bluuebunny/crossref_metadata_2025_split huggingface dataset:
The architecture of collaboration
Authors: Fjeldstad Øystein D. , Snow Charles C. , Miles Raymond E. , Lettl Christopher 
Published: April 2012

AbstractFirms increasingly face competitive pressures related to rapid and continuous adaptation to a complex, dynamic, and highly interconnected global environment. Pressing challenges include keeping pace with shorter product life cycles, incorporating multiple technologies into the design of new products, cocreating products and services with customers and partners, and leveraging the growth of scientific and technical knowledge in many sectors. In response, we observe experimentation with new organization designs that are fundamentally different from existing forms of organizing. We propose that these new designs are based on an actor‐oriented architectural scheme composed of three main elements: (1) actors who have the capabilities and values to self‐organize; (2) commons where the actors accumulate and share resources; and (3) protocols, processes, and infrastructures that enable multi‐actor collaboration. We demonstrate the usefulness of the actor‐oriented scheme by applying it to organizations drawn from four different sectors: global professional services, open source software development, computer equipment, and national defense. We discuss the implications of the actor‐oriented architectural scheme for future research on organizational forms as well as for managers who are involved in designing organizations. Copyright © 2012 John Wiley & Sons, Ltd.
Nanotoxicity: How the Body Develops A Way to Reduce the Toxicity of Carbon Nanotubes
Authors: Riehemann Kristina 
Published: April 2012

AbstractThe interaction of nanoparticles with cells and organisms are often the focus of biomedical, material, and environmental research. This article highlights a paper by Yuliang Zhao, Chunying Chen, Ruhong Zhou, and co‐workers (Proc. Natl. Acad. Sci. USA 2011, 108, 16968), which brings a new aspect to the discussion about purpose and mechanisms underlying the reaction of an organism with nanoparticles. The interactions of carbon nanotubes with cells were investigated with regard to the defense mechanisms of the body against foreign materials developed during evolution. Such mechanisms are not only important for nanotoxicity research, but also for targeting nanoparticles in medical applications. The cited article thus gives a new focus to an important aspect of nanotechnology, which will determine the application aspects of this technology in future: the approach of biological systems to nanosized particles.
Response to Intervention and the Changing Roles of Schoolwide Personnel
Authors: Bean Rita , Lillenstein Jennifer 
Published: April 2012

AbstractInterviews and observations were conducted in five schools using a Response to Instruction and Invention framework to investigate (a) changes in role‐ expectations and functions for educators, (b) perceptions about their changing roles, and (c) skills needed to be effective in this systemic effort to improve literacy instruction for all students. Findings included: changes in role‐expectations are essential and inevitable. Essential skill sets included: in‐depth understanding of literacy assessment and instruction and of how to differentiate instruction, ability to use data for instructional decision making, increased collaboration and reflective dialogue, and a commitment to life‐long learning. Shared leadership was evident in all schools, with all personnel involved in efforts to improve literacy learning.
Lymphovascular invasion is a pathological feature related to aggressive cancer behavior and predicts early recurrence in prostate cancer
Authors: Luo Hao Lun , Chiang Po Hui , Chen Yen Ta , Cheng Yuan Tso 
Published: April 2012

AbstractIn order to determine the prognostic impact of lymphovascular invasion (LVI) in patients after radical prostatectomy, the retrospective data from our institution has been analyzed. From 1998 to 2010, 117 patients underwent radical prostatectomy. A total of 87 patients were included in this retrospective study. The relationship between LVI and advanced prostate cancer characteristics was evaluated by χ2 test. The Kaplan‐Meier method and meta‐analysis were used to describe the impact of LVI invasion upon early biochemical failure after radical prostatectomy. LVI was observed in patients with clinically or pathologically aggressive prostate cancer including patients of higher preoperative risk group, higher preoperative PSA, advanced Gleason grade, and pathological T3 disease. LVI is also associated with early biochemical failure rate both in our report and in the literature. Therefore, LVI is a pathological feature which indicates prognosis correlates with aggressive prostate cancer behavior and results in early biochemical failure after radical prostatectomy.
Fluconazole exposure rather than clonal spreading is correlated with the emergence of Candida glabrata with cross‐resistance to triazole antifungal agents
Authors: Chen Tun‐Chieh , Chen Yen‐Hsu , Chen Yee‐Chun , Lu Po‐Liang 
Published: April 2012

AbstractThe emergence of antifungal resistance in Candida species has raised concern in recent years, especially resistance toward triazole. Several newer triazole antifungal agents have been introduced which have a broader spectrum for fungal infections, such as voriconazole. However, cross‐resistance among triazoles is a major concern with regard to their clinical application. Antifungal susceptibility was performed using E‐test for 166 clinical isolates (29 blood and 137 nonblood isolates) in 2003 and 2004. We applied pulsed‐field gel electrophoresis for genotyping. Ninety isolates of C. albicans, 47 isolates of C. tropicalis, 27 isolates of C. glabrata, and two isolates of C. krusei were included. All isolates were susceptible to amphotericin B. Eleven (40.7%) of the 27 C. glabrata had intermediate resistance to caspofungin. Forty‐seven (28.3%) of the 166 isolates were not susceptible to fluconazole, including two C. albicans, 16 C. tropicalis, 27 C. glabrata, and two C. krusei isolates. All except seven of the C. glabrata isolates were susceptible to voriconazole. All the triazole drugs had a positive correlation among their minimum inhibitory concentrations (MICs). Fluconazole MIC was a good predictor for susceptibility to voriconazole, as determined using a receiver operating characteristic curve. Furthermore, a high diversity of pulsotypes for the 27 clinical isolates of C. glabrata was observed. Previous fluconazole exposure within 3 months was associated with reduced triazole susceptibility for C. glabrata. We demonstrated a significant positive correlation of MIC values among the four tested triazole drugs. No amphotericin B and caspofungin resistant isolates were found in this study. The cross‐resistance to triazole among C. glabrata isolates was associated with previous fluconazole exposure as opposed to clonal spreading. Selection pressure due to fluconazole use may play a major role in triazole cross‐resistance.
The alteration of plasma TGF‐β1 levels in patients with brain tumors after tumor removal
Authors: Loh Joon‐Khim , Lieu Ann‐Shung , Su Yu‐Feng , Cheng Chi‐Yun , Tsai Tai‐Hsin , Lin Chih‐Lung , Lee Kung‐Shing , Hwang Shiuh‐Lin , Kwan Aij‐Lie , Wang Chih‐Jen , Hong Yi‐Ren , Howng Shen‐Long , Chio Chung‐Ching 
Published: April 2012

AbstractTransforming growth factor (TGF) β1 may be a candidate for a serologic tumor marker. In this study, the plasma levels of TGF‐β1 in patients with brain tumors were measured using enzyme‐linked immunosorbent assay before and after tumor removal. Patients were divided into four groups, the control group and the benign, malignant, and metastatic brain tumor groups. All brain tumor groups showed significant increases in the levels of TGF‐β1 before tumor removal (6.36 ± 3.94, 17.0 ± 9.7, and 12.2 ± 10.3 ng/ml for the benign, malignant, and metastatic groups, respectively). When compared with the results obtained in the control group (1.12 ± 0.74 ng/ml), significant decreases in TGF‐β1 concentrations after total tumor removal were found in both the benign and malignant brain tumor groups (2.55 ± 2.00 and 8.93 ± 5.73 ng/ml, respectively; p = 0.0001 and p = 0.003, respectively). On the other hand, plasma TGF‐β1 levels in the metastatic brain tumor group showed a slight but significant increase (14.7 ± 9.3 ng/ml, p = 0.035) after tumor removal. In a case of low‐grade astrocytoma, plasma levels of TGF‐β1 were found to be 3.6 and 1.1 ng/ml before and after tumor removal, respectively. However, recurrent tumor was noted in this patient 7 months later, and the levels of TGF‐β1 were 26.2 and 8.4 ng/ml before and after the second operation, respectively. The data show that plasma TGF‐β1 was elevated in the circulation of patients with brain tumors and that significant decreases in TGF‐β1 levels were observed after the removal of benign and malignant tumors. The results also suggest that TGF‐β1 may be a useful serologic marker for brain tumors.
EMPIRICAL TESTS OF INTEREST-RELATIVE INVARIANTISM
Authors: Sripada Chandra Sekhar , Stanley Jason 
Published: April 2012

AbstractAccording to Interest-Relative Invariantism, whether an agent knows that p, or possesses other sorts of epistemic properties or relations, is in part determined by the practical costs of being wrong about p. Recent studies in experimental philosophy have tested the claims of IRI. After critically discussing prior studies, we present the results of our own experiments that provide strong support for IRI. We discuss our results in light of complementary findings by other theorists, and address the challenge posed by a leading intellectualist alternative to our view.
United States – Certain Measures Affecting Imports of Poultry from China: the fascinating case that wasn't
Authors: REGAN DONALD H. 
Published: April 2012

AbstractUS–Poultry (China) was the first Panel decision dealing with an origin-specific SPS measure, or with what the United States referred to as an ‘equivalence regime’. More specifically, it was the first instance in which the basis for the challenged measure was the claimed inability of the complainant country to enforce its own food-safety rules. Unfortunately, as the litigation developed, the very interesting novel issues raised by such a measure were not discussed. This essay discusses those novel issues – in particular, what sort of scientific justification or risk assessment should be required for a measure like this, and what SPS Article 4 says about equivalence regimes. The essay also criticizes the Panel's analysis of some of the issues the Panel does discuss, such as the meaning of the ‘appropriate level of protection’ in SPS 5.5 and 5.6, and the relationship between the SPS and GATT XX(b).
United States – Anti-Dumping Measures on Polyethylene Retail Carrier Bags from Thailand: a cat in the bag
Authors: PRUSA THOMAS J. , VERMULST EDWIN 
Published: April 2012

AbstractThis paper analyzes the dispute between Thailand and the United States regarding the method of calculating the anti-dumping duty on polyethylene retail carrier bags from Thailand. In December 2006, after a series of WTO Appellate Body reports, the United States ceased zeroing in original investigations. The United States implemented the policy change prospectively, that is only for future cases. Consequently, the margins in this case remained unchanged because they had been calculated in 2004. Thailand challenged the United States' use of zeroing in the final determination. The US did not contest the claim. The Panel confirmed that zeroing was used and, following the long line of Appellate Body rulings, found the United States' practice inconsistent with Article 2.4.2 of the Anti-Dumping Agreement. After the Panel Report was adopted, the United States retroactively applied the policy change to the facts of this case and recalculated the margins without zeroing. The relative simplicity of the panel proceeding and the United States' willingness to amend the calculations following the adoption of the Panel Report may invite other WTO members to pursue a similar course of action in instances where their exporters have been subjected to US zeroing.
Fast cloud adjustment to increasing CO2 in a superparameterized climate model
Authors: Wyant Matthew C. , Bretherton Christopher S. , Blossey Peter N. , Khairoutdinov Marat 
Published: April 2012

Two‐year simulation experiments with a superparameterized climate model, SP‐CAM, are performed to understand the fast tropical (30S‐30N) cloud response to an instantaneous quadrupling of CO2 concentration with SST held fixed at present‐day values. The greenhouse effect of the CO2 perturbation quickly warms the tropical land surfaces by an average of 0.5 K. This shifts rising motion, surface precipitation, and cloud cover at all levels from the ocean to the land, with only small net tropical‐mean cloud changes. There is a widespread average reduction of about 80 m in the depth of the trade inversion capping the marine boundary layer (MBL) over the cooler subtropical oceans. One apparent contributing factor is CO2‐enhanced downwelling longwave radiation, which reduces boundary‐layer radiative cooling, a primary driver of turbulent entrainment through the trade inversion. A second contributor is a slight CO2‐induced heating of the free troposphere above the MBL, which strengthens the trade inversion and also inhibits entrainment. There is a corresponding downward displacement of MBL clouds with a very slight decrease in mean cloud cover and albedo. Two‐dimensional cloud‐resolving model (CRM) simulations of this MBL response are run to steady state using composite SP‐CAM simulated thermodynamic and wind profiles from a representative cool subtropical ocean regime, for the control and 4xCO2 cases. Simulations with a CRM grid resolution equal to that of SP‐CAM are compared with much finer resolution simulations. The coarse‐resolution simulations maintain a cloud fraction and albedo comparable to SP‐CAM, but the fine‐resolution simulations have a much smaller cloud fraction. Nevertheless, both CRM configurations simulate a reduction in inversion height comparable to SP‐CAM. The changes in low cloud cover and albedo in the CRM simulations are small, but both simulations predict a slight reduction in low cloud albedo as in SP‐CAM.
Genome Replikin Count Predicts Increased Infectivity/Lethality of Viruses
Authors: Bogoch Samuel , Bogoch Elenore 
Published: April 2012

AbstractThe genomes of all groups of viruses whose sequences are listed on Pubmed, specimens since 1918, analyzed by a software from Bioradar UK Ltd., contain Replikins which range in concentration from a Replikin Count (number of Replikins per 100 amino acids) of less than 1 to 30 (see accompanying communications for higher Counts in tuberculosis, malaria, and cancer, associated with higher lethality). Counts of less than 4.0 were found in ‘resting’ virus states; Counts greater than 4.0, found to be associated with rapid replication, were found invariably to accompany or to predict virus outbreaks, by as much as two years, in viral hosts examined from salmon, to birds, to livestock, to humans. X-ray diffraction showed Replikins to be on the surface of the hemagglutinin gene of influenza and to spread as the Count increased from 3.2 to 10.1, prior to, then during, the 2009 H1N1 influenza pandemic. The degree of lethality of these outbreaks was found to be a function of the statistically significant increase in Replikin Count, particularly in the influenza polymerase gene p B1 or its equivalent in other viruses. Prediction up to two years in advance of the outbreak, and the geographic location of the outbreak, now done in 7/7 trials (see Bogoch, Nature Precedings), has permitted the solid phase synthesis of Replikin vaccines in 7 days, with time to permit manufacture, adequate testing for safety and efficacy, and distribution freeze-dried to all populations. These completely synthetic Replikins vaccines so far have been shown to be effective against Taura Syndrome virus in shrimp, and H5N1 in chickens. Thus for the first time this new technology provides the practical possibility to prevent pandemics rather than just to react to them.
Word-Finding Intervention for Children With Specific Language Impairment: A Multiple Single-Case Study
Authors: Bragard Anne , Schelstraete Marie-Anne , Snyers Perrine , James Deborah G. H. 
Published: April 2012

Purpose
This study examined the effectiveness of a combined phonological and semantic intervention for children with specific language impairment who had word-finding difficulties (WFDs).

Method
To evaluate the intervention, a multiple single-case design was implemented with 4 children, ages 9;6 (years;months) to 13;9, who had WFDs. Some items were trained using a phonological intervention; others were trained using a semantic one. Lexical access outcomes were measured using a picture-naming test at pre- and posttesting.

Results
Three children exhibited a significant reduction in WFDs on the intervention words after 6 sessions. These effects were present at posttest and 6 months later for the treated words only and not the control words. Each child responded differently to the intervention, and these response patterns seemed to be related to each child’s linguistic profile.

Conclusion
This intervention seemed to achieve long-lasting reductions in children’s WFDs. The differential responses to phonological and semantic intervention imply the need to tailor intervention for differing children by matching it to their linguistic profile.
Use of a Structured Panel Process to Define Quality Metrics for Antimicrobial Stewardship Programs
Authors: Morris Andrew M. , Brener Stacey , Dresser Linda , Daneman Nick , Dellit Timothy H. , Avdic Edina , Bell Chaim M. 
Published: April 2012

Introduction.Antimicrobial stewardship programs are being implemented in health care to reduce inappropriate antimicrobial use, adverse events, Clostridium difficile infection, and antimicrobial resistance. There is no standardized approach to evaluate the impact of these programs.Objective.To use a structured panel process to define quality improvement metrics for evaluating antimicrobial stewardship programs in hospital settings that also have the potential to be used as part of public reporting efforts.Design.A multiphase modified Delphi technique.Setting.Paper-based survey supplemented with a 1-day consensus meeting.Participants.A 10-member expert panel from Canada and the United States was assembled to evaluate indicators for relevance, effectiveness, and the potential to aid quality improvement efforts.Results.There were a total of 5 final metrics selected by the panel: (1) days of therapy per 1000 patient-days; (2) number of patients with specific organisms that are drug resistant; (3) mortality related to antimicrobial-resistant organisms; (4) conservable days of therapy among patients with community-acquired pneumonia (CAP), skin and soft-tissue infections (SSTI), or sepsis and bloodstream infections (BSI); and (5) unplanned hospital readmission within 30 days after discharge from the hospital in which the most responsible diagnosis was one of CAP, SSTI, sepsis or BSI. The first and second indicators were also identified as useful for accountability purposes, such as public reporting.Conclusion.We have successfully identified 2 measures for public reporting purposes and 5 measures that can be used internally in healthcare settings as quality indicators. These indicators can be implemented across diverse healthcare systems to enable ongoing evaluation of antimicrobial stewardship programs and complement efforts for improved patient safety.
CONTRA: copy number analysis for targeted resequencing
Authors: Li Jason , Lupat Richard , Amarasinghe Kaushalya C. , Thompson Ella R. , Doyle Maria A. , Ryland Georgina L. , Tothill Richard W. , Halgamuge Saman K. , Campbell Ian G. , Gorringe Kylie L. 
Published: April 2012

AbstractMotivation: In light of the increasing adoption of targeted resequencing (TR) as a cost-effective strategy to identify disease-causing variants, a robust method for copy number variation (CNV) analysis is needed to maximize the value of this promising technology.Results: We present a method for CNV detection for TR data, including whole-exome capture data. Our method calls copy number gains and losses for each target region based on normalized depth of coverage. Our key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. Our methods are made available via CONTRA (COpy Number Targeted Resequencing Analysis), a software package that takes standard alignment formats (BAM/SAM) and outputs in variant call format (VCF4.0), for easy integration with other next-generation sequencing analysis packages. We assessed our methods using samples from seven different target enrichment assays, and evaluated our results using simulated data and real germline data with known CNV genotypes.Availability and implementation: Source code and sample data are freely available under GNU license (GPLv3) at http://contra-cnv.sourceforge.net/Contact: Jason.Li@petermac.orgSupplementary information: Supplementary data are available at Bioinformatics online.
The Helicase and RNaseIIIa Domains of Arabidopsis Dicer-Like1 Modulate Catalytic Parameters during MicroRNA Biogenesis
Authors: Liu Chenggang , Axtell Michael J. , Fedoroff Nina V. 
Published: April 2012

Abstract
Dicer-Like1 (DCL1), an RNaseIII endonuclease, and Hyponastic Leaves1 (HYL1), a double-stranded RNA-binding protein, are core components of the plant microRNA (miRNA) biogenesis machinery. hyl1 null mutants accumulate low levels of miRNAs and display pleiotropic developmental phenotypes. We report the identification of five new hyl1 suppressor mutants, all of which are alleles of DCL1. These new alleles affect either the helicase or the RNaseIIIa domains of DCL1, highlighting the critical functions of these domains. Biochemical analysis of the DCL1 suppressor variants reveals that they process the primary transcript (pri-miRNA) more efficiently than wild-type DCL1, with both higher K cat and lower K m values. The DCL1 variants largely rescue wild-type miRNA accumulation levels in vivo, but do not rescue the MIRNA processing precision defects of the hyl1 null mutant. In vitro, the helicase domain confers ATP dependence on DCL1-catalyzed MIRNA processing, attenuates DCL1 cleavage activity, and is required for precise MIRNA processing of some substrates.