bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying evenness and linking it to diversity, beta diversity, and similarity
Authors: Chao Anne , Ricotta Carlo 
Published: July 2019

AbstractAn enormous number of measures based on different criteria have been proposed to quantify evenness or unevenness among species relative abundances in an assemblage. However, a unified approach that can encompass most of the widely used indices is still lacking. Here, we first present some basic requirements for an evenness measure. We then propose that unevenness among species relative abundances in an assemblage can be measured by a normalized divergence between the vector of species relative abundances and the mean vector, where the mean vector represents the species relative abundances of a completely even assemblage. Thus, evenness among species relative abundances is measured by the corresponding normalized extent of closeness between these two vectors. We consider five divergence measures, leading to five classes of evenness indices. All our evenness measures are in terms of diversity (Hill number) of order q > 0 (here q controls the weighting of species relative abundances) and species richness (diversity of order q = 0). We propose quantifying evenness through a continuous profile that depicts evenness as a function of diversity order q > 0. The profiles can be easily and visually compared across multiple assemblages. Our evenness indices satisfy all the requirements presented in this paper and encompass many widely used evenness measures as special cases. When there are multiple assemblages, the abundance‐based Jaccard‐ and Sørensen‐type dissimilarity measures (which are monotonic functions of beta diversity) can be expressed as weighted averages of the individual species’ compositional unevenness values; here, each individual species’ compositional unevenness is calculated based on that species’ abundances among assemblages. The contribution of a species to each dissimilarity measure can be clearly disentangled and quantified in terms of this single species’ compositional unevenness among assemblages. Thus, our framework links the concepts of evenness, diversity, beta diversity, and similarity. Moreover, the framework can be readily extended to a phylogenetic version. A real data example is used to illustrate our approach. We also discuss some criteria and other measures that were previously proposed in the literature.
Increased ILC3s associated with higher levels of IL‐1β aggravates inflammatory arthritis in mice lacking phagocytic NADPH oxidase
Authors: Chan Tzu‐Yi , Yen Chia‐Liang , Huang Ya‐Fang , Lo Pei‐Chi , Nigrovic Peter A. , Cheng Chia‐Ying , Wang Wei‐Zhi , Wu Szu‐Yu , Shieh Chi‐Chang 
Published: July 2019

AbstractThe role of redox regulation in immune‐mediated arthritis has been previously described. However, the relationship between innate immune cells, including innate lymphoid cells (ILCs) and phagocyte‐derived ROS, in this process remains unclear. Here, we characterize ILCs and measure the IL‐1 family cytokines along with other cytokines relevant to ILC functions and development in serum‐induced arthritic joints in wild type and phagocytic NADPH oxidase (NOX2)‐deficient Ncf1−/− mice. We found more severe serum‐induced joint inflammation and increased NCR+ ILC3s in inflamed joints of Ncf1−/− mice. Furthermore, in vitro stimulation with IL‐1β on Tbet+ ILC1s from joints facilitated their differentiation into ROR‐γt+ ILC3s. Moreover, treatment with IL‐1 antagonists effectively lowered the proportions of NCR+ ILC3s and IL‐17A producing ILC3s in Ncf1−/− arthritic mice and ameliorated the joint inflammation. These results suggest that NOX2 is an essential regulator of ILC transdifferentiation and may mediate this process in a redox‐dependent manner through IL‐1β production in the inflammatory joint. Our findings shed important light on the role of ILCs in the initiation and progression in tissue inflammation and delineate a novel innate immune cell‐mediated pathogenic mechanism through which redox regulation may determine the direction of immune responses in joints.
Use of recycled aggregates in pressed fly ash geopolymer concrete
Authors: Wongsa Ampol , Siriwattanakarn Apinun , Nuaklong Peem , Sata Vanchai , Sukontasukkul Piti , Chindaprasirt Prinya 
Published: July 2019

AbstractIn this study, the physical, mechanical, and thermal properties of pressed geopolymer concrete (PRGC) mixed with recycled concrete aggregate (RC) and recycled concrete block aggregate (RB) were investigated. Lignite coal fly ash, sodium hydroxide solution (NaOH), and sodium silicate solution were used as source materials to make geopolymer paste. The effect of fly ash to aggregate ratios and concentrations of NaOH on PRGC properties were tested. Test results were also compared to those of PRGCs mixed with conventional aggregate (limestone dust, SD). The test results showed that PRGCs containing RC and RB exhibited lower dry density, thermal conductivity, and compressive strength than those of PRGCs containing SD. Nevertheless, the compressive strength of PRGCs mixed with recycled aggregates was close to the compressive strength for moderate strength lightweight concrete as per ACI 213. Moreover, the lower thermal conductivity and dry density indicated better insulating properties than that of PRGCs containing SD. The developed PRGCs containing RC and RB in the study can be used for the manufacturing of hollow geopolymer‐based concrete block which are green material with improved insulating properties.
Acute promyelocytic leukemia with a cryptic insertion of RARA into TBL1XR1
Authors: Osumi Tomoo , Watanabe Akihiro , Okamura Kohji , Nakabayashi Kazuhiko , Yoshida Masanori , Tsujimoto Shin‐ichi , Uchiyama Meri , Takahashi Hiroyuki , Tomizawa Daisuke , Hata Kenichiro , Kiyokawa Nobutaka , Kato Motohiro 
Published: July 2019

AbstractAcute promyelocytic leukemia (APL) is cytogenetically characterized by the t(15;17) (q24;q21), although cases without this translocation exist. These cases are referred to as “cryptic” or “masked” translocations. Additionally, fewer than 5% of APL cases have another partner gene fused to the RARA gene. The TBL1XR1‐RARA fusion gene has recently been reported as a novel RARA‐associated fusion gene. We report a case with TBL1XR1‐RARA and a masked translocation that was not detected by conventional tests for RARA‐associated translocations. Three‐year‐old girl was diagnosed with APL based morphological findings, although conventional tests for RARA‐associated chimeric genes were negative. She received all‐trans retinoic acid treatment, but that was not effective. She achieved a complete remission (CR) by conventional multidrug chemotherapy, but had extramedullary relapse 2 years after onset. She underwent cord blood transplantation (CBT) in her second CR and is currently alive. To investigate the underlying pathogenesis of this unique case, we performed whole‐genome sequencing and found a cryptic insertion of RARA gene into the TBL1XR1 gene. The transcript of the chimeric gene, TBL1XR1‐RARA, was confirmed as an in‐frame fusion by RT‐PCR. In conclusion, we found using next‐generation sequencing (NGS) a TBL1XR1‐RARA fusion in a child with variant APL without the classic karyotype. Cryptic insertion could also occur in cases other than APL with PML‐RARA. Variant APL has many variants and NGS analysis should therefore be considered for APL variant cases, even for those without RARA translocation detected by conventional analysis.
Cut and covered: Subfossil trees in buried soils reflect medieval forest composition and exploitation of the central European uplands
Authors: Kaiser Knut , Hrubý Petr , Tolksdorf Johann Friedrich , Alper Götz , Herbig Christoph , Kočár Petr , Petr Libor , Schulz Lars , Heinrich Ingo 
Published: July 2019

AbstractKnowledge of historic changes in vegetation, relief, and soil is key in understanding how the uplands in central Europe have changed during the last millennium, being an essential requirement for measures on forest conversion and nature conservation in that area. Evidence of forest‐clearing horizons from the medieval period could be systematically documented at four low‐ to mid‐altitudinal sites (360–640 meters above mean sea level) in the Harz (Harz Mountains), Erzgebirge (Ore Mountains), and Českomoravská vrchovina (Bohemian‐Moravian Highlands). Subfossil trees with traces of human cutmarks and burning were recovered from buried wet‐organic soils (paleosols) within a context of mining and settlement archaeology, applying a multiproxy‐approach by using data from archaeology, paleobotany, geochronology, dendrochronology, and pedology. Tree stumps and trunks, as well as small‐scale wood remains represent an in situ record of local conifer stands (spruce, fir, and pine). Some deciduous tree taxa also occur. Dating of the tree remains yielded ages from the 10th/11th to the 13th/14th centuries A.D. After deforestation, the tree remains were buried by technogenic and alluvial–colluvial deposits. The reconstructed conifer‐dominated woodlands on wet soils mirror the local vegetation structure immediately before the medieval deforestation. As such wet sites are common in the uplands, conifers were significantly present in the natural vegetation even at mid and lower altitudes.
Astroglial endfeet exhibit distinct Ca2+ signals during hypoosmotic conditions
Authors: Eilert‐Olsen Martine , Hjukse Jarand B. , Thoren Anna E. , Tang Wannan , Enger Rune , Jensen Vidar , Pettersen Klas H. , Nagelhus Erlend A. 
Published: July 2019

AbstractAstrocytic endfeet cover the brain surface and form a sheath around the cerebral vasculature. An emerging concept is that endfeet control blood–brain water transport and drainage of interstitial fluid and waste along paravascular pathways. Little is known about the signaling mechanisms that regulate endfoot volume and hence the width of these drainage pathways. Here, we used the genetically encoded fluorescent Ca2+ indicator GCaMP6f to study Ca2+ signaling within astrocytic somata, processes, and endfeet in response to an osmotic challenge known to induce cell swelling. Acute cortical slices were subjected to artificial cerebrospinal fluid with 20% reduction in osmolarity while GCaMP6f fluorescence was imaged with two‐photon microscopy. Ca2+ signals induced by hypoosmotic conditions were observed in all astrocytic compartments except the soma. The Ca2+ response was most prominent in subpial and perivascular endfeet and included spikes with single peaks, plateau‐type elevations, and rapid oscillations, the latter restricted to subpial endfeet. Genetic removal of the type 2 inositol 1,4,5‐triphosphate receptor (IP3R2) severely suppressed the Ca2+ responses in endfeet but failed to affect brain water accumulation in vivo after water intoxication. Furthermore, the increase in endfoot Ca2+ spike rate during hypoosmotic conditions was attenuated in mutant mice lacking the aquaporin‐4 anchoring molecule dystrophin and after blockage of transient receptor potential vanilloid 4 channels. We conclude that the characteristics and underpinning of Ca2+ responses to hypoosmotic stress differ within the astrocytic territory and that IP3R2 is essential for the Ca2+ signals only in subpial and perivascular endfeet.
A comparison of automated lesion segmentation approaches for chronic stroke T1‐weighted MRI data
Authors: Ito Kaori L. , Kim Hosung , Liew Sook‐Lei 
Published: July 2019

AbstractAccurate stroke lesion segmentation is a critical step in the neuroimaging processing pipeline for assessing the relationship between poststroke brain structure, function, and behavior. Many multimodal segmentation algorithms have been developed for acute stroke neuroimaging, yet few algorithms are effective with only a single T1‐weighted (T1w) anatomical MRI. This is a critical gap because multimodal MRI is not commonly available due to time and cost constraints in the stroke rehabilitation setting. Although several attempts to automate the segmentation of chronic lesions on single‐channel T1w MRI have been made, these approaches have not been systematically evaluated on a large dataset. We performed an exhaustive review of the literature and identified one semiautomated and three fully automated approaches for segmentation of chronic stroke lesions using T1w MRI within the last 10 years: Clusterize, automated lesion identification (ALI), Gaussian naïve Bayes lesion detection (lesionGnb), and lesion identification with neighborhood data analysis (LINDA). We evaluated each method on a large T1w stroke dataset (N = 181). LINDA was the most computationally expensive approach, but performed best across the three main evaluation metrics (median values: dice coefficient = 0.50, Hausdorff's distance = 36.34 mm, and average symmetric surface distance = 4.97 mm). lesionGnb had the highest recall/least false negatives (median = 0.80). However, across the automated methods, many lesions were either misclassified (ALI: 28, lesionGnb: 39, LINDA: 45) or not identified (ALI: 24, LINDA: 23, lesionGnb: 0). Segmentation accuracy in all automated methods were influenced by size (small: worst) and stroke territory (brainstem, cerebellum: worst) of the lesion. To facilitate reproducible science, our analysis files have been made publicly available online.
Freeze‐dry processing of three‐dimensional cell constructs for bone graft materials
Authors: Sasaki Jun‐Ichi , Yoshimoto Itsumi , Katata Chihiro , Tsuboi Ririko , Imazato Satoshi 
Published: July 2019

AbstractFreeze‐dry processing improves the operability and stability of cell‐based biomaterials and facilitates sterilization for clinical application. However, there is no established freeze‐drying protocol for engineered tissues. Recently, we reported that biomimetic bone tissues can be fabricated using scaffold‐free three‐dimensional (3D) cell constructs with potential applications as bone graft materials. The purpose of this study was to assess the influence of freeze drying on the morphology and components of 3D cell constructs. Cell constructs freeze dried in phosphate buffered saline (PBS) maintained organic and inorganic components; whereas sodium citrate buffer (SCB)‐treated constructs had significantly lower amounts of calcium and bone‐related proteins. Alkaline phosphatase (ALP) activity in cell constructs was maintained by freeze drying in 10% sucrose‐containing PBS, whereas cell constructs treated with PBS without sucrose or with sucrose‐containing SCB showed significant reductions of ALP activity. In this study, we found that sucrose‐containing phosphate buffer was suitable for freeze drying to maintain minerals and protein functions within 3D cell constructs, whereas citrate buffer was inappropriate. The insights gained by this study may facilitate the development of novel cell‐based biomaterials fabricated by tissue engineering approaches and bone graft biomaterials.
Changes in glucose‐lipid metabolism, insulin resistance, and inflammatory factors in patients with autoimmune thyroid disease
Authors: Lei Yi , Yang Jun , Li Hua , Zhong Haihua , Wan Qin 
Published: July 2019

AbstractBackgroundAutoimmune thyroid disease (AITD) is a common organ‐specific autoimmune disorder, and genetic, environmental, and endogenous factors are responsible for initiation of thyroid autoimmunity. Some AITD patients suffer from a certain degree of glucose‐lipid metabolism disorder. This study aims to explore the changes in glucose‐lipid metabolism, insulin resistance, and inflammatory factors in patients with AITD.MethodsA total of 91 patients with Hashimoto's thyroiditis were retrospectively analyzed and divided into hypothyroidism group (n = 42) and normal thyroid group (n = 49), while 50 healthy people were selected as control group. The changes in glucose‐lipid metabolism, insulin resistance, and inflammatory factors in each group were compared, and their correlations with the thyroid function were analyzed.ResultsThe levels of serum interleukin‐6 (IL‐6), tumor necrosis factor‐α (TNF‐α), IL‐12, IL‐10, (FINS), and homeostasis model assessment of insulin resistance (HOMA‐IR) were gradually declined in sequence of hypothyroidism group, normal thyroid group, and control group (P < 0.05). In hypothyroidism group, the levels of serum‐free triiodothyronine (FT3), free thyroxine (FT4), (TC), triglyceride (TG), and low‐density lipoprotein cholesterol (LDL‐C) were significantly lower than those in normal thyroid group (P < 0.05), while the level of serum thyroid stimulating hormone (TSH) was significantly higher than that in normal thyroid group (P < 0.05). However, the fasting blood glucose and 2‐hour postprandial blood glucose levels had no statistically significant differences among the three groups (P > 0.05).ConclusionAutoimmune thyroid disease patients are prone to fat metabolism disorder, and the serum thyroid hormone level has a close correlation with blood lipid metabolism, insulin metabolism, and inflammatory factors.
Characterization of human pegivirus infection in liver transplantation recipients
Authors: Izumi Takuma , Sakata Kazuhito , Okuzaki Daisuke , Inokuchi Shoichi , Tamura Tomokazu , Motooka Daisuke , Nakamura Shota , Ono Chikako , Shimokawa Masahiro , Matsuura Yoshiharu , Mori Masaki , Fukuhara Takasuke , Yoshizumi Tomoharu 
Published: July 2019

AbstractApproximately 2% of healthy persons are infected with human pegivirus (HPgV). HPgV is transmitted via vertical, sexual, and blood‐borne routes. Recently, the association of HPgV infection with the risk of lymphoma was reported. Here, we examined the prevalence of chronic HPgV infection in liver transplantation (LT) recipients and patients with hepatectomy and the influence of HPgV infection after LT on clinical and perioperative factors. We enrolled 313 LT recipients and 187 patients with hepatectomy who received care at the Kyusyu University Hospital between May 1997 and September 2017. Of the 313 recipients and 187 patients enrolled in this study, 44 recipients (14.1%) and 2 patients (1.1%) had HPgV viremia, respectively. There was no significant association between HPgV infection and LT outcomes. Interestingly, one recipient was infected with HPgV during the peritransplant period, which was likely transmitted via blood transfusion because HPgV RNA was detected from the blood bag transfused to the recipient during LT. We reviewed the available literature on the prevalence HPgV infections in other organ‐transplanted patients and whether they impacted clinical outcomes. They also had the higher prevalence of HPgV infection, while it appears to be of low or no consequences. In addition, HPgV infection induced the upregulation of interferon‐stimulated gene (ISG) expression in peripheral blood mononuclear cells. LT recipients had higher HPgV viremia compared to patients with hepatectomy. Although HPgV infection was not associated with LT‐related outcomes, it induced ISG expression in recipients.
Secondary Perforation Risk in Plate Osteosynthesis of Unstable Proximal Humerus Fractures: A Biomechanical Investigation of the Effect of Screw Length
Authors: Ciric Daniel , Mischler Dominic , Qawasmi Feras , Wenzel Lisa , Richards R. Geoff , Gueorguiev Boyko , Windolf Markus , Varga Peter 
Published: July 2019

ABSTRACTSecondary perforation of screws into the joint surface is a commonly reported mechanical fixation failure mode in locked plating of proximal humerus fractures (PHF). This study investigated the influence that screws tip to joint distance (TJD) has on the biomechanical risk of secondary screw perforation and the stability of PHF. Ten pairs of cadaveric proximal humeri with a wide range of bone mineral density were used. Each specimen was osteotomized and instrumented with the PHILOS plate, simulating a highly unstable 3‐part fracture. Bones were randomized into a long screw group (LSG) with 4 mm TJD, or a short screw group (SSG) with 8 mm TJD. A custom biomechanical setup was used to test the samples to failure cyclically with a constant valley load and an increasing ramp. The number of cycles to the initial screw loosening event was significantly higher for the LSG (mean ± standard deviation: 17,532 ± 6,458) compared with the SSG (11,102 ± 5,440) (p < 0.01). The mode of failure during testing was lateral‐inferior displacement combined with varus collapse, with calcar screws perforating first. The number of cycles to failure event for LSG (27,849 ± 5,648) was not significantly different compared with SSG (28,782 ± 7,307) (p = 0.50). Screws that purchase closer to the joint had better initial stability and resistance against loosening. Placing longer screws, within limits dictated by the surgical guide, is expected to decrease the risk of secondary perforation failures in unstable PHF. These findings require clinical corroboration. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:2625–2633, 2019
The use of interdental brushes or oral irrigators as adjuvants to conventional oral hygiene associated with recurrence of periodontitis in periodontal maintenance therapy: A 6‐year prospective study
Authors: Costa Fernando Oliveira , Costa Amanda Almeida , Cota Luís Otávio Miranda 
Published: July 2019

AbstractBackgroundProspective studies investigating the influence of adjuvants to oral hygiene procedures on the recurrence of periodontitis (RP) during periodontal maintenance therapy (PMT) programs have not been previously reported. The aim of this study was to compare the effect of oral irrigator devices or interdental brushes as adjuncts to toothbrushing associated with dental flossing to improving periodontal condition and reducing RP among individuals under PMT.MethodsFrom a 6‐year prospective PMT cohort study (n = 268), 142 individuals who attended at least one PMT visit within 12 months were determined to be eligible. According to oral hygiene adjuvants use, they were categorized into three groups: 1) manual brushing/dental flossing + interdental brushes (BDF + Ib; n = 44); 2) manual brushing/dental flossing + oral irrigator (BDF + Oi; n = 36); and 3) only manual brushing/dental flossing (BDF; n = 62). Full‐mouth periodontal examination and oral hygiene habits were evaluated at two time points: T1 (after active periodontal therapy) and T2 (6 years).ResultsRP was significantly higher among BDF when compared with BDF + Ib and BDF + Oi. The final logistic model in T2 for RP included the following items: manual brushing/dental flossing alone (odds ratio [OR] = 1.94); age > 50 years (OR = 1.98), smoking (OR = 3.51), bleeding on probing >30% sites (OR = 4.10), and the interaction between manual brushing/dental flossing alone and smoking (OR = 6.1). A protective effect on RP was observed in BDF + Oi individuals (OR = 0.52).ConclusionsBDF + Ib and BDF + Oi individuals presented lower rates of RP and better periodontal condition when compared to BDF individuals. Including these adjuvants to conventional oral hygiene have shown to improve biofilm control during PMT leading to a better periodontal status maintenance.