bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competition between items in working memory leads to forgetting
Authors: Lewis-Peacock Jarrod A. , Norman Kenneth A. 
Published: December 2014

AbstractSwitching attention from one thought to the next propels our mental lives forward. However, it is unclear how this thought-juggling affects our ability to remember these thoughts. Here we show that competition between the neural representations of pictures in working memory can impair subsequent recognition of those pictures. We use pattern classifiers to decode functional magnetic resonance imaging (fMRI) data from a retro-cueing task where participants juggle two pictures in working memory. Trial-by-trial fluctuations in neural dynamics are predictive of performance on a surprise recognition memory test: trials that elicit similar levels of classifier evidence for both pictures (indicating close competition) are associated with worse memory performance than trials where participants switch decisively from thinking about one picture to the other. This result is consistent with the non-monotonic plasticity hypothesis, which predicts that close competition can trigger weakening of memories that lose the competition, leading to subsequent forgetting.
The tumour suppressor DLC2 ensures mitotic fidelity by coordinating spindle positioning and cell–cell adhesion
Authors: Vitiello Elisa , Ferreira Jorge G. , Maiato Helder , Balda Maria S. , Matter Karl 
Published: December 2014

AbstractDividing epithelial cells need to coordinate spindle positioning with shape changes to maintain cell–cell adhesion. Microtubule interactions with the cell cortex regulate mitotic spindle positioning within the plane of division. How the spindle crosstalks with the actin cytoskeleton to ensure faithful mitosis and spindle positioning is unclear. Here we demonstrate that the tumour suppressor DLC2, a negative regulator of Cdc42, and the interacting kinesin Kif1B coordinate cell junction maintenance and planar spindle positioning by regulating microtubule growth and crosstalk with the actin cytoskeleton. Loss of DLC2 induces the mislocalization of Kif1B, increased Cdc42 activity and cortical recruitment of the Cdc42 effector mDia3, a microtubule stabilizer and promoter of actin dynamics. Accordingly, DLC2 or Kif1B depletion promotes microtubule stabilization, defective spindle positioning, chromosome misalignment and aneuploidy. The tumour suppressor DLC2 and Kif1B are thus central components of a signalling network that guides spindle positioning, cell–cell adhesion and mitotic fidelity.
Atomic and electronic structures of an extremely fragile liquid
Authors: Kohara Shinji , Akola Jaakko , Patrikeev Leonid , Ropo Matti , Ohara Koji , Itou Masayoshi , Fujiwara Akihiko , Yahiro Jumpei , Okada Junpei T. , Ishikawa Takehiko , Mizuno Akitoshi , Masuno Atsunobu , Watanabe Yasuhiro , Usuki Takeshi 
Published: December 2014

AbstractThe structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia–Thornton number–number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr–O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr–O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid.
Anesthetic Diffusion Through Lipid Membranes Depends on the Protonation Rate
Authors: Pérez-Isidoro Rosendo , Sierra-Valdez F. J. , Ruiz-Suárez J. C. 
Published: December 2014

AbstractHundreds of substances possess anesthetic action. However, despite decades of research and tests, a golden rule is required to reconcile the diverse hypothesis behind anesthesia. What makes an anesthetic to be local or general in the first place? The specific targets on proteins, the solubility in lipids, the diffusivity, potency, action time? Here we show that there could be a new player equally or even more important to disentangle the riddle: the protonation rate. Indeed, such rate modulates the diffusion speed of anesthetics into lipid membranes; low protonation rates enhance the diffusion for local anesthetics while high ones reduce it. We show also that there is a pH and membrane phase dependence on the local anesthetic diffusion across multiple lipid bilayers. Based on our findings we incorporate a new clue that may advance our understanding of the anesthetic phenomenon.
The insulinotrophic effect of insulin-like peptide 5 in vitro and in vivo
Authors: Luo Xiao , Li Ting , Zhu Yue , Dai Yunbin , Zhao Jianwei , Guo Zhan-Yun , Wang Ming-Wei 
Published: December 2014

Insulin-like peptide 5 (INSL5), a member of the insulin/relaxin superfamily, can activate the G-protein-coupled receptor relaxin/insulin-like family peptide receptor 4 (RXFP4), but its precise biological functions are largely unknown. Recent studies suggest that INSL5/RXFP4 is involved in the control of food intake and glucose homoeostasis. We report in the present study that RXFP4 is present in the mouse insulinoma cell line MIN6 and INSL5 augments glucose-stimulated insulin secretion (GSIS) both in vitro and in vivo. RXFP4 is also expressed in the mouse intestinal L-cell line GLUTag and INSL5 is capable of potentiating glucose-dependent glucagon-like peptide-1 (GLP-1) secretion in GLUTag cells. We propose that the insulinotrophic effect of INSL5 is probably mediated through stimulation of insulin/GLP-1 secretion and the INSL5/RXFP4 system may be a potential therapeutic target for Type 2 diabetes.
The glutaredoxin mono- and di-thiol mechanisms for deglutathionylation are functionally equivalent: implications for redox systems biology
Authors: Mashamaite Lefentse N. , Rohwer Johann M. , Pillay Ché S. 
Published: December 2014

Glutathionylation plays a central role in cellular redox regulation and anti-oxidative defence. Grx (Glutaredoxins) are primarily responsible for reversing glutathionylation and their activity therefore affects a range of cellular processes, making them prime candidates for computational systems biology studies. However, two distinct kinetic mechanisms involving either one (monothiol) or both (dithiol) active-site cysteines have been proposed for their deglutathionylation activity and initial studies predicted that computational models based on either of these mechanisms will have different structural and kinetic properties. Further, a number of other discrepancies including the relative activity of active-site mutants and contrasting reciprocal plot kinetics have also been reported for these redoxins. Using kinetic modelling, we show that the dithiol and monothiol mechanisms are identical and, we were also able to explain much of the discrepant data found within the literature on Grx activity and kinetics. Moreover, our results have revealed how an apparently futile side-reaction in the monothiol mechanism may play a significant role in regulating Grx activity in vivo.
The library's role in the management and funding of open access publishing
Authors: LARA Kate 
Published: December 2014

ABSTRACTThis survey presents information on library management of open access resources, institutional involvement in open access funding, and the role librarians see themselves playing in this model in the future. 149 responses from 30 different countries were included. 94% of respondents were librarians, and the remaining 6% consisted of faculty, students, and other library staff. Results showed that most libraries are cataloging open access journals, though they usually represent only 1–5% of total listings. The responsibility for funding open access is more likely to fall on the author or a granting organization than the library or institution. 23% of libraries in this survey help finance open access, and one‐third of these had established criteria for funding. While librarians disagreed on the appropriate level of their involvement in the publishing process and financing of article charges, the majority viewed the library as an important advocate for open access publishing in their institution.
Penetration of Nigerian predatory biomedical open access journals 2007–2012: a bibliometric study
Authors: NWAGWU Williams EZINWA , OJEMENI Obinna 
Published: December 2014

ABSTRACTThis paper presents the bibliometric characteristics of 32 biomedical open access journals published by Academic Journals and International Research Journals – the two Nigerian publishers in Jeffery Beall's list of 23 predatory open access publishers in 2012. Data about the journals and the authors of their articles were collected from the websites of the publishers, Google Scholar and Web of Science. As at December 2012, the journals had together produced a total of 5,601 papers written by 5,599 authors, and received 12,596 citations. Authors from Asia accounted for 56.79% of the publications; those from Africa wrote 28.35% while Europe contributed 7.78%. Authors from Africa accounted for 18.25% of the citations these journals received, and this is about one‐third the number of citations by authors in Asia (54.62%). At country level, India ranks first in the top 10 citer countries, while Nigeria, the host country of the journals, ranked eighth. More in‐depth studies are required to develop further information about the journals such as how much scientific information the journals contain, as well as the science literacy of the authors and the editorial.
A biophysical approach to predicting protein-DNA binding energetics
Authors: Locke George , Morozov Alexandre V. 
Published: December 2014

AbstractSequence-specific interactions between proteins and DNA play a central role in DNA replication, repair, recombination, and control of gene expression. These interactions can be studiedin vitrousing microfluidics, protein-binding microarrays (PBMs), and other high-throughput techniques. Here we develop a biophysical approach to predicting protein-DNA binding specificities from high-throughputin vitrodata. Our algorithm, called BindSter, accommodates multiple protein species competing for access to DNA and alternative binding modes of the same protein, while rigorously taking into account all sterically allowed configurations of DNA-bound particles. BindSter can be used with a hierarchy of protein-DNA interaction models of increasing complexity. We observe that the quality of BindSter predictions does not change significantly as some of the energy parameters vary over a sizable range. To take this degeneracy into account, we have developed a graphical representation of parameter uncertainties, called IntervalLogo. We find that our simplest model, in which each nucleotide in the binding site is treated independently, performs better than previous biophysical approaches. The extensions of this model, in which contributions of longer words are also considered, result in further improvements, underscoring the importance of higherorder effects in protein-DNA energetics. In contrast, we find little evidence for multiple binding modes for the transcription factors (TFs) in our dataset. Furthermore, there is limited consistency in predictions for the same TF utilizing microfluidics and PBM experimental platforms.
Common binding by redundant group B Sox proteins is evolutionarily conserved inDrosophila
Authors: Carl Sarah H. , Russell Steven 
Published: December 2014

AbstractBackgroundGroup B Sox proteins are a highly conserved group of transcription factors that act extensively to coordinate nervous system development in higher metazoans while showing both co-expression and functional redundancy across a broad group of taxa. InDrosophila melanogaster, the two group B Sox proteins Dichaete and SoxNeuro show widespread common binding across the genome. While some instances of functional compensation have been observed inDrosophila, the function of common binding and the extent of its evolutionary conservation is not known.ResultsWe used DamID-seq to examine the genome-wide binding patterns of Dichaete and SoxNeuro in four species ofDrosophila. Through a quantitative comparison of Dichaete binding, we evaluated the rate of binding site turnover across the genome as well as at specific functional sites. We also examined the presence of Sox motifs within binding intervals and the correlation between sequence conservation and binding conservation. To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species.ConclusionWe find that, while the regulatory networks driven by Dichaete and SoxNeuro are largely conserved across the drosophilids studied, binding site turnover is widespread and correlated with phylogenetic distance. Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites. We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important. Our analysis provides insights into the evolution of group B Sox function, highlighting the specific conservation of shared binding sites and suggesting alternative sources of neofunctionalisation between paralogous family members.
Measurement of Phenotype and Absolute Number of Circulating Heparin-Binding Hemagglutinin, ESAT-6 and CFP-10, and Purified Protein Derivative Antigen-Specific CD4 T Cells Can Discriminate Active from Latent Tuberculosis Infection
Authors: Hutchinson Paul , Barkham Timothy M. S. , Tang Wenying , Kemeny David M. , Chee Cynthia Bin-Eng , Wang Yee T. 
Published: December 2014

ABSTRACTThe tuberculin skin test (TST) and interferon gamma (IFN-γ) release assays (IGRAs) are used as adjunctive tests for the evaluation of suspected cases of active tuberculosis (TB). However, a positive test does not differentiate latent from active TB. We investigated whether flow cytometric measurement of novel combinations of intracellular cytokines and surface makers on CD4 T cells could differentiate between active and latent TB after stimulation withMycobacterium tuberculosis-specific proteins. Blood samples from 60 patients referred to the Singapore Tuberculosis Control Unit for evaluation for active TB or as TB contacts were stimulated with purified protein derivative (PPD), ESAT-6 and CFP-10, or heparin-binding hemagglutinin (HBHA). The CD4 T cell cytokine response (IFN-γ, interleukin-2 [IL-2], interleukin-17A [IL-17A], interleukin-22 [IL-22], granulocyte-macrophage colony-stimulating factor [GM-CSF], and tumor necrosis factor alpha [TNF-α]) and surface marker expression (CD27, CXCR3, and CD154) were then measured. We found that the proportion of PPD-specific CD4 T cells, defined as CD154+TNF-α+cells that were negative for CD27 and positive for GM-CSF, gave the strongest discrimination between subjects with latent and those with active TB (area under the receiver operator characteristic [ROC] curve of 0.9277;P< 0.0001). Also, the proportions and absolute numbers of HBHA-specific CD4 T cells were significantly higher in those with latent TB infection, particularly CD154+TNF-α+IFN-γ+IL-2+and CD154+TNF-α+CXCR3+. Finally, we found that the ratio of ESAT-6- and CFP-10-responding to HBHA-responding CD4 T cells was significantly different between the two study populations. In conclusion, we found novel markers ofM. tuberculosis-specific CD4 cells which differentiate between active and latent TB.
Seroprevalence of Cytomegalovirus among Children 1 to 5 Years of Age in the United States from the National Health and Nutrition Examination Survey of 2011 to 2012
Authors: Lanzieri Tatiana M. , Kruszon-Moran Deanna , Amin Minal M. , Bialek Stephanie R. , Cannon Michael J. , Carroll Margaret D. , Dollard Sheila C. 
Published: December 2014

ABSTRACTCytomegalovirus (CMV) seroprevalence among U.S. children 1 to 5 years old was assessed in the National Health and Nutrition Examination Survey of 2011 to 2012. The overall seroprevalence (95% confidence interval) of IgG was 20.7% (14.4 to 28.2%), that of IgM was 1.1% (0.4 to 2.4%), and that of low IgG avidity was 3.6% (1.7 to 6.6%), corresponding to a 17.3% (10.1 to 26.7%) prevalence of recent infection among IgG-positive children.
Tsukamurella pulmonis Bloodstream Infection Identified by
secA1
Gene Sequencing
Authors: Pérez del Molino Bernal Inmaculada C. , Cano María E. , García de la Fuente Celia , Martínez-Martínez Luis , López Mónica , Fernández-Mazarrasa Carlos , Agüero Jesús 
Published: December 2014

ABSTRACT

Recurrent bloodstream infections caused by a Gram-positive bacterium affected an immunocompromised child.
Tsukamurella pulmonis
was the microorganism identified by
secA1
gene sequencing. Antibiotic treatment in combination with removal of the subcutaneous port healed the patient.
Molecular Epidemiology and Genetic Diversity of Fluoroquinolone-Resistant Escherichia coli Isolates from Patients with Community-Onset Infections in 30 Chinese County Hospitals
Authors: Zhao Lina , Zhang Jing , Zheng Beiwen , Wei Zeqing , Shen Ping , Li Sujuan , Li Lanjuan , Xiao Yonghong 
Published: December 2014

ABSTRACT

The high frequency of fluoroquinolone resistance in
Escherichia coli
is a feature of clinical bacteriology in China, where the molecular epidemiology and genetic characteristics of this resistance in county hospitals remain unclear. A total of 590 nonduplicate
E. coli
isolates from 30 county hospitals located across seven Chinese regions were examined for plasmid-mediated quinolone resistance (PMQR) genes and mutations in quinolone resistance-determining regions (QRDRs). Multilocus sequence typing (MLST) and phylogenetic analysis of fluoroquinolone-resistant isolates were used to determine their genetic relatedness. The ciprofloxacin resistance rate of community-onset
E. coli
was 51.2%, and at least one PMQR gene was carried by 220 (37.3%) isolates. These included
qnr
(3.7%),
aac(6
′
)-Ib-cr
(19.7%),
qepA
(14.4%), and
oqxAB
(3.8%). Two novel
oqxB
mutants were identified and named
oqxB20
and
oqxB29
. From 60 sequence types (STs) isolated, 5 novel STs (ST4499 to ST4503) were identified. ST1193 (7.9%) was the second most abundant ST among fluoroquinolone-resistant isolates (ST131 was the most common, with 14.6%), and this is the first report of it in China. This is also the first report of ST2115 and ST3014 isolates from human samples. Ciprofloxacin-resistant
E. coli
isolates fell mainly into phylogroups B2 and D. The rates of fluoroquinolone resistance and the prevalence of PMQR genes in community-onset
E. coli
isolates from Chinese county hospitals were high. The wide-ranging molecular epidemiology of
E. coli
isolates from scattered locations across China indicates that fluoroquinolone resistance evolved from different sources.
Hepatitis C Virus Genotype 7, a New Genotype Originating from Central Africa
Authors: Murphy Donald G. , Sablon Erwin , Chamberland Jasmine , Fournier Eric , Dandavino Raymond , Tremblay Cécile L. 
Published: December 2014

ABSTRACT
We report a new hepatitis C virus (HCV) genotype identified in patients originating from the Democratic Republic of Congo. The prototype QC69 virus is shown to be a new lineage distinct from genotypes 1 to 6. Three additional patients were also found to be infected by a virus from this lineage, confirming its circulation in humans. We propose that these viruses be classified into HCV genotype 7.
Proposing an Empirically Justified Reference Threshold for Blood Culture Sampling Rates in Intensive Care Units
Authors: Karch André , Castell Stefanie , Schwab Frank , Geffers Christine , Bongartz Hannah , Brunkhorst Frank M. , Gastmeier Petra , Mikolajczyk Rafael T. 
Published: December 2014

ABSTRACT
Early and appropriate blood culture sampling is recommended as a standard of care for patients with suspected bloodstream infections (BSI) but is rarely taken into account when quality indicators for BSI are evaluated. To date, sampling of about 100 to 200 blood culture sets per 1,000 patient-days is recommended as the target range for blood culture rates. However, the empirical basis of this recommendation is not clear. The aim of the current study was to analyze the association between blood culture rates and observed BSI rates and to derive a reference threshold for blood culture rates in intensive care units (ICUs). This study is based on data from 223 ICUs taking part in the German hospital infection surveillance system. We applied locally weighted regression and segmented Poisson regression to assess the association between blood culture rates and BSI rates. Below 80 to 90 blood culture sets per 1,000 patient-days, observed BSI rates increased with increasing blood culture rates, while there was no further increase above this threshold. Segmented Poisson regression located the threshold at 87 (95% confidence interval, 54 to 120) blood culture sets per 1,000 patient-days. Only one-third of the investigated ICUs displayed blood culture rates above this threshold. We provided empirical justification for a blood culture target threshold in ICUs. In the majority of the studied ICUs, blood culture sampling rates were below this threshold. This suggests that a substantial fraction of BSI cases might remain undetected; reporting observed BSI rates as a quality indicator without sufficiently high blood culture rates might be misleading.
Isolation and Enrichment of Cryptosporidium DNA and Verification of DNA Purity for Whole-Genome Sequencing
Authors: Guo Yaqiong , Li Na , Lysén Colleen , Frace Michael , Tang Kevin , Sammons Scott , Roellig Dawn M. , Feng Yaoyu , Xiao Lihua 
Published: December 2014

ABSTRACT

Whole-genome sequencing of
Cryptosporidium
spp. is hampered by difficulties in obtaining sufficient, highly pure genomic DNA from clinical specimens. In this study, we developed procedures for the isolation and enrichment of
Cryptosporidium
genomic DNA from fecal specimens and verification of DNA purity for whole-genome sequencing. The isolation and enrichment of genomic DNA were achieved by a combination of three oocyst purification steps and whole-genome amplification (WGA) of DNA from purified oocysts. Quantitative PCR (qPCR) analysis of WGA products was used as an initial quality assessment of amplified genomic DNA. The purity of WGA products was assessed by Sanger sequencing of cloned products. Next-generation sequencing tools were used in final evaluations of genome coverage and of the extent of contamination. Altogether, 24 fecal specimens of
Cryptosporidium parvum
,
C. hominis
,
C. andersoni
,
C. ubiquitum
,
C. tyzzeri
, and
Cryptosporidium
chipmunk genotype I were processed with the procedures. As expected, WGA products with low (<16.0) threshold cycle (

C
T

) values yielded mostly
Cryptosporidium
sequences in Sanger sequencing. The cloning-sequencing analysis, however, showed significant contamination in 5 WGA products (proportion of positive colonies derived from
Cryptosporidium
genomic DNA, ≤25%). Following this strategy, 20 WGA products from six
Cryptosporidium
species or genotypes with low (mostly <14.0)

C
T

values were submitted to whole-genome sequencing, generating sequence data covering 94.5% to 99.7% of
Cryptosporidium
genomes, with mostly minor contamination from bacterial, fungal, and host DNA. These results suggest that the described strategy can be used effectively for the isolation and enrichment of
Cryptosporidium
DNA from fecal specimens for whole-genome sequencing.