bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prävention – eine Notwendigkeit in einer Gesellschaft des langen Lebens
Authors: Lehr Ursula 
Published: January 2012

Einleitung
Wir werden älter als es Generationen vor uns waren und sind dabei gesünder und kompetenter. Das verdanken wir gesundheitsförderlichen Umweltbedingungen, den Fortschritten der Medizin und Medizintechnik, der Pharmazie, aber auch einem gesünderen Lebensstil. Die zunehmende Langlebigkeit und die altersstrukturellen Veränderungen unterstreichen die Forderung, alles zu tun, um möglichst gesund und kompetent alt zu werden, um möglichst selbständig und selbstbestimmt sein Leben auch als 80 oder 90-Jähriger führen zu können. Dies ist nur möglich durch einen Ausbau von Prävention auf nahezu allen Gebieten des Lebens. Sowohl als Einzelner in der Individual-, als auch als Gesellschaft in der Verhältnisprävention.
Informierte Entscheidung bei Darmkrebsfrüherkennung: Ausweg aus der Unmündigkeit
Authors: Steckelberg Anke , Bunge Martina 
Published: January 2012

Einleitung
Bürger haben ein Recht auf Evidenz-basierte Informationen als Voraussetzung für informierte Entscheidungen. In einer randomisiert-kontrollierten Studie wurden die Effekte einer Evidenz-basierten Information zur Darmkrebsfrüherkennung mit einer Standardinformation verglichen. Der primäre Endpunkt war die informierte Entscheidung. 1586 Versicherte der Gmündener Ersatzkasse (GEK) wurden randomisiert. Die Evidenz-basierte Information führte signifikant häufiger zu informierten Entscheidungen.
Initial Recovery Trajectories Among Patients With Hip Fracture: A Conceptual Approach to Exploring Comparative Effectiveness in Postacute Care
Authors: Aronow Harriet U. , Sharkey Phoebe , Siebens Hilary C. , Horn Susan D. , Smout Randall J. , DeJong Gerben , Munin Michael C. , Radnay Craig S. 
Published: January 2012

ObjectiveTo assess whether clusters of patients with hip fracture and with distinct initial recovery trajectories (IRT) could be identified by using practice‐based evidence data and to examine the validity of these data.DesignAnalysis of multisite prospective observational cohort study database.SettingEighteen skilled nursing and inpatient rehabilitation facilities.PatientsPatients with hip fractures (N = 226) treated with joint replacement and admitted to skilled nursing or inpatient rehabilitation facilities, subset (n = 85), with telephone follow‐up results approximately 8 months after rehabilitation discharge. Patients' ages were 76.8 ± 11.4 years; the majority were women (78%) and white (87%).MethodsMeasurements included medical severity by using the Comprehensive Severity Index and functional levels by using Functional Independence Measure (FIM). The IRT was calculated for each patient as the rate of change in function from the time of surgery to rehabilitation admission. We used cluster analysis to partition patients into subsets that shared common IRT scores. Validity was explored by comparing subgroups across patient characteristics and treatment patterns. Significance was defined as P ≤ .05.Main Outcomes MeasurementsIRT grouping, Comprehensive Severity Index, FIM, discharge location, living location at follow‐up.ResultsWe identified 3 patient clusters with differentiated IRT scores: group 1: 4.96 ± 2.45 (range, 0.4‐8.6) FIM point change per day; group 2: 12.42 ± 2.51 (range, 8.9‐17.0); group 3: 26.80 ± 13.78 (range, 17.5‐70.0). Clinical group validation was established from statistically different Comprehensive Severity Index scores on admission; FIM scores at admission, discharge, and follow‐up; and discharge and 8‐month living settings. Calculation of IRT recovery curves by using FIM scores and associated time in days through logarithmic regression curves confirmed each group's IRT remained distinct through rehabilitation and follow‐up.ConclusionsThe IRT concept appears to be valid in patients with hip fracture who were treated with hip arthroplasty, and may assist in evaluating and comparing the effectiveness of postacute rehabilitation services.
Results of U-Pb dating of zircon and baddeleyite from the Noril’sk-1 ultramafic-mafic intrusion (Russia)
Authors: Malitch K.N. , Badanina I.Yu. , Belousova E.A. , Tuganova E.V. 
Published: January 2012

Abstract
We present for the first time the mineralogical and isotope-geochemical particularities of zircon and baddeleyite from various rocks of the economic ore-bearing Noril’sk-1 intrusion located in the northwestern part of the Siberian platform. The ultramafic-mafic Noril’sk-1 intrusion hosts one of the world’s major economic platinum-group-element (PGE)-Cu-Ni sulphide deposits.
A detailed study of crystal morphology and internal structure identify four zircon populations, characterized by different U-Pb (SHRIMP-II) ages. The U-Pb ages of baddeleyite and the defined zircon populations cover a significant time span (from 290 ± 2.8 to 226.7 ± 0.9 Ma). The established U-Pb ages imply that crystallization of baddeleyite and zircon populations corresponds to several stages of protracted evolution of the ore-forming magmatic system (290 ± 2.8, 261.3 ± 1.6, 245.7 ± 1.1, 236.5 ± 1.8, and 226.7 ± 0.9 Ma, respectively) that served as the favorable factor for accumulation of magmas and ores of unique scales and concentrations.
The Early Proterozoic Primorskii complex of rapakivi granites (western Cisbaikalia): geochemistry, crystallization conditions, and ore potential
Authors: Savel’eva V.B. , Bazarova E.P. 
Published: January 2012

Abstract
The Primorskii complex in western Cisbaikalia, which formed in the Early Proterozoic at the postcollisional stage in the Siberian craton evolution, comprises rapakivi granites, equigranular biotitic and leucocratic granites, and alaskites. It is a K-rich granitoid assemblage with a medium and high alkalinity, whose F, Ba, Pb, REE, Zr, Th, and Zn contents exceed the clarkes. The complex consists of three plutons: Bugul’deika–Anga, Ulan-Khan, and Trekhgolovyi, which formed in two intrusive stages. The evolution of the main-stage composition was marked by an increase in silica content, with a similtaneous increase in agpaite and Fe contents and a decrease in Na2O/K2O. The Bugul’deika–Anga and Trekhgolovyi plutons are the most contrasting in composition and crystallization conditions. The former originated from a weakly differentiated water-undersaturated melt, which crystallized at medium depths (Ptot = 3–4 kbar). The crystallization was unaccompanied by considerable accumulation of granitophile elements (the concentration index (CI) of granitophile elements is ~3) in the leucogranites, except the alaskites, which crystallized in the upper part of the magma chamber (CI = 5). The Trekhgolovyi pluton originated from a leucogranitic melt enriched in Cs, Li, Rb, and Sn, which crystallized at a low Ptot (~2 kbar). The average contents of some elements in the leucogranites are higher than their clarkes in Ca-poor granites: by a factor of 4 for Sn, 3.8 for Th, 2.7 for Rb, 2.5 for Cs, and 2 for F (CI ≈ 9). The final-stage granites in the Trekhgolovyi pluton are associated with quartz-muscovitic (±topaz, fluorite) greisens, which contain cassiterite, columbite, ilmenorutile, wolframite, bismuthinite, and other minerals. The data suggest that the Trekhgolovyi pluton has a Sn potential.
The U-Pb geochronology of the Mukhal alkaline massif (western Transbaikalia)
Authors: Doroshkevich A.G. , Ripp G.S. , Sergeev S.A. , Konopel’ko D.L. 
Published: January 2012

Abstract
We present results of U-Pb (SHRIMP II) geochronological study of the rocks of the Mukhal alkaline massif in the Vitim alkaline province, western Transbaikalia. The available K-Ar and Rb-Sr dates for the alkaline rocks (Saizhen complex) of the Vitim province, including the Mukhal massif, vary over a broad range of values. The obtained age of crystallization of the Mukhal urtites refines the time when the regional alkaline magmatism began. The age of zircons and magmatic processes within the Barguzin area (315–275 Ma) is close to the peak of main events, which occurred between 295 and 275 Ma. These processes took place at the early stage of evolution of the Late Paleozoic rift system in Central Asia, whose activity was associated with the activity of mantle superplume.
The geoelectric structure at the site of “Crystal” underground nuclear explosion (Western Yakutia) from TEM data
Authors: Kozhevnikov N.O. , Antonov E.Yu. , Artamonova S.Yu. , Plotnikov A.E. 
Published: January 2012

Abstract
The resistivity pattern at the site of the “Crystal” underground nuclear explosion (Daldyn–Alakit district of Yakutia) of 1974 which led to an accident has been imaged using TEM data. The local background pattern corresponds to a three-or four-layer earth with a conductor at the base. The uppermost layer, with a resistivity of tens to hundreds of ohm · m, has its bottom at 190–260 m asl and consists of perennially frozen Late Cambrian carbonates. The resistivity structure of shallow subsurface at the blast epicenter remained unperturbed though being subject to mechanic and thermal effects. The bottom of the second layer is at 20 to 190 m below the sealevel and its resistivity is 7–10 ohm · m. It is composed of frost-bound and unfrozen cold rocks that belong to a Late Cambrian water-bearing sequence (an aquifer). The third and fourth layers make up the conducting base of the section (0.2–1.4 ohm · m) while the conductor’s top matches the table of a Middle Cambrian aquifer. Anomalous transient response at the site prompts the existence of a local conductor possibly produced by highly saline waters in the containment cavity and in deformed rocks around it. However, the resistivity is too low (0.02 ohm · m) to be accounted for by any model available at the present state of knowledge. Another problem is to explain how the brines circulating at large depths may have reached the explosion cavity and the surrounding strained zones. The study has provided a first idea of the background resistivity distribution and its UNE-induced changes.
High-temperature conductivity of magnetite ores in relation to their genesis and mineral composition (by the example of the Goroblagodatskoe skarn-magnetite deposit)
Authors: Bakhterev V.V. , Kuznetsov A.Zh. 
Published: January 2012

Abstract
Samples of magnetite ores of different parageneses and mineral compositions from the Goroblagodatskoe skarn-magnetite deposit were studied by physical and mineralogo-petrographic methods. Electrical-resistance curves were obtained for an ore containing 80–90% magnetite for the temperature range 20–800 ºC. Three groups of samples were recognized according to the pattern of temperature curves and electrical resistance: sulfide-free, sulfide-containing (pyrrhotite), and variolitic ores. The parameters of high-temperature conductivity (activation energy E0 and coefficient of electrical resistance logR0) have been determined. A linear relationship between E0 and logR0 (logR0= a – bE0) has been established for magnetite ores of all mineral types. The coefficient a varies from 1.92 to 4.80 depending on the type and mineral composition of magnetite ores. The coefficient b is nearly constant for all studied samples, 6.65. The figurative points of the samples in the E0–logR0 coordinates lie in the field bounded by the straight lines logR0= 4.80 – 6.65E0 and logR0= 1.92 – 6.65E0. The samples of magnetite ores of the skarn and hydrosilicate paragenesis with visible pyrrhotite inclusions and samples of variolitic ores form an individual group in the above field. Within the group, the ores are also subdivided into garnet-magnetite (skarn paragenesis), epidote-chlorite-magnetite (hydrosilicate paragenesis), pyroxene-magnetite, and orthoclase-magnetite (variolitic ores).
Determinants of Producers' Participation in Agricultural Cooperatives: Evidence from Northern China
Authors: Zheng Shi , Wang Zhigang , Awokuse Titus O. 
Published: January 2012

AbstractAgricultural producer cooperatives are of great significance to the development of agricultural productivity and can provide improved economic welfare benefits to farmers. However, such organizations have not been well‐developed in China. While China's new Cooperatives Law of 2007 has generated interest among scholars, very few empirical analyses have focused on the role of cooperatives in China's agricultural sector. The main objective of this study is to investigate the determinants of farmers' perception and their decision to participate in cooperatives, using a unique dataset from recently collected survey data of farming households in China's Jilin Province. The empirical results from probit and logit regression models suggest that educational attainment, risk comfort level, farm expansion, operational costs, geographic location and crop types are significant factors that influence producers' perception of cooperatives, as well as their participation behavior.
Robust rank aggregation for gene list integration and meta-analysis
Authors: Kolde Raivo , Laur Sven , Adler Priit , Vilo Jaak 
Published: January 2012

Abstract
Motivation: The continued progress in developing technological platforms, availability of many published experimental datasets, as well as different statistical methods to analyze those data have allowed approaching the same research question using various methods simultaneously. To get the best out of all these alternatives, we need to integrate their results in an unbiased manner. Prioritized gene lists are a common result presentation method in genomic data analysis applications. Thus, the rank aggregation methods can become a useful and general solution for the integration task.
Results: Standard rank aggregation methods are often ill-suited for biological settings where the gene lists are inherently noisy. As a remedy, we propose a novel robust rank aggregation (RRA) method. Our method detects genes that are ranked consistently better than expected under null hypothesis of uncorrelated inputs and assigns a significance score for each gene. The underlying probabilistic model makes the algorithm parameter free and robust to outliers, noise and errors. Significance scores also provide a rigorous way to keep only the statistically relevant genes in the final list. These properties make our approach robust and compelling for many settings.
Availability: All the methods are implemented as a GNU R package RobustRankAggreg, freely available at the Comprehensive R Archive Network http://cran.r-project.org/.
Contact: vilo@ut.ee
Supplementary information Supplementary data are available at Bioinformatics online.
BOCTOPUS: improved topology prediction of transmembrane β barrel proteins
Authors: Hayat Sikander , Elofsson Arne 
Published: January 2012

Abstract
Motivation: Transmembrane β barrel proteins (TMBs) are found in the outer membrane of Gram-negative bacteria, chloroplast and mitochondria. They play a major role in the translocation machinery, pore formation, membrane anchoring and ion exchange. TMBs are also promising targets for antimicrobial drugs and vaccines. Given the difficulty in membrane protein structure determination, computational methods to identify TMBs and predict the topology of TMBs are important.
Results: Here, we present BOCTOPUS; an improved method for the topology prediction of TMBs by employing a combination of support vector machines (SVMs) and Hidden Markov Models (HMMs). The SVMs and HMMs account for local and global residue preferences, respectively. Based on a 10-fold cross-validation test, BOCTOPUS performs better than all existing methods, reaching a Q3 accuracy of 87%. Further, BOCTOPUS predicted the correct number of strands for 83% proteins in the dataset. BOCTOPUS might also help in reliable identification of TMBs by using it as an additional filter to methods specialized in this task.
Availability: BOCTOPUS is freely available as a web server at: http://boctopus.cbr.su.se/. The datasets used for training and evaluations are also available from this site.
Contact: arne@bioinfo.se
Supplementary information: Supplementary data are available at Bioinformatics online.
Roundup 2.0: enabling comparative genomics for over 1800 genomes
Authors: DeLuca Todd F. , Cui Jike , Jung Jae-Yoon , St. Gabriel Kristian Che , Wall Dennis P. 
Published: January 2012

Abstract
Summary: Roundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based on any group of genomes. Annotated query results may be viewed in a variety of ways including as clusters of orthologs and as phylogenetic profiles. Genomic results may be downloaded in formats suitable for functional as well as phylogenetic analysis, including the recent OrthoXML standard. In addition, gene IDs can be retrieved using FASTA sequence search. All source code and orthologs are freely available.
Availability: http://roundup.hms.harvard.edu
Contact: dpwall@hms.harvard.edu; todd_deluca@hms.harvard.edu
nEASE: a method for gene ontology subclassification of high-throughput gene expression data
Authors: Chittenden Thomas W. , Howe Eleanor A. , Taylor Jennifer M. , Mar Jessica C. , Aryee Martin J. , Gómez Harold , Sultana Razvan , Braisted John , Nair Sarita J. , Quackenbush John , Holmes Chris 
Published: January 2012

Abstract
Summary: High-throughput technologies can identify genes whose expression profiles correlate with specific phenotypes; however, placing these genes into a biological context remains challenging. To help address this issue, we developed nested Expression Analysis Systematic Explorer (nEASE). nEASE complements traditional gene ontology enrichment approaches by determining statistically enriched gene ontology subterms within a list of genes based on co-annotation. Here, we overview an open-source software version of the nEASE algorithm. nEASE can be used either stand-alone or as part of a pathway discovery pipeline.
Availability: nEASE is implemented within the Multiple Experiment Viewer software package available at http://www.tm4.org/mev.
Contact: cholmes@stats.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Mining and evaluation of molecular relationships in literature
Authors: Senger Christian , Grüning Björn A. , Erxleben Anika , Döring Kersten , Patel Hitesh , Flemming Stephan , Merfort Irmgard , Günther Stefan 
Published: January 2012

Abstract
Motivation: Specific information on newly discovered proteins is often difficult to find in literature. Particularly if only sequences and no common names of proteins or genes are available, preceding sequence similarity searches can be crucial for the process of information collection. In drug research, it is important to know whether a small molecule targets only one specific protein or whether similar or homologous proteins are also influenced that may account for possible side effects.
Results: prolific (protein-literature investigation for interacting compounds) provides a one-step solution to investigate available information on given protein names, sequences, similar proteins or sequences on the gene level. Co-occurrences of UniProtKB/Swiss-Prot proteins and PubChem compounds in all PubMed abstracts are retrievable. Concise ‘heat-maps’ and tables display frequencies of co-occurrences. They provide links to processed literature with highlighted found protein and compound synonyms. Evaluation with manually curated drug–protein relationships showed that up to 69% could be discovered by automatic text-processing. Examples are presented to demonstrate the capabilities of prolific.
Availability: The web-application is available at http://prolific.pharmaceutical-bioinformatics.de and a web service at http://www.pharmaceutical-bioinformatics.de/prolific/soap/prolific.wsdl.
Contact: stefan.guenther@pharmazie.uni-freiburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Application of canonical correlation analysis for identifying viral integration preferences
Authors: Gumus Ergun , Kursun Olcay , Sertbas Ahmet , Ustek Duran 
Published: January 2012

Abstract
Motivation: Gene therapy aims at using viral vectors for attaching helpful genetic code to target genes. Therefore, it is of great importance to develop methods that can discover significant patterns around viral integration sites. Canonical correlation analysis is an unsupervised statistical tool that is used to describe the relations between two related views of the same semantic object, which fits well for identifying such salient patterns.
Results: Proposed method is demonstrated on a sequence dataset obtained from a study on HIV-1 preferred integration regions. The subsequences on the left and right sides of the integration points are given to the method as the two views, and statistically significant relations are found between sequence-driven features derived from these two views, which suggest that the viral preference must be the factor responsible for this correlation. We found that there are significant correlations at x=5 indicating a palindromic behavior surrounding the viral integration site, which complies with the previously reported results.
Availability: Developed software tool is available at http://ce.istanbul.edu.tr/bioinformatics/hiv1/
Contact: egumus@istanbul.edu.tr
Common large-scale responses to climate and fishing across Northwest Atlantic ecosystems
Authors: Shackell Nancy L. , Bundy Alida , Nye Janet A. , Link Jason S. 
Published: January 2012

Abstract
Shackell, N. L., Bundy, A., Nye, J. A., and Link, J. S. 2012. Common large-scale responses to climate and fishing across Northwest Atlantic ecosystems. – ICES Journal of Marine Science, 69: 151–152. Investigating whether there were common biological responses to climate and fishing across seven Northwest Atlantic ecosystems, a minimum/maximum autocorrelation factor analysis of biological indicators for each region revealed a common primary multivariate trend of a rapid change during the 1980s and early 1990s. There was a strong common pattern in the biological indicators responsible for the primary multivariate temporal trend in the five more northerly regions: an increase in the abundance of phytoplankton, an increase in biomass at mid-trophic levels, and a decline in predatory groundfish size. The common associations between patterns and drivers were fishing indices and the Atlantic Multidecadal Oscillation, but all associations weakened when co-varying drivers were held constant. The results are consistent with known long-term effects of intense fishing, such as a decline in average fish size and changes in species composition. Less fishing pressure has allowed some regions to recover to former predatory biomass levels since the late 1990s, but the bulk of the biomass consists of fewer species. However, fishing was not the only driver, and a more mechanistic understanding of how the climate affects lower trophic levels is needed to contextualize climate effects in heavily fished ecosystems.