bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate change will increase savannas at the expense of forests and treeless vegetation in tropical and subtropical Americas
Authors: Anadón José D. , Sala Osvaldo E. , Maestre Fernando T. 
Published: January 2015

Summary

Transition areas between biomes are particularly sensitive to environmental changes. Our understanding of the impacts of ongoing climate change on terrestrial ecosystems has significantly increased during the last years. However, it is largely unknown how climatic change will affect transitions among major vegetation types.

We modelled the distribution of three alternative states (forest, savanna and treeless areas) in the tropical and subtropical Americas by means of climate‐niche modelling. We studied how such distribution will change by the year 2070 by using 17 downscaled and calibrated global climate models from the Coupled Model Intercomparison Project Phase 5 and the latest scenarios provided by the 5th Assessment Report of the IPCC.

Our results support the savannization of the tropical and subtropical Americas because of climate change, with an increase in savannas mainly at the expense of forests.

Our models predict an important geographical shift in the current distribution of transition areas between forest and savannas, which is much less pronounced in the case of those between savannas and treeless areas. Largest shifts, up to 600 km northward, are predicted in the forest–savanna transitions located in the eastern Amazon.

Our findings indicate that climate change will promote a shift towards more unstable states: the extent of the transition areas will notably increase, and largely stable forest areas are predicted to shrink dramatically.

Synthesis. Our work explores dimensions of the impact of climate change on biomes that have received little attention so far. Our results indicate that climate change will not only affect the extent of savanna, forest and treeless areas in the tropical and subtropical Americas, but also will: (i) promote a significant geographical shift and an increase of the extent of transition areas between biomes and (ii) decrease the stability of the equilibrium between forest, savanna and treeless areas, yielding a more unpredictable system.
SecReT6: a web‐based resource for type VI secretion systems found in bacteria
Authors: Li Jun , Yao Yufeng , Xu H. Howard , Hao Limin , Deng Zixin , Rajakumar Kumar , Ou Hong‐Yu 
Published: January 2015

SummarySecReT6 (http://db‐mml.sjtu.edu.cn/SecReT6/) is an integrated database providing comprehensive information on type VI secretion systems (T6SSs) in bacteria. T6SSs are a class of sophisticated cell contact‐dependent apparatuses involved in mediating antagonistic or synergistic communications between bacteria and/or bacteria and eukaryotes. These apparatuses have recently been found to be widely distributed among Gram‐negative bacterial species. SecReT6 offers a unique, readily explorable archive of known and putative T6SSs, and cognate effectors found in bacteria. It currently contains data on 11 167 core T6SS components mapping to 906 T6SSs found in 498 bacterial strains representing 240 species, as well as a collection of over 600 directly relevant references. Also collated and archived were 1340 diverse candidate secreted effectors which were experimentally shown and/or predicted to be delivered by T6SSs into target eukaryotic and/or prokaryotic cells as well as 196 immunity proteins. A broad range of T6SS gene cluster detection and comparative analysis tools are readily accessible via SecReT6, which may aid identification of effectors and immunity proteins around the T6SS core components. This database will be regularly updated to ensure its ongoing maximal utility and relevance to the scientific research community.
Identification of Bioactive Peptide Sequences from Amaranth (Amaranthus hypochondriacus) Seed Proteins and Their Potential Role in the Prevention of Chronic Diseases
Authors: Montoya‐Rodríguez Alvaro , Gómez‐Favela Mario A. , Reyes‐Moreno Cuauhtémoc , Milán‐Carrillo Jorge , González de Mejía Elvira 
Published: February 2015

AbstractAmaranth (Amaranthus hypochondriacus) is a pseudocereal with higher protein concentration than most cereal grains. Enzymatic hydrolysis and food processing could produce biopeptides from amaranth proteins; however, there is limited information about the bioactivity of peptides from amaranth proteins. The objective of this comprehensive review was to determine bioactive peptide sequences in amaranth proteins that may prevent cardiovascular disease, cancer, and diabetes. Amaranth proteins, reported in UniProt database, were evaluated for potential bioactive peptide using BIOPEP database. The 15 main proteins present in amaranth seed are 11S globulin, 7S globulin, α‐amylase inhibitor, trypsin inhibitor, antimicrobial proteins, nonspecific lipid‐transfer‐protein‐1, superoxide dismutase, ring‐zinc finger protein, prosystemin, amaranth albumin 1, glucose‐1‐phosphate adenyltransferase, glucosyltransferase, polyamine oxidase, granule‐bound starch synthase 1, and acetolactate synthase. All proteins showed high occurrence frequencies of angiotensin‐converting enzyme‐inhibitor peptides (A = 0.161 to 0.362), as well as of dipeptidyl peptidase IV inhibitor (A = 0.003 to 0.087). Other proteins showed antioxidative (A = 0.012 to 0.063) and glucose uptake‐stimulating activity (A = 0.023 to 0.042), and also antithrombotic (A = 0.002 to 0.031) and anticancer sequences (A = 0.001 to 0.042). The results of this study support the concept that amaranth grain could be part of a “healthy” diet and thereby prevent chronic human diseases.
Hypothermia Secondary to Glioblastoma Multiforme? Autopsy Findings in Two Cases
Authors: Morgan Matthew , Schwartz Liliana , Duflou Johan 
Published: January 2015

AbstractDeath due to accidental primary hypothermia in cold climates is relatively common, with previous case series reflecting this. In contrast, hypothermia‐related death as a result of an underlying medical cause, such as a brain tumor, is rare. The literature clearly illustrates a theoretical causal relationship between brain neoplasms and hypothermia through the infiltration of the hypothalamus; however, the number of reported cases is minimal. Two cases are presented where autopsy confirmed hypothermia as the cause of death with both cases revealing widespread glioblastoma multiforme in the brain. Both decedents were elderly with a number of comorbidities identified during autopsy that could explain death; however, hypothermia was deemed the most likely cause. It is proposed that both decedents died of hypothermia as a result of the tumor's effect on thermoregulation. These cases underline the importance of forensic pathologists to be aware of the relationship between brain tumors and hypothermia and to not dismiss death as being due to other disease processes.
Comparison of the C‐MAC video laryngoscope with direct Macintosh laryngoscopy in the emergency department
Authors: Vassiliadis John , Tzannes Alex , Hitos Kerry , Brimble Jessica , Fogg Toby 
Published: January 2015

AbstractObjectiveTo investigate the first pass success rate, airway grade and complications in two tertiary EDs with the C‐MAC video laryngoscope (VL), when compared with standard direct laryngoscopy (DL).MethodsThis was a retrospective analysis of prospectively collected data entered into an airway registry database in the EDs of Royal North Shore and St George Hospitals (SGH) over a 30 month period. Doctors had the choice of using either DL using a Macintosh or Miller blade or a C‐MAC VL for the intubation.ResultsSix hundred and nineteen consecutive patients were recruited. There was no statistical difference between VL and DL in grade of view obtained, P = 0.526. Chance of intubation success increased by more than threefold by using a C‐MAC VL in the setting of a grade III/IV (total of 109) on DL (OR = 3.06; 95% CI: 1.52–6.17; P = 0.002).ConclusionThis is the first observational study of airway management comparing the C‐MAC VL with DL blades in an Australian ED population. Our findings revealed that although the C‐MAC VL overall did not provide an enhanced view of the larynx over the Macintosh DL, it was superior to DL when the grade was at least grade III. Currently we are unable to reliably predict the grade by any algorithm prior to intubation. Findings from this study suggest that the C‐MAC VL should be considered as the first line laryngoscope in all ED intubations not just the ones predicted to be difficult.
Diagnosing Acute Heart Failure in Patients With Undifferentiated Dyspnea: A Lung and Cardiac Ultrasound (LuCUS) Protocol
Authors: Russell Frances M. , Ehrman Robert R. , Cosby Karen , Ansari Asim , Tseeng Stephanie , Christain Errick , Bailitz John 
Published: January 2015

AbstractObjectivesThe primary goal of this study was to determine accuracy for diagnosing acutely decompensated heart failure (ADHF) in the undifferentiated dyspneic emergency department (ED) patient using a lung and cardiac ultrasound (LuCUS) protocol. Secondary objectives were to determine if US findings acutely change management and if findings are more accurate than clinical gestalt.MethodsThis was a prospective, observational study of adult patients presenting to the ED with undifferentiated dyspnea. The intervention consisted of a 12‐view LuCUS protocol performed by experienced emergency physician sonographers. The primary objective was measured by comparing US findings to the final diagnosis independently determined by two physicians blinded to the LuCUS result. Acute treatment changes based on US findings were tracked in real time through a standardized data collection form.ResultsData on 99 patients were analyzed; ADHF was the final diagnosis in 36%. The LuCUS protocol had sensitivity of 83% (95% confidence interval [CI] = 67% to 93%), specificity of 83% (95% CI = 70% to 91%), positive likelihood ratio of 4.8 (95% CI = 2.7 to 8.3), and negative likelihood ratio of 0.20 (95% CI = 0.09 to 0.42). Forty‐seven percent of patients had changes in acute management, and 42% had changes in acute treatment. Observed agreement for the LuCUS protocol was 93% between coinvestigators. Overall, accuracy improved by 20% (83% vs. 63%, 95% CI = 8% to 31% for the difference) over clinical gestalt alone.ConclusionsThe LuCUS protocol may accurately identify ADHF and may improve acute clinical management in dyspneic ED patients. This protocol has improved diagnostic accuracy over clinical gestalt alone.
The Effect of Traumatic Lumbar Puncture on Hospitalization Rate for Febrile Infants 28 to 60 Days of Age
Authors: Pingree Elizabeth W. , Kimia Amir A. , Nigrovic Lise E. 
Published: January 2015

AbstractObjectivesThe authors measured the effect of a traumatic or unsuccessful lumbar puncture (LP) on the management of febrile infants.MethodsThis was a 10‐year retrospective cross‐sectional study of low‐risk infants by the “Boston” criteria 28 to 60 days of age presenting to the emergency department for evaluation of fever. “Normal LP” infants had cerebrospinal fluid (CSF) WBC < 10 × 106 cells/L. “Traumatic” or “unsuccessful LP” infants had CSF red blood cell count ≥ 10 × 109 cells/L or no CSF cell counts obtained, respectively. A serious bacterial infection (SBI) was defined as growth of a bacterial pathogen from culture. The hospitalization and SBI rates were compared between infants with normal versus traumatic or unsuccessful LPs.ResultsOf the 929 study infants, 756 (81.4%) had normal LPs, and 173 (18.6%) had traumatic or unsuccessful LPs. Infants with traumatic or unsuccessful LPs had a higher hospitalization rate (72.3% traumatic or unsuccessful LP vs. 18.1% normal LP; difference = 54.1%; 95% confidence interval [CI] = 46.4% to 60.8%), but a similar SBI rate (2.9% vs. 4.1%; difference = 1.2%; 95% CI = –2.7% to 3.6%). No infant had proven bacterial meningitis (0% risk, 95% CI = 0 to 0.3%).ConclusionsLow‐risk infants aged 28 to 60 days with traumatic or unsuccessful LPs are more frequently hospitalized, although SBI rates were similar to those of infants with normal LPs.
The Transfer Instability Index: A Novel Metric of Emergency Department Transfer Relationships
Authors: Kindermann Dana R. , Mutter Ryan L. , Houchens Robert L. , Barrett Marguerite L. , Pines Jesse M. 
Published: January 2015

AbstractObjectivesIn this study, the objective was to characterize emergency department (ED) transfer relationships and study the factors that predict the stability of those relationships. A metric is derived for ED transfer relationships that may be useful in assessing emergency care regionalization and as a resource for future emergency medicine research.MethodsEmergency department records at transferring hospitals were linked to ED and inpatient records at receiving hospitals in nine U.S. states using the 2010 Healthcare Cost and Utilization Project State Emergency Department Databases and State Inpatient Databases, the American Hospital Association Annual Survey, and the Trauma Information Exchange Program. Using the Clinical Classification Software to categorize conditions, high transfer rate conditions were placed into nine clinical groups. The authors created a new measure, the “transfer instability index,” which estimates the effective number of “transfer partners” for each sending ED: this is designed to measure the stability of outgoing transfer relationships, where higher values of the index indicate less stable relationships. The index provides a measure of how many hospitals a transferring hospital sends its patients to (weighted by how often each transfer partner is used). Regression was used to analyze factors associated with higher values of the index.ResultsSending hospitals had a median of 3.5 effective transfer partners across all conditions. The calculated transfer instability indices varied from 1 to 2.4 across disease categories. In general, higher index values were associated with treating a higher proportion of publicly insured patients: 10 and 12% increases in the Medicare and Medicaid share of ED encounters, respectively, were associated with 10 and 14% increases in the effective number of transfer partners. This public insurance effect held while studying all conditions together as well as within individual disease categories, such as cardiac, neurologic, and traumatic conditions.ConclusionsUnited States EDs that transfer patients to other hospitals often have multiple transfer partners. The stability of the transfer relationship, assessed by the transfer instability index, differs by condition. Less stable transfer relationships (i.e., hospitals with greater numbers of transfer partners) were more common in EDs with higher proportions of publicly insured patients.
Long‐term outcomes for patients with acute myeloid leukemia: A single‐center experience from AIIMS, India
Authors: Bahl Ankur , Sharma Atul , Raina Vinod , Kumar Lalit , Bakhshi Sameer , Gupta Ritu , Kumar Rajeev 
Published: January 2015

AbstractAimTo analyze clinicopathological characteristics of acute myeloid leukemia (AML) patients and to evaluate long‐term outcome of these patients presented to single tertiary care center in India.MethodsWe evaluated outcomes of 480 patients (age 8–60 years), classified into good, intermediate and poor risk according to cytogenetic results. Standard “3 + 7” induction therapy with dose of daunorubicin ranging from 45 to 90 mg/m2 followed by two to three courses of high‐dose cytarabine (12–18 g/m2) as consolidation therapy was given to majority.ResultsThe complete remission rate of the treated population (407 patients) was 70% with 84.8% in good risk, 67.9% in intermediate risk and 54.2% in poor risk (P = 0.0001). Induction mortality was 18.4%. One hundred twenty‐nine patients relapsed with median treatment free interval of 10.4 months. At a median follow‐up of 34.5 months, the median overall survival (OS) was 20.6 months with an estimated 5‐year survival rate of 35.5%. No difference was found in OS between the three risk groups; however, patients with intermediate risk had a better leukemia‐free survival (LFS) in comparison to good risk. Multivariate analysis showed age, performance status, treatment completion and hematopoietic stem cell transplant affecting OS, while only treatment completion affected LFS.ConclusionThis is one of the largest single‐center studies reflecting more accurately the outcome of AML in India. These results are likely due to uniform treatment protocols, intensification of induction and post‐remission treatments with comprehensive supportive care.
miRNA–Target Gene Regulatory Networks: A Bayesian Integrative Approach to Biomarker Selection with Application to Kidney Cancer
Authors: Chekouo Thierry , Stingo Francesco C. , Doecke James D. , Do Kim-Anh 
Published: January 2015

Summary
The availability of cross-platform, large-scale genomic data has enabled the investigation of complex biological relationships for many cancers. Identification of reliable cancer-related biomarkers requires the characterization of multiple interactions across complex genetic networks. MicroRNAs are small non-coding RNAs that regulate gene expression; however, the direct relationship between a microRNA and its target gene is difficult to measure. We propose a novel Bayesian model to identify microRNAs and their target genes that are associated with survival time by incorporating the microRNA regulatory network through prior distributions. We assume that biomarkers involved in regulatory networks are likely associated with survival time. We employ non-local prior distributions and a stochastic search method for the selection of biomarkers associated with the survival outcome. We use KEGG pathway information to incorporate correlated gene effects within regulatory networks. Using simulation studies, we assess the performance of our method, and apply it to experimental data of kidney renal cell carcinoma (KIRC) obtained from The Cancer Genome Atlas. Our novel method validates previously identified cancer biomarkers and identifies biomarkers specific to KIRC progression that were not previously discovered. Using the KIRC data, we confirm that biomarkers involved in regulatory networks are more likely to be associated with survival time, showing connections in one regulatory network for five out of six such genes we identified.
Classification of Longitudinal Data Through a Semiparametric Mixed-Effects Model Based on Lasso-Type Estimators
Authors: Arribas-Gil Ana , De la Cruz Rolando , Lebarbier Emilie , Meza Cristian 
Published: January 2015

SummaryWe propose a classification method for longitudinal data. The Bayes classifier is classically used to determine a classification rule where the underlying density in each class needs to be well modeled and estimated. This work is motivated by a real dataset of hormone levels measured at the early stages of pregnancy that can be used to predict normal versus abnormal pregnancy outcomes. The proposed model, which is a semiparametric linear mixed-effects model (SLMM), is a particular case of the semiparametric nonlinear mixed-effects class of models (SNMM) in which finite dimensional (fixed effects and variance components) and infinite dimensional (an unknown function) parameters have to be estimated. In SNMM's maximum likelihood estimation is performed iteratively alternating parametric and nonparametric procedures. However, if one can make the assumption that the random effects and the unknown function interact in a linear way, more efficient estimation methods can be used. Our contribution is the proposal of a unified estimation procedure based on a penalized EM-type algorithm. The Expectation and Maximization steps are explicit. In this latter step, the unknown function is estimated in a nonparametric fashion using a lasso-type procedure. A simulation study and an application on real data are performed.
Differential Plasticity in the Recovery of Adopted Children After Early Adversity
Authors: Palacios Jesús , Román Maite , Moreno Carmen , León Esperanza , Peñarrubia María‐Gracia 
Published: January 2015

AbstractResearch on adoption is contributing to our understanding of developmental plasticity. As early adversity is usually involved in adoption, researchers can study both the negative consequences of such adversity and the catch‐up processes that follow once children are integrated into a protective, loving, and stimulating family context. In this article, we analyze postadoption recovery in three developmental domains: growth, neuropsychological development, and attachment. Given the existence of differential plasticity within each of these domains, generalizations about physical, neuropsychological, and emotional recovery should be avoided.
Pathogenesis of atopic dermatitis
Authors: Peng W. , Novak N. 
Published: February 2015

SummaryAtopic dermatitis (AD) is the most common allergic inflammatory skin disease. Interactions of genetic, environmental and immunological factors result in the initiation and progress of AD. Although the clinical picture, characterized by acute flare‐ups of eczematous, pruritic lesions on dry skin at typical predilection such as the flexural folds, is quite homogenous, the trigger factors of the disease are diverse and the pathophysiologic network involved is complex. Therefore, first attempts have been made to classify subtypes of AD based on the most relevant causal factors in the individual patient. To optimize such a stratification of patients, detailed knowledge about cofactors impacting on manifestation of AD as well as impairment of the course of the disease is indispensable. AD shares general features of barrier dysfunction and skin inflammation with other inflammatory diseases of the skin such as psoriasis or allergic contact dermatitis, but a plethora of disease‐specific genetic, immunologic and environmental factors have been identified in AD as well. It is the purpose of this review to illustrate key concepts of the pathogenesis of AD. Important findings of recent years will be summarized and cofactors of the pathogenesis will be controversially discussed. We will summarize knowledge on pathogenic factors on the immunologic level contributing to skin barrier dysfunction in AD and the role of the microbiome as first line of defence. Furthermore, we will elucidate the role of innate lymphoid cells in AD and outline the pattern of T helper cell subtypes present in the skin during different stages of AD.