bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significance and roles of synonymous codon usage in the evolutionary process of Proteus
Authors: Jin Li , Gao Han , Cao Xiaoan , Han Shengyi , Xu Long , Ma Zhongren , Shang Youjun , Ma Xiao‐xia 
Published: March 2020

AbstractProteus spp. bacteria frequently serve as opportunistic pathogens that can infect many animals and show positive survival and existence in various natural environments. The evolutionary pattern of Proteus spp. is an unknown topic, which benefits understanding the different evolutionary dynamics for excellent bacterial adaptation to various environments. Here, the eight whole genomes of different Proteus species were analyzed for the interplay between nucleotide usage and synonymous codon usage. Although the orthologous average nucleotide identity and average nucleotide identity display the genetic diversity of these Proteus species at the genome level, the principal component analysis further shows that these species sustain the specific genetic niche at the aspect of synonymous codon usage patterns. Interestingly, although these Proteus species have A/T rich genes with underrepresented G (guanine) or C (cytosine) at the third codon positions and overrepresented A or T at these positions, some synonymous codons with A or T end are obviously suppressed in usage. The overall codon usage pattern reflected by the effective number of codons (ENC) has a significantly positive correlation with GC3 content (GC content at the third codon position), and ENC has a significantly negative correlation with the adaptation index for these species. These results suggest that the mutation pressure caused by nucleotide composition constraint serves as a dominant evolutionary dynamic driving evolutionary trend of Proteus spp., along with other selections related to natural selection, replication and fine‐tune translation, and so on. Taken together, the analyses help to understand the evolutionary interplay between nucleotide and codon usage at the gene level of Proteus.
Inter‐segmental foot kinematics during gait in elderly females according to the severity of hallux valgus
Authors: Kim Eo Jin , Shin Hyuck Soo , Takatori Naoko , Yoo Hyo Jeong , Cho Yun Jae , Yoo Won Joon , Lee Dong Yeon 
Published: March 2020

AbstractThe objective of this study was to find the effect of hallux valgus (HV) deformity on the inter‐segmental motion of the foot using an MFM with a 15‐marker set (DuPont Foot Model, DuFM) in comparison with age and sex controlled healthy adults. Fifty‐eight female symptomatic HV patients and 50 female asymptomatic older female volunteers were included in this study. According to the radiographic hallux valgus angle (HVA), the study population was divided into severe HV (SHV, HVA ≥ 40°, n = 25), moderate HV (MHV, 20° ≤ HVA < 40°, n = 47), and control (CON, n = 36). MHV group was divided into symptomatic MHV group (S‐MHV, n = 33) and asymptomatic MHV group (A‐MHV, n = 14) according to the symptoms associated with HV. For temporal parameters, gait speed and stride length were diminished according to the severity of HV deformity. Sagittal range of motion of hallux and hindfoot decreased significantly in SHV group. Loss of push‐off during the preswing phase was observed and forefoot adduction motion during terminal stance was decreased in SHV group. In a subgroup analysis of MHV, asymptomatic HV minimally affects gait and inter‐segmental motion during gait. HV deformity affects gait parameters and inter‐segmental motion of the foot during gait in proportion to the severity of the deformity. However, the effect of MHV itself on foot kinematics might be limited while pain or arthritic change of the joint might cause changes in gait in patients with symptomatic HV.
Fracture risk assessment and clinical decision making for patients with metastatic bone disease
Authors: Damron Timothy A. , Mann Kenneth A. 
Published: March 2020

AbstractMetastatic breast, prostate, lung, and other cancers often affect bone, causing pain, increasing fracture risk, and decreasing function. Management of metastatic bone disease (MBD) is clinically challenging when there is potential but uncertain risk of pathological fracture. Management of MBD has become a major focus within orthopedic oncology with respect to fracture and impending fracture care. If impending skeletal‐related events (SREs), particularly pathologic fracture, could be predicted, increasing evidence suggests that prophylactic surgical treatment improves patient outcomes. However, current fracture risk assessment and radiographic metrics do not have high accuracy and have not been combined with relevant patient survival tools. This review first explores the prevalence, incidence, and morbidity of MBD and associated SREs for different cancer types. Strengths and limitations of current fracture risk scoring systems for spinal stability and long bone fracture are highlighted. More recent computed tomography (CT)‐based structural rigidity analysis (CTRA) and finite element (FE) analysis methods offer advantages of increased specificity (true negative rate), but are limited in availability. Other fracture prediction approaches including parametric response mapping and positron emission tomography/computed tomography measures show early promise. Substantial new information to inform clinical decision‐making includes measures of survival, clinical benefits, and economic analysis of prophylactic treatment compared to after‐fracture stabilization. Areas of future research include use of big data and machine learning to predict SREs, greater access and refinement of CTRA/FE approaches, combination of clinical survival prediction tools with radiographically based fracture risk assessment, and net benefit analysis for fracture risk assessment and prophylactic treatment.
Determination of skin penetration profiles by confocal Raman microspectroscopy: Evaluation of interindividual variability and interlab comparability
Authors: Binder Lisa , Valenta Claudia , Lunter Dominique 
Published: March 2020

AbstractConfocal Raman microspectroscopy is being increasingly used to investigate the skin penetration of actives and excipients. The aim of the present study was to compare results obtained with skin from different donors, acquired with two Raman systems: the RiverD gen2 Skin Composition Analyzer and the WiTec alpha 500 instrument. To elucidate the interindividual variability between the skin donors and to find out whether the two systems would give similar results in skin penetration analysis, we compared the penetration of the model drug procaine from hydrogel formulations with or without the penetration enhancer POE‐23‐lauryl ether. Penetration was investigated with both systems on skin from three different skin donors, each. Penetration plots were prepared by plotting the signal intensity of a typical peak of procaine against the skin depth. We then calculated the enhancement ratio from the areas under the curves of the penetration plots of procaine that had penetrated from the formulation with or without the enhancer. They ranged between 2.0 and 3.1 for the WiTec system and between 2.1 and 3.1 for the RiverD system. Thus, we found that both systems provide similar estimations of the skin penetration of procaine.
Self‐Diverting Acid System with Retarding Function for Heterogeneous Carbonate Reservoirs Stimulation
Authors: Mao Jincheng , Wang Chen , Yang Xiaojiang , Zhang Heng , Zhang Wenlong , Zhang Chong , Lin Chong 
Published: March 2020

AbstractMatrix acidization, an important technology for reservoir stimulation, has encountered challenges regarding heterogeneity. In addition to not achieving desired results, conventional acidization makes reservoir heterogeneity more prominent. In this study, we investigated the efficacy of a surfactant‐based functional acid system for uniform acidization in carbonate reservoirs. The two surfactants used in such acid systems are industrial initial products, which can be converted to a hydrochloride surfactant in hydrochloric acid. The conversion alters viscosity in reaction processes and can slow down reaction rates to allow for deeper rock penetration while at the same time forcing fresh acid into the untreated areas. The acid system can enhance well production considerably. It was found that the surfactant solution exhibited a relatively high viscosity at 90°C and is conducive to acid diverting. The retarding rate of the acid system was found to be up to 48%, allowing for deeper penetration. Parallel core flood testing indicates that the acid system exhibits superior diverting performance when compared to regular acid at 20 wt% HCl.
Effect of Harvest on a Brown Bear Population in Alaska
Authors: Brockman Chris , Guttery Michael R. , Dale Bruce W. , Schwanke Rebecca A. , Tobey Robert W. , Koons David N. 
Published: March 2020

ABSTRACTThere is a long and contentious history of brown bear (Ursus arctos) harvest management in Alaska, USA, the state that hosts the largest brown bear population in North America. In the mid‐1990s, the Alaska Board of Game set the population objective for brown bears in Game Management Unit 13 A, located in interior southcentral Alaska, to be reduced by 50% to improve survival of moose (Alces alces) calves. The Board began further liberalizing brown bear harvest regulations for the unit beginning in regulatory year 1995, though adult females and their dependent offspring (i.e., cubs <2 yrs old) were protected. To evaluate progress toward this abundance objective, we captured and collared bears between 2006 and 2011 and conducted a capture‐mark‐resight density survey during summer 2011 for comparison to a similar baseline survey conducted in 1998. We report the results of the density survey and vital rates estimated from resight histories of collared bears and harvest information spanning from 1985 (10 years before establishment of the population objective) to 2012. There was a 25–40% reduction in abundance between 1998 and 2011. Population growth rates derived from density estimates and a matrix population projection model indicated that the population declined by 2.3–4.2% annually. We estimated harvest rates to be 8–15% annually, but harvest composition data indicated no changes in skull size, age distribution, or overall sex ratio. There was evidence of an increase in the proportion of older females in the harvest. Demographic analysis indicated high reproductive output and recruitment, potentially indicating a density‐dependent compensatory response to reduced population size. Despite 13 years of harvest rates in excess of what had previously been considered to be sustainable for this population, the objective of reducing bear abundance by 50% had not been achieved as of 2011. The protection of females and dependent offspring in our study population appears to be a sufficient safeguard against a precipitous population decline while still permitting progress toward the population objective through high harvest on other segments of the population. © 2020 The Wildlife Society.
The vulnerability of calcareous soils exposed to Mg‐enriched irrigation water
Authors: Abdollahpour Mostafa , Rahnemaie Rasoul , Lützenkirchen Johannes 
Published: March 2020

AbstractDue to imbalanced groundwater withdrawal, Mg concentration has relatively increased in the majority of irrigation waters in arid and semiarid regions, which may negatively affect soil properties and productivity. Therefore, this study was aimed at understanding to what extent varying Ca to Mg ratios in the calcareous soil solution alter the ratio on the exchangeable sites. To do so, four calcareous soils were equilibrated with eight Ca to Mg ratios and then the relative adsorption of Ca and Mg ions on the exchangeable sites and the CEC of soil samples were measured using a modified silver‐thiourea method. To quantitatively explain our observations, we used the Gaines–Thomas equation, and its parameters were independently derived from the dissolution/precipitation reactions of carbonate minerals. Our results showed that among Ca and Mg, the one that had the lowest concentration in the soil solution was preferably adsorbed at exchangeable sites. The modeling results indicated that Ca and Mg ions are adsorbed with wide ranges of adsorption energies, which on the macroscopic scale are interpreted as ion preference. Ion pair formation of Ca and Mg with Cl in the soil solution had no significant effect on their surface reactions. In addition, modeling indicated that at high Ca or Mg concentration, the surface species stoichiometry may gradually change from bidentate to monodentate to accommodate more ions. Thus, it can be concluded that by application of Mg‐enriched irrigation water the risk for Mg accumulation in calcareous soils is highly increased which in turn increases the risk for soil degradation and indirectly for soil sodification.
Grazing significantly increases root shoot ratio but decreases soil organic carbon in Qinghai‐Tibetan Plateau grasslands: A hierarchical meta‐analysis
Authors: Yan Liang , Li Yong , Wang Li , Zhang Xiaodong , Wang Jinzhi , Wu Haidong , Yan Zhongqing , Zhang Kerou , Kang Xiaoming 
Published: March 2020

AbstractThe Qinghai‐Tibetan Plateau (QTP) is the most expansive area of alpine grasslands worldwide, which have been grazed for thousands of years. Distinct environmental conditions render QTP grasslands vulnerable to disturbances. Intensified grazing in the area has led to its degradation in recent decades. However, the effects of grazing on grassland production, soil carbon, and nitrogen contents, their relationships and the factors influencing the grasslands of QTP have yet to be determined. In this study, we evaluated the effect of grazing by using a hierarchical meta‐analysis, and explored relation of response variables by structural equation modeling. In all, grazing significantly decreased the aboveground biomass (−38%), total biomass (TB) (−14%), litter (−63%), soil organic carbon (SOC) (−20%), and total nitrogen (TN) (−15%). The root shoot ratio was increased (75%). Grazing intensity exerted significant effects, and mean annual temperature and altitude influenced the responses to a certain degree. Specifically, the response of the root shoot ratio, which can affect the responses of SOC and TN, was significantly higher in the QTP grasslands. Our findings elucidated the response patterns, specialties, relationships, and factors influencing the QTP grasslands, which need to be considered in the development of process‐based models and the sustainable use of alpine grasslands on QTP in the future.
Two‐Way Reversible Shape Memory Properties of Benzoyl Peroxide Crosslinked Poly(ethylene‐co‐vinyl acetate) under Different Stress Conditions
Authors: Hui Jin , Xia Hong , Fu Yaqin , Qiu Yiping , Ni Qing‐Qing 
Published: March 2020

AbstractTwo‐way (reversible) chemically crosslinked semicrystalline shape memory polymers are synthesized using poly(ethylene‐co‐vinyl acetate) (PEVA) with benzoyl peroxide (BPO). The two‐way shape memory effect (2W‐SME) is achieved under both constant stress and stress‐free conditions. It is found that the stress‐free 2W‐SME can be achieved by the relationship between the initial prestretching strain (Rprestretch) and recovery strain (Rrec). Under the same prestretching stress, the stress‐free two‐way shape memory behavior can be controlled by variation of Rrec using a different setting temperature (Tset) in the recovery process. More importantly, the driving force and recovery force, as one of the key indicators for two‐way shape memory materials, are investigated, and they significantly change depending on the BPO content. The sample with high BPO content shows excellent high‐temperature creep resistant performance. A highly crosslinked structure can suppress viscous flow and provides sufficient force to allow the sample to recover its initial shape after crystal melting. Therefore, the PEVA/BPO samples are able to contract during heating. The presence of an oriented crystal structure with high applied stress that causes sample elongation during cooling is also investigated. These findings for PEVA/BPO two‐way shape memory polymers will contribute to their applications as soft actuators in various fields.
Striatal Dopamine Denervation Impairs Gait Automaticity in Drug‐Naïve Parkinson's Disease Patients
Authors: Hirata Kosei , Hattori Takaaki , Kina Satoko , Chen Qingmeng , Ohara Masahiro , Yokota Takanori 
Published: March 2020

AbstractBackgroundGait automaticity, which is impaired in patients with Parkinson's disease (PD), can be quantified by gait variability analysis. Among the 3 regions of the striatum (sensorimotor, executive, and limbic), the sensorimotor region may play a crucial role in motor automaticity in healthy individuals. However, neural correlates of impaired gait automaticity are poorly investigated in PD.ObjectiveWe aimed to examine the relationship between gait automaticity and striatal dopaminergic depletion in drug‐naïve PD patients.MethodsA total of 21 drug‐naïve PD patients and 12 healthy controls were enrolled. Gait parameters were measured via wearable inertial sensors under fast‐paced gait or cognitive dual‐task conditions, and their respective coefficient of variation (CV) and dual‐task cost were calculated. The extent of striatal dopaminergic depletion was evaluated by dopamine transporter (DAT) imaging with single‐photon emission computed tomography using N‐ω‐fluoropropyl‐2β‐carbomethoxy‐3β‐(4‐[123I]iodophenyl)nortropane. Correlation between DAT uptake and gait variables was analyzed using the region‐of‐interest analysis for the 3 right or left striatal regions and voxel‐based analysis.ResultsPD had higher mean bilateral CV and dual‐task cost of stride length than healthy controls. The mean bilateral CV of stride length was negatively correlated with DAT uptake in the bilateral executive regions of the striatum. Voxel‐based analysis revealed a negative correlation between the mean bilateral CV of stride length and DAT uptake in the anteromedial striatum.ConclusionsDopaminergic denervation in the anteromedial striatum, a part of the executive region, is associated with impaired gait automaticity in drug‐naïve PD patients. This region may compensate for the posterior sensorimotor striatum, maintaining gait automaticity. © 2020 International Parkinson and Movement Disorder Society
Label‐free in situ pH monitoring in a single living cell using an optical nanoprobe
Authors: Yang Qingbo , Zhang Xiaobei , Song Yang , Li Ke , Shi Honglan , Xiao Hai , Ma Yinfa 
Published: March 2020

AbstractIntracellular pH plays critical roles in cell and tissue functions during processes such as metabolism, proliferation, apoptosis, ion transportation, endocytosis and muscle contraction. It is thus an important biomarker that can readily be used to monitor the physiological status of a cell. Thus, disrupted intracellular pH may serve as an early indicator of cell dysfunction and deterioration. Various methods have been developed to detect cellular pH, such as pH‐sensitive labelling reagents with fluorescent or Raman signals. However, excessive cellular uptake of these reagents will not only disrupt cell viability but also compromise effective long‐term monitoring. Here, we present a novel fibre‐optic fluorescent nanoprobe with a high spatial resolution for label‐free, subcellular pH sensing. The probe has a fast response time (~20 s) with minimum invasiveness and excellent pH resolution (0.02 pH units) within a biologically relevant pH environment ranging from 6.17 to 8.11. Its applicability was demonstrated on cultured A549 lung cancer cells, and its efficacy was further testified in two typical cytotoxic cases using carbonylcyanide 3‐chlorophenyl hydrazine, titanium dioxide and nanoparticles. The probe can readily detect the pH variations among cells under toxin/nanoparticles administration, enabling direct monitoring of the early onset of physiological or pathological events with high spatiotemporal resolution. This platform has excellent promise as a minimum invasive diagnostic tool for pH‐related cellular mechanism studies, such as inflammation, cytotoxicity, drug resistance, carcinogenesis and stem cell differentiation.
Weather‐data‐based model: an approach for forecasting leaf and stripe rust on winter wheat
Authors: Rodríguez‐Moreno Victor M. , Jiménez‐Lagunes Alejandro , Estrada‐Avalos Juan , Mauricio‐Ruvalcaba Jorge E. , Padilla‐Ramírez José S. 
Published: March 2020

AbstractClassification and regression trees (CARTs) for data analysis, an hourly weather dataset, and a 3 year field incidence and severity dataset of winter wheat rust were integrated to forecast pathogens’ presence/absence. The field dataset of incidence and severity was collected for three production cycles. Measured records of 88 Automatic Meteorological Stations and the indirect weather dataset generated in the Weather Research and Forecasting environment interpolated to each Automatic Meteorological Station location were analysed in the Python ecosystem. The focal point of the analysis was the severity of the disease. The analysis of direct weather data revealed the association of leaf rust severity with a night temperature of <14.25°C and global radiation of <521.67 W·m–2, while the estimated dataset showed that its severity is better explained by the dew point temperature of <13.7°C and a mean temperature of <19.06°C. The direct dataset also indicated that stripe rust severity was associated with relative humidity of <88.73%, global radiation of <597.39 W·m–2 and dew point temperature of <16.09°C, whereas the estimated data revealed that pathogen severity is better explained by a model composed of a dew point temperature of <14.6°C, night temperature of <20.4°C and a maximum temperature of <27.9°C. The severity and intensity analysis indicated the pathogen's preference for non‐dry ambient conditions and the preference of stripe rust pathogen for humid and warmer temperatures than leaf rust. The weather thresholds of both pathogens, and CART analysis, unveiled that winter wheat rust can be forecasted. This constitutes the foundation of a more efficient extension programme based on the internet of things.
In Silico Prediction of Metabolic Epoxidation for Drug‐like Molecules via Machine Learning Methods
Authors: Hu Jiajing , Cai Yingchun , Li Weihua , Liu Guixia , Tang Yun 
Published: March 2020

AbstractEpoxidation is one of the reactions in drug metabolism. Since epoxide metabolites would bind with proteins or DNA covalently, drugs should avoid epoxidation metabolism in the body. Due to the instability of epoxide, it is difficult to determine epoxidation experimentally. In silico models based on big data and machine learning methods are hence valuable approaches to predict whether a compound would undergo epoxidation. In this study, we collected 884 epoxidation data manually from various sources, and finally got 829 unique sites of epoxidation. Three types of molecular fingerprints with different lengths (1024, 2048 or 4096 bits) were used to describe the reaction sites. Six machine learning methods were used to build the classification models. The training set and test set were randomly divided into 8 : 2, and 54 models were constructed and evaluated. Four best models were selected for feature selection. The features were then chosen and verified by external validation set. The resulted optimal model had the accuracy and AUC (area under the curve) values at 0.873 and 0.944 for the test set, 0.838 and 0.987 for the external validation set, respectively. The models built in this study could accurately predict whether a compound will undergo epoxidation and which part is most susceptible to epoxidation, which is of great significance for drug design.