bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Combination of Biomarkers to Herald the Onset of Sepsis Prior to the Manifestation of Symptoms
Authors: Dolin Hallie H. , Papadimos Thomas J. , Stepkowski Stanislaw , Chen Xiaohuan , Pan Zhixing K. 
Published: October 2017

ABSTRACT
Sepsis, which kills over 200,000 patients and costs over $20 billion in the United States alone, presents a constant but preventable challenge in the healthcare system. Among the more challenging problems that it presents is misdiagnosis due to conflation with other inflammatory processes, as its mechanisms are identical to those of other inflammatory states. Unfortunately, current biomarker tests can only assess the severity and mortality risk of each case, whereas no single test exists that can predict sepsis prior to the onset of symptoms for the purpose of pre-emptive care and monitoring. We propose that a single test utilizing three, rather than two, biomarkers that appear most quickly in the blood and are the most specific for sepsis rather than trauma, may improve diagnostic accuracy and lead to lessened patient morbidity and mortality. Such a test would vastly improve patient outcomes and quality of life, prevent complications for sepsis survivors, and prevent hospital readmissions, saving the American healthcare system money. This review summarizes the current use of sepsis biomarkers to prognosticate morbidity and mortality, and rejects the current single-biomarker and even combination biomarker tests as non-specific and inaccurate for current patient needs/pro-inflammatory cytokines, general markers of inflammation, and proteins specific to myeloid cells (and therefore to infection) are discussed. Ultimately, the review suggests a three-biomarker test of procalcitonin (PCT), interleukin-6 (IL-6), and soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) to diagnose sepsis before the onset of symptoms.
Perioperative and Long-term Outcome of the Warshaw Technique in Laparoscopic Spleen-preserving Distal Pancreatectomy
Authors: Suzumura Kazuhiro , Hatano Etsuro , Okada Toshihiro , Fujimoto Jiro 
Published: October 2017

Purpose:
The purpose of this study was to compare the safety and outcomes of laparoscopic splenic vessel preservation (Lap-SVP) to those of laparoscopic Warshaw technique (Lap-WT).

Materials and Methods:
Fourteen patients underwent Lap-SVP and 5 patients underwent Lap-WT. Their clinical data and outcomes of the 2 procedures were compared.

Results:
The operative time, intraoperative blood loss, clinically relevant pancreatic fistula, and the rate of splenic infarction were significantly higher in the patients who underwent Lap-WT than in those who underwent Lap-SVP. In both groups, the platelet count ratio and splenic volume ratio at 1 month after the operation did not differ from the preoperative values. Two patients in the Lap-WT group experienced splenic infarction, and could be observed without any treatment.

Conclusions:
The long-term outcome of Lap-WT was relevant. Therefore, Lap-WT could be a treatment option for patients who may not have undergone Lap-SVP.
Systemic Inflammation in Lewy Body Diseases
Authors: King Eleanor , Thomas Alan 
Published: October 2017

Abstract:
Few studies have investigated the role of inflammation in Lewy body dementia (LBD) and variable results have been found. We systematically reviewed the literature for evidence of systemic inflammatory changes in dementia with Lewy bodies and Parkinson disease dementia. Owing to the low number of studies we also included Parkinson disease. Key terms were used to search the relevant databases. Titles and abstracts were screened and potentially relevant articles were reviewed in full. References of included studies and relevant reviews were searched. The database search returned 2166 results, 46 of which were finally included in the systematic review. These studies showed a general increase in inflammatory markers in the peripheral blood, most notably interleukin-1β (IL-1β), tumor necrosis factor-α, IL-6, and IL-10. Studies examining cerebrospinal fluid found IL-1β, IL-6, and transforming growth factor-β1 to be particularly increased, and interferon-γ decreased. C-reactive protein levels were increased, particularly in Parkinson disease dementia. These results provide evidence that LBD is associated with an increased inflammatory response. Furthermore, there may be a stronger general inflammatory response in LBD than in Parkinson disease, while complex changes occur in the individual cytokines.
Flexible clock systems: adjusting the temporal programme
Authors: van der Veen Daan R. , Riede Sjaak J. , Heideman Paul D. , Hau Michaela , van der Vinne Vincent , Hut Roelof A. 
Published: October 2017

Under natural conditions, many aspects of the abiotic and biotic environment vary with time of day, season or even era, while these conditions are typically kept constant in laboratory settings. The timing information contained within the environment serves as critical timing cues for the internal biological timing system, but how this system drives daily rhythms in behaviour and physiology may also depend on the internal state of the animal. The disparity between timing of these cues in natural and laboratory conditions can result in substantial differences in the scheduling of behaviour and physiology under these conditions. In nature, temporal coordination of biological processes is critical to maximize fitness because they optimize the balance between reproduction, foraging and predation risk. Here we focus on the role of peripheral circadian clocks, and the rhythms that they drive, in enabling adaptive phenotypes. We discuss how reproduction, endocrine activity and metabolism interact with peripheral clocks, and outline the complex phenotypes arising from changes in this system. We conclude that peripheral timing is critical to adaptive plasticity of circadian organization in the field, and that we must abandon standard laboratory conditions to understand the mechanisms that underlie this plasticity which maximizes fitness under natural conditions.This article is part of the themed issue ‘Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals’.
CLASP stabilizes microtubule plus ends created by serving to drive cortical array reorientation
Authors: Lindeboom Jelmer J. , Nakamura Masayoshi , Saltini Marco , Hibbel Anneke , Walia Ankit , Ketelaar Tijs , Emons Anne Mie C. , Sedbrook John C. , Kirik Viktor , Mulder Bela M. , Ehrhardt David W. 
Published: October 2017

AbstractCentral to building and reorganizing cytoskeletal arrays is the creation of new polymers. While nucleation has been the major focus of study for new microtubule generation, severing has been proposed as an alternative mechanism to create new polymers, a mechanism recently shown to drive the reorientation of cortical arrays of higher plants in response to blue light perception. As severing produces new plus ends behind the stabilizing GTP-cap, an important and unanswered question is how these are stabilizedin vivoto promote net microtubule generation. Here we identify the conserved protein CLASP as a potent stabilizer of new plus ends created by katanin severing and find that CLASP is required for rapid cortical array reorientation. Inclaspmutants both rescue of shrinking plus ends and the regrowth of plus ends immediately after severing are reduced, computational modeling reveals that it is the specific stabilization of severed ends that explains CLASP’s function in promoting microtubule amplification by severing and cortical array reorientation.
Distress feeding of depredatory birds in Sunflower and Sorghum protected by bioacoustics
Authors: Mahesh S.S. , Vasudeva Rao V. , Surender G. , Kiran kumar D.A. , Swamy K. 
Published: October 2017

ABSTRACTOne of the most ignored aspects of bioacoustic technology employed worldwide is lack of understanding between acclimatisation and distress feeding by depredatory birds. Acclimatisation results in gradual increase in resistance to bioacoustics in comparison to distress feeding, which makes sudden surge in instances of feeding by depredatory birds. Acclimatisation and distress feeding are independent functions of feeding behaviour. Distress feeding in itself is a function of physiological conditions of bird, extent of cropped area, distance traveled to obtain food, population dynamics, other natural habitats and cropping pattern in an area and is greatly influenced by them. There are no studies conducted to understand the distress feeding of birds in agricultural landscape. Experiments proved that bioacoustics could offer protection against distress feeding by birds although at reduced efficiency.
Re-Identification of Individuals in Genomic Data-Sharing Beacons via Allele Inference
Authors: Thenen Nora von , Ayday Erman , Ercument Cicek A. 
Published: October 2017

AbstractGenomic datasets are often associated with sensitive phenotypes. Therefore, the leak of membership information is a major privacy risk. Genomic beacons aim to provide a secure, easy to implement, and standardized interface for data sharing by only allowing yes/no queries on the presence of specific alleles in the dataset. Previously deemed secure against re-identification attacks, beacons were shown to be vulnerable despite their stringent policy. Recent studies have demonstrated that it is possible to determine whether the victim is in the dataset, by repeatedly querying the beacon for his/her single nucleotide polymorphisms (SNPs). In this work, we propose a novel re-identification attack and show that the privacy risk is more serious than previously thought. Using the proposed attack, even if the victim systematically hides informative SNPs (i.e., SNPs with very low minor allele frequency -MAF-), it is possible to infer the alleles at positions of interest as well as the beacon query results with very high confidence. Our method is based on the fact that alleles at different loci are not necessarily independent. We use the linkage disequilibrium and a high-order Markov chain-based algorithm for the inference. We show that in a simulated beacon with 65 individuals from the CEU population, we can infer membership of individuals with 95% confidence with only 5 queries, even when SNPs with MAF less than 0.05 are hidden. This means, we need less than 0.5% of the number of queries that existing works require, to determine beacon membership under the same conditions. We further show that countermeasures such as hiding certain parts of the genome or setting a query budget for the user would fail to protect the privacy of the participants under our adversary model.
Combined analysis of genome sequencing and RNA-motifs reveals novel damaging non-coding mutations in human tumors
Authors: Singh Babita , Trincado Juan L. , Tatlow PJ , Piccolo Stephen R. , Eyras Eduardo 
Published: October 2017

AbstractA major challenge in cancer research is to determine the biological and clinical significance of somatic mutations in non-coding regions. This has been studied in terms of recurrence, functional impact, and association to individual regulatory sites, but the combinatorial contribution of mutations to common RNA regulatory motifs has not been explored. We developed a new method, MIRA, to perform the first comprehensive study of significantly mutated regions (SMRs) affecting binding sites for RNA-binding proteins (RBPs) in cancer. Extracting signals related to RNA-related selection processes and using RNA sequencing data from the same samples we identified alterations in RNA expression and splicing linked to mutations on RBP binding sites. We found SRSF10 and MBNL1 motifs in introns, HNRPLL motifs at 5’ UTRs, as well as 5’ and 3’ splice-site motifs, among others, with specific mutational patterns that disrupt the motif and impact RNA processing. MIRA facilitates the integrative analysis of multiple genome sites that operate collectively through common RBPs and can aid in the interpretation of non-coding variants in cancer. MIRA is available athttps://github.com/comprna/mira.
Vagal nerve stimulation triggers widespread responses and alters large-scale functional connectivity in the rat brain
Authors: Cao Jiayue , Lu Kun-Han , Powley Terry L. , Liu Zhongming 
Published: October 2017

AbstractVagus nerve stimulation (VNS) is a therapy for epilepsy and depression. However, its efficacy varies and its mechanism remains unclear. Prior studies have used functional magnetic resonance imaging (fMRI) to map brain activations with VNS in human brains, but have reported inconsistent findings. The source of inconsistency is likely attributable to the complex temporal characteristics of VNS-evoked fMRI responses that cannot be fully explained by simplified response models in the conventional model-based analysis for activation mapping. To address this issue, we acquired 7-Tesla blood oxygenation level dependent fMRI data from anesthetized Sprague–Dawley rats receiving electrical stimulation at the left cervical vagus nerve. Using spatially independent component analysis, we identified 20 functional brain networks and detected the network-wise activations with VNS in a data-driven manner. Our results showed that VNS activated 15 out of 20 brain networks, and the activated regions covered >76% of the brain volume. The time course of the evoked response was complex and distinct across regions and networks. In addition, VNS altered the strengths and patterns of correlations among brain networks relative to those in the resting state. The most notable changes in network-network interactions were related to the limbic system. Together, such profound and widespread effects of VNS may underlie its unique potential for a wide range of therapeutics to relieve central or peripheral conditions.
An Early Devonian permineralized rhyniopsid from the Battery Point Formation of Gaspé (Canada)
Authors: Pfeiler Kelly C. , Tomescu Alexandru M.F. 
Published: October 2017

AbstractThe Emsian deposits of the Battery Point Formation (GaspéCanada) host the most diverse Early Devonian flora in North America. While most of this diversity has been described from plant compressions, the permineralized component of the flora is incompletely explored. Based on >15 axes studied in serial sections, we describe a new anatomically preserved rhyniopsid from the Battery Point Formation,Eddianna gaspianagen. & sp. nov..Eddiannaaxes are up to 2 mm in diameter and have a well-developed terete xylem strand with potential centrarch maturation (comprising 80% of the cross sectional surface area) that featuresSennicaulis-type tracheid wall thickenings. A thin layer interpreted as phloem is preserved around the central xylem and an irregular sclerenchymatous cortex forms longitudinal anastomosing ridges on the outside of the axes. The anatomy ofEddiannaaxes suggests that they represent lower portions, specialized in efficient water transfer, of a larger plant whose distal regions have yet to be discovered.Eddianna, the first permineralized rhyniopsid described from the Battery Point Formation, is one of only four anatomically preserved plants reported from this unit. These fossils reiterate the potential for additional discoveries of anatomically preserved plants in the Battery Point Formation.
Investigating low-velocity fluid flow in tumours using convection-MRI
Authors: Walker-Samuel Simon , Roberts Thomas A. , Ramasawmy Rajiv , Burrell Jake , Johnson S. Peter , Siow Bernard , Richardson Simon , Gonçalves Miguel , Pendsé Douglas , Robinson Simon P. , Pedley R. Barbara , Lythgoe Mark F. 
Published: October 2017

AbstractSeveral distinct fluid flow phenemena occur in solid tumours, including intravascular blood flow and interstitial convection. To probe low-velocity flow in tumors resulting from raised interstitial fluid pressure, we have developed a novel magnetic resonance imaging (MRI) technique named convection-MRI. It uses a phase-contrast acquisition with a dual-inversion vascular nulling preparation to separate intra- and extra-vascular flow. Here, we report the results of experiments in flow phantoms, numerical simulations and tumor xenograft models to investigate the technical feasibility of convection-MRI. We report a good correlation between estimates of effective fluid pressure from convection-MRI with gold-standard, invasive measurements of interstitial fluid pressure in mouse models of human colorectal carcinoma and show that convection-MRI can provide insights into the growth and response to vascular-targeting therapy in colorectal cancers.
Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis
Authors: Davidson Nadia M , Oshlack Alicia 
Published: October 2017

AbstractBackgroundRNA-Seq analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating assembled transcriptome with reference annotation are lacking.FindingsNecklace is a software pipeline that runs genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential expression testing.ConclusionsNecklace allows a comprehensive transcriptome to be built from a combination of assembled and annotated transcripts which results in a more comprehensive transcriptome for the majority of organisms. In addition RNA-seq data is mapped back to this newly created superTranscript reference to enable differential expression testing with standard methods. Necklace is available fromhttps://github.com/Oshlack/necklace/wikiunder GPL 3.0.
Vital signs analysis algorithm detects inflammatory response in premature infants with late onset sepsis and necrotizing enterocolitis
Authors: Mithal Leena B. , Yogev Ram , Palac Hannah L. , Kaminsky Daniel , Gur Ilan , Mestan Karen K. 
Published: October 2017

BackgroundNonspecific clinical signs and suboptimal diagnostic tests limit accurate identification of late onset sepsis (LOS) and necrotizing enterocolitis (NEC) in premature infants, resulting in significant morbidity and antibiotic overuse. An infant’s systemic inflammatory response may be identified earlier than clinical suspicion through analysis of multiple vital signs by a computerized algorithm (RALIS).AimTo evaluate the revised RALIS algorithm for detection of LOS and NEC in preterm infants.MethodsIn this nested case-control study, VS data (heart rate, respiratory rate, temperature, desaturations, bradycardias) were extracted from medical records of infants 23-32 weeks gestation. RALIS generated an output, with score >5 triggering an alert. Patient episodes were classified based on culture, radiograph, and antibiotic data into categories: LOS, expanded LOS, NEC, and controls. Paired t-tests, linear regression and cross-validation analyses were used to evaluate the relationship between RALIS alert and LOS/NEC.ResultsAmong 155 infants with 161 episodes, there were 41 expanded LOS (+ blood, CSF, urine, respiratory culture), 31 LOS (+ blood, CSF, urine), 9 NEC, and 93 controls. RALIS alert was 43.1+/-79 hours before culture in LOS (p=0.012). There was a significant association between RALIS alert and LOS/NEC (β=0.72, p<0.0001). Sensitivity and specificity for LOS/NEC were 84% and 80%, (PPV=63%; NPV=93%). The regression model demonstrated an AUC of 89.9%.ConclusionsFor infants <32 weeks, RALIS detects systemic inflammatory responses in LOS and NEC in the first month of life. The algorithm identifies infection earlier than clinical suspicion, even for NEC with negative cultures. RALIS has high NPV to rule-out LOS and NEC, and may, after prospective validation, aid in antibiotic treatment decisions.
Cis-regulatory evolution integrated the Bric-à-brac transcription factors into a novel fruit fly gene regulatory network
Authors: Roeske Maxwell J. , Camino Eric M. , Grover Sumant , Rebeiz Mark , Williams Thomas M. 
Published: October 2017

AbstractGene expression evolution through gene regulatory network (GRN) changes has gained appreciation as a driver of morphological evolution. However, understanding how GRNs evolve is hampered by finding relevantcis-regulatory element (CRE) mutations, and interpreting the protein-DNA interactions they alter. We investigated evolutionary changes in the duplicated Bric-à-brac (Bab) transcription factors and a key Bab target gene in a GRN underlying the novel dimorphic pigmentation ofD. melanogasterand its relatives. It has remained uncertain how Bab was integrated within the pigmentation GRN. Here we show that Bab gained a role in sculpting sex-specific pigmentation through the evolution of binding sites in a CRE of the pigment-promotingyellowgene and without any noteworthy changes to Bab protein coding sequences. This work demonstrates how a new trait can evolve by incorporating existing transcription factors into a GRN through CRE evolution, an evolutionary path likely to predominate newly evolved functions of transcription factors.
Rab5 and Alsin regulate stress-activated cytoprotective signaling on mitochondria
Authors: Hsu FoSheng , Spannl Stephanie , Ferguson Charles , Hyman Tony , Parton Robert G. , Zerial Marino 
Published: October 2017

AbstractMitochondrial stress response is essential for cell survival, and damaged mitochondria are a hallmark of neurodegenerative diseases. It is thus fundamental to understand how mitochondria relay information within the cell. Here, by investigating mitochondrial-endosome contact sites we made the surprising observation that the small GTPase Rab5 translocates from early endosomes to the outer mitochondrial membrane upon oxidative stress. This is accompanied by an increase in Rab5-positive endosomes in contact with mitochondria. Interestingly, activation of Rab5 on mitochondria depend on the Rab5-GEF ALS2/Alsin, which is encoded by a gene mutated in amyotrophic lateral sclerosis (ALS). Alsin-/-human induced pluripotent stem cell-derived spinal motor neurons cannot relocate Rab5 to mitochondria and display increased susceptibility to oxidative stress. These findings define a novel pathway whereby Alsin catalyzes assembly of the Rab5 endocytic machinery on mitochondria. Defects in stress-sensing by endosomes could be crucial for mitochondrial quality control during the onset of ALS.
A dynamical model of TCRβgene recombination: Coupling the initiation of Dβ-Jβrearrangement to TCRβallelic exclusion
Authors: Jaeger Sébastien , Lima Ricardo , Meyroneinc Arnaud , Bonnet Marie , Ugalde Edgardo , Ferrier Pierre 
Published: October 2017

AbstractOne paradigm of random monoallelic gene expression is that of T-cell receptor (TCR)βallelic exclusion in T lymphocytes. However, the dynamics that sustain asymmetric choice in TCRβdual allele usage and the production of TCRβmonoallelic expressing T-cells remain poorly understood. Here, we develop a computational model to explore a scheme of TCRβallelic exclusion based on the stochastic initiation of DNA rearrangement [V(D)J recombination] at homologous alleles in T-cell progenitors, and thus account for the genotypic profiles typically associated with allelic exclusion in differentiated T-cells. Disturbances in these dynamics at the level of an individual allele have limited consequences on these pro1les, robust feature of the system that is underscored by our simulations. Our study predicts a biological system in which locus-specific, prime epigenetic allelic activation effects set the stage to both optimize the production of TCRβallelically excluded T-cells and curtail the emergence of their allelically included counterparts.