bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discrimination of influenza A subtype by antibodies recognizing host‐specific amino acids in the viral nucleoprotein
Authors: Miyoshi‐Akiyama Tohru , Yamashiro Tetsu , Mai Le Quynh , Narahara Kenji , Miyamoto Akitomo , Shinagawa Shingo , Mori Sunao , Kitajima Hirotake , Kirikae Teruo 
Published: February 2012

Please cite this paper as: Miyoshi‐Akiyama et al. (2012) Discrimination of influenza A subtype by antibodies recognizing host‐specific amino acids in the viral nucleoprotein. Influenza and Other Respiratory Viruses 6(6), 434–441.Background  Nucleoprotein (NP) of influenza viruses is utilized to differentiate between the A, B, and C viral serotypes. The availability of influenza genome sequence data has allowed us to identify specific amino acids at particular positions in viral proteins, including NP, known as “signature residues,” which can be used to discriminate human influenza A viruses from H5N1 highly pathogenic avian influenza in human cases (HPAI) and pandemic H1N1(2009) (H1N1/2009) viruses.Methods  Screening and epitope mapping of monoclonal antibodies (mAb) against NP of influenza A, which reacted differently with NP from human influenza A virus from HPAI and H1N1/2009 A virus. To identify the epitope(s) responsible for the discrimination of viral NP by mAbs, we prepared mutant NP proteins in the 293 cell expression system because some of the mAbs reacted with non‐linear epitopes.Results and Conclusions  In the present study, we identified 3 mAbs. The results of epitope mapping showed that the epitopes were located at the signature residues. These results indicated that signature residues of NP could discriminate influenza A viruses from different origin.
Glycoalkaloids (α‐Chaconine and α‐Solanine) Contents of Selected Pakistani Potato Cultivars and Their Dietary Intake Assessment
Authors: Aziz Abdul , Randhawa Muhammad Atif , Butt Masood Sadiq , Asghar Ali , Yasin Muhammad , Shibamoto Takayuki 
Published: February 2012

Abstract:  Glycoalkaloids (α‐solanine and α‐chaconine) are naturally occurring toxic compounds in potato tuber (Solanum tuberosum L.) that cause acute intoxication in humans after their consumption. Present research was conducted to evaluate α‐chaconine, α‐solanine, and total glycoalkaloids (TGAs) contents in the peel and flesh portions by high‐performance liquid chromatography method in selected Pakistani potato cultivars. The α‐solanine content varies 45.98 ± 1.63 to 2742.60 ± 92.97 mg/100 g of dry weight (DW) in peel and from 4.01 ± 0.14 to 2466.56 ± 87.21 mg/100 g of DW in flesh. Similarly, α‐chaconine content varied from 4.42 ± 0.16 to 6818.40 ± 211.07 mg/100 g of DW in potato peel and from 3.94 ± 0.14 to 475.33 ± 16.81 mg/100 g DW in flesh portion. The TGA concentration varied from 177.20 ± 6.26 to 5449.90 ± 192.68 mg/100 g of DW in peel and from 3.08 ± 0.11 to 14.69 ± 0.52 mg/100 g of DW in flesh portion of all the potato cultivars tested. All the potato cultivars contained lower concentration of TGA than the limits recommended as safe, except 2 cultivars, that is FD8‐3 (2539.18 ± 89.77 mg/100 g of DW) and Cardinal (506.16 ± 17.90 mg/kg). The dietary intake assessment of potato cultivars revealed that Cardinal, FD 35‐36, FD 8‐3, and FD 3‐9 contained higher amount of TGA in whole potato, although FD 8‐3 only possessed higher content of TGA (154.93 ± 7.75) in its flesh portion rendering it unfit for human consumption.Practical Application:  This paper was based on the research conducted on toxic compounds present in all possible potato cultivars in Pakistan. Actually, we quantify the toxic compounds (glycoalkaloids) of potato cultivars through HPLC and their dietary assessment. This paper revealed safety assessment and their application in food industries especially potato processing.
Comparison of Stream Invertebrate Response Models for Bioassessment Metrics1
Authors: Waite Ian R. , Kennen Jonathan G. , May Jason T. , Brown Larry R. , Cuffney Thomas F. , Jones Kimberly A. , Orlando James L. 
Published: February 2012

Waite, Ian R., Jonathan G. Kennen, Jason T. May, Larry R. Brown, Thomas F. Cuffney, Kimberly A. Jones, and James L. Orlando, 2012. Comparison of Stream Invertebrate Response Models for Bioassessment Metrics. Journal of the American Water Resources Association (JAWRA) 48(3): 570‐583. DOI: 10.1111/j.1752‐1688.2011.00632.xAbstract:  We aggregated invertebrate data from various sources to assemble data for modeling in two ecoregions in Oregon and one in California. Our goal was to compare the performance of models developed using multiple linear regression (MLR) techniques with models developed using three relatively new techniques: classification and regression trees (CART), random forest (RF), and boosted regression trees (BRT). We used tolerance of taxa based on richness (RICHTOL) and ratio of observed to expected taxa (O/E) as response variables and land use/land cover as explanatory variables. Responses were generally linear; therefore, there was little improvement to the MLR models when compared to models using CART and RF. In general, the four modeling techniques (MLR, CART, RF, and BRT) consistently selected the same primary explanatory variables for each region. However, results from the BRT models showed significant improvement over the MLR models for each region; increases in R2 from 0.09 to 0.20. The O/E metric that was derived from models specifically calibrated for Oregon consistently had lower R2 values than RICHTOL for the two regions tested. Modeled O/E R2 values were between 0.06 and 0.10 lower for each of the four modeling methods applied in the Willamette Valley and were between 0.19 and 0.36 points lower for the Blue Mountains. As a result, BRT models may indeed represent a good alternative to MLR for modeling species distribution relative to environmental variables.
Dissolved Organic Carbon and Estrogen Transport in Surface Runoff From Agricultural Land Receiving Poultry Litter1
Authors: Dutta Sudarshan , Inamdar Shreeram , Tso Jerry , Aga Diana S. , Sims J. Tom 
Published: February 2012

Dutta, Sudarshan, Shreeram Inamdar, Jerry Tso, Diana S. Aga, and J. Tom Sims, 2012. Dissolved Organic Carbon and Estrogen Transport in Surface Runoff from Agricultural Land Receiving Poultry Litter. Journal of the American Water Resources Association (JAWRA) 48(3): 558‐569. DOI: 10.1111/j.1752‐1688.2011.00634.xAbstract:  Dissolved organic carbon (DOC) provides a reactive substrate for the transport of organic contaminants with runoff. Very few studies have investigated the export of DOC from agricultural land, especially those receiving manure applications. We investigated exports of DOC in surface runoff from agricultural fields receiving various treatments of poultry litter (raw vs. pelletized). In addition, we also investigated how estrogens in runoff were associated with DOC. Different forms of estrogens studied were: estrone, 17β‐estradiol, estriol, and their conjugates. Experimental agricultural plots were 12 m × 5 m long and had reduced tillage and no‐till management practices. The aromatic content of DOC was characterized using specific ultraviolet absorbance (SUVA). Flow‐weighted concentrations of DOC and SUVA in surface runoff from plots with poultry litter were significantly (p ≤ 0.10) greater than the control (no litter) plots. Compared to pelletized poultry litter, reduced‐tillage plots with raw litter yielded higher DOC concentrations and SUVA values. No significant differences (p ≥ 0.10) in DOC and SUVA were observed between litter treatments for plots with no‐till. Total estrogen concentrations (including all forms) were positively and significantly (p ≤ 0.10) correlated with DOC. These results can help select and guide agricultural management practices that can reduce the exports of DOC and associated contaminant from agricultural land receiving manure applications.
Distributed Hydrologic Modeling in the Suburban Landscape: Assessing Parameter Transferability from Gauged Reference Catchments1
Authors: Mittman Tamara , Band Lawrence E. , Hwang Taehee , Smith Monica Lipscomb 
Published: February 2012

Mittman, Tamara, Lawrence E. Band, Taehee Hwang, and Monica Lipscomb Smith, 2012. Distributed Hydrologic Modeling in the Suburban Landscape: Assessing Parameter Transferability from Gauged Reference Catchments. Journal of the American Water Resources Association (JAWRA) 48(3): 546‐557. DOI: 10.1111/j.1752‐1688.2011.00636.xAbstract:  Distributed, process‐based models of catchment hydrologic response are potentially useful tools for the assessment of Low Impact Development (LID) techniques in urbanized catchments. Their application is often limited, however, by the lack of continuous streamflow records to calibrate poorly constrained parameters. This article examines the transferability of soil and groundwater parameters from a forested reference catchment to a nearby suburban catchment. We use the Regional Hydro‐Ecologic Simulation System (RHESSys) to develop hydrologic models of one gauged forested and one ungauged suburban catchment within the Baltimore Ecosystem Study (BES) study area. We use a parameter uncertainty framework to calibrate soil and groundwater parameters for the forested catchment, and discrete measurements of streamflow from the suburban catchment to assess parameter transferability. Results indicate that the transfer of soil and groundwater parameters from forested reference to nearby suburban catchments is viable, with performance measures for the suburban catchment often exceeding those for the forested catchment. We propose that the simplification of hydrologic processes in urbanized catchments may account for the increase in model performance in the suburban catchment.
Lack of adverse effect of anti‐tumor necrosis factor‐α biologics in treatment of rheumatoid arthritis: 5 years follow‐up
Authors: Dewedar Ahmed M. , Shalaby Medhat A. , Al‐Homaid Sulaiman , Mahfouz Ahmed M. , Shams Osama A. , Fathy Ahmed 
Published: February 2012

AbstractBackgroundRheumatoid arthritis (RA) is a chronic, systemic inflammatory disorder affecting synovial joints and many other organs. Most patients seen in clinical settings have a progressive chronic disease, with radiographic damage, frequent work disability, incremental functional declines and increased mortality rates. The introduction of the biological drugs in treatment of RA has played an important role in prevention of destructive effects of the disease but may have serious adverse effects due to their powerful inhibition of the immune system.ObjectivesTo study the adverse effects (ADEs) of three different tumor necrosis factor α inhibitor (TNFi) drugs (infliximab, adalimumab and etanercept) in RA patients for 5 years in the south‐west area of Saudi Arabia.MethodsTwo groups of RA patients were included in this study: The first group included 112 patients, representing the biologics group. These patients received biological therapy plus disease modifying anti‐rheumatic drugs (DMARDs): 56 patients received infliximab (IFX), 36 patients received adalimumab (ADL) and 20 patients received etanercept (ETN). The second group also included 112 patients, representing the control group: RA patients treated only with the traditional DMARDs. ADEs were classified into mild and severe.ResultsThe mild ADEs which had been recorded during 5 years of follow‐up in patients receiving TNFi, were onycholysis (1.8%), positive tuberculin test (1.8%) and small vessel vasculitis (1.8%). Statistically, there were insignificant differences in the mild ADEs except for upper respiratory tract infection that was significantly higher in the control group. Severe ADEs included pneumonia (1.8%) and solid tumor (1.8%) and there were no significant differences between the biologics and control groups. Also there were no significant statistical differences for the ADEs, mild or severe, between the three biologics, infliximab, adalimumab and etanercept. Occurrence of ADEs did not correlate to methotrexate dose, steroid dose or rheumatoid factor positivity.ConclusionsOur results indicate that the use of TNFi therapy appeared to be as safe as traditional DMARDs in treatment of rheumatoid arthritis patients and long‐term follow‐up with careful examination is essential to pick up any abnormal ADEs.
Urine sVCAM‐1 and sICAM‐1 levels are elevated in lupus nephritis
Authors: Howe Hwee Siew , Kong Kok Ooi , Thong Bernard YH , Law Weng Giap , Chia Faith L. A. , Lian Tsui Yee , Lau Tang Ching , Chng Hiok Hee , Leung Bernard P. L. 
Published: February 2012

AbstractAimWe sought to evaluate the relationship of urine levels of soluble cellular adhesion molecules sVCAM‐1 (vascular) and sICAM‐1 (intercellular) in systemic lupus erythematosus (SLE) patients with or without lupus nephritis, and to explore their correlation with renal disease activity.MethodsPaired serum and urine samples of 121 Asian SLE patients, and urine samples of 19 normal healthy controls were collected. Demographic data, disease activity and damage scores, and selected laboratory parameters, including levels of anti‐double stranded DNA antibody, complements C3, C4, and creatinine were captured. Renal disease activity was scored with renal SLE Activity Measure revised (rSLAM‐R). Serum and urine sVCAM‐1 and sICAM‐1 levels were assayed by enzyme‐linked immunosorbent assay.ResultsUrinary sVCAM‐1 and sICAM‐1 were elevated in SLE patients compared to controls. Significantly higher levels of urine sVCAM‐1 found in patients with active lupus nephritis correlated with rSLAM‐R. In addtion, significantly more patients with active lupus nephritis had detectable levels of urine sICAM‐1, but no correlation with renal activity was observed.ConclusionUrinary sVCAM‐1 may serve as a potential biomarker for early diagnosis of lupus nephritis as levels correlated with even mild abnormalities of urine sediment. In addition, both urine sVCAM‐1 and sICAM‐1 levels may be useful in identifying patients at risk of lupus nephritis.
Present status of insulin therapy for type 2 diabetes treated by general practitioners and diabetes specialists in Japan: Third report of a cross‐sectional survey of 15,652 patients
Authors: Arai Keiko , Takai Masahiko , Hirao Koichi , Matsuba Ikuro , Matoba Kiyokazu , Takeda Hiroshi , Kanamori Akira , Yamauchi Mikio , Mori Hisao , Terauchi Yasuo 
Published: February 2012

AbstractAims/Introduction:  Insulin therapy is often required to achieve good glycemic control in patients with type 2 diabetes mellitus. However, some providers, particularly general practitioners (GPs), are reluctant to prescribe insulin to their patients. The aim of the present study was to clarify any differences in, as well as any problems associated with, insulin therapy in patients with type 2 diabetes being treated by either a GP or a diabetes specialist in Japan.Materials and Methods:  Of 15,652 patients across 721 clinics and hospitals, 15,350 were diagnosed with type 2 diabetes (14,312 by GPs and 1038 by specialists). Data regarding glycated hemoglobin (HbA1c) levels, age, height, bodyweight and treatment modality were collected for each patient.Results: Of the patients with type 2 diabetes, 9.1 and 22.9% had been prescribed insulin monotherapy, and 38.8 and 37.0% were also receiving insulin with an oral antidiabetic (OAD) by GPs or specialists, respectively. Diabetes specialists prescribed analog insulin more frequently than did GPs. GPs chose premixed insulin more frequently than did specialists, and this factor correlated with higher HbA1c levels. A younger age and daily insulin dose in groups being treated by both providers were correlated with high HbA1c levels on insulin monotherapy. Neither type of insulin nor OAD was correlated with HbA1c on insulin plus OAD therapy.Conclusions: To achieve better glycemic control with insulin therapy, sufficient insulin dose and intensive treatment regimen, in addition to lifestyle interventions, might be necessary. (J Diabetes Invest, doi: 10.1111/j.2040‐1124.2012.00198.x, 2012)
Population-based resequencing analysis of wild and cultivated barley revealed weak domestication signal of selection and bottleneck in theRrs2scald resistance gene region
Authors: Fu Yong-Bi 
Published: February 2012

Many plant disease resistance (R) genes have been cloned, but the potential of utilizing these plant R-gene genomic resources for genetic inferences of plant domestication history remains unexplored. A population-based resequencing analysis of the genomic region near the Rrs2 scald resistance gene was made in 51 accessions of wild and cultivated barley from 41 countries. Fifteen primer pairs were designed to sample the genomic region with a total length of 10 406 bp. More nucleotide diversity was found in wild (π = 0.01846) than cultivated (π = 0.01507) barley samples. Three distinct groups of 29 haplotypes were detected for all 51 samples, and they were well mixed with wild and cultivated barley samples from different countries and regions. The neutrality tests by Tajima’s D were not significant, but a significant (P < 0.05) case by Fu and Li’s D* and F* was found in the barley cultivar samples. The estimate of selection intensity by Ka/Kswas 0.691 in wild barley and 0.580 in cultivated barley. The estimate of the minimum recombination events was 16 in wild barley and 19 in cultivated barley. A coalescence simulation revealed a bottleneck intensity of 1.5 to 2 since barley domestication. Together, the domestication signal in the genomic region was weak both in human selection and domestication bottleneck.
Under-representation of repetitive sequences in whole-genome shotgun sequence databases: an illustration using a recently acquired transposable element
Authors: Koga Akihiko 
Published: February 2012

It is widely accepted in a conceptual framework that repetitive sequences, especially those with high sequence homogeneity among copies, tend to be under-represented in whole-genome shotgun sequence databases, because of the difficulty of assembling sequence reads into contigs. Although this is easily inferred, there is no quantitative illsutration of this phenomenon. An example using a currently used database is expected to contribute to the intuitive understanding of how serious the under-representation is. The present study provides the first quantitative example (in the case of 16 copies of virtually identical, 4.7-kb sequences in a genome of 7 × 108bp) by comparing the results of BLAST searches of a sequence database (contig N50; 9.8 kb) with those of Southern blot analysis of genomic DNA. This has revealed that the internal regions of the repetitive sequences are under-represented to a striking extent.
Salt tectonics on passive margins: examples from Santos, Campos and Kwanza basins
Authors: Quirk Dave G. , Schødt Niels , Lassen Birgitte , Ings Steven J. , Hsu Dan , Hirsch Katja K. , Von Nicolai Christina 
Published: February 2012

Abstract

Salt flows downslope, irrespective of overburden. In salt basins on passive margins, the salt will tilt and flow towards the ocean immediately after continental rifting has ended due to thermal subsidence. Using real examples, as well as physical and numerical models, tilting is shown to be relatively rapid, enhanced by isostatic rebound updip and loading downdip where salt pools and inflates behind an outer high. In the Santos, Campos and Kwanza basins, this outer high is represented by an embryonic mid-Atlantic ridge, amplified in height by the differential weight of the inflating salt. Widespread extension and translation of overburden, utilizing both seaward- and landward-dipping normal faults, characterizes the early evolution of the inboard region. Inflation and contraction occur outboard, the effects of which tend to expand in a landward direction over time. Rapid accumulation of salt implies wholesale dewatering of pre-salt sediments, the water possibly permeating the salt once it has reached a burial depth of
c.
3 km. The process of thermal subsidence, salt drainage and isostatic amplification is an efficient mechanism for moving sediment on passive margins tens of kilometres seaward during a relatively short period and helps explain why great thicknesses of salt can accumulate there in the first place.
Flip-flop salt tectonics
Authors: Quirk David G. , Pilcher Robin S. 
Published: February 2012

Abstract
This paper describes a common type of salt wall found in extensional regimes which possess the characteristics: cover strata truncated against both flanks; an asymmetric appearance in cross-section caused by normal fault-related growth patterns; and at least one unconformity and onlap surface separating strata which are tilted in opposite directions. This type of structure evolves by a process known as flip-flop salt tectonics starting with a roller where a normal fault detaches down one flank of the embryonic salt body. The structure grows as salt flows towards the low-stress zone below the crest of the footwall causing it to swell and tilt backwards until it becomes gravitationally unstable, until the cover strata on one or both sides welds out or until the salt emerges at surface. Further growth is then accommodated by switching to a new counter-dipping fault that detaches on the opposite flank of the salt body leading to a flip in hanging-wall/footwall polarity marked by an unconformity and onlap surface. The salt body continues to grow beneath the new footwall, causing partial inversion of the old hanging wall. Additional switches may occur, leading to tall flip-flop structures until the source of salt is depleted.
Halokinetic effects on submarine channel equilibrium profiles and implications for facies architecture: conceptual model illustrated with a case study from Magnolia Field, Gulf of Mexico
Authors: Kane Ian A. , McGee David T. , Jobe Zane R. 
Published: February 2012

Abstract
In Magnolia Field, deepwater sediments were affected during deposition by allochthonous salt. Pleistocene channel systems developed on a salt flank and were initially deeply incised close to the salt but progressively avulsed down the lateral slope, each time with decreasing depth of incision. Following this degradational stage, a lobe developed on top of the channel fills and a large-scale aggradational system developed. A conceptual model of submarine channel development adjacent to active topography has been developed from this dataset. Channels may become deeply entrenched during stages of salt growth, but only where flow frequency and magnitude are sufficient to outpace topographic growth. Where flows are less frequent topographic growth may present a barrier to successive flows, causing avulsion. The large-scale cycles of salt growth and withdrawal commonly recognized in subsurface systems, combined with eustatic sea-level changes, may result in a cyclic style of evolution whereby channels initially become entrenched and/or step away from the growing topography, switching to backfilling as salt growth slows or pauses, followed by a distributive-style as the entire system backsteps. During salt withdrawal the equilibrium profile may become relatively raised and channels may develop an aggradational style. In these settings, significant cross-channel facies asymmetry may result.