bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recognizing economic value in multifunctional buffers in the lower Mississippi river basin
Authors: Xu Hui , Wu May , Ha Miae 
Published: August 2018

AbstractIntegrating conservation practices with bioenergy has been recommended as a promising strategy to improve bioeconomy and water quality but the literature on the economics of this strategy is limited. This study evaluated the value proposition of reducing nutrient loss from cropland by implementing switchgrass riparian buffers in the Lower Mississippi River Basin (LMRB). Nutrient loss was simulated by using the Soil and Water Assessment Tool. The value proposition of nutrient abatement was quantified by estimating (1) value of trapped nutrients as fertilizer and (2) potential net returns of harvesting switchgrass as bioenergy feedstock at different farm‐gate prices. Results suggest that switchgrass buffers may reduce mean annual total nitrogen and total phosphorus loads from cropland in the LMRB by 23% and 31%, respectively. The value of trapped nutrients is considerable (mean = $69 ha−1 year−1) but far less than the cost of implementing a switchgrass buffer (mean = $163 ha−1 year−1). At biomass prices of $20, $40, $60, and $80 per dry‐ton, mean net returns of switchgrass buffers (without considering land‐use change from cropland to buffers) were estimated to be around −$66, $199, $463, and $727 ha−1 year−1, respectively. Total net returns for the LMRB may be reduced by 20% if switchgrass is grown without the addition of commercial fertilizer. The results highlight the potential of switchgrass buffers for improving water sustainability of both agricultural and bioenergy production. The value proposition of switchgrass buffers is nevertheless sensitive to future feedstock price. The impact of fertilizer prices change and forgone income on benefit analysis is also presented. © 2018 The Authors. Biofuels, Bioproducts, and Biorefining published by Society of Chemical Industry and John Wiley & Sons, Ltd.
The predictive ability of childhood animal cruelty methods for later interpersonal crimes
Authors: Hensley Christopher , Ketron Joseph B. 
Published: August 2018

AbstractResearch on the topic of childhood animal cruelty methods and their link to interpersonal violence is sparse. Most of the studies that do exist focus only on the frequencies of different methods of childhood animal cruelty. Only two studies to date have examined the predictive nature of these methods for later violence toward humans. One of these previous studies found that drowning and having sex with animals were predictive of later human violence, while the other found that sex with animals and the age at which the offenders began committing animal cruelty were its only statistically significant predictors. Using data collected from 257 anonymous self‐reports by male inmates at a medium‐security prison in a Southern state, we investigate the predictive ability of several retrospectively identified childhood animal cruelty methods (i.e., drowning, hitting/beating, hitting with rocks, shooting, kicking, choking, burning, stabbing, having sex, and starving/neglecting) for later violent crimes toward humans. Regression analyses revealed that recurrent (i.e., more than once) childhood animal cruelty and stabbing animals were the only statistically significant variables in the model that predicted recurrent interpersonal violence in adulthood.
Designing web‐games for transportation engineering education
Authors: Wang Qichao , Abbas Montasir 
Published: August 2018

AbstractThis paper presents the gamification of transportation engineering education. We identified what the authors deemed to be the key hard concepts in the taught course and designed five web‐games targeting five areas within transportation engineering. The developed games were tested with undergraduate students. The results show that the games can enhance the students’ understanding of the hard concepts.
“Inverse” Frustrated Lewis Pairs: An Inverse FLP Approach to the Catalytic Metal Free Hydrogenation of Ketones
Authors: Mummadi Suresh , Brar Amandeep , Wang Guoqiang , Kenefake Dustin , Diaz Rony , Unruh Daniel K. , Li Shuhua , Krempner Clemens 
Published: August 2018

AbstractFor the first time have boron‐containing weak Lewis acids been demonstrated to be active components of Frustrated Lewis Pair (FLP) catalysts in the hydrogenation of ketones to alcohols. Combining the organosuperbase (pyrr)3P=NtBu with the Lewis acid 9‐(4‐CF3‐C6H4)‐BBN generated an “inverse” FLP catalyst capable of hydrogenating a range of aliphatic and aromatic ketones including N‐, O‐ and S‐functionalized substrates and bio‐mass derived ethyl levulinate. Initial computational and experimental studies indicate the mechanism of catalytic hydrogenation with “inverse” FLPs to be different from conventional FLP catalysts that contain strong Lewis acids such as B(C6F5)3.
Improved RNA‐seq Workflows Using CyVerse Cyberinfrastructure
Authors: Chougule Kapeel M. , Wang Liya , Stein Joshua C. , Wang Xiaofei , Devisetty Upendra Kumar , Klein Robert R. , Ware Doreen 
Published: August 2018

AbstractRNA‐seq is a vital method for understanding gene structure and expression patterns. Typical RNA‐seq analysis protocols use sequencing reads of length 50 to 150 nucleotides for alignment to the reference genome and assembly of transcripts. The resultant transcripts are quantified and used for differential expression and visualization. Existing tools and protocols for RNA‐seq are vast and diverse; given their differences in performance, it is critical to select an analysis protocol that is scalable, accurate, and easy to use. Tuxedo, a popular alignment‐based protocol for RNA‐seq analysis, has been updated with HISAT2, StringTie, StringTie‐merge, and Ballgown, and the updated protocol outperforms its predecessor. Similarly, new pseudo‐alignment‐based protocols like Kallisto and Sleuth reduce runtime and improve performance. However, these tools are challenging for researchers lacking command‐line experience. Here, we describe two new RNA‐seq analysis protocols, in which all tools are deployed on CyVerse Cyberinfrastructure with user‐friendly graphical user interfaces, and validate their performance using plant RNA‐seq data. © 2018 by John Wiley & Sons, Inc.
Installing, Maintaining, and Using a Local Copy of BLAST for Compute Cluster or Workstation Use
Authors: Ladunga Istvan 
Published: August 2018

AbstractThe Basic Local Alignment Search Tool (BLAST) is the first resource to computationally characterize a novel amino acid or nucleic acid sequence. BLAST plays important roles in genomics, transcriptomics, and protein science. For numerous academic and commercial researchers, neither BLAST Web servers nor cloud resources satisfy the requirements of high‐throughput comparative genomic pipelines or company policies. For such users, this unit describes how to install BLAST locally, either on a standalone workstation, or preferably on a compute cluster. We provide practical guidance for the planning and the installation under the LINUX, Windows, and Mac OS X operating systems. We propose strategies for downloading existing and generating new sequence databases in BLAST format. © 2018 by John Wiley & Sons, Inc.
A stochastic scheduled operation of wind farm based on scenarios of the generated power with copula
Authors: Yoshida Kotaro , Negishi Shintaro , Takayama Satoshi , Ishigame Atsushi 
Published: August 2018

AbstractRecently, the penetration of wind farm (WF) has been increasing because of the global warming and the lack of the fossil energy resource. However, WF output fluctuate due to the weather and the seasonality. Specially, the long‐term fluctuation is called “Ramp event.” It's difficult for WF output to dispatch to the power grid without controlling the ramp events. This article proposes the method of scheduled operation to mitigate the ramp events and reduce the imbalance energy with the stochastic programming. In this method, it's necessary to use the WF output scenarios. However, there has never been studied the method of generating scenarios with the temporal correlation so far. Therefore, we propose the production method of generating scenarios considering the temporal correlation with copula. Finally, this article shows the validity and the effectiveness of these methods through computational simulations using the integrated WF data of Tohoku area.
LC–MS/MS glycomics of idiopathic rapid eye movement sleep behavior disorder
Authors: Dong Xue , Mondello Stefania , Kobeissy Firas , Talih Farid , Ferri Raffaele , Mechref Yehia 
Published: August 2018

AbstractIdiopathic REM sleep behavior disorder (iRBD) is now considered a prodromal stage of an α‑synucleinopathy‐related to neurodegenerative disease such as Parkinson's diseases. Emerging evidence has shown that post‐translational modification or glycosylation are implicated in dynamic disease mechanisms and the onset of many pathological conditions. We hypothesized that the characterization of the glycosylation pattern of patients with RBD would be of great value to understand the pathophysiology and underlying mechanisms and represent potentially useful biomarkers for disease‐associated molecular changes. To test this hypothesis, we assessed the serum glycome of patients with RBD and compared to that of healthy controls. NanoRPLC–MS was used to generate quantitative N‐glycan profiles while high‐temperature PGC‐LC–MS platform was employed to generate quantitative isomeric N‐glycan profiles. By analyzing permethylated glycans derived from human blood sera on C18‐LC–MS/MS, we identified 59 N‐glycan structures in healthy (control) cohort, 56 N‐glycans in RBD cohort. Sixteen N‐glycans structures were found to be significantly altered in the RBD cohort (p < 0.05). N‐glycans with the composition of HexNAc4Hex5Fuc1, HexNAc5Hex5, and HexNAc4Hex5Fuc1NeuAc1 presented the most substantial difference between controls and RBD patients (p < 0.01). HexNAc4Hex5Fuc1NeuAc1 showed a relatively high abundance (3.1 ± 0.7% in the control cohort versus 4 ± 3% in the idiopathic RBD cohort). These N‐glycans can be potential diagnostic biomarker candidates and provide a window into underlying neurodegenerative processes in patients with idiopathic RBD. In addition, 7 N‐glycan isomers were significantly different between controls and RBD patients (p < 0.05). HexNAc4Hex5Fuc1NeuAc1 (4511‐2) and HexNAc4Hex5Fuc1 NeuAc2 (4512‐2) showed the most substantial difference between the control and idiopathic RBD cohorts (p < 0.001). Levels of both these two isomeric structures were higher in the idiopathic RBD cohort. Further larger studies are required to assess the reproducibility of these findings and to elucidate the role played by the changes in glycan structures in the pathogenetic mechanisms of RBD. This information will be instrumental in developing molecular therapeutic targets to promote neuroprotection and prevention of neurodegeneration.
Synergistic effect of organophosphate functionalized montmorillonite on properties and water resistance of intumescent flame‐retarded SEBS
Authors: Li Jun , Li Xiaoyan , Wei Qian , Yang Jian , Qiu Biwei , Xu Jianjun , Wang Xia 
Published: August 2018

SummaryPolystyrene‐b‐(ethylene‐co‐butylene)‐b‐styrene (SEBS) is a widely used thermoplastic elastomer. However, it suffers from poor flame retardancy. Proper combination of organic‐modified montmorillonite and intumescent flame retardant (IFR) works but is not stable due to easy absorption of moisture. In this study, a novel and stable halogen‐free flame‐retardant system is demonstrated by encapsulating a hydrophobic organophosphate, ie, bisphenol A bis (diphenyl phosphate) (BDP) into a stable micelle and then “attaching” the BDP micelles to the montmorillonite (called: side‐intercalation). The resulted BDP modified montmorillonite (BMMT) has a large inter‐platelet spacing and demonstrated synergistic effect with IFR on flame retardancy, tensile property, and water resistance for the composite with SEBS. In addition to more homogeneous dispersion of IFR and BMMT, a longer‐lasting interfacial interaction between IFR and SEBS matrix with addition of small amount of BMMT also plays the role. The results suggest that BMMT can serve as an effective additive for formulating novel halogen‐free flame retardants for the SEBS to meet increasingly stricter environmental requirements.
New records and a key to the species ofMalmidea(lichenized Ascomycota) from India
Authors: Joseph Siljo , Nayaka Sanjeeva , Randive Pallavi , Upreti D. K. 
Published: August 2018

Six species of the genusMalmidea,M. atlantica(M. Cáceres & Lücking) M. Cáceres & Kalb,M. duplomarginata(Papong & Kalb) Kalb & Papong,M. hypomelaena(Nyl.) Kalb & Lücking,M. papillosaWeerak. & Aptroot,M. subaurigera(Vain.) Kalbet al., andM. variabilisKalb, are reported as new records to India. A key to all known Indian species ofMalmideais provided.
Impact of age on mid‐ to long‐term outcomes of transvaginal native tissue repair for apical vaginal prolapse
Authors: Kissane Lindsay M. , Meyer Isuzu , Martin Kimberly D. , Tan Jubilee C. , Miller Kathryn , Richter Holly E. 
Published: August 2018

AimsTo compare surgical success rates in older versus younger women a minimum of 3 years post transvaginal native tissue repair for apical prolapse. Post‐operative symptom severity and quality of life improvement, surgical complications and retreatment were also examined.MethodsWomen who underwent transvaginal native tissue repair for apical prolapse between 2011 and 2013 were eligible. Subjects completed the pelvic floor distress inventory (PFDI‐20), pelvic floor impact questionnaire (PFIQ‐7), and patient global impression of improvement (PGI‐I), and were categorized as “younger” (age <70) or “older” (age ≥70). The primary outcome of surgical success was defined as the absence of bulge symptoms and no re‐treatment for prolapse.ResultsOf 641 eligible patients, response rate was 51.0%. 62.7% of subjects had hysterectomy prior to index surgery. Surgical success was noted in 72.9% of younger and 82.2% of older subjects (Adjusted odds ratio [aOR] 1.72, 95% CI [0.93, 3.17]). Older women had greater improvement from baseline in PFDI‐20 score (−87.5 [IQR 74.0] vs −54.2 [IQR 80.2], P = 0.01). Retreatment rate and surgical complication rates were similar between groups (both P > 0.05).ConclusionsOlder and younger women had similar surgical success rates a minimum of 3 years post‐operative; however, older women had a greater overall symptom severity improvement. This information may be helpful in counseling older women regarding surgical expectations and decision‐making.
A quasi‐incompressible and quasi‐inextensible element formulation for transversely isotropic materials
Authors: Dal H. 
Published: August 2018

SummaryThe contribution presents a new finite element formulation for quasi‐inextensible and quasi‐incompressible finite hyperelastic behavior of transeversely isotropic materials and addresses its computational aspects. The material formulation is presented in purely Eulerian setting and based on the additive decomposition of the free energy function into isotropic and anisotropic parts, where the former is further decomposed into isochoric and volumetric parts. For the quasi‐incompressible response, the Q1P0 element formulation is outlined briefly, where the pressure‐type Lagrange multiplier and its conjugate enter the variational formulation as an extended set of variables. Using the similar argumentation, an extended Hu‐Washizu–type mixed variational potential is introduced, where the volume averaged fiber stretch and fiber stress are additional field variables. Within this context, the resulting Euler‐Lagrange equations and the element formulation resulting from the extended variational principle are derived. The numerical implementation exploits the underlying variational structure, leading to a canonical symmetric structure. The efficiency of the proposed approached is demonstrated through representative boundary value problems. The superiority of the proposed element formulation over the standard Q1 and Q1P0 element formulation is studied through convergence analyses. The proposed finite element formulation is modular and exhibits very robust performance for fiber reinforced elastomers in the inextensibility limit.
Shifting weaning practices in Early Neolithic Cis‐Baikal, Siberia: New insights from stable isotope analysis of molar micro‐samples
Authors: Scharlotta Ian , Goude Gwenaëlle , Herrscher Estelle , Bazaliiskii Vladimir I. , Weber Andrzej W. 
Published: August 2018

AbstractReconstructing individual dietary histories at Shamanka II, an Early Neolithic (7000–5700 cal. BP) Kitoi hunter‐gatherer cemetery in Cis‐Baikal, Siberia, revealed surprising intrapopulation variability in childhood diets. Stable isotope analytical data produced by micro‐sampled first molars identified changes in both the timing and rate of weaning for different individuals. Further, examination within the framework of a high‐resolution radiocarbon chronology identified shifting practices between two phases of cemetery use, and additional links with mortuary treatment that indicates differences relating to group and/or family structure. The differential treatment of infants, correlated with the complex hunter‐gatherer social structure, and subsequent burial treatment evident at this cemetery are investigated in light of regional dietary trends.
Childhood cancer incidence and survival in Thailand: A comprehensive population‐based registry analysis, 1990–2011
Authors: Bidwell Serena S. , Peterson Catherine C. , Demanelis Kathryn , Zarins Katie R. , Meza Rafael , Sriplung Hutcha , Wiangnon Surapon , Chotsampancharoen Thirachit , Chitapanarux Imjai , Pongnikorn Donsuk , Daoprasert Karnchana , Suwanrungruang Krittika , Chansaard Wasan , Rozek Laura S. 
Published: August 2018

AbstractBackgroundSoutheast Asia is undergoing a transition from infectious to chronic diseases, including a dramatic increase in adult cancers. Childhood cancer research in Thailand has focused predominantly on leukemias and lymphomas or only examined children for a short period of time. This comprehensive multisite study examined childhood cancer incidence and survival rates in Thailand across all International Classification of Childhood Cancer (ICCC) groups over a 20‐year period.MethodsCancer cases diagnosed in children ages 0‐19 years (n = 3574) from 1990 to 2011 were extracted from five provincial population‐based Thai registries, covering approximately 10% of the population. Descriptive statistics of the quality of the registries were evaluated. Age‐standardized incidence rates (ASRs) were calculated using the Segi world standard population, and relative survival was computed using the Kaplan‐Meier method. Changes in incidence and survival were analyzed using Joinpoint Regression and reported as annual percent changes (APC).ResultsThe ASR of all childhood cancers during the study period was 98.5 per million person‐years with 91.0 per million person‐years in 1990–2000 and 106.2 per million person‐years in 2001–2011. Incidence of all childhood cancers increased significantly (APC = 1.2%, P < 0.01). The top three cancer groups were leukemias, brain tumors, and lymphomas. The 5‐year survival for all childhood cancers significantly improved from 39.4% in 1990–2000 to 47.2% in 2001–2011 (P < 0.01).ConclusionsBoth childhood cancer incidence and survival rates have increased, suggesting improvement in the health care system as more cases are identified and treated. Analyzing childhood cancer trends in low‐ and middle‐income countries can improve understanding of cancer etiology and pediatric health care disparities.
Alternate gas washout indices: Assessment of ventilation inhomogeneity in mild to moderate pediatric cystic fibrosis lung disease
Authors: Nyilas Sylvia , Bigler Anja , Yammine Sophie , Kieninger Elisabeth , Rochat Isabelle , Ramsey Kathryn , Casaulta Carmen , Moeller Alexander , Latzin Philipp , Singer Florian 
Published: August 2018

AbstractIntroductionNormalized phase III slope (SnIII) indices from multiple breath washout (MBW) estimate ventilation inhomogeneity. Alternate (*) protocols for SnIII indices exist, however the utility of these outcomes in children with mild‐to‐moderate cystic fibrosis (CF) is unknown.MethodsWe measured nitrogen MBW and spirometry in 135 children (43 controls) aged 4‐18 years. We assessed validity, practicability, and reliability of SnIII protocols. Outcomes included the ability to detect abnormal lung function, test agreement, measurement duration, intra‐test repeatability, and quality.ResultsLung clearance index (LCI) was abnormal in 80 (87%), Scond in 55 (60%), Scond* in 17 (19%), Sacin in 10 (11%), Sacin* in 11 (12%), and FEV1 in 28 (30%). Alternate protocols reduced measurement duration. Agreement of indices to detect abnormal lung function was poor. The quality of analysis and repeatability deteriorated with the alternate technique compared to standard.ConclusionIn children with mild‐to‐moderate CF lung disease, alternate protocols seem practical but clinimetric properties of standard SnIII protocols are preferable.
Structural enzymology binding studies of the peptide‐substrate‐binding domain of human collagen prolyl 4‐hydroxylase (type‐II): High affinity peptides have a PxGP sequence motif
Authors: Murthy Abhinandan V. , Sulu Ramita , Koski M. Kristian , Tu Hongmin , Anantharajan Jothi , Sah‐Teli Shiv K. , Myllyharju Johanna , Wierenga Rik K. 
Published: August 2018

AbstractThe peptide‐substrate‐binding (PSB) domain of collagen prolyl 4‐hydroxylase (C‐P4H, an α2β2 tetramer) binds proline‐rich procollagen peptides. This helical domain (the middle domain of the α subunit) has an important role concerning the substrate binding properties of C‐P4H, although it is not known how the PSB domain influences the hydroxylation properties of the catalytic domain (the C‐terminal domain of the α subunit). The crystal structures of the PSB domain of the human C‐P4H isoform II (PSB‐II) complexed with and without various short proline‐rich peptides are described. The comparison with the previously determined PSB‐I peptide complex structures shows that the C‐P4H‐I substrate peptide (PPG)3, has at most very weak affinity for PSB‐II, although it binds with high affinity to PSB‐I. The replacement of the middle PPG triplet of (PPG)3 to the nonhydroxylatable PAG, PRG, or PEG triplet, increases greatly the affinity of PSB‐II for these peptides, leading to a deeper mode of binding, as compared to the previously determined PSB‐I peptide complexes. In these PSB‐II complexes, the two peptidyl prolines of its central P(A/R/E)GP region bind in the Pro5 and Pro8 binding pockets of the PSB peptide‐binding groove, and direct hydrogen bonds are formed between the peptide and the side chains of the highly conserved residues Tyr158, Arg223, and Asn227, replacing water mediated interactions in the corresponding PSB‐I complex. These results suggest that PxGP (where x is not a proline) is the common motif of proline‐rich peptide sequences that bind with high affinity to PSB‐II.