bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stress Survival of a Genetically Engineered Pseudomonas in Soil Slurries: Cytochrome P‐450cam‐Catalyzed Dehalogenation of Chlorinated Hydrocarbons
Authors: Rattan Kavita , Shanker Rishi , Khanna Purushottam , Atkins William M. 
Published: July 2002

AbstractBiological treatment of hazardous chemical wastes has potential as an effective, practical, and economically viable process in above the ground treatment systems that consist of both genetically engineered microorganisms (GEMs) and bioreactors with process control instruments to create ideal conditions for biodegradation. A strain of Pseudomonas putida coexpressing cytochrome P‐450cam and luciferase (lux) that provides both the reductive detoxification potential of the hemoprotein and a mechanism for its reduction in the absence of “normal” P‐450 redox partners was evaluated for its ability to survive and remain metabolically competent under nutrient stress in soil slurry microcosms. More than 74% of the cells of engineered Pseudomonas were culturable after 7 days of multiple nutrient (C,N,P) starvation. The diagnostic luminescence and carbon monoxide‐difference spectra for the two engineered traits could be detected in a significant fraction of the surviving population. The GEM could be revived after repeated desiccation and starvation using Luria broth, benzoate, or citrate as nutrients. Soil slurries inoculated with the GEM transformed hexachloroethane (HCE) to tetrachloroethylene (tetraCE) 8–10‐fold faster than uninoculated slurries. The GEM also transformed the insecticide, γ‐HCH (γ‐3,4,5,6‐hexachlorocyclhexene), to γ‐3,4,5,6‐tetrachlorocyclohexene (γtetraCH) in soil slurries under subatmospheric conditions. These results indicate that GEMs can be constructed with broad substrate range detoxification catalysts such as cytochrome P‐450 for remediation.
Global form perception: interactions between luminance and texture information
Authors: Van Der Zwan Rick , Badcock David R , Parkin Brent 
Published: July 2002

Purpose: This experiment reports the independence of first‐ and second‐order processing mechanisms in form perception. Methods: Symmetrical dot patterns were created using either luminance‐increment dots (luminance above background), or texture‐defined dots (average luminance equal to background). The proportion of luminance increment or texture dots defining each pattern was varied among fields of noise dots of the same type to determine symmetry detection thresholds. Results: Differences in detection thresholds were found between luminance‐ and texture‐defined patterns. Further, symmetry detection thresholds for luminance‐increment dot patterns were resistant to noise defined by dots of opposite contrast polarity (luminance‐decrement dots) or texture, while texture‐defined patterns were resistant to neither texture nor luminance‐decrement noise. Conclusions: These data suggest that symmetry perception, along with other types of form perception, use both first‐ and second‐order processing mechanisms. The data are compatible with a second‐order system that includes a negative half‐wave rectifying non‐linearity.
URINARY ALBUMIN IS A POWERFUL INDICATOR OF POOR HEALTH AND RISK FOR PREMATURE DEATH AMONG ABORIGINES (A)
Authors: We Hoy , Z Wang , P Baker , S McDonald , Jd Mathews , P. Van Buynder 
Published: July 2002

Background: Adult death rates of A in the NT are increased 3‐6‐fold. Albuminuria (high albumin/creatinine ratio, ACR, gm/mol) is also pervasive & progressive. In a study of one community, ACR correlated with indices of poor health, including early malnutrition, increasing BP, glycemia and dyslipidemia, heavy drinking, & infections, and it predicts not only renal failure, but natural death (McDonald et al CEPP 1999). We further develop this last association and discuss its implications.Methods: 763 adults (20+ yr)were screened & followed for 1‐8 yr (mean 4.3) yr, until death, renal failure, start of treatment or close‐out in April ‘98.Results: Twelve people started dialysis: all had ACR 100+ at baseline. There were 61 natural deaths; 21 were cardiovascular (CV), 40 others were due to lung disease, infections, liver disease, amyloidosis, cancer etc. Death rates (CV and nonCV) correlated with increasing baseline ACR over a continuum in nondiabetics and diabetics. People with baseline ACR < 3.4 had a death rate of 4.7./1000 person yr, the referent group, while hazard ratios for natural death of persons with baseline ACRs of 3.4‐33, 34‐99 and 100+ were 2.3 (95% CI 0.98‐5.3), 3.2 (1.3‐7.9) and 5.1(2.1‐12.8) respectively (p = .0029) after accounting for age and sex. The population attributable risk for natural death or dialysis marked by ACR 3.4+ was 0.67 (CI .37‐.83), and for natural death alone was 0.59 (.22‐.79) after accounting for age, sex, diabetes & hyper‐tension. The excess CV mortality of diabetics was entirely represented by their higher baseline ACRs.Conclusion:.
Much of the excess mortality in this group is predicted by albumin‐uria. Thus the kidney, whose maturation is very sensitive to early environment, and has vast vascular networks, high blood flow, high metabolic rate, and concentrating, phagocytic & endocrine functions, seems an exquisite marker of general health in A people. The ACR is a simple, reproducible, cheap test, which has wide potential application in definition of community health profiles and trends, and in defining diagnosis and prognosis. Initiation and titration of treatment might be guided by the ACR, and arrest of its progression results in dramatic reductions in natural deaths and renal failure.(Hoy et al, ANZSN '99).
Automatic numerical integration techniques for polyatomic molecules
Authors: Pérez-Jordá José M. , Becke Axel D. , San-Fabián Emilio 
Published: July 2002

We describe a new algorithm for the generation of 3D grids for the numerical evaluation of multicenter molecular integrals in density functional theory. First, we use the nuclear weight functions method of Becke [A. D. Becke, J. Chem. Phys. 88, 2547 (1988)] to decompose a multicenter integral ∫F(r) dr into a sum of atomic-like single-center integrals. Then, we apply automatic numerical integration techniques to evaluate each of these atomic-like integrals, so that the total integral is approximated as ∫F(r) dr≊∑iωiF(ri). The set of abscissas ri and weights ωi constitutes the 3D grid. The 3D atomic-like integrals are arranged as three successive monodimensional integrals, each of which is computed according to a recently proposed monodimensional automatic numerical integration scheme which is able to determine how many points are needed to achieve a given accuracy. When this monodimensional algorithm is applied to 3D integration, the 3D grids obtained adapt themselves to the shape of the integrand F(r), and have more points in more difficult regions.
The function F(r), which, upon numerical integration, yields the 3D grid, is called the generating function of the grid. We have used promolecule densities as generating functions, and have checked that grids generated from promolecule densities are also accurate for other integrands. Our scheme is very reliable in the sense that, given a relative tolerance ε, it generates 3D grids which are able to approximate multicenter integrals with relative errors smaller than ε for all the molecules tested in this work. Coarser or finer grids can be obtained using greater or smaller tolerances. For a series of 21 molecules, the average number of points per atom for ε=2.0⋅10−3, ε=2.0⋅10−4, ε=2.0⋅10−5, ε=2.0⋅10−6, and ε=2.0⋅10−7 is respectively 3141 (2.9⋅10−4), 10271 (2.4⋅10−5), 27184 (3.1⋅10−6), 72266 (1.9⋅10−7), and 164944 (5.2⋅10−9) (in parentheses are the maximum errors obtained when integrating the density). It is possible to reduce the number of points in the grid by taking advantage of molecular symmetry. It seems that our method achieves a given accuracy with fewer points than other recently proposed methods.
Reaction of Cl with vibrationally excited CH4 and CHD3: State-to-state differential cross sections and steric effects for the HCl product
Authors: Simpson William R. , Rakitzis T. Peter , Kandel S. Alex , Orr-Ewing Andrew J. , Zare Richard N. 
Published: July 2002

The mechanism for the reaction of atomic chlorine with vibrationally excited methane is investigated by measurement of correlated state and scattering distributions using the method of core extraction (see preceding paper). Laser photolysis of molecular chlorine creates monoenergetic chlorine atoms (≳98% Cl 2P3/2) that react with vibrationally excited methane molecules prepared by linearly polarized infrared laser excitation. The resulting HCl product population distributions are determined by (2+1) resonance-enhanced multiphoton ionization (REMPI), and the differential cross section for each product rovibrational state is measured by core extraction. Approximately 30% of the product is formed in HCl(υ=1,J) with a cold rotational distribution; the remaining population is formed in HCl(υ=0,J) and is more rotationally excited. We observe a rich variation of the scattered flux that is dependent on the internal-energy state of the product. The HCl(υ=1) product is sharply forward scattered for low J and becomes nearly equally forward–backward scattered for high J; the HCl(υ=0,J) product is back and side scattered. The reactions of Cl with C–H stretch-excited methane (CH4) and C–H stretch-excited CHD3 are found to have similar angular and internal-state distributions. Observation of the spatial anisotropy of the HCl(υ=0, J=3) product shows that significant vibrational excitation of the methyl fragment does not occur.
The measured spatial anisotropy is most consistent with a model in which backscattered HCl(υ=0, J=3) is formed in coincidence with slight methyl vibrational excitation and the forward-scattered HCl(υ=0, J=3) is formed in coincidence with no methyl excitation. The approach of the attacking chlorine atom with respect to the C–H stretch direction can be varied by rotating the plane of polarization of the infrared excitation. A marked steric effect is observed in which Cl atoms approaching perpendicular to the C–H stretch preferentially yield forward-scattered HCl(υ=1) product. On the other hand, the reaction is weakly dependent on the rotational quantum state of CH4(υ3=1,J), and on the rotational polarization. The data are consistent with a model that has a widely open ‘‘cone of acceptance’’ in which the impact parameter controls the internal-state and scattering distributions of the HCl product.
Computational space reduction and parallelization of a new clustering approach for large groups of sequences.
Authors: Trelles O , Andrade M A , Valencia A , Zapata E L , Carazo J M 
Published: July 2002

Abstract
MOTIVATION: The explosive growth of the biological sequences databases stimulated by genome projects has modified the framework of several applications in the biological sequence analysis area. In most cases, this new scenario is characterized by studies on large sets of sequences, suggesting the need for effective and automatic methods for their clustering. A more effective clustering of the database could be followed by the application of common family analysis schemes to the groups so formed. RESULTS: In this work, we present a new strategy to reduce the computational cost associated with the clustering of large sets of sequences which are expected to contain several families. The strategy is based on the grouping of the sequences into families by using a dynamic threshold on a pairwise sequence similarity criterion. Routine clustering of large data sets can now be done very efficiently. The method developed here achieves a computational space reduction of about an order of magnitude over more traditional ones of all-versus-all comparisons. The outcome of this approach produces family groupings that reproduce closely already accepted biological results. Our work includes a parallel implementation for distributed memory multiprocessors with a dynamic scheduling strategy for performance optimization. AVAILABILITY: By anonymous ftp at ftp.ac.uma.es (/pub/ots/pCluster directory), or from our Web site http://www.cnb. uam.es/www/software/software_index.html CONTACT: ots@ac.uma.es
A metadata approach to query interoperation between molecular biology databases.
Authors: Cheung K H , Nadkarni P M , Shin D G 
Published: July 2002

Abstract
MOTIVATION: Molecular biology databases have been proliferating rapidly. Their heterogeneity and complexity pose a great challenge to efforts in database interoperation. To minimize the efforts of interoperating heterogeneous databases, it is useful to develop a system that lets a user of a particular genomic database access another related database as if the latter is structurally similar to the former. RESULTS: We extend a structurally simple model-the entity-attribute-value (EAV) model-to describe uniformly metadata relating to individual databases. Such metadata, which are necessary for performing database comparisons, include descriptions of primitive database objects (including entities, attributes, domain values and entity relationships) and specification of correspondences among the database objects. We show how to decompose SQL queries and map them from one database to another based on the EAV representation of the basic database objects. A prototype system is implemented to demonstrate query interoperation between two chromosome map databases. AVAILABILITY: Freely available (Cold Fusion source code and an Access database containing the mapping knowledge) upon request from the author. CONTACT: kei.cheung@yale.edu
Short‐chain dehydrogenase/reductase (SDR) relationships: A large family with eight clusters common to human, animal, and plant genomes
Authors: Kallberg Yvonne , Oppermann Udo , Jörnvall Hans , Persson Bengt 
Published: July 2002

AbstractThe progress in genome characterizations has opened new routes for studying enzyme families. The availability of the human genome enabled us to delineate the large family of short‐chain dehydrogenase/reductase (SDR) members. Although the human genome releases are not yet final, we have already found 63 members. We have also compared these SDR forms with those of three model organisms: Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana. We detect eight SDR ortholog clusters in a cross‐genome comparison. Four of these clusters represent extended SDR forms, a subgroup found in all life forms. The other four are classical SDRs with activities involved in cellular differentiation and signalling. We also find 18 SDR genes that are present only in the human genome of the four genomes studied, reflecting enzyme forms specific to mammals. Close to half of these gene products represent steroid dehydrogenases, emphasizing the regulatory importance of these enzymes.
Evaluating the success of upland hay meadow restoration in the North Pennines, United Kingdom, using green hay transfer
Authors: Starr‐Keddle Ruth E. 
Published: February 2022

Abstract

Traditionally managed mesotrophic species‐rich upland hay meadows conforming to the National Vegetation Classification (NVC) MG3b are one of the rarest grassland types in the United Kingdom, with substantial declines in botanical diversity over the last 50 years. Intensive spring grazing, earlier cut dates and increases in soil fertility cause a decline in characteristic positive indicator species in MG3b meadows, shifting communities from species‐rich MG3b, to NVC MG6 meadows, and finally to species‐poor NVC MG7 meadows.

The North Pennines Area of Outstanding Natural Beauty (AONB) Partnership's Hay Time project aimed to improve the knowledge of upland hay meadows, and to investigate the success of seed addition of key positive indicator species. A landscape‐scale restoration programme was undertaken between 2006 and 2012, harvesting seed from 82 species‐rich donor meadows and spreading seed onto 89 receptor meadows (222.82 ha). Seed was harvested as green hay, using two types of donors: MG6 (classed as restoration, with species such as Rhinanthus minor) and MG3b (classed as enhancement, with species such as Geranium sylvaticum). All 89 meadows were monitored, with a baseline botanical survey and a repeat survey 3–5 years after seed addition. In addition, 41 meadows that did not have seed addition were monitored (controls).

Species richness, diversity and floristic composition improved in 77 meadows 3–5 years after seed addition. Eighteen plant species had an increase in frequency in the receptor meadows but did not increase in frequency in the control meadows. The most successful were eight positive indicators which were annuals or fast‐growing perennial plants (Anthoxanthum odoratum, Euphrasia spp., Myosotis discolor, Plantago lanceolata, Ranunculus acris, R minor, Trifolium dubium and Trifolium pratense). However, rarer characteristic MG3b plants such as Alchemilla spp., G. sylvaticum and Cirsium heterophyllum showed little signs of establishing.

Botanical evidence is demonstrating that seed addition using green hay is a successful way of restoring meadows to an MG6 community. What is now needed is an effective method to establish characteristic MG3b plants. Hand‐collecting seeds and establishing plug plants, alongside seed addition and maintaining traditional management practises, is one possible way forward.
Wide‐Bandgap Double Perovskites with Multiple Longitudinal‐Optical Phonon Scattering
Authors: Wang Liangling , Zheng Wei , Vitale Francesco , Zhang Xiangzhou , Li Xiuling , Ji Yanchen , Liu Zhen , Ghaebi Omid , Plass Christian T. , Domes Robert , Frosch Torsten , Soavi Giancarlo , Wendler Elke , Zhang Yuhai , Ronning Carsten 
Published: February 2022

AbstractAlloyed lead‐free double perovskites display intense photoluminescence, are environmentally friendly, and their devices show long‐term operation. Thanks to these properties, which make them excellent warm white‐emitting materials, they have recently received great attention in lighting applications. An important factor to tune the optical properties of alloyed lead‐free double perovskites is the presence of self‐trapped excitons. Here, it is demonstrated that in lead‐free double perovskites, the strong electron–phonon coupling plays a crucial role in the generation of self‐trapped excitons. The strong electron–phonon coupling is confirmed by a large Huang–Rhys factor and by the presence of multiphonon transitions. In particular, sharp emission lines superimposed on the broad photoluminescence emission band of one of these samples (Cs2Ag0.6Na0.4InCl6 0.5%Bi) are observed; these are due to the strong coupling of longitudinal‐optical phonons with excited electronic states caused by the tetragonally distorted AgCl6 octahedrons. Such a strong coupling of longitudinal‐optical phonons to electrons can effectively modulate the photophysical properties of alloyed double perovskites, and its understanding is, thus, of paramount importance for the design of future optoelectronic devices.
Screening and enrollment of underrepresented ethnocultural and educational populations in the Alzheimer's Disease Neuroimaging Initiative (ADNI)
Authors: Ashford Miriam T. , Raman Rema , Miller Garrett , Donohue Michael C. , Okonkwo Ozioma C. , Mindt Monica Rivera , Nosheny Rachel L. , Coker Godfrey A. , Petersen Ronald C. , Aisen Paul S. , Weiner Michael W. ,   the Alzheimer's Disease Neuroimaging Initiative
Published: February 2022

AbstractIntroductionAn analysis of the ethnocultural and socioeconomic composition of Alzheimer's Disease Neuroimaging Initiative (ADNI) participants is needed to assess the generalizability of ADNI data to diverse populations.MethodsADNI data collected between October 2004 and November 2020 were used to determine ethnocultural and educational composition of the sample and differences in the following metrics: screening, screen fails, enrollment, biomarkers.ResultsOf 3739 screened individuals, 11% identified as being from ethnoculturally underrepresented populations (e.g., Black, Latinx) and 16% had <12 years of education. Of 2286 enrolled participants, 11% identified as ethnoculturally underrepresented individuals and 15% had <12 years of education. This participation is considerably lower than US Census data for adults 60+ (ethnoculturally underrepresented populations: 25%; <12 years of education: 4%). Individuals with <12 years of education failed screening at a higher rate.DiscussionOur findings suggest that ADNI results may not be entirely generalizable to ethnoculturally diverse and low education populations.
Study on dust occurrence and transportation related to boundary layer height in Northwest China
Authors: Tan Ziyuan , Ma Minjin , Huang Wanlong , Tan Changrong , Zhao Zhenzhu , Ding Fan 
Published: February 2022

AbstractBoundary layer development has a significant influence on dust emission and transportation. The effects of surface heat flux on distribution of dust related to BLH (boundary layer height) during a dust event in Northwest China are discussed by numerical simulation. The results show that: the dust emissions start in Dunhuang and strengthen in Minqin with large dust emission fluxes (as high as 3000 μg m−2 s−1) and surface wind speed (up to 20 m s−1). The dust at the early stage mainly concentrates below 500 m above the ground, then lifts over 3000 m above the ground at the strengthening stage, and the concentration in high value center is more than 24,000 μg m−3 at the dust source Dunhuang. The high dust concentration in Minqin maintains at about 1000 m above the ground. Weak dust emission in Minqin makes the dust concentration near the ground less than that in the upper air. The BLH in the high dust concentration center is higher than that in the surrounding area at the emission stage in Dunhuang. Sensitivity experiment with turning off surface heat flux shows obvious decrease of the dust concentration in Dunhuang, with more than four times reduction of the surface dust concentration. The BLH near the high dust concentration area reduces significantly in the sensitivity experiment. However, the gap between the two experiments reduces with the dust development. The BLH in the sensitivity experiment has small spatial differences with uniform distribution in Dunhuang. It means that the thermodynamic contribution is main reason for the distribution differences. The two experiments in Minqin also show that the height of high concentration dust has a difference of about 500 m. The dust lifts with the boundary layer development, but shows different distribution characteristics and influencing factors between Dunhuang and Minqin.
Does social distancing affect the processing of brand logos?
Authors: D'Ascenzo Stefania , Scerrati Elisa , Villani Caterina , Galatolo Renata , Lugli Luisa , Nicoletti Roberto 
Published: February 2022

AbstractSocial distancing and isolation have been imposed to contrast the spread of COVID‐19. The present study investigates whether social distancing affects our cognitive system, in particular the processing of different types of brand logos in different moments of the pandemic spread in Italy. In a size discrimination task, six different logos belonging to three categories (letters, symbols, and social images) were presented in their original format and spaced. Two samples of participants were tested: one just after the pandemic spread in Italy, the other one after 6 months. Results showed an overall distancing effect (i.e., spaced stimuli are processed slower than original ones) that interacted with the sample, revealing a significant effect only for participants belonging to the second sample. However, both groups showed a distancing effect modulated by the type of logo as it only emerged for social images. Results suggest that social distancing behaviors have been integrated in our cognitive system as they appear to affect our perception of distance when social images are involved.