ricin’s entry into cells, hinders its intracellular routing, and can protect even after ricin is present in the target organelle, providing evidence that the major site of neutralization is intracellular. These data add toxins to the list of pathogenic agents that can be neutralized intracellularly and explain the in vivo efficacy of delayed administration of anti-toxin Abs. The results encourage the use of post-exposure passive Ab therapy, and show the importance of the A chain as a target of Abs.
Comments on Two-Loop Four-Particle Amplitude in Superstring Theory

It is shown that the four-particle amplitude of superstring theory at two loops obtained in [1, 2] is equivalent to the previously obtained results in [3, 4, 5]. Here the Z2 symmetry in hyperelliptic Riemann surface plays an important role in the proof. In some previous papers [1, 2, 6] we have computed explicitly the two loop n-particle amplitude in superstring theory for all n ≤ 4 by using the newly obtained measure of D’Hoker and Phong [7, 8, 9, 10] (for a recent review see [11, 12]). The new measure of D’Hoker and Phong is unambiguous and slice-independent. For all n ≤ 3 we proved that the n-particle amplitudes are identically zero. A simple expression was also obtained for the 4-particle amplitude which is independent of the insertion points of the supermoduli. ∗Supported in part by fund from the National Natural Science Foundation of China with grant Number 90103004.
Prediction of Monomer Isomery in Florine: A Workflow Dedicated to Nonribosomal Peptide Discovery

Nonribosomal peptides represent a large variety of natural active compounds produced by microorganisms. Due to their specific biosynthesis pathway through large assembly lines called NonRibosomal Peptide Synthetases (NRPSs), they often display complex structures with cycles and branches. Moreover they often contain non proteogenic or modified monomers, such as the D-monomers produced by epimerization. We investigate here some sequence specificities of the condensation (C) and epimerization (E) domains of NRPS that can be used to predict the possible isomeric state (D or L) of each monomer in a putative peptide. We show that C- and E- domains can be divided into 2 sub-regions called Up-Seq and Down-Seq. The Up-Seq region corresponds to an InterPro domain (IPR001242) and is shared by C- and E-domains. The Down-Seq region is specific to the enzymatic activity of the domain. Amino-acid signatures (represented as sequence logos) previously described for complete C-and E-domains have been restricted to the Down-Seq region and amplified thanks to additional sequences. Moreover a new Down-Seq signature has been found for Ct-domains found in fungi and responsible for terminal cyclization of the peptides. The identification of these signatures has been included in a workflow named Florine, aimed to predict nonribosomal peptides from NRPS sequence analyses. In some cases, the prediction of isomery is guided by genus-specific rules. Florine was used on a Pseudomonas genome to allow the determination of the type of pyoverdin produced, the update of syringafactin structure and the identification of novel putative products.
Invasive Pneumococcal Disease in HIV-Infected Adults: Clinical Changes After the Introduction of the Pneumococcal Conjugate Vaccine in Children

BackgroundFew data exist on the implications of widespread use of 7-valent pneumococcal conjugate vaccine in children in the invasive pneumococcal disease (IPD) in HIV-infected adults. We conducted a multicenter study to analyze differences in clinical presentation of IPD between HIV-infected and non–HIV-infected adults in the prevaccine and postvaccine era. MethodsStudy of all cases of IPD in HIV-infected adults diagnosed since 1996 to 2010. Episodes were classified into prevaccine (1996–2001), early postvaccine (2002–2004), and late postvaccine period (2005–2010). For each case, we identified an HIV-negative control patient with IPD matched by hospital, age, and vaccine period. ResultsTwo hundred twenty-one episodes of IPD in HIV-infected patients were diagnosed. The incidence of IPD decreased from 7.81 to 3.69 episodes per 1000 patient-years (−53%; 95% confidence interval: −65% to −36%, P < 0.001) between prevaccine and late postvaccine period. There was an 81% (95% confidence interval: −88% to −69%, P < 0.001) decrease of IPD caused by vaccine serotypes. In late postvaccine period IPD in HIV-infected patients was associated to higher rates of respiratory failure (28.4% vs. 48.4%, P = 0.011), greater intensive care unit admission (8.2% vs. 21.7%, P = 0.02) and a higher need for mechanical ventilation (5.9% vs. 16.3%, P = 0.033). In the prevaccine period, non–HIV-infected patients had a more severe illness than in those with HIV infection; however, these differences disappeared in the late postvaccine period. ConclusionsIn the late postvaccine era, the incidence of IPD in HIV-infected patients has decreased, however, clinical presentation seems to have changed to a more severe illness. The widespread use of highly active antiretroviral therapy, polyssacharide vaccine, and 7-valent pneumococcal conjugate vaccine has contributed to these changes.
Teratogenic Effects of Long Term Consumption of Potassium Benzoate on Eye Development in Balb/c Fetal Mice

Objective(s): Potassium benzoate (PB) is used as a substitute preservative for sodium benzoate primarily in dietetic foods where the sodium content is minimized. There are few reports about the teratogenic effects of PB. The purpose of this study is to investigate the teratogenic effects of PB on eye development in balb/c mice fetuses. Materials and Methods: Thirty female mice were divided to two experimental and one control groups (N=10/grp). Experimental groups I and II received daily intraperitoneal (IP) injections of 280 and 560 mg/kg of PB, respectively; while the control group received normal saline. Injections were done for 10 days before mating and from gestation days (GD) 6 through 15. Dams were Caesarean sectioned on GD 18. Eye development was externally examined. After measuring weight and crown-rump length of the fetuses, the tissue sections of the eyes were prepared and stained with hematoxylin-eosin. Histopathologic and morphologic changes were recorded. The data was analyzed by ANOVA and Mann Whitney statistical tests using SPSS (version 15). Results: Fetuses with eye malformations observed in both experimental groups of I and II. The incidence of these malformations was significantly increased in fetuses of experimental group II as compared with the control group (P<0.05). Histopathological evaluations of the malformed eyes showed deformed lens, retinal folds with undeveloped layers associated with hemorrhage. Conclusion: Our results suggest that PB can induce teratogenic effects on the eye development of mice fetuses. Therefore, more concise studies are needed regarding its specific and general effects conducted.
Object recognition in wikimage data based on local invariant image features

Object recognition is an essential task in content-based image retrieval and classification. This paper deals with object recognition in WIKImage data, a collection of publicly available annotated Wikipedia images. WIKImage comprises a set of 14 binary classification problems with significant class imbalance. Our approach is based on using the local invariant image features and we have compared 3 standard and widely used feature types: SIFT, SURF and ORB. We have examined how the choice of representation affects the k-nearest neighbor data topology and have shown that some feature types might be more appropriate than others for this particular problem. In order to assess the difficulty of the data, we have evaluated 7 different k-nearest neighbor classification methods and shown that the recently proposed hubness-aware classifiers might be used to either increase the accuracy of prediction, or the macro-averaged F-score. However, our results indicate that further improvements are possible and that including the textual feature information might prove beneficial for system performance.
High SUVmax on FDG-PET Indicates Pleomorphic Subtype in Epithelioid Malignant Pleural Mesothelioma: Supportive Evidence to Reclassify Pleomorphic as Nonepithelioid Histology

Background: We have recently proposed to reclassify the pleomorphic subtype of epithelioid malignant pleural mesothelioma (MPM) as nonepithelioid (biphasic/sarcomatoid) histology because of its similarly poor prognosis. We sought to investigate whether preoperative maximum standardized uptake value (SUVmax) on 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET) correlates with histologic subtype in MPM. Methods: Clinical data were collected for 78 patients with MPM who underwent preoperative FDG-PET. We retrospectively classified the epithelioid tumors into five subtypes: trabecular, tubulopapillary, micropapillary, solid, and pleomorphic. Tumors were categorized by SUVmax into two groups: low (<10.0) and high (≥10.0). Results: The median overall survival of epithelioid tumors with high SUVmax (n = 12) was significantly shorter (7.1 months) than that of epithelioid tumors with low SUVmax (n = 54, 18.9 months, p < 0.001) and comparable to nonepithelioid tumors (n = 12, 7.2 months). Epithelioid tumors with pleomorphic subtype (n = 9) had marginally higher SUVmax (mean ± SD: 10.6 ± 5.9) than epithelioid nonpleomorphic subtype (n = 57, 6.5 ± 3.2, p = 0.050), and were comparable to that of nonepithelioid tumors (n = 12, 9.1 ± 4.8). Among the epithelioid tumors with high SUVmax (n = 12), 50% (n = 6) showed pleomorphic subtype. In contrast, among epithelioid tumors with low SUVmax (n = 54), 6% (n = 3) showed epithelioid pleomorphic subtypes (p = 0.001). A positive correlation between mitotic count and SUVmax was observed (r = 0.30, p = 0.010). Conclusions: Pleomorphic subtype of epithelioid MPM showed higher SUVmax than the epithelioid nonpleomorphic subtype and was similar to nonepithelioid histology. Preoperative SUVmax on FDG-PET in epithelioid MPM can indicate patients with pleomorphic subtype with poor prognosis, supporting their reclassification as nonepithelioid.
Orographically Anchored El Niño Effect on Summer Rainfall in Central China

AbstractYear-to-year variations in summer precipitation have great socioeconomic impacts on China. Historical rainfall variability over China is investigated using a newly released high-resolution dataset. The results reveal summer-mean rainfall anomalies associated with ENSO that are anchored by mountains in central China east of the Tibetan Plateau. These orographically anchored hot spots of ENSO influence are poorly represented in coarse-resolution datasets so far in use. In post–El Nino summers, an anomalous anticyclone forms over the tropical northwest Pacific, and the anomalous southwesterlies on the northwest flank cause rainfall to increase in mountainous central China through orographic lift. At upper levels, the winds induce additional adiabatic updraft by increasing the eastward advection of warm air from Tibet. In post–El Nino summers, large-scale moisture convergence induces rainfall anomalies elsewhere over flat eastern China, which move northward from June to August and amount to little in .
A Neural Basis for the Acquired Capability for Suicide

The high rate of fatal suicidal behavior (SB) in men is an urgent issue as highlighted in the public eye via news sources and media outlets. In this study, we have attempted to address this issue and understand the neural substrates underlying the gender differences in the rate of fatal SB. The Interpersonal–Psychological Theory of Suicide has proposed an explanation for the seemingly paradoxical relationship between gender and SB, i.e., greater non-fatal suicide attempts by women but higher number of deaths by suicide in men. This theory states that possessing suicidal desire (due to conditions such as depression) alone is not sufficient for a lethal suicide attempt. It is imperative for an individual to have the acquired capability for suicide (ACS) along with suicidal desire in order to die by suicide. Therefore, higher levels of ACS in men may explain why men are more likely to die by suicide than women, despite being less likely to experience suicidal ideation or depression. In this study, we used activation likelihood estimation meta-analysis to investigate a potential ACS network that involves neural substrates underlying emotional stoicism, sensation-seeking, pain tolerance, and fearlessness of death, along with a potential depression network that involves neural substrates that underlie clinical depression. Brain regions commonly found in ACS and depression networks for males and females were further used as seeds to obtain regions functionally and structurally connected to them. We found that the male-specific networks were more widespread and diverse than the female-specific ones. Also, while the former involved motor regions, such as the premotor cortex and cerebellum, the latter was dominated by limbic regions. This may support the fact that suicidal desire generally leads to fatal/decisive action in males, while, in females, it manifests as depression, ideation, and generally non-fatal actions. The proposed model is a first attempt to characterize the neural networks underlying gender differences in SB. Future studies should examine the proposed network to better characterize and refine this network using tasks specifically targeted toward constructs underlying ACS.
Controlling air and burned gas masses of turbocharged VVT SI engines

In this paper, we propose a strategy to control the in-cylinder air and burned gas masses inside the combustion chambers of turbocharged VVT SI engines. We coordinate existing low-level controllers acting separately on the throttle, the waste gate and on the VVT actuators. Coordination is obtained by updating the set points based on real-time measurements. The objective is to improve transients response. The effect of the implicit feedback loop is analyzed by the small-gain theorem.
A possible interrelation between the estimated luminosity distances and internal extinctions of type Ia supernovae

We studied the statistical properties of the luminosity distance and internal extinction data of type Ia supernovae in the lists published by Tonry et al. (2003) and Barris et al. (2004). After selecting the luminosity distance in an empty Universe as a reference level we divided the sample into low z < 0.25 and high z ≥ 0.25 parts. We further divided these subsamples by the median of the internal extinction. Performing sign tests using the standardized residuals between the estimated logarithmic luminosity distances and those of an empty universe, on the four subsamples separately, we recognized that the residuals were distributed symmetrically in the low redshift region, independently from the internal extinction. On the contrary, the low extinction part of the data of z ≥ 0.25 clearly showed an excess of the points with respect to an empty Universe which was not the case in the high extinction region. This diversity pointed to an interrelation between the estimated luminosity distance and internal extinction. To characterize quantitatively this interrelation we introduced a hidden variable making use of the technics of factor analysis. After subtracting that part of the residual which was explained by the hidden variable we obtained luminosity distances which were already free from interrelation with internal extinction. Fitting the corrected luminosity distances with cosmological models we concluded that the SN Ia data alone did not exclude the possibility of the Λ = 0 solution. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Lidocaine elimination and monoethylglycinexylidide formation in patients with chronic hepatitis or cirrhosis.

BACKGROUND/AIMS The aim of this study was to evaluate the relationship between plasma elimination of lidocaine and monoethylglycinexylidide (MEGX) formation, which is considered to be a quantitative liver function test. METHODOLOGY The study included ten healthy subjects and 54 patients: 27 with chronic hepatitis and 27 with cirrhosis. Lidocaine and MEGX were measured at 0, 2, 5, 10, 15, 30 min and then every 30 min for 180 min using the TDX system. RESULTS In cirrhotic patients, the lidocaine half-life of the slow decline phase of the plasma disappearance curve (beta-HL) and the lidocaine half-life of hepatic elimination from the second compartment (K20-HL) proved to be significantly abnormal, as did all parameters of MEGX formation. In chronic hepatitis, both the lidocaine kinetics and the MEGX formation parameters were within the normal range. In chronic hepatitis patients, MEGX formation (AUC 0-180) was significantly correlated to K20-HL (rs = -0.633, p < 0.001) and to the rapid decline phase of the plasma disappearance curve (alpha-HL, rs = -0.483, p < 0.05). In cirrhotic patients, MEGX was significantly correlated to K20-HL (rs = -0.423, p < 0.05) and to beta-HL (rs = -0.500, p < 0.01). CONCLUSIONS These results show that in chronic active hepatitis, MEGX formation from lidocaine is maintained as a metabolic process, whereas it is altered in cirrhotic patients. The interrelationship between lidocaine elimination and MEGX formation were somewhat different in the two liver diseases.