bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilizing organic and organometallic structural data in powder diffraction
Authors: Cole Jason C. , Kabova Elena A. , Shankland Kenneth 
Published: October 2014

The Cambridge Structural Database (CSD) is a database of small molecule organic and organometallic crystal structures elucidated using X-Ray and neutron crystallography. The CSD is distributed alongside a system of software (the Cambridge Structural Database System) to academic and industrial users. The system contains a number of applications (in particular DASH, ConQuest, and Mogul) that can be used to aid crystallographers in the solution and refinement of crystal structures from powder diffraction data, and in the interpretation of crystal structure models (in particular, Mercury). This publication uses a racemic form of ornidazole (Z′ = 3) to illustrate the efficacy of DASH in the crystal structure solution from powder diffraction data. Furthermore, numerous features in Mogul and Mercury that aid crystal structure solution and interpretation of crystallographic data are revised. Finally, a review of a new method for using database-derived geometric information directly in structural solution is presented.
Query Complexity of Sampling and Small Geometric Partitions
Authors: GOYAL NAVIN , RADEMACHER LUIS , VEMPALA SANTOSH 
Published: October 2014

In this paper we study the following problem.Discrete partitioning problem (DPP). Let$\mathbb{F}_q$Pndenote then-dimensional finite projective space over$\mathbb{F}_q$. For positive integerk⩽n, let {Ai}i= 1Nbe a partition of ($\mathbb{F}_q$Pn)ksuch that:(1)for alli⩽N,Ai= ∏j=1kAji(partition into product sets),(2)for alli⩽N, there is a (k− 1)-dimensional subspaceLi⊆$\mathbb{F}_q$Pnsuch thatAi⊆ (Li)k.What is the minimum value ofNas a function ofq, n, k? We will be mainly interested in the casek=n.DPP arises in an approach that we propose for proving lower bounds for the query complexity of generating random points from convex bodies. It is also related to other partitioning problems in combinatorics and complexity theory. We conjecture an asymptotically optimal partition for DPP and show that it is optimal in two cases: when the dimension is low (k=n= 2) and when the factors of the parts are structured, namely factors of a part are close to being a subspace. These structured partitions arise naturally as partitions induced by query algorithms. Our problem does not seem to be directly amenable to previous techniques for partitioning lower bounds such as rank arguments, although rank arguments do lie at the core of our techniques.
Using Mixed Methods to Assess Pediatric Disaster Preparedness in the Hospital Setting
Authors: Burke Rita V. , Kim Tae Y. , Bachman Shelby L. , Iverson Ellen I. , Berg Bridget M. 
Published: October 2014

AbstractIntroductionChildren are particularly vulnerable during disasters and mass-casualty incidents. Coordinated multi-hospital training exercises may help health care facilities prepare for pediatric disaster victims.ProblemThe purpose of this study was to use mixed methods to assess the disaster response of three hospitals, focusing on pediatric disaster victims.MethodsA full-functional disaster exercise involving a simulated 7.8-magnitude earthquake was conducted at three Los Angeles (California USA) hospitals, one of which is a freestanding designated Level I Pediatric Trauma Center. Exercise participants provided quantitative and qualitative feedback regarding their perceptions of pediatric disaster response during the exercise in the form of surveys and interviews. Additionally, trained observers provided qualitative feedback and recommendations regarding aspects of emergency response during the exercise, including communication, equipment and supplies, pediatric safety, security, and training.ResultsAccording to quantitative participant feedback, the disaster exercise enhanced respondents’ perceived preparedness to care for the pediatric population during a mass-casualty event. Further, qualitative feedback from exercise participants and observers revealed opportunities to improve multiple aspects of emergency response, such as communication, equipment availability, and physician participation. Additionally, participants and observers reported opportunities to improve safety and security of children, understanding of staff roles and responsibilities, and implementation of disaster triage exercises.ConclusionConsistent with previous investigations of pediatric disaster preparedness, evaluation of the exercise revealed several opportunities for all hospitals to improve their ability to respond to the needs of pediatric victims. Quantitative and qualitative feedback from both participants and observers was useful for comprehensively assessing the exercise's successes and obstacles. The present study has identified several opportunities to improve the current state of all hospitals’ pediatric disaster preparedness, through increased training on pediatric disaster triage methods and additional training on the safety and security of children. Regular assessment and evaluation of supplies, equipment, leadership assignments, and inter-hospital communication is also suggested to optimize the effectiveness and efficiency of response to pediatric victims in a disaster.BurkeRV, KimTY, BachmanSL, IversonEI, BergBM. Using mixed methods to assess pediatric disaster preparedness in the hospital setting. Prehosp Disaster Med. 2014;29(6): 1-7.
The stability of seeds in external beam prostate radiotherapy and implications of migration in current practice: a systematic review
Authors: Soprun K. , Sale C. , Knight K. 
Published: October 2014

AbstractPurposeTo determine and summarise the literature on prostatic seed stability by investigating seed marker migration and loss in prostate cancer patients. In addition, documenting the implications of significant seed migration and loss in clinical practise.MethodsPubMed and Sciencedirect databases were used to locate papers on the stability of gold seed markers in prostate patients treated with external beam radiation therapy. The search found 3,238 articles and ten articles were selected and reviewed based on inclusion and exclusion criteria for the scope of this literature review.ResultsMinimal migration and loss of seeds was observed in the literature reviewed, with the majority of authors reporting <2·0 mm migration within the prostate; however, there were individual cases reported outside of the 2·0 mm threshold. It was also found that significant migration had an impact on image matching, as well as, planning treatment volume margins.ConclusionSeed stability within the prostate has been proven, with most authors reporting minimal migration within a 2·0 mm threshold and minimal loss of seeds. Although individual cases can have significant migration and loss, if marker migration exceeds the 2·0 mm threshold, a protocol is required to deal with both non-significant and significant migration.
Erratum: Microorganisms persist at record depths in the subseafloor of the Canterbury Basin
Authors: Ciobanu Maria-Cristina , Burgaud Gaëtan , Dufresne Alexis , Breuker Anja , Rédou Vanessa , Ben Maamar Sarah , Gaboyer Frédéric , Vandenabeele-Trambouze Odile , Lipp Julius Sebastian , Schippers Axel , Vandenkoornhuyse Philippe , Barbier Georges , Jebbar Mohamed , Godfroy Anne , Alain Karine 
Published: October 2014

Abstract
Correction to: The ISME Journal (2014) 8, 1370–1380; doi:10.1038/ismej.2013.250; published online 16 January 2014 Since the publication of this article, it has come to the authors’ attention that the study accession number deposited in the Sequence Read Archive was omitted from the article. The study accession number is ERP002102.
Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community
Authors: Klümper Uli , Riber Leise , Dechesne Arnaud , Sannazzarro Analia , Hansen Lars H , Sørensen Søren J , Smets Barth F 
Published: October 2014

Abstract
Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids.
RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells
Authors: Arora Rajika , Lee Yongwoo , Wischnewski Harry , Brun Catherine M. , Schwarz Tobias , Azzalin Claus M. 
Published: October 2014

AbstractA fraction of cancer cells maintain telomeres through the telomerase-independent, ‘Alternative Lengthening of Telomeres’ (ALT) pathway. ALT relies on homologous recombination (HR) between telomeric sequences; yet, what makes ALT telomeres recombinogenic remains unclear. Here we show that the RNA endonuclease RNaseH1 regulates the levels of RNA–DNA hybrids between telomeric DNA and the long noncoding RNA TERRA, and is a key mediator of telomere maintenance in ALT cells. RNaseH1 associated to telomeres specifically in ALT cells and its depletion led to telomeric hybrid accumulation, exposure of single-stranded telomeric DNA, activation of replication protein A at telomeres and abrupt telomere excision. Conversely, overexpression of RNaseH1 weakened the recombinogenic nature of ALT telomeres and led to telomere shortening. Altering cellular RNaseH1 levels did not perturb telomere homoeostasis in telomerase-positive cells. RNaseH1 maintains regulated levels of telomeric RNA–DNA hybrids at ALT telomeres to trigger HR without compromising telomere integrity too severely.
A novel set of symmetric methylene blue derivatives exhibits effective bacteria photokilling — a structure — response study
Authors: Gollmer Anita , Felgenträger Ariane , Bäumler Wolfgang , Maisch Tim , Späth Andreas 
Published: October 2014

Abstract
This study focuses on the structure—response relationship of symmetrically substituted phenothiazinium dyes. Four hydrophilic derivatives with the ability of additional hydrogen bonding (5, 6) or additional electrostatic interaction (3, 4) were synthesized, photophysically characterized and compared to the parent compound methylene blue (MB, 1) and a lipophilic derivative (2) without additional coordination sites. Derivative 5 was most effective against Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli reaching a maximum photodynamic efficacy of >5log10 steps (≥99.999%) of bacteria killing in 10 minutes (5 µM, 30 J cm−2) without inherent dark toxicity after one single treatment with the incoherent light source PDT1200 (λmax = 660 nm, 50 mW cm−2). Interestingly, one derivative with two additional primary positive charges (3) showed selective killing of Escherichia coli (5 µM, 30 J cm−2, 4log10 steps inactivation (≥99.99%)) and no antimicrobial effect on Staphylococcus aureus. This might allow the development of a new generation of photosensitizers with higher antimicrobial efficacy and selectivity for future applications.
Cytoglobin ligand binding regulated by changing haem-co-ordination in response to intramolecular disulfide bond formation and lipid interaction
Authors: Beckerson Penny , Wilson Michael T. , Svistunenko Dimitri A. , Reeder Brandon J. 
Published: October 2014

Cytoglobin (Cygb) is a hexa-co-ordinate haem protein from the globin superfamily with a physiological function that is unclear. We have previously reported that the haem co-ordination is changed in the presence of lipids, potentially transforming the redox properties of the protein and hence the function of Cygb in vivo. Recent research suggests that the protein can exist in a number of states depending on the integrity and position of disulfide bonds. In the present study, we show that the monomeric protein with an internal disulfide bond between the two cysteine residues Cys38 and Cys83, interacts with lipids to induce a change in haem co-ordination. The dimeric protein with intermolecular disulfide bonds and monomeric protein without an intramolecular disulfide bond does not exhibit these changes in haem co-ordination. Furthermore, monomeric Cygb with an intramolecular disulfide bond has significantly different properties, oxidizing lipid membranes and binding ligands more rapidly as compared with the other forms of the protein. The redox state of these cysteine residues in vivo is therefore highly significant and may be a mechanism to modulate the biochemical properties of the haem under conditions of stress.
CDK5 activator protein p25 preferentially binds and activates GSK3β
Authors: Chow Hei-Man , Guo Dong , Zhou Jie-Chao , Zhang Guan-Yun , Li Hui-Fang , Herrup Karl , Zhang Jie 
Published: October 2014

SignificanceCDK5 and GSK3β are recognized as interrelated kinases; they share a strong structural resemblance, and both are known tau kinases that contribute to the etiology of Alzheimer’s disease. We report here that p25 but not p35, the normal cyclin-like activator of CDK5, unexpectedly binds to GSK3β in the AXIN-binding region. The binding of p25 increases GSK3β activity and alters its substrate specificity. Results, both in vivo and in vitro, suggest that many of the effects of p25 previously assumed to be due to hyperactivation of CDK5 must now be reexamined for the potential role of altered GSK3β activity. This result carries important implications for how we approach disease-modifying strategies for the treatment of Alzheimer’s and other neurodegenerative diseases.
Trait-based diversification shifts reflect differential extinction among fossil taxa
Authors: Wagner Peter J. , Estabrook George F. 
Published: October 2014

Significance
Shifts in biological diversity often are associated with particular anatomical traits. Anatomical data from over 300 clades of brachiopods, molluscs, arthropods, echinoderms, and chordates show that trait-based diversification shifts are common at even fairly low (genus and species) taxonomic levels. Cambrian taxa present the lone major exception. Among post-Cambrian taxa, diversification shifts correlate strongly with elevated net extinction of primitive taxa rather than elevated net speciation of derived taxa or increased morphological disparity among derived taxa. This finding emphasizes the importance of extinction in shaping morphological and phylogenetic diversity among closely related species and genera as well as suggests another way in which Cambrian evolution was unique.
Motive attribution asymmetry for love vs. hate drives intractable conflict
Authors: Waytz Adam , Young Liane L. , Ginges Jeremy 
Published: October 2014

SignificancePolitical conflict between American Democrats and Republicans and ethnoreligious conflict between Israelis and Palestinians seem intractable, despite the availability of reasonable compromise solutions in both cases. This research demonstrates a fundamental cognitive bias driving such conflict intractability: Adversaries attribute their ingroup’s actions to ingroup love more than outgroup hate and attribute their outgroup’s actions to outgroup hate more than ingroup love. This biased attributional pattern increases beliefs and intentions associated with conflict intractability, including unwillingness to negotiate and unwillingness to vote for compromise solutions. In addition, offering financial incentives for accuracy in evaluating one’s outgroup mitigates this biased attributional pattern and its consequences. Understanding this bias and how to alleviate it can contribute to conflict resolution on a global scale.
Learning regulatory programs by threshold SVD regression
Authors: Ma Xin , Xiao Luo , Wong Wing Hung 
Published: October 2014

Significance
With the increase in high-throughput data in genomic studies, the study of regulatory relationships between multidimensional predictors and responses is becoming a common task. Although high-dimensional data hold promise for revealing rich and complex regulations, it remains challenging to infer the relations between tens of thousands of responses and thousands of predictors, as the desired signal must be searched among an overwhelming number of irrelevant responses. Here we show that by formulating the regulatory programs as hidden-intermediate nodes in a linear network, a sparsity-inducing modeling and inference approach is effective in extracting the regulatory relations among very high-dimensional responses and predictors, even when the sample size is much lower.
Beasts, Beliefs, Intentions, Norms
Authors: Checkland David 
Published: October 2014

“Terms that have histories cannot be defined.” – Nietzsche“[T]he reality to which we were attending seemed to resist our thinking it.” – Cora Diamond[1] Much has been learned in recent decades about the behaviour and abilities of many species of non-human animals. Increasingly many who reflect on the abilities of languageless animals are uncomfortable with a once prevalent dichotomy of either assigning these abilities to the realm of mere (usually “associative”) mechanism or granting such creatures full rationality and more or less the entire range of abilities that involves. This has lead to no little reflection and debate regarding how to proceed in studying animal “cognition,” and about what counts as adequately or accurately explaining animal behaviour. I cautiously hope herein to contribute to the clarity of what is already a discussion too rich and complex to do any justice to here. Little of what I say will be original, but the particular way of approaching the issues herein may shed some light on why certain issues have endured.
Curcumin enhances the production of major structural components of elastic fibers, elastin, and fibrillin-1, in normal human fibroblast cells
Authors: Lee Shu-Mei , Chiang Shu-Hua , Wang Hsun-Yen , Wu Pey-Shiuan , Lin Chih-Chien 
Published: October 2014

Abstract
Curcumin is the major component of the yellow extract derived from the rhizome of the Curcuma longa, which is also a main bioactive polyphenol and has been generally used as a spice, food additive, and herbal medicine. In this presented study, we found that curcumin can enhance the production of major structural components of elastic fibers, elastin, and fibrillin-1, in normal human fibroblast cells via increasing ELN and FBN1 promoters’ activities. With 2 μM curcumin treatment, the enhanced tropoelastin and fibrillin-1 protein amounts in Detroit 551 cells were approximately 134 and 130% of control, respectively. Therefore, our results demonstrated that curcumin may be used as a functional compound and applied to drugs, foods, and cosmetics in the future.
Implementation of an Enhanced Safety-Engineered Sharp Device Oversight and Bloodborne Pathogen Protection Program at a Large Academic Medical Center
Authors: Talbot Thomas R. , Wang Deede , Swift Melanie , St. Jacques Paul , Johnson Susan , Brinsko Vicki , Thayer Valerie , Dail Teresa , Feistritzer Nancye , Polancich Shea 
Published: October 2014

Objective.Exposure of healthcare personnel to bloodborne pathogens (BBPs) can be prevented in part by using safety-engineered sharp devices (SESDs) and other safe practices, such as double gloving. In some instances, however, safer devices and practices cannot be utilized because of procedural factors or the lack of a manufactured safety device for the specific clinical use. In these situations, a standardized system to examine requests for waiver from expected practices is necessaryDesign.Before-after program analysis.Setting.Large academic medical center.Interventions.Vanderbilt University Medical Center developed a formalized system for an improved waiver process, including an online submission and tracking site, and standards surrounding implementation of core safe practices. The program’s impact on sharp device injuries and utilization of double gloving and blunt sutures was examined.Results.Following implementation of the enhanced program, there was an increase in the amount of undergloves and blunt sutures purchased for surgical procedures, suggesting larger utilization of these practices. The rate of sharp device injuries of all at-risk employees decreased from 2.32% to 2.12%, but this decline was not statistically significant (P = .14). The proportion of reported injuries that were deemed preventable significantly decreased from 72.7% (386/531) before implementation to 63.9% (334/523; P = .002) after implementation of the enhanced program.Conclusions.An enhanced BBP protection program was successful at providing guidance to increase safe practices and at improving the management of SESD waiver requests and was associated with a reduction in preventable sharp device injuries.
Seed: a user-friendly tool for exploring and visualizing microbial community data
Authors: Beck Daniel , Dennis Christopher , Foster James A. 
Published: October 2014

Summary: In this article we present Simple Exploration of Ecological Data (Seed), a data exploration tool for microbial communities. Seed is written in R using the Shiny library. This provides access to powerful R-based functions and libraries through a simple user interface. Seed allows users to explore ecological datasets using principal coordinate analyses, scatter plots, bar plots, hierarchal clustering and heatmaps.
Availability and implementation: Seed is open source and available at https://github.com/danlbek/Seed.
Contact: danlbek@gmail.com
Supplementary information: Supplementary Data are available at Bioinformatics online.