bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environment and the Lifetime of Tropical Deep Convection in a Cloud-Permitting Regional Model Simulation
Authors: Hagos Samson , Feng Zhe , McFarlane Sally , Leung L. Ruby 
Published: May 2013

Abstract
By applying a cloud-tracking algorithm to tropical convective systems in a regional high-resolution model simulation, this study documents the environmental conditions before and after convective systems are initiated over ocean and land by following them during their lifetime. The comparative roles of various mechanisms of convection–environment interaction on the longevity of convective systems are quantified. The statistics of lifetime, maximum area, and propagation speed of the simulated deep convection agree well with geostationary satellite observations.
Among the environmental variables considered, lifetime of convective systems is found to be most related to midtropospheric moisture before as well as after the initiation of convection. Over ocean, convective systems enhance surface fluxes through the associated cooling and drying of the boundary layer as well as increased wind gusts. This process appears to play a minor positive role in the longevity of systems. For systems of equal lifetime, those over land tend to be more intense than those over ocean especially during the early stages of their life cycle. Both over ocean and land, convection is found to transport momentum vertically to increase low-level shear and decrease upper-level shear, but no discernible effect of shear on the lifetime of the convective systems is found.
Informing Hydrometric Network Design for Statistical Seasonal Streamflow Forecasts
Authors: Rosenberg Eric A. , Wood Andrew W. , Steinemann Anne C. 
Published: May 2013

Abstract
A hydrometric network design approach is developed for enhancing statistical seasonal streamflow forecasts. The approach employs gridded, model-simulated water balance variables as predictors in equations generated via principal components regression in order to identify locations for additional observations that most improve forecast skill. The approach is applied toward the expansion of the Natural Resources Conservation Service (NRCS) Snowpack Telemetry (SNOTEL) network in 24 western U.S. basins using two forecasting scenarios: one that assumes the currently standard predictors of snow water equivalent and water year-to-date precipitation and one that considers soil moisture as an additional predictor variable. Resulting improvements are spatially and temporally analyzed, attributed to dominant predictor contributions, and evaluated in the context of operational NRCS forecasts, ensemble-based National Weather Service (NWS) forecasts, and historical as-issued NRCS/NWS coordinated forecasts. Findings indicate that, except for basins with sparse existing networks, substantial improvements in forecast skill are only possible through the addition of soil moisture variables. Furthermore, locations identified as optimal for soil moisture sensor installation are primarily found in regions of low to mid elevation, in contrast to the higher elevations where SNOTEL stations are traditionally situated. The study corroborates prior research while demonstrating that soil moisture data can explicitly improve operational water supply forecasts (particularly during the accumulation season), that statistical forecasts are comparable in skill to ensemble-based forecasts, and that simulated hydrologic data can be combined with observations to improve statistical forecasts. The approach can be generalized to other settings and applications involving the use of point observations for statistical prediction models.
A Free-Floating PIV System: Measurements of Small-Scale Turbulence under the Wind Wave Surface
Authors: Wang Binbin , Liao Qian , Xiao Jianen , Bootsma Harvey A. 
Published: May 2013

Abstract
An in situ free-floating underwater miniature particle image velocimetry (UWMPIV) system is developed and applied to measure the structure of turbulence in the aqueous side of the wind wave surface boundary layer. The UWMPIV system provides a direct way to measure the aqueous side turbulence dissipation rate and vortex structures immediately below the air–water interface, which are important parameters that determine the gas exchange rate across the air–water interface subjected to a low-to-moderate wind shear. The impact of platform motion on the measurement of small-scale turbulence is discussed and found to be insignificant. A series of field experiments under a near “zero-fetch” wind wave condition and one open water experiment under a low wind condition were conducted on Lake Michigan to demonstrate the capabilities of the free-floating particle image velocimetry (PIV) system. The dissipation rate estimated with a “direct method” and with a “spectra fitting” method are compared. Vertical profiles of the turbulence dissipation rate suggest a power-law dependency with depth below the water surface. Surface shear velocities estimated through the aqueous side Reynolds stress distribution agreed well with wind stresses estimated by the classic drag law for zero-fetch wind wave conditions, where the primary source of turbulence was wind shear. For the open water experiment under a very low wind condition, a high dissipation rate was observed near the water surface, suggesting a high turbulence production rate by surface waves, and the profile of dissipation rate showed a slower decay rate with depth in the presence of waves.
Pearls and pitfalls in experimental in vivo models of migraine: Dural trigeminovascular nociception
Authors: Akerman Simon , Holland Philip R , Hoffmann Jan 
Published: May 2013

Background Migraine is a disorder of the brain and is thought to involve activation of the trigeminovascular system, which includes the peripheral afferent projection to the nociceptive specific dura mater, as well as the central afferent projection to the trigeminal nucleus caudalis. Stimulation of the blood vessels of the dura mater produces pain in patients that is referred to the head similar to headache. Headache mechanisms The likely reason for the pain is because the vascular structures of the dura mater, including the superior sagittal sinus and middle meningeal artery, are richly innervated by a plexus of largely unmyelinated sensory nerve fibers from the ophthalmic division of the trigeminal ganglion. Methodology Stimulation of these nociceptive specific nerve fibers is painful and produces neuronal activation in the trigeminal nucleus caudalis. Preclinical models of headache have taken advantage of this primarily nociceptive pathway, and various animal models use dural trigeminovascular nociception to assay aspects of head pain. These assays measure responses at the level of the dural vasculature and the central trigeminal nucleus caudalis as a correlate of trigeminovascular activation thought to be involved in headache. Summary This review will summarize the history of the development of models of dural trigeminovascular nociception, including intravital microscopy and laser Doppler flowmetry at the level of the vasculature, and electrophysiology and Fos techniques used to observe neuronal activation at the trigeminal nucleus caudalis. It will also describe some of pitfalls of these assays and developments for the future.
Pearls and pitfalls: Neurostimulation in headache
Authors: Jürgens Tim P , Leone Massimo 
Published: May 2013

Context A variety of neuromodulatory approaches available today has broadened our therapeutic options significantly especially in drug refractory patients with chronic cluster headache and chronic migraine. Overview It is a dynamic field with a current trend to non-invasive transcutaneous stimulation approaches. However, sound studies providing evidence for the widespread use of these novel approaches are sparse. For invasive approaches, occipital nerve stimulation is now widely considered the treatment of first choice in chronic trigeminal autonomic cephalgias and – with limitations – chronic migraine. Although equally effective, deep brain stimulation is considered second-line treatment in cluster headache because of its potentially life-threatening side effects. Most recently, stimulation of the sphenopalatine ganglion has also been shown to effectively abort acute cluster headache attacks. Interesting other upcoming approaches include transcutaneous supraorbital nerve stimulation and transcutaneous vagal nerve stimulation. Conclusion Pearls and pitfalls of common invasive and non-invasive neuromodulatory approaches and open questions are summarised in this review along with recommendations for future studies.
Intermolecular interactions of the malate synthase of Paracoccidioides spp
Authors: de Oliveira Karine Martins , da Silva Neto Benedito Rodrigues , Parente Juliana Alves , da Silva Roosevelt Alves , Quintino Guilherme Oliveira , Voltan Aline Raquel , Mendes-Giannini Maria José Soares , de Almeida Soares Célia Maria , Pereira Maristela 
Published: May 2013

Abstract

Background
The fungus Paracoccidioides spp is the agent of paracoccidioidomycosis (PCM), a pulmonary mycosis acquired by the inhalation of fungal propagules. Paracoccidioides malate synthase (PbMLS) is important in the infectious process of Paracoccidioides spp because the transcript is up-regulated during the transition from mycelium to yeast and in yeast cells during phagocytosis by murine macrophages. In addition, PbMLS acts as an adhesin in Paracoccidioides spp. The evidence for the multifunctionality of PbMLS indicates that it could interact with other proteins from the fungus and host. The objective of this study was to identify and analyze proteins that possibly bind to PbMLS (PbMLS-interacting proteins) because protein interactions are intrinsic to cell processes, and it might be possible to infer the function of a protein through the identification of its ligands.

Results
The search for interactions was performed using an in vivo assay with a two-hybrid library constructed in S. cerevisiae; the transcripts were sequenced and identified. In addition, an in vitro assay using pull-down GST methodology with different protein extracts (yeast, mycelium, yeast-secreted proteins and macrophage) was performed, and the resulting interactions were identified by mass spectrometry (MS). Some of the protein interactions were confirmed by Far-Western blotting using specific antibodies, and the interaction of PbMLS with macrophages was validated by indirect immunofluorescence and confocal microscopy. In silico analysis using molecular modeling, dynamics and docking identified the amino acids that were involved in the interactions between PbMLS and PbMLS-interacting proteins. Finally, the interactions were visualized graphically using Osprey software.

Conclusion
These observations indicate that PbMLS interacts with proteins that are in different functional categories, such as cellular transport, protein biosynthesis, modification and degradation of proteins and signal transduction. These data suggest that PbMLS could play different roles in the fungal cell.
Polymorphisms of PTPN11 gene could influence serum lipid levels in a sex-specific pattern
Authors: Jia Zhi-Fang , Cao Xue-Yuan , Cao Dong-Hui , Kong Fei , Kharbuja Punyaram , Jiang Jing 
Published: May 2013

Abstract

Background
Previous studies have reported that different genotypes of PTPN11 gene (protein tyrosine phosphatase, non-receptor 11) were associated with different levels of serum lipids. The aim of this study was to explore the relationship between single nucleotide polymorphisms (SNPs) of PTPN11 and serum lipids in Northeast Chinese.

Methods
A total of 1003 subjects, 584 males and 419 females, were included in the study and their serum lipids were determined. Five htSNPs (rs2301756, rs12423190, rs12229892, rs7958372 and rs4767860) of PTPN11 gene were genotyped using TaqMan assay method.

Results
All of the five SNPs were in Hardy-Weinberg equilibrium. The male subjects had higher triglyceride (TG), higher low-density lipoprotein cholesterol (LDL-C) and lower high-density lipoprotein cholesterol (HDL-C) level than females. In males, rs4767860 was found to be associated with serum TG and total cholesterol (TC) levels and rs12229892 was associated with TC level. However, these significant associations could not be observed in females. In females, rs2301756 was found to be associated with TG and rs7958372 was associated with LDL-C level. Haplotype analysis showed that the GCGTG haplotype was associated with slightly higher TG level and ATGCG with higher TC level.

Conclusions
SNPs of PTPN11 may play a role in serum lipids in a sex-specific pattern. However, more studies are needed to confirm the conclusion and explore the underlying mechanism.
SF2/ASF binding region within JC virus NCCR limits early gene transcription in glial cells
Authors: Uleri Elena , Regan Patrick , Dolei Antonina , Sariyer Ilker Kudret 
Published: May 2013

AbstractBackgroundPatients undergoing immune modulatory therapies for the treatment of autoimmune diseases such as multiple sclerosis, and individuals with an impaired-immune system, most notably AIDS patients, are in the high risk group of developing progressive multifocal leukoencephalopathy (PML), a fatal demyelinating disease of the white matter caused by human neurotropic polyomavirus, JC virus. It is now widely accepted that pathologic strains of JCV shows unique rearrangements consist of deletions and insertions within viral NCCR. While these kinds of rearrangements are related to viral tropism and pathology of the disease, their roles in molecular regulation of JCV gene expression and replication are unclear. We have previously identified SF2/ASF as a negative regulator of JCV gene expression in glial cells. This negative impact of SF2/ASF was dependent on its ability to bind a specific region mapped to the tandem repeat within viral promoter. In this report, functional role of SF2/ASF binding region in viral gene expression and replication was investigated by using deletion mutants of viral regulatory sequences.ResultsThe second 98-base-pair tandem repeat on Mad1 strain was first mutated by deletion and named Mad1-(1X98). In addition to this mutant, the CR3 region which served the binding side for SF2/ASF was also mutated and named Mad1-ΔCR3 (1X73). Both mutations were tested for SF2/ASF binding by ChIP assay. While SF2/ASF was associated with Mad1-WT and Mad1-(1X98), its interaction was completely abolished on Mad1-ΔCR3 (1X73) construct as expected. Surprisingly, reporter gene analysis of Mad1-(1X98) and Mad1-ΔCR3 (1X73) early promoter sequences showed two and three fold increase in promoter activities, respectively. The impact of “CR3” region on JCV propagation was also tested on the viral background. While replication of Mad1-(1X98) strain in glial cells was similar to Mad1-WT strain, propagation of Mad1-ΔCR3 (1X73) was less productive. Further analysis of the transcription mediated by Mad1-ΔCR3 (1X73) NCCR revealed that late gene expression was significantly affected.ConclusionsThe results of this study reveal a differential role of CR3 region within JCV NCCR in expression of JCV early and late genes.
Human monoclonal ScFv that bind to different functional domains of M2 and inhibit H5N1 influenza virus replication
Authors: Pissawong Tippawan , Maneewatch Santi , Thueng-in Kanyarat , Srimanote Potjanee , Dong-din-on Fonthip , Thanongsaksrikul Jeeraphong , Songserm Thaweesak , Tongtawe Pongsri , Bangphoomi Kunan , Chaicumpa Wanpen 
Published: May 2013

AbstractBackgroundNovel effective anti-influenza agent that tolerates influenza virus antigenic variation is needed. Highly conserved influenza virus M2 protein has multiple pivotal functions including ion channel activity for vRNP uncoating, anti-autophagy and virus assembly, morphogenesis and release. Thus, M2 is an attractive target of anti-influenza agents including small molecular drugs and specific antibodies.MethodsFully human monoclonal single chain antibodies (HuScFv) specific to recombinant and native M2 proteins of A/H5N1 virus were produced fromhuscfv-phagemid transformedE. coliclones selected from a HuScFv phage display library using recombinant M2 of clade 1 A/H5N1 as panning antigen. The HuScFv were tested for their ability to inhibit replication of A/H5N1 of both homologous and heterologous clades. M2 domains bound by HuScFv of individualE. coliclones were identified by phage mimotope searching and computerized molecular docking.ResultsHuScFv derived from fourhuscfv-phagemid transformedE. coliclones (no. 2, 19, 23 and 27) showed different amino acid sequences particularly at the CDRs. Cells infected with A/H5N1 influenza viruses (both adamantane sensitive and resistant) that had been exposed to the HuScFv had reduced virus release and intracellular virus. Phage peptide mimotope search and multiple alignments revealed that conformational epitopes of HuScFv2 located at the residues important for ion channel activity, anti-autophagy and M1 binding; epitopic residues of HuScFv19 located at the M2 amphipathic helix and cytoplasmic tail important for anti-autophagy, virus assembly, morphogenesis and release; epitope of HuScFv23 involved residues important for the M2 activities similar to HuScFv2 and also amphipathic helix residues for viral budding and release while HuScFv27 epitope spanned ectodomain, ion channel and anti-autophagy residues. Results of computerized homology modelling and molecular docking conformed to the epitope identification by phages.ConclusionsHuScFv that bound to highly conserved epitopes across influenza A subtypes and human pathogenic H5N1clades located on different functional domains of M2 were produced. The HuScFv reduced viral release and intracellular virus of infected cells. While the molecular mechanisms of the HuScFv await experimental validation, the small human antibody fragments have high potential for developing further as a safe, novel and mutation tolerable anti-influenza agent especially against drug resistant variants.
In vitro evaluation of anti-infective activity of a Lactobacillus plantarum strain against Salmonella enterica serovar Enteritidis
Authors: Das Jugal Kishore , Mishra Debasmita , Ray Pratikshya , Tripathy Prangya , Beuria Tushar K , Singh Neera , Suar Mrutyunjay 
Published: May 2013

Abstract

Background

Salmonella enterica serovar Enteritidis infections are known to exhibit worldwide prevalence with increased morbidity and mortality. The conventional strategies like antibiotic therapy and vaccination have not only proved to be of sub-optimal efficacy but also led to the development of multidrug resistant strains of Salmonella. Antimicrobial activities of probiotics against various enteropathogens and other health promoting effects have assumed greater significance in recent years. The present study aims to evaluate the efficacy of a Lactobacillus plantarum strain (KSBT 56, isolated from a traditional food product of India), in preventing Salmonella enterica serovar Enteritidis growth and pathogenicity in vitro.

Methods and results
The cell free culture supernatant (CFCS) of KSBT 56 strain notably inhibited the growth of Salmonella Enteritidis without affecting the growth of other gram-positive lactic acid bacteria. The isolated KSBT 56 strain produces lactic acid similar to other standard probiotic strains like Lactobacillus plantarum MTCC 1407. The free radical production by KSBT 56 strain was studied by using sodC mutant of S. Enteritidis, which exhibited reduced growth in the presence of CFCS of the KSBT 56 strain, indicating the inhibitory activity of free radicals on the growth of S. Enteritidis. Our results also showed a significant reduction in the biofilm forming ability of Salmonella Enteritidis in the presence of the KSBT 56 strain (2 log cfu/ml, p = 0.01). Further, the anti-infective characteristics of KSBT 56 strain was validated by gentamicin protection assay which revealed 80% reduction in the invasion of Salmonella Enteritidis to HCT-116 cell line (Salmonella Enteritidis and KSBT 56 in a 1:1 ratio) and delayed addition of Salmonella Enteritidis by 1 h. Similarly, the reduced adhesion of Salmonella to the HCT-116 cells was observed along with the down regulation of hilA gene of Salmonella Pathogenicity Island 1 (SPI1) indicating that they might have acted synergistically to decrease the invasion of the pathogen into the cell line.

Conclusions
KSBT 56 strain effectively inhibited the growth, invasion and the biofilm forming ability of Salmonella Enteritidis without inhibiting the growth of other Lactobacillus strains. Overall, our result suggested that KSBT 56 can be used as a potential probiotic strain with considerable beneficial effects on the host.
Negative Charge and Solvent Effects on Electronic Excited-State Hydrogen Bonding of 2′-Deoxycytidine 5′-Monophosphate (dCMP) in Aqueous Solution
Authors: Zhang Xiaoyu , Zhang Weiping 
Published: May 2013

Abstract
Time-dependent density functional theory (TDDFT) was applied to study the influence of negative charge and solvent effects on the hydrogen-bonding dynamics of 2′-deoxycytidine 5′-monophosphate (dCMP) in electronically excited states. The intramolecular hydrogen bond O5–H2···O3 would be weakened with the strengthening of the hydration. Moreover, the greater the negative charge, the stronger the intramolecular hydrogen bond O5–H2···O3 is in [dCMP-H]−/2−–nH2O (n = 1, 2, 3) complexes. We concluded that the negative charge site of the phosphate would be the preferable site of hydration. In comparison with hydrogen-bonded [dCMP-H]−–nH2O (n = 0, 1, 2, 3) complexes, the excitation energies of complexes [dCMP-H]2−–nH2O (n = 0, 1, 2, 3) are lower except for individual excited states, that is to say, the increase of negative charge can make the related electronic spectra shift to red and hydrogen bonds strengthen. According to the results of calculated absorption spectra, the solvent effects by the polarizible continuum model (PCM) can lead to the electronic spectra blue shift.
A Facile Synthesis of Monodispersed Carbon-encapsulated Copper Nanoparticles with Excellent Oxidation Resistance from a Refluxing-derived Precursor
Authors: Meng Xiaopeng , Wen Jiqiu , Yao Yadong , Ding Yi , Gong Yichao , Zou Changwu , Yin Guangfu , Liao Xiaoming , Huang Zhongbing , Chen Xianchun 
Published: May 2013

Abstract
Carbon-encapsulated copper nanoparticles (CECNPs) are synthesized from a precursor derived easily through a refluxing method. The as-synthesized CECNPs are monodispersed with a uniform size distribution and obvious core–shell structure. The formation process of the CECNPs is investigated, and the possible mechanism is proposed. Furthermore, TG-DSC measurements, in conjunction with the corresponding XRD patterns, reveal that the as-synthesized CECNPs show excellent oxidation resistance to temperatures up to 900 °C.
Transformation of Gold(I)–cyclo[–Met–Met–] Complex Supramolecular Fibers into Aligned Gold Nanoparticles
Authors: Furutani Masahiro , Kudo Kazuaki 
Published: May 2013

Abstract
A cyclic dipeptide cyclo[–l-methionyl–l-methionyl–] and gold(I) cation were found to form a complex in a 1:2 ratio. Pouring a DMF solution of the complex into ethyl acetate afforded fibers with lengths of more than 20 µm and 100–400 nm in width, which consisted of fibrous nanostructures 50–100 nm in diameter. Treatment of this supramolecular fiber with catechol gave linearly aligned Au nanoparticles on the original fibers.
Organic Semiconductor Molecules with Nonaromatic Core of 1,4-Dithiin
Authors: Ito Hiroki , Watanabe Daichi , Yamamoto Tatsuya , Tsushima Noboru , Muraoka Hiroki , Ogawa Satoshi 
Published: May 2013

Abstract
Novel thiophene-condensed 1,4-dithiin derivatives having styryl or phenyl groups were synthesized, and their spectroscopic and electrochemical properties were investigated. Organic field-effect transistor (OFET) devices using these derivatives exhibited typical p-type FET characteristics, though the core units of both molecules were not aromatic compounds.