bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noninvasive white blood cell quantification in umbilical cord blood collection bags with quantitative oblique back‐illumination microscopy
Authors: Casteleiro Costa Paloma , Ledwig Patrick , Bergquist Austin , Kurtzberg Joanne , Robles Francisco E. 
Published: February 2020

BACKGROUNDUmbilical cord blood has become an important source of hematopoietic stem and progenitor cells for therapeutic applications. However, cord blood banking (CBB) grapples with issues related to economic viability, partially due to high discard rates of cord blood units (CBUs) that lack sufficient total nucleated cells for storage or therapeutic use. Currently, there are no methods available to assess the likelihood of CBUs meeting storage criteria noninvasively at the collection site, which would improve CBB efficiency and economic viability.MATERIALS AND METHODSTo overcome this limitation, we apply a novel label‐free optical imaging method, called quantitative oblique back‐illumination microscopy (qOBM), which yields tomographic phase and absorption contrast to image blood inside collection bags. An automated segmentation algorithm was developed to count white blood cells and red blood cells (RBCs) and assess hematocrit. Fifteen CBUs were measured.RESULTSqOBM clearly differentiates between RBCs and nucleated cells. The cell‐counting analysis shows an average error of 13% compared to hematology analysis, with a near‐perfect, one‐to‐one relationship (slope = 0.94) and strong correlation coefficient (r = 0.86). Preliminary results to assess hematocrit also show excellent agreement with expected values. Acquisition times to image a statistically significant number of cells per CBU were approximately 1 minute.CONCLUSIONqOBM exhibits robust performance for quantifying blood inside collection bags. Because the approach is automated and fast, it can potentially quantify CBUs within minutes of collection, without breaching the CBUs' sterile environment. qOBM can reduce costs in CBB by avoiding processing expenses of CBUs that ultimately do not meet storage criteria.
Automatic Extraction of Engineering Rules From Unstructured Text: A Natural Language Processing Approach
Authors: Ye Xinfeng , Lu Yuqian 
Published: February 2020

Abstract
Manufacturers use cloud manufacturing platforms to offer their services. The literature has suggested a semantic web-based cloud manufacturing framework, in which engineering knowledge is modeled using structured syntax. Translating engineering rules to semantic rules by human is a painstaking task and prone to mistakes. We present a scheme that treats converting engineering knowledge into semantic rules as a machine translation task and uses neural machine translation techniques to carry out the conversion.
Exploring Sample/Feature Hybrid Transfer for Gear Fault Diagnosis Under Varying Working Conditions
Authors: Shen Fei , Langari Reza , Yan Ruqiang 
Published: February 2020

AbstractUnknown environmental noise and varying operation conditions negatively affect gear fault diagnosis (GFD) performance. In this paper, the sample/feature hybrid transfer learning (TL) strategies are adopted for GFD under varying working conditions, where source working conditions are considered to help the learning of target working conditions. Here, a multiple domains-feature vector is extracted where certain insensitive features offset the adverse effects of varying working conditions on sensitive features, including time domain, frequency domain, noise domain, and torque domain. Before TL, the signed-rank and chi-square test-based similarity estimation frame is adopted to select source data sets, aiming to reduce the possibility of negative transfer. Then, the hybrid transfer model, including the fast TrAdaBoost and partial model-based transfer (PMT) algorithm, is carried out, whose weights are allocated in sample and feature, respectively. Related experiments were conducted on the drivetrain dynamics simulator, which proves that feature transfer is more suitable for low-quality source domains while sample transfer is more suitable for high-quality source domains. Compared with non-transfer strategy, transfer learning is a useful tool to solve a practical GFD problem when facing with multiple working conditions, thus enhancing the universality and application value in fault diagnosis field.
Computational Design and Analysis of a Magic Snake
Authors: Li Zilong , Hou Songming , Bishop Thomas C. 
Published: February 2020

Abstract
The Magic Snake (Rubik’s Snake) is a toy that was invented decades ago. It draws much less attention than Rubik’s Cube, which was invented by the same professor, Erno Rubik. The number of configurations of a Magic Snake, determined by the number of discrete rotations about the elementary wedges in a typical snake, is far less than the possible configurations of a typical cube. However, a cube has only a single three-dimensional (3D) structure while the number of sterically allowed 3D conformations of the snake is unknown. Here, we demonstrate how to represent a Magic Snake as a one-dimensional (1D) sequence that can be converted into a 3D structure. We then provide two strategies for designing Magic Snakes to have specified 3D structures. The first enables the folding of a Magic Snake onto any 3D space curve. The second introduces the idea of “embedding” to expand an existing Magic Snake into a longer, more complex, self-similar Magic Snake. Collectively, these ideas allow us to rapidly list and then compute all possible 3D conformations of a Magic Snake. They also form the basis for multidimensional, multi-scale representations of chain-like structures and other slender bodies including certain types of robots, polymers, proteins, and DNA.
Erupted zircon record of continental crust formation during mantle driven arc flare-ups
Authors: Attia Snir , Cottle John M. , Paterson Scott R. 
Published: February 2020

Abstract
Coupled zircon U-Pb age, trace-element, and Lu-Hf isotope analyses from central Sierra Nevada (eastern California, USA) metavolcanic strata reveal the expression of three Mesozoic arc flare-ups in the volcanic record over ∼150 m.y. of magmatic activity. Zircon εHf(i) values vary up to 20 epsilon units within individual samples and coeval sample populations but show no clear links with other geochemical indices, requiring both mixing and fractionation for arc magma genesis. Zircon compositions show repeated temporal trends across flare-ups: Hf isotopes spanning evolved to juvenile values converge to more juvenile compositions, middle rare earth element (MREE) depletion and heavy REE slopes increase during flare-up main phases, and highly variable U/Yb values converge to low values as flare-ups conclude. Despite pervasive contamination, juvenile source magmas dominate magmas erupted throughout the entirety of high-magma-addition episodes. Arc flare-ups thus represent ∼30 m.y. of increased mantle magma input that represents significant continental crust formation in Cordilleran arcs.
Serum zonulin and its diagnostic performance in non-coeliac gluten sensitivity
Authors: Barbaro Maria Raffaella , Cremon Cesare , Morselli-Labate Antonio Maria , Di Sabatino Antonio , Giuffrida Paolo , Corazza Gino Roberto , Di Stefano Michele , Caio Giacomo , Latella Giovanni , Ciacci Carolina , Fuschi Daniele , Mastroroberto Marianna , Bellacosa Lara , Stanghellini Vincenzo , Volta Umberto , Barbara Giovanni 
Published: February 2020

ObjectiveNon-coeliac gluten sensitivity (NCGS) is characterised by intestinal and extraintestinal symptoms related to the ingestion of gluten-containing foods, in the absence of coeliac disease (CD) and wheat allergy. No biomarkers are available to diagnose NCGS and the gold standard double-blind placebo-controlled gluten challenge is clinically impractical. The aim of our work was to investigate the role of serum zonulin as a diagnostic biomarker of NCGS and to develop a diagnostic algorithm.DesignIn a multicentre study, we enrolled 86 patients with either self-reported or double-blind confirmed NCGS, 59 patients with diarrhoea-predominant IBS (IBS-D), 15 patients with CD and 25 asymptomatic controls (AC). Zonulin serum levels were assessed and the associated diagnostic power calculated. Clinical and symptomatic data were recorded. The effect of diet on zonulin levels was evaluated in a subgroup of patients with NCGS.ResultsCompared with ACs, the NCGS, irrespective of modality of diagnosis, and patients with CD had significantly increased levels of zonulin, as did both NCGS and patients with CD compared with participants with IBS-D. Self-reported NCGS showed increased zonulin levels compared with double-blind confirmed and not-confirmed NCGS. Six-month wheat avoidance significantly reduced zonulin levels only in HLA-DQ2/8-positive participants with NCGS. The diagnostic accuracy of zonulin levels in distinguishing NCGS from IBS-D was 81%. After exclusion of CD, a diagnostic algorithm combining zonulin levels, symptoms and gender improved the accuracy to 89%.ConclusionZonulin can be considered a diagnostic biomarker in NCGS and combined with demographic and clinical data differentiates NCGS from IBS-D with high accuracy. Wheat withdrawal was associated with a reduction in zonulin levels only in NCGS carrying HLA genotype.
Associations between metabolites and pancreatic cancer risk in a large prospective epidemiological study
Authors: Stolzenberg-Solomon Rachael , Derkach Andriy , Moore Steven , Weinstein Stephanie J , Albanes Demetrius , Sampson Joshua 
Published: February 2020

ObjectiveTo assess whether prediagnostic metabolites were associated with incident pancreatic ductal adenocarcinoma (PDAC) in a prospective cohort study.DesignWe conducted an untargeted analysis of 554 known metabolites measured in prediagnostic serum (up to 24 years) to determine their association with incident PDAC in a nested case-control study of male smokers (372 matched case-control sets) and an independent nested case-control study that included women and non-smokers (107 matched sets). Metabolites were measured using Orbitrap Elite or Q-Exactive high-resolution/accurate mass spectrometers. Controls were matched to cases by age, sex, race, date of blood draw, and follow-up time. We used conditional logistic regression adjusted for age to calculate ORs and 95% CIs for a 1 SD increase in log-metabolite level separately in each cohort and combined the two ORs using a fixed-effects meta-analysis.ResultsThirty-one metabolites were significantly associated with PDAC at a false discovery rate <0.05 with 12 metabolites below the Bonferroni-corrected threshold (p<9.04×10–5). Similar associations were observed in both cohorts. The dipeptides glycylvaline, aspartylphenylalanine, pyroglutamylglycine, phenylalanylphenylalanine, phenylalanylleucine and tryptophylglutamate and amino acids aspartate and glutamate were positively while the dipeptides tyrosylglutamine and α-glutamyltyrosine, fibrinogen cleavage peptide DSGEGDFXAEGGGVR and glutathione-related amino acid cysteine-glutathione disulfide were inversely associated with PDAC after Bonferroni correction. Five top metabolites demonstrated significant time-varying associations (p<0.023) with the strongest associations observed 10–15 years after participants’ blood collection and attenuated thereafter.ConclusionOur results suggest that prediagnostic metabolites related to subclinical disease, γ-glutamyl cycle metabolism and adiposity/insulin resistance are associated with PDAC.
First-principles study on composition-dependent properties of quaternary InP1−x−yNxBiy alloys
Authors: Chen Yingjie , Zhu Pengfei , Wu Liyuan , Chen Xianchun , Lu Pengfei 
Published: February 2020

The content of bismuth and nitrogen can strongly affect the physical properties of III–V semiconductors and have a decisive impact on their performance in applications. Using first-principles calculations, we systematically study the geometry, electronic and optical properties of [Formula: see text] aligned in special quasirandom structures (SQS). The incorporation of a small amount of N and Bi can effectively tune the band gap of pristine InP. For the same number of P atoms being substituted, co-doping mode reduced the bond length disparity and the corresponding formation energy was also smaller than that of only nitrogen doped. Since the bismuth doped increases spin-orbit splitting energy [Formula: see text], the Auger recombination and intervalence band absorption (IVBA) processes are found to be suppressed for quaternary [Formula: see text] (4.40 [Formula: see text]m), [Formula: see text] (12.04 [Formula: see text]m) and [Formula: see text] (9.12 [Formula: see text]m) alloys, which provides new feasibility in the future mid-wavelength infrared and long-wavelength infrared (MWIR/LWIR) device applications.
Controllable Electrochemical Synthesis of Ag Hierarchical Micro/Nanostructures with High SERS-Activity
Authors: Zhou Huayu , Wang Jingjing , Yang Qiong , Chen Menglei , Song Changsheng , Pan Jiaqi , Chen Qing , Li Chaorong 
Published: February 2020

We report a one-step electrochemical deposition technique to prepare three-dimensional (3D) Ag hierarchical micro/nanostructured film consisting of well-crystallized Ag nanosheets grown on an indium tin oxide (ITO) conductive substrate. The Ag hierarchical micro/nanostructures were fabricated in the mixed solution of AgNO3 and sodium citrate in a constant current system at room temperature. Through reduction of Ag[Formula: see text] electrodeposited on the surface of ITO substrate, nanoparticles were grown to form nanosheets which further combined into 3D sphere-like microstructures. The 3D Ag micro/nanostructures have many sharp edges and nanoscale gaps which can give rise to good Raman-enhanced effect. Due to localized surface plasmon resonance (LSPR) effects, these special Ag micro/nanostructures exhibited good Raman-enhanced performance. Using Rhodamine 6G (R6G) molecules as probe molecule, we studied the influence of excitation wavelength on Raman enhancement. The results showed that the 532[Formula: see text]nm excitation wavelength is the best to obtain the strongest Raman signal and to reduce the influence of other impurity peaks. Using the as-synthesized Ag hierarchical micro/nanostructures, we can detect the 10[Formula: see text][Formula: see text]mol/L R6G aqueous solution, exhibiting great Raman-enhanced effect.
DNA damage-free iPS cells exhibit potential to yield competent cardiomyocytes
Authors: Miller Jessica M. , Mardhekar Nikhil M. , Pretorius Danielle , Krishnamurthy Prasanna , Rajasekaran Namakkal Soorappan , Zhang Jianyi , Kannappan Ramaswamy 
Published: February 2020

DNA damage accrued in induced pluripotent stem cell (iPSC)-derived cardiomyocytes during in vitro culture practices lessens their therapeutic potential. We determined whether DNA-damage-free iPSCs (DdF-iPSCs) can be selected using stabilization of p53, a transcription factor that promotes apoptosis in DNA-damaged cells, and differentiated them into functionally competent DdF cardiomyocytes (DdF-CMs). p53 was activated using Nutlin-3a in iPSCs to selectively kill the DNA-damaged cells, and the stable DdF cells were cultured further and differentiated into CMs. Both DdF-iPSCs and DdF-CMs were then characterized. We observed a significant decrease in the expression of reactive oxygen species and DNA damage in DdF-iPSCs compared with control (Ctrl) iPSCs. Next-generation RNA sequencing and Ingenuity Pathway Analysis revealed improved molecular, cellular, and physiological functions in DdF-iPSCs. The differentiated DdF-CMs had a compact beating frequency between 40 and 60 beats/min accompanied by increased cell surface area. Additionally, DdF-CMs were able to retain the improved molecular, cellular, and physiological functions after differentiation from iPSCs, and, interestingly, cardiac development network was prominent compared with Ctrl-CMs. Enhanced expression of various ion channel transcripts in DdF-CMs implies DdF-CMs are of ventricular CMs and mature compared with their counterparts. Our results indicated that DdF-iPSCs could be selected through p53 stabilization using a small-molecule inhibitor and differentiated into ventricular DdF-CMs with fine-tuned molecular signatures. These iPSC-derived DdF-CMs show immense clinical potential in repairing injured myocardium. NEW & NOTEWORTHY Culture-stress-induced DNA damage in stem cells lessens their performance. A robust small-molecule-based approach, by stabilizing/activating p53, to select functionally competent DNA-damage-free cells from a heterogeneous population of cells is demonstrated. This protocol can be adopted by clinics to select DNA-damage-free cells before transplanting them to the host myocardium. The intact DNA-damage-free cells exhibited with fine-tuned molecular signatures and improved cellular functions. DNA-damage-free cardiomyocytes compared with control expressed superior cardiomyocyte functional properties, including, but not limited to, enhanced ion channel signatures. These DNA-intact cells would better engraft, survive, and, importantly, improve the cardiac function of the injured myocardium.
Build-a-Mouse: Melanoma Modeling Picks up Speed
Authors: Thorkelsson Andres , Merlino Glenn , Michael Helen 
Published: February 2020

Abstract
The study by Bok and colleagues in this issue introduces a new paradigm for generating new mouse models for melanoma research. Genetically engineered mouse models (GEMM) have been crucial for understanding tumor initiation and modeling potential therapies, but are time consuming to create. Bok and colleagues generated and validated high-contribution chimeric GEMM models using common melanoma GEMMs as a starting point and added additional CRISPR, Cre-inducible, and Dox-inducible alleles. This rapid method for generating new models has the potential to revolutionize mouse modeling for melanoma.
See related article by Bok et al., p. 912
Single-Cell Genomic Characterization Reveals the Cellular Reprogramming of the Gastric Tumor Microenvironment
Authors: Sathe Anuja , Grimes Susan M. , Lau Billy T. , Chen Jiamin , Suarez Carlos , Huang Robert J. , Poultsides George , Ji Hanlee P. 
Published: February 2020

Abstract

Purpose:
The tumor microenvironment (TME) consists of a heterogenous cellular milieu that can influence cancer cell behavior. Its characteristics have an impact on treatments such as immunotherapy. These features can be revealed with single-cell RNA sequencing (scRNA-seq). We hypothesized that scRNA-seq analysis of gastric cancer together with paired normal tissue and peripheral blood mononuclear cells (PBMC) would identify critical elements of cellular deregulation not apparent with other approaches.

Experimental Design:
scRNA-seq was conducted on seven patients with gastric cancer and one patient with intestinal metaplasia. We sequenced 56,167 cells comprising gastric cancer (32,407 cells), paired normal tissue (18,657 cells), and PBMCs (5,103 cells). Protein expression was validated by multiplex immunofluorescence.

Results:
Tumor epithelium had copy number alterations, a distinct gene expression program from normal, with intratumor heterogeneity. Gastric cancer TME was significantly enriched for stromal cells, macrophages, dendritic cells (DC), and Tregs. TME-exclusive stromal cells expressed distinct extracellular matrix components than normal. Macrophages were transcriptionally heterogenous and did not conform to a binary M1/M2 paradigm. Tumor DCs had a unique gene expression program compared to PBMC DCs. TME-specific cytotoxic T cells were exhausted with two heterogenous subsets. Helper, cytotoxic T, Treg, and NK cells expressed multiple immune checkpoint or co-stimulatory molecules. Receptor–ligand analysis revealed TME-exclusive intercellular communication.

Conclusions:
Single-cell gene expression studies revealed widespread reprogramming across multiple cellular elements in the gastric cancer TME. Cellular remodeling was delineated by changes in cell numbers, transcriptional states, and intercellular interactions. This characterization facilitates understanding of tumor biology and enables identification of novel targets including for immunotherapy.
Deriving a Passive Surveillance Stroke Severity Indicator From Routinely Collected Administrative Data: The PaSSV Indicator
Authors: Yu Amy Y. X. , Austin Peter C. , Rashid Mohammed , Fang Jiming , Porter Joan , Hill Michael D. , Kapral Moira K. 
Published: February 2020

Background:
Adjusting for stroke severity is crucial for stroke outcomes research. However, this information is not available in administrative healthcare data. We aimed to derive an indicator of baseline stroke severity using these data.

Methods and Results:
We identified patients with stroke enrolled in a population-based registry in Ontario, Canada, and used the Canadian Neurological Scale (CNS), documented in the registry, as a measure of stroke severity. We derived an estimated CNS from a linear regression model in which we regressed the observed CNS on predictor variables: age, sex, arrival by ambulance, interhospital transfer, mechanical ventilation, and an emergency department triage score. The effect of stroke severity on the estimated hazard ratios for 30-day mortality was determined in 3 Cox-proportional hazards models with (1) no CNS, (2) observed CNS, and (3) estimated CNS, all adjusted for age, sex, Charlson index, and stroke type. We assessed model discrimination using C statistics. To assess for construct validity, we repeated these analyses in a subset of patients with documented National Institute of Health Stroke Scale and in a cohort of patients with stroke external to the registry. We derived the estimated stroke severity in 41 481 patients (48.7% female, median age of 75 years [interquartile range, 64– 83]). The magnitude of the association between stroke severity and mortality was similar for the observed and estimated CNS. The discriminative ability of the Cox-proportional hazards models to predict mortality was highest when the observed CNS was included (C statistic, 0.82 [95% CI, 0.81–0.82]), moderate with estimated CNS (0.76 [0.75–0.76]), and lowest without CNS (0.69 [0.69–0.70]. Our findings were replicated with the National Institute of Health Stroke Scale and in the external cohort.

Conclusions:
We derived an estimated measure of stroke severity using administrative data. This can be applied for risk adjustment in population-based stroke outcomes research and in assessments of health system performance.