bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal Piecewise Linear Regression Algorithm for QSAR Modelling
Authors: Cardoso‐Silva Jonathan , Papadatos George , Papageorgiou Lazaros G. , Tsoka Sophia 
Published: September 2018

AbstractQuantitative Structure‐Activity Relationship (QSAR) models have been successfully applied to lead optimisation, virtual screening and other areas of drug discovery over the years. Recent studies, however, have focused on the development of models that are predictive but often not interpretable. In this article, we propose the application of a piecewise linear regression algorithm, OPLRAreg, to develop both predictive and interpretable QSAR models. The algorithm determines a feature to best separate the data into regions and identifies linear equations to predict the outcome variable in each region. A regularisation term is introduced to prevent overfitting problems and implicitly selects the most informative features. As OPLRAreg is based on mathematical programming, a flexible and transparent representation for optimisation problems, the algorithm also permits customised constraints to be easily added to the model. The proposed algorithm is presented as a more interpretable alternative to other commonly used machine learning algorithms and has shown comparable predictive accuracy to Random Forest, Support Vector Machine and Random Generalised Linear Model on tests with five QSAR data sets compiled from the ChEMBL database.
Taurine is Involved in Energy Metabolism in Muscles, Adipose Tissue, and the Liver
Authors: Wen Chaoyue , Li Fengna , Zhang Lingyu , Duan Yehui , Guo Qiuping , Wang Wenlong , He Shanping , Li Jianzhong , Yin Yulong 
Published: September 2018

AbstractEnergy metabolism is a basic and general process, by which the body acquires and uses energy to maintain normal function, and taurine plays a vital role in energy metabolism. Taurine deficiency may cause a weak energy metabolism and energy metabolism dysfunction. Taurine biosynthetic ability is limited, and its supplementation in the diet can strengthen energy metabolism in muscle performance, cardiac function, liver activity, and adipose tissue. Combining taurine with other drugs may have a superior effect in energy metabolism. In many metabolic disorders, taurine, or the combination of taurine with other drugs, also functions as a repair treatment for damaged tissues, and acts as a promoter for the balance of energy metabolism. The present study discusses the potential roles of taurine in energy metabolism.
Effects of Dietary Carbohydrate/Lipid Ratios on Growth, Feed Utilization, Hematology Parameters, and Intestinal Digestive Enzyme Activities of Juvenile Hybrid Grouper (Brown-Marbled Grouper Epinephelus fuscoguttatus ♀ × Giant Grouper E. lanceolatus ♂)
Authors: Gao Yujie , Luo Yuan , Li Xiaojun , Dong Yu , Liao Yan , Yao Wei , Jin Zibo , Wu Xiaoyi 
Published: September 2018

Abstract
An 8-week growth trial was conducted to investigate the effects of dietary carbohydrate (CHO)/lipid (L) ratios on growth, feed utilization, hematology parameters, and intestinal digestive enzyme activities of juvenile hybrid grouper (Brown-marbled Grouper Epinephelus fuscoguttatus ♀ × Giant Grouper E. lanceolatus ♂). Seven isoproteic (53.5% dietary crude protein) and isoenergetic (3.6 kcal/g dry matter) experimental diets were formulated containing various CHO/L ratios: 0.03 (0.5% CHO/16% L); 0.36 (5% CHO/14% L); 0.79 (9.5% CHO/12% L); 1.4 (14% CHO/10% L); 2.31 (18.5% CHO/8% L); 3.83 (23% CHO/6% L); and 6.88 (27.5% CHO/4% L). Fifteen juvenile hybrid grouper (average initial body weight ± SE = 10.16 ± 0.16 g) were stocked in small floating cages. Triplicate groups of fish were fed each dietary treatment to apparent satiation twice daily (0800 and 1600 hours). Results showed that weight gain (WG; %), daily feed intake (DFI), feed conversion ratio (FCR), and protein efficiency ratio (PER) were significantly affected by different experimental diet treatments. Fish that were fed diets with CHO/L ratios of 3.83 and 6.88 had lower WG and PER but higher DFI and FCR than fish that received diets with other CHO/L ratios. Intraperitoneal fat ratio and whole-body lipid content significantly decreased with increasing dietary CHO/L ratios. Hepatic glycogen content increased with increases in dietary digestible CHO level. Fish that received lower CHO/L ratios had lower plasma glucose concentrations than fish that were fed diets with higher CHO/L ratios. As dietary CHO/L ratio increased, intestinal lipase activity decreased, but intestinal α-amylase activity increased. In conclusion, dietary energy from lipid could be partially replaced by that from digestible CHO without significant negative effects on growth performance of hybrid grouper. Furthermore, partial replacement of dietary lipid by CHO was beneficial for reducing fish adiposity through avoiding excessive lipid deposition in the abdominal cavity as well as in other tissues. We recommend 2.31 as a suitable dietary CHO/L ratio for hybrid grouper, since higher ratios (3.83 and 6.68) depressed fish growth performance.
Comparison of Lake and River Fishery Performance between Two Strains of Steelhead in Eastern Lake Michigan
Authors: Prichard Carson G. , Dexter James L. , Ledet Neil D. , O'Neal Richard , Wolgamood Martha , VanAmberg Jan P. , Jonas Jory L. 
Published: September 2018

Abstract
Management of fish species for which alternative genetic strains can be considered should be informed by indicators of strain-specific fishery performance. We compared how two strains of steelhead Oncorhynchus mykiss supported indices of angler satisfaction (catch rate and size) and motivation (effort) in the Lake Michigan basin. We assessed 10 years of recreational angling data collected for the Little Manistee River steelhead strain (LMR-STS) and Skamania steelhead strain (SKA-STS), which were tagged and stocked as paired groups in the St. Joseph and Manistee rivers. The LMR-STS were stocked to enhance fall/winter and spring river fisheries, and SKA-STS were stocked to create river/inshore summer fisheries; both were also intended to contribute to the recreational fishery of Lake Michigan. Summer angler effort exceeded spring effort on the St. Joseph River, whereas spring effort exceeded summer effort on the Manistee River. In spring river fisheries, catch rates of LMR-STS were higher than those of SKA-STS. In summer fisheries on the Manistee River, catch rates of SKA-STS exceeded those of LMR-STS. In summer on the St. Joseph River, catch rates of LMR-STS and SKA-STS were equivalent. In spring/summer, steelhead of either strain stocked in the St. Joseph River were caught equally among eight of nine ports surveyed. The CPUE of Manistee River-stocked SKA-STS was higher than that of LMR-STS in the Lake Michigan fishery. Catch statistics in both rivers and in Lake Michigan indicate that the two strains provide similar opportunities for trophy-sized steelhead. Our findings suggest that LMR-STS are favored for the St. Joseph River fishery and may represent a better total return on investment in the Lake Michigan basin.
Estimating Resting Energy Expenditure in Obesity
Authors: Foster Gary D. , McGuckin Brian G. 
Published: September 2018

FOSTER, GARY D. AND BRIAN G. MCGUCKIN. Estimating resting energy expenditure in obesity. Obes Res. 2001;9:367S–372S.In the treatment of obesity, assessment of resting energy expenditure (REE) can provide the basis for prescribing an individualized energy intake to attain a desired level of energy deficit. Indirect calorimetry is the most frequently used method to measure REE, but the great expense of equipment precludes its widespread use. As a result, REE is often estimated by predictive formulas based on weight, height, age, and gender. This paper examines the accuracy of these formulas in estimating REE among obese patients, discusses the assumptions underlying their use, and reviews the need for technological advances that will make the assessment of REE accurate, portable, and inexpensive.
Towards measuring growth rates of pathogens during infections by D2O‐labeling lipidomics
Authors: Neubauer Cajetan , Sessions Alex L. , Booth Ian R. , Bowen Benjamin P. , Kopf Sebastian H. , Newman Dianne K. , Dalleska Nathan F. 
Published: September 2018

RationaleMicrobial growth rate is an important physiological parameter that is challenging to measure in situ, partly because microbes grow slowly in many environments. Recently, it has been demonstrated that generation times of S. aureus in cystic fibrosis (CF) infections can be determined by D2O‐labeling of actively synthesized fatty acids. To improve species specificity and allow growth rate monitoring for a greater range of pathogens during the treatment of infections, it is desirable to accurately quantify trace incorporation of deuterium into phospholipids.MethodsLipid extracts of D2O‐treated E. coli cultures were measured on liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS) instruments equipped with time‐of‐flight (TOF) and orbitrap mass analyzers, and used for comparison with the analysis of fatty acids by isotope‐ratio gas chromatography (GC)/MS. We then developed an approach to enable tracking of lipid labeling, by following the transition from stationary into exponential growth in pure cultures. Lastly, we applied D2O‐labeling lipidomics to clinical samples from CF patients with chronic lung infections.ResultsLipidomics facilitates deuterium quantification in lipids at levels that are useful for many labeling applications (>0.03 at% D). In the E. coli cultures, labeling dynamics of phospholipids depend largely on their acyl chains and between phospholipids we notice differences that are not obvious from absolute concentrations alone. For example, cyclopropyl‐containing lipids reflect the regulation of cyclopropane fatty acid synthase, which is predominantly expressed at the beginning of stationary phase. The deuterium incorporation into a lipid that is specific for S. aureus in CF sputum indicates an average generation time of the pathogen on the order of one cell doubling per day.ConclusionsThis study demonstrates how trace level measurement of stable isotopes in intact lipids can be used to quantify lipid metabolism in pure cultures and provides guidelines that enable growth rate measurements in microbiome samples after incubation with a low percentage of D2O.
Impact of nitrate contamination on the analysis of carbon and oxygen isotopes in carbonate and a low‐temperature phosphoric acid digestion approach for online sample preparation
Authors: Hu Bin , Gao Jianfei , Fan Changfu , Li Yanhe , Qin Yan , Zhao Yue , Tian Yourong 
Published: September 2018

RationaleHigh‐temperature phosphoric acid digestion combined with continuous‐flow isotope ratio mass spectrometry (CF‐IRMS) is one of the standard methods for the determination of carbon and oxygen isotopes in carbonate. However, the routine purification protocol has not been tested by samples with nitrate contamination. Here we show that the standard protocol is not capable of measuring such samples with satisfactory accuracy and precision.MethodsWe tested the low‐temperature (25°C) phosphoric acid digestion method combined with CF‐IRMS for the measurement of natural carbonate samples with ~1% nitrate concentration and nitrate‐doped carbonate standards. We also recorded the Raman spectra of the gases extracted from the nitrate‐doped carbonate standards to identify the gas species that affect the results.ResultsThe accuracy and precision of δ18O values for nitrate‐doped carbonate standards digested at 72°C are much poorer than routine measurements. For the measurements of doped standards reacted at 25°C, the accuracy and precision of the δ13C and δ18O values are indistinguishable from normal results. Raman spectra demonstrate that NO2 generated from high‐temperature digestion is the possible interference species for oxygen isotope measurement.ConclusionsLow‐temperature digestion is a reliable method for the measurement of carbon and oxygen isotopes in nitrate‐contaminated carbonate samples because the formation of NO2 can be largely reduced. This approach can be applied to some nitrate‐rich speleothems, evaporites and other samples with nitrate contamination.
Pulsed capillary introduction applied to a miniature mass spectrometer for efficient liquid analysis
Authors: Shi Wenyan , Lu Xinqiong , Zhang Jianchao , Yu Quan , Wang Xiaohao 
Published: September 2018

RationaleCapillary sampling of liquids for direct mass spectrometry (MS) analysis is introduced. The low transfer rate of the solution in the capillary will affect the analytical sensitivity and the response time; hence a pulsed capillary introduction (PCI) method was proposed and characterized.MethodsThe experiments were carried out using a miniature quadrupole mass spectrometer, and liquid can be spontaneously drawn into the vacuum chamber for subsequent ionization and detection. A simple up‐and‐down motor platform was used to control the brief contact of the capillary inlet with the liquid sample and implement pulsed injection. The pulsed sampling parameters were optimized based on the characterization and dynamic study of liquid transfer in capillaries.ResultsCompared with continuous capillary introduction (CCI), PCI can reduce the response time of MS analysis from more than half a minute to a few seconds. In addition, it provides better detection sensitivity as the ion signals of all solution components are enhanced and the acquired limit of detection (LOD) of toluene is about eight times lower than CCI analysis. For each analysis, the consumed sample volume is only a few nanoliters and the absolute consumption of the analyte can reach the femtogram level.ConclusionsThe proposed PCI method is proved to be successful in improving the sampling efficiency when performing direct liquid analysis without increasing the vacuum load. A miniature MS instrument with a proper capillary inlet can possess flexible operation modes to meet different application demands.
Biomarkers for Progenitor and Differentiated Epithelial Cells in the Human Meibomian Gland
Authors: Xie Hua-Tao , Sullivan David A. , Chen Di , Hatton Mark P. , Kam Wendy R. , Liu Yang 
Published: September 2018

Abstract
The meibomian gland (MG) is a sebaceous gland that secretes through a holocrine process. Because such secretion requires the destruction of MG acinar epithelial cells, they need constant renewal and differentiation. The processes that promote these regenerative events in the human MG are unknown, nor is it known how to distinguish MG progenitor and differentiated cells. We discovered that Lrig1 and DNase2 serve as biomarkers for human MG progenitor and differentiated cells, respectively. Lrig1 is expressed in MG basal epithelial cells in the acinar periphery, a location where progenitor cells originate in sebaceous glands. DNase2 is expressed in the differentiated epithelial cells of the MG central acinus. Furthermore, proliferation stimulates, and differentiation suppresses, Lrig1 expression in human MG epithelial cells. The opposite is true for DNase2 expression. Our biomarker identification may have significant value in clinical efforts to restore MG function and to regenerate MGs after disease-induced dropout.
Prospects for the Use of Induced Pluripotent Stem Cells in Animal Conservation and Environmental Protection
Authors: Stanton Morgan M. , Tzatzalos Evangeline , Donne Matthew , Kolundzic Nikola , Helgason Ingvar , Ilic Dusko 
Published: September 2018

Summary
Stem cells are unique cell populations able to copy themselves exactly as well as specialize into new cell types. Stem cells isolated from early stages of embryo development are pluripotent, i.e., can be differentiated into multiple different cell types. In addition, scientists have found a way of reverting specialized cells from an adult into an embryonic-like state. These cells, that are as effective as cells isolated from early embryos, are termed induced pluripotent stem cells (iPSCs). The potency of iPSC technology is recently being employed by researchers aimed at helping wildlife and environmental conservation efforts. Ambitious attempts using iPSCs are being made to preserve endangered animals as well as reanimate extinct species, merging science fiction with reality. Other research to sustain natural resources and promote animal welfare are exploring iPSCs for laboratory grown animal products without harm to animals offering unorthodox options for creating meat, leather, and fur. There is great potential in iPSC technology and what can be achieved in consumerism, animal welfare, and environmental protection and conservation. Here, we discuss current research in the field of iPSCs and how these research groups are attempting to achieve their goals. Stem Cells Translational Medicine 2019;8:7–13
Cell-Based Therapies: The Nonresponder
Authors: Caplan Arnold I. 
Published: September 2018

Summary
Cell-based therapies have come of age and several phase III trials are now being conducted. Cell-based therapies, especially involving mesenchymal stem cells (MSCs), have substantial nonresponder rates, as has been reported in some current clinical trials. This high rate is expected as the MSCs are neither tuned for each of the diseases that are being treated nor for the huge variance in the genetics and response characteristics of the individual patients being treated. Such nonresponders might be used as a control group, thus eliminating the need for placebo controls.
Diet Variability of Steelhead/Rainbow Trout in a Coastal Basin in Central California: Relative Importance of Seasonal, Spatial, and Ontogenetic Variation
Authors: Rundio David E. , Lindley Steven T. 
Published: September 2018

AbstractDiets of stream‐dwelling salmonids vary at multiple spatial and temporal scales, but the relative importance of different sources of variation has rarely been evaluated for a population. In a small coastal basin in central California, we sampled diets of steelhead/Rainbow Trout Oncorhynchus mykiss monthly for a year from two reaches that differed in the presence of streambed travertine (calcium carbonate) to determine the relative magnitude of spatial, seasonal, and ontogenetic variation in consumption and diet composition. Seasonal parameters (cosine function terms for months in periodic regression and multivariate models) and fish size (FL) were greater sources of variation than differences between the two study reaches, and seasonal and ontogenetic patterns were evident despite high interindividual variability. Seasonal parameters explained the most variation in diet composition, which varied in an orderly pattern over the year. Consumption was highest in spring and summer for both aquatic and terrestrial prey, and seasonal parameters accounted for more variation than fish size for consumption of aquatic prey but this was reversed for terrestrial prey and total consumption. The main ontogenetic trend was increased consumption of terrestrial invertebrates: from 15‐20% of the energy consumed by 60–100‐mm fish to 60% of the energy consumed by fish larger than 160 mm. In addition, diet breadth (taxonomic richness and prey size) and the degree of variation among individuals also increased with fish size. Diet differences between sites were relatively small and included higher consumption of aquatic invertebrates at the site without travertine in 4 months and modest differences in the relative abundances of common prey taxa. Although seasonal and ontogenetic patterns were evident, interindividual variation was the dominant scale of diet variation, and diets of individual fish ranged from specialized to generalized relative to the population. Based on these findings, O. mykiss appeared to be opportunistic feeders that took advantage of diverse aquatic and terrestrial prey available in these study reaches.
Can Polymer Solar Cells Open the Path to Sustainable and Efficient Photovoltaic Windows Fabrication?
Authors: Vohra Varun 
Published: September 2018

AbstractSunlight is among the most abundant energy sources available on our planet. Finding adequate solutions to properly and efficiently harvest it is of major importance to potentially solve the global energy crisis. Polymer solar cells have been introduced in the late 20th century as low‐cost and easily processed alternative to the state‐of‐the‐art silicon photovoltaics. Their power conversion efficiencies, which were initially rather low, are constantly improving and now reach values close to 15 %. As their optical properties can be easily tuned, designing active layer which absorb homogeneously throughout the visible spectrum is relatively simple. These peculiar characteristics enable the possibility to fabricate visibly transparent solar cells with high color rendering indices which can be employed as photovoltaic windows. After reviewing some of the most successful examples of polymer solar cell‐based transparent photovoltaic window fabrication, I will discuss the possibility to produce these devices in a sustainable and/or eco‐friendly manner while maintaining their performances.
X‐Ray Scattering and Imaging Studies of Electrode Structure and Dynamics
Authors: You Hoydoo 
Published: September 2018

AbstractWe will review structures and dynamics of electrode interfaces studied in situ using x‐ray scattering and imaging techniques. The examples cover single‐crystal and nanocrystal structures relevant to electrocatalytic activities, anodic oxidation and corrosion, aqueous dissolution reactions, surface reconstructions, and surface modifications by under potential deposition. The x‐ray techniques include the widely used traditional surface x‐ray scattering, such as crystal truncation rods and x‐ray reflectivity, as well as recently developed resonance surface scattering, coherent surface x‐ray photon correlation spectroscopy, coherent x‐ray Bragg diffraction imaging, and surface ptychography. Results relevant to various electrochemical phenomena will be highlighted.
Perspective to the Potential Use of Graphene in Li‐Ion Battery and Supercapacitor
Authors: Tian Jiarui , Yang Zhoufei , Yin Zefang , Ye Zhenzhen , Wang Jin , Cui Chaojie , Qian Weizhong 
Published: September 2018

AbstractGraphene is a hot star in materials science with various potential application aspects, including in Li‐ion battery and supercapacitor. The burst of scientific papers in this area seems to validate the performance of graphene, but also arouses large dispute. Herein, we share our judgment of these trends to all, encouraging the discussion and enhancing the understanding of the structure‐performance relationship of graphene.