bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased frequency of PD-1hiCXCR5- T cells and B cells in patients with newly diagnosed IgA nephropathy
Authors: Wang Xin , Li Tao , Si Rui , Chen Jinyun , Qu Zhihui , Jiang Yanfang 
Published: January 2020

AbstractRecent research has identified a population of PD-1hiCXCR5− ‘peripheral helper’ T (Tph) cells that simulate plasma cell differentiation by interactions between IL-21 and SLAMF5. However, the alteration of circulating Tph and CD138+ B in IgA nephropathy (IgAN) remains poorly understood. Flow cytometry analysis was used to measure the frequency of circulating PD-1hiCXCR5− T cells and CD138+ B cells in 37 patients with IgAN and 23 healthy controls (HCs). Estimated glomerular filtration rate (eGFR), 24 h urinary protein and serum cytokine concentrations were measured. The percentage of different subsets of circulating PD-1hiCXCR5− T cells and CD138+ B cells were significantly higher in patients with IgAN compared to HCs. Pretreatment, the percentage of different subsets of circulating PD-1hiCXCR5− T cells and CD138+ B cells were negatively correlated with eGFR, the percentage of circulating CD138+ B cells was positively correlated with 24-h urinary protein concentration, and the percentage of circulating PD-1hiCXCR5−, CD28+ and ICOS+ T cells. Posttreatment, the percentage of different subsets of circulating PD-1hiCXCR5− T cells and CD138+ B cells and serum IL-21 concentration were significantly reduced. Different subsets of circulating PD-1hiCXCR5− T cells contribute to the progression and pathogenesis of IgAN by regulating the differentiation of CD138+ B cells through a combination of surface molecules.
Cross section measurements of 151Eu(3He,5n) reaction: new opportunities for medical alpha emitter 149Tb production
Authors: Moiseeva A. N. , Aliev R. A. , Unezhev V. N. , Zagryadskiy V. A. , Latushkin S. T. , Aksenov N. V. , Gustova N. S. , Voronuk M. G. , Starodub G. Ya. , Ogloblin A. A. 
Published: January 2020

AbstractMethod for production of alpha emitter 149Tb by irradiation of 151Eu with 70 MeV 3He nuclei is proposed. For the first time, the cross sections for the formation of isotopes 149,150,151,152Tb were measured experimentally using a stack foil technique in the 3He particles energy range 70 → 12 MeV. The thick target yield of 149Tb is 39 MBq/μAh, or 230 MBq/μA 149Tb at saturation. The optimal energy range from the point of view of radioisotopic purity is 70 → 40 MeV. At these conditions about 150 MBq/μA 149Tb can be produced in 8 hours irradiation, which is sufficient for therapeutic applications. The main impurities are 150Tb (~100% in activity) and 151Tb (~30% in activity). The proposed method surpasses its counterparts by the high content of the target isotope in the natural mixture and the simplicity of the radiochemical separation of 149Tb from the bulk target material.
Phytoavailability of bound residue of Carbendazim to Chinese cabbage (Brassica campestris ssp.chinensis) coexisted with Superabsorbent polymers
Authors: Yang Yatian , Wang Haiyan , Li Wei , Chen Yan , Guo Wei , Gu Xin , Ye Qingfu 
Published: January 2020

AbstractUnderstanding the bioavailability and phytotoxicity of Carbendazim (MBC) bound residues (BR) in soils incubated with different Superabsorbent polymer (SAP) amendment on succeeding crops is essential to assess their environmental fate and risks. In our research, we studied the morphological characteristics and 14C-accumulation of Chinese cabbage and released BR in three typical cultivated soils. The plant dry weight was in order of superabsorbent-hydrogels formulations (HMBC) > MBC > MBC and SAP (MBC-SAP) at 35 d in basic soil 3 (S3), with 675.40 ± 29.07 mg/plant.d.w, 575.93 ± 25.35 mg/plant.d.w and 427.86 ± 18.79 mg/plant.d.w. The whole plant accumulated 2-fold more BR when grew in neutral soil 2 (S2) treated with SAP than MBC at 7 d. The root accumulated a greater proportion of 14C-MBC residue than shoot, with order of MBC-SAP > MBC > HMBC at 21d. The results indicate MBC-BR could be released and accumulated in plant. HMBC promoted the Chinese cabbage growth with lowest 14C accumulation, while MBC-SAP inhibited plant growth with the highest 14C uptake. The released BR rate was 61.43 ± 3.75% of initial BR in MBC-SAP, with 2-fold higher than MBC and HMBC. It is assumed HMBC could be a potential environmentally friendly measure for rational use of pesticides in future.
Warming and drying over the central Himalaya caused by an amplification of local mountain circulation
Authors: Norris Jesse , Carvalho Leila M. V. , Jones Charles , Cannon Forest 
Published: January 2020

AbstractClimatic changes over the central Himalaya are critical for water resources in downstream regions where hundreds of millions of people live. Warming and drying in this region have both occurred in recent decades, but the associated meteorological factors are difficult to diagnose based on observations from unevenly distributed weather stations, reanalyses, and global climate models that poorly reproduce the orographic diurnal cycle. Here, recent trends in the summer diurnal cycle over the central Himalaya are investigated using a 36-year high-resolution dynamical downscaling. We illustrate contrasting trends over the diurnal cycle of circulation and convection over the Himalaya. In the daytime, warming of the slopes has enhanced anabatic upslope winds. At night, clearer skies have radiatively cooled the slopes, enhancing katabatic downslope winds. The enhanced upslope winds have prevented any drying over the mountains in the daytime, while the enhanced downslope winds are associated with significant nocturnal drying at high elevations. This amplification in the diurnal cycle is critical for projecting the future hydroclimate over the region’s complex terrain.
Effects of melatonin on the proliferation and differentiation of rat adipose-derived stem cells
Authors: Zaminy Arash , Kashani Iraj Ragerdi , Barbarestani Mohammad , Hedayatpour Azim , Mahmoudi Reza , Vardasbi Safoura , Shokrgozar Mohammad Ali 
Published: January 2020

ABSTRACT
Background: Osteogenesis driven by adipose-derived stem cells (ADSCs) is regulated by physiological and pathological factors. Accumulating evidence from in vitro and in vivo experiments suggests that melatonin may have an influence on bone formation. However, little is known about the effects of melatonin on osteogenesis, which thus remains to be elucidated. This study was performed to determine whether melatonin at physiological concentrations (0.01-10 nM) could affect the in vitro proliferation and osteogenic differentiation of rat ADSCs.Materials and Methods: ADSCs were isolated from the fat of adult rats. After cell expansion in culture media and through three passages, osteogenesis was induced in a monolayer culture using osteogenic medium with or without melatonin at physiological concentrations (0.01-10 nM). After four weeks, the cultures were examined for mineralization by Alizarin Red S and von Kossa staining and for alkaline phosphatase (ALP) activity using an ALP kit. Cell viability and apoptosis were also assayed by 3-(4, 5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTT) assay and flow cytometry, respectively.Results: The results indicated that at physiological concentrations, melatonin suppressed proliferation and differentiation of ADSCs. These data indicate that ADSCs exposed to melatonin, had a lower ALP activity in contrast to the cells exposed to osteogenic medium alone. Similarly, mineral deposition (calcium level) also decreased in the presence of melatonin. Flow cytometry confirmed that cell growth had decreased and that the numbers of apoptotic cells had increased.Conclusion: These results suggest that the physiological concentration of melatonin has a negative effect on ADSC osteogenesis.
Effect of Smoking Cessation on the Pharmacokinetics and Pharmacodynamics of Clopidogrel after PCI: The Smoking Cessation Paradox Study
Authors: Ramotowski Bogumił , Gurbel Paul A. , Tantry Udaya , Bracha Jan S. , Karaźniewicz-Łada Marta , Lewandowski Zbigniew , Budaj Andrzej 
Published: January 2020

Abstract
Background Cigarette smoking is associated with enhanced clopidogrel effect and platelet inhibition. However, the effect of smoking cessation on clopidogrel pharmacokinetics (PK) and pharmacodynamics (PD) is unknown. We aimed to determine the effect of smoking cessation, confirmed by cotinine measurement, on clopidogrel PK and PD after percutaneous coronary intervention (PCI).
Methods and Results Following successful PCI, patients treated with 75 mg/day clopidogrel who reported smoking ≥10 cigarettes/day with NicAlert urine cotinine level 6 were enrolled. Clopidogrel and its metabolite concentrations, VerifyNow P2Y12 reaction units (PRUs), and NicAlert levels were measured in the study group before and at 30 days after smoking cessation and in a control group. CYP1A2 and CYP2C19 genotypes were determined. At 30-day visit (n = 87), 45 patients continued smoking, whereas 42 patients stopped smoking. Baseline PRUs were similar between groups. At 30 days, the smoking cessation group had higher PRUs (150.5 ± 68.6 vs. 118.4 ± 65.9, p = 0.03), greater absolute PRU change (27.7 ± 39.8 vs. −12.9 ± 55.4, p = 0.0002), greater change of PRUs adjusted for baseline platelet reactivity (38.6 ± 10.0, p < 0.01), greater risk of high platelet reactivity (HPR) (odds ratio: 10.14 [1.52–67.5], p = 0.017), and a trend towards decreased H3 clopidogrel metabolite levels (−3.41 ng/mL [−11.00 to 0.54 ng/mL], p = 0.072). CYP2C19 LoF carriers who stopped smoking had the highest PRUs, whereas those with the wild type who continued smoking had the lowest PRUs (p < 0.008).
Conclusion Smoking cessation in clopidogrel-treated patients after PCI is associated with increased platelet reactivity and greater risk of HPR. Alternative P2Y12 inhibitors may be considered in selected patients who stop smoking after PCI.
Biosynthesis of silver nanoparticle from pomelo (Citrus Maxima) and their antibacterial activity against acidovorax oryzae RS-2
Authors: Ali Khattak Arif , Yao Rong , Wu Wenge , Masum Md Mahidul Islam , Luo Jinyan , Wang Yanli , Zhang Yang , An Qianli , Sun Guochang , Li Bin 
Published: January 2020

Abstract
Silver nanoparticles (AgNPs), synthesized with plant materials, are considered to be an emerging field of agriculture for their eco-friendly and outstanding antibacterial attributes. In this study, we synthesized AgNPs using pomelo (Citrus maxima) fruit extract as a biological capping and reducing material. The particle size was determined as 11.3–12.8 nm by using UV–vis spectrophotometer, TEM and x-ray diffraction analysis. UV–vis spectrophotometer analysis also confirmed the formation of AgNPs in colloidal solution and showed a maximum absorption at 426 nm. Fourier transform infrared spectra was used to analysed the involvement of biological molecule in AgNPs synthesis. The minimum inhibitory concentration of AgNPs against Acidovorax oryzae strain RS-2 was determined as 25 μg ml−1 by agar well diffusion and bacterial growth assay. In addition, bacterial viability and swarming motility were significantly inhibited by AgNPs. Compared with the control, 25 μg ml−1 of AgNPs lower bacterial biofilm formation up to 68.24%. The bacterial cell wall damaged by AgNPs was observed t TEM. Furthermore, AgNPs treatment resulted into the down regulation of expression of many type VI secretion system related genes, suggesting that AgNPs also have an effect on the virulence of bacteria. The overall conclusion of this study suggests that AgNPs can play an important role in controlling A. oryzae.
Nonlinear optical absorption and asymmetric charge carrier conduction in chemical vapor deposited single-layer graphene
Authors: Thomas Subin , Nalini Savitha , Jayaraj M K , L S Vikas , K Rajeev Kumar 
Published: January 2020

Abstract
In this work, we report the nonlinear optical absorption and asymmetric charge carrier conduction in single layer graphene films deposited by chemical vapor deposition (CVD) technique on copper foils with pretreated surface. XRD texture and pole figure analysis of the substrate are utilized for the visualization of the effect of the pretreatment on the substrate. The synthesised graphene is employed as a channel layer in a back gated field-effect transistor and the asymmetric behavior of charge carriers is analyzed. Nonlinear optical response of graphene is recorded after transferring it onto a quartz substrate. Open aperture Z-scan technique yields a nonlinear absorption coefficient of 5.34 × 106 cm GW−1. The film exhibits saturable absorption in the visible range with a saturation intensity as low as 0.134 GW cm−2.
Mechanism of silver/glass interaction in the metallization of crystalline silicon solar cells
Authors: Sun Xinjie , Yao Shanshan , Xing Juanjuan , Zhang Jiefeng , Yang Yunxia , Li Hongbo , Tong Hua , Yuan Xiao 
Published: January 2020

Abstract
In order to reveal the interaction between solid substances (Ag powder and glass frit) during the metallization of crystalline silicon solar cells, the effect of glass frit on the Ag powder sintering and the mechanism of Ag colloid formation in glass phase were investigated. The results show that the Ag powder could grow into larger grains as mixed with a certain amount of glass frit, because the corrosion of Ag by glass melt enabled early start of Ag sintering. This makes the internal grain size and electric resistivity of sintered Ag lines to be closely related to the glass content in the silver paste. Subsequently, it was found that the formation of Ag colloid in glass phase is a physical process rather than a chemical transformation process. Taking Pb-B-Zn-Al composite oxide glasses for exemplification, a feasible strategy of raising the solubility of Ag in glass melt is proposed.
Bilateral Breast Reconstruction With Profunda Artery Perforator Flaps and Immediate Implant Augmentation
Authors: Chu Carrie K , DeFazio Michael , Largo Rene D , Ross Merrick 
Published: January 2020

Abstract
The smaller volume of the profunda artery perforator (PAP) flap relative to that of abdominal flaps limits the size of breast reconstruction that may be achieved. Immediate implant augmentation of abdominal free flaps has been performed, but immediate implant augmentation of PAP flaps has never been described. A 54-year-old woman with BRCA2 mutation, submuscular implants, and previous abdominoplasty presented for nipple-sparing mastectomies (NSM). Autologous tissue volume was inadequate to support reconstruction to the desired size. She wished to avoid serial expansion. Skin quality was unsuitable for direct-to-implant reconstruction. The patient underwent bilateral NSM. The previous implants were removed with capsule preservation. Bilateral PAP flaps were harvested and anastomosed to the internal mammary vessels. Moderate classic profile 170-mL smooth round silicone implants were placed into the existing capsule pockets with lateral capsulorraphy. There were no flap, implant, or infectious complications. Initial mastectomy skin and nipple ischemia completely resolved without necrosis. Donor site healing was uneventful. At 8 months, the reconstruction is supple and the implants remain well-positioned without rippling. One minor revision was performed for fat grafting and to correct lateral nipple deviation. PAP flap breast reconstruction with immediate implant augmentation is technically feasible. Advantages include improved prosthetic coverage, allowing for immediate reconstruction to a larger size with reduced concern regarding mastectomy skin necrosis and threat to the device, optimal implant camouflage, and improved substrate for secondary fat grafting if necessary.
Level of Evidence: 5
Bridging-induced microphase separation: photobleaching experiments, chromatin domains and the need for active reactions
Authors: Brackley C A , Marenduzzo D 
Published: January 2020

Abstract
We review the mechanism and consequences of the ‘bridging-induced attraction’, a generic biophysical principle that underpins some existing models for chromosome organization in 3D. This attraction, which was revealed in polymer physics-inspired computer simulations, is a generic clustering tendency arising in multivalent chromatin-binding proteins, and it provides an explanation for the biogenesis of nuclear bodies and transcription factories via microphase separation. Including post-translational modification reactions involving these multivalent proteins can account for the fast dynamics of the ensuing clusters, as is observed via microscopy and photobleaching experiments. The clusters found in simulations also give rise to chromatin domains that conform well with the observation of A/B compartments in HiC experiments.
incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs
Authors: Retwitzer Matan Drory , Reinharz Vladimir , Churkin Alexander , Ponty Yann , Waldispühl Jérôme , Barash Danny 
Published: January 2020

AbstractSummaryRNA design has conceptually evolved from the inverse RNA folding problem. In the classical inverse RNA problem, the user inputs an RNA secondary structure and receives an output RNA sequence that folds into it. Although modern RNA design methods are based on the same principle, a finer control over the resulting sequences is sought. As an important example, a substantial number of non-coding RNA families show high preservation in specific regions, while being more flexible in others and this information should be utilized in the design. By using the additional information, RNA design tools can help solve problems of practical interest in the growing fields of synthetic biology and nanotechnology. incaRNAfbinv 2.0 utilizes a fragment-based approach, enabling a control of specific RNA secondary structure motifs. The new version allows significantly more control over the general RNA shape, and also allows to express specific restrictions over each motif separately, in addition to other advanced features.Availability and implementationincaRNAfbinv 2.0 is available through a standalone package and a web-server at https://www.cs.bgu.ac.il/incaRNAfbinv. Source code, command-line and GUI wrappers can be found at https://github.com/matandro/RNAsfbinv.Supplementary informationSupplementary data are available at Bioinformatics online.
Lineage EM algorithm for inferring latent states from cellular lineage trees
Authors: Nakashima So , Sughiyama Yuki , Kobayashi Tetsuya J 
Published: January 2020

Abstract

Summary
Phenotypic variability in a population of cells can work as the bet-hedging of the cells under an unpredictably changing environment, the typical example of which is the bacterial persistence. To understand the strategy to control such phenomena, it is indispensable to identify the phenotype of each cell and its inheritance. Although recent advancements in microfluidic technology offer us useful lineage data, they are insufficient to directly identify the phenotypes of the cells. An alternative approach is to infer the phenotype from the lineage data by latent-variable estimation. To this end, however, we must resolve the bias problem in the inference from lineage called survivorship bias. In this work, we clarify how the survivorship bias distorts statistical estimations. We then propose a latent-variable estimation algorithm without the survivorship bias from lineage trees based on an expectation–maximization (EM) algorithm, which we call lineage EM algorithm (LEM). LEM provides a statistical method to identify the traits of the cells applicable to various kinds of lineage data.

Availability and implementation
An implementation of LEM is available at https://github.com/so-nakashima/Lineage-EM-algorithm.

Supplementary information
Supplementary data are available at Bioinformatics online.
Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency
Authors: Hiranniramol Kasidet , Chen Yuhao , Liu Weijun , Wang Xiaowei 
Published: January 2020

Abstract

Motivation
The development of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) technology has provided a simple yet powerful system for targeted genome editing. In recent years, this system has been widely used for various gene editing applications. The CRISPR editing efficacy is mainly dependent on the single guide RNA (sgRNA), which guides Cas9 for genome cleavage. While there have been multiple attempts at improving sgRNA design, there is a pressing need for greater sgRNA potency and generalizability across various experimental conditions.

Results
We employed a unique plasmid library expressed in human cells to quantify the potency of thousands of CRISPR/Cas9 sgRNAs. Differential sequence and structural features among the most and least potent sgRNAs were then used to train a machine learning algorithm for assay design. Comparative analysis indicates that our new algorithm outperforms existing CRISPR/Cas9 sgRNA design tools.

Availability and implementation
The new sgRNA design tool is freely accessible as a web application, http://crispr.wustl.edu.

Supplementary information
Supplementary data are available at Bioinformatics online.
Autophagy-mediated regulation of neutrophils and clinical applications
Authors: Yu Yao , Sun Bingwei 
Published: January 2020

AbstractAutophagy, an adaptive catabolic process, plays a cytoprotective role in enabling cellular homeostasis in the innate and adaptive immune systems. Neutrophils, the most abundant immune cells in circulation, are professional killers that orchestrate a series of events during acute inflammation. The recent literature indicates that autophagy has important roles in regulating neutrophil functions, including differentiation, degranulation, metabolism and neutrophil extracellular trap formation, that dictate neutrophil fate. It is also becoming increasingly clear that autophagy regulation is critical for neutrophils to exert their immunological activity. However, evidence regarding the systematic communication between neutrophils and autophagy is insufficient. Here, we provide an updated overview of the function of autophagy as a regulator of neutrophils and discuss its clinical relevance to provide novel insight into potentially relevant treatment strategies.