bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precise diagnosis of three top cancers using dbGaP data
Authors: Liu Xu-Qing , Liu Xin-Sheng , Rong Jian-Ying , Gao Feng , Wu Yan-Dong , Deng Chun-Hua , Jiang Hong-Yan , Li Xiao-Feng , Chen Ye-Qin , Zhao Zhi-Guo , Liu Yu-Ting , Chen Hai-Wen , Li Jun-Liang , Huang Yu , Ji Cheng-Yao , Liu Wen-Wen , Luo Xiao-Hu , Xiao Li-Li 
Published: January 2021

AbstractThe challenge of decoding information about complex diseases hidden in huge number of single nucleotide polymorphism (SNP) genotypes is undertaken based on five dbGaP studies. Current genome-wide association studies have successfully identified many high-risk SNPs associated with diseases, but precise diagnostic models for complex diseases by these or more other SNP genotypes are still unavailable in the literature. We report that lung cancer, breast cancer and prostate cancer as the first three top cancers worldwide can be predicted precisely via 240–370 SNPs with accuracy up to 99% according to leave-one-out and 10-fold cross-validation. Our findings (1) confirm an early guess of Dr. Mitchell H. Gail that about 300 SNPs are needed to improve risk forecasts for breast cancer, (2) reveal an incredible fact that SNP genotypes may contain almost all information that one wants to know, and (3) show a hopeful possibility that complex diseases can be precisely diagnosed by means of SNP genotypes without using phenotypical features. In short words, information hidden in SNP genotypes can be extracted in efficient ways to make precise diagnoses for complex diseases.
Completeness of open access FluNet influenza surveillance data for Pan-America in 2005–2019
Authors: Simpson Ryan B. , Gottlieb Jordyn , Zhou Bingjie , Hartwick Meghan A. , Naumova Elena N. 
Published: January 2021

AbstractFor several decades, the World Health Organization has collected, maintained, and distributed invaluable country-specific disease surveillance data that allow experts to develop new analytical tools for disease tracking and forecasting. To capture the extent of available data within these sources, we proposed a completeness metric based on the effective time series length. Using FluNet records for 29 Pan-American countries from 2005 to 2019, we explored whether completeness was associated with health expenditure indicators adjusting for surveillance system heterogeneity. We observed steady improvements in completeness by 4.2–6.3% annually, especially after the A(H1N1)-2009 pandemic, when 24 countries reached > 95% completeness. Doubling in decadal health expenditure per capita was associated with ~ 7% increase in overall completeness. The proposed metric could navigate experts in assessing open access data quality and quantity for conducting credible statistical analyses, estimating disease trends, and developing outbreak forecasting systems.
Enzymatic defense of Cyperus brevifolius in hydrocarbons stress environment and changes in soil properties
Authors: Chakravarty Paramita , Deka Hemen 
Published: January 2021

AbstractHydrocarbons or crude oil contamination of soil is still a burning problem around the globe. The herbs competent that are to survive in hydrocarbons contaminated habitats have some adaptive advantages to cope up with the adverse situations prevailing in that environment. In the present study, the adaptive response of Cyperus brevifolius in the heavily polluted soil with crude oil has been investigated in terms of survivability, changes in productivity, antioxidants, phytochemicals and functional group pro files of the plant species. Besides, changes in enzymes, beneficial bacterial population and physico-chemical conditions of contaminated soil were also studied during 60 days of experimental trials. The results showed significant enhancement in activities of soil dehydrogenase, urease, alkaline phosphatase, catalase, and amylase whereas reduction in cellulase, polyphenol oxidase and peroxidase activities. There was a significant increase in nitrogen fixing, phosphate and potassium solubilizing bacterial population, improvement in physico-chemical conditions and a decrease in total oil and grease (TOG) levels. Besides there was significant variations in the productivity parameters and antioxidant profiles of Cyperus brevifolius in hydrocarbons stress condition suggesting enzymatic defense of the herb. The fourier-transform infrared (FT-IR) analysis indicated uptake and metabolism of some hydrocarbon components by the experimental plant from the hydrocarbons polluted soil.
Consistent choice of landscape urbanization level across the annual cycle in a migratory waterbird species
Authors: Chyb Amelia , Jedlikowski Jan , Włodarczyk Radosław , Minias Piotr 
Published: January 2021

AbstractRapid urbanization has a great impact on avian distribution, ecology, habitat selection, and behavior. Recent avian studies indicated that individuals remain consistent in their behavioral responses to human disturbance across short periods of time. However, there is still little information about keeping consistent behaviors in distinct locations across different stages of the annual cycle. In this study, we aimed to test for long-term consistency in habitat selection with respect to urbanization in a migratory waterbird species, the Eurasian cootFulica atra. For this purpose, we individually marked ca. 300 coots from four populations that varied in urbanization level and tracked their habitat preferences during the non-breeding season. We found that individuals from urban breeding populations selected habitats with a higher share of artificial areas during the non-breeding season, when compared to non-urban individuals. Also, a comparison of non-breeding sites selected by birds from our study populations with random sites showed that urban birds selected sites with higher urbanization level than resulting from random availability. Finally, we found a seasonal variation in habitat preferences in coots—individuals from all study populations selected more urbanized areas as the non-breeding season progressed. The results indicate that birds are able to remain consistent in habitat preferences not only at a large geographical scale, but also across different seasons. Marked between-population variation in habitat selection across the annual cycle may reflect personality differences of coots from urban and non-urban populations, and it stays in line with the personality-matching habitat choice hypothesis.
CHA2DS2-VASc score in acute ischemic stroke with atrial fibrillation: results from the Clinical Research Collaboration for Stroke in Korea
Authors: Lee Hak-Loh , Kim Joon-Tae , Lee Ji Sung , Kim Beom Joon , Park Jong-Moo , Kang Kyusik , Lee Soo Joo , Kim Jae Guk , Cha Jae-Kwan , Kim Dae-Hyun , Park Tai Hwan , Park Sang-Soon , Lee Kyung Bok , Lee Jun , Hong Keun-Sik , Cho Yong-Jin , Park Hong-Kyun , Lee Byung-Chul , Yu Kyung-Ho , Oh Mi Sun , Kim Dong-Eog , Ryu Wi-Sun , Choi Jay Chol , Kwon Jee-Hyun , Kim Wook-Joo , Shin Dong-Ick , Sohn Sung Il , Hong Jeong-Ho , Park Man-Seok , Choi Kang-Ho , Cho Ki-Hyun , Lee Juneyoung , Bae Hee-Joon 
Published: January 2021

AbstractWe investigated a multicenter registry to identify estimated event rates according to CHA2DS2-VASc scores in patients with acute ischemic stroke (AIS) and atrial fibrillation (AF). The additional effectiveness of antiplatelets (APs) plus oral anticoagulants (OACs) compared with OACs alone considering the CHA2DS2-VASc scores was also explored. This study retrospectively analyzed a multicenter stroke registry between Jan 2011 and Nov 2017, identifying patients with acute ischemic stroke with AF. The primary outcome event was a composite of recurrent stroke, myocardial infarction, and all-cause mortality within 1 year. A total of 7395 patients (age, 73 ± 10 years; men, 54.2%) were analyzed. The primary outcome events at one year ranged from 5.99% (95% CI 3.21–8.77) for a CHA2DS2-VASc score of 0 points to 30.45% (95% CI 24.93–35.97) for 7 or more points. After adjustments for covariates, 1-point increases in the CHA2DS2-VASc score consistently increased the risk of primary outcome events (aHR 1.10 [1.06–1.15]) at 1-year. Among OAC-treated patients at discharge (n = 5500), those treated with OAC + AP (vs. OAC alone) were more likely to experience vascular events, though among patients with a CHA2DS2-VASc score of 5 or higher, the risk of primary outcome in the OAC + AP group was comparable to that in the OAC alone group (Pint = 0.01). Our study found that there were significant associations of increasing CHA2DS2-VASc scores with the increasing risk of vascular events at 1-year in AIS with AF. Further study would be warranted.
New combination chemotherapy of cisplatin with an electron-donating compound for treatment of multiple cancers
Authors: Zhang Qinrong , Lu Qing-Bin 
Published: January 2021

AbstractCisplatin is the first and most widely used platinum-based chemotherapy drug and is the cornerstone agent in treating a broad spectrum of cancers. However, its clinical application is often limited by severe toxic side effects and drug resistance. Based on the discovered dissociative electron transfer mechanism of cisplatin, a novel combination of cisplatin with [9-(2-carboxyphenyl)-6-diethylamino-3-xanthenylidene]-diethylammonium chloride (basic violet 10, BV10) is proposed to potentiate the chemotherapeutic effect of cisplatin. Here, we show that this combination enhances the anti-cancer effect of cisplatin in both in vitro cell lines and in vivo xenograft mouse models of cisplatin-sensitive and -resistant lung, ovarian and cervical cancers while introducing minimal additional toxic side effects. Furthermore, femtosecond time-resolved laser spectroscopic measurements demonstrate that cisplatin reacts with BV10 via an electron transfer mechanism. These results indicate that the combination of cisplatin with BV10 is promising for improving the chemotherapy of cancers with various extents of cisplatin resistance.
Formation environments and mechanisms of multistage paleokarst of Ordovician carbonates in Southern North China Basin
Authors: Zhang Haitao , Xu Guangquan , Liu Mancai , Wang Minhua 
Published: January 2021

AbstractWith the reduction of oil and gas reserves and the increase of mining difficulty in Northern China, the carbonate rocks in Southern North China Basin are becoming a significant exploration target for carbonate reservoirs. However, the development characteristics, formation stages, formation environments and mechanisms of the carbonate reservoirs in Southern North China Basin are still unclear, which caused the failures of many oil and gas exploration wells. This study focused on addressing this unsolved issue from the Ordovician carbonate paleokarst in the Huai-Fu Basin, which is located in the southeast of Southern North China Basin and one of the key areas for oil and gas exploration. Based on petrology, mineralogy and geochemical data, pore types, distribution characteristics, and formation stages of the Ordovician paleokarst were analyzed. Then, in attempt to define the origins of porosity development, the formation environments and mechanisms were illustrated. The results of this study showed that pore types of the Ordovician carbonates in the Huai-Fu Basin are mainly composed of intragranular pores, intercrystalline (intergranular) pores, dissolution pores (vugs), fractures, channels, and caves, which are usually in fault and fold zones and paleoweathering crust. Furthermore, five stages and five formation environments of the Ordovician paleokarst were identified. Syngenetic karst, eogenetic karst, and paleoweathering crust karst were all developed in a relatively open near-surface environment, and their formations are mainly related to meteoric water dissolution. Mesogenetic karst was developed in a closed buried environment, and its formation is mainly related to the diagenesis of organic matters and thermochemical sulfate reduction in the Permian-Carboniferous strata. Hydrothermal (water) karst was developed in a deep-buried and high-temperature environment, where hydrothermal fluids (waters) migrated upward through structures such as faults and fractures to dissolve carbonate rocks and simultaneously deposited hydrothermal minerals and calcites. Lastly, a paleokarst evolution model, combined with the related porosity evolution processes, nicely revealed the Ordovician carbonate reservoir development. This study provides insights and guidance for further oil and gas exploration in the Southern North China Basin, and also advances our understanding of the genesis of carbonate paleokarst around the world.
Effects of cannabis on visual function and self-perceived visual quality
Authors: Ortiz-Peregrina Sonia , Ortiz Carolina , Casares-López Miriam , Jiménez José R. , Anera Rosario G. 
Published: January 2021

AbstractCannabis is one of the most used drugs of abuse in the world. The objective of this study was to analyze the effects of smoking cannabis on vision and to relate these to those perceived by the user. Thirty-one cannabis users participated in this study. Visual function assessment was carried out in a baseline session as well as after smoking cannabis. We evaluated static visual acuity, contrast sensitivity, stereoacuity, accommodative response, straylight, night-vision disturbances (halos) and pupil size. The participants were also divided into two groups depending on whether they perceived their vision to have worsened after smoking cannabis. A logistic regression analysis was employed to identify which visual test could best predict self-perceived visual effects. The study found that smoking cannabis has significant adverse effects on all the visual parameters analyzed (p < 0.05). Self-perceived visual quality results revealed that about two thirds of the sample think that smoking cannabis impairs their vision. Contrast sensitivity, specifically for the spatial frequency 18 cpd, was identified as the only visual parameter significantly associated with self-perceived visual quality (Odds Ratio: 1.135; p = 0.040). Smoking cannabis is associated with negative effects on visual function. Self-perceived visual quality after smoking cannabis could be related to impaired contrast sensitivity.
Operant and classical learning principles underlying mind–body interaction in pain modulation: a pilot fMRI study
Authors: Lee In-Seon , Jung Won-Mo , Lee Ye-Seul , Wallraven Christian , Chae Younbyoung 
Published: January 2021

AbstractThe operant conditioning has been less studied than the classical conditioning as a mechanism of placebo-like effect, and two distinct learning mechanisms have never been compared to each other in terms of their neural activities. Twenty-one participants completed cue-learning based pain rating tasks while their brain responses were measured using functional magnetic resonance imaging. After choosing (instrumental) or viewing (classical) one of three predictive cues (low- and high-pain cues with different level of certainty), they received painful stimuli according to the selected cues. Participants completed the same task during the test session, except that they received only a high pain stimulus regardless of the selected cues to identify the effects of two learning paradigms. While receiving a high pain stimulation, low-pain cue significantly reduced pain ratings compared to high-pain cue, and the overall ratings were significantly lower under operant than under classical conditioning. Operant behavior activated the temporoparietal junction significantly more than the passive behavior did, and neural activity in the primary somatosensory cortex was significantly reduced during pain in instrumental as compared with classical conditioning trials. The results suggest that pain modulation can be induced by classical and operant conditioning, and mechanisms of attention and context change are involved in instrumental learning.
Hydrodynamic particle focusing enhanced by femtosecond laser deep grooving at low Reynolds numbers
Authors: Zhang Tianlong , Namoto Misuzu , Okano Kazunori , Akita Eri , Teranishi Norihiro , Tang Tao , Anggraini Dian , Hao Yansheng , Tanaka Yo , Inglis David , Yalikun Yaxiaer , Li Ming , Hosokawa Yoichiroh 
Published: January 2021

AbstractMicrofluidic focusing of particles (both synthetic and biological), which enables precise control over the positions of particles in a tightly focused stream, is a prerequisite step for the downstream processing, such as detection, trapping and separation. In this study, we propose a novel hydrodynamic focusing method by taking advantage of open v-shaped microstructures on a glass substrate engraved by femtosecond pulse (fs) laser. The fs laser engraved microstructures were capable of focusing polystyrene particles and live cells in rectangular microchannels at relatively low Reynolds numbers (Re). Numerical simulations were performed to explain the mechanisms of particle focusing and experiments were carried out to investigate the effects of groove depth, groove number and flow rate on the performance of the groove-embedded microchannel for particle focusing. We found out that 10-µm polystyrene particles are directed toward the channel center under the effects of the groove-induced secondary flows in low-Re flows, e.g. Re < 1. Moreover, we achieved continuous focusing of live cells with different sizes ranging from 10 to 15 µm, i.e. human T-cell lymphoma Jurkat cells, rat adrenal pheochromocytoma PC12 cells and dog kidney MDCK cells. The glass grooves fabricated by fs laser are expected to be integrated with on-chip detection components, such as contact imaging and fluorescence lifetime-resolved imaging, for various biological and biomedical applications, where particle focusing at a relatively low flow rate is desirable.
Livestock integration into soybean systems improves long-term system stability and profits without compromising crop yields
Authors: de Albuquerque Nunes Pedro Arthur , Laca Emilio Andrés , de Faccio Carvalho Paulo César , Li Meng , de Souza Filho William , Robinson Kunrath Taise , Posselt Martins Amanda , Gaudin Amélie 
Published: January 2021

AbstractClimate models project greater weather variability over the coming decades. High yielding systems that can maintain stable crop yields under variable environmental scenarios are critical to enhance food security. However, the effect of adding a trophic level (i.e. herbivores) on the long-term stability of agricultural systems is not well understood. We used a 16-year dataset from an integrated soybean-beef cattle experiment to measure the impacts of grazing on the stability of key crop, pasture, animal and whole-system outcomes. Treatments consisted of four grazing intensities (10, 20, 30 and 40 cm sward height) on mixed black oat (Avena strigosa) and Italian ryegrass (Lolium multiflorum) pastures and an ungrazed control. Stability of both human-digestible protein production and profitability increased at moderate to light grazing intensities, while over-intensification or absence of grazing decreased system stability. Grazing did not affect subsequent soybean yields but reduced the chance of crop failure and financial loss in unfavorable years. At both lighter and heavier grazing intensities, tradeoffs occurred between the stability of herbage production and animal live weight gains. We show that ecological intensification of specialized soybean systems using livestock integration can increase system stability and profitability, but the probability of win–win outcomes depends on management.
Predictors for bronchoalveolar lavage recovery failure in diffuse parenchymal lung disease
Authors: Koda Keigo , Hozumi Hironao , Yasui Hideki , Suzuki Yuzo , Karayama Masato , Furuhashi Kazuki , Enomoto Noriyuki , Fujisawa Tomoyuki , Inui Naoki , Nakamura Yutaro , Suda Takafumi 
Published: January 2021

AbstractBronchoalveolar lavage (BAL) plays a role in the diagnosis of diffuse parenchymal lung diseases (DPLD); however, poor BAL fluid (BALF) recovery results in low diagnostic reliability. BAL is relatively safe, but its indications should be carefully considered in patients with risks. Therefore, estimating the likelihood of recovery failure is helpful in clinical practice. This study aimed to clarify predictors of BALF recovery failure and to develop its simple-to-use prediction models. We detected the predictors applying a logistic regression model on clinical, physiological, and radiological data from 401 patients with DPLD (derivation cohort). The discrimination performance of the prediction models using these factors was evaluated by the c-index. In the derivation cohort, being a man, the forced expiratory volume in one second/forced vital capacity, and a BAL target site other than right middle lobe or left lingula were independent predictors. The c-indices of models 1 and 2 that we developed were 0.707 and 0.689, respectively. In a separate cohort of 234 patients (validation cohort), the c-indices of the models were 0.689 and 0.670, respectively. In conclusion, we developed and successfully validated simple-to-use prediction models useful for pulmonologists considering BAL indications or target sites, based on independent predictors for BALF recovery failure.
Rotatable central composite design versus artificial neural network for modeling biosorption of Cr6+ by the immobilized Pseudomonas alcaliphila NEWG-2
Authors: Saber WesamEldin I. A. , El-Naggar Noura El-Ahmady , El-Hersh Mohammed S. , El-khateeb Ayman Y. , Elsayed Ashraf , Eldadamony Noha M. , Ghoniem Abeer Abdulkhalek 
Published: January 2021

AbstractHeavy metals, including chromium, are associated with developed industrialization and technological processes, causing imbalanced ecosystems and severe health concerns. The current study is of supreme priority because there is no previous work that dealt with the modeling of the optimization of the biosorption process by the immobilized cells. The significant parameters (immobilized bacterial cells, contact time, and initial Cr6+ concentrations), affecting Cr6+ biosorption by immobilized Pseudomonas alcaliphila, was verified, using the Plackett–Burman matrix. For modeling the maximization of Cr6+ biosorption, a comparative approach was created between rotatable central composite design (RCCD) and artificial neural network (ANN) to choose the most fitted model that accurately predicts Cr6+ removal percent by immobilized cells. Experimental data of RCCD was employed to train a feed-forward multilayered perceptron ANN algorithm. The predictive competence of the ANN model was more precise than RCCD when forecasting the best appropriate wastewater treatment. After the biosorption, a new shiny large particle on the bead surface was noticed by the scanning electron microscopy, and an additional peak of Cr6+ was appeared by the energy dispersive X-ray analysis, confirming the role of the immobilized bacteria in the biosorption of Cr6+ ions.