bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neighborhood Socioeconomic Status and All-Cause Mortality
Authors: Bosma Hans , Dike van de Mheen H. , Borsboom Gerard J. J. M. , Mackenbach Johan P. 
Published: July 2002

Abstract
This study sought to determine the contribution of neighborhood socioeconomic status to all-cause mortality and to explore its correlates. As part of the longitudinal “Gezondheid en LevensOmstandigheden Bevolking en omstreken” (GLOBE) study in the Netherlands, 8,506 randomly selected men and women aged 15–74 years from 86 neighborhoods in the city of Eindhoven reported on their socioeconomic status in the 1991 baseline survey. During the 6-year follow-up, 487 persons died. Neighborhood socioeconomic status was derived from individual reports on socioeconomic status. Its effect on mortality was stringently controlled for four individual-level socioeconomic indicators. Persons living in a neighborhood with a high percentage of unemployed/disabled or poor persons had a higher mortality risk than did those living in a neighborhood with a low percentage of unemployed/disabled or poor persons. This was independent of individual socioeconomic characteristics, including individual unemployment/disability or reports of severe financial problems. Educational and occupational neighborhood indicators were similarly, but less strongly, related to mortality. The prevalence of poor housing conditions, social disintegration, and unhealthy psychologic profiles and behaviors was higher in neighborhoods with a low socioeconomic status. Contextual effects of socioeconomic status may thus be due to one or more of these specific circumstances. The findings indicate potential public health benefits of modifying socioeconomic characteristics of areas.
Incidence of Transitional Cell Carcinoma and Arsenic in Drinking Water: A Follow-up Study of 8,102 Residents in an Arseniasis-endemic Area in Northeastern Taiwan
Authors: Chiou Hung-Yi , Chiou Shu-Ti , Hsu Yi-Hsiang , Chou Yi-Li , Tseng Chin-Hsiao , Wei Min-Li , Chen Chien-Jen 
Published: July 2002

Abstract
A significant association between ingested arsenic and bladder cancer has been reported in an arseniasis-endemic area in southwestern Taiwan, where many households share only a few wells in their villages. In another arseniasis-endemic area in northeastern Taiwan, each household has its own well for obtaining drinking water. In 1991–1994, the authors examined risk of transitional cell carcinoma (TCC) in relation to ingested arsenic in a cohort of 8,102 residents in northeastern Taiwan. Estimation of each study subject's individual exposure to inorganic arsenic was based on the arsenic concentration in his or her own well water, which was determined by hydride generation combined with atomic absorption spectrometry. Information on duration of consumption of the well water was obtained through standardized questionnaire interviews. The occurrence of urinary tract cancers was ascertained by follow-up interview and by data linkage with community hospital records, the national death certification profile, and the cancer registry profile. Cox proportional hazards regression analysis was used to estimate multivariate-adjusted relative risks and 95% confidence intervals. There was a significantly increased incidence of urinary cancers for the study cohort compared with the general population in Taiwan (standardized incidence ratio = 2.05; 95% confidence interval (CI): 1.22, 3.24). A significant dose-response relation between risk of cancers of the urinary organs, especially TCC, and indices of arsenic exposure was observed after adjustment for age, sex, and cigarette smoking. The multivariate-adjusted relative risks of developing TCC were 1.9, 8.2, and 15.3 for arsenic concentrations of 10.1–50.0, 50.1–100, and &gt;100 µg/liter, respectively, compared with the referent level of ≤10.0 µg/liter.
Plasma Concentrations of Carotenoids, Retinol, and Tocopherols in Preeclamptic and Normotensive Pregnant Women
Authors: Zhang Cuilin , Williams Michelle A. , Sanchez Sixto E. , King Irena B. , Ware-Jauregui Suzie , Larrabure Gloria , Bazul Victor , Leisenring Wendy M. 
Published: July 2002

Abstract
This case-control study was conducted in Lima, Peru, from June 1997 through January 1998 to assess whether plasma concentrations of carotenoids (α-carotene, β-carotene, lycopene, lutein, zeaxanthin, β-cryptoxanthin), retinol, and tocopherols (α-tocopherol and γ-tocopherol) are decreased in women with preeclampsia. A total of 125 pregnant women with preeclampsia and 179 normotensive pregnant women were included. Plasma concentrations of antioxidants were determined using high performance liquid chromatography. After adjusting for maternal demographic, behavioral, and reproductive characteristics and total plasma lipid concentrations, the authors found a linear increase in risk of preeclampsia with increasing concentrations of α-tocopherol (odds ratio of the highest quartile = 3.13; 95% confidence interval: 1.06, 9.23, with the lowest quartile as the reference group; p value of the test of linear trend = 0.040). The risk of preeclampsia decreased across increasing quartiles of concentrations for retinol (odds ratio of the highest quartile = 0.32; 95% confidence interval: 0.15, 0.69, with the lowest quartile as the reference group; p value of the test of linear trend = 0.001). Some of these results are inconsistent with the prevailing hypothesis that preeclampsia is an antioxidant-deficient state. Preliminary findings confirm an earlier observation of increased plasma concentrations of α-tocopherol among women with preeclampsia as compared with normotensive pregnant women.
Estimating the Relative Incidence of Heroin Use: Application of a Method for Adjusting Observed Reports of First Visits to Specialized Drug Treatment Agencies
Authors: Hickman Matthew , Seaman Shaun , de Angelis Daniela 
Published: July 2002

Abstract
In this paper, the authors propose a method for estimating the incidence of heroin use by adjusting reported numbers of heroin users visiting drug treatment agencies for the time lag between onset of heroin use and first treatment request (lag distribution). The adjusted incidence is relative, since it represents the number of individuals beginning heroin use in each year whose cases will be reported within 8 years of starting use. Users with longer lag times or whose cases are never reported are excluded. Utilizing data from southeastern England (1991–1998), the authors analyzed the effects of covariates (sex, age group, ethnic group, route of consumption, and year of onset of drug use) on the lag distribution. Trends in the adjusted incidence of heroin use were very different for injectors and noninjectors: Incidence among injectors seemed to be stable, while in noninjectors it increased twofold between 1991 and 1996–1997. These results must be interpreted cautiously, especially in relation to the wider context of underlying trends in the population. Potential biases derive from underreporting and from changes in the proportion of heroin users in treatment. The lag correction method adds substantially to the value of routine treatment data, at least for heroin use, and is potentially the best method for obtaining estimates of incidence.
Family Size, Day-Care Attendance, and Breastfeeding in Relation to the Incidence of Childhood Asthma
Authors: Infante-Rivard Claire , Amre Devendra , Gautrin Denyse , Malo Jean-Luc 
Published: July 2002

Abstract
A hypothesis has been suggested stating that children exposed early to infections are less likely to develop atopy or asthma. The authors investigated the relation between risk of childhood asthma and number of siblings as well as day-care attendance, as factors possibly increasing the likelihood of early infections, and breastfeeding as a factor reducing them. A case-control study was carried out in Montréal, Canada, between 1988 and 1995 that included 457 children diagnosed with asthma at 3–4 years of age and 457 healthy controls. Cases followed for 6 years were later classified as persistent or transient by the symptoms and use of medication after diagnosis. Among cases diagnosed at 3–4 years of age, the adjusted odds ratio for asthma was 0.54 (95% confidence interval (CI): 0.36, 0.80) for one sibling and 0.49 (95% CI: 0.30, 0.81) for two or more. The adjusted odds ratio for day-care attendance before 1 year of age was 0.59 (95% CI: 0.40, 0.87). Results were similar with persistent cases. Among transient cases (who possibly had an infection with wheezing at 3–4 years of age), day-care attendance and a short duration of breastfeeding resulted in increased risk. The results support the hypothesis that opportunity for early infections reduces the risk of asthma.
Polymer chromosome models and Monte Carlo simulations of
radiation breaking DNA
Authors: L.Ponomarev A. , K.Sachs R. 
Published: July 2002

Abstract
Motivation: Chromatin breakage by ionizing radiation is relevant to studies of carcinogenesis, tumor radiotherapy, biodosimetry and molecular biology. This article focuses on computer analysis of chromosome irradiation in mammalian cells.
Methods: Polymer physics and Monte Carlo numerical methods are used to develop a coarse-grained computational approach. Chromatin is modeled as a random walk on a cubic lattice, and the radiation tracks hitting the chromatin are modeled as straight lines hitting lattice sites. Each track can make a cluster of DSBs on a chromosome.
Results: The results obtained replace conjectured DNA fragment-size distribution functions in the recently developed RLC formalism by more mechanistically motivated distributions. The discrete lattice algorithm reproduces features of current radiation experiments relevant to chromatin on large scales. It approximates the continuous formalism and experimental data with adequate precision. It was also found that assuming either fixed chromatin with correlations among different clusters of DSBs or moving chromatin with no such correlations gives virtually identical numerical predictions.
Availability: This set of subroutines comprises the DNABreak package available at the UC Berkeley mathematical radiobiology site: http://math.berkeley.edu/~sachs/ponomarev/artem.index.html
Contact: alp17@math.berkeley.edu
Abbreviations: Mbp, megabasepair; DSB, DNA double strand break; RLC, randomly-located-clusters Sachs et al. (1999);PBC, periodic boundary conditions Binder (1995); RW, random walk Sokal (1995); size, genomic content in Mbp.
Alignment of 3D structures of macromolecular assemblies
Authors: Lanzavecchia Salvatore , Cantele Francesca , Bellon Pier Luigi 
Published: July 2002

Abstract
Motivation: A number of macromolecular assemblies are being reconstructed in 3D from electron micrographs. The analysis yields a 3D matrix representing the protein density map. In reconstruction processes and in comparing the results of different experiments, it is often necessary to obtain all models oriented the same way in three dimensions. The problem is not trivial since there exist no 3D counterpart of correlation analysis used for 2D images. It is usually solved by time consuming trial and error algorithms.
Results: 3D density distributions can be brought to a ‘canonical’ orientation. The tensor of inertia of the distribution is determined and its eigenvectors are oriented along the coordinate axes. The method is fast and essentially free of reference. It is suitable for structures whose inertial axes do not completely degenerate as they do in icosahedral viruses or if symmetry is cubic. Applications are presented for asymmetric objects and for molecules possessing symmetry axes higher than twofold.
Implementation: The implementation simply requires the accumulation of the inertial tensor and its diagonalisation. Volume data rotation has been already illustrated in this journal by the authors.
Availability: The software is available upon request to the authors.
Contact: salvator@csmtbo.mi.cnr.it
* To whom correspondence should be addressed.
Extensive feature detection of N-terminal protein sorting
signals
Authors: Bannai Hideo , Tamada Yoshinori , Maruyama Osamu , Nakai Kenta , Miyano Satoru 
Published: July 2002

Abstract
Motivation: The prediction of localization sites of various proteins is an important and challenging problem in the field of molecular biology. TargetP, by Emanuelsson et al. (J. Mol. Biol. , 300, 1005–1016, 2000) is a neural network based system which is currently the best predictor in the literature for N-terminalsorting signals. One drawback of neural networks, however, is that it is generally difficult to understand and interpret how and why they make such predictions. In this paper, we aim to generate simple and interpretable rules as predictors, and still achieve a practical prediction accuracy. We adopt an approach which consists of an extensive search for simple rules and various attributes which is partially guided by human intuition.
Results: We have succeeded in finding rules whose prediction accuracies come close to that of TargetP, while still retaining a very simple and interpretable form. We also discuss and interpret the discovered rules.
Availability: An (experimental) web service usingrules obtained by our method is provided at http://hypothesiscreator.net/iPSORT/.
Contact: bannai@ims.u-tokyo.ac.jp
Multiple sequence alignment using partial order graphs
Authors: Lee Christopher , Grasso Catherine , Sharlow Mark F. 
Published: July 2002

Abstract
Motivation: Progressive Multiple Sequence Alignment (MSA) methods depend on reducing an MSA to a linear profile for each alignment step. However, this leads to loss of information needed for accurate alignment, and gap scoring artifacts.
Results: We present a graph representation of an MSA that can itself be aligned directly by pairwise dynamic programming, eliminating the need to reduce the MSA to a profile. This enables our algorithm (Partial Order Alignment (POA)) to guarantee that the optimal alignment of each new sequence versus each sequence in the MSA will be considered. Moreover, this algorithm introduces a new edit operator, homologous recombination, important for multidomain sequences. The algorithm has improved speed (linear time complexity) over existing MSA algorithms, enabling construction of massive and complex alignments (e.g. an alignment of 5000 sequences in 4 h on a Pentium II). We demonstrate the utility of this algorithm on a family of multidomain SH2 proteins, and on EST assemblies containing alternative splicing and polymorphism.
Availability: The partial order alignment program POA is available at http://www.bioinformatics.ucla.edu/poa.
Contact: leec@mbi.ucla.edu
* To whom correspondence should be addressed.
2 Current address: center for Applied Mathematics, 657 Rhodes Hall, Cornell University, Ithaca NY 14853, USA.
Environments of Crystallization and Compositional Diversity of Mauna Loa Xenoliths
Authors: GAFFNEY AMY M. 
Published: July 2002

Abstract
Two picrite flows from the SW rift zone of Mauna Loa contain xenoliths of dunite, harzburgite, lherzolite, plagioclase-bearing lherzolite and harzburgite, troctolite, gabbro, olivine gabbro, and gabbronorite. Textures and olivine compositions preclude a mantle source for the xenoliths, and rare earth element concentrations of xenoliths and clinopyroxene indicate that the xenolith source is not old oceanic crust, but rather a Hawaiian, tholeiitic-stage magma. Pyroxene compositions, phase assemblages and textural relationships in xenoliths indicate at least two different crystallization sequences. Calculations using the pMELTS algorithm show that the two sequences result from crystallization of primitive Mauna Loa magmas at 6 kbar and 2 kbar. Independent calculations of olivine Ni–Fo compositional variability in the plagioclase-bearing xenoliths over these crystallization sequences are consistent with observed olivine compositional variability. Two parents of similar bulk composition, but which vary in Ni content, are necessary to explain the olivine compositional variability in the dunite and plagioclase-free peridotitic xenoliths. Xenoliths probably crystallized in a small magma storage area beneath the rift zone, rather than the large sub-caldera magma reservoir. Primitive, picritic magmas are introduced to isolated rift zone storage areas during periods of high magma flux. Subsequent eruptions reoccupy these areas, and entrain and transport xenoliths to the surface.
Alkaline phosphatase from the hyperthermophilic bacterium T. maritima requires cobalt for activity
Authors: Wojciechowski Cheryl L. , Cardia James P. , Kantrowitz Evan R. 
Published: July 2002

AbstractThe hyperthermophilic bacterium Thermotoga maritima encodes a gene sharing sequence similarities with several known genes for alkaline phosphatase (AP). The putative gene was isolated and the corresponding protein expressed in Escherichia coli, with and without a predicted signal sequence. The recombinant protein showed phosphatase activity toward the substrate p‐nitrophenyl‐phosphate with a kcat of 16 s−1 and a Km of 175 μM at a pH optimum of 8.0 when assayed at 25°C. T. maritima phosphatase activity increased at high temperatures, reaching a maximum kcat of 100 s−1, with a Km of 93 μM at 65°C. Activity was stable at 65°C for >24 h and at 90°C for 5 h. Phosphatase activity was dependent on divalent metal ions, specifically Co(II) and Mg(II). Circular dichroism spectra showed that the enzyme gains secondary structure on addition of these metals. Zinc, the most common divalent metal ion required for activity in known APs, was shown to inhibit the T. maritima phosphatase enzyme at concentrations above 0.3 moles Zn: 1 mole monomer. All activity was abolished in the presence of 0.1 mM EDTA. The T. maritima AP primary sequence is 28% identical when compared with E. coli AP. Based on a structural model, the active sites are superimposable except for two residues near the E. coli AP Mg binding site, D153 and K328 (E. coli numbering) corresponding to histidine and tryptophan in T. maritima AP, respectively. Sucrose‐density gradient sedimentation experiments showed that the protein exists in several quaternary forms predominated by an octamer.
Cancer Risk in Children of Mothers With Epilepsy and High-Dose Folic Acid Use During Pregnancy
Authors: Vegrim Håkon Magne , Dreier Julie Werenberg , Alvestad Silje , Gilhus Nils Erik , Gissler Mika , Igland Jannicke , Leinonen Maarit K. , Tomson Torbjörn , Sun Yuelian , Zoega Helga , Christensen Jakob , Bjørk Marte-Helene 
Published: September 2022

ImportanceWomen with epilepsy are recommended high doses of folic acid before and during pregnancy owing to risk of congenital anomalies associated with antiseizure medications. Whether prenatal exposure to high-dose folic acid is associated with increases in the risk of childhood cancer is unknown.ObjectiveTo assess whether high-dose folic acid supplementation in mothers with epilepsy is associated with childhood cancer.Design, Setting, and ParticipantsObservational cohort study conducted with nationwide registers in Denmark, Norway, and Sweden from 1997 to 2017. Analyses were performed during January 10, 2022, to January 31, 2022. Mother-child pairs were identified in medical birth registers and linked with information from patient, prescription, and cancer registers, as well as with sociodemographic information from statistical agencies, and were categorized by maternal diagnosis of epilepsy. The study population consisted of 3 379 171 children after exclusion of 126 711 children because of stillbirth or missing or erroneous values on important covariates.ExposuresMaternal prescription fills for high-dose folic acid tablets (≥1 mg daily) between 90 days before pregnancy start and birth.Main Outcomes and MeasuresFirst onset of childhood cancer at younger than 20 years. Cox proportional hazards models were used to calculate adjusted hazard ratios with corresponding 95% CIs, adjusted for potential confounders. Cumulative incidence at aged 20 years was used as a measure of absolute risk.ResultsThe median age at the end of follow-up in the study population of 3 379 171 children was 7.3 years (IQR, 3.5-10.9 years). Among the 27 784 children (51.4% male) born to mothers with epilepsy, 5934 (21.4%) were exposed to high-dose folic acid (mean dose, 4.3 mg), with 18 exposed cancer cases compared with 29 unexposed, producing an adjusted hazard ratio of 2.7 (95% CI, 1.2-6.3), absolute risk if exposed of 1.4% (95% CI, 0.5%-3.6%), and absolute risk if unexposed of 0.6% (95% CI, 0.3%-1.1%). In children of mothers without epilepsy, 46 646 (1.4%) were exposed to high-dose folic acid (mean dose, 2.9 mg), with 69 exposed and 4927 unexposed cancer cases and an adjusted hazard ratio of 1.1 (95% CI, 0.9-1.4; absolute risk, 0.4% [95% CI, 0.3%-0.5%]). There was no association between children born to mothers with epilepsy who were prenatally exposed to antiseizure medications, but not high-dose folic acid, and an increased risk of cancer (absolute risk, 0.6%; 95% CI, 0.2%-1.3%).Conclusions and RelevancePrenatal exposure to high-dose folic acid was associated with increased risk of cancer in children of mothers with epilepsy.
DNA Immobilization
Authors: Wittmann Christine 
Published: September 2022

Abstract
Immobilized DNA is used for various purposes, starting with the development of DNA chips and microarrays, and reaching to methods for gene delivery and DNA‐based vaccines. The broad application range for all of these DNA‐based systems can still be found in the medical area (e.g. diagnostics and therapeutics, combined ‘theranostics’). Furthermore, in particular, DNA sensors are described to ensure food safety. Hence, strategies for DNA immobilization are described in this article, with a strong focus on immobilization chemistry. Various immobilization techniques (e.g. via physical adsorption, covalent, affinity binding, and matrix entrapment/encapsulation) are already well established. The ‘top‐down’ techniques can be distinguished from the ‘bottom‐up’ techniques that started at the beginning of DNA chip development. Suitable synthetic and artificial DNA structures (e.g. DNA origami) are developed and become adapted to existing DNA platforms. Surfaces used for DNA immobilization comprise carbonaceous materials, silica and silicon surfaces, gold, and metal surfaces, in addition to (bio)polymers. More recently, nanostructures for drug and gene delivery via liposomes and cationic polymers are on focus to generate therapeutic devices and vaccines. Overall, the main aim of this article is to provide an overview of the methods currently used for DNA immobilization regarding the variety of DNA and surface structures for different applications.
Prescribed performance control of Euler–Lagrange systems with input saturation and output constraints
Authors: Zhang Jie , Yang Jing , Zhang Zhongcai , Wu Yuqiang 
Published: September 2022

SummaryIn this article, we investigate the performance‐guaranteed tracking control for Euler–Lagrange (EL) systems subject to input saturation and output constraints. The prescribed performance and output constraints are first considered for EL systems with input saturation. Time‐varying barrier Lyapunov function (BLF) is employed to ensure constraint satisfaction. An adaptive control method for EL systems with saturation is put forward by adding a speed transformation into the BLF and designing auxiliary variables to the system. Subsequently, neural network is introduced to compensate for uncertainties of systems. In combination with backstepping technique, it is demonstrated that the controller not only guarantees that the tracking error converges to a preset compact set near zero at a specified decay rate, but also ensures that the output always stays within a given boundary. Simulation results further demonstrate the effectiveness of the proposed control scheme.