bluuebunny/crossref_metadata_2025_split huggingface dataset:
SurpriseMe: an integrated tool for network community structure characterization using Surprise maximization
Authors: Aldecoa Rodrigo , Marín Ignacio 
Published: December 2013

Abstract
Summary: Detecting communities and densely connected groups may contribute to unravel the underlying relationships among the units present in diverse biological networks (e.g. interactomes, coexpression networks, ecological networks). We recently showed that communities can be precisely characterized by maximizing Surprise, a global network parameter. Here, we present SurpriseMe, a tool that integrates the outputs of seven of the best algorithms available to estimate the maximum Surprise value. SurpriseMe also generates distance matrices that allow visualizing the relationships among the solutions generated by the algorithms. We show that the communities present in small- and medium-sized networks, with up to 10 000 nodes, can be easily characterized: on standard PC computers, these analyses take less than an hour. Also, four of the algorithms may rapidly analyze networks with up to 100 000 nodes, given enough memory resources. Because of its performance and simplicity, SurpriseMe is a reference tool for community structure characterization.
Availability and implementation: SurpriseMe is implemented in Perl and C/C++. It compiles and runs on any UNIX-based operating system, including Linux and Mac OS/X, using standard libraries. The source code is freely and publicly available under the GPL 3.0 license at http://github.com/raldecoa/SurpriseMe/releases.
Contact: imarin@ibv.csic.es
Observing the quantum anomalous Hall effect
Authors: Wang Ling 
Published: December 2013

Abstract
Soon after the article ‘Experimental Observation of the Quantum Anomalous Hall Effect (QAHE) in a Magnetic Topological Insulator’ was published online in Science, Qikun Xue, the team leader of this fabulous work from Tsinghua University, was flooded with requests for interviews. This is not so surprising. Physicists have been waiting for the observation of the QAHE for over 20 years, and, until 2013, there had been few groundbreaking experimental results. ‘The honor absolutely belongs to the entire group, especially our budding scientists’, Xue declared, Xucun Ma and Ke He, two scientists of Institute of Physics, CAS, are certainly among them. In 2009, Ma and He commenced their journey to find a unique material that could demonstrate the QAHE under the leadership of Xue.
Sufficient Amounts of Functional HOP2/MND1 Complex Promote Interhomolog DNA Repair but Are Dispensable for Intersister DNA Repair during Meiosis in Arabidopsis
Authors: Uanschou Clemens , Ronceret Arnaud , Von Harder Mona , De Muyt Arnaud , Vezon Daniel , Pereira Lucie , Chelysheva Liudmila , Kobayashi Wataru , Kurumizaka Hitoshi , Schlögelhofer Peter , Grelon Mathilde 
Published: December 2013

Abstract
During meiosis, homologous recombination (HR) is essential to repair programmed DNA double-strand breaks (DSBs), and a dedicated protein machinery ensures that the homologous chromosome is favored over the nearby sister chromatid as a repair template. The HOMOLOGOUS-PAIRING PROTEIN2/MEIOTIC NUCLEAR DIVISION PROTEIN1 (HOP2/MND1) protein complex has been identified as a crucial factor of meiotic HR in Arabidopsis thaliana, since loss of either MND1 or HOP2 results in failure of DNA repair. We isolated two mutant alleles of HOP2 (hop2-2 and hop2-3) that retained the capacity to repair meiotic DSBs via the sister chromatid but failed to use the homologous chromosome. We show that in these alleles, the recombinases RADIATION SENSITIVE51 (RAD51) and DISRUPTED MEIOTIC cDNA1 (DMC1) are loaded, but only the intersister DNA repair pathway is activated. The hop2-2 phenotype is correlated with a decrease in HOP2/MND1 complex abundance. In hop2-3, a truncated HOP2 protein is produced that retains its ability to bind to DMC1 and DNA but forms less stable complexes with MND1 and fails to efficiently stimulate DMC1-driven D-loop formation. Genetic analyses demonstrated that in the absence of DMC1, HOP2/MND1 is dispensable for RAD51-mediated intersister DNA repair, while in the presence of DMC1, a minimal amount of functional HOP2/MND1 is essential to drive intersister DNA repair.
Exploring the consequences of reducing survey effort for detecting individual and temporal variability in survival
Authors: Lahoz‐Monfort José J. , Harris Michael P. , Morgan Byron J. T. , Freeman Stephen N. , Wanless Sarah 
Published: December 2013

SummaryLong‐term monitoring programmes often involve substantial input of skilled staff time. In mark–recapture studies, considerable effort is usually devoted to both marking and recapturing/resighting individuals. Given increasing budgetary constraints, it is essential to streamline field protocols to minimize data redundancy while still achieving targets such as detecting trends or ecological effects.We evaluated different levels of field effort investment in marking and resighting individuals by resampling existing mark–recapture–recovery data to construct plausible scenarios of changes in field protocols. We demonstrate the method with 26 years data from a common guillemotUria aalgemonitoring programme at a majorNorthSea colony. We also assess the impact of stopping the ringing of chicks on our ability to study population demography using integrated population models (IPM) fitted to data including information on breeding adults. Different data sets were removed artificially to explore the ability to compensate for missing data.Current ringing effort at this colony appears adequate but resighting effort could be halved while still maintaining the capacity to monitor first‐year survival and detect the effect of hatch date on survival prospects.TheIPMappears robust for estimating survival, productivity or abundance of the breeding population, but has limited capacity to recover year‐specific first‐year survival when chick data are omitted. If productivity were not monitored, the inclusion of chick data would be essential to estimate it, albeit imprecisely.Synthesis and applications. Post‐study evaluation can help streamline existing long‐term environmental monitoring programmes. To our knowledge, this study is the first use of data thinning of existing mark–recapture–recovery data to identify potential field effort reductions. We also highlight how alternative monitoring scenarios can be evaluated with integrated population models when data are collected on different aspects of demography and abundance. When effort reduction is necessary, both approaches provide decision‐support tools for adjusting field protocols to collect demographic data. The framework has broad applicability to other taxa and demographic parameters, provided suitable long‐term data are available, and we discuss its use in different contexts.
Factors Related to Public Health Data Sharing between Local and State Health Departments
Authors: Vest Joshua R. , Issel L. Michele 
Published: December 2013

ObjectivePublic health organizations increasingly face the need to be able to share data among themselves and ultimately with other providers. We examined what factors contribute to public health organizations' data exchange capabilities.Data SourcesNational Association of County and City Health Officials' 2008 National Profile of Local Health Departments survey was linked to the Association of State and Territorial Health Official's 2007 Profile of State Public Health Survey.Study DesignWe conducted a cross‐sectional analysis of organizational factors associated with gaps in data sharing between state health agencies (SHAs) and local health departments (LHDs) in the areas of childhood immunizations, vital records, and reportable conditions.Data CollectionBased on reported information system (IS) capabilities, we created a binary variable that measured whether bidirectional data sharing was structurally possible between an LHD and its respective SHA.Principal FindingsThe proportion of LHDs experiencing a data sharing gap was 34.0 percent for immunizations, 69.8 percent for vital records, and 81.8 percent for reportable conditions. Increased SHA technological capacity and size reduced the odds of gaps.ConclusionsImproving the IS capabilities of public health agencies may be the key to their remaining relevant in the currently evolving health care system.
White But Not Quite: Normalizing Colonial Conquests Through Spatial Mimicry
Authors: Ram Mori 
Published: December 2013

AbstractThe role of mimicry in the construction and deconstruction of social identities has enriched our understanding of power relations considerably. However, as a spatial practice, mimicry has received scant consideration. In what ways can space itself become an object of mimicry? What strategies and practices are involved in this process and with what political objectives? The current paper treats these questions by analyzing processes of mimetic spatial production aiming to transform the Israeli‐occupied territory of Mount Hermon into an “ordinary” western ski resort. Yet this concerted effort produces a variety of tensions and contradictions that ultimately undo the normalization of the colonial space, comprising a test case of the convoluted ways in which mimicry of space, not merely in space, generates various forms of slippage, excess and ambivalence.
Barrio Women's Invited and Invented Spaces Against Urban Elitisation in Chacao, Venezuela
Authors: Velásquez Atehortúa Juan 
Published: December 2013

AbstractOutright victories against urban elitisation are rare in the current urban revolution. This article highlights how urban elitisation is confronted in Chacao, the most elite and urban part of Venezuela. Initially it reviews how this urban elitisation created the main economic, political and military strongholds of the opposition to the Bolivarian revolution. Then, in contesting it, the urban and Bolivarian revolutions feed each other through women's participation in invited and invented spaces of citizenship. From such spaces, Chacao women in their settler's movement organised struggles of insurgent citizenship to stop elitist urban renewal agendas and develop further forms of insurgent urbanism to conduct an urban renewal from below and establish a New Socialist Community for 600 families. They emerged as a revolutionary class to implement Bolivarian policies addressing the inefficiency and opportunism of the bureaucratic state and contesting urban elitisation with an anti‐capitalist and anti‐imperialist insurgent urbanism.
Rheumatoid arthritis and outcomes in first and subsequent births based on data from a national birth registry
Authors: Wallenius Marianne , Salvesen Kjell Å. , Daltveit Anne K. , Skomsvoll Johan F. 
Published: December 2013

AbstractObjectiveTo examine associations between rheumatoid arthritis (RA) and pregnancy outcomes in first and subsequent births.DesignCohort study.SettingStudy based on data registered in the Medical Birth Registry of Norway from the period 1 December 1998 to 31 December 2009.PopulationSingleton births in women recorded with RA (n = 1496) and reference deliveries from the general population (n = 625 642).MethodsOutcomes of first and subsequent births were analyzed separately. First birth was defined as the first delivery of nulliparous women. Associations between RA and maternal and perinatal outcomes were assessed in logistic regression analyses and adjusted for maternal age at delivery, gestational age, smoking habits and for previous cesarean section when relevant.Main outcome measuresMaternal and perinatal outcomes.ResultsVaginal bleeding was observed more often among women with RA both in first pregnancy [adjusted odds ratio (aOR) 1.8, 95% CI 1.3–2.4] and in subsequent pregnancies (aOR 1.4, 95% CI 1.1–1.9). Elective cesarean section was more common among women with RA both in the first birth (aOR 2.0, 95% CI 1.4–2.8) and in subsequent births (aOR 1.5, 95% CI 1.2–2.0). Preterm delivery was more frequent among women with RA than the reference population in first pregnancy (aOR 1.5, 95% CI 1.1–2.0) and in subsequent pregnancies (aOR 1.5, 95% CI 1.1–1.9).ConclusionComplications and poor pregnancy outcomes were more often observed in women with RA and the greatest differences were observed in the first pregnancy.
Cytotoxicity of Lidocaine to Human Corneal Endothelial Cells In Vitro
Authors: Yu Hao‐Ze , Li Yi‐Han , Wang Rui‐Xin , Zhou Xin , Yu Miao‐Miao , Ge Yuan , Zhao Jun , Fan Ting‐Jun 
Published: December 2013

AbstractLidocaine has been reported to induce apoptosis on rabbit corneal endothelial cells. However, the apoptotic effect and exact mechanism involved in cytotoxicity of lidocaine are not well‐established in human corneal endothelial (HCE) cells. In this study, we investigated the apoptosis‐inducing effect of lidocaine on HCE cells in vitro. After HCE cells were treated with lidocaine at concentrations of 0.15625–10.0 g/l, the morphology and ultrastructure of the cells were observed by inverted light microscope and transmission electron microscope (TEM). Cell viability was measured by MTT assay, and the apoptotic ratio was evaluated with flow cytometry and fluorescent microscopic counting after FITC–Annexin V/PI and AO/EB staining. DNA fragmentation was detected by electrophoresis, and the activation of caspases was evaluated by ELISA. In addition, changes in mitochondrial membrane potential were determined by JC‐1 staining. Results suggest that lidocaine above 1.25 g/l reduced cellular viability and triggered apoptosis in HCE cells in a time‐ and dose‐dependent manner. Diminishment of ΔΨm and the activation of caspases indicate that lidocaine‐induced apoptosis was caspase dependent and may be related to mitochondrial pathway.
Cost of illness for bipolar disorder: a systematic review of the economic burden
Authors: Kleine‐Budde Katja , Touil Elina , Moock Jörn , Bramesfeld Anke , Kawohl Wolfram , Rössler Wulf 
Published: December 2013

ObjectivesRecent reviews lack important information on the high cost‐of‐illness worldwide for bipolar disorder (BD). Therefore, the present study systematically analyzed those costs, their driving components, and the methodological quality with which the few existing cost‐of‐illness investigations have been performed.MethodsIn June 2012, we conducted a systematic literature review of electronic databases to identify relevant cost‐of‐illness studies published since 2000. Their methodological quality was assessed. Costs were standardized by first extrapolating them to 2009 using country‐specific gross domestic product inflators and then converting them into US dollars via purchasing power parities (PPP).ResultsThe main characteristics of 22 studies were evaluated. Ignoring outliers, costs per capita ranged from 8,000 to 14,000 US$‐PPP for overall direct healthcare, from 4,000 to 5,000 US$‐PPP for direct mental healthcare, and from 2,500 to 5,000 US$‐PPP for direct BD‐related care. Indirect costs ranged from 2,000 to 11,000 US$‐PPP. Inpatient care was the main cost driver in three studies; drug costs, in two studies. Methodological quality was deemed satisfactory.ConclusionsThe cost variance was great between studies. This was likely due to differences in methodology rather than healthcare systems, thereby making such comparisons difficult. The results showed that BD has a substantial economic burden on society. To gain more evidence, international standardized checklists are needed when undertaking cost‐of‐illness studies.
Control of voice gender in pre‐pubertal children
Authors: Cartei Valentina , Cowles Wind , Banerjee Robin , Reby David 
Published: December 2013

Adult listeners are capable of identifying the gender of speakers as young as 4 years old from their voice. In the absence of a clear anatomical dimorphism in the dimensions of pre‐pubertal boys' and girls' vocal apparatus, the observed gender differences may reflect children's regulation of their vocal behaviour. A detailed acoustic analysis was conducted of the utterances of 34 6‐ to 9‐year‐old children, in their normal voices and also when asked explicitly to speak like a boy or a girl. Results showed statistically significant shifts in fundamental and formant frequency values towards those expected from the sex dimorphism in adult voices. Directions for future research on the role of vocal behaviours in pre‐pubertal children's expression of gender are considered.
Molecular Dynamics Simulations of Certain RGD‐Based Peptides from Kistrin Provide Insight into the Higher Activity of REI‐RGD34 Protein at Higher Temperature
Authors: Upadhyay Sanjay K. 
Published: December 2013

To determine the bioactive conformation required to bind with receptor αIIbβ3, the peptide sequence RIPRGDMP from Kistrin was inserted into CDR 1 loop region of REI protein, resulting in REI‐RGD34. The activity of REI‐RGD34 was observed to increase at higher temperature towards the receptor αIIbβ3. It could be justified in either way: the modified complex forces the restricted peptide to adapt bioactive conformation or it unfolds the peptide in a way that opens its binding surface with high affinity for receptor. Here, we model the conformational preference of RGD sequence in RIPRGDMP at 25 and 42 °C using multiple MD simulations. Further, we model the peptide sequence RGD, PRGD and PRGDMP from kistrin to observe the effect of flanking residues on conformational sampling of RGD. The presence of flanking residues around RGD peptide greatly influenced the conformational sampling. A transition from bend to turn conformation was observed for RGD sequence at 42 °C. The turn conformation shows pharmacophoric parameters required to recognize the receptor αIIbβ3. Thus, the temperature‐dependent activity of RIPRGDMP when inserted into the loop region of REI can be explained by the presence of the turn conformation. This study will help in designing potential antagonist for the receptor αIIbβ3.
Development of Rapid Temporal Processing and Its Impact on Literacy Skills in Primary School Children
Authors: Steinbrink Claudia , Zimmer Karin , Lachmann Thomas , Dirichs Martin , Kammer Thomas 
Published: December 2013

In a longitudinal study, auditory and visual temporal order thresholds (TOTs) were investigated in primary school children (N = 236; mean age at first data point = 6;7) at the beginning of Grade 1 and the end of Grade 2 to test whether rapid temporal processing abilities predict reading and spelling at the end of Grades 1 and 2. Auditory and visualTOTs differed but showed comparable developmental trajectories over 20 months. VisualTOTs were not predictive of literacy measures; auditoryTOTs in Grade 1 were the best predictor. Interestingly, they were related to spelling in Grade 2 while auditoryTOTs in Grade 2 were not, suggesting that rapid auditory processing abilities have a causal influence on literacy development.
Gender‐Based Relationship Efficacy: Children's Self‐Perceptions in Intergroup Contexts
Authors: Zosuls Kristina M. , Field Ryan D. , Martin Carol Lynn , Andrews Naomi C. Z. , England Dawn E. 
Published: December 2013

This research introduces a new construct, gender‐based relationship efficacy, which refers to beliefs about one's ability to relate to own‐ and other‐gender peers. Study 1 investigated 204 fourth graders (Mage = 9.56) and confirmed that own‐gender and other‐gender relationship efficacy represent distinguishable aspects of preadolescents' social competency beliefs that are differentially related to outcomes with own‐ and other‐gender peers, including outcome expectancies and friendships with own‐ and other‐gender peers. Study 2 provided further evidence of the distinctiveness of relationship efficacy for own‐ and other‐gender peers among 403 seventh (Mage = 12.48) and 453 eighth (Mage = 13.50) graders and found gender and age differences. Developmental changes and implications for research on intergroup relationships are discussed.
White blood cell subtypes, insulin resistance and β‐cell dysfunction in high‐risk individuals – the PROMISE cohort
Authors: Lee Chee‐Tin Christine , Harris Stewart B. , Retnakaran Ravi , Gerstein Hertzel C. , Perkins Bruce A. , Zinman Bernard , Hanley Anthony J. 
Published: December 2013

SummaryBackgroundHigher white blood cell count (WBC) is associated with incident type 2 diabetes; however, little is known about the potential relationship of WBC subtypes with metabolic abnormalities underlying diabetes.DesignCross‐sectional analysis.ParticipantsSix hundred and fifty‐six nondiabetic participants in the Prospective Metabolism and Islet Cell Evaluation cohort.MeasurementsGranulocytes (basophils, neutrophils and eosinophils), lymphocytes and monocytes were measured in fasting blood samples. Neutrophil lymphocyte ratio (NLR) is the ratio of neutrophil to lymphocyte. Insulin resistance was measured by insulin sensitivity index (ISOGTT) and homeostasis model assessment of insulin resistance (HOMA‐IR). Beta‐cell dysfunction was measured by insulinogenic index (IGI) divided by HOMA‐IR (IGI/IR) and Insulin Secretion Sensitivity Index‐2 (ISSI‐2).ResultsAll WBC subtypes were inversely associated with ISOGTT [β = −0·12 (−0·15, −0·083) for granulocytes, β = −0·23 (−0·31, −0·15) for lymphocytes, β = −0·67 (−1·00, −0·34) for monocytes] and positively associated with HOMA‐IR [β = 0·11 (0·074, 0·15) for granulocytes, β = 0·22 (0·14, 0·30) for lymphocytes, β = 0·64 (0·33, 0·97) for monocytes]. Granulocytes and lymphocytes were inversely associated with IGI/IR [β = −0·10 (−0·15, −0·047), β = −0·23 (−0·35, −0·11), respectively] and ISSI‐2 [β = −0·048 (−0·074, −0·022), β = −0·14 (−0·19, −0·089), respectively]. BMI attenuated the associations of monocytes with IGI/IR and ISSI‐2, and those of NLR with ISOGTT and HOMA‐IR. NLR was not associated with IGI/IR and ISSI‐2.ConclusionsAll WBC subtypes were independently associated with insulin resistance, whereas granulocytes and lymphocytes, but not monocytes, were associated with β‐cell dysfunction. NLR was not associated with β‐cell dysfunction, and its association with insulin resistance was confounded by obesity.
Brain‐derived neurotrophic factor is expressed in rat and human placenta and its serum levels are similarly regulated throughout pregnancy in both species
Authors: Garcés María F. , Sanchez Elizabeth , Torres‐Sierra Alejandra L. , Ruíz‐Parra Ariel I. , Angel‐Müller Edith , Alzate Juan P. , Sánchez Ángel Y. , Gomez Martín A. , Romero Ximena C. , Castañeda Zoila E. , Sanchez‐Rebordelo Estrella , Diéguez Carlos , Nogueiras Rubén , Caminos Jorge E. 
Published: December 2013

SummaryObjectivePregnancy is characterized by several metabolic changes that promote fat gain and later onset of insulin resistance. As Brain‐derived neurotrophic factor (BDNF) decreases hyperglycaemia and hyperphagia, we aimed to investigate the potential role of placental and circulating BDNF levels in these pregnancy‐related metabolic changes in rats and humans.Design and methodsWe identified the mRNA and protein expression of placental BDNF and its receptor TrkB using real‐time PCR, Western blot and immunohistochemical approaches in both rat and humans. Serum BDNF was measured by ELISA. We also did a longitudinal prospective cohort study in 42 pregnant women to assess BDNF levels and correlations with other metabolic parameters.ResultsWe found that BDNF and TrkB are expressed in both rat and human placenta. In rat, both placental mRNA and serum levels are increased throughout pregnancy, whereas their protein levels are significantly decreased at the end of gestation. Serum BDNF levels in pregnant women are significantly lower in the first trimester when compared to the second and third trimester (P < 0·0148, P < 0·0012, respectively). Serum BDNF levels were negatively correlated with gestational age at birth and fasting glucose levels.ConclusionOur findings suggest that both BDNF and its receptor TrkB are expressed in rodent and human placenta being regulated during pregnancy. Taken together, these findings support a role of BDNF in the regulation of several metabolic functions during pregnancy.