bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel tumor-immune microenvironment (TIME)-on-Chip mimics three dimensional neutrophil-tumor dynamics and neutrophil extracellular traps (NETs)-mediated collective tumor invasion
Authors: Surendran Vikram , Rutledge Dylan , Colmon Ramair , Chandrasekaran Arvind 
Published: February 2021

Abstract
Neutrophils are the most abundant type of leukocytes in the blood, traditionally regarded as the first immune responders to infections and inflammations. In the context of tumors, neutrophils have been shown to possess both tumor-promoting and tumor-limiting properties. A better understanding of the inter-cellular dynamics between the neutrophils and aggregated tumors could possibly shed light on the different modalities of neutrophil involvement in tumor progression. To study in-vitro the interactional dynamics of neutrophils and growing tumor aggregates, in this work, we engineered a novel, microfluidics-integrated, three-dimensional (3D) tumor-immune microenvironment (TIME)-on-Chip device, and we investigated the effect of neutrophils on the inception of collective 3D invasion of ovarian tumor cells. Herein, tumor spheroids generated and cultured on hydrogel based multi-microwell plates, and embedded within collagen matrix of defined thickness, were magnetically hybrid-integrated with a 3D bioprinting enabled microfluidic system fabricated on a porous membrane and carrying neutrophils. This setting recreated a typical TIME in-vitro to model dynamic neutrophil migration and 3D tumor invasion. Using this device, we observed that neutrophils respond to the growing tumor spheroids through both chemotaxis and generation of neutrophil extracellular traps (NETs). The formation of NETs stimulated the reciprocation of tumor cells from their aggregated state to collectively invade into the surrounding collagen matrix, in a manner more significant compared to their response to known tumor-derived stimulants such as transforming growth factor and Interleukin- 8. This effect was reversed by drug-induced inhibition of NETs formation, suggesting that induction of NETs by cancer cells could be a pro-migratory tumor behavior. Further, we additionally report a previously unidentified, location-dictated mechanism of NETosis, in which NETs formation within the stromal extracellular collagen matrix around the spheroids, and not tumor-contacted NETs, is important for the induction of collective invasion of the ovarian tumor cells, thus providing a rationale for new anti-tumor therapeutics research.
Quantum spatial correlations imaging through thick scattering media: experiments and comparison with simulations of the biphoton wave function
Authors: Soro Gnatiessoro , Lantz Eric , Mosset Alexis , Devaux Fabrice 
Published: February 2021

Abstract
We first extend our recent experiments of spatial quantum correlations imaging through thin scattering media to the case where two phase scattering plates placed respectively in the image and the Fourier planes of the biphoton source, mimics a thick scattering medium. Spatial correlations between twin photons are still detected at the quantum level but no more in the form of two-photon speckle-like patterns. However, we show that spatial entanglement of very-high dimensionality can be retrieved through thick scattering media with moderate losses and without any fair sampling assumption in the space and time domains. Second, a numerical simulation of the biphoton wave function is developed and applied to our experimental situation, with a good agreement.
Chlorin e6-1,3-diphenylisobenzofuran polymer hybrid nanoparticles for singlet oxygen-detection photodynamic abaltion
Authors: Wang Xiao-Hui , Wei Xiao-Fei , Liu Jin-Hua , Yang Wei , Liu Yuan-An , Cheng Kun , He Xiao-Ying , Fu Xiu-Li , Zhang Yu , Zhang Hong-Xin 
Published: February 2021

Abstract
A dual-functional nanosysterm is developed by means of Chlorin e6 (Ce6) as photosensitizer and 1,3-Diphenylisobenzofuran (DPBF) as fluorescent singlet oxygen (1O2) probe. Under 660 nm laser irradiation, Ce6 exhibites efficient 1O2 generation, and subsequently the production of 1O2 is assessed by the ratiometric fluorescence of PFO and DPBF under one-photon and two-photon excitation mode. The nanoparticles with excellent biocompatibility can be internalized into Hela cells and applied for tumor treatment. For intracellular PDT, the nanoparticles perform a high phototoxicity, while the PDT proccess can be evaluated in time by monitoring fluorescence signals of DPBF. This theranostic nanosysterm provides a facile strategy to fabricate 1O2-detection PDT, which can realize accurate and efficient photodynamic therapy based on singlet oxygen detection.
Hydrodynamic lubrication analysis of water-lubricated bearings with partial microgroove considering wall slip
Authors: Feng Wei , Han Yanfeng , Xiang Guo , Wang Jiaxu 
Published: February 2021

Abstract
In the present works, the Reynolds equation considering the partial wall slip is used to study the hydrodynamic lubrication performance of Partial Microgroove Water-lubricated Bearings (PMWB). Based on the developed model, the hydrodynamic performances of partial microgroove water-lubricated bearings with three microgroove distributions are systematically compared. The results show that herringbone-groove bearing yields the maximum load capacity, followed by spiral-groove bearings and straight-groove bearings. Furthermore, numerical results also show that wall slip can enhance the load capacity for all three partial microgroove distributions. In addition, the effects of the groove depth and the groove angle, eccentricity ratio and slip arrangement on the lubrication performance of the microgroove bearings are studied. The simulation results indicate that the eccentricity ratio significantly affects the lubrication performance of partial microgroove water-lubricated bearings considering wall slip, while the groove depth and the angle only slightly affect the lubrication performance. Moreover, the slip arrangement is less sensitive to the depth and angle of groove than eccentricity ratio. The parametric study demonstrates that the load capacity of PMWB will decline at a relatively large eccentricity ratio.
Investigation of the experiment and simulation on TiH2 powder packing by a novel irregular 3D model
Authors: Zhang Bing , Liu Shaopeng , Xia Jing , Chen Yungui , Tang Yongbai 
Published: February 2021

Abstract
Density and porosity have an important influence on powder metallurgy products, and it is feasible to predict the tap density of powder by simulating the packing of powder. Analysis models of spherical and simple geometric have been developed to predict the packing density of the powder. In this study, a novel particle model with complex three-dimensional (3D) morphology was established to simulate the packing process of titanium hydride powder with binary particle size distribution. The results have indicated that when the particle size ratio and the volume ratio of fine powder to coarse powder were 1:3 and 1:1, respectively, the sintered sample reaches its optimum sintered density of 99.24%. Compared with these samples sintered by single-scale powder, the size and distribution of residual pores reduced significantly with the application of mixed powders, which is beneficial to the mechanical properties of powder metallurgy products.
Synthesis and optical properties of GdVO4: Eu3+ phosphor
Authors: Thakur Himani , Singh Rajesh Kumar , Gathania Arvind K 
Published: February 2021

Abstract
In the present work, we have synthesized GdVO4 doped Eu3+ using a facile sol-gel method and analysed the effect of concentration variation and annealing temperature on the optical properties. Tetragonal (I41/amd) zircon type crystal structure of the material was confirmed by x-ray diffraction (XRD) study. The photoluminescence (PL) spectra were recorded with an ultraviolet (UV) excitation of wavelength 325 nm. GdVO4 doped Eu3+ (1 mol%) gives prominent red emission. This optimized sample was annealed at different temperature and as annealing temperature raises, the crystallinity of the material increases resulting in the improved emission intensity. The emission spectra of this phosphor exhibit intense peaks at wavelengths 593 nm (orange) and 618 nm (red) which corresponds to 5D0-7F1, 5D0 -7F2 transitions of Eu3+ ions. 5D0 -7F2, the electric dipole transition is dominant indicating that Eu3+ ions situated at a non-centrosymmetric site in the crystal structure. GdVO4: Eu3+(1 mol%) annealed at 800 °C gives eminent red emission which can be further used as the potential candidate for bioimaging, lighting, temperature sensing and display devices.
De novopurine biosynthesis is a major driver of chemoresistance in glioblastoma
Authors: Shireman Jack M , Atashi Fatemeh , Lee Gina , Ali Eunus S , Saathoff Miranda R , Park Cheol H , Savchuk Sol , Baisiwala Shivani , Miska Jason , Lesniak Maciej S , James C David , Stupp Roger , Kumthekar Priya , Horbinski Craig M , Ben-Sahra Issam , Ahmed Atique U 
Published: February 2021

AbstractGlioblastoma is a primary brain cancer with a near 100% recurrence rate. Upon recurrence, the tumour is resistant to all conventional therapies, and because of this, 5-year survival is dismal. One of the major drivers of this high recurrence rate is the ability of glioblastoma cells to adapt to complex changes within the tumour microenvironment. To elucidate this adaptation's molecular mechanisms, specifically during temozolomide chemotherapy, we used chromatin immunoprecipitation followed by sequencing and gene expression analysis. We identified a molecular circuit in which the expression of ciliary protein ADP-ribosylation factor-like protein 13B (ARL13B) is epigenetically regulated to promote adaptation to chemotherapy. Immuno-precipitation combined with liquid chromatography-mass spectrometry binding partner analysis revealed that that ARL13B interacts with the purine biosynthetic enzyme inosine-5′-monophosphate dehydrogenase 2 (IMPDH2). Further, radioisotope tracing revealed that this interaction functions as a negative regulator for purine salvaging. Inhibition of the ARL13B-IMPDH2 interaction enhances temozolomide-induced DNA damage by forcing glioblastoma cells to rely on the purine salvage pathway. Targeting the ARLI3B-IMPDH2 circuit can be achieved using the Food and Drug Administration-approved drug, mycophenolate mofetil, which can block IMPDH2 activity and enhance the therapeutic efficacy of temozolomide. Our results suggest and support clinical evaluation of MMF in combination with temozolomide treatment in glioma patients.
A Genome-Wide Association Study Identifies Novel Susceptibility loci in Chronic Chagas Cardiomyopathy
Authors: Casares-Marfil Desiré , Strauss Mariana , Bosch-Nicolau Pau , Lo Presti María Silvina , Molina Israel , Chevillard Christophe , Cunha-Neto Edecio , Sabino Ester , Ribeiro Antonio Luiz P , González Clara Isabel , Martín Javier , Acosta-Herrera Marialbert 
Published: February 2021

Abstract

Background
Chagas disease is an infectious disease caused by the parasite Trypanosoma cruzi and is endemic from Latin American countries. The goal of our study was to identify novel genetic loci associated with chronic Chagas cardiomyopathy development in Chagas disease patients from different Latin American populations.

Methods
We performed a cross-sectional, nested case-control study including 3 sample collections from Colombia, Argentina, and Bolivia. Samples were genotyped to conduct a genome-wide association study (GWAS). These results were meta-analyzed with summary statistic data from Brazil, gathering a total of 3413 Chagas disease patients. To identify the functional impact of the associated variant and its proxies, we performed an in silico analysis of this region.

Results
The meta-analysis revealed a novel genome-wide statistically significant association with chronic Chagas cardiomyopathy development in rs2458298 (OR = 0.90, 95%CI = 0.87–0.94, P-value = 3.27 × 10-08), nearby the SAC3D1 gene. In addition, further in silico analyses displayed functional relationships between the associated variant and the SNX15, BAFT2, and FERMT3 genes, related to cardiovascular traits.

Conclusions
Our findings support the role of the host genetic factors in the susceptibility to the development of the chronic cardiac form of this neglected disease.
Palace versus City: Wilhelm II's Terrace Project,1892–1901
Authors: Klahr Douglas 
Published: February 2021

Abstract
Through archival research covering ministerial letters, parliamentary records and legal texts, this article reconstructs an unprecedented delimitation of royal property ownership that occurred near the end of the 450-year Hohenzollern dynasty in Berlin. The property owner was Wilhelm II, whose proposed terrace project alongside the Berliner Schloss raised issues regarding building line, pavement, street paving and the land beneath the street. A series of legal arguments between the Kaiser’s Oberhofmarschall and Prussian ministers of state resolved these matters, but not before this modest building project had produced concerns within Berlin’s city assembly and the Prussian House of Representatives about threats to ministerial accountability, a tenet of the Prussian Constitution.
Dissemination of carbapenem resistance and plasmids encoding carbapenemases in Gram-negative bacteria isolated in India
Authors: Manohar Prasanth , Leptihn Sebastian , Lopes Bruno S , Nachimuthu Ramesh 
Published: February 2021

Abstract

Background
Carbapenem resistance in Gram-negative bacteria is an ongoing public health problem of global dimensions leaving very few treatment options for infected patients.

Objectives
To study the dissemination of plasmid-borne carbapenemase genes in Gram-negative bacteria from a diagnostic centre in Tamil Nadu, India.

Methods
A total of 151 non-repetitive isolates belonging to 10 genera were collected between January 2015 and December 2016 from a diagnostic centre in Tamil Nadu. The isolates included Escherichia coli (n = 57), Klebsiella pneumoniae (n = 45), Pseudomonas aeruginosa (n = 10), Salmonella Typhi (n = 8), Enterobacter cloacae (n = 8), Acinetobacter baumannii (n = 7), Serratia marcescens (n = 5), Achromobacter xylosoxidans (n = 5), Proteus mirabilis (n = 5), Klebsiella oxytoca (n = 5) and Elizabethkingia meningoseptica (n = 1).

Results
Of the 151 isolates, 71% (n = 107) and 68% (n = 103) were found to be resistant to meropenem and imipenem, respectively. The most prevalent β-lactamase gene was blaNDM-1 (n = 22), followed by blaOXA-181 (n = 21), blaGES-1 (n = 11), blaOXA-51 (n = 9), blaGES-9 (n = 8), blaOXA-23 (n = 7) and blaIMP-1 (n = 3). We also observed blaOXA-23 in E. coli (n = 4), and three K. pneumoniae were positive for both, blaOXA-23 and blaOXA-51. Plasmid incompatibility (inc/rep) typing results showed that the resistance genes (n = 11) were present in the isolates carrying plasmid-types IncX, IncA/C, IncFIA-FIB and IncFIIA. The plasmid-borne resistance genes in E. coli and K. pneumoniae were transferred to susceptible E. coli AB1157.

Conclusions
This study highlights the prevalence of carbapenem resistance and the acquisition of plasmid-borne carbapenemase genes in Gram-negative bacteria isolated at this centre.
WblA, a global regulator of antibiotic biosynthesis in Streptomyces
Authors: Nah Hee-Ju , Park Jihee , Choi Sisun , Kim Eung-Soo 
Published: February 2021

Abstract
Streptomyces species are soil-dwelling bacteria that produce vast numbers of pharmaceutically valuable secondary metabolites (SMs), such as antibiotics, immunosuppressants, antiviral, and anticancer drugs. On the other hand, the biosynthesis of most SMs remains very low due to tightly controlled regulatory networks. Both global and pathway-specific regulators are involved in the regulation of a specific SM biosynthesis in various Streptomyces species. Over the past few decades, many of these regulators have been identified and new ones are still being discovered. Among them, a global regulator of SM biosynthesis named WblA was identified in several Streptomyces species. The identification and understanding of the WblAs have greatly contributed to increasing the productivity of several Streptomyces SMs. This review summarizes the characteristics and applications on WblAs reported to date, which were found in various Streptomyces species and other actinobacteria.
Ear, nose, and throat
Authors: Steventon Nicholas 
Published: February 2021

AbstractThis chapter in the Oxford Handbook of Clinical Specialties explores the ear, nose, and throat (ENT) specialty. It outlines examination in the ENT in general and investigates each area in depth. The ear is explored including hearing tests, painful ears (otalgia), discharging ears, otitis media, and fluid in the middle ear. Deafness in childhood and adults is discussed, as well as tinnitus, acoustic neuroma, noise-induced hearing loss, and vertigo. The nose is explored, including the paranasal sinuses, nasal injury, foreign bodies, and nosebleed. The throat is investigated, including sore throat, stridor, hoarseness (dysphonia), dysphagia, cancer, palsy, neck lumps, and salivary glands. Dentistry for doctors is also explored.
Trauma
Authors: Clutton Juliet 
Published: February 2021

AbstractThis chapter in the Oxford Handbook of Clinical Specialties explores trauma. It looks at describing an X-ray and whether a patient needs an X-ray or computed tomography scan. It discusses management and complications of fractures as well as complex regional pain syndromes. It explores trauma to the arm, shoulder, elbow, and forearm, as well as distal radial and ulnar fractures, and hand fractures and injuries. It reviews proximal femoral fractures and hip fractures in the elderly, as well as injuries to the knee, and ankle and foot strains and fractures. It describes injuries to the face, neck, and eye, as well as nerve injury, including testing peripheral nerve motor functions, dermatomes and peripheral nerves, nerve compression and syndromes, injuries to the brachial plexus, and spinal cord injury.
Doctors’ health & performance
Authors: Baldwin Andrew , Myers Gil 
Published: February 2021

AbstractThis chapter in the Oxford Handbook of Clinical Specialties explores the subject of doctors’ health and performance. It discusses doctors’ mental health and how to look after it, and how to manage stress and recognize and avoid burnout. It investigates resilience, difficulties encountered by trainees, manipulative patients, and boundary setting. It explores the concept of being a good doctor, appraisal, revalidation, clinical governance, and managing uncertainty and risk, as well as organizations that can help, and an overview of some useful apps.
Ribosome Profiling Reveals a Dichotomy Between Ribosome Occupancy of Nuclear-Encoded and Mitochondrial-Encoded OXPHOS mRNA Transcripts in a Striatal Cell Model of Huntington Disease
Authors: Subramaniam S , Shahani N 
Published: February 2021

AbstractHuntington disease (HD) is caused by an expanded polyglutamine mutation in huntingtin (mHTT), which promotes a prominent atrophy in the striatum and subsequent psychiatric, cognitive, and choreiform movements. Multiple lines of evidence point to an association between HD and aberrant striatal mitochondrial functions. However, present knowledge about whether (or how) mitochondrial mRNA translation is differentially regulated in HD remains unclear. We have recently applied ribosome profiling (Ribo-Seq), a technique based on the high-throughput sequencing of ribosome-protected mRNA fragments, to analyze detailed snapshots of ribosome occupancy of the mitochondrial mRNA transcripts in control and HD striatal cells. Ribo-seq data revealed almost unaltered ribosome occupancy on the nuclear-encoded mitochondrial transcripts involved in oxidative phosphorylation (OXPHOS) and only a mild reduction in ribosome occupancy on a few selected transcripts (SHDA, Ndufv1, Timm23, Tomm5, and Mrps22) in HD cells. By contrast, ribosome occupancy of mitochondrially encoded OXPHOS mRNAs (mtNd-1, mtNd-2, mtNd-4, mtNd-4l, mtNd-5, mtNd-6, mt-Co1, mtCyt b, and mt-ATP8) was dramatically increased, implying widespread dichotomous effects on ribosome occupancy and OXPHOS mRNA translation in HD. Thus, mHTT may command signals that specifically regulate translation of the mitochondrial OXPHOS transcripts and influence HD pathogenesis.
Improving sequence-based modeling of protein families using secondary structure quality assessment
Authors: Malbranke Cyril , Bikard David , Cocco Simona , Monasson Rémi 
Published: February 2021

AbstractMotivationModeling of protein family sequence distribution from homologous sequence data recently received considerable attention, in particular for structure and function predictions, as well as for protein design. In particular, Direct Coupling Analysis, a method to infer effective pairwise interactions between residues, was shown to capture important structural constraints and to successfully generate functional protein sequences. Building on this and other graphical models, we introduce a new framework to assess the quality of the secondary structures of the generated sequences with respect to reference structures for the family.ResultsWe introduce two scoring functions characterizing the likeliness of the secondary structure of a protein sequence to match a reference structure, called Dot Product and Pattern Matching. We test these scores on published experimental protein mutagenesis and design dataset, and show improvement in the detection of non-functional sequences. We also show that use of these scores help rejecting non-functional sequences generated by graphical models (Restricted Boltzmann Machines) learned from homologous sequence alignments.AvailabilitySupplementary Materials, Data and Code available athttps://github.com/CyrilMa/ssqa.Contactcyril.malbranke@ens.frAbstract Figure
Tools enabling flexible approaches to high-resolution subtomogram averaging
Authors: Burt Alister , Gaifas Lorenzo , Dendooven Tom , Gutsche Irina 
Published: February 2021

AbstractCryo-electron tomography and subtomogram averaging are increasingly used for macromolecular structure determinationin situ. Here we introduce a set of computational tools and resources designed to enable flexible approaches to subtomogram averaging. In particular, our tools simplify metadata handling, increase automation, and interface theDynamosoftware package with theWarp-Relion-Mpipeline. We provide a framework forab initioand geometrical approaches to subtomogram averaging combining tools from these packages. We illustrate the power of working within the framework enabled by our developments by applying it toEMPIAR-10164, a publicly available dataset containing immature HIV-1 virus-like particles, and a challengingin situdataset containing chemosensory arrays in bacterial minicells. Additionally, we establish an open and collaborative online platform for sharing knowledge and tools related to cryo-electron tomography data processing. To this platform, we contribute a comprehensive guide to obtaining state-of-the-art results fromEMPIAR-10164.