bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surveying Southern Mongolia: application of multivariate classification methods in drylands with low diversity and long floristic gradients
Authors: Wesche Karsten , von Wehrden Henrik 
Published: July 2011

AbstractQuestion: How do standard multivariate classification algorithms perform for Mongolian dryland vegetation characterized by low diversity and very long floristic gradients?Location: Southern Mongolian Gobi.Methods: We compared several widely used classification methods based on 1231 relevés obtained with a similar sampling method. We applied agglomerative cluster algorithms (flexible beta/FLEX, average linkage/UPGMA, weighted linkage/WPGMA, complete linkage, Ward's clustering) and a divisive classification technique (TWINSPAN); data were reduced to presence/absence. We compared results against a published phytosociological classification (PHYTO), against environmental background data, and with respect to the presence of significant indicator species.Results: Complete linkage was inferior to other methods. TWINSPAN, UPGMA, flexible beta and WPGMA gave partly similar clusters, with FLEX and WARD showing the highest pair‐wise similarity. Classifications of all methods except CL partly agreed with PHYTO classification. Clusters of all methods had significant indicator species, but Ward's method had the highest number of indicator species, followed by the PHYTO classification and FLEX, TWINSPAN, UPGMA and WPGMA. The latter four methods all yielded clusters that differed in terms of precipitation, but TWINSPAN, FLEX and Ward's method performed best under this criterion. PHYTO and CL ranked last in partitioning the precipitation gradient. Comparisons with ordinations indicated that classification algorithms capture the main floristic gradient but were less successful than the phytosociological approach to elucidate the finer structures.Conclusion: Performance of classification methods differed depending on the applied validation approach and we thus caution against uncritically adopting a single evaluation/validation criterion. Most numerical approaches can aid sorting of large data sets, while details of manual syntaxonomic classifications are not easily reproduced. Choice of the most appropriate classification and validation method thus clearly depends on the overall aim of a given study.
Effects of a combination of hinokitiol (β‐thujaplicin) and an organic acid mixture on ruminal fermentation in heifers fed a high‐grain diet
Authors: ISHII Junichiro , OMURA Hiroshi , MITSUI Tadao , EGUCHI Norichika , UENO Takashi , GOTO Hisaya , ITO Hiroshi 
Published: July 2011

ABSTRACTThis study evaluated the effects of hinokitiol (a natural antibacterial compound extracted from Thujopsis dolabrata var. hondai) and an organic acid mixture (citrate content 50%) on ruminal fermentation. Antibacterial properties were examined by measuring minimal inhibitory concentration. Hinokitiol at 1.56 µg/mL or an organic acid mixture at 1600 µg/mL inhibited Streptococcus bovis growth. The combination of 0.78 µg/mL hinokitiol and 200 µg/mL of an organic acid mixture also inhibited S. bovis growth. Both hinokitiol and the hinokitiol and an organic acid mixture combination showed strong antibacterial properties on Gram‐positive bacteria such as S. bovis, but relatively weak antibacterial activities on Gram‐negative bacteria such as Megasphaera elsdenii. Three ruminally cannulated heifers were fed a bloat‐producing diet containing barley, pelleted alfalfa meal, soybean meal and salt without long‐cut roughage to investigate the ruminal characteristics in vivo. Feeding to heifers a bloat‐producing diet containing 7.8 mg/kg hinokitiol and 0.2% of an organic acid mixture significantly decreased the increase in stable ingesta volume. Hinokitiol or an organic acid mixture did not affect ruminal volatile fatty acids, protozoa and bacteria. These results suggest that a combination of hinokitiol and an organic acid mixture might reduce frothy bloat in cattle fed high‐grain diets.
Quaternary structure, conformational variability and global motions of phosphoglucosamine mutase
Authors: Mehra‐Chaudhary Ritcha , Mick Jacob , Tanner John J. , Beamer Lesa J. 
Published: July 2011

Phosphoglucosamine mutase (PNGM) is a bacterial enzyme that participates in the peptidoglycan biosynthetic pathway. Recent crystal structures of PNGM from two bacterial pathogens, Bacillus anthracis and Francisella tularensis, have revealed key structural features of this enzyme for the first time. Here, we follow up on several novel findings from the crystallographic studies, including the observation of a structurally conserved interface between polypeptide chains and conformational variability of the C‐terminal domain. Small‐angle X‐ray scattering of B. anthracis PNGM shows that this protein is a dimer in solution. Comparisons of the four independent polypeptide chains from the two structures reveals conserved residues and structural changes involved in the conformational variability, as well as a significant rotation of the C‐terminal domain, of nearly 60°, between the most divergent conformers. Furthermore, the fluctuation dynamics of PNGM are examined via normal mode analyses. The most mobile region of the protein is its C‐terminal domain, consistent with observations from the crystal structures. Large regions of correlated, collective motions are identified exclusively for the dimeric state of the protein, comprising both contiguous and noncontiguous structural domains. The motions observed in the lowest frequency normal mode of the dimer result in dynamically coupled opening and closing of the two active sites. The global motions identified in this study support the importance of the conformational change of PNGM in function, and suggest that the dimeric state of this protein may confer advantages consistent with its evolutionary conservation.Structured digital abstract
PNGM binds to PNGM by x ray scattering (View interaction)
Crystal structure of Cu / Zn superoxide dismutase from Taenia solium reveals metal‐mediated self‐assembly
Authors: Hernández‐Santoyo Alejandra , Landa Abraham , González‐Mondragón Edith , Pedraza‐Escalona Martha , Parra‐Unda Ricardo , Rodríguez‐Romero Adela 
Published: July 2011

Taenia solium is the cestode responsible for porcine and human cysticercosis. The ability of this parasite to establish itself in the host is related to its evasion of the immune response and its antioxidant defence system. The latter includes enzymes such as cytosolic Cu/Zn superoxide dismutase. In this article, we describe the crystal structure of a recombinant T. solium Cu/Zn superoxide dismutase, representing the first structure of a protein from this organism. This enzyme shows a different charge distribution at the entrance of the active channel when compared with human Cu/Zn superoxide dismutase, giving it interesting properties that may allow the design of specific inhibitors against this cestode. The overall topology is similar to other superoxide dismutase structures; however, there are several His and Glu residues on the surface of the protein that coordinate metal ions both intra‐ and intermolecularly. Interestingly, one of these ions, located on the β2 strand, establishes a metal‐mediated intermolecular β–β interaction, including a symmetry‐related molecule. The factors responsible for the abnormal protein–protein interactions that lead to oligomerization are still unknown; however, high metal levels have been implicated in these phenomena, but exactly how they are involved remains unclear. The present results suggest that this structure could be useful as a model to explain an alternative mechanism of protein aggregation commonly observed in insoluble fibrillar deposits.Database
The atomic coordinates and structure factors have been deposited in the Protein Data Bank under the accession number 3MND.Structured digital abstract
Cu/Zn SOD binds to Cu/Zn SOD by dynamic light scattering (View Interaction 1, 2)
Cu/Zn SOD binds to Cu/Zn SOD by mass spectrometry studies of complexes (View interaction)
Cu/Zn SOD binds to Cu/Zn SOD by molecular sieving (View Interaction 1, 2)
Cu/Zn SOD binds to Cu/Zn SOD by x‐ray crystallography (View interaction)
Formation of the Galactic bulge from a two-component stellar disc: explaining cylindrical rotation and a vertical metallicity gradient
Authors: Bekki Kenji , Tsujimoto Takuji 
Published: July 2011

Abstract
Recent observational studies have revealed that the Galactic bulge has cylindrical rotation and a steeper vertical metallicity gradient. We adopt two representative models for the bulge formation and thereby investigate whether the two models can explain both the observed cylindrical rotation and vertical metallicity gradient in a self-consistent manner. One is the ‘pure disc scenario’ (PDS) in which the bulge is formed from a pure thin stellar disc through spontaneous bar instability. The other is the ‘two-component disc scenario’ (TCDS) in which the bulge is formed from a disc composed of thin and thick discs through bar instability. Our numerical simulations show that although the PDS can reproduce the cylindrical rotation, it shows a rather flatter vertical metallicity gradient that is inconsistent with observations. The derived flatter metallicity gradient is due to the vertical mixing of stars with different initial metallicities by the stellar bar. This result implies that the bulge cannot be simply formed from a pure thin stellar disc. On the other hand, the bulge formed from the two-component disc in the TCDS can explain both the observed cylindrical rotation and vertical metallicity gradient of the Galactic bulge reasonably well. In the TCDS, more metal-poor stars at higher ∣z∣ (vertical distance), which originate from the already dynamically hotter thick disc, cannot be strongly influenced by vertical mixing of the bar so that they can stay in situ for longer time-scales and thus keep the lower metallicity at higher ∣z∣. Consequently, the vertical metallicity gradient of the bulge composed of initially thin and thick disc stars cannot be so flattened, even if the gradient of the thin disc can be flattened significantly by the bar in the TCDS. We therefore suggest that a significant fraction of the present Galactic bulge is composed of stars initially in the inner part of the thick disc and thus that these bulge stars and the thick disc have a common origin. We also suggest that the Galaxy might well have experienced some merger events that could dynamically heat up its inner regions until ∼10 Gyr ago.
Numerical convergence in self-gravitating disc simulations: initial conditions and edge effects
Authors: Paardekooper Sijme-Jan , Baruteau Clément , Meru Farzana 
Published: July 2011

Abstract
We study the numerical convergence of hydrodynamical simulations of self-gravitating accretion discs, in which a simple cooling law is balanced by shock heating. It is well known that there exists a critical cooling time-scale for which shock heating can no longer compensate for the energy losses, at which point the disc fragments. The numerical convergence of previous results of this critical cooling time-scale was questioned recently using smoothed particle hydrodynamics (SPH). We employ a two-dimensional grid-based code to study this problem and find that for smooth initial conditions, fragmentation is possible for slower cooling as the resolution is increased, in agreement with recent SPH results. We show that this non-convergence is at least partly due to the creation of a special location in the disc, the boundary between the turbulent and the laminar region, when cooling towards a gravito-turbulent state. Converged results appear to be obtained in setups where no such sharp edges appear, and we then find a critical cooling time-scale of ∼4Ω−1, where Ω is the local angular velocity.
Liver X Receptor Activation Enhances Blood–Brain Barrier Integrity in the Ischemic Brain and Increases the Abundance of ATP‐Binding Cassette Transporters ABCB1 and ABCC1 on Brain Capillary Cells
Authors: ElAli Ayman , Hermann Dirk M. 
Published: July 2011

AbstractThe blood–brain barrier (BBB) consists of dense contacts between endothelial cells, the tight junctions, which are complemented by membrane‐bound transporters belonging to the ATP‐binding cassette (ABC) transporter family. Liver X receptors (LXR) have previously been shown to stabilize the integrity of atherosclerotic noncerebral arteries. Their effects on ischemic cerebral vessels are still unknown. By delivering LXR agonists, T0901317 and GW3965, to mice submitted to 30 minutes intraluminal middle cerebral artery occlusion, we show that LXR activation reduces brain swelling and decreases BBB permeability by upregulating LXR's target calpastatin that deactivates calpain‐1/2, stabilizing p120 catenin. p120 catenin specifically interacts with RhoA and Cdc42, inactivating the former and overactivating the latter, thus restoring the postischemic expression, phosphorylation and interaction of the tight junction proteins occludin and zona occludens‐1. Moreover, LXR activation deactivates matrix metalloproteases‐2/9 and inhibits microvascular apoptosis by deactivating JNK1/2 and caspase‐3. In addition to the cholesterol transporters ABCA1 and ABCG1, which have previously been shown to be upregulated by LXR in noncerebral vessels, LXR activation increases the abundance of the drug transporters ABCB1 and ABCC1 on ischemic brain capillaries, as we further show. That LXR activation promotes endothelial integrity in different ways makes this receptor attractive as target for stroke therapies.
Distinct Spatio‐Temporal Extracellular Matrix Accumulation within Demyelinated Spinal Cord Lesions in Theiler's Murine Encephalomyelitis
Authors: Haist Verena , Ulrich Reiner , Kalkuhl Arno , Deschl Ulrich , Baumgärtner Wolfgang 
Published: July 2011

AbstractThe accumulation of extracellular matrix (ECM) and glial scar formation are considered important factors for the failure of regeneration in central nervous system (CNS) injury and multiple sclerosis. Theiler's murine encephalomyelitis (TME) as a model of multiple sclerosis served to evaluate the spatio‐temporal course of ECM alterations in demyelinating conditions. Microarray analysis revealed only mildly upregulated gene expression of ECM molecules, their biosynthesis pathways and pro‐fibrotic factors, while upregulation of matrix remodeling enzymes was more prominent. Immunohistochemistry demonstrated progressive accumulation of chondroitin sulfate proteoglycans, glycoproteins and collagens within demyelinated TME lesions, paralleling the development of astrogliosis. Deposition of collagen IV, laminin, perlecan and tenascin‐C started 28 days postinfection (dpi), collagen I, decorin, entactin and neurocan accumulated from 56 dpi on, and fibronectin from 98 dpi on. The basement membrane (BM) molecules collagen IV, entactin, fibronectin, laminin and perlecan showed perivascular and parenchymal deposition, while the non‐BM components collagen I, decorin, neurocan and tenascin‐C only accumulated in a nonvascular pattern in demyelinated areas. Contrary, phosphacan expression progressively decreased during TME. The immunoreactivity of aggrecan and brevican remained unchanged. The spatio‐temporal association of matrix accumulation with astrogliosis suggests a mainly astrocytic origin of ECM deposits, which in turn may contribute to remyelination failure in TME.
Characterization of Influenza A Outbreaks in Minnesota Swine Herds and Measures Taken to Reduce the Risk of Zoonotic Transmission
Authors: Beaudoin A. , Johnson S. , Davies P. , Bender J. , Gramer M. 
Published: July 2011

SummaryInfluenza A virus infections commonly cause respiratory disease in swine and can be transmitted between people and pigs, with potentially novel strains introduced into herds and spilling back into the human population. The goals of this study were to characterize influenza infections in Minnesota pigs and assess biosecurity measures used by swine workers. Veterinarians submitting influenza‐positive swine samples to the University of Minnesota Veterinary Diagnostic Laboratory between October 2007 and April 2009 were surveyed regarding disease‐related information and biosecurity procedures at each farm. Influenza‐positive samples were submitted year‐round, peaking in spring and fall. H1N1 was the most commonly detected subtype (56%), followed by H3N2 (14%) and H1N2 (12%). Most positive submissions were associated with illness in growing pigs (median age 8.8 weeks, IQR 5–15). Median morbidity and mortality were 25% (IQR 10–48) and 2% (IQR 0.5–3.5), respectively. Vaccination of sows and growing pigs was conducted at 71% and 7.9% of the swine farms, respectively. Specialized footwear was reported as the most common form of protective equipment used by workers. Employee vaccination for seasonal influenza was 19%. The sow vaccination rate in this study is consistent with national data, although growing pig vaccination is lower than the national average. Seasonal and age trends identified here may provide diagnostic guidance when growing pigs experience respiratory disease. Inconsistent use of protective equipment and employee vaccination at swine farms indicates the need for further discussion and research of approaches to minimize interspecies influenza transmission on swine farms.
Are diagrams always helpful tools? Developmental and individual differences in the effect of presentation format on student problem solving
Authors: Booth Julie L. , Koedinger Kenneth R. 
Published: July 2011

Background. High school and college students demonstrate a verbal, or textual, advantage whereby beginning algebra problems in story format are easier to solve than matched equations (Koedinger & Nathan, 2004). Adding diagrams to the stories may further facilitate solution (Hembree, 1992; Koedinger & Terao, 2002). However, diagrams may not be universally beneficial (Ainsworth, 2006; Larkin & Simon, 1987).Aims. To identify developmental and individual differences in the use of diagrams, story, and equation representations in problem solving. When do diagrams begin to aid problem‐solving performance? Does the verbal advantage replicate for younger students?Sample. Three hundred and seventy‐three students (121 sixth, 117 seventh, 135 eighth grade) from an ethnically diverse middle school in the American Midwest participated in Experiment 1. In Experiment 2, 84 sixth graders who had participated in Experiment 1 were followed up in seventh and eighth grades.Method. In both experiments, students solved algebra problems in three matched presentation formats (equation, story, story + diagram).Results. The textual advantage was replicated for all groups. While diagrams enhance performance of older and higher ability students, younger and lower‐ability students do not benefit, and may even be hindered by a diagram's presence.Conclusions. The textual advantage is in place by sixth grade. Diagrams are not inherently helpful aids to student understanding and should be used cautiously in the middle school years, as students are developing competency for diagram comprehension during this time.
The effect of an expressive writing intervention (EWI) on stress in infertile couples undergoing assisted reproductive technology (ART) treatment: A randomized controlled pilot study
Authors: Matthiesen Signe , Klonoff‐Cohen Hillary , Zachariae Robert , Jensen‐Johansen Mikael B. , Nielsen Berit K. , Frederiksen Yoon , Schmidt Lone , Ingerslev Hans Jakob 
Published: July 2011

Objectives. Infertile couples undergoing fertility treatments may experience stress and could benefit from psychological intervention. Expressive Writing Intervention (EWI) has shown promising results on various psychological outcomes, yet only one study has applied the method to infertility‐related stress. Our aim was to assess feasibility and effectiveness of EWI for patients in treatment with Assisted Reproductive Technology (ART).Design and participants. Patients enrolling in their first ART treatment at the fertility clinic, Aarhus University Hospital, Denmark were offered to participate. A total of 82 participants (45 women, 37 men), mean age: 33.17, were randomized to home‐based EWI or neutral writing control group and completed an infertility‐related stress questionnaire at treatment enrollment, 3 weeks later (at the time of down regulation), and 6 weeks after the intervention. The intervention took place 2 weeks after treatment start.Results. Mixed between‐within ANOVA showed a main effect of time (Wilks Lambda = 0.68, F(2,28) = 6.48) as well as a significant interaction effect between group (control/ EWI) and time (Wilks Lambda = 0.83, F(2,28) = 2.92). Infertility‐related stress decreases were observed after the intervention in the EWI group compared to controls. Six weeks after the intervention, stress tended to increase in both groups, with the control group, follow‐up stress levels exceeding baseline stress scores, whereas the follow‐up scores of EWI‐participants’ did not exceed baseline levels.Conclusions. Our preliminary results suggest EWI to be a feasible, cost‐effective, and efficient method for alleviating infertility‐related stress, although results should be considered preliminary and further testing with a larger sample is warranted.
Victim responsibility, credibility, and verdict in a simulated rape case: Application of Weiner's attribution model
Authors: Sperry Kathryn , Siegel Jason T. 
Published: July 2011

Purpose. Victims of rape are often attributed a certain amount of responsibility, which is often translated into reduced victim credibility and fewer convictions in the courtroom. The purpose of the present study was to apply Weiner's attribution model to the literature on rape blame to understand why victim blame impacts credibility and verdict. Weiner's model posits that perceptions of a target's responsibility will lead to less sympathy and therefore reduced willingness to help the target. In line with this model, it was hypothesized that sympathy for a rape victim mediates the relationship between victim responsibility and: (a) willingness to help the victim, (b) credibility, and (c) verdict.Methods. Participants read a 1,000‐word transcript of a rape trial and made judgements regarding the victim's responsibility for the rape, sympathy for the victim, willingness to help the victim, perceived witness credibility, and verdict. The victim's responsibility for the rape was manipulated between subjects.Results. The hypotheses were supported: sympathy mediated the relationships between perceived victim responsibility and: (a) willingness to help the victim, (b) credibility, and (c) verdict. Using EQS, two models are presented (one hypothesized and one modified) that further delineate these relationships.Conclusions. The present study applied a well‐established theory in social psychology to further understand the relationship between victim blame, willingness to help, victim credibility, and verdict. In line with Weiner's attribution model, sympathy for the victim played a key role in those relationships. Implications of these findings for legal professionals are discussed.