Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal Structure of Crataeva tapia Bark Protein (CrataBL) and Its Effect in Human Prostate Cancer Cell Lines

A protein isolated from the bark of Crataeva tapia (CrataBL) is both a Kunitz-type plant protease inhibitor and a lectin. We have determined the amino acid sequence and three-dimensional structure of CrataBL, as well as characterized its selected biochemical and biological properties. We found two different isoforms of CrataBL isolated from the original source, differing in positions 31 (Pro/Leu); 92 (Ser/Leu); 93 (Ile/Thr); 95 (Arg/Gly) and 97 (Leu/Ser). CrataBL showed relatively weak inhibitory activity against trypsin (Kiapp = 43 µM) and was more potent against Factor Xa (Kiapp = 8.6 µM), but was not active against a number of other proteases. We have confirmed that CrataBL contains two glycosylation sites and forms a dimer at high concentration. The high-resolution crystal structures of two different crystal forms of isoform II verified the β-trefoil fold of CrataBL and have shown the presence of dimers consisting of two almost identical molecules making extensive contacts (∼645 Å2). The structure differs from those of the most closely related proteins by the lack of the N-terminal β-hairpin. In experiments aimed at investigating the biological properties of CrataBL, we have shown that addition of 40 µM of the protein for 48 h caused maximum growth inhibition in MTT assay (47% of DU145 cells and 43% of PC3 cells). The apoptosis of DU145 and PC3 cell lines was confirmed by flow cytometry using Annexin V/FITC and propidium iodide staining. Treatment with CrataBL resulted in the release of mitochondrial cytochrome c and in the activation of caspase-3 in DU145 and PC3 cells.
Exploring commonalities across participants in the neural representation of objects

The question of whether the neural encodings of objects are similar across different people is one of the key questions in cognitive neuroscience. This article examines the commonalities in the internal representation of objects, as measured with fMRI, across individuals in two complementary ways. First, we examine the commonalities in the internal representation of objects across people at the level of interobject distances, derived from whole brain fMRI data, and second, at the level of spatially localized anatomical brain regions that contain sufficient information for identification of object categories, without making the assumption that their voxel patterns are spatially matched in a common space. We examine the commonalities in internal representation of objects on 3T fMRI data collected while participants viewed line drawings depicting various tools and dwellings. This exploratory study revealed the extent to which the representation of individual concepts, and their mutual similarity, is shared across participants. Hum Brain Mapp, 2011. © 2011 Wiley‐Liss, Inc.
A clinicopathologic study of 92 cases of granulosa cell tumor of the ovary with special reference to the factors influencing prognosis

Ninety‐two cases of granulosa cell tumor of the ovary have been studied. The clinical and pathologic data from this group were similar to that obtained in previous series. Because of the long natural history of many granulosa cell tumors, crude death rates over a relatively short period give little indication of the true malignant potential of these neoplasms and hence corrected survival rates were calculated; these show that, if no patient died from any other disease, approximately half of the women with this neoplasm would die, as a result of the tumor, within 20 years. Factors indicating a relatively poor survival rate were: age over 40 at the time of diagnosis, a presentation with abdominal symptoms, a palpable mass, a solid large tumor, bilateral tumors, extraovarian spread, and numerous mitotic figures in the tumor. It is suggested that all granulosa cell tumors should be considered as malignant and that the factors pointing to a poor prognosis are those indicating that a particular tumor has been diagnosed at a late stage in its natural history, either because it has been present for a long time or because it is highly malignant. There are no definite criteria for defining the prognosis in a case in which the tumor has been removed at any early stage in its natural life history.
The isolation and biologic activities of purified secretory IgA and IgG anti-Salmonella typhimurium "O" antibodies from rabbit intestinal fluid and colostrum.

Direct contact of external secretory tissue with living, but not with dead, Salmonella typhimurium stimulated formation of high concentrations of anti-“O” antibodies in the small intestinal fluid and colostrum. Purified IgG and IgA anti-S. typhimurium “O” antibodies were isolated from these fluids and their activities measured on a molar basis. Serum and exocrine IgG molecules had identical complement-dependent bactericidal, opsonization and PCA reactions. Exocrine IgA antibodies showed little or no activity in these biologic assays but did exert a similar suppressive effect upon antibody formation after intravenous injection or oral administration, as did exocrine IgG antibodies. Both IgA and IgG molecules had similar specific agglutination activities.
DNA methylation as a marker for prenatal smoke exposure in adults

Prenatal cigarette smoke is an environmental stressor that has a profound effect on DNA methylation in the exposed offspring. We have previously shown that some of these effects persist throughout childhood and into adolescence. Of interest is whether these signals persist into adulthood. We conducted an analysis to investigate associations between reported maternal smoking in pregnancy and DNA methylation in peripheral blood of women in the Avon Longitudinal Study of Parents and Children (ALSPAC) (n=754; mean age 30 years). We observed associations at 15 CpG sites in 11 gene regions, MYO1G, FRMD4A, CYP1A1, CNTNAP2, ARL4C, AHRR, TIFAB, MDM4, AX748264, DRD1, FTO (FDR < 5%). All but two of these CpG sites have previously been identified in relation to prenatal smoke exposure in the offspring at birth and the majority showed persistent hypermethylation among the offspring of smokers. We confirmed that most of these associations were not driven by own smoking and that they were still present 18 years later (N = 656; mean age 48 years). In addition, we replicated findings of a persistent methylation signal related to prenatal smoke exposure in peripheral blood among men in the ALSPAC cohort (N = 230; mean age 53 years). For both participant groups, there was a strong signal of association above that expected by chance at CpG sites previously associated with prenatal smoke exposure in newborns (Wilcoxon rank sum p-value < 2.2 × 10−4). Furthermore, we found that a prenatal smoking score, derived by combining methylation values at these CpG sites, could predict whether the mothers of the ALSPAC women smoked during pregnancy with an AUC 0.69 (95% 0.67, 0.73).
Toward a Theory of Conflict Cultures in Organizations

Research on conflict management in organizations is thriving, yet historically it has been primarily micro in its orientation, focusing almost exclusively on individual and small group processes. Although a micro approach to conflict management is certainly valid, from a levels of analysis perspective, by limiting the focus on conflict management to the individual and small group level, current conflict management paradigms may be underspecified (House et al., 1995). Many phenomena in organizations - whether it is innovation, leadership, or job attitudes, involve multiple levels of analysis, and conflict management should be of no exception. In this theory paper, we introduce a complementary macro theory of conflict cultures, or shared norms that specify how conflict should be managed in organizational settings. We propose a typology that includes four distinct organizational conflict cultures, collaborative conflict cultures, avoidant conflict cultures, passive-aggressive conflict cultures, and dominating conflict cultures, which are differentiated by two dimensions - active versus passive conflict management norms, and prosocial versus antisocial conflict management norms. We discuss top down processes (e.g., leadership, organizational structure and rewards, industry and societal factors) and bottom-up processes (e.g., personality, demographics, values) that facilitate the development of distinct conflict cultures. We explore organizational outcomes of conflict cultures as well as moderators of proposed effects. We conclude with theoretical and practical implications of a conflict culture perspective.
Video Segmentation by MAP Labeling of Watershed Segments

This paper addresses the problem of spatio-temporal segmentation of video sequences. An initial intensity segmentation method (watershed segmentation) provides a number of initial segments which are subsequently labeled, with a known number of labels, according to motion information. The label field is modeled as a Markov random field where the statistical spatial and and temporal interactions are expressed on the basis of the initial watershed segments. The labeling criterion is the maximization of the conditional a posteriori probability of the label field given the motion hypotheses, the estimate of the label field of the previous frame, and the image intensities. For the optimization, an iterative motion estimation-labeling algorithm is proposed and experimental results are presented.
Stroke: Highlights of Selected Articles

Various radiographic methods have been performed to identify vul-nerable plaque in carotid arteries. Positron emission tomography using 18 fluoro-2-deoxy- d -glucose radiotracer can detect inflammation in carotid plaques. The presence of microembolic signals (MES) seen on transcranial Doppler is a strong predictor of stroke in asymptomatic carotid artery disease. In this study by Müller et al, 18 fluoro-2-deoxy- d -glucose positron emission tomography–computed tomography and MES were performed in patients with 50% to 99% symptomatic or asymptomatic stenosis. MES-positive lesions were found in 16% of stenoses. There was significantly more MES-positive stenosis in the symptomatic group compared with the asymptomatic group (25% versus 9%). Target:background ratio values, the measure of 18 fluoro-2-deoxy- d -glucose uptake, were higher in symptomatic when compared with asymptomatic stenosis and in MES-positive compared with MES-negative plaques. Target:background ratio val-ues were also higher in asymptomatic MES-positive stenosis when compared with that in MES negative. These results show that 18 flu-oro-2-deoxy- d -glucose positron emission tomography–computed tomography can identify high-risk carotid plaques. Additional larger prospective studies are needed to validate these results before incor-porating it into everyday clinical practice. See p 3561.
Expression of conditional fear with and without awareness

Conditional responding during simple Pavlovian conditioning is often characterized as a form of implicit memory. The extent to which this type of associative learning is independent of awareness is an issue of continuing debate. Previous studies have demonstrated conditioning in the absence of awareness. However, their results have been questioned based on methodological concerns with postexperimental questionnaires. In the present study, skin conductance response (SCR) and unconditioned stimulus (UCS) expectancy were measured concurrently as participants were exposed to a differential delay fear conditioning procedure in which one tone (CS+) predicted a loud white noise, whereas a second tone (CS-) was presented alone. UCS predictability was varied on a trial-by-trial basis by presenting conditioned stimuli (CSs) at volumes just above or below the perceptual threshold. Differential UCS expectancy (awareness) was observed only on perceived trials, whereas differential SCR developed on both perceived and unperceived trials. Although perceived stimuli elicited larger SCRs, the magnitude of conditioning, indexed by differential conditioned response expression (conditioned SCR to CS+ minus the SCR to CS-), was not influenced by stimulus perception. These data indicate that conditional fear can be expressed when individuals are unaware of fear-eliciting stimuli and suggest that the degree of conditioning is independent of awareness during differential Pavlovian fear conditioning.
Changes in spontaneous and LPS-induced ex vivo cytokine production and mRNA expression in male and female athletes following prolonged exhaustive exercise.

PURPOSE The capacity of whole blood cultures to produce cytokines in response to endotoxin (LPS) was studied in athletes before, 30 min after, 3 h after and 24 h after a half-marathon run. METHODS Eight well trained men and 8 well trained women (6 of them in the late luteal phase of their cycle) participated. EDTA blood was incubated with or without LPS for 1 h, and cytokine concentration and gene expression were determined. To quantify LPS-dependent release on a per monocyte basis (LDR), the mean values of the difference (delta) between cytokine concentration in stimulated and unstimulated cultures, normalized to monocyte numbers, were calculated. RESULTS LDR of TNF-alpha was significantly reduced by exercise with identical kinetic in men and women. TNF-alpha mRNA expression was slightly down-regulated following exercise (P < 0.05), but significantly so only in women. LDR of IL-6 was also reduced, but with a faster kinetic in women than in men. Similarly, 30 min post-exercise; LDR and spontaneous release of IL-1ra were significantly less in women than men. Concomitantly, IL-Ira mRNA was significantly elevated in unstimulated and in stimulated cultures in men only. IL-10 and IL-10 mRNA were significantly induced 30 min following exercise in absence of any detectable LDR. Women showed significantly lower levels than men. LDR and spontaneous release of IL-8 was enhanced in men and TGF-beta1 in women. A significant up-regulation was seen in unstimulated IL-8 mRNA for women and LPS-stimulated IL-8 mRNA expression for men following exercise. CONCLUSION Altogether, LPS-dependent ex vivo cytokine release was strongly influenced by exercise and these changes could only in part be attributed to changes in messenger RNA. Results for IL-1ra, IL-6 and IL-10 pointed to a less pronounced anti-inflammatory response in women as compared with men. Our results also indicate an early production of IL-10 by peripheral blood cells in response to exercise.
Characterization of metal‐resistant plant‐growth promoting Bacillus weihenstephanensis isolated from serpentine soil in Portugal

A metal‐resistant bacterial strain SM3 isolated from a serpentine soil in the north‐east of Portugal was characterized as Bacillus weihenstephanensis based on the morphological and biochemical characteristics and on the comparative analysis of the partial 16S ribosomal DNA sequence. Bacillus weihenstephanensis SM3 showed a high degree of resistance to nickel (1500 mg l–1), copper (500 mg l–1) and zinc (700 mg l–1) and also to antibiotics (ampicillin, penicillin, kanamycin and streptomycin). Strain SM3 has also exhibited the capability of solubilizing phosphate and producing indole‐3‐acetic acid (IAA) both in the absence and in the presence of metals (Ni, Cu and Zn). A pot experiment was conducted to elucidate the effects of strain SM3 on plant growth and uptake of Ni, Cu or Zn by Helianthus annuus. Inoculation with strain SM3 increased the shoot and root biomass of H. annuus grown in both non‐contaminated and contaminated soil. Furthermore, strain SM3 increased the accumulation of Cu and Zn in the root and shoot systems. A batch experiment was also conducted to assess the metal mobilization potential of strain SM3 in soil. Inoculation with this strain increased the concentrations of water soluble Ni, Cu and Zn in soil. Metal solubilization by this bacterial strain may be an important process to promote the uptake of heavy metals by plants. This study elucidates the multifarious role of strain SM3 in plant growth promotion and its metal mobilizing potential. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Bone marrow-derived cell regulation of skeletal muscle regeneration

Limb regeneration requires the coordination of multiple stem cell populations to recapitulate the process of tissue formation. Therefore, bone marrow (BM) ‐derived cell regulation of skeletal muscle regeneration was examined in mice lacking the CC chemokine receptor 2 (CCR2). Myofiber size, numbers of myogenic progenitor cells (MPCs), and recruitment of BM‐derived cells and macrophages were assessed after cardiotoxin‐induced injury of chimeric mice produced by transplanting BM from wild‐type (WT) or CCR2−/− mice into irradiated WT or CCR2−/− host mice. Regardless of the host genotype, muscle regeneration and recruitment of BM‐derived cells and macrophages were similar in mice replenished with WT BM, whereas BM‐derived cells and macrophage accumulation were decreased and muscle regeneration was impaired in all animals receiving CCR2−/− BM. Furthermore, numbers of MPCs (CD34+/Sca‐1−/CD45− cells) were significantly increased in mice receiving CCR2−/− BM despite the decreased size of regenerated myofibers. Thus, the expression of CCR2 on BM‐derived cells regulated macrophage recruitment into injured muscle, numbers of MPC, and the extent of regenerated myofiber size, all of which were independent of CCR2 expression on host‐derived cells. Future studies in regenerative medicine must include consideration of the role of BM‐derived cells, possibly macrophages, in CCR2‐dependent events that regulate effective skeletal muscle regeneration. —Sun, D. , Martinez, C. O. , Ochoa, O. , Ruiz‐Willhite, L. , Bonilla, J. R, Centonze, V. E. , Waite, L. L. , Michalek, J. E. , McManus, L. M. , Shireman, P. K. Bone marrow‐derived cell regulation of skeletal muscle regeneration. FASEB J. 23, 382–395 (2009)
Test Set Diameter: Quantifying the Diversity of Sets of Test Cases

A common and natural intuition among software testers is that test cases need to differ if a software system is to be tested properly and its quality ensured. Consequently, much research has gone into formulating distance measures for how test cases, their inputs and/or their outputs differ. However, common to these proposals is that they are data type specific and/or calculate the diversity only between pairs of test inputs, traces or outputs. We propose a new metric to measure the diversity of sets of tests: the test set diameter (TSDm). It extends our earlier, pairwise test diversity metrics based on recent advances in information theory regarding the calculation of the normalized compression distance (NCD) for multisets. A key advantage is that TSDm is a universal measure of diversity and so can be applied to any test set regardless of data type of the test inputs (and, moreover, to other test-related data such as execution traces). But this universality comes at the cost of greater computational effort compared to competing approaches. Our experiments on four different systems show that the test set diameter can help select test sets with higher structural and fault coverage than random selection even when only applied to test inputs. This can enable early test design and selection, prior to even having a software system to test, and complement other types of test automation and analysis. We argue that this quantification of test set diversity creates a number of opportunities to better understand software quality and provides practical ways to increase it.
Out-Patient Detoxification in Chronic Migraine: Comparison of Strategies

Chronic migraine (CM) patients frequently overuse symptomatic medications (SM). These medications may create a cycle of rebound, worsening of headache and withdrawal symptoms that perpetuate the headache itself. In addition, the overuse of such substances is believed to counteract the efficacy of preventive treatments. We conducted a prospective randomized open-label trial comparing approaches to out-patient management in 150 CM patients (125 women, 25 men; ages 18-80 years, mean 40.3 ± 13.8) with overuse of SM. In each group, 50 patients received education and orientation and were then abruptly withdrawn from all SM. Immediately following withdrawal, the first group took prednisone (60 mg/day 2 days, 40 mg/day 2 days and 20 mg/day 2 days) for 6 days, the second group did not have any regular medications to take and the third group took naratriptan (2.5 mg twice a day) during this initial period. All patients had similar profiles of headache characteristics and consumption (quality and quantity) of SM before initiation of the treatment, but most were not severe headache sufferers, heavy SM overusers or were overusing opioids. After 5 weeks the headache frequency and intensity, the prevalence and frequency of withdrawal symptoms and consumption of rescue medications during the first 6 days were compared between groups. In addition, adherence to treatment (who returned or not and for which reasons, between groups) and headache frequency, week by week, among the groups of patients were also compared. Forty-four (88%) patients from the prednisone group, 41 (82%) from the ‘nothing’ group and 35 (70%) from the naratriptan group adhered to the treatment and returned. The were no differences between groups with regard to treatment adherence (P = 0.072), headache frequency as well as intensity (P = 0.311) and decreasing of days with headache after 5 weeks and weekly (P = 0.275). However, the incidence of withdrawal symptoms and consumption of rescue drugs was higher among the patients who did not take regular medications during the first 6 days (P = 0.0001 and P = 0.006). We concluded that CM patients with moderate overuse of SM other than opioids may be detoxified on an out-patient basis regardless of the strategy adopted with regard to the use of regular drugs during the initial days of withdrawal, but prednisone and naratriptan may be useful for reducing withdrawal symptoms and rescue medication consumption. Further controlled studies are necessary to confirm these observations.
Correlation between facial involuntary movements and abnormalities of blink and corneal reflexes in Huntington's chorea

Blink and corneal reflexes were studied in 11 patients with Huntington's chorea and the results compared with the severity of the disease. The latency of the R2 component of the blink reflex was delayed and the duration of R2 and of the corneal reflex (CR) prolonged. A greater habituation of the R2 component was found in the patients with involuntary movements in the face, and in some patients a long‐lasting depression of R2 was present. A correlation was found between: (a) severity of involuntary face movements and R2 and CR latency and (b) severity of involuntary movements in the neck and latency of R2.