Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting changes in streaming data with information-theoretic windowing

This study addresses the problem of detecting change points in streaming data. Herein, we focus on detecting changes with low complexity and high accuracy to manage large-volume, high-velocity data. To this end, we propose a novel method of detecting changes via data compression, by introducing minimum description length (MDL) change statistics to an adaptive windowing regime. The time complexity of the resulting algorithm, Sequential Compression with Adaptive Windowing (SCAW), is optimal except for a logarithmic factor, and is theoretically justified through exponential upper bounds on error probabilities. Moreover, SCAW can be used to detect arbitrary types of changes by choosing an appropriate compressor. We also introduce the notion of asymptotic reliability as a criterion of change point detection algorithms, and determine SCAW's parameter using this criterion. Finally, we demonstrate the effectiveness of the proposed method in experiments using synthetic and real-world data from markets and industrial machinery.
Regulation of Sos Activity by Intramolecular Interactions

ABSTRACT The guanine nucleotide exchange factor Sos mediates the coupling of receptor tyrosine kinases to Ras activation. To investigate the mechanisms that control Sos activity, we have analyzed the contribution of various domains to its catalytic activity. Using human Sos1 (hSos1) truncation mutants, we show that Sos proteins lacking either the amino or the carboxyl terminus domain, or both, display a guanine nucleotide exchange activity that is significantly higher compared with that of the full-length protein. These results demonstrate that both the amino and the carboxyl terminus domains of Sos are involved in the negative regulation of its catalytic activity. Furthermore, in vitro Ras binding experiments suggest that the amino and carboxyl terminus domains exert negative allosteric control on the interaction of the Sos catalytic domain with Ras. The guanine nucleotide exchange activity of hSos1 was not augmented by growth factor stimulation, indicating that Sos activity is constitutively maintained in a downregulated state. Deletion of both the amino and the carboxyl terminus domains was sufficient to activate the transforming potential of Sos. These findings suggest a novel negative regulatory role for the amino terminus domain of Sos and indicate a cooperation between the amino and the carboxyl terminus domains in the regulation of Sos activity.
Construction and validation of a prognostic model across several studies, with an application in superficial bladder cancer

Many models for clinical prediction (prognosis or diagnosis) are published in the medical literature every year but few such models find their way into clinical practice. The reason may be that since in most cases models have not been validated in independent data, they lack generality and/or credibility. In this paper we consider the situation in which several compatible, independent data sets relating to a given disease with a time‐to‐event endpoint are available for analysis. The aim is to construct and evaluate a single prognostic model. Building a multivariable model from the available prognostic factors is accomplished within the Cox proportional hazards framework, stratifying by study. Non‐linear relationships with continuous predictors are modelled by using fractional polynomials. To assess the discrimination or separation of a survival model, we use the D statistic of Royston and Sauerbrei. D may be interpreted as the separation (log hazard ratio) between the survival distributions for two independent prognostic groups. To evaluate the generality of a prognostic model across the data sets, we propose ‘internal–external cross‐validation’ on D: each study is omitted in turn, the model parameters are estimated from the remaining studies and D is evaluated in the omitted study. Because the linear predictor of a survival model tells only part of the story, we also suggest a method for investigating heterogeneity in the baseline distribution function across studies which involves fitting completely specified, flexible parametric survival models (Royston and Parmar). Our final models combine the prognostic index (obtained with stratification by study) with the pooled baseline survival distribution (estimated parametrically). By applying this methodology, we construct two prognostic scores in superficial bladder cancer. The simpler of the two scores is more suited to clinical application. We show that a three‐group prognostic classification scheme based on either score produces well‐separated survival curves for each of the data sets, despite identifiable heterogeneity among the baseline distribution functions and to a lesser extent among the prognostic indexes for the individual studies. Copyright © 2004 John Wiley & Sons, Ltd.
Photolithographic Patterning of C2C12 Myotubes using Vitronectin as Growth Substrate in Serum‐Free Medium

The C2C12 cell line is frequently used as a model of skeletal muscle differentiation. In our serum‐free defined culture system, differentiation of C2C12 cells into myotubes required surface‐bound signals such as substrate‐adsorbed vitronectin or laminin. On the basis of this substrate requirement of myotube formation, we developed a photolithography‐based method to pattern C2C12 myotubes, where myotubes formed exclusively on vitronectin surface patterns. We have determined that the optimal line width to form single myotubes is approximately 30 μm. To illustrate a possible application of this method, we patterned myotubes on the top of commercial substrate‐embedded microelectrodes. In contrast to previous experiments where cell patterning was achieved by selective attachment of the cells to patterned surfaces in a medium that contained all of the factors necessary for differentiation, this study illustrates that surface patterning of a signaling molecule, which is essential for skeletal muscle differentiation in a defined system, can result in the formation of aligned myotubes on the patterns. This technique is being developed for applications in cell biology, tissue engineering, and robotics.
Relationship between NFKB1 -94 insertion/deletion ATTG polymorphism and susceptibility of cervical squamous cell carcinoma risk.

BACKGROUND A very high expression of nuclear factor-kappa B protein (nuclear p50, encoded by NFKB1) in high-grade squamous intraepithelial lesion and invasive cancers has been observed. The aim of this study was to determine whether the functional NFKB1 -94 insertion/deletion ATTG polymorphism (rs28362491) is associated with cervical squamous cell carcinoma (CSCC). MATERIALS AND METHODS PCR-polyacrylamide gel electrophoresis method was used to genotype the NFKB1 -94 insertion/deletion ATTG polymorphism in 233 women with CSCC and 365 ethnicity-matched healthy control women. The genotyping method was confirmed by the DNA sequencing analysis. RESULTS The frequency of ATTG(2)/ATTG(2) genotype and ATTG(2) allele in the CSCC patients was significantly higher than that of controls, indicating that the -94 insertion/deletion ATTG polymorphism in NFKB1 promoter was associated with CSCC [P = 0.001, odds ratio (OR) = 2.560, 95% confidence interval (CI) 1.459-4.492 and P = 0.001, OR = 1.493, 95% CI 1.168-1.908, respectively]. Results of stratified analyses revealed that this polymorphism is associated with younger age (< or =35 years) and positive parametrial invasion but not with tumor differentiation, high clinical stage or lymph node status. CONCLUSION Our results indicate that the functional NFKB1 -94 insertion/deletion ATTG polymorphism is associated with CSCC, especially with younger age (< or =35 years) and positive parametrial invasion of CSCC patients.
Pattern and Predictors of Weight Gain During Pregnancy Among HIV-1–Infected Women from Tanzania

Progression of HIV disease is often accompanied by weight loss and wasting. Gestational weight gain is a strong determinant of maternal and neonatal outcomes; however, the pattern and predictors of weight gain during pregnancy among HIV-positive women are unknown. We obtained monthly anthropometric measurements in a cohort of 957 pregnant women from Tanzania who were HIV infected. We estimated the weekly rate of weight gain at various points during the second and third trimesters of pregnancy and computed rate differences between levels of sociodemographic, nutritional, immunologic, and parasitic variables at the first prenatal visit. The change in mid-upper arm circumference (MUAC) from baseline to delivery was also examined. The rate of weight gain decreased progressively during pregnancy. There was an average decline of 1 cm in MUAC between weeks 12 and 38. Lower level of education and helminthic infections at first visit were associated with decreased adjusted rates of weight gain during the third trimester. High baseline MUAC, not contributing to household income, lower serum retinol and selenium concentrations, advanced clinical stage of HIV disease, and malaria infection were related to decreased rates of weight gain during the second trimester. Low baseline CD4 T-cell counts were related to a poorer pattern of weight gain throughout pregnancy. Prevention and treatment of parasitic infections and improvement of nutritional status are likely to enhance the pattern of gestational weight gain among HIV-infected women.
Alkalophilic Bacillus firmus RAB generates variants which can grow at lower Na+ concentrations than the parental strain

Obligately alkalophilic Bacillus firmus RAB cannot grow well on media containing less than 5 mM Na+. However, variant strains can be isolated on plates containing 2 to 3 mM Na+. These variants are observed only rarely in cultures that are plated before being subjected to repeated transfers in liquid medium. Cultures which have been transferred several times produce variants at an apparent frequency of 2 X 10(-4). Most of these variants are unstable, generating parental types at the high frequency of 10%; however, stable variants can be isolated. These strains grow better than the parental strain at very high pH values in the presence of 5 mM Na+ and have enhanced activity of the Na+ -H+ antiporter that has been implicated in pH homeostasis. By contrast, Na+ -coupled solute uptake is indistinguishable from that of the parental strain, and no obvious changes in the respiratory chain components are apparent in reduced versus oxidized difference spectra. The membranes of the variants show a marked enhancement, on sodium dodecyl sulfate-polyacrylamide gradient electrophoresis, in one polypeptide band with a molecular weight in the range of 90,000. The findings are discussed from the point of view of genetic mechanisms that might confer adaptability to even more extreme environments than usual and in view of earlier models relating the Na+ -translocating activities of the alkalophiles.
Admission volume is associated with mortality of neonatal respiratory failure in emerging neonatal intensive care units

Abstract Objective: The aim of this survey was to explore the relationship between admission volume and mortality of neonates with hypoxemic respiratory failure (NRF) in emerging neonatal intensive care units (NICUs). Methods: NRF from 55 NICUs were retrospectively included with death risk as the major outcome. Perinatal comorbidities, underlying disease severity, respiratory support, facility utilization, and economic burden in the early postnatal period were compared among five NICU admission volume categories defined by NRF incidence, with score for neonatal acute physiology perinatal extension II (SNAPPE-II) also assessed as initial severity. Results: Compared to NICUs with NRF < 50 cases/year, NRF incidence, NRF/NICU, NRF/NICU admissions, and magnitude of ventilator use were several times higher, and mortality rates 20–50% lower, in NICUs of 150–199 and ≥200 cases/year (p < .01), even after adjustment with SNAPPE-II in stratified ranges. Median SNAPPE-II values, which correlated with the death rate of NRF (r = .282, p < .001), were lower in NICUs of 150–199 and ≥200 than in <50, 50–99, and 100–149 categories (13 versus 18, p < .01). NRF mortalities were not correlated with the proportion of very low birth weight patients in each category. Conclusions: Neonates in NICUs with smaller NRF admission volume and decreased magnitude of ventilator use had a higher risk of death as assessed by SNAPPE-II, which should be targeted in the quality improvement of newly established, resource-limited NICUs.
Mating system of an exceptional primate, the olive colobus (Procolobus verus)

In the olive colobus (Procolobus verus), many groups have multiple males and the males have large testes. This indicates that even though this species lives in small groups, single males do not monopolize the groups. We investigated the strategies employed by males to secure their mating success, and sought to determine whether the lack of male monopolization was a result of female mating strategies, as indicated by the exaggerated sexual swellings of the females. Four study groups were monitored for demographic changes, and group composition was determined in six additional groups in Taï National Park, Ivory Coast, between 1994 and 1999. Social behavior was recorded by scan and focal sampling in the study groups. The almost permanent association of olive colobus with Diana monkeys (Cercopithecus diana) in effect provided males a resource at which they could expect females to visit and sometimes even permanently join them, as well as protection from predators. As alternative strategies for obtaining females, one male took over the group of another male and one male immigrated into a bisexual group. Within bi‐male groups, dominant males mated most frequently and males defended their groups during intergroup interactions. Lone females that visited groups or solitary males had a swelling more often than expected, and generally mated with the males they visited. Females had long receptive periods, several consecutive receptive cycles, and some overlap in receptive periods within groups. Females mated with extragroup males, and during infertile periods. We concluded that the males used the Diana monkeys for safety reasons and to obtain mating partners, and that female reproductive biology and behavior prevented the monopolization of groups of females by single males. Our data were inconclusive as regards the benefits to females of avoiding monopolization by males. Am. J. Primatol. 62:261–273, 2004. © 2004 Wiley‐Liss, Inc.
Common Alterations in PBP1a from Resistant Streptococcus pneumoniae Decrease Its Reactivity toward β-Lactams

The development of high level β-lactam resistance in the pneumococcus requires the expression of an altered form of PBP1a, in addition to modified forms of PBP2b and PBP2x, which are necessary for the appearance of low levels of resistance. Here, we present the crystal structure of a soluble form of PBP1a from the highly resistant Streptococcus pneumoniae strain 5204 (minimal inhibitory concentration of cefotaxime is 12 mg·liter-1). Mutations T371A, which is adjacent to the catalytic nucleophile Ser370, and TSQF(574–577)NTGY, which lie in a loop bordering the active site cleft, were investigated by site-directed mutagenesis. The consequences of these substitutions on reaction kinetics with β-lactams were probed in vitro, and their effect on resistance was measured in vivo. The results are interpreted in the framework of the crystal structure, which displays a narrower, discontinuous active site cavity, compared with that of PBP1a from the β-lactam susceptible strain R6, as well as a reorientation of the catalytic Ser370.
Lectin, a possible basis for symbiosis between bacteria and sponges

From the marine sponge Halichondria panicea a lectin was isolated and characterized. The homogeneous lectin (composed of protein to 80.7% and of neutral carbohydrates to 14.1%) had a molecular weight of 78,000 (determined by gel filtration) and consisted of four subunits with a molecular weight of 21,000 each (determined by gel electrophoresis in the presence of sodium dodecyl sulfate). The hemagglutinating activity was only slightly dependent upon ionic strength and incubation temperature and did not require divalent cations, but it was inhibited by reagents for thiol groups. The Halichondria lectin was completely inhibited in hemagglutination competition experiments in the presence of fetuin, D-galacturonic acid, D-glucuronic acid, polygalacturonic acid, or L-fucose. The purified Halichondria lectin did not cause reaggregation of dissociated H. panicea cells. From the same sponge species bacteria were isolated and identified as Pseudomonas insolita. These bacteria were cultivated in marine broth 2216. Under these culture conditions the bacteria grew only in the presence of the homologous lectin; the lectin-caused effect was not abolished by D-glucuronic acid or D-galacturonic acid. However, after addition of a polysaccharide-containing fraction isolated from P. insolita, the lectin-caused, growth-promoting effect was abolished. Other lectins were found to exhibit no growth-promoting effect. On the basis of colony counts, P. insolita was the predominant bacterial species in the sponge extract; 1.9 X 10(6) Pseudomonas colonies were measured in extracts isolated from 1 g of sponge. The assumption of an interrelationship between the sponge and the bacterium is supported by the results indicating that the Halichondria lectin has no effect on the growth of such bacteria isolated from six other marine sponge species. Evidence is presented which indicates that the Halichondria lectin is not utilized during growth of the Pseudomonas species. Lectin activity was detected on the surface of mucoid cells from H. panicea. From the data obtained the possibility is discussed that the Halichondria lectin is a basis for a symbiotic relationship between the sponge and the bacterium.
An inordinate fondness for beetles? Variation in seasonal dietary preferences of night‐roosting big brown bats (Eptesicus fuscus)

Generalist species with numerous food web interactions are thought to provide stability to ecosystem dynamics; however, it is not always clear whether habitat generality translates into dietary diversity. Big brown bats are common across North America and employ a flexible foraging strategy over water, dense forests, forest edges and rural and urban settings. Despite this generalist use of habitat, they are paradoxically characterized as beetle specialists. However, hard carapaces may preferentially survive digestion leading to over‐representation during morphological analysis of diet. This specialization has not been evaluated independently using molecular analysis and species‐level identification of prey. We used next‐generation sequencing to assess the diet of big brown bats. Beetles were consumed in the highest frequency but Lepidoptera species richness was highest among identified prey. The consumption of species showed strong seasonal and annual variation. While Coleoptera consumption varied, Lepidoptera and Ephemeroptera were relatively constant dietary components. Dietary diversity increased in late summer when insect diversity decreases. Our results indicate that big brown bats are dietary generalists and, while beetles are an important component of the diet, Lepidoptera are equally important, and Lepidoptera and Ephemeroptera are the only stable prey resource exploited. As resources become limited, big brown bats may respond by increasing the species richness of prey and thus their connectedness in the ecosystem. This characterization of diet corresponds well with a generalist approach to foraging, making them an important species in encouraging and maintaining ecosystem stability.
Analysis of Gene Expression and Ig Transcription in PU.1/Spi-B-Deficient Progenitor B Cell Lines1

A number of presumptive target genes for the Ets-family transcription factor PU.1 have been identified in the B cell lineage. However, the precise function of PU.1 in B cells has not been studied because targeted null mutation of the PU.1 gene results in a block to lymphomyeloid development at an early developmental stage. In this study, we take advantage of recently developed PU.1−/−Spi-B−/− IL-7 and stromal cell-dependent progenitor B (pro-B) cell lines to analyze the function of PU.1 and Spi-B in B cell development. We show that contrary to previously published expectations, PU.1 and/or Spi-B are not required for Ig H chain (IgH) gene transcription in pro-B cells. In fact, PU.1−/−Spi-B−/− pro-B cells have increased levels of IgH transcription compared with wild-type pro-B cells. In addition, high levels of Igκ transcription are induced after IL-7 withdrawal of wild-type or PU.1−/−Spi-B−/− pro-B cells. In contrast, we found that Igλ transcription is reduced in PU.1−/−Spi-B−/− pro-B cells relative to wild-type pro-B cells after IL-7 withdrawal. These results suggest that Igλ, but not IgH or Igκ, transcription, is dependent on PU.1 and/or Spi-B. The PU.1−/−Spi-B−/− pro-B cells have other phenotypic changes relative to wild-type pro-B cells including increased proliferation, increased CD25 expression, decreased c-Kit expression, and decreased RAG-1 expression. Taken together, our observations suggest that reduction of PU.1 and/or Spi-B activity in pro-B cells promotes their differentiation to a stage intermediate between late pro-B cells and large pre-B cells.
The Impact of Non-interest Income on the Efficiency of China's Banking Sector

This paper investigates the impact of non-interest income on bank efficiency based on data from China banking sector during the period 1996~2010 by establishing DEA model and Panel-Tobit model. The efficiency levels of China banking sector are estimated by employing traditional DEA model, which only considers loans and investments as the output variables, and alternative DEA model, which considers non-interest income as an additional output variable. The results of parametric and non-parametric univariate tests on the efficiency scores show that there are no significant differences in mean and median efficiency calculated from traditional and alternative DEA models. In other words, the inclusion of non-interest income in output vector does not have a statistically significant influence on the efficiency of China banking sector. Additionally, we normalize each bank’s efficiency score under these two DEA models in order to avoid potential estimation bias due to the fact that the alternative DEA model has one more output variable than the traditional DEA model, and the findings suggest that only a small proportion of banks present an increase in efficiency level with inclusion of non-interest income, while no significant changes are seen on most banks’ efficiency levels. Also, further analysis by establishing Panel-Tobit regression model finds that the relationship between the share of noninterest income to the net operating revenue and the bank efficiency score is not significant, which suggests that the bank efficiency doesn’t increase significantly with the increasing non-interest income share. Furthermore, the bank efficiency also does not present a significant increase with the time. Overall, our findings suggest that the inclusion of non-interest income does not significantly increase the efficiency level of China banking sector.