bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stratigraphic architecture resulting from dune interactions: White Sands Dune Field, New Mexico
Authors: Brothers Sarah C. , Kocurek Gary , Brothers Thomas C. , Buynevich Ilya V. 
Published: August 2016

ABSTRACTAeolian dune interactions provide the dynamics for field‐scale pattern emergence and evolution within a set of boundary conditions. Although morphologies for a spectrum of dune interactions are recognized, associated stratigraphic architectures are unknown and have probably been misidentified in the rock record. A unique data set for the White Sands Dune Field in New Mexico (USA) allowed for a detailed analysis in which the morphological evolution of defect and bedform repulsion interactions is chronicled over a decadal time‐series of images and coupled with the resulting stratigraphic architecture, documented from cross‐strata exposed in interdune areas and ground‐penetrating radar imaging of dune interiors. Defect and bedform repulsions represent a class of interactions in which the faster‐migrating dune termination or defect (defect repulsion), or pair of defects (bedform repulsion), collides with the target dune downwind. Results document that during the collision, the defect(s) of the impactor dune recombine(s) with a segment of the target dune, and the redundant target dune segment is ejected as a parabolic‐shaped ejecta dune. The ejecta dune assumes a more barchanoid shape as it migrates downwind. The interaction architecture consists of lateral truncation of the target set by an interaction bounding surface. Defect cross‐strata tangentially approach the surface in plan‐view, and downlap onto the surface in cross‐section. The orientation of the defect cross‐strata is at an acute angle to the trend of the interaction surface. Orientations of the defect cross‐strata, which represent the defect approach angle, and the target dune cross‐strata, which represent the general dune migration direction, diverge at a high angle. Defect cross‐strata typically consist of wind‐ripple laminae, in contrast to the target set that may house grainflow cross‐strata. In the transport direction, the erosional interaction surface curves to become subparallel to subjacent and superjacent cross‐strata where the defect and target unify into a single lee face.
A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA‐seq profiling
Authors: Klepikova Anna V. , Kasianov Artem S. , Gerasimov Evgeny S. , Logacheva Maria D. , Penin Aleksey A. 
Published: August 2016

SummaryArabidopsis thaliana is a long established model species for plant molecular biology, genetics and genomics, and studies of A. thaliana gene function provide the basis for formulating hypotheses and designing experiments involving other plants, including economically important species. A comprehensive understanding of the A. thaliana genome and a detailed and accurate understanding of the expression of its associated genes is therefore of great importance for both fundamental research and practical applications. Such goal is reliant on the development of new genetic and genomic resources, involving new methods of data acquisition and analysis. We present here the genome‐wide analysis of A. thaliana gene expression profiles across different organs and developmental stages using high‐throughput transcriptome sequencing. The expression of 25 706 protein‐coding genes, as well as their stability and their spatiotemporal specificity, was assessed in 79 organs and developmental stages. A search for alternative splicing events identified 37 873 previously unreported splice junctions, approximately 30% of them occurred in intergenic regions. These potentially represent novel spliced genes that are not included in the TAIR10 database. These data are housed in an open‐access web‐based database, TraVA (Transcriptome Variation Analysis, http://travadb.org/), which allows visualization and analysis of gene expression profiles and differential gene expression between organs and developmental stages.
Gastric carcinoma in canines and humans, a review
Authors: Hugen S. , Thomas R. E. , German A. J. , Burgener I. A. , Mandigers P. J. J. 
Published: August 2016

AbstractGastric carcinoma (GC) is the most common neoplasm in the stomach of dogs. Although incidence in the general population is reported to be low, breed‐specific GC has a high incidence. Median age at presentation ranges from 8 to approximately 10 years. The disease is mostly located in the lesser curvature and antropyloric region of the stomach. Unfortunately, diagnosis is usually made when the disease is at an advanced stage and, therefore, prognosis is poor. Due to similarities in clinical presentation, diagnosis, histology and prognosis, canine GC may serve as a valuable model for human GC. Extensive pedigrees of canine gastric carcinoma cases could reveal insights for human gastric carcinoma. Putative species differences include the role of Helicobacter in pathogenesis, the wide array of genetic data and screening available for humans, and treatment protocols that are available for human GC.
Evaluation ofPax5expression and comparison with BLA.36 and CD79αcy in feline non‐Hodgkin lymphoma
Authors: Felisberto R. , Matos J. , Alves M. , Cabeçadas J. , Henriques J. 
Published: August 2016

AbstractPaired box gene 5 (Pax5) is a widely used B‐cell marker for human and canine non‐Hodgkin's lymphoma (nHL); however, in the literature there is only one case report using Pax5 in a cat B‐cell lymphoma. The purposes of this study were to investigate the expression and detection of B‐cell specific activator protein (BSAP) using a monoclonal anti‐Pax5 antibody in felinenHL(FnHL) tissue samples to evaluate its diagnostic relevance as a B‐cell marker. A total of 45FnHLsamples in 45 cats were evaluated. B‐cell lymphoma was the most common immunophenotype (51.1%) for all the samples and T‐cell the most common immunophenotype (64.3%) for the gastrointestinal (GI) form. Pax5 stained 82.6% of all B‐cell lymphomas and no expression was found in any of the T‐cell lymphomas. Anti‐Pax5 antibody staining inFnHLis similar to that reported in human and canine counterparts and may offer an excellent B‐cell marker in cats.
Diagnostic performance of molecular and conventional methods for identification of dermatophyte species from clinically infected Arabian horses in Egypt
Authors: Tartor Yasmine H. , El Damaty Hend M. , Mahmmod Yasser S. 
Published: August 2016

BackgroundRapid and accurate identification of dermatophytes is crucial for the effective control of disease outbreaks. Current methods based on culture and microscopic characteristics may require weeks before positive identification is made.ObjectivesTo (i) identify the most common pathogenic dermatophytes affecting Arabian horses; (ii) compare the performance of direct microscopy (DM), culture, PCR using hair samples (PCRhair) and PCR based on culture isolates (PCRculture) for the diagnosis of dermatophytosis.MethodsSamples of hair and crusts of skin lesions from Arabian horses were collected on a monthly basis by scraping skin of affected horses. Samples were divided into three portions: the first portion was used for microscopic examination, the second for culture and the third portion for PCR amplification of intergenic spacer (ITS) regions.ResultsOut of 200 horses examined, 70 (35%) showed cutaneous lesions characteristic of dermatophytosis. DM revealed that 70.4% were positive for fungal elements and 85.7% were culture positive. The identified species were Microsporum canis, Trichophyton verrucosum, T. mentagrophytes var. mentagrophytes and M. equinum. Among 25 selected samples, 64, 92, 91.3 and 52% were positive for dermatophytes, as determined by DM, culture, PCRculture and PCRhair, respectively.ConclusionsThe dermatophytes M. canis, T. verrucosum, T. mentagrophytes var. mentagrophytes and M. equinum were the most common cause of dermatophytosis in Arabian horses. Although the number of samples was small, the ITS‐based PCR may be a useful diagnostic tool when combined with culture.
In Vitro Biomechanical Testing of the Tube Knot
Authors: Chang Stephany , Dong Fanglong , Lagman Minette , Schmidt Peggy L. , Irizarry Kristopher L. , Schulz David , Fahie Maria A. 
Published: August 2016

ObjectiveTo compare in vitro biomechanical properties of the tube knot (TB) to a crimp clamp (CC) system, and square knot (SQ) using 3 monofilament materials.Study DesignIn vitro biomechanical study.Sample PopulationSuture loops (n=20 per material/knot construct).MethodsMonotonic tensile loading (300 mm/min single pull to failure) was performed on knots tied using 3 knots (TB, 5‐throw SQ, and CC system) with each of 3 materials (40# Securos® nylon, #2 polypropylene, and #2 nylon). Ultimate tensile strength, elongation, and stiffness were measured and compared by sequential 1‐ and 2‐way ANOVA.ResultsUltimate tensile strength was greatest with 40# nylon CC (mean ± SD, 293.6 ± 26.2 N), followed by TB (289.8 ± 9.2 N) and SQ (252.2 ± 8.5 N) with no significant difference between CC and TB. TB with #2 polypropylene (158.1 ± 7.4 N) and #2 nylon (126.3 ± 5.5 N) had significantly greater tensile strength than SQ with #2 polypropylene (143.6 ± 5.3 N) and #2 nylon (110.7 ± 6.2 N). Elongation at failure was significantly greater in 40# nylon TB (25.3 ± 3.2 mm) and SQ (10.8 ± 1.6 mm) compared to CC (5.3 ± 1.0 mm). Both material and knotting method had an effect on ultimate tensile strength, elongation at failure, and stiffness, based on 2‐way ANOVA.ConclusionUltimate tensile strength of TB was equivalent to that of CC; however, elongation at failure was greatest for TB, which may be of concern for clinical applications.
Assessment of water quality in the vicinity of peat extraction sites: The case of Pien‐Saimaa, Finland
Authors: Sääksjärvi Eija , Reinikainen Satu‐Pia , Louhi‐Kultanen Marjatta 
Published: August 2016

AbstractPeatlands have an important global role as carbon sinks. Locally, however, peat bog extraction can cause pollution in nearby watercourses. The aim of this study is to investigate the application of multivariate methods in the renovation and protection of eutrophic lakes surrounded by agricultural and peat extraction areas. The analytical data used in the study originated from a national water quality database and the period studied was 2000–2013. Multivariate methods: Principal Component Analysis (PCA) and Parallel Factor Analysis (PARAFAC) were applied to solve interactions of variables and pollution sources in a complex water ecosystem. Leaching from the peat bog area was found to be the main source of iron, which has an important role as a precipitator of phosphorus in loose sediment and in water. Nutrient ratios had no direct correlation to algae blooms, but high ratios indicated an increased likelihood of an upcoming bloom.
Relationships between environmental metrics and water temperature: a case study of Polish lowland rivers
Authors: Łaszewski Maksym 
Published: August 2016

AbstractThe article presents relations between environmental metrics and water temperature in small Polish lowland rivers and describes their spatial temperature patterns. Water temperature data was obtained from measurements conducted on nine sites during summer of 2015 with the use of digital data loggers. Selected environmental metrics in the catchments areas were calculated and correlated with water temperature parameters. The results showed that water temperature patterns were generally similar across catchments, except for sites with strong human influence, which caused a decrease in the number and power of statistically significant relationships between environmental metrics and water temperature parameters. The best‐explained water temperature parameter was the minimum and mean daily range, while the best environmental predictors were the Strahler order, catchment area, mean catchment elevation and forested area. Most of the relations proved to be theoretically justified and could be used to further improve temperature monitoring studies and the management of water resources.
Pulmonary Deposition and Elimination of Liposomal Amikacin for Inhalation and Effect on Macrophage Function after Administration in Rats
Authors: Malinin Vladimir , Neville Mary , Eagle Gina , Gupta Renu , Perkins Walter R. 
Published: August 2016

ABSTRACT

Pulmonary nontuberculous mycobacterial (PNTM) infections represent a treatment challenge. Liposomal amikacin for inhalation (LAI) is a novel formulation currently in development for the treatment of PNTM infections. The pulmonary deposition and elimination of LAI and its effect on macrophage function were evaluated in a series of preclinical studies in healthy rats. The pulmonary deposition of LAI was evaluated in female rats (
n
= 76) treated with LAI by nebulizer at 10 mg/kg of body weight per day or 90 mg/kg per day for 27 days, followed by dosing of dually labeled LAI (LAI with a lipid label plus an amikacin label) on day 28 with subsequent lung histological and amikacin analyses. In a separate study for assessment of alveolar macrophage function, rats (
n
= 180) received daily treatment with LAI at 90 mg/kg per day or 1.5% saline over three 30-day treatment periods followed by 30-day recovery periods; phagocytic and
Saccharomyces cerevisiae
(yeast) killing capabilities and inflammatory mediator release were assessed at the end of each period. LAI demonstrated equal dose-dependent deposition across all lung lobes and regions. Lipid and amikacin labels showed diffuse extracellular colocalization, followed by macrophage uptake and gradual amikacin elimination. Macrophages demonstrated accumulation of amikacin during treatment periods and nearly complete elimination during recovery periods. No evidence of an inflammatory response was seen. No differences in microsphere uptake or yeast killing were seen between LAI-treated and control macrophages. Neither LAI-treated nor control macrophages demonstrated constitutive inflammatory mediator release; however, both showed normal mediator release on lipopolysaccharide stimulation. LAI is readily taken up by macrophages in healthy rats without compromising macrophage function.
Trivalency of a Nanobody Specific for the Human Respiratory Syncytial Virus Fusion Glycoprotein Drastically Enhances Virus Neutralization and Impacts Escape Mutant Selection
Authors: Palomo Concepción , Mas Vicente , Detalle Laurent , Depla Erik , Cano Olga , Vázquez Mónica , Stortelers Catelijne , Melero José A. 
Published: August 2016

ABSTRACT
ALX-0171 is a trivalent Nanobody derived from monovalent Nb017 that binds to antigenic site II of the human respiratory syncytial virus (hRSV) fusion (F) glycoprotein. ALX-0171 is about 6,000 to 10,000 times more potent than Nb017 in neutralization tests with strains of hRSV antigenic groups A and B. To explore the effect of this enhanced neutralization on escape mutant selection, viruses resistant to either ALX-0171 or Nb017 were isolated after serial passage of the hRSV Long strain in the presence of suboptimal concentrations of the respective Nanobodies. Resistant viruses emerged notably faster with Nb017 than with ALX-0171 and in both cases contained amino acid changes in antigenic site II of hRSV F. Detailed binding and neutralization analyses of these escape mutants as well as previously described mutants resistant to certain monoclonal antibodies (MAbs) offered a comprehensive description of site II mutations which are relevant for neutralization by MAbs and Nanobodies. Notably, ALX-0171 showed a sizeable neutralization potency with most escape mutants, even with some of those selected with the Nanobody, and these findings make ALX-0171 an attractive antiviral for treatment of hRSV infections.
Griffithsin-Modified Electrospun Fibers as a Delivery Scaffold To Prevent HIV Infection
Authors: Grooms Tiffany N. , Vuong Hung R. , Tyo Kevin M. , Malik Danial A. , Sims Lee B. , Whittington Carli P. , Palmer Kenneth E. , Matoba Nobuyuki , Steinbach-Rankins Jill M. 
Published: August 2016

ABSTRACT

Despite current prophylactic strategies, sexually transmitted infections (STIs) remain significant contributors to global health challenges, spurring the development of new multipurpose delivery technologies to protect individuals from and treat virus infections. However, there are few methods currently available to prevent and no method to date that cures human immunodeficiency virus (HIV) infection or combinations of STIs. While current oral and topical preexposure prophylaxes have protected against HIV infection, they have primarily relied on antiretrovirals (ARVs) to inhibit infection. Yet continued challenges with ARVs include user adherence to daily treatment regimens and the potential toxicity and antiviral resistance associated with chronic use. The integration of new biological agents may avert some of these adverse effects while also providing new mechanisms to prevent infection. Of the biologic-based antivirals, griffithsin (GRFT) has demonstrated potent inhibition of HIV-1 (and a multitude of other viruses) by adhering to and inactivating HIV-1 immediately upon contact. In parallel with the development of GRFT, electrospun fibers (EFs) have emerged as a promising platform for the delivery of agents active against HIV infection. In the study described here, our goal was to extend the mechanistic diversity of active agents and electrospun fibers by incorporating the biologic GRFT on the EF surface rather than within the EFs to inactivate HIV prior to cellular entry. We fabricated and characterized GRFT-modified EFs (GRFT-EFs) with different surface modification densities of GRFT and demonstrated their safety and efficacy against HIV-1 infection
in vitro
. We believe that EFs are a unique platform that may be enhanced by incorporation of additional antiviral agents to prevent STIs via multiple mechanisms.
Identification of Nafamostat as a Potent Inhibitor of Middle East Respiratory Syndrome Coronavirus S Protein-Mediated Membrane Fusion Using the Split-Protein-Based Cell-Cell Fusion Assay
Authors: Yamamoto Mizuki , Matsuyama Shutoku , Li Xiao , Takeda Makoto , Kawaguchi Yasushi , Inoue Jun-ichiro , Matsuda Zene 
Published: August 2016

ABSTRACT

Middle East respiratory syndrome (MERS) is an emerging infectious disease associated with a relatively high mortality rate of approximately 40%. MERS is caused by MERS coronavirus (MERS-CoV) infection, and no specific drugs or vaccines are currently available to prevent MERS-CoV infection. MERS-CoV is an enveloped virus, and its envelope protein (S protein) mediates membrane fusion at the plasma membrane or endosomal membrane. Multiple proteolysis by host proteases, such as furin, transmembrane protease serine 2 (TMPRSS2), and cathepsins, causes the S protein to become fusion competent. TMPRSS2, which is localized to the plasma membrane, is a serine protease responsible for the proteolysis of S in the post-receptor-binding stage. Here, we developed a cell-based fusion assay for S in a TMPRSS2-dependent manner using cell lines expressing
Renilla
luciferase (RL)-based split reporter proteins. S was stably expressed in the effector cells, and the corresponding receptor for S, CD26, was stably coexpressed with TMPRSS2 in the target cells. Membrane fusion between these effector and target cells was quantitatively measured by determining the RL activity. The assay was optimized for a 384-well format, and nafamostat, a serine protease inhibitor, was identified as a potent inhibitor of S-mediated membrane fusion in a screening of about 1,000 drugs approved for use by the U.S. Food and Drug Administration. Nafamostat also blocked MERS-CoV infection
in vitro
. Our assay has the potential to facilitate the discovery of new inhibitors of membrane fusion of MERS-CoV as well as other viruses that rely on the activity of TMPRSS2.
Activity of Tedizolid in Methicillin-Resistant Staphylococcus aureus Experimental Foreign Body-Associated Osteomyelitis
Authors: Park Kyung-Hwa , Greenwood-Quaintance Kerryl E. , Mandrekar Jayawant , Patel Robin 
Published: August 2016

ABSTRACT

We compared tedizolid alone and tedizolid with rifampin to rifampin and vancomycin plus rifampin in a rat model of methicillin-resistant
Staphylococcus aureus
(MRSA) foreign body-associated osteomyelitis. The study strain was a prosthetic joint infection-associated isolate. Steady-state pharmacokinetics for intraperitoneal administration of tedizolid, vancomycin, and rifampin were determined in uninfected rats. MRSA was inoculated into the proximal tibia, and a wire was implanted. Four weeks later, the rats were treated intraperitoneally for 21 days with tedizolid (
n
= 14), tedizolid plus rifampin (
n
= 11), rifampin (
n
= 16), or vancomycin plus rifampin (
n
= 13). Seventeen rats received no treatment. After treatment, quantitative bone cultures were performed. Blood was obtained for determination of drug trough concentrations in the tedizolid and tedizolid plus rifampin groups. The mean peak plasma concentration and mean area under the concentration-time curve from time zero to 24 h for tedizolid were 12 μg/ml and 60 μg · h/ml, respectively. The bacterial loads in all treatment groups were significantly lower than those in the control group; those in the tedizolid- plus rifampin-treated animals were not significantly different from those in the vancomycin- plus rifampin-treated animals. The range of mean plasma trough concentrations in the tedizolid group was 0.44 to 0.73 μg/ml. Although neither tedizolid nor vancomycin resistance was detected in isolates recovered from bones, rifampin resistance was detected in 10 animals (63%) in the rifampin group, 8 animals (73%) in the tedizolid plus rifampin group, and a single animal (8%) in the vancomycin plus rifampin group. Tedizolid alone or tedizolid combined with rifampin was active in a rat model of MRSA foreign body-associated osteomyelitis. The emergence of rifampin resistance was noted in animals receiving tedizolid plus rifampin.