Miracle-dz/UniFAR-FTUs huggingface dataset:
The Coevolution of Networks and Political Attitudes

How do attitudes and social affiliations coevolve? A long stream of research has focused on the relationship between attitudes and social affiliations. However, in most of this research the causal relationship between views and affiliations is difficult to discern definitively: Do people influence each other's views so that they converge over time or do they primarily affiliate (by choice or happenstance) with those of similar views? Here we use longitudinal attitudinal and whole network data collected at critical times (notably, at the inception of the system) to identify robustly the determinants of attitudes and affiliations. We find significant conformity tendencies: Individuals shift their political views toward the political views of their associates. This conformity is driven by social ties rather than task ties. We also find that political views are notably unimportant as a driver for the formation of relationships.
Aberrant Promoter Hypermethylation of Multiple Genes in Gallbladder Carcinoma and Chronic Cholecystitis

Purpose: Aberrant methylation of 5′ gene promoter regions is an epigenetic phenomenon that is a major mechanism for silencing of tumor suppressor genes in many cancer types. There is limited information about the molecular changes involved in the pathogenesis of gallbladder carcinoma (GBC), including methylation status. Experimental Design: We investigated the aberrant promoter methylation profile of 24 known or suspected tumor suppressor genes in 50 GBCs and compared those results with the findings in 25 chronic cholecystitis (CC) specimens without cancer. The methylation-specific polymerase chain reaction and combined restriction analysis methods were used to detect methylation, and the results were confirmed by sequencing of cloned polymerase chain reaction products. Results: In GBC, gene methylation frequencies varied from 0% to 80%. Ten genes demonstrated relatively high frequencies of aberrant methylation: SHP1 (80%), 3-OST-2 (72%), CDH13 (44%), P15INK4B (44%), CDH1 (38%), RUNX3 (32%), APC (30%), RIZ1 (26%), P16INK4A (24%), and HPP1 (20%). Eight genes (P73, RARβ2, SOCS-1, DAPK, DcR2, DcR1, HIN1, and CHFR) showed low frequencies (2–14%) of methylation, and no methylation of the remaining six genes (TIMP-3, P57, RASSF1A, CRBP1, SYK, and NORE1) was detected. In CC, methylation was detected for seven genes: SHP1 (88%), P15INK4B (28%), 3-OST-2 (12%), CDH1 (12%), CDH13 (8%), DcR2 (4%), and P16INK4A (4%). Significantly higher frequencies of methylation in GBC compared with CC were detected for eight genes (3-OST-2, CDH13, CDH1, RUNX3, APC, RIZ1, P16INK4A, and HPP1). Of those, four genes showed frequent methylation (>30%) in GBCs. The mean methylation index, an expression of the amount of methylated genes by case, was significantly higher in GBC (0.196 ± 0.013) compared with CC (0.065 ± 0.008; P < 0.001). Conclusions: Our study constitutes the most comprehensive methylation profile report available in GBC and demonstrates that this neoplasm has a distinct pattern of abnormal gene methylation. Whereas gallbladders from healthy individual were not available, our finding of methylation in CC cases without cancer suggests that this phenomenon represents an early event in the pathogenesis of GBC.
The activity of plasma membrane H+‐ATPase is strongly stimulated during Saccharomyces cerevisiae adaptation to growth under high copper stress, accompanying intracellular acidification

For the adaptation of cells of Saccharomyces cerevisiae, a period of latency is necessary before exponential growth is resumed in a medium supplemented with a highly inhibitory concentration of copper. In this work, we have examined some physiological responses occurring during this period of adaptation. The results revealed that plasma membrane H+‐ATPase (PM‐ATPase) activity is strongly stimulated (up to 24‐fold) during copper‐induced latency in growth medium with glucose, reaching maximal levels when the cells were about to start inhibited exponential growth. This in vivo activation of the ATPase activity by copper was accompanied by the stimulation of the H+‐pumping activity of the enzyme in vivo and was essentially due to the increase of the apparent Vmax for MgATP. Although the exact molecular basis of the reported plasma membrane ATPase activation was not clarified, no increase in the mRNA levels from the encoding genes PMA1 and PMA2 was apparently detected during copper‐induced latency. The physiological response reported here may allow the cells to cope with copper‐induced lipid peroxidation and consequent decrease in plasma membrane lipid ordering and increase in the non‐specific permeability to protons. The consequences of these copper deleterious effects were revealed by the decrease of the intracellular pH (pHi) of the yeast population, from approximately pHi 6 to pHi 5, during copper‐induced latency in growth medium at pH 4.3. The time‐dependent patterns of plasma membrane ATPase activation and of the decrease of pHi during the period of adaptation to growth with copper correlate, suggesting that the regulation of this membrane enzyme activity may be triggered by intracellular acidification. Consistent with this idea, when exponential growth under copper stress was resumed and the pHi of the yeast population recovered up to physiological values, plasma membrane ATPase activity simultaneously decreased from the highly stimulated level attained during the adaptation period of latency. Copyright © 2001 John Wiley & Sons, Ltd.
Application of DInSAR-GPS Optimization for Derivation of Fine-Scale Surface Motion Maps of Southern California

A method based on random field theory and Gibbs-Markov random fields equivalency within Bayesian statistical framework is used to derive 3-D surface motion maps from sparse global positioning system (GPS) measurements and differential interferometric synthetic aperture radar (DInSAR) interferogram in the southern California region. The minimization of the Gibbs energy function is performed analytically, which is possible in the case when neighboring pixels are considered independent. The problem is well posed and the solution is unique and stable and not biased by the continuity condition. The technique produces a 3-D field containing estimates of surface motion on the spatial scale of the DInSAR image, over a given time period, complete with error estimates. Significant improvement in the accuracy of the vertical component and moderate improvement in the accuracy of the horizontal components of velocity are achieved in comparison with the GPS data alone. The method can be expanded to account for other available data sets, such as additional interferograms, lidar, or leveling data, in order to achieve even higher accuracy
Early inner retinal thinning and cardiovascular autonomic dysfunction in type 2 diabetes

Background To investigate changes in the neural retina according to the presence of retinal nerve fiber layer (RNFL) defects in type 2 diabetes, and to determine the association between inner retina thickness and the severity of diabetic complications. Methods We studied non-glaucomatous patients with type 2 diabetes and control subjects Circumpapillary RNFL and macula ganglion cell-inner plexiform layer (GCIPL) thicknesses were measured by spectral-domain optical coherence tomography. In patients with type 2 diabetes, a cardiovascular autonomic function test (AFT) was performed, which included the heart rate parameter of beat-beat variation—with deep breathing, in response to the Valsalva maneuver, and on postural change from lying to standing. The results of each test were scored as 0 for normal and 1 for abnormal. A total AFT score of 1 was defined as early cardiovascular autonomic neuropathy (CAN), and an AFT score≥ 2 as definite CAN. Results We compared control eyes (n = 70), diabetic eyes with RNFL defects (n = 47), and eyes without RNFL defects (n = 30). The average RNFL and GCIPL thicknesses were significantly different among groups (all, P<0.05). On post-hoc testing, diabetic eyes with RNFL defects had a significantly thinner average GCIPL thickness than those without RNFL defects. On multivariate analyses, significantly thinner average GCIPL was seen in early CAN staging (B = -4.32, P = 0.016) and in definite CAN staging (B = -10.33, P<0.001), compared with no CAN involvement, after adjusting for confounding parameters. Conclusions Cardiovascular autonomic dysfunction was associated with early neurodegenerative changes in type 2 diabetes.
Chronic Myeloid Leukemia Patients Sensitive and Resistant to Imatinib Treatment Show Different Metabolic Responses

The BCR-ABL tyrosine kinase inhibitor imatinib is highly effective for chronic myeloid leukemia (CML). However, some patients gradually develop resistance to imatinib, resulting in therapeutic failure. Metabonomic and genomic profiling of patients' responses to drug interventions can provide novel information about the in vivo metabolism of low-molecular-weight compounds and extend our insight into the mechanism of drug resistance. Based on a multi-platform of high-throughput metabonomics, SNP array analysis, karyotype and mutation, the metabolic phenotypes and genomic polymorphisms of CML patients and their diverse responses to imatinib were characterized. The untreated CML patients (UCML) showed different metabolic patterns from those of healthy controls, and the discriminatory metabolites suggested the perturbed metabolism of the urea cycle, tricarboxylic acid cycle, lipid metabolism, and amino acid turnover in UCML. After imatinib treatment, patients sensitive to imatinib (SCML) and patients resistant to imatinib (RCML) had similar metabolic phenotypes to those of healthy controls and UCML, respectively. SCML showed a significant metabolic response to imatinib, with marked restoration of the perturbed metabolism. Most of the metabolites characterizing CML were adjusted to normal levels, including the intermediates of the urea cycle and tricarboxylic acid cycle (TCA). In contrast, neither cytogenetic nor metabonomic analysis indicated any positive response to imatinib in RCML. We report for the first time the associated genetic and metabonomic responses of CML patients to imatinib and show that the perturbed in vivo metabolism of UCML is independent of imatinib treatment in resistant patients. Thus, metabonomics can potentially characterize patients' sensitivity or resistance to drug intervention.
Sex differences in blood pressure control: are T lymphocytes the missing link?

See related article, pp 384–390 There is an ever expanding literature base implicating T lymphocytes in the development and progression of numerous cardiovascular diseases, including hypertension. T lymphocytes contribute to the development of hypertension in genetic, angiotensin II (Ang-II), and salt-sensitive male experimental animals.1 Among the most definitive studies implicating T lymphocytes in hypertension are studies conducted in Rag-1−/− mice, which lack B and T lymphocytes. Guzik et al2 were the first to demonstrate that these mice have a blunted hypertensive response to Ang-II infusion. Adoptive transfer of T lymphocytes into male Rag−/− mice restored the hypertensive response to Ang-II; adoptive transfer of B lymphocytes did not alter the blood pressure (BP) response. Although low-grade inflammation, and T lymphocytes in particular, are now a recognized hallmark of hypertension, the majority of basic science literature in this field has been conducted exclusively in males, despite the fact that females account for ≈50% of all hypertensive cases in the United States. Therefore, it was with great interest that we read the study by Pollow et al3 in the current issue of Hypertension , which was designed to determine (1) whether there are sex differences in the ability of T lymphocytes to induce Ang-II–dependent hypertension and (2) whether sex affects central or renal T lymphocytes infiltration after Ang-II hypertension. Of particular interest, they found that male mice exhibited a significant increase in BP and renal damage to Ang-II after the adoptive transfer of CD3+ T lymphocytes from wild-type male mice. In contrast, BP responses and renal injury to Ang-II were not significantly altered in female Rag−/− mice after adoptive transfer of T lymphocytes from males. Male Rag−/− mice also had greater renal CD3+, CD4+, CD8+, and T-regulatory cells (Tregs) …
Three-Dimensional Projective Geometry with Geometric Algebra

The line geometric model of 3-D projective geometry has the nice property that the Lie algebra sl(4) of 3-D projective transformations is isomorphic to the bivector algebra of CL(3,3), and line geometry is closely related to the classical screw theory for 3-D rigid-body motions. The canonical homomorphism from SL(4) to Spin(3,3) is not satisfying because it is not surjective, and the projective transformations of negative determinant do induce orthogonal transformations in the Pl\"ucker coordinate space of lines. This paper presents our contributions in developing a rigorous and convenient algebraic framework for the study of 3-D projective geometry with Clifford algebra. To overcome the unsatisfying defects of the Pl\"ucker correspondence, we propose a group Pin^{sp}(3,3) with Pin(3,3) as its normal subgroup, to quadruple-cover the group of 3-D projective transformations and polarities. We construct spinors in factored form that generate 3-D reflections and rigid-body motions, and extend screw algebra from the Lie algebra of rigid-body motions to other 6-D Lie subalgebras of sl(4), and construct the corresponding cross products and virtual works.
Nanomechanics of flexoelectric switching

We examine the phenomenon of flexoelectric switching of polarization in ultrathin films of barium titanate induced by a tip of an atomic force microscope (AFM). The spatial distribution of the tip-induced flexoelectricity is computationally modeled both for perpendicular mechanical load (point measurements) and for sliding load (scanning measurements), and compared with experiments. We find that (i) perpendicular load does not lead to stable ferroelectric switching in contrast to the load applied in the sliding contact load regime, due to nontrivial differences between the strain distributions in both regimes: ferroelectric switching for the perpendicular load mode is impaired by a strain gradient inversion layer immediately underneath the AFM tip; while for the sliding load regime, domain inversion is unimpaired within a greater material volume subjected to larger values of the mechanically induced electric field that includes the region behind the sliding tip; (ii) beyond a relatively small value of an applied force, increasing mechanical pressure does not increase the flexoelectric field inside the film, but results instead in a growing volume of the region subjected to such field that aids domain nucleation processes; and (iii) the flexoelectric coefficients of the films are of the order of few nC/m, which is much smaller than for bulk BaTiO3 ceramics, indicating that there is a “flexoelectric size effect” that mirrors the ferroelectric one
Cigarette Smoking and Lung Cancer: Modeling Total Exposure and Intensity

Investigators typically analyze cigarette smoking using smoking duration and intensity (number of cigarettes smoked per day) as risk factors. However, odds ratios (OR) for categories of intensity either adjusted for, or jointly with, duration of smoking may be distorted by differences in total pack-years of exposure to cigarette smoke. To study effects of intensity, we apply a linear excess OR model to compare total exposure delivered at low intensity for a long period of time with an equal total exposure delivered at high intensity for a short period of time to data from a large case-control study of lung cancer. The excess OR per pack-year increases with intensity for subjects who smoke ≤20 cigarettes per day and decreases with intensity for subjects who smoke >20 cigarettes per day. The intensity patterns are homogeneous by histologic type of lung cancer, suggesting that observed differences in risks by histologic type are related to total smoking exposure or smoking duration and not smoking intensity. At lower smoking intensities, there is an “exposure enhancement” effect such that for equal total exposure, the excess OR per pack-year increases with intensity. At higher smoking intensities, there is a “reduced potency” or “wasted exposure” effect such that for equal total exposure, the excess OR per pack-year decreases with intensity (i.e., smoking at a lower intensity for longer duration is more deleterious than smoking at a higher intensity for shorter duration). (Cancer Epidemiol Biomarkers Prev 2006;15(3):517–23)
Remifentanil and propofol for sedation in children and young adolescents undergoing diagnostic flexible bronchoscopy

Flexible fibreoptic bronchoscopy (FOB) has become a useful diagnostic and therapeutic procedure in children. We investigated 26 patients (3–14 years) for FOB using a new sedation strategy. All patients received oral premedication and inhalation of topical anaesthetic. Sedation for bronchoscopy was achieved with a continuous infusion of remifentanil and intermittent boluses of propofol. Propofol injection was repeated if sedation was inadequate. Sedation could be successfully performed in all children without adverse effects. Endtidal CO2 concentration and arterial oxygen saturation remained stable throughout the study. All children were awake 5±1.3 min after stopping remifentanil infusion. Sedation with remifentanil/propofol is a new sedation strategy for diagnostic flexible paediatric bronchoscopy in children with spontaneous ventilation.
Are Correlations of Stock Returns Justified by Subsequent Changes in National Outputs?

In an integrated world capital market, the same pricing kernel is applicable to all securities. We apply this idea to the stock returns of different countries. We investigate the underlying determinants of cross-country stock return correlations. First, we determine, for a given, measured degree of commonality of country outputs, what should be the degree of correlation of national stock returns. To that end, we develop a model containing a statistical model for output and an intertemporal financial market model for stock returns. We then match the correlations generated by the model with measured correlations. We find that actual correlations can be matched to what they should be in a unified market but that they are much larger than they should be in fully segmented financial markets.
Microbiological biodiversity in poultry and paddy straw wastes in composting systems

Immense quantity of waste is generated in association with poultry meat egg and crop production. The potential risks due to disposal of these wastes are magnified as a result of dense refinement of poultry production and the decreasing amount of land available for waste disposal. The study aims at studying the microbiological biodiversity of poultry waste and paddy straw based co-composting system. The predominant microflora of the poultry manure were bacteria, fungi, enteric bacteria and spore forming bacteria whose population was high at the initiation of composting but decreased significantly as the compost approached maturity. The initial load of inherent enteric groups of bacteria in poultry waste, that also includes some pathogenic ones, is considerably reduced and some new vital groups contributed to compost quality as the microbiological biodiversity sets in the system and becomes stable. Major fraction of nitrogen of poultry waste was subjected to ammonia volatilization and a fraction of it conserved by co-composting it in conjunction with wastes having low nitrogen contents. In the treatment T1 and T5, where poultry manure and paddy straws alone were composted, 60 and 30 percent of organic carbon, respectively, was lost over a period of six months. Whereas in treatments T2,T3 and T4, poultry manure and paddy straw were co-composted in the ratio of 3:1, 2:2 and 1:3, respectively, 51.4,45.0 and 37.0 percent of carbon, respectively, was lost during decomposition. The C: N ratio in all the treatments decreased significantly to 18.3 for T1, 24.7 for T2, 27.0 for T3, 34.9 for T4 and 38.5 for T5 at the end of composting period.
Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species

Significance Mechanisms of competition are not well-studied in the mammalian gut microbiota, especially among abundant species of this ecosystem. Theoretical models predict that antagonistic mechanisms should profoundly affect member fitness, yet identification and experimental analyses of such factors are few. Here we show that the abundant gut species Bacteroides fragilis produce T6SSs that deploy previously undescribed toxins able to antagonize numerous species of human gut Bacteroidales. We show that these systems are synthesized in the mammalian gut and allow a producing strain to outcompete a sensitive isogenic strain. Our data support that GA3 T6SSs likely allow the producing B. fragilis strain to create a protected niche in the human colon. Type VI secretion systems (T6SSs) are multiprotein complexes best studied in Gram-negative pathogens where they have been shown to inhibit or kill prokaryotic or eukaryotic cells and are often important for virulence. We recently showed that T6SS loci are also widespread in symbiotic human gut bacteria of the order Bacteroidales, and that these T6SS loci segregate into three distinct genetic architectures (GA). GA1 and GA2 loci are present on conserved integrative conjugative elements (ICE) and are transferred and shared among diverse human gut Bacteroidales species. GA3 loci are not contained on conserved ICE and are confined to Bacteroides fragilis. Unlike GA1 and GA2 T6SS loci, most GA3 loci do not encode identifiable effector and immunity proteins. Here, we studied GA3 T6SSs and show that they antagonize most human gut Bacteroidales strains analyzed, except for B. fragilis strains with the same T6SS locus. A combination of mutation analyses, trans-protection analyses, and in vitro competition assays, allowed us to identify novel effector and immunity proteins of GA3 loci. These proteins are not orthologous to known proteins, do not contain identified motifs, and most have numerous predicted transmembrane domains. Because the genes encoding effector and immunity proteins are contained in two variable regions of GA3 loci, GA3 T6SSs of the species B. fragilis are likely the source of numerous novel effector and immunity proteins. Importantly, we show that the GA3 T6SS of strain 638R is functional in the mammalian gut and provides a competitive advantage to this organism.
The 'why' and 'why not' of job search behaviour: Their relation to searching, unemployment experience, and well-being

Two studies (n = 273 and 254) used self-determination theory (SDT) to examine unemployed people's motivation both to search and not to search for a job. The self-regulation questionnaire format (Ryan & Connell, 1989) was used to assess participants' autonomous and controlled job-search motivation (the ‘why’ of job search) as well as their amotivation for searching. Additionally, both autonomous and controlled motivation for not searching (the ‘why not’ of job search) was assessed. Results provide validity for these five motivational constructs and indicate, in line with SDT, that the constructs predicted reports of search behaviour, affective experiences, and well-being. The addition of autonomous and controlled motivation for not searching contributed additional predictive power beyond the motivational constructs that focused only on searching. Copyright © 2004 John Wiley & Sons, Ltd.