bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of grain quality in terms of functional group response to elevated [CO2], water, and nitrogen using a meta‐analysis: Grain protein, zinc, and iron under future climate
Authors: Al‐Hadeethi Ikhlas , Li Yan , Odhafa Abdul Kareem H. , Al‐Hadeethi Hanan , Seneweera Saman , Lam Shu K. 
Published: June 2019

AbstractThe increasing [CO2] in the atmosphere increases crop productivity. However, grain quality of cereals and pulses are substantially decreased and consequently compromise human health. Meta‐analysis techniques were employed to investigate the effect of elevated [CO2] (e[CO2]) on protein, zinc (Zn), and iron (Fe) concentrations of major food crops (542 experimental observations from 135 studies) including wheat, rice, soybean, field peas, and corn considering different levels of water and nitrogen (N). Each crop, except soybean, had decreased protein, Zn, and Fe concentrations when grown at e[CO2] concentration (≥550 μmol/mol) compared to ambient [CO2] (a[CO2]) concentration (≤380 μmol/mol). Grain protein, Zn, and Fe concentrations were reduced under e[CO2]; however, the responses of protein, Zn, and Fe concentrations to e[CO2] were modified by water stress and N. There was an increase in Fe concentration in soybean under medium N and wet conditions but nonsignificant. The reductions in protein concentrations for wheat and rice were ~5%–10%, and the reductions in Zn and Fe concentrations were ~3%–12%. For soybean, there was a small and nonsignificant increase of 0.37% in its protein concentration under medium N and dry water, while Zn and Fe concentrations were reduced by ~2%–5%. The protein concentration of field peas decreased by 1.7%, and the reductions in Zn and Fe concentrations were ~4%–10%. The reductions in protein, Zn, and Fe concentrations of corn were ~5%–10%. Bias in the dataset was assessed using a regression test and rank correlation. The analysis indicated that there are medium levels of bias within published meta‐analysis studies of crops responses to free‐air [CO2] enrichment (FACE). However, the integration of the influence of reporting bias did not affect the significance or the direction of the [CO2] effects.
Possible precision medicine implications from genetic testing using combined detection of sequence and intragenic copy number variants in a large cohort with childhood epilepsy
Authors: Truty Rebecca , Patil Nila , Sankar Raman , Sullivan Joseph , Millichap John , Carvill Gemma , Entezam Ali , Esplin Edward D. , Fuller Amy , Hogue Michelle , Johnson Britt , Khouzam Amirah , Kobayashi Yuya , Lewis Rachel , Nykamp Keith , Riethmaier Darlene , Westbrook Jody , Zeman Michelle , Nussbaum Robert L. , Aradhya Swaroop 
Published: June 2019

AbstractObjectiveMolecular genetic etiologies in epilepsy have become better understood in recent years, creating important opportunities for precision medicine. Building on these advances, detailed studies of the complexities and outcomes of genetic testing for epilepsy can provide useful insights that inform and refine diagnostic approaches and illuminate the potential for precision medicine in epilepsy.MethodsWe used a multi‐gene next‐generation sequencing (NGS) panel with simultaneous sequence and exonic copy number variant detection to investigate up to 183 epilepsy‐related genes in 9769 individuals. Clinical variant interpretation was performed using a semi‐quantitative scoring system based on existing professional practice guidelines.ResultsMolecular genetic testing provided a diagnosis in 14.9%‐24.4% of individuals with epilepsy, depending on the NGS panel used. More than half of these diagnoses were in children younger than 5 years. Notably, the testing had possible precision medicine implications in 33% of individuals who received definitive diagnostic results. Only 30 genes provided 80% of molecular diagnoses. While most clinically significant findings were single‐nucleotide variants, ~15% were other types that are often challenging to detect with traditional methods. In addition to clinically significant variants, there were many others that initially had uncertain significance; reclassification of 1612 such variants with parental testing or other evidence contributed to 18.5% of diagnostic results overall and 6.1% of results with precision medicine implications.SignificanceUsing an NGS gene panel with key high‐yield genes and robust analytic sensitivity as a first‐tier test early in the diagnostic process, especially for children younger than 5 years, can possibly enable precision medicine approaches in a significant number of individuals with epilepsy.
Chronic Hepatitis B Prevalence Among Foreign‐Born and U.S.‐Born Adults in the United States, 1999‐2016
Authors: Le Michael H. , Yeo Yee Hui , Cheung Ramsey , Henry Linda , Lok Anna S. , Nguyen Mindie H. 
Published: June 2019

Hepatitis B virus (HBV) infection remains a major global health problem, exacerbated by poor linkage to care. We aimed to determine the prevalence of HBV infection, exposure, self‐reported vaccination, vaccine‐induced immunity, disease awareness, and treatment in the United States by birthplace and race/ethnicity during 1999‐2016. A total of 47,628 adult participants in the National Health and Nutrition Examination Survey who completed HBV core antibody (anti‐HBc) and surface antigen (HBsAg) tests and 47,618 adults who completed HBV surface antibody (anti‐HBs) and anti‐HBc tests were included in the analysis. HBV infection was defined by positive HBsAg and past exposure by positive anti‐HBc. Vaccine‐mediated immunity was defined by positive anti‐HBs and negative anti‐HBc. No significant change in the prevalence of HBV infection was observed between 1999 and 2016 (P = 0.442), affecting 0.35% (95% confidence interval [CI], 0.28‐0.45) or 0.84 million adults. In contrast, a significant decrease in HBV exposure and increase in vaccine‐mediated immunity was observed. U.S.‐born persons had significantly lower prevalence of HBV infection and exposure as well as higher prevalence of vaccine‐mediated immunity and self‐reported vaccination than foreign‐born persons. Prevalence of HBV infection was highest in non‐Hispanic Asians in both foreign‐ (3.85%; 95% CI, 2.97‐4.97) and U.S.‐born (0.79%; 95% CI, 0.17‐3.59) persons during 2011‐2016. Among infected persons, liver disease awareness was only 15.19%, and treatment rate was only 4.60%. Conclusion: This study revealed disparities of HBV infection among ethnic/racial groups and between U.S.‐born and foreign‐born persons. Awareness of liver disease and treatment rate among infected persons was dismal.
Study of the physical and chemical changes during the maturation of three cocoa clones, EET8, CCN51, and ICS60
Authors: Cubillos Bojacá Andrés F , García Muñoz María C , Calvo Salamanca Ana M , Carvajal Rojas Guillermo H , Tarazona‐Díaz Martha P 
Published: June 2019

AbstractBACKGROUNDColombia is known for its production of fine and aromatic cocoa; however, the lack of homogeneity in the ripeness stage of cocoa fruit affects the final quality of cocoa beans. Therefore, the aim of this work was to identify parameters that can be use as indicators of ripeness in cocoa fruit in order to homogenize the characteristics of raw cocoa used in the production of cocoa‐products industry. The parameters evaluated were fruit, seed and pod weight, firmness, color, polar and equatorial diameters of the fruit, seed moisture content, total titratable acidity, pH, and total soluble solids of pulp.RESULTSFactors such as seed weight, firmness, diameters, total soluble solids, pH, and acidity were affected by the clone factor, whereas seed weight, pH, and total titratable acidity were affected by ripeness stage.CONCLUSIONIdentification of indicators of ripeness for cocoa fruit is a complex task due to the influence of the clone on the evolution of the physicochemical characteristics of cocoa fruit during its maturation process. Thus, indicators must be developed for each clone, and at least two parameters among color, pH, and total titratable acidity should be used to determine the ripeness stage of cocoa fruit. © 2019 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Quantification of pulsed saturation transfer at 1.5T and 3T
Authors: Chan Rachel W. , Myrehaug Sten , Stanisz Greg J. , Sahgal Arjun , Lau Angus Z. 
Published: June 2019

PurposeTo compare magnetization transfer (MT) and CEST effects between 1.5T and 3T in phantom and in vivo experiments.MethodsA pulsed saturation scheme using block‐shaped pulses separated by gaps was used to overcome the single RF amplifier duty cycle limitations of a clinical 1.5T scanner. Modeling was performed by incorporating the extended phase graph formalism into a Bloch‐McConnell simulation. Two saturation pulse types (with long and short pulses) were used. Estimated parameters for MT (the semi‐solid pool fraction, M0B; the semi‐solid transverse relaxation time, T2B) and CEST (asymmetry; areas) were compared between 1.5T and 3T in phantoms and in the healthy brain.ResultsImproved fits were shown after inclusion of extended phase graphs. Semi‐solid pool fractions in phantom (for agar with ammonium chloride) were higher for short compared to long pulses at 3T (by 19% over all concentrations) and higher at 1.5T compared to 3T (by 5%) using short pulses. In the in vivo experiments, differentiation of white and gray matter was seen in the brain at both field strengths with improved white–gray matter contrast at 3T. In white matter, the mean semi‐solid fractions were 18 ± 2% at 3T and 15 ± 2% at 1.5T. The CEST asymmetry in white matter was negative (−4.9 ± 0.4%) at 3T and zero (0.0 ± 0.3%) at 1.5T.ConclusionsThe pulsed saturation method with short pulses, using the extended phase graph formalism in the Bloch McConnell simulations, led to improved model fits to the data, when compared to those without extended phase graphs.
Increased precision in the intravascular arterial input function with flow compensation
Authors: Bourassa‐Moreau Benoît , Lebel Réjean , Gilbert Guillaume , Mathieu David , Lepage Martin 
Published: June 2019

PurposeIn this study, we investigate the effects of pulsatile flow and inflow on dynamic susceptibility‐contrast MRI intravascular arterial input function measurement in human brain arteries and measure how they are affected by first‐order flow compensation.MethodsA dual‐echo single‐shot EPI sequence with alternating flow compensation gradients was used to acquire dynamic susceptibility‐contrast images with electrocardiogram monitoring. The dynamic signal variations measured inside the middle cerebral and internal carotid arteries were associated to the pulsatile arterial blood velocities measured with a single‐slice quantitative flow sequence throughout the cardiac cycle.ResultsMajor inverse correlations between intravascular signal and blood velocity were found for the standard single‐shot EPI sequence. Flow compensation reduces these correlated variations that contribute to signal physiological noise. This causes a significant twofold increase of intravascular SNR in the middle cerebral and the internal carotid arteries (2.3 ± 0.9, P = 0.03) and (2.0 ± 0.9, P = 0.04), respectively; and reduced phase SD for the internal carotid arteries (0.72 ± 0.14, P = 0.004). The correction proposed in this work translates into a quantitative arterial input function with reduced noise in the internal carotid arteries.ConclusionThe physiological noise added by pulsatile flow and inflow for intravascular arterial input function measurement in the brain arteries is significantly reduced by flow compensation.
Optimization of peptidic HIV‐1 fusion inhibitor T20 by phage display
Authors: Chen Gang , Cook Jonathan D. , Ye Wei , Lee Jeffrey E. , Sidhu Sachdev S. 
Published: June 2019

AbstractThe HIV fusion inhibitor T20 has been approved to treat those living with HIV/AIDS, but treatment gives rise to resistant viruses. Using combinatorial phage‐displayed libraries, we applied a saturation scan approach to dissect the entire T20 sequence for binding to a prefusogenic five‐helix bundle (5HB) mimetic of HIV‐1 gp41. Our data set compares all possible amino acid substitutions at all positions, and affords a complete view of the complex molecular interactions governing the binding of T20 to 5HB. The scan of T20 revealed that 12 of its 36 positions were conserved for 5HB binding, which cluster into three epitopes: hydrophobic epitopes at the ends and a central dyad of hydrophilic residues. The scan also revealed that the T20 sequence was highly adaptable to mutations at most positions, demonstrating a striking structural plasticity that allows multiple amino acid substitutions at contact points to adapt to conformational changes, and also at noncontact points to fine‐tune the interface. Based on the scan result and structural knowledge of the gp41 fusion intermediate, a library was designed with tailored diversity at particular positions of T20 and was used to derive a variant (T20v1) that was found to be a highly effective inhibitor of infection by multiple HIV‐1 variants, including a common T20‐escape mutant. These findings show that the plasticity of the T20 functional sequence space can be exploited to develop variants that overcome resistance of HIV‐1 variants to T20 itself, and demonstrate the utility of saturation scanning for rapid epitope mapping and protein engineering.
Enabling full‐length evolutionary profiles based deep convolutional neural network for predicting DNA‐binding proteins from sequence
Authors: Chauhan Sucheta , Ahmad Shandar 
Published: June 2019

AbstractSequence based DNA‐binding protein (DBP) prediction is a widely studied biological problem. Sliding windows on position specific substitution matrices (PSSMs) rows predict DNA‐binding residues well on known DBPs but the same models cannot be applied to unequally sized protein sequences. PSSM summaries representing column averages and their amino‐acid wise versions have been effectively used for the task, but it remains unclear if these features carry all the PSSM's predictive power, traditionally harnessed for binding site predictions. Here we evaluate if PSSMs scaled up to a fixed size by zero‐vector padding (pPSSM) could perform better than the summary based features on similar models. Using multilayer perceptron (MLP) and deep convolutional neural network (CNN), we found that (a) Summary features work well for single‐genome (human‐only) data but are outperformed by pPSSM for diverse PDB‐derived data sets, suggesting greater summary‐level redundancy in the former, (b) even when summary features work comparably well with pPSSM, a consensus on the two outperforms both of them (c) CNN models comprehensively outperform their corresponding MLP models and (d) actual predicted scores from different models depend on the choice of input feature sets used whereas overall performance levels are model‐dependent in which CNN leads the accuracy.
Review: Endophytic microbes and their potential applications in crop management
Authors: White James F , Kingsley Kathryn L , Zhang Qiuwei , Verma Rajan , Obi Nkolika , Dvinskikh Sofia , Elmore Matthew T , Verma Satish K , Gond Surendra K , Kowalski Kurt P 
Published: June 2019

AbstractEndophytes are microbes (mostly bacteria and fungi) present asymptomatically in plants. Endophytic microbes are often functional in that they may carry nutrients from the soil into plants, modulate plant development, increase stress tolerance of plants, suppress virulence in pathogens, increase disease resistance in plants, and suppress development of competitor plant species. Endophytic microbes have been shown to: (i) obtain nutrients in soils and transfer nutrients to plants in the rhizophagy cycle and other nutrient‐transfer symbioses; (ii) increase plant growth and development; (iii) reduce oxidative stress of hosts; (iv) protect plants from disease; (v) deter feeding by herbivores; and (vi) suppress growth of competitor plant species. Because of the effective functions of endophytic microbes, we suggest that endophytic microbes may significantly reduce use of agrochemicals (fertilizers, fungicides, insecticides, and herbicides) in the cultivation of crop plants. The loss of endophytic microbes from crop plants during domestication and long‐term cultivation could be remedied by transfer of endophytes from wild relatives of crops to crop species. Increasing atmospheric carbon dioxide levels could reduce the efficiency of the rhizophagy cycle due to repression of reactive oxygen used to extract nutrients from microbes in roots. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Middle‐Latitudinal Band Structure Observed in the Nighttime Ionosphere
Authors: Zhong Jiahao , Lei Jiuhou , Yue Xinan , Luan Xiaoli , Dou Xiankang 
Published: June 2019

AbstractIn this study, the Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) electron densities (Ne) from 200 to 800 km during 2006–2017 are used to investigate the middle‐latitudinal band structure of the nighttime ionosphere. The main results are as follows. (1) In the nighttime, the Ne at about ±40° geomagnetic latitudes is generally greater, especially in the topside ionosphere. (2) Double bands of relatively high Ne are seen at all longitudes during the equinoxes, while only one latitudinal band is clearly visible at specific longitudes in the winter hemisphere during the solstices. (3) The middle‐latitudinal band structure of the topside ionosphere is more pronounced at later local times (LTs) at night and under lower solar activity. (4) The middle‐latitudinal band structure mainly occurs at 23‐05 LT. (5) The seasonal/longitudinal variations of the middle‐latitudinal band structure are consistent with those of the plasmaspheric total electron content at low latitudes and upward field‐aligned winds at middle latitudes. (6) At the middle‐latitudinal bands, the downward plasma diffusion from the plasmasphere provides stable plasma source to the topside ionosphere, while the upward plasma motion due to the neutral winds is the primary source for the F2 peak region. (7) The plasma sources for the middle‐latitudinal band structures at different altitude regions are probably different, so that the resulting measurements might be due to a coalescing of these two completely different mechanisms. (8) The modulated recombination rates due to the thermospheric dynamics could also reinforce this structure.
Bumpy Topographic Effects on the Transbasin Evolution of Large‐Amplitude Internal Solitary Wave in the Northern South China Sea
Authors: Xie Jieshuo , He Yinghui , Cai Shuqun 
Published: June 2019

AbstractThe bumpy continental slope/shelf topography is a quite common feature in the northern South China Sea (SCS), yet its effect on the shoaling internal solitary waves (ISWs) remains poorly understood. Therefore, numerical simulations by a fully nonlinear, nonhydrostatic model are carried out to explore the bumpy continental slope/shelf topographic effects on the transbasin evolution of large‐amplitude ISW in the northern SCS. It is found that the prominent bumps over both continental slope and shelf regions play significant roles in modulating the evolution of transbasin ISW in the northern SCS. The bump over the continental slope is capable of triggering a solitary‐like mode‐2 internal wave packet, while the bump over the continental shelf can result in three wave groups, including a leading group of rank‐ordered mode‐1 ISW packet and two following groups of non‐rank‐ordered mode‐1 ISW packet and mode‐2 internal waves. The bumps can cause a peak‐to‐peak difference of the energy decay rate of ISW up to 10–20 kW/m over continental slope region and 3–5 kW/m over continental shelf region. The wave kinetic energy (KE) is found to exceed the available potential energy (APE) by as much as 50% over the continental shelf break region. Over the shelf region, however, the bumps can first make the KE drop to as low as only 80% of the APE, but later the KE might bounce back to approximately 1.1–1.2 times of the APE. Both onshore‐ and offshore‐propagating beam‐like disturbances are found to be excited by the bumps. Except for the onshore‐propagating mode‐2 ISW packet, the reflected offshore‐propagating waves in different internal modes are also formed. These onshore‐ and offshore‐propagating multimodal internal waves can be clarified by the beam scattering and local generation mechanism.
Climate Sensitivity From Both Physical and Carbon Cycle Feedbacks
Authors: Goodwin Philip , Williams Richard G. , Roussenov Vassil M. , Katavouta Anna 
Published: June 2019

AbstractThe surface warming response to anthropogenic forcing is highly sensitive to the strength of feedbacks in both the physical climate and carbon cycle systems. However, the definitions of climate feedback, λClimate in W·m−2·K−1, and climate sensitivity, SClimate in K/(W/m2), explicitly exclude the impact of carbon cycle feedbacks. Here we provide a new framework to incorporate carbon feedback into the definitions of climate feedback and sensitivity. Applying our framework to the Global Carbon Budget reconstructions reveals a present‐day terrestrial carbon feedback of λCarbon = 0.31 ± 0.09 W·m−2·K−1 and an ocean carbon feedback of −0.06 to 0.015 W·m−2·K−1 in Earth system models. Observational constraints reveal a combined climate and carbon feedback of λClimate+Carbon = 1.48 W·m−2·K−1 with a 95% range of 0.76 to 2.32 W·m−2·K−1 on centennial time scales, corresponding to a combined climate and carbon sensitivity of SClimate+Carbon = 0.67 K/(W/m2) with a 95% range of 0.43 to 1.32 K/(W/m2).
Weaker Than Weakest: On the Strength of Shear Zones
Authors: Stenvall Christian A. , Fagereng Åke , Diener Johann F. A. 
Published: June 2019

AbstractThin, laterally continuous ultramylonites within kilometer‐scale ductile shear zones may control middle to lower crustal strength where deformation is localized. Interconnected phyllosilicate networks are commonly suggested to be the weakest geometry a shear zone can reach, yet fine‐grained polyphase mixtures are commonly found in the cores of high‐strain zones. We study a continental strike‐slip shear zone which deformed granulite facies quartzofeldspathic migmatitic gneisses at retrograde amphibolite to greenschist facies conditions. A brittle feldspar framework and interconnected phyllosilicate networks control the strength of the lower strain protomylonites and mylonites, respectively, whereas the ultramylonites comprise a fine‐grained mixture of the host rock minerals. The localization of strain in ultramylonites demonstrates how fine‐grained polyphase mixtures can be weaker than, and supersede, interconnected phyllosilicate networks with increasing shear strain. This contradicts the common assumption that interconnected layers of phyllosilicates is the weakest state a shear zone can reach.
Investigations on water–LiBr‐based absorption refrigerator with solar parabolic dish in cogeneration mode
Authors: Abdul Shukoor Pathuthara , Reddy Kalvala Srinivas 
Published: June 2019

Here, performance of 11 kW solar‐powered lithium bromide water absorption chillers in cogeneration mode is investigated. A 40 m2 solar parabolic dish of 19 kWth capacity is used for both processes heating and cooling. Extensive thermodynamic design and analysis are carried out, and the results obtained are validated. Parabolic dish and cavity receiver are sized for Chennai (13°N, 80.18°E), India. In the present analysis, a new performance parameter COPWE is introduced by replacing the thermal input component in the calculation of COP, by an equivalent amount of high‐grade energy. Both physical and chemical exergy at all state points of the chiller are estimated and found that total irreversibility is about 2.37 kW in desorber followed by absorber which is 0.41 kW. The developed model estimates solution concentration at the exit of solution expansion valve (SEV) that is important since it affects absorption of refrigerant in the absorber.