bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seven decades of chemotherapy clinical trials: a pan-cancer social network analysis
Authors: Li Xuanyi , Sigworth Elizabeth A. , Wu Adrianne H. , Behrens Jess , Etemad Shervin A. , Nagpal Seema , Go Ronald S. , Wuichet Kristin , Chen Eddy J. , Rubinstein Samuel M. , Venepalli Neeta K. , Tillman Benjamin F. , Cowan Andrew J. , Schoen Martin W. , Malty Andrew , Greer John P. , Fernandes Hermina D. , Seifter Ari , Chen Qingxia , Chowdhery Rozina A. , Mohan Sanjay R. , Dewdney Summer B. , Osterman Travis , Ambinder Edward P. , Buchbinder Elizabeth I. , Schwartz Candice , Abraham Ivy , Rioth Matthew J. , Singh Naina , Sharma Sanjai , Gibson Michael K. , Yang Peter C. , Warner Jeremy L. 
Published: October 2020

AbstractClinical trials establish the standard of cancer care, yet the evolution and characteristics of the social dynamics between the people conducting this work remain understudied. We performed a social network analysis of authors publishing chemotherapy-based prospective trials from 1946 to 2018 to understand how social influences, including the role of gender, have influenced the growth and development of this network, which has expanded exponentially from fewer than 50 authors in 1946 to 29,197 in 2018. While 99.4% of authors were directly or indirectly connected by 2018, our results indicate a tendency to predominantly connect with others in the same or similar fields, as well as an increasing disparity in author impact and number of connections. Scale-free effects were evident, with small numbers of individuals having disproportionate impact. Women were under-represented and likelier to have lower impact, shorter productive periods (P < 0.001 for both comparisons), less centrality, and a greater proportion of co-authors in their same subspecialty. The past 30 years were characterized by a trend towards increased authorship by women, with new author parity anticipated in 2032. The network of cancer clinical trialists is best characterized as strategic or mixed-motive, with cooperative and competitive elements influencing its appearance. Network effects such as low centrality, which may limit access to high-profile individuals, likely contribute to the observed disparities.
Plasmonically enhanced mid-IR light source based on tunable spectrally and directionally selective thermal emission from nanopatterned graphene
Authors: Shabbir Muhammad Waqas , Leuenberger Michael N. 
Published: October 2020

AbstractWe present a proof of concept for a spectrally selective thermal mid-IR source based on nanopatterned graphene (NPG) with a typical mobility of CVD-grown graphene (up to 3000 $$\hbox {cm}^2\,\hbox {V}^{-1}\,\hbox {s}^{-1}$$

cm
2

V

-
1

s

-
1

), ensuring scalability to large areas. For that, we solve the electrostatic problem of a conducting hyperboloid with an elliptical wormhole in the presence of an in-plane electric field. The localized surface plasmons (LSPs) on the NPG sheet, partially hybridized with graphene phonons and surface phonons of the neighboring materials, allow for the control and tuning of the thermal emission spectrum in the wavelength regime from $$\lambda =3$$

λ
=
3

to 12 $$\upmu$$
μ
m by adjusting the size of and distance between the circular holes in a hexagonal or square lattice structure. Most importantly, the LSPs along with an optical cavity increase the emittance of graphene from about 2.3% for pristine graphene to 80% for NPG, thereby outperforming state-of-the-art pristine graphene light sources operating in the near-infrared by at least a factor of 100. According to our COMSOL calculations, a maximum emission power per area of $$11\times 10^3$$

11
×

10
3

W/$$\hbox {m}^2$$

m
2

at $$T=2000$$

T
=
2000

K for a bias voltage of $$V=23$$

V
=
23

V is achieved by controlling the temperature of the hot electrons through the Joule heating. By generalizing Planck’s theory to any grey body and deriving the completely general nonlocal fluctuation-dissipation theorem with nonlocal response of surface plasmons in the random phase approximation, we show that the coherence length of the graphene plasmons and the thermally emitted photons can be as large as 13 $$\upmu$$
μ
m and 150 $$\upmu$$
μ
m, respectively, providing the opportunity to create phased arrays made of nanoantennas represented by the holes in NPG. The spatial phase variation of the coherence allows for beamsteering of the thermal emission in the range between $$12^\circ$$

12
∘

and $$80^\circ$$

80
∘

by tuning the Fermi energy between $$E_F=1.0$$

E
F

=
1.0

eV and $$E_F=0.25$$

E
F

=
0.25

eV through the gate voltage. Our analysis of the nonlocal hydrodynamic response leads to the conjecture that the diffusion length and viscosity in graphene are frequency-dependent. Using finite-difference time domain calculations, coupled mode theory, and RPA, we develop the model of a mid-IR light source based on NPG, which will pave the way to graphene-based optical mid-IR communication, mid-IR color displays, mid-IR spectroscopy, and virus detection.
Higher cytolytic score correlates with an immunosuppressive tumor microenvironment and reduced survival in glioblastoma
Authors: Haddad Alexander F. , Chen Jia-Shu , Oh Taemin , Pereira Matheus P. , Joshi Rushikesh S. , Aghi Manish K. 
Published: October 2020

AbstractCytolytic score (CYT), calculated from mRNA expression levels of granzyme and perforin, positively correlates with CD8+ T cell infiltration/activity in a variety of cancers. Unlike other cancers, higher CYT has been associated with worse prognosis in glioblastoma (GBM). To address this discrepancy, we sought to investigate the relationship between CYT and immune checkpoint gene score (ICGscore), as well as their correlation with patient survival and tumor immune cell infiltration. Clinical and RNA-sequencing data for patients with newly diagnosed GBM were obtained from The Cancer Genome Atlas. Maximally-selected rank statistics was used to dichotomize subgroups. CIBERSORT was used to estimate abudence of immune cell-types. Spearman correlation was used to characterize the relationship between CYT and ICGscore. Kaplan–Meier curves were generated for survival analysis. Overall, 28/151 patients had high CYT. High CYT was associated with a mesenchymal subtype (p < 0.001) and worse survival (7.45 vs. 12.2 months, p < 0.001). There were no differences in patient demographics, IDH/MGMT mutation status, or treatment. On subgroup analysis, patients with high CYT/ICGscore had significantly increased CD8+ infiltration (p < 0.001), as expected, and worse survival (HR 0.445, p < 0.01). Furthermore, CYT strongly correlated with ICGscore (RS = 0.675, p < 0.001). The high CYT/ICGscore subgroup was associated with greater infiltration of M2 macrophages (p = 0.011) and neutrophils (p = 0.055). Our study highlights a multidimensional immunosuppressive GBM microenvironment in patients with higher CYT and potentially identifies patients with high CYT/ICGscore as a subgroup that may particularly benefit from multi-faceted immunotherapies, given their already elevated tumor CD8+ T cell levels.
Protein conformational entropy is not slaved to water
Authors: Marques Bryan S. , Stetz Matthew A. , Jorge Christine , Valentine Kathleen G. , Wand A. Joshua , Nucci Nathaniel V. 
Published: October 2020

AbstractConformational entropy can be an important element of the thermodynamics of protein functions such as the binding of ligands. The observed role for conformational entropy in modulating molecular recognition by proteins is in opposition to an often-invoked theory for the interaction of protein molecules with solvent water. The “solvent slaving” model predicts that protein motion is strongly coupled to various aspects of water such as bulk solvent viscosity and local hydration shell dynamics. Changes in conformational entropy are manifested in alterations of fast internal side chain motion that is detectable by NMR relaxation. We show here that the fast-internal side chain dynamics of several proteins are unaffected by changes to the hydration layer and bulk water. These observations indicate that the participation of conformational entropy in protein function is not dictated by the interaction of protein molecules and solvent water under the range of conditions normally encountered.
Floquet-engineered quantum walks
Authors: Katayama Haruna , Hatakenaka Noriyuki , Fujii Toshiyuki 
Published: October 2020

AbstractThe quantum walk is the quantum-mechanical analogue of the classical random walk, which offers an advanced tool for both simulating highly complex quantum systems and building quantum algorithms in a wide range of research areas. One prominent application is in computational models capable of performing any quantum computation, in which precisely controlled state transfer is required. It is, however, generally difficult to control the behavior of quantum walks due to stochastic processes. Here we unveil the walking mechanism based on its particle-wave duality and then present tailoring quantum walks using the walking mechanism (Floquet oscillations) under designed time-dependent coins, to manipulate the desired state on demand, as in universal quantum computation primitives. Our results open the path towards control of quantum walks.
Pore-scale experimental investigation of oil recovery enhancement in oil-wet carbonates using carbonaceous nanofluids
Authors: Zhang Bingjun , Mohamed Abdelhalim I. A. , Goual Lamia , Piri Mohammad 
Published: October 2020

AbstractThis study investigates the pore-scale displacement mechanisms of crude oil in aged carbonate rocks using novel engineered carbon nanosheets (E-CNS) derived from sub-bituminous coal. The nanosheets, synthesized by a simple top-down technique, were stable in brine without any additional chemicals. Owing to their amphiphilic nature and nano-size, they exhibited dual properties of surfactants and nanoparticles and reduced the oil/brine interfacial tension (IFT) from 14.6 to 5.5 mN/m. X-ray micro-computed tomography coupled with miniature core-flooding was used to evaluate their ability to enhance oil recovery. Pore-scale displacement mechanisms were investigated using in-situ contact angle measurements, oil ganglia distribution analysis, and three-dimensional visualization of fluid occupancy maps in pores of different sizes. Analysis of these maps at the end of various flooding stages revealed that the nanofluid invaded into medium and small pores that were inaccessible to base brine. IFT reduction was identified as the main displacement mechanism responsible for oil recovery during 1 to 8 pore volumes (PVs) of nanofluid injection. Subsequently, wettability alteration was the dominant mechanism during the injection of 8 and 32 PVs, decreasing the average contact angle from 134° (oil wet) to 85° (neutral wet). In-situ saturation data reveals that flooding with only 0.1 wt% of E-CNS in brine resulted in incremental oil production of 20%, highlighting the significant potential of this nanofluid as a recovery agent.
Magnetic resonance fingerprinting of the pancreas at 1.5 T and 3.0 T
Authors: Serrao Eva M. , Kessler Dimitri A. , Carmo Bruno , Beer Lucian , Brindle Kevin M. , Buonincontri Guido , Gallagher Ferdia A. , Gilbert Fiona J. , Godfrey Edmund , Graves Martin J. , McLean Mary A. , Sala Evis , Schulte Rolf F. , Kaggie Joshua D. 
Published: October 2020

AbstractMagnetic resonance imaging of the pancreas is increasingly used as an important diagnostic modality for characterisation of pancreatic lesions. Pancreatic MRI protocols are mostly qualitative due to time constraints and motion sensitivity. MR Fingerprinting is an innovative acquisition technique that provides qualitative data and quantitative parameter maps from a single free‐breathing acquisition with the potential to reduce exam times. This work investigates the feasibility of MRF parameter mapping for pancreatic imaging in the presence of free-breathing exam. Sixteen healthy participants were prospectively imaged using MRF framework. Regions-of-interest were drawn in multiple solid organs including the pancreas and T1and T2 values determined. MRF T1and T2mapping was performed successfully in all participants (acquisition time:2.4–3.6 min). Mean pancreatic T1values were 37–43% lower than those of the muscle, spleen, and kidney at both 1.5 and 3.0 T. For these organs, the mean pancreatic T2values were nearly 40% at 1.5 T and < 12% at 3.0 T. The feasibility of MRF at 1.5 T and 3 T was demonstrated in the pancreas. By enabling fast and free-breathing quantitation, MRF has the potential to add value during the clinical characterisation and grading of pathological conditions, such as pancreatitis or cancer.
Population genomics in two cave-obligate invertebrates confirms extremely limited dispersal between caves
Authors: Balogh Andras , Ngo Lam , Zigler Kirk S. , Dixon Groves 
Published: October 2020

AbstractCaves offer selective pressures that are distinct from the surface. Organisms that have evolved to exist under these pressures typically exhibit a suite of convergent characteristics, including a loss or reduction of eyes and pigmentation. As a result, cave-obligate taxa, termed troglobionts, are no longer viable on the surface. This circumstance has led to an understanding of highly constrained dispersal capabilities, and the prediction that, in the absence of subterranean connections, extreme genetic divergence between cave populations. An effective test of this model would involve (1) common troglobionts from (2) nearby caves in a cave-dense region, (3) good sample sizes per cave, (4) multiple taxa, and (5) genome-wide characterization. With these criteria in mind, we used RAD-seq to genotype an average of ten individuals of the troglobiotic spider Nesticus barri and the troglobiotic beetle Ptomaphagus hatchi, each from four closely located caves (ranging from 3 to 13 km apart) in the cave-rich southern Cumberland Plateau of Tennessee, USA. Consistent with the hypothesis of highly restricted dispersal, we find that populations from separate caves are indeed highly genetically isolated. Our results support the idea of caves as natural laboratories for the study of parallel evolutionary processes.
mRNA and miRNA expression profile reveals the role of miR-31 overexpression in neural stem cell
Authors: Li Pengfei , Gao Yuantao , Li Xiao , Tian Feng , Wang Fei , Wang Yali , Zhao Bichun , Zhang Ruxin , Wang Chunfang 
Published: October 2020

AbstractA detailed understanding of the character and differentiation mechanism of neural stem cells (NSCs) will help us to effectively utilize their transplantation to treat spinal cord injury. In previous studies, we found that compared with motor neurons (MNs), miR-31 was significantly high-expressed in NSCs and might play an important role in the proliferation of NSCs and the differentiation into MNs. To better understand the role of miR-31, we characterized the mRNA and miRNAs expression profiles in the early stage of spinal cord-derived NSCs after miR-31 overexpression. There were 35 mRNAs and 190 miRNAs differentially expressed between the miR-31 overexpression group and the control group. Compared with the control group, both the up-regulated mRNAs and miRNAs were associated with the stemness maintenance of NSCs and inhibited their differentiation, especially to MNs, whereas the down-regulated had the opposite effect. Further analysis of the inhibition of miR-31 in NSCs showed that interfering with miR-31 could increase the expression of MNs-related genes and produce MNs-like cells. All these indicated that miR-31 is a stemness maintenance gene of NSCs and has a negative regulatory role in the differentiation of NSCs into MNs. This study deepens our understanding of the role of miR-31 in NSCs, provides an effective candidate target for effectively inducing the differentiation of NSCs into MNs, and lays a foundation for the effective application of NSCs in clinic.
Risk of genotoxic damage in schoolchildren exposed to organochloride pesticides
Authors: Anguiano-Vega Gerardo Alfonso , Cazares-Ramirez Linette Hazel , Rendon-Von Osten Jaime , Santillan-Sidon Alma Patricia , Vazquez-Boucard Celia Gloria 
Published: October 2020

AbstractThis study identified and determined organochloride pesticide (OCs) concentrations in hair samples from children at two elementary schools: one exposed to fumigations in agricultural fields, the other unexposed. Three concentrations of OCs levels in the hair were compared (high, medium, low), and total nuclear abnormalities in buccal cells were determined: micronuclei (MNi), condensed chromatin, karyorrhexis, pyknosis, binucleate cells, karyolysis, lobed nuclei, and apoptosis. No significant differences were found for the presence of MNi between the schoolchildren from the exposed and unexposed schools, but the prevalence of OCs in both schools was over 50%, as well as the frequencies of MNi in the children were over 58%. Findings show a significant difference between the frequency of MNi in the total sample of schoolchildren (exposed school + unexposed school) in relation to the concentration of OCs detected in their hair. The children from exposed school that showed the higher concentrations of OCs in hair had higher levels of genotoxic damage in the buccal cells; compared against children with lower concentrations of OCs. The most frequent nuclear abnormalities in the exposed children were lobed nuclei (79.4%), binucleate cells (66.66%), apoptosis (65.07), and MNi (58.7%). We determined the prevalence ratio (PR) and prevalence odds ratio (POR) for the presence of MNi in buccal cells in relation to the OCs concentrations in the hair samples. Both ratios were high for MNi [PR 3.93, 95% confidence interval (CI) 1.97–7.84, p = 0.0003; and POR 7.97, 95% CI 2.62–24.28, p = 0.0003], indicating a 7.97 times greater risk that the exposed children will present > 0.2% of MNi when OCs concentrations exceed 0.447 μg/g. These indicators may be useful biomarkers of genotoxic damage in children exposed to persistent, highly-toxic compounds. Results suggest the potential risk to which those schoolchildren are exposed on a daily basis due to fumigations in nearby agricultural fields.
Graphene/silver nanoflower hybrid coating for improved cycle performance of thermally-operated soft actuators
Authors: Piao Chengxu , Suk Ji Won 
Published: October 2020

AbstractTwisted and coiled actuators (TCAs), fabricated by twisting cheap nylon sewing threads, have attracted a great deal of attention for their use as artificial muscles or soft actuators. Since the dynamic behavior of a thermally-operated TCA is governed by its thermal properties, graphene and silver nanoflowers (AgNFs) were spray-coated onto the surface of an actuator to achieve enhanced heat transfer. Addition of AgNFs improves interfacial thermal contacts between graphene flakes, while pristine graphene flakes have extremely high in-plane thermal conductivity. Thus, the synergistic effect of graphene and AgNFs reduced the total cycle time of the TCA by up to 38%. Furthermore, when a pulsed current with a 40% duty cycle was applied to the TCA, the graphene/AgNF-coated TCA exhibited a threefold larger peak-to-peak amplitude of the displacement oscillation of the actuator, as compared to that of the non-coated TCA, which demonstrates that the combination of graphene and AgNFs effectively reduced a cooling time of the TCA. This work shows great potential for a simple coating of graphene and AgNFs to produce high-performance thermally-operated soft actuators.
Non-invasive detection of EGFR mutations by cell-free loop-mediated isothermal amplification (CF-LAMP)
Authors: Arjuna Srividya , Venkataram Rajesh , Dechamma Pandyanda Nanjappa , Chakraborty Gunimala , Babu Nishith , D’Cruz Audrey , Hosmane Giridhar Belur , Chakraborty Anirban 
Published: October 2020

AbstractTargeting epidermal growth factor receptor (EGFR) through tyrosine kinase inhibitors (TKI) is a successful therapeutic strategy in non-small cell lung cancer. However, the response to TKI therapy depends on specific activating and acquired mutations in the tyrosine kinase domain of the EGFR gene. Therefore, confirming the EGFR status of patients is crucial, not only for determining the eligibility, but also for monitoring the emergence of mutations in patients under TKI therapy. In this study, our aim was to develop a cost effective, yet sensitive, technique that allows the detection of therapeutically-relevant EGFR hotspot mutations at isothermal conditions in a non-invasive manner. Previously, we developed an allele-specific loop-mediated isothermal amplification (AS-LAMP) assay for screening germline and somatic de novo T790M EGFR mutation in lung cancer patients. In this study, we used cell free DNA as a template in AS-LAMP assay (CF-LAMP) for non-invasive detection of two hotspot EGFR mutations (T790M, and L858R) and compared its efficiency with ultrasensitive droplet digital PCR (ddPCR) assay. The results of CF-LAMP assay were consistent with those obtained in ddPCR assay, indicating the robustness of the method. CF-LAMP may serve as a valuable and cost-effective alternative for liquid biopsy techniques used in molecular diagnosis of non-small cell lung cancer.
Isolation and enrichment of melanocytes from human corneal limbus using CD117 (c-Kit) as selection marker
Authors: Polisetti Naresh , Schlötzer-Schrehardt Ursula , Reinhard Thomas , Schlunck Günther 
Published: October 2020

AbstractLimbal melanocytes (LM) are located in the basal epithelial layer of the corneoscleral limbus and interact with adjacent limbal epithelial progenitor cells. The exploration of their biological role in the maintenance of the limbal stem cell niche has been limited by the difficulty of LM isolation and cultivation. Here, we report on a facile protocol for the efficient isolation and enrichment of pure populations of human LMs by fluorescence-activated cell sorting (FACS) using antibodies raised against the cell surface marker CD117 (c-Kit). The enriched LMs retain self-renewal capacity and sustained melanin production, and are suitable to study the potential of LMs in stem cell-based corneal tissue engineering.
Self-propelling and rolling of a sessile-motile aggregate of the bacterium Caulobacter crescentus
Authors: Zeng Yu , Liu Bin 
Published: October 2020

AbstractActive dispersal of microorganisms is often attributed to the cells’ motile organelles. However, much less is known about whether sessile cells can access such motility through aggregation with motile counterparts. Here, we show that the rosette aggregates of the bacterium Caulobacter crescentus, although predominantly sessile, can actively disperse through the flagellar motors of motile members. Comparisons in kinematics between the motile rosettes and solitary swimming cells indicate that the rosettes can be powered by as few as a single motor. We further reconstructed the 3D movements of the rosettes to reveal that their proximity to a solid-liquid interface promotes a wheel-like rolling, as powered by the flagellar torque. This rolling movement also features a sequence of sharp turns, a reorientation mechanism distinct from that of swimming cells. Overall, our study elucidates an unexplored regime of aggregation-based motility that can be widely applied to sessile-motile composites.