bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trade-offs in a Tempest: Stakeholder Influence on Hurricane Evacuation Decisions
Authors: Dye Karen Chinander , Eggers J. P. , Shapira Zur 
Published: February 2014

Stakeholders often control vital resources for decision makers, and this can lead decision makers to take stakeholder opinions into account when making important decisions. This process can be complicated by a number of factors. First, many important decisions involve risk and uncertainty. When the outcome is uncertain, how does a decision maker take the views of stakeholders into account? Second, many decision makers are accountable to multiple different stakeholder groups with different preferences. How do these heterogeneous stakeholder groups affect the process of decision making? More generally, do these stakeholder considerations lead to decisions that are not socially optimal? We explore these and related questions by focusing on a specific type of high-stakes decision making in a context featuring significant risk and heterogeneous stakeholders—the decision to evacuate a community during the threat of a hurricane hitting land. There is research on weather forecasting techniques and individual evacuation behavior; however, there is no research on the behavior of local officials in making hurricane evacuation decisions. These decisions provide an excellent context for an exploration into the specific processes by which stakeholder considerations may affect the process of decision making. This study offers a simple model of the process underlying evacuation decision making. The model focuses on how the evacuation threshold is set based on the anticipated costs of Type I versus Type II errors. We then use the model—supplemented with rich qualitative and quantitative data—to offer a series of propositions about the conditions under which nonsocially optimal evacuation decisions may be made. This paper contributes to the literature on decision making by offering a simple model that integrates decision making and stakeholder considerations and by offering specific and novel propositions about this integration.
Synthesis and fundamental HSQC NMR data of monolignol β-glycosides, dihydromonolignol β-glycosides and p-hydroxybenzaldehyde derivative β-glycosides for the analysis of phenyl glycoside type lignin-carbohydrate complexes (LCCs)
Authors: Miyagawa Yasuyuki , Mizukami Takahito , Kamitakahara Hiroshi , Takano Toshiyuki 
Published: February 2014

Abstract
Twelve monolignol (coniferyl alcohol, sinapyl alcohol and p-coumaryl alcohol) β-glycosides (β-glucosides, β-galactosides, β-xylosides and β-mannosides) were synthesised to obtain fundamental NMR data for the analysis of phenyl glycoside type lignin-carbohydrate complexes (LCCs). That is, the 1,2-trans glycosides (the β-glucosides, β-galactosides and β-xylosides) and the 1,2-cis glycosides (the β-mannosides) were synthesized by means of Koenig-Knorr glycosylation and β-selective Mitsunobu glycosylation strategies, respectively. In addition, dihydromonolignol and p-hydroxybenzaldehyde derivative β-glycosides were also prepared from the corresponding monolignol glycosides and their intermediates, respectively. The correlation observed for the C1β-H1β bonds of the sugar moieties in the HSQC spectra of the all β-glycosides varied and were in the range of δ
C/δ
H 96–104/4.7–5.4 ppm. Especially, it was found that the correlations derived from the C1β-H1β bonds of the guaiacyl and p-hydroxyphenyl β-mannosides were close to those derived from the C1α-H1α bonds of the 4-O-methyl-α-D-glucuronic acid moieties described in the literature.
Sequence Profiling of the Saccharomyces cerevisiae Genome Permits Deconvolution of Unique and Multialigned Reads for Variant Detection
Authors: Jubin Claire , Serero Alexandre , Loeillet Sophie , Barillot Emmanuel , Nicolas Alain 
Published: February 2014

Abstract
Advances in high-throughput sequencing (HTS) technologies have accelerated our knowledge of genomes in hundreds of organisms, but the presence of repetitions found in every genome raises challenges to unambiguously map short reads. In particular, short polymorphic reads that are multialigned hinder our capacity to detect mutations. Here, we present two complementary bioinformatics strategies to perform more robust analyses of genome content and sequencing data, validated by use of the Saccharomyces cerevisiae fully sequenced genome. First, we created an annotated HTS profile for the reference genome, based on the production of virtual HTS reads. Using variable read lengths and different numbers of mismatches, we found that 35 nt-reads, with a maximum of 6 mismatches, targets 89.5% of the genome to unique (U) regions. Longer reads consisting of 50−100 nt provided little additional benefits on the U regions extent. Second, to analyze the remaining multialigned (M) regions, we identified the intragenomic single-nucleotide variants and thus defined the unique (MU) and multialigned (MM) subregions, as exemplified for the polymorphic copies of the six flocculation genes and the 50 Ty retrotransposons. As a resource, the coordinates of the U and M regions of the yeast genome have been added to the Saccharomyces Genome Database (www.yeastgenome.org). The benefit of this advanced method of genome annotation was confirmed by our ability to identify acquired single nucleotide polymorphisms in the U and M regions of an experimentally sequenced variant wild-type yeast strain.
unfulfilledInteracting Genes Display Branch-Specific Roles in the Development of Mushroom Body Axons inDrosophila melanogaster
Authors: Bates Karen E , Sung Carl , Hilson Liam , Robinow Steven 
Published: February 2014

AbstractThe mushroom body (MB) of Drosophila melanogaster is an organized collection of interneurons that is required for learning and memory. Each of the three subtypes of MB neurons, γ, α´/β´, and α/β, branch at some point during their development, providing an excellent model in which to study the genetic regulation of axon branching. Given the sequential birth order and the unique patterning of MB neurons, it is likely that specific gene cascades are required for the different guidance events that form the characteristic lobes of the MB. The nuclear receptor UNFULFILLED (UNF), a transcription factor, is required for the differentiation of all MB neurons. We have developed and used a classical genetic suppressor screen that takes advantage of the fact that ectopic expression of unf causes lethality to identify candidate genes that act downstream of UNF. We hypothesized that reducing the copy number of unf-interacting genes will suppress the unf-induced lethality. We have identified 19 candidate genes that when mutated suppress the unf-induced lethality. To test whether candidate genes impact MB development, we performed a secondary phenotypic screen in which the morphologies of the MBs in animals heterozygous for unf and a specific candidate gene were analyzed. Medial MB lobes were thin, missing, or misguided dorsally in five double heterozygote combinations (;unf/+;axin/+, unf/+;Fps85D/+, ;unf/+;Tsc1/+, ;unf/+;Rheb/+, ;unf/+;msn/+). Dorsal MB lobes were missing in ;unf/+;DopR2/+ or misprojecting beyond the termination point in ;unf/+;Sytβ double heterozygotes. These data suggest that unf and unf-interacting genes play specific roles in axon development in a branch-specific manner.
Maintaining Two Mating Types: Structure of the Mating Type Locus and Its Role in Heterokaryosis inPodospora anserina
Authors: Grognet Pierre , Bidard Frédérique , Kuchly Claire , Tong Laetitia Chan Ho , Coppin Evelyne , Benkhali Jinane Ait , Couloux Arnaud , Wincker Patrick , Debuchy Robert , Silar Philippe 
Published: February 2014

AbstractPseudo-homothallism is a reproductive strategy elected by some fungi producing heterokaryotic sexual spores containing genetically different but sexually compatible nuclei. This lifestyle appears as a compromise between true homothallism (self-fertility with predominant inbreeding) and complete heterothallism (with exclusive outcrossing). However, pseudohomothallic species face the problem of maintaining heterokaryotic mycelia to fully benefit from this lifestyle, as homokaryons are self-sterile. Here, we report on the structure of chromosome 1 in mat+ and mat− isolates of strain S of the pseudohomothallic fungus Podospora anserina. Chromosome 1 contains either one of the mat+ and mat− mating types of P. anserina, which is mostly found in nature as a mat+/mat− heterokaryotic mycelium harboring sexually compatible nuclei. We identified a “mat” region ∼0.8 Mb long, devoid of meiotic recombination and containing the mating-type idiomorphs, which is a candidate to be involved in the maintenance of the heterokaryotic state, since the S mat+ and S mat− strains have different physiology that may enable hybrid-vigor-like phenomena in the heterokaryons. The mat region contains 229 coding sequences. A total of 687 polymorphisms were detected between the S mat+ and S mat− chromosomes. Importantly, the mat region is colinear between both chromosomes, which calls for an original mechanism of recombination inhibition. Microarray analyses revealed that 10% of the P. anserina genes have different transcriptional profiles in S mat+ and S mat−, in line with their different phenotypes. Finally, we show that the heterokaryotic state is faithfully maintained during mycelium growth of P. anserina, yet mat+/mat+ and mat−/mat− heterokaryons are as stable as mat+/mat− ones, evidencing a maintenance of heterokaryosis that does not rely on fitness-enhancing complementation between the S mat+ and S mat− strains.
TargetOrtho: A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets
Authors: Glenwinkel Lori , Wu Di , Minevich Gregory , Hobert Oliver 
Published: February 2014

AbstractThe identification of the regulatory targets of transcription factors is central to our understanding of how transcription factors fulfill their many key roles in development and homeostasis. DNA-binding sites have been uncovered for many transcription factors through a number of experimental approaches, but it has proven difficult to use this binding site information to reliably predict transcription factor target genes in genomic sequence space. Using the nematode Caenorhabditis elegans and other related nematode species as a starting point, we describe here a bioinformatic pipeline that identifies potential transcription factor target genes from genomic sequences. Among the key features of this pipeline is the use of sequence conservation of transcription-factor-binding sites in related species. Rather than using aligned genomic DNA sequences from the genomes of multiple species as a starting point, TargetOrtho scans related genome sequences independently for matches to user-provided transcription-factor-binding motifs, assigns motif matches to adjacent genes, and then determines whether orthologous genes in different species also contain motif matches. We validate TargetOrtho by identifying previously characterized targets of three different types of transcription factors in C. elegans, and we use TargetOrtho to identify novel target genes of the Collier/Olf/EBF transcription factor UNC-3 in C. elegans ventral nerve cord motor neurons. We have also implemented the use of TargetOrtho in Drosophila melanogaster using conservation among five species in the D. melanogaster species subgroup for target gene discovery.
Photodynamic Therapy During Supportive Periodontal Care: Clinical, Microbiologic, Immunoinflammatory, and Patient‐Centered Performance in a Split‐Mouth Randomized Clinical Trial
Authors: Kolbe Maria F. , Ribeiro Fernanda V. , Luchesi Vanessa H. , Casarin Renato C. , Sallum Enilson A. , Nociti Francisco H. , Ambrosano Gláucia M.B. , Cirano Fabiano R. , Pimentel Suzana P. , Casati Marcio Z. 
Published: February 2014

Background: This study investigates the effect of photodynamic therapy (PDT) as monotherapy during supportive periodontal therapy.Methods: A split‐mouth, randomized controlled trial was conducted in patients with chronic periodontitis (N = 22) presenting at least three residual pockets (probing depth [PD] ≥5 mm with bleeding on probing [BOP]). The selected sites randomly received the following: 1) PDT; 2) photosensitizer (PS); or 3) scaling and root planing (SRP). At baseline and 3 and 6 months, clinical, microbiologic (real‐time polymerase chain reaction analyses), cytokine pattern (multiplexed bead immunoassay), and patient‐centered (regarding morbidity) evaluations were performed.Results: All therapies promoted similar improvements in clinical parameters throughout the study (P <0.05), except that BOP was not reduced in the PS protocol (P >0.05). Lower levels of Aggregatibacter actinomycetemcomitans were observed in the PDT and SRP protocols at 3 months when compared with the PS protocol (P <0.05). An inferior frequency detection of Porphyromonas gingivalis was observed in the PDT protocol at 3 and 6 months and in the SRP protocol at 6 months from baseline (P <0.05). In addition, PDT protocol presented inferior frequency of P. gingivalis at 3 months when compared with the other therapies (P <0.05). Only patients in the PDT protocol exhibited augmented levels of anti‐inflammatory interleukin (IL)‐4 and reduced proinflammatory IL‐1β and IL‐6 throughout the study (P <0.05). Intergroup analyses showed reduced IL‐10 and increased interferon‐γ and IL‐1β levels in the PS protocol when compared with the other therapies during follow‐ups (P <0.05). No differences in morbidity were observed between the therapies (P >0.05), although the need for anesthesia was higher in SRP‐treated sites (P <0.05).Conclusion: PDT as an exclusive therapy may be considered a non‐invasive alternative for treating residual pockets, offering advantages in the modulation of cytokines.
The Pharmacogenetics of Type 2 Diabetes: A Systematic Review
Authors: Maruthur Nisa M. , Gribble Matthew O. , Bennett Wendy L. , Bolen Shari , Wilson Lisa M. , Balakrishnan Poojitha , Sahu Anita , Bass Eric , Kao W.H. Linda , Clark Jeanne M. 
Published: February 2014

OBJECTIVE
We performed a systematic review to identify which genetic variants predict response to diabetes medications.

RESEARCH DESIGN AND METHODS
We performed a search of electronic databases (PubMed, EMBASE, and Cochrane Database) and a manual search to identify original, longitudinal studies of the effect of diabetes medications on incident diabetes, HbA1c, fasting glucose, and postprandial glucose in prediabetes or type 2 diabetes by genetic variation. Two investigators reviewed titles, abstracts, and articles independently. Two investigators abstracted data sequentially and evaluated study quality independently. Quality evaluations were based on the Strengthening the Reporting of Genetic Association Studies guidelines and Human Genome Epidemiology Network guidance.

RESULTS
Of 7,279 citations, we included 34 articles (N = 10,407) evaluating metformin (n = 14), sulfonylureas (n = 4), repaglinide (n = 8), pioglitazone (n = 3), rosiglitazone (n = 4), and acarbose (n = 4). Studies were not standalone randomized controlled trials, and most evaluated patients with diabetes. Significant medication–gene interactions for glycemic outcomes included 1) metformin and the SLC22A1, SLC22A2, SLC47A1, PRKAB2, PRKAA2, PRKAA1, and STK11 loci; 2) sulfonylureas and the CYP2C9 and TCF7L2 loci; 3) repaglinide and the KCNJ11, SLC30A8, NEUROD1/BETA2, UCP2, and PAX4 loci; 4) pioglitazone and the PPARG2 and PTPRD loci; 5) rosiglitazone and the KCNQ1 and RBP4 loci; and 5) acarbose and the PPARA, HNF4A, LIPC, and PPARGC1A loci. Data were insufficient for meta-analysis.

CONCLUSIONS
We found evidence of pharmacogenetic interactions for metformin, sulfonylureas, repaglinide, thiazolidinediones, and acarbose consistent with their pharmacokinetics and pharmacodynamics. While high-quality controlled studies with prespecified analyses are still lacking, our results bring the promise of personalized medicine in diabetes one step closer to fruition.
Agritourism in Italy and the Local Impact Referring To Itria Valley. The Organic Firm “Raggio Verde” And Its Ecological Agritourism Project
Authors: Ciervo Margerita 
Published: February 2014

AbstractThe aim of this article, using a paradigmatic approach, is to understand the evolution of agritouristic activity in Italy, to evaluate the possible local impacts referring to Itria Valley and considering the case of study of the organic firm “Raggio Verde” in Cisternino (Brindisi, Italy) with its project of multifunctional initiatives through the creation of an organic ecological agritourism. The thesis supported is that the local impact of the agritouristic activity is different according to the reference’s paradigm (market liberalism or ecological-territorial) and to the agritourism model (with reference to environmental and social relations, and to the dependence’s level from external sources). The methodology is inductive, based on qualitative and quantitative analysis, on indirect, direct and participant observation by a research on the field.
Descriptions of digenean parasites from three snail species, Bithynia fuchsiana (Morelet), Parafossarulus striatulus Benson and Melanoides tuberculata Müller, in North Vietnam
Authors: Besprozvannykh V. , Ngo H. , Ha N. , Hung N. , Rozhkovan K. , Ermolenko A. 
Published: February 2014

Abstract
For first time, 3 species of prosobranchial snails (Bithynia fuchsiana, Parafossarulus striatulus (Bithyniidae) and Melanoides tuberculata (Thiaridae)) from North Vietnam were studied for presence of the parthenitae and cercariae of Trematoda. The morphology of 12 species of larvae belonging to 8 families (Cyathocotylidae, Pleurogenidae, Lecithodendriidae, Paramphistomidae, Heterophyidae, Notocotylidae, Psilostomidae and Echinostomatidae) was described. Data on the life cycles of 3 species (Echinochasmus japonicus, Notocotylus intestinalis and Sphaeridiotrema monorchis) as well as molecular data on 28S rDNA were obtained. There was no intraspecific variability found in any of the sequences examined. The 28S rDNA sequence length determined for N. intestinalis was 1315 bp, while that of S. monorchis was 1292 bp, and that of E. japonicus was 1288 bp.
Application of LSVT BIG Intervention to Address Gait, Balance, Bed Mobility, and Dexterity in People With Parkinson Disease: A Case Series
Authors: Janssens Jorina , Malfroid Klaartje , Nyffeler Thomas , Bohlhalter Stephan , Vanbellingen Tim 
Published: February 2014

Background and Purpose
Lee Silverman Voice Treatment Big (LSVT BIG) is characterized by intensive exercising of high-amplitude movements to overcome bradykinesia and hypokinesia in patients with Parkinson disease (PD). The aim of the present case series was to explore possible beneficial effects of LSVT BIG training on gait, balance, bed mobility, and dexterity.

Case Description
Three patients with mild to moderate PD (all male; aged 52, 54, and 70 years; Hoehn & Yahr stages I–III) completed a 4-week LSVT BIG training program (16 individual 1-hour sessions) and an intensive home training program in accordance with the LSVT BIG protocol. Two certified LSVT BIG physical therapists delivered the LSVT BIG training sessions.

Outcomes
The outcome measures for gait and balance included the Functional Gait Assessment (FGA), Functional Reach Test (FRT), Timed “Up & Go” Test (TUG), Freezing of Gait Questionnaire (FOGQ), and motor score on part III of the Unified Parkinson's Disease Rating Scale (UPDRS III). Bed mobility was addressed using the Lindop Parkinson's Disease Mobility Assessment (LPA). The Nine-Hole Peg Test (9HPT) was used to measure dexterity. The 3 patients performed better on balance and gait assessments, as indicated by increased scores on the FRT and FGA (all 3 patients) and decreased scores on the TUG, FOGQ, and UPDRS III, of which scores of the FRT and UPDRS III achieved the minimal detectable change. Furthermore, the patients were quicker in tasks related to bed mobility (LPA). The patients' dexterity skills did not improve for their dominant (right) hand (9HPT).

Discussion
This case series suggests that the LSVT BIG may be beneficial for gait, balance, and bed mobility. Future work is needed to ascertain the effectiveness by means of randomized controlled trials.
Interrater and Intrarater Reliability of Common Clinical Standing Balance Tests for People With Hip Osteoarthritis
Authors: Choi Yik Ming , Dobson Fiona , Martin Joel , Bennell Kim L. , Hinman Rana S. 
Published: February 2014

Background
Hip osteoarthritis (OA) is a common musculoskeletal condition affecting older individuals. Clinical balance tests are frequently used to assess standing balance in these people. There is insufficient information regarding the reliability of these tests.

Objective
The aim of this study was to estimate reliability and measurement error of 4 common clinical standing balance tests in people with hip OA.

Design
A prospective study was conducted with repeated measures between 2 independent raters within 1 session and within 1 rater over a 1-week interval.

Methods
Thirty people with hip OA were evaluated. Reliability was estimated for the Four-Square Step Test, Step Test, Functional Reach Test, and Timed Single-Leg Stance Test using intraclass correlation coefficients (ICC [2,1]). Measurement error was expressed as standard error of measurement and minimal detectable change.

Results
The Four-Square Step Test, Step Test, and Timed Single-Leg Stance Test were sufficiently reliable between raters (ICC=.85–.94, lower 1-sided 95% confidence interval [95% CI]=.71–.89), whereas the Step Test (standing on study limb) and Timed Single-Leg Stance Test (standing on nonstudy limb) were sufficiently reliable within a rater over a 1-week interval (ICC=.91, lower 1-sided 95% CI=.80–.83). The Step Test (standing on study limb) and Timed Single-Leg Stance Test (standing on nonstudy limb) achieved optimal levels of reliability (ICC &gt;.90, lower 1-sided 95% CI &gt;.70), with acceptable measurement error (&lt;10%) for clinical outcome measures. The Functional Reach Test was not sufficiently reliable. A ceiling effect was detected for the Timed Single-Leg Stance Test.

Limitations
Reliability was assessed only between 2 raters during a single session and within 1 rater over a 1-week interval, which limits generalizability.

Conclusions
The Step Test (standing on study limb) is recommended as a highly reliable test with acceptable measurement error for assessing standing balance in people with hip OA.