bluuebunny/crossref_metadata_2025_split huggingface dataset:
Macrophage stimulating agent soluble yeast β‐1,3/1,6‐glucan as a topical treatment of diabetic foot and leg ulcers: A randomized, double blind, placebo‐controlled phase II study
Authors: Zykova Svetlana N , Balandina Ksenia A , Vorokhobina Natalia V , Kuznetsova Alla V , Engstad Rolf , Zykova Tatiana A 
Published: December 2013

AbstractAims/IntroductionDysregulated inflammatory response is believed to be an important factor in the pathogenesis of several late complications of diabetes mellitus. β‐Glucans are potent inducers of immune function. The present randomized, double blind, two‐center, placebo‐controlled study was undertaken to explore safety, tolerability and efficacy of soluble β‐1,3/1,6‐glucan (SBG) as a local treatment of diabetic foot ulcers.Materials and MethodsA total of 60 patients with type 1 or 2 diabetes and lower extremity ulcers (Wagner grade 1–2, Ankle/Brachial Index ≥0.7) received SBG or a comparator product (methylcellulose) locally three times weekly up to 12 weeks in addition to conventional management scheme. A total of 54 patients completed the study.ResultsA tendency for shorter median time to complete healing in the SBG group was observed (36 vs 63 days, P = 0.130). Weekly percentage reduction in ulcer size was significantly higher in the SBG group than in the methylcellulose group between weeks 1–2, 3–4 and 5–6 (P < 0.05). The proportion of ulcers healed by week 12 was also in favor of SBG (59% vs 37%, P = 0.09), with a significantly higher healing incidence in the SBG group at week 8 (44% vs 17%, P = 0.03). SBG was safe and well tolerated. There was a clinically significant difference regarding the incidence of serious adverse events in favor of the SBG treatment.ConclusionsLocal treatment of diabetic lower extremity ulcers with β‐1,3/1,6‐polyglucose shows good safety results. This β‐glucan preparation shows promising potential as a treatment accelerating cutaneous healing. Further studies are required to confirm this effect. This trial was registered with ClinicalTrials.gov (no. NCT00288392).
Designing Processing and Fermentation Conditions for Long‐Life Set Yoghurt for Made‐in‐Transit (MIT) Product
Authors: Nor‐Khaizura M‐A‐R. , Flint S.H. , McCarthy O.J. , Palmer J.S. , Golding M. , Jaworska A. 
Published: December 2013

AbstractExtending yoghurt fermentations could facilitate yoghurt distribution by allowing the fermentation to occur during transportation – a concept known as “made‐in‐transit” (MIT). The objective was to determine the starter culture composition, inoculum size and fermentation temperature for extending yoghurt fermentations to 168 h. The yoghurt was processed using a milk base sterilized by ultra‐high temperature (UHT) treatment at 138C for 6 s. Factorial experiments for yoghurt processing were designed with starter culture combinations of STLB (Streptococcus thermophilus with Lactobacillus delbrueckii subsp. bulgaricus) and STLA (S. thermophilus with L. acidophilus), inoculum sizes of 2.0 and 0.2% (v/v) and fermentation temperatures of 25 or 35C. The fermentation was monitored over 168 h using pH, starter culture concentration and firmness. The combination of STLA, and a 0.2% inoculum, fermented at 25C extended the yoghurt fermentation to 168 h; however, no gel formed. The best product was produced with a STLB starter combination of 2.0% inoculum fermented at 35C for 24 h. This shows the constraints and limitations of applying the MIT concept to a fermented food.Practical ApplicationsYoghurt produced using an extended fermentation time to allow fermentation during transportation, could allow product to be shipped to distant markets and extend the shelf life in the market. A UHT‐treated milk base will be needed to ensure no growth of contaminants, and this will also help to ensure a longer product shelf life. The fermentation conditions obtained in this study provide an opportunity for extending the yoghurt market reach by up to 7 days (168 h) of transportation.
Accumulation of periplasmic enterobactin impairs the growth and morphology of Escherichia coli tolC mutants
Authors: Vega Daniel E. , Young Kevin D. 
Published: December 2013

SummaryTolC is the outer membrane component of tripartite efflux pumps, which expel proteins, toxins and antimicrobial agents from Gram‐negative bacteria. Escherichia coli tolC mutants grow well and are slightly elongated in rich media but grow less well than wild‐type cells in minimal media. These phenotypes have no physiological explanation as yet. Here, we find that tolC mutants have highly aberrant shapes when grown in M9‐glucose medium but that adding iron restores wild‐type morphology. When starved for iron, E. coli tolC mutants synthesize but cannot secrete the siderophore enterobactin, which collects in the periplasm. tolC mutants unable to synthesize enterobactin display no growth or morphological defects, and adding exogenous enterobactin recreates these aberrations, implicating this compound as the causative agent. Cells unable to import enterobactin across the outer membrane grow normally, whereas cells that import enterobactin only to the periplasm become morphologically aberrant. Thus, tolC mutants grown in low iron conditions accumulate periplasmic enterobactin, which impairs bacterial morphology, possibly by sequestering iron and inhibiting an iron‐dependent reaction involved in cell division or peptidoglycan synthesis. The results also highlight the need to supply sufficient iron when studying TolC‐directed export or efflux, to eliminate extraneous physiological effects.
A universe of dwarfs and giants: genome size and chromosome evolution in the monocot familyMelanthiaceae
Authors: Pellicer Jaume , Kelly Laura J. , Leitch Ilia J. , Zomlefer Wendy B. , Fay Michael F. 
Published: December 2013

SummarySince the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process.Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclearDNAcontents.Melanthiaceae are the most diverse family in terms of genome size, withC‐values ranging more than 230‐fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor (MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change.Genome evolution inMelanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramaticDNAaccumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes.
The protein phosphatase subunit PP2A‐B′γ is required to suppress day length‐dependent pathogenesis responses triggered by intracellular oxidative stress
Authors: Li Shengchun , Mhamdi Amna , Trotta Andrea , Kangasjärvi Saijaliisa , Noctor Graham 
Published: December 2013

Summary

Oxidative stress responses are influenced by growth day length, but little is known about how this occurs. A combined reverse genetics, metabolomics and proteomics approach was used to address this question in Arabidopsis thaliana.

A catalase‐deficient mutant (cat2), in which intracellular oxidative stress drives pathogenesis‐related responses in a day length‐dependent manner, was crossed with a knockdown mutant for a specific type 2A protein phosphatase subunit (pp2a‐b′γ). In long days (LD), the pp2a‐b′γ mutation reinforced cat2‐triggered pathogenesis responses.

In short days (SD), conditions in which pathogenesis‐related responses were not activated in cat2, the additional presence of the pp2a‐b′γ mutation allowed lesion formation, PATHOGENESIS‐RELATED GENE1 (PR1) induction, salicylic acid (SA) and phytoalexin accumulation and the establishment of metabolite profiles that were otherwise observed in cat2 only in LD. Lesion formation in cat2 pp2a‐b′γ in SD was genetically dependent on SA synthesis, and was associated with decreased PHYTOCHROME A transcripts. Phosphoproteomic analyses revealed that several potential protein targets accumulated in the double mutant, including recognized players in pathogenesis and key enzymes of primary metabolism.

We conclude that the cat2 and pp2a‐b′γ mutations interact synergistically, and that PP2A‐B′γ is an important player in controlling day length‐dependent responses to intracellular oxidative stress, possibly through phytochrome‐linked pathways.
The effect of arginine on oral biofilm communities
Authors: Nascimento M.M. , Browngardt C. , Xiaohui X. , Klepac‐Ceraj V. , Paster B.J. , Burne R.A. 
Published: December 2013

SummaryAlkali production by oral bacteria via the arginine deiminase system (ADS) increases the pH of oral biofilms and reduces the risk for development of carious lesions. This study tested the hypothesis that increased availability of arginine in the oral environment through an exogenous source enhances the ADS activity levels in saliva and dental plaque. Saliva and supra‐gingival plaque samples were collected from 19 caries‐free (CF) individuals (DMFT = 0) and 19 caries‐active (CA) individuals (DMFT ≥ 2) before and after treatment, which comprised the use of a fluoride‐free toothpaste containing 1.5% arginine, or a regular fluoride‐containing toothpaste twice daily for 4 weeks. ADS activity was measured by quantification of ammonia produced from arginine by oral samples at baseline, after washout period, 4 weeks of treatment, and 2 weeks post‐treatment. Higher ADS activity levels were observed in plaque samples from CF compared to those of CA individuals (P = 0.048) at baseline. The use of the arginine toothpaste significantly increased ADS activity in plaque of CA individuals (P = 0.026). The plaque microbial profiles of CA treated with the arginine toothpaste showed a shift in bacterial composition to a healthier community, more similar to that of CF individuals. Thus, an anti‐caries effect may be expected from arginine‐containing formulations due in large part to the enhancement of ADS activity levels and potential favorable modification to the composition of the oral microbiome.
Evaluation of endocrine function in children admitted to pediatric intensive care unit
Authors: Aydın Banu Küçükemre , Demirkol Demet , Baş Firdevs , Türkoğlu Ümit , Kumral Alkın , Karaböcüoğlu Metin , Çıtak Agop , Darendeliler Feyza 
Published: December 2013

AbstractBackgroundAlthough studied widely in adulthood, little is known about endocrinological disorders during critical illnesses in childhood. The aims of this study were to define the endocrinological changes in patients admitted to pediatric intensive care unit (PICU) and to identify their effects on prognosis.MethodsForty patients with a mean age of 5.1 years admitted to PICU were enrolled in the study. Blood samples were taken at admission and at 24 and 48 h to measure cortisol, adrenocorticotropic hormone (ACTH), prolactin, growth hormone (GH), GH binding protein (GHBP), insulin‐like growth factor‐binding protein‐3 (IGFBP‐3) and interleukin‐6 (IL‐6). The severity of the patient's condition was assessed using pediatric risk of mortality (PRISM) and pediatric logistic organ dysfunction (PELOD) scores.ResultsPRISM and PELOD scores were significantly higher in non‐survivors. Cortisol, ACTH, prolactin, GH, GHBP, IGFBP‐3 and IL‐6 were not significantly different between the survivors and non‐survivors. There was a negative correlation between baseline IGFBP‐3 and PRISM scores. A positive correlation was seen between cortisol level at 24 h and PRISM score. On multivariate linear regression analysis, PRISM score was best explained by ACTH and cortisol at 24 h. A positive weak correlation was detected between IL‐6 at 24 h and PELOD scores.ConclusionsAlthough there was no difference between survivors and non‐survivors regarding the studied endocrine parameters, there were associations between cortisol, ACTH, IL‐6 and IGFBP‐3 and risk assessment scores, and, given that these scores correlated with mortality, these parameters might be useful as prognostic factors.
Last millennium development and dynamics of vegetated linear dunes inferred from ground‐penetrating radar and optically stimulated luminescence ages
Authors: Roskin Joel , Blumberg Dan G. , Katra Itzhak 
Published: December 2013

AbstractUsing ground‐penetrating radar, optically stimulated luminescence dating, particle‐size distribution and morphological analysis, the study of the construction phases of a vegetated linear dune in the arid north‐western Negev dunefield of Israel during the last millennium improves current knowledge about vegetated linear dunes that developed in the late Pleistocene. Vertical accretion in rapid pulses forming horizontally bedded units along the axis of vegetated linear dunes, regardless of their age, was found to be characteristic of vegetated linear dunes. The combination of the unique topographic feature of a longitudinal 5 m step‐like fall in dune crest elevation with the substantial narrowing of dune width constitutes a distinct morphological marker for interpreting local dune growth and stabilization of the last, albeit localized, dune mobilization episode at ca 0·5 ka. Evidence for lateral dune migration was not observed. Where local sediment supply exists, short episodes of powerful winds within the Holocene (with recurrence intervals separated by hundreds of years) can lead to the construction of vegetated linear dunes. The spatially constrained extent of such young dunes in the north‐western Negev may be due to limited sand availability because most of the Negev dunes were stable during the Holocene. These findings imply that vegetated linear dune construction can occur in glacial and interglacial (including Holocene) environments in semi‐arid to arid climates if certain conditions are met. In times of increased wind power during the Anthropocene, a period characterized by simultaneous rises in the human impact on the landscape and in climate variability (i.e. drought), local growth of vegetated linear dunes can be expected. This study demonstrates that ground‐penetrating radar is a reliable tool for interpreting the shallow internal structure of young vegetated linear dunes.
An example of a highly bioturbated, storm‐influenced shoreface deposit: Upper Jurassic Ula Formation, Norwegian North Sea
Authors: Baniak Greg M. , Gingras Murray K. , Burns Beverly A. , George Pemberton S. 
Published: December 2013

AbstractIntegrated ichnological and sedimentological analyses of core samples from the Upper Jurassic Ula Formation in the Norwegian Central Graben were undertaken to quantify the influence of storm waves on sedimentation. Two main facies associations (offshore and shoreface) that form a progradational coarsening upward succession are recognizable within the cores. The offshore deposits are characterized by massive to finely laminated mudstones and fine‐grained sandstones, within a moderately to highly bioturbated complex. The trace fossil assemblage is dominated by deposit‐feeding structures (for example, Planolites, Phycosiphon and Rosselia) and constitutes an expression of the proximal Zoophycos to distal Cruziana ichnofacies. The absence of grazing behaviours and dominance of deposit‐feeding ichnofossils is a reflection of the increased wave energies present (i.e. storm‐generated currents) within an offshore setting. The shoreface succession is represented by highly bioturbated fine‐grained to medium‐grained sandstones, with intervals of planar and trough cross‐bedding, thin pebble lags and bivalve‐rich shell layers. The ichnofossil assemblage, forming part of the Skolithos ichnofacies, is dominated by higher energy Ophiomorpha nodosa ichnofossils and lower energy Ophiomorpha irregulaire and Siphonichnus ichnofossils. The presence of sporadic wave‐generated sedimentary structures and variability in ichnofossil diversity and abundance attests to the influence of storm‐generated currents during deposition. As a whole, the Ula Formation strongly reflects the influence of storm deposits on sediment deposition; consequently, storm‐influenced shoreface most accurately describes these depositional environments.
Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective
Authors: van Heeswijk Wally C. , Westerhoff Hans V. , Boogerd Fred C. 
Published: December 2013

SUMMARYWe present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism inEscherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.
Incorporating Genomics into Breast Cancer Clinical Trials and Care
Authors: Tabchy Adel , Ma Cynthia X. , Bose Ron , Ellis Matthew J. 
Published: December 2013

Abstract
Advances in DNA sequencing provide the potential for clinical assays that are timely and affordable and use small amounts of clinical material. The hypothesis has therefore been raised that marked improvements in patient outcomes will result when DNA diagnostics are matched to an armamentarium of targeted agents. While this may be partially true, much of the novel biology uncovered by recent sequencing analysis is poorly understood and not druggable with existing agents. Significant other challenges remain before these technologies can be successfully implemented in the clinic, including the predictive accuracy of pathway-based models, distinguishing drivers from passenger mutations, development of rational combinations, addressing genomic heterogeneity, and molecular evolution/resistance mechanisms. Developments in regulatory science will also need to proceed in parallel to scientific advances so that targeted treatment approaches can be delivered to small subsets of patients with defined biology and drug reimbursement is available for individuals whose tumor carries a mutation that has been successfully targeted in another malignancy, as long as they agree to participate in an outcome registry. Clin Cancer Res; 19(23); 6371–9. ©2013 AACR.
Tackling the Diversity of Triple-Negative Breast Cancer
Authors: Turner Nicholas C. , Reis-Filho Jorge S. 
Published: December 2013

AbstractTriple-negative breast cancer (TNBC) comprises a highly diverse collection of cancers. Here, we review this diversity both in terms of gene expression subtypes and the repertoire of genetic events. Transcriptomic analyses of TNBC have revealed at least six subtypes, with the luminal androgen receptor (luminal AR) or molecular apocrine cancers forming a distinct group within triple-negative disease. Distinct from the gene expression subtypes, a diverse set of genetic events have been described in TNBC, with a number of potentially targetable genetic events found although all at relatively low frequency. Clinical trials to define the clinical utility of therapies targeting these low-frequency events will require substantial screening efforts to identify sufficient patients. Set against the diversity of TNBC, clinical studies of patients with triple-negative disease will need to be either focused on molecularly defined subsets with upfront molecular stratification, or powered for a secondary endpoint analysis of a molecularly defined subset. Such approaches will be crucial to realize the potential of precision medicine for patients with TNBCs. Clin Cancer Res; 19(23); 6380–8. ©2013 AACR.
Correlating Storm Surge Heights with Tropical Cyclone Winds at and before Landfall
Authors: Needham Hal F. , Keim Barry D. 
Published: December 2013

Abstract
This paper investigates relationships between storm surge heights and tropical cyclone wind speeds at 3-h increments preceding landfall. A unique dataset containing hourly tropical cyclone position and wind speed is used in conjunction with a comprehensive storm surge dataset that provides maximum water levels for 189 surge events along the U.S. Gulf Coast from 1880 to 2011. A landfall/surge classification was developed for analyzing the relationship between surge magnitudes and prelandfall winds. Ten of the landfall/surge event types provided useable data, producing 117 wind–surge events that were incorporated into this study. Statistical analysis indicates that storm surge heights correlate better with prelandfall tropical cyclone winds than with wind speeds at landfall. Wind speeds 18 h before landfall correlated best with surge heights. Raising wind speeds to exponential powers produced the best wind–surge fit. Higher wind–surge correlations were found when testing a more recent sample of data that contained 63 wind–surge events since 1960. The highest correlation for these data was found when wind speeds 18 h before landfall were raised to a power of 2.2, which provided R2 values that approached 0.70. The R2 values at landfall for these same data were only 0.44. Such results will be useful to storm surge modelers, coastal scientists, and emergency management personnel, especially when tropical cyclones rapidly strengthen or weaken while approaching the coast.