bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applications, challenges, and needs for employing synthetic biology beyond the lab
Authors: Brooks Sierra M. , Alper Hal S. 
Published: March 2021

AbstractSynthetic biology holds great promise for addressing global needs. However, most current developments are not immediately translatable to ‘outside-the-lab’ scenarios that differ from controlled laboratory settings. Challenges include enabling long-term storage stability as well as operating in resource-limited and off-the-grid scenarios using autonomous function. Here we analyze recent advances in developing synthetic biological platforms for outside-the-lab scenarios with a focus on three major application spaces: bioproduction, biosensing, and closed-loop therapeutic and probiotic delivery. Across the Perspective, we highlight recent advances, areas for further development, possibilities for future applications, and the needs for innovation at the interface of other disciplines.
Uncontrolled asthma: a retrospective cohort study in Japanese patients newly prescribed with medium-/high-dose ICS/LABA
Authors: Inoue Hiromasa , Milligan Ki Lee , McConnon Aine , Yoshisue Hajime , Loefroth Emil , McSharry Martin , Yokoyama Akihito , Ichinose Masakazu 
Published: March 2021

AbstractMany asthma patients remain uncontrolled despite guideline-based therapies. We examined real-life asthma control in Japanese patients prescribed with inhaled corticosteroid/long-acting β2-agonist (ICS/LABA). Patients (≥12 years) with ≥2 asthma diagnoses, newly initiated on medium-/high-dose ICS/LABA (Japanese asthma guidelines), from 01 April 2009 to 31 March 2015 were included, using Japan Medical Data Center Claims Database. Primary objective: proportion of patients with uncontrolled asthma in the year following ICS/LABA initiation. Secondary objectives: predictors of uncontrolled asthma and healthcare resource utilization. In medium-dose (N = 24,937) and high-dose (N = 8661) ICS/LABA cohorts, 23% and 21% patients, respectively, were uncontrolled. Treatment step up and exacerbation were most common indicators of uncontrolled asthma. Predictors of uncontrolled asthma, analyzed by multivariable Cox model, included systemic corticosteroid use, exacerbation history, comorbidities, and being female. In both cohorts, healthcare resource utilization was higher in patients with uncontrolled asthma. Over 20% patients with persistent asthma who initiated medium- or high-dose ICS/LABA were uncontrolled, highlighting unmet need for novel therapies in these patients.
Next generation methodology for updating HA vaccines against emerging human seasonal influenza A(H3N2) viruses
Authors: Allen James D. , Ross Ted M. 
Published: March 2021

AbstractWhile vaccines remain the best tool for preventing influenza virus infections, they have demonstrated low to moderate effectiveness in recent years. Seasonal influenza vaccines typically consist of wild-type influenza A and B viruses that are limited in their ability to elicit protective immune responses against co-circulating influenza virus variant strains. Improved influenza virus vaccines need to elicit protective immune responses against multiple influenza virus drift variants within each season. Broadly reactive vaccine candidates potentially provide a solution to this problem, but their efficacy may begin to wane as influenza viruses naturally mutate through processes that mediates drift. Thus, it is necessary to develop a method that commercial vaccine manufacturers can use to update broadly reactive vaccine antigens to better protect against future and currently circulating viral variants. Building upon the COBRA technology, nine next-generation H3N2 influenza hemagglutinin (HA) vaccines were designed using a next generation algorithm and design methodology. These next-generation broadly reactive COBRA H3 HA vaccines were superior to wild-type HA vaccines at eliciting antibodies with high HAI activity against a panel of historical and co-circulating H3N2 influenza viruses isolated over the last 15 years, as well as the ability to neutralize future emerging H3N2 isolates.
Superimposed gratings induce diverse response patterns of gamma oscillations in primary visual cortex
Authors: Wang Bin , Han Chuanliang , Wang Tian , Dai Weifeng , Li Yang , Yang Yi , Yang Guanzhong , Zhong Lvyan , Zhang Yange , Wu Yujie , Wang Gang , Yu Hongbo , Xing Dajun 
Published: March 2021

AbstractStimulus-dependence of gamma oscillations (GAMMA, 30–90 Hz) has not been fully understood, but it is important for revealing neural mechanisms and functions of GAMMA. Here, we recorded spiking activity (MUA) and the local field potential (LFP), driven by a variety of plaids (generated by two superimposed gratings orthogonal to each other and with different contrast combinations), in the primary visual cortex of anesthetized cats. We found two distinct narrow-band GAMMAs in the LFPs and a variety of response patterns to plaids. Similar to MUA, most response patterns showed that the second grating suppressed GAMMAs driven by the first one. However, there is only a weak site-by-site correlation between cross-orientation interactions in GAMMAs and those in MUAs. We developed a normalization model that could unify the response patterns of both GAMMAs and MUAs. Interestingly, compared with MUAs, the GAMMAs demonstrated a wider range of model parameters and more diverse response patterns to plaids. Further analysis revealed that normalization parameters for high GAMMA, but not those for low GAMMA, were significantly correlated with the discrepancy of spatial frequency between stimulus and sites’ preferences. Consistent with these findings, normalization parameters and diversity of high GAMMA exhibited a clear transition trend and region difference between area 17 to 18. Our results show that GAMMAs are also regulated in the form of normalization, but that the neural mechanisms for these normalizations might differ from those of spiking activity. Normalizations in different brain signals could be due to interactions of excitation and inhibitions at multiple stages in the visual system.
Curcumin promotes oligodendrocyte differentiation and their protection against TNF-α through the activation of the nuclear receptor PPAR-γ
Authors: Bernardo Antonietta , Plumitallo Cristina , De Nuccio Chiara , Visentin Sergio , Minghetti Luisa 
Published: March 2021

AbstractCurcumin is a compound found in the rhizome of Curcuma longa (turmeric) with a large repertoire of pharmacological properties, including anti-inflammatory and neuroprotective activities. The current study aims to assess the effects of this natural compound on oligodendrocyte progenitor (OP) differentiation, particularly in inflammatory conditions. We found that curcumin can promote the differentiation of OPs and to counteract the maturation arrest of OPs induced by TNF-α by a mechanism involving PPAR-γ (peroxisome proliferator activated receptor), a ligand-activated transcription factor with neuroprotective and anti-inflammatory capabilities. Furthermore, curcumin induces the phosphorylation of the protein kinase ERK1/2 known to regulate the transition from OPs to immature oligodendrocytes (OLs), by a mechanism only partially dependent on PPAR-γ. Curcumin is also able to raise the levels of the co-factor PGC1-α and of the cytochrome c oxidase core protein COX1, even when OPs are exposed to TNF-α, through a PPAR-γ-mediated mechanism, in line with the known ability of PPAR-γ to promote mitochondrial integrity and functions, which are crucial for OL differentiation to occur. Altogether, this study provides evidence for a further mechanism of action of curcumin besides its well-known anti-inflammatory properties and supports the suggested therapeutic potential of this nutraceutical in demyelinating diseases.
Identifying gene expression patterns associated with drug-specific survival in cancer patients
Authors: Neary Bridget , Zhou Jie , Qiu Peng 
Published: March 2021

AbstractThe ability to predict the efficacy of cancer treatments is a longstanding goal of precision medicine that requires improved understanding of molecular interactions with drugs and the discovery of biomarkers of drug response. Identifying genes whose expression influences drug sensitivity can help address both of these needs, elucidating the molecular pathways involved in drug efficacy and providing potential ways to predict new patients’ response to available therapies. In this study, we integrated cancer type, drug treatment, and survival data with RNA-seq gene expression data from The Cancer Genome Atlas to identify genes and gene sets whose expression levels in patient tumor biopsies are associated with drug-specific patient survival using a log-rank test comparing survival of patients with low vs. high expression for each gene. This analysis was successful in identifying thousands of such gene–drug relationships across 20 drugs in 14 cancers, several of which have been previously implicated in the respective drug’s efficacy. We then clustered significant genes based on their expression patterns across patients and defined gene sets that are more robust predictors of patient outcome, many of which were significantly enriched for target genes of one or more transcription factors, indicating several upstream regulatory mechanisms that may be involved in drug efficacy. We identified a large number of genes and gene sets that were potentially useful as transcript-level biomarkers for predicting drug-specific patient survival outcome. Our gene sets were robust predictors of drug-specific survival and our results included both novel and previously reported findings, suggesting that the drug-specific survival marker genes reported herein warrant further investigation for insights into drug mechanisms and for validation as biomarkers to aid cancer therapy decisions.
A pilot trial of intravital microscopy in the study of the tumor vasculature of patients with peritoneal carcinomatosis
Authors: Gabriel Emmanuel M. , Kim Minhyung , Fisher Daniel T. , Mangum Catherine , Attwood Kristopher , Ji Wenyan , Mukhopadhyay Debabrata , Bagaria Sanjay P. , Robertson Matthew W. , Dinh Tri A. , Knutson Keith L. , Skitzki Joseph J. , Wallace Michael B. 
Published: March 2021

AbstractAberrancies in the tumor microvasculature limit the systemic delivery of anticancer agents, which impedes tumor response. Using human intravital microscopy (HIVM), we hypothesized that HIVM would be feasible in patients with peritoneal carcinomatosis (PC). During cytoreductive surgery with hyperthermic intraperitoneal chemotherapy for PC, HIVM was performed in both tumor and non-tumor areas. The primary outcome was HIVM feasibility to measure vessel characteristics. We secondarily evaluated associations between HIVM vessel characteristics and oncologic outcomes (RECIST response to neoadjuvant therapy and disease-specific survival). Thirty patients with PC were enrolled. Nineteen patients (63.3%) received neoadjuvant therapy. HIVM was feasible in all patients. Compared to non-tumor (control) areas, PC areas had a lower density of functional vessels, higher proportion of non-functional vessels, smaller lumenal diameters, and lower blood flow velocity. Qualitative differences in these vessel characteristics were observed among patients who had partial response, stable disease, or progressive disease after receiving neoadjuvant therapy. However, no statistically significant relationships were found between HIVM vessel characteristics and oncologic outcomes. These novel findings comprise the first-in-human, real-time evidence of the microscopic differences between normal and tumor-associated vessels and form the basis for our larger, ongoing clinical trial appropriately powered to determine the clinical utility of HIVM (NCT03823144).
Ab initio study of the structure, elastic, and electronic properties of Ti3(Al1−nSin)C2 layered ternary compounds
Authors: Ahams S. T. , Shaari A. , Ahmed R. , Pattah N. F. Abdul , Idris M. C. , Haq B. U. 
Published: March 2021

AbstractThe MAX phase materials such as layered ternary carbides that simultaneously exhibit characteristics of metallic and ceramic materials have received substantial interest in recent years. Here, we present a systematic investigation of the electronic, structural stabilities, and elastic properties of Ti3(Al1−nSin)C2 (n = 0,1) MAX phase materials using the ab initio method via a plane-wave pseudopotential approach within generalized-gradient-approximations. The computed electronic band structures and projected density of states show that both Ti3SiC2 and Ti3AlC2 are metallic materials with a high density of states at the Fermi level emanating mainly from Ti-3d. Using the calculated elastic constants, the mechanical stability of the compounds was confirmed following the Born stability criteria for hexagonal structures. The Cauchy pressure and the Pugh’s ratio values establish the brittle nature of the Ti3SiC2 and Ti3AlC2 MAX phase materials. Due to their intriguing physical properties, these materials are expected to be suitable for applications such as thermal shock refractories and electrical contact coatings.
COVID-19 in South Africa: outbreak despite interventions
Authors: Schröder Malte , Bossert Andreas , Kersting Moritz , Aeffner Sebastian , Coetzee Justin , Timme Marc , Schlüter Jan 
Published: March 2021

AbstractThe future dynamics of the Corona Virus Disease 2019 (COVID-19) outbreak in African countries is largely unclear. Simultaneously, required strengths of intervention measures are strongly debated because containing COVID-19 in favor of the weak health care system largely conflicts with socio-economic hardships. Here we analyze the impact of interventions on outbreak dynamics for South Africa, exhibiting the largest case numbers across sub-saharan Africa, before and after their national lockdown. Past data indicate strongly reduced but still supracritical growth after lockdown. Moreover, large-scale agent-based simulations given different future scenarios for the Nelson Mandela Bay Municipality with 1.14 million inhabitants, based on detailed activity and mobility survey data of about 10% of the population, similarly suggest that current containment may be insufficient to not overload local intensive care capacity. Yet, enduring, slightly stronger or more specific interventions, combined with sufficient compliance, may constitute a viable option for interventions for South Africa.
Numerical simulation of wind field and sand flux in crescentic sand dunes
Authors: Zhang Huiwen , Wu Zhen , Hu Jing , Zhang Zhiping , Xiao Bin , Ma Jianping 
Published: March 2021

AbstractSand flux is the key factor to determine the migration of sand dunes and the erosion to the surrounding environment. There are crescent-shaped sand dunes of various scales in the desert, and there are significant differences in spatial wind field and sand flux among them. However, due to the difficulty of monitoring, it is difficult to continuously observe the spatial wind field and sand flux around the larger crescentic dunes. On the basis of the Reynolds-Average Navier–Stokes (RA-NS) equation and the stress and sand flux model, the distribution of wind field and sand flux of a circular dune with a height of 4.2 m and a length of about 100 m during the four evolutionary periods of the evolution into a crescentic dune was simulated in this study. By comparing with the measured results, we verified that the closer to the leeward side, the more the simulated values of the velocity in wind field and sand flux were in line with the measured results. In order to further analyze the influence of the height of dune and other relevant parameters on sand flux, we simulated the influence on wind field and sand flux by changing the air viscosity and wind velocity of upper boundary. We found that the air viscosity mainly affected the amount of deposited sand on the leeward side of sand dune, while the increase of wind velocity would undoubtedly increase the sand flux of the whole sand dune. In addition, the simulation results also showed that the influence of changes in height of dune on the turbulent intensity of leeward side was very significant, and the turbulent intensity increased with the height of dune. The height changes of tall dunes gradually affected the transport of sand caused by wind flow behind the leeward side because that the rotation of the wind flow would form new vortexes at the large pores behind the leeward side, which would increase the turbulent energy in space and thus would increase the distance of migration of the lifting sand. While the low sand dunes could not form extra small vortexes at the bottom of the leeward side, so the wind velocity was small and the eddy currents behind the leeward side were more stable. The simulation results indicated that wind velocity was not the only reason for increasing the amount of sand flux, and the fluctuation of wind flow caused by turbulence could also stimulate the movement of sand particles on the ground.
Comparative transcriptome profiles of large and small bodied large-scale loaches cultivated in paddy fields
Authors: Zhao Liulan , He Kuo , Xiao Qing , Liu Qiao , Luo Wei , Luo Jie , Fu Hongmei , Li Jiayao , Wu Xugan , Du Jun , Gong Quan , Wang Xun , Yang Song 
Published: March 2021

AbstractFish culture in paddy fields is a traditional aquaculture mode, which has a long history in East Asia. Large-scale loach (Paramisgurnus dabryanus) fast growth is suitable for paddy fields aquaculture in China. The objective of this study was to identify differential expression genes (DEGs) in the brain, liver and muscle tissues between large (LG, top 5% of maximum total length) and small (SG, top 5% of minimum total length) groups using RNA-seq. In total, 150 fish were collected each week and 450 fish were collected at twelfth week from three paddy fields for all the experimental. Histological observation found that the muscle fibre diameter of LG loaches was greater than that of SG loaches. Transcriptome results revealed that the high expression genes (HEGs) in LG loaches (fold change ≥ 2, p < 0.05) were mainly concentrated in metabolic pathways, such as “Thyroid hormone signalling pathway”, “Citrate cycle (TCA cycle)”, “Carbon metabolism”, “Fatty acid metabolism”, and “Cholesterol metabolism”, and the HEGs in SG loaches were enriched in the pathways related to environmental information processing such as “Cell adhesion molecules (CAMs)”, “ECM− receptor interaction” and “Rap1 signalling pathway”; cellular processes such as “Tight junction”, “Focal adhesion”, “Phagosome” and “Adherens junction”. Furthermore, IGFs gene family may play an important role in loach growth for their different expression pattern between the two groups. These findings can enhance our understanding about the molecular mechanism of different growth and development levels of loaches in paddy fields.
Impact of bariatric surgery on obstructive sleep apnea severity and continuous positive airway pressure therapy compliance—prospective observational study
Authors: Nastałek Paweł , Polok Kamil , Celejewska-Wójcik Natalia , Kania Aleksander , Sładek Krzysztof , Małczak Piotr , Major Piotr 
Published: March 2021

AbstractTo evaluate association between bariatric surgery and changes in obstructive sleep apnea (OSA) severity and sleep architecture was as well as to asses continuous positive airway pressure (CPAP) effectiveness and compliance. We enrolled patients undergoing bariatric surgery. Polysomnography was performed in each patient preoperatively and 12 months after the procedure in a subgroup of patients diagnosed with OSA. STOP-BANG, Epworth Sleepiness Scale (ESS) and Berlin questionnaire scores were obtained pre- and postoperatively. CPAP compliance data was recorded during follow-up hospitalization. Among 44 patients with median age of 49.5 years, predominantly women (68.2%) pre- and postoperative polysomnography was performed. We observed significant improvement in STOP-BANG (6.0 vs. 3.0, p < 0.001) and ESS (12.0 vs. 5.0, p < 0.001) scores, apnea–hypopnea index (44.9 vs. 29.2, p < 0.001), oxygen desaturation index (43.6 vs. 18.3, p < 0.001) and sleep architecture parameters. CPAP compliance was poor with a median percentage of days with CPAP use accounting to 49.3%. Bariatric surgery is associated with a significant decrease in the number of sleep-related respiratory disturbances, as well as improvement of sleep efficiency. Postoperative CPAP therapy compliance was poor despite low rate of OSA resolution. This study suggests that patients with OSA undergoing bariatric surgery require postoperative reassessment.
Optimized anti-reflection core-shell microspheres for enhanced optical trapping by structured light beams
Authors: Shahabadi Vahid , Madadi Ebrahim , Abdollahpour Daryoush 
Published: March 2021

AbstractIn this paper, we study the optical trapping of anti-reflection core-shell microspheres by regular Gaussian beam and several structured beams including radially polarized Gaussian, petal, and hard-aperture-truncated circular Airy beams. We show that using an appropriate anti-reflection core-shell microsphere for the optical trapping by several structured light beams can dramatically enhance the strength of the trap compared to the trapping by the common Gaussian beam. The optimal core-shell thickness ratio that minimizes the scattering force is obtained for polystyrene-silica and anatase-amorphous titania microspheres, such that the core-shells act as anti-reflection coated microspheres. We show that the trapping strength of the anti-reflection coated microparticles trapped by the common Gaussian beam is enhanced up to 2-fold compared to that of trapped uncoated microparticles, while the trapping of anti-reflection coated microparticles, by the radially polarized beam, is strengthened up to 4-fold in comparison to that of the trapped uncoated microparticles by the Gaussian beam. Our results indicate that for anatase-amorphous titania microparticles highest trap strength is obtained by radially polarized beam, while for the polystyrene-silica microparticles, the strongest trapping is achieved by the petal beam.
Direct UV written waveguides and Bragg gratings in doped planar silica using a 213 nm laser
Authors: Ahmed Q. Salman , Gow Paul C. , Holmes Christopher , Mennea Paolo L. , Field James W. , Bannerman Rex H.S. , Smith Devin H. , Gawith Corin B.E. , Smith Peter G.R. , Gates James C. 
Published: March 2021

AbstractIn this paper, the first demonstration of simultaneous UV written Bragg gratings and waveguides in germanium and boron‐doped planar silica is presented using a 5th harmonic solid‐state nanosecond laser operating at 213 nm wavelength. The fabrication of high‐quality gratings by using a high peak power density, yielding sufficient uniformity and without any surface damage is demonstrated. The photosensitivity of the doped silica layer is investigated by measuring the local effective refractive index of the optical modes. The written gratings are used to measure grating refractive index modulation, grating detuning bandwidth and the waveguide propagation loss with a minimum value of 0.28 0.07 dB cm. This paper shows that this new generation of pulsed UV lasers is a promising alternative for conventional longer wavelength CW laser sources used in small spot direct grating writing in doped silica.