bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new deep learning method for image deblurring in optical microscopic systems
Authors: Zhao Huangxuan , Ke Ziwen , Chen Ningbo , Wang Songjian , Li Ke , Wang Lidai , Gong Xiaojing , Zheng Wei , Song Liang , Liu Zhicheng , Liang Dong , Liu Chengbo 
Published: December 2019

AbstractDeconvolution is the most commonly used image processing method in optical imaging systems to remove the blur caused by the point‐spread function (PSF). While this method has been successful in deblurring, it suffers from several disadvantages, such as slow processing time due to multiple iterations required to deblur and suboptimal in cases where the experimental operator chosen to represent PSF is not optimal. In this paper, we present a deep‐learning‐based deblurring method that is fast and applicable to optical microscopic imaging systems. We tested the robustness of proposed deblurring method on the publicly available data, simulated data and experimental data (including 2D optical microscopic data and 3D photoacoustic microscopic data), which all showed much improved deblurred results compared to deconvolution. We compared our results against several existing deconvolution methods. Our results are better than conventional techniques and do not require multiple iterations or pre‐determined experimental operator. Our method has several advantages including simple operation, short time to compute, good deblur results and wide application in all types of optical microscopic imaging systems. The deep learning approach opens up a new path for deblurring and can be applied in various biomedical imaging fields.
Interaction of MOPS buffer with glass–ceramic scaffold: Effect of (PO4)3− ions in SBF on kinetics and morphology of formatted hydroxyapatite
Authors: Horkavcová Diana , Rohanová Dana , Stříbny Adam , Schuhladen Katharina , Boccaccini Aldo Roberto , Bezdička Petr 
Published: December 2019

AbstractThe international standard ISO 23317:2014 for the in vitro testing of inorganic biomaterials in simulated body fluid (SBF) uses TRIS buffer to maintain neutral pH. In our previous papers, we investigated the interaction of a glass–ceramic scaffold with TRIS and HEPES buffers. Both of them speeded up glass–ceramic dissolution and hydroxyapatite (HAp) precipitation, thereby demonstrating their unsuitability for the in vitro testing of highly reactive biomaterials. In this article, we tested MOPS buffer (3‐[N‐morpholino] propanesulfonic acid), another amino acid from the group of “Goods buffers”. A highly reactive glass–ceramic scaffold (derived from Bioglass®) was exposed to SBF under static–dynamic conditions for 13/15 days. The kinetics and morphology of the newly precipitated HAp were studied using two different concentrations of (PO4)3− ions in SBF. The pH value and the SiIV, Ca2+, and (PO4)3− concentrations in the SBF leachate samples were measured every day (AAS, spectrophotometry). The glass–ceramic scaffold was monitored by SEM/EDS, XRD, WD‐XRF, and BET before and after 1, 3, 7, 11, and 13/15 days of exposure. As in the case of TRIS and HEPES, the preferential dissolution of the glass–ceramic crystalline phase (Combeite) was observed, but less intensively. The lower concentration of (PO4)3− ions slowed down the kinetics of HAp precipitation, thereby causing the disintegration of the scaffold structure. This phenomenon shows that the HAp phase was predominately generated by the presence of (PO4)3− ions in the SBF, not in the glass–ceramic material. Irrespective of this, MOPS buffer is not suitable for the maintenance of pH in SBF.
Some results on the Ryser design conjecture
Authors: Parulekar Tushar D. , Sane Sharad S. 
Published: December 2019

AbstractA Ryser design has equally many points as blocks with the provision that every two blocks intersect in a fixed number of points . An improper Ryser design has only one replication number and is thus symmetric design. A proper Ryser design has two replication numbers. The only known construction of a Ryser design is the complementation of a symmetric design. Such a Ryser design is called a Ryser design of type 1. Let denote a Ryser design of order , index and replication numbers . Let denote the number of points of with replication number (with ). Call a block small (respectively large) if (respectively ) and average if . Let denote the integer and let denote the rational number . Main results of the present article are the following. For every block , (this improves an earlier known inequality ). If there is no small block (respectively no large block) in , then (respectively ). With an extra assumption an earlier known upper bound on is improved from a cubic to a quadratic in . It is also proved that if and if equals or , then is of type 1. Finally, a Ryser design with points is shown to be of type 1.
Evaluating hypercoagulability in new‐onset systemic lupus erythematosus patients using thromboelastography
Authors: Gong Huiyun , Shi Ce , Zhou Zhuochao , Teng Jialin , Sun Yue , Yang Chengde , Wang Xuefeng , Ye Junna 
Published: December 2019

AbstractBackgroundThromboelastography (TEG) can reflect the coagulation status in vivo, from clot formation to clot lysis. In the present study, we aimed to evaluate the function of TEG in detecting coagulation in patients with SLE and sought to explore the correlation between clinical and laboratory data.MethodsA total of 41 patients with new‐onset SLE who had not undergone treatment and 56 healthy controls were included. TEG and other laboratory tests were performed, and clinical data were collected.ResultsA significant difference in the TEG reaction time and TEG achievement of clot firmness was observed between the groups. Moreover, these parameters were correlated with the lupus anticoagulant levels, platelet count, 24‐hour urinary total protein quantity, and systemic lupus erythematosus disease activity index.ConclusionOur study demonstrated the prospective value of TEG in evaluating hypercoagulability in patients with SLE.
Derivation of notochordal cells from human embryonic stem cells reveals unique regulatory networks by single cell‐transcriptomics
Authors: Diaz‐Hernandez Martha E. , Khan Nazir M. , Trochez Camila M. , Yoon Tim , Maye Peter , Presciutti Steven M. , Gibson Greg , Drissi Hicham 
Published: December 2019

AbstractIntervertebral disc degeneration (IDD) is a public health dilemma as it is associated with low back and neck pain, a frequent reason for patients to visit the physician. During IDD, nucleus pulposus (NP), the central compartment of intervertebral disc (IVD) undergo degeneration. Stem cells have been adopted as a promising biological source to regenerate the IVD and restore its function. Here, we describe a simple, two‐step differentiation strategy using a cocktail of four factors (LDN, AGN, FGF, and CHIR) for efficient derivation of notochordal cells from human embryonic stem cells (hESCs). We employed a CRISPR/Cas9 based genome‐editing approach to knock‐in the mCherry reporter vector upstream of the 3′ untranslated region of the Noto gene in H9‐hESCs and monitored notochordal cell differentiation. Our data show that treatment of H9‐hESCs with the above‐mentioned four factors for 6 days successfully resulted in notochordal cells. These cells were characterized by morphology, immunostaining, and gene and protein expression analyses for established notochordal cell markers including FoxA2, SHH, and Brachyury. Additionally, pan‐genomic high‐throughput single cell RNA‐sequencing revealed an efficient and robust notochordal differentiation. We further identified a key regulatory network consisting of eight candidate genes encoding transcription factors including PAX6, GDF3, FOXD3, TDGF1, and SOX5, which are considered as potential drivers of notochordal differentiation. This is the first single cell transcriptomic analysis of notochordal cells derived from hESCs. The ability to efficiently obtain notochordal cells from pluripotent stem cells provides an additional tool to develop new cell‐based therapies for the treatment of IDD.
Calcium signaling and regulation of neutrophil functions: Still a long way to go
Authors: Hann J. , Bueb J.-L. , Tolle F. , Bréchard S. 
Published: December 2019

Abstract
Neutrophils are the most abundant leukocytes in blood and disruption in their functions often results in an increased risk of serious infections and inflammatory autoimmune diseases. Following recent discoveries in their influence over disease progression, a resurgence of interest for neutrophil biology has taken place. The multitude of signaling pathways activated by the engagement of numerous types of receptors, with which neutrophils are endowed, reflects the functional complexity of these cells. It is therefore not surprising that there remains a huge lack in the understanding of molecular mechanisms underlining neutrophil functions. Moreover, studies on neutrophils are undoubtedly limited by the difficulty to efficiently edit the cell's genome. Over the past 30 years, compelling evidence has clearly highlighted that Ca2+-signaling is governing the key processes associated with neutrophil functions. The confirmation of the role of an elevation of intracellular Ca2+ concentration has come from studies on NADPH oxidase activation and phagocytosis. In this review, we give an overview and update of our current knowledge on the role of Ca2+ mobilization in the regulation of pro-inflammatory functions of neutrophils. In particular, we stress the importance of Ca2+ in the formation of NETs and cytokine secretion in the light of newest findings. This will allow us to embrace how much further we have to go to understand the complex dynamics of Ca2+-dependent mechanisms in order to gain more insights into the role of neutrophils in the pathogenesis of inflammatory diseases. The potential for therapeutics to regulate the neutrophil functions, such as Ca2+ influx inhibitors to prevent autoimmune and chronic inflammatory diseases, has been discussed in the last part of the review.
Diversity of extracellular matrix morphology in vertebrate skeletal muscle
Authors: Sleboda David A. , Stover Kristin K. , Roberts Thomas J. 
Published: December 2019

AbstractExisting data suggest the extracellular matrix (ECM) of vertebrate skeletal muscle consists of several morphologically distinct layers: an endomysium, perimysium, and epimysium surrounding muscle fibers, fascicles, and whole muscles, respectively. These ECM layers are hypothesized to serve important functional roles within muscle, influencing passive mechanics, providing avenues for force transmission, and influencing dynamic shape changes during contraction. The morphology of the skeletal muscle ECM is well described in mammals and birds; however, ECM morphology in other vertebrate groups including amphibians, fish, and reptiles remains largely unexamined. It remains unclear whether a multilayered ECM is a common feature of vertebrate skeletal muscle, and whether functional roles attributed to the ECM should be considered in mechanical analyses of non‐mammalian and non‐avian muscle. To explore the prevalence of a multilayered ECM, we used a cell maceration and scanning electron microscopy technique to visualize the organization of ECM collagen in muscle from six vertebrates: bullfrogs (Lithobates catesbeianus), turkeys (Meleagris gallopavo), alligators (Alligator mississippiensis), cane toads (Rhinella marina), laboratory mice (Mus musculus), and carp (Cyprinus carpio). All muscles studied contained a collagen‐reinforced ECM with multiple morphologically distinct layers. An endomysium surrounding muscle fibers was apparent in all samples. A perimysium surrounding groups of muscle fibers was apparent in all but carp epaxial muscle; a muscle anatomically, functionally, and phylogenetically distinct from the others studied. An epimysium was apparent in all samples taken at the muscle periphery. These findings show that a multilayered ECM is a common feature of vertebrate muscle and suggest that a functionally relevant ECM should be considered in mechanical models of vertebrate muscle generally. It remains unclear whether cross‐species variations in ECM architecture are the result of phylogenetic, anatomical, or functional differences, but understanding the influence of such variation on muscle mechanics may prove a fruitful area for future research.
Risk factors for development of ventricular tachycardia in patients with ventricular premature contraction with a structurally normal heart
Authors: Nomura Yuichi , Seki Syunji , Hazeki Daisuke , Ueno Kentaro , Tanaka Yuji , Masuda Kiminori , Nishibatake Makoto , Yoshinaga Masao 
Published: December 2019

AbstractBackgroundWe examined risk factors for development of ventricular tachycardia (VT) in pediatric patients with ventricular premature contractions (VPCs) and a structurally normal heart.MethodsThe subjects were 81 844 first graders and 88 244 seventh graders of Kagoshima City School‐based cardiovascular screening (SCV‐screening) between 2001 and 2015. We retrospectively reviewed the clinical data of students who were diagnosed as having VPC.ResultsVentricular premature contractions were observed in 134 first graders (0.16%) and 270 seventh graders (0.31%). On the screening electrocardiograms (ECGs), 43 patients (11%) showed bi‐/trigemini, three patients (0.7%) showed a couplet, and one patient showed VT. We obtained 166 patients' follow‐up information and evaluated 59 patients (36%) as improved, 97 patients (58%) as no change, and 10 patients (6%) as worsened (couplets, five; triplets, two; VT, three). We assumed that these worsened patients have risk factors for development of VT. Comparing the findings of SCV‐screening ECGs of risk patients with the others, a significant difference was observed only in the number of VPCs (per 10 seconds) (mean ± SD; 4.3 ± 2.6 vs 1.8 ± 1.4, P < .0001). A logistic regression analysis revealed that the number of VPCs was significant (P < .001, odds ratio; 2.01, 95% confidence intervals; 1.46‐2.93). Receiver operating characteristics analysis showed an adequate cut‐off number of three VPCs for the risk, the sensitivity was 89% and the specificity was 77%.ConclusionsOf the patients with VPC and a structurally normal heart, a few patients developed VT. Careful observation is important in patients who had three or more VPCs on SCV‐screening ECG.
Biocorrosion inhibition of Cu70:Ni30 by Bacillus subtilis strain S1X and Pseudomonas aeruginosa strain ZK biofilms
Authors: Wadood Hafiz Zeshan , Rajasekar Aruliah , Farooq Ameeq , Ting Yen‐Peng , Sabri Anjum Nasim 
Published: December 2019

AbstractMicrobiologically influenced corrosion (MIC) or biocrorrosion is a cause of huge economic set back for industries around the globe. The present work deals with the study of corrosion of copper alloy (Cu–Ni 70:30) in the presence of bacterial biofilms produced by Bacillus subtilis strain S1X and Pseudomonas aeruginosa strain ZK. MIC was investigated using electrochemical techniques such as potentiodynamic polarization and electrochemical impedance spectroscopy, and through analytical techniques such as scanning electron microscopy (SEM), Fourier‐transform infrared spectroscopy (FTIR), and atomic force microscopy (AFM). The Cu–Ni coupons were exposed to bacteria in minimal salt medium supplemented with NaCl for a period of 15 days. AFM and FTIR analysis revealed formation of a thick biofilm on the surface of the Cu alloy in bacterial inoculated systems. The electrochemical results demonstrated a decreased current density and corrosion rate for the systems with bacterial biofilms. These findings were supported by the results of SEM and weight loss studies. The results showed the inhibition of corrosion for Cu–Ni in biotic conditions (with biofilms) as compared with abiotic conditions (without biofilms).
The role of ENSO flavours and TNA on recent droughts over Amazon forests and the Northeast Brazil region
Authors: Jimenez Juan C. , Marengo Jose A. , Alves Lincoln M. , Sulca Juan C. , Takahashi Ken , Ferrett Samantha , Collins Matthew 
Published: December 2019

AbstractAmazon tropical forests and the semiarid Northeast Brazil (NEB) region have registered very severe droughts during the last two decades, with a frequency that may have exceeded natural climate variability. Severe droughts impact the physiological response of Amazon forests, decreasing the availability to absorb atmospheric CO2, as well as biodiversity and increasing risk of fires. Droughts on this region also affect population by isolating them due to anomalous low river levels. Impacts of droughts over NEB region are related to water and energy security and subsistence agriculture. Most drought episodes over Amazonia and NEB are associated with El Niño (EN) events, anomalous warming over the Tropical North Atlantic (TNA), and even an overlapping among them. However, not all the dry episodes showed a large‐scale pattern linked to a canonical EN event or warm TNA episodes. For instance, dry episodes linked to EN events present distinct spatial patterns of precipitation anomalies depending on EN type (Central‐Pacific vs. Eastern‐Pacific EN), and NEB region experienced a severe drought in 2012 that is not attributed to EN or warm TNA events. Even in the case of the strong EN in 2015/16, some regional impacts have not been explained by EN contribution. This paper discusses the effects of CP and EP EN events, and the role of warm TNA events on tropical Walker and Hadley circulation leading to drought over Amazonia and NEB regions.
The relationship of three‐dimensional joint space width on weight‐bearing CT with pain and physical function
Authors: Kothari Mayank D. , Rabe Kaitlin G. , Anderson Donald D. , Nevitt Michael C. , Lynch John A. , Franz Hayden , A. Segal Neil 
Published: December 2019

AbstractLimitations of plain radiographs may contribute to poor sensitivity in the detection of knee osteoarthritis and poor correlation with pain and physical function. Three‐dimensional (3D) joint space width (JSW), measured from weight‐bearing computed tomography (CT) images, may yield a more accurate correlation with patients’ symptoms. We assessed the cross‐sectional association between 3D JSW and self‐reported pain and physical function. Five hundred twenty eight knees (57% women) were analyzed from Multicenter Osteoarthritis Study participants. An upright weight‐bearing CT scanner was used to acquire bilateral, weight‐bearing, fixed‐flexion images of the knees. A 3D dataset was reconstructed from cone beam projections and JSW was calculated across the joint surface. The percentages of the apposed medial tibiofemoral joint surface with JSW less than 2.0 and 2.5 mm, respectively, were calculated. Pain and physical function were measured using Western Ontario and McMaster Universities Osteoarthritis Index. Participants who reported greater pain severity tended to have a greater joint area with JSW less than 2.0 mm (P = .07 for the highest vs the lowest tertile). Participants who reported greater functional limitations had a greater joint area with JSW less than 2.0 mm (P = .02 for the highest vs the lowest tertile). There appears to be an association between the medial tibiofemoral area with JSW less than 2.0 mm and pain and physical function.
MicroCT vascular network analysis program: Development, validation, and comparison to manufacturer software
Authors: Peters John , Vest Luke , Schuelke Matthew , Zustiak Silviya P. , Hall Andrew F. , McBride‐Gagyi Sarah 
Published: December 2019

AbstractThe dependence on angiogenesis for bone repair makes accurate measuring of vascular networks of great importance to orthopedic researchers. A three‐dimensional imaging modality like microcomputed tomography (µCT) would better capture these networks than histology. There are commercially available programs to analyze vessel networks in three dimensions, but these may be too costly for laboratories. Alternatively, µCT trabecular software could be used but may not be appropriate. The goal of this project was to develop a vascular network analysis protocol based on freely or commonly available software and compare its performance to that of a µCT trabecular analysis software. The protocol developed, called vascular network analysis or VNA, relies on two modules in Fiji ImageJ and a custom MATLAB program. We validated the software and compared it to a µCT trabecular analysis program (MicroCT) using in silico models of increasing complexity and differing homogeneity. In general, VNA outcomes were significantly different from true values, but most were within an acceptable percent error (<10%). VNA and MicroCT performed almost identically for volume but significantly differently for average vessel diameter. For the homogenous models, the average diameters differed only slightly but were starkly different for the heterogeneous models. In the most heterogeneous system, the MicroCT software overestimated average diameter by about 650% from true. VNA was within 1% of true for the same model. In conclusion, we have developed a program to analyze vascular networks from MicroCT scans which is easily accessible, insensitive to network homogeneity, and of higher accuracy compared to a µCT trabecular analysis software.
Key Determinants for Achieving Enteral Autonomy and Reduced Parenteral Nutrition Exposure in Pediatric Intestinal Failure
Authors: Enman Macie A. , Wilkinson Linda T. , Meloni Katie B. , Shroyer Michelle C. , Jackson Tracy F. , Aban Inmaculada , Dimmitt Reed A. , Martin Colin A. , Galloway David P. 
Published: December 2019

AbstractBackgroundWe sought to evaluate the relationship between determinants of intestinal failure (IF) and achieving enteral autonomy from parenteral nutrition (PN) in a large single‐center cohort of children.MethodsThis is a retrospective chart review of pediatric subjects enrolled in a database for the Center for Advanced Intestinal Rehabilitation at Children's of Alabama from 1989 to 2016. IF was defined as dependence on PN for >60 days. Subjects were included if they were followed since birth or infancy for a minimum of 3 months and sufficient documentation of study variables were available. Gestational age, race, diagnosis, anatomy (percent small and large bowel remaining, presence of ileocecal valve [ICV]), county of residence (rural/urban), and days of PN use were recorded. Kaplan‐Meier curves and parametric survival regression models were used to investigate the relationship between the demographic and clinical variables with the length of PN use.ResultsInitially, 290 subjects were available to review. After inclusion/exclusion were applied, 158 subjects remained. Gestational age, diagnosis (necrotizing enterocolitis), small‐bowel length (>50%), and presence of an ICV were all positive predictors for reaching enteral autonomy. Residual colon length was associated with shorter duration of PN in days.ConclusionEnteral autonomy is a key outcome among children with IF. In our cohort, we found that gestational age, diagnosis, remaining small bowel, and presence of ICV are positive predictors for reaching this important milestone. Colon length is also an important factor with respect to duration of PN in days.