bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial distribution, source identification, and risk assessment of organochlorines in wild tilapia from Guangxi, South China
Authors: Ding Yang , Wu Zhiqiang , Zhang Ruijie , Kang Yaru , Yu Kefu , Wang Yinghui , Zheng Xiaobo , Huang Liangliang , Zhao Lichao 
Published: September 2020

AbstractSeventy-five wild tilapia samples from six rivers (ten sites) in Guangxi province were collected and analyzed for 53 organochlorine compounds. DDTs, endosulfan, and PCBs were the most dominant compounds found in this study. Tiandong County (TD) and Guigang City (GG) sites were found to be heavily contaminated with high levels of endosulfan (385–925 ng/g lw) and/or DDTs (20.1–422 ng/g lw). The diagnostic ratios indicated that the residues of DDTs and endosulfan in wild tilapia are associated with historical applications as well as the recent introduction of technical DDTs and endosulfan at some sampling sites. The correlation between total length, body mass, and organochlorines (OCs) was higher than the correlation between age and lipid content. There was no significant correlation between organochlorine pesticides (OCPs) and lipid content. Therefore, for organisms, the feeding intensity (related to length and mass) of fish could better reflect degree of pollution than exposure time (age) of fish. The hazardous ratios for the 50th and 95th percentile data of OCPs and PCBs in fish were both below 1, suggesting that daily exposure to OCPs and PCBs yields a lifetime cancer risk lower than 1 in 10,000.
Age-dependent decline in stress response capacity revealed by proteins dynamics analysis
Authors: Chen Kaiyue , Shen Wenting , Zhang Zhiwen , Xiong Fangzheng , Ouyang Qi , Luo Chunxiong 
Published: September 2020

AbstractThe aging process is regarded as the progressive loss of physiological integrity, leading to impaired biological functions and the increased vulnerability to death. Among various biological functions, stress response capacity enables cells to alter gene expression patterns and survive when facing internal and external stresses. Here, we explored changes in stress response capacity during the replicative aging of Saccharomyces cerevisiae. To this end, we used a high-throughput microfluidic device to deliver intermittent pulses of osmotic stress and tracked the dynamic changes in the production of downstream stress-responsive proteins, in a large number of individual aging cells. Cells showed a gradual decline in stress response capacity of these osmotic-related downstream proteins during the aging process after the first 5 generations. Among the downstream stress-responsive genes and unrelated genes tested, the residual level of response capacity of Trehalose-6-Phosphate Synthase (TPS2) showed the best correlation with the cell remaining lifespan. By monitor dynamics of the upstream transcription factors and mRNA of Tps2, it was suggested that the decline in downstream stress response capacity was caused by the decline of translational rate of these proteins during aging.
New insights into the biodiversity of coliphages in the intestine of poultry
Authors: Sørensen Patricia E. , Van Den Broeck Wim , Kiil Kristoffer , Jasinskyte Dziuginta , Moodley Arshnee , Garmyn An , Ingmer Hanne , Butaye Patrick 
Published: September 2020

AbstractDespite phages’ ubiquitous presence and great importance in shaping microbial communities, little is known about the diversity of specific phages in different ecological niches. Here, we isolated, sequenced, and characterized 38 Escherichia coli-infecting phages (coliphages) from poultry faeces to gain a better understanding of the coliphage diversity in the poultry intestine. All phages belonged to either the Siphoviridae or Myoviridae family and their genomes ranged between 44,324 and 173,384 bp, with a G+C content between 35.5 and 46.4%. Phylogenetic analysis was performed based on single “marker” genes; the terminase large subunit, portal protein, and exonucleases, as well as the full draft genomes. Single gene analysis resulted in six distinct clusters. Only minor differences were observed between the different phylogenetic analyses, including branch lengths and additional duplicate or triplicate subclustering. Cluster formation was according to genome size, G+C content and phage subfamily. Phylogenetic analysis based on the full genomes supported these clusters. Moreover, several of our Siphoviridae phages might represent a novel unclassified phage genus. This study allowed for identification of several novel coliphages and provides new insights to the coliphage diversity in the intestine of poultry. Great diversity was observed amongst the phages, while they were isolated from an otherwise similar ecosystem.
The immune response after noise damage in the cochlea is characterized by a heterogeneous mix of adaptive and innate immune cells
Authors: Rai Vikrant , Wood Megan B. , Feng Hao , Schabla Nathan. M. , Tu Shu , Zuo Jian 
Published: September 2020

AbstractCells of the immune system are present in the adult cochlea and respond to damage caused by noise exposure. However, the types of immune cells involved and their locations within the cochlea are unclear. We used flow cytometry and immunostaining to reveal the heterogeneity of the immune cells in the cochlea and validated the presence of immune cell gene expression by analyzing existing single-cell RNA-sequencing (scRNAseq) data. We demonstrate that cell types of both the innate and adaptive immune system are present in the cochlea. In response to noise damage, immune cells increase in number. B, T, NK, and myeloid cells (macrophages and neutrophils) are the predominant immune cells present. Interestingly, immune cells appear to respond to noise damage by infiltrating the organ of Corti. Our studies highlight the need to further understand the role of these immune cells within the cochlea after noise exposure.
Experimental autoimmune encephalomyelitis is associated with changes of the microbiota composition in the gastrointestinal tract
Authors: Johanson David M. , Goertz Jennifer E. , Marin Ioana A. , Costello John , Overall Christopher C. , Gaultier Alban 
Published: September 2020

AbstractThe gut microbiome is known to be sensitive to changes in the immune system, especially during autoimmune diseases such as Multiple Sclerosis (MS). Our study examines the changes to the gut microbiome that occur during experimental autoimmune encephalomyelitis (EAE), an animal model for MS. We collected fecal samples at key stages of EAE progression and quantified microbial abundances with 16S V3–V4 amplicon sequencing. Our analysis of the data suggests that the abundance of commensal Lactobacillaceae decreases during EAE while other commensal populations belonging to the Clostridiaceae, Ruminococcaceae, and Peptostreptococcaceae families expand. Community analysis with microbial co-occurrence networks points to these three expanding taxa as potential mediators of gut microbiome dysbiosis. We also employed PICRUSt2 to impute MetaCyc Enzyme Consortium (EC) pathway abundances from the original microbial abundance data. From this analysis, we found that a number of imputed EC pathways responsible for the production of immunomodulatory compounds appear to be enriched in mice undergoing EAE. Our analysis and interpretation of results provides a detailed picture of the changes to the gut microbiome that are occurring throughout the course of EAE disease progression and helps to evaluate EAE as a viable model for gut dysbiosis in MS patients.
Identifying a stochastic clock network with light entrainment for single cells of Neurospora crassa
Authors: Caranica C. , Al-Omari A. , Schüttler H.-B. , Arnold J. 
Published: September 2020

AbstractStochastic networks for the clock were identified by ensemble methods using genetic algorithms that captured the amplitude and period variation in single cell oscillators of Neurosporacrassa. The genetic algorithms were at least an order of magnitude faster than ensemble methods using parallel tempering and appeared to provide a globally optimum solution from a random start in the initial guess of model parameters (i.e., rate constants and initial counts of molecules in a cell). The resulting goodness of fit $${x}^{2}$$

x

2

was roughly halved versus solutions produced by ensemble methods using parallel tempering, and the resulting $${x}^{2}$$

x

2

per data point was only $${\chi }^{2}/n$$

χ

2

/
n

= 2,708.05/953 = 2.84. The fitted model ensemble was robust to variation in proxies for “cell size”. The fitted neutral models without cellular communication between single cells isolated by microfluidics provided evidence for only one Stochastic Resonance at one common level of stochastic intracellular noise across days from 6 to 36 h of light/dark (L/D) or in a D/D experiment. When the light-driven phase synchronization was strong as measured by the Kuramoto (K), there was degradation in the single cell oscillations away from the stochastic resonance. The rate constants for the stochastic clock network are consistent with those determined on a macroscopic scale of 107 cells.
Modeling HIV-1 neuropathogenesis using three-dimensional human brain organoids (hBORGs) with HIV-1 infected microglia
Authors: dos Reis Roberta S. , Sant Shilpa , Keeney Hannah , Wagner Marc C. E. , Ayyavoo Velpandi 
Published: September 2020

AbstractHIV-1 associated neurocognitive disorder (HAND) is characterized by neuroinflammation and glial activation that, together with the release of viral proteins, trigger a pathogenic cascade resulting in synaptodendritic damage and neurodegeneration that lead to cognitive impairment. However, the molecular events underlying HIV neuropathogenesis remain elusive, mainly due to lack of brain-representative experimental systems to study HIV-CNS pathology. To fill this gap, we developed a three-dimensional (3D) human brain organoid (hBORG) model containing major cell types important for HIV-1 neuropathogenesis; neurons and astrocytes along with incorporation of HIV-infected microglia. Both infected and uninfected microglia infiltrated into hBORGs resulting in a triculture system (MG-hBORG) that mirrors the multicellular network observed in HIV-infected human brain. Moreover, the MG-hBORG model supported productive viral infection and exhibited increased inflammatory response by HIV-infected MG-hBORGs, releasing tumor necrosis factor (TNF-α) and interleukin-1 (IL-1β) and thereby mimicking the chronic neuroinflammatory environment observed in HIV-infected individuals. This model offers great promise for basic understanding of how HIV-1 infection alters the CNS compartment and induces pathological changes, paving the way for discovery of biomarkers and new therapeutic targets.
Copaifera spp. oleoresins impair Toxoplasma gondii infection in both human trophoblastic cells and human placental explants
Authors: Teixeira Samuel Cota , de Souza Guilherme , Borges Bruna Cristina , de Araújo Thádia Evelyn , Rosini Alessandra Monteiro , Aguila Fábio Alves , Ambrósio Sergio Ricardo , Veneziani Rodrigo Cassio Sola , Bastos Jairo Kenupp , Silva Marcelo José Barbosa , Martins Carlos Henrique Gomes , de Freitas Barbosa Bellisa , Ferro Eloisa Amália Vieira 
Published: September 2020

AbstractThe combination of pyrimethamine and sulfadiazine is the standard care in cases of congenital toxoplasmosis. However, therapy with these drugs is associated with severe and sometimes life-threatening side effects. The investigation of phytotherapeutic alternatives to treat parasitic diseases without acute toxicity is essential for the advancement of current therapeutic practices. The present study investigates the antiparasitic effects of oleoresins from different species ofCopaiferagenus againstT. gondii. Oleoresins fromC. reticulata,C. duckei,C. paupera,andC. pubiflorawere used to treat human trophoblastic cells (BeWo cells) and human villous explants infected withT. gondii.Our results demonstrated that oleoresins were able to reduceT. gondiiintracellular proliferation, adhesion, and invasion. We observed an irreversible concentration-dependent antiparasitic action in infected BeWo cells, as well as parasite cell cycle arrest in the S/M phase. The oleoresins altered the host cell environment by modulation of ROS, IL-6, and MIF production in BeWo cells. Also,Copaiferaoleoresins reduced parasite replication and TNF-α release in villous explants. Anti-T. gondiieffects triggered by the oleoresins are associated with immunomodulation of the host cells, as well as, direct action on parasites.
Beta-blockers and renin-angiotensin system inhibitors in acute myocardial infarction managed with inhospital coronary revascularization
Authors: Sim Hui Wen , Zheng Huili , Richards A. Mark , Chen Ruth W. , Sahlen Anders , Yeo Khung-Keong , Tan Jack W. , Chua Terrance , Tan Huay Cheem , Yeo Tiong Cheng , Ho Hee Hwa , Liew Boon-Wah , Foo Ling Li , Lee Chi-Hang , Hausenloy Derek J. , Chan Mark Y. 
Published: September 2020

AbstractPivotal trials of beta-blockers (BB) and angiotensin converting enzyme inhibitors/angiotensin receptor blockers (ACEI/ARB) in acute myocardial infarction (AMI) were largely conducted prior to the widespread adoption of early revascularization. A total of 15,073 patients with AMI who underwent inhospital coronary revascularization from January 2007 to December 2013 were analyzed. At 12 months, BB was significantly associated with a lower incidence of major adverse cardiovascular events (MACE, adjusted HR 0.80, 95% CI 0.70–0.93) and all-cause mortality (adjusted HR 0.69, 95% CI 0.55–0.88), while ACEI/ARB was significantly associated with lower all-cause mortality (adjusted HR 0.80, 95% CI 0.66–0.98) and heart failure (HF) hospitalization (adjusted HR 0.80, 95% CI 0.68–0.95). Combined BB and ACEI/ARB use was associated with the lowest incidence of MACE (adjusted HR 0.70, 95% CI 0.57–0.86), all-cause mortality (adjusted HR 0.55, 95% CI 0.40–0.77) and HF hospitalization (adjusted HR 0.64, 95% CI 0.48–0.86). This were consistent for left ventricular ejection fraction < 50% or ≥ 50%. In conclusion, in AMI managed with revascularization, both BB and ACEI/ARB were associated with a lower incidence of 12-month all-cause mortality. Combined BB and ACEI/ARB was associated with the lowest incidence of all-cause mortality and HF hospitalization.
Characterization of the nucleotide-binding domain NsrF from the BceAB-type ABC-transporter NsrFP from the human pathogen Streptococcus agalactiae
Authors: Furtmann Fabia , Porta Nicola , Hoang Dai Tri , Reiners Jens , Schumacher Julia , Gottstein Julia , Gohlke Holger , Smits Sander H. J. 
Published: September 2020

AbstractTreatment of bacterial infections is a great challenge of our era due to the various resistance mechanisms against antibiotics. Antimicrobial peptides are considered to be potential novel compound as antibiotic treatment. However, some bacteria, especially many human pathogens, are inherently resistant to these compounds, due to the expression of BceAB-type ABC transporters. This rather new transporter family is not very well studied. Here, we report the first full characterization of the nucleotide binding domain of a BceAB type transporter from Streptococcus agalactiae, namely SaNsrF of the transporter SaNsrFP, which confers resistance against nisin and gallidermin. We determined the NTP hydrolysis kinetics and used molecular modeling and simulations in combination with small angle X-ray scattering to obtain structural models of the SaNsrF monomer and dimer. The fact that the SaNsrFH202A variant displayed no ATPase activity was rationalized in terms of changes of the structural dynamics of the dimeric interface. Kinetic data show a clear preference for ATP as a substrate, and the prediction of binding modes allowed us to explain this selectivity over other NTPs.
Axial growth and refractive change in white European children and young adults: predictive factors for myopia
Authors: McCullough Sara , Adamson Gary , Breslin Karen M. M. , McClelland Julie F. , Doyle Lesley , Saunders Kathryn J. 
Published: September 2020

AbstractThis report describes development of spherical equivalent refraction (SER) and axial length (AL) in two population-based cohorts of white, European children. Predictive factors for myopic growth were explored. Participants were aged 6–7- (n = 390) and 12–13-years (n = 657) at baseline. SER and AL were assessed at baseline and 3, 6 and 9 years prospectively. Between 6 and 16 years: latent growth mixture modelling identified four SER classes (Persistent Emmetropes-PEMM, Persistent Moderate Hyperopes-PMHYP, Persistent High Hyperopes-PHHYP and Emerging Myopes-EMYO) as optimal to characterise refractive progression and two classes to characterise AL. Between 12 and 22-years: five SER classes (PHHYP, PMHYP, PEMM, Low Progressing Myopes-LPMYO and High Progressing Myopes-HPMYO) and four AL classes were identified. EMYO had significantly longer baseline AL (≥ 23.19 mm) (OR 2.5, CI 1.05–5.97) and at least one myopic parent (OR 6.28, CI 1.01–38.93). More myopic SER at 6–7 years (≤ + 0.19D) signalled risk for earlier myopia onset by 10-years in comparison to baseline SER of those who became myopic by 13 or 16 years (p ≤ 0.02). SER and AL progressed more slowly in myopes aged 12–22-years (− 0.16D, 0.15 mm) compared to 6–16-years (− 0.41D, 0.30 mm). These growth trajectories and risk criteria allow prediction of abnormal myopigenic growth and constitute an important resource for developing and testing anti-myopia interventions.
Skin-conformable printed supercapacitors and their performance in wear
Authors: Railanmaa Anna , Soltani Ayat , Lehtimäki Suvi , Pournoori Nazanin , Keskinen Jari , Hokka Mikko , Lupo Donald 
Published: September 2020

AbstractWearable sensors and electronic systems are of great interest these days, but their viability depends on the availability of compatible energy storage solutions. Such sensors can either be integrated into clothing or attached directly to the skin, each case presenting a different set of requirements for the devices. In this work, we examine the performance of printed supercapacitors while attached to the skin. The devices are manufactured from benign materials, such as water, carbon and sodium chloride, and worn on the forearm or chest for 24 h for durability testing. The supercapacitors exhibit excellent mechanical durability and stay well attached under all test conditions. Electrically, the supercapacitors exhibit reliable capacitive function throughout the test period; other key parameters such as equivalent series resistance and leakage current are affected but to a minimal extent. The movement and deformation of the supercapacitor show good compatibility with the skin, as shown by the Digital Image Correlation full field strain measurements on and around the capacitor. The supercapacitors deform with the skin and do not hinder normal movement or function.
A novel, multi-level approach to assess allograft incorporation in revision total hip arthroplasty
Authors: Rolvien Tim , Friesecke Christian , Butscheidt Sebastian , Gehrke Thorsten , Hahn Michael , Püschel Klaus 
Published: September 2020

AbstractThe successful use of allografts in reconstructive orthopedic surgery, including revision total hip arthroplasty (THA), has been outlined repeatedly. Nonetheless, as previous studies were primarily based on clinical follow-ups, we aimed to create an algorithm that accurately determines the extent of allograft incorporation in the acetabulum and femur using a suite of high-resolution imaging techniques. This study is based on a large patient database including > 4,500 patient data with previous revision THA and simultaneous use of allografts. While the database was continuously matched with the deceased individuals at the local forensic medicine department, complete hips were retrieved in case of a positive match. A positive match was achieved for n = 46 hips at a mean follow-up of 11.8 ± 5.1 years. Comprehensive imaging included contact radiography, high-resolution computed tomography (HR-pQCT), undecalcified histology of ground sections and quantitative backscattered electron imaging (qBEI). We here define a histomorphometric toolkit of parameters to precisely characterize the incorporation of structural (bulk) and morselized (chip) allografts in the acetabulum (n = 38) and femur (n = 8), including the defect area and interface length, microstructural and cellular bone turnover parameters as well as overlap and fibrosis thickness. This collection of samples, through its unique study design and precise definition of incorporation parameters, will provide the scientific community with a valuable source for further in-depth investigation of allograft incorporation and, beyond that, the regenerative potential of this osteoconductive scaffold.
Repeated intravesical injections of platelet-rich plasma improve symptoms and alter urinary functional proteins in patients with refractory interstitial cystitis
Authors: Jiang Yuan-Hong , Kuo Yuh-Chen , Jhang Jia-Fong , Lee Cheng-Ling , Hsu Yung-Hsiang , Ho Han-Chen , Kuo Hann-Chorng 
Published: September 2020

AbstractRepeated intravesical injections of autologous platelet-rich plasma (PRP) have been shown to improve symptoms in patients with interstitial cystitis/bladder pain syndrome (IC/BPS); however, there is a paucity of objective evidence of the effectiveness of this therapy. In this study, we investigated the changes in urinary markers after PRP treatment. Forty patients with IC/BPS who were refractory to conventional therapy received four injections of PRP at monthly intervals; 10 mL PRP solution with 2.5 times the peripheral blood platelet concentration was used. Urine levels of thirteen functional proteins, growth factors, and cytokines were assessed at baseline and at the 4th PRP injection. The clinical parameters included visual analog scale (VAS) pain score, daily urinary frequency, nocturia episodes, functional bladder capacity, and global response assessment (GRA). The GRA and symptom score significantly decreased post-treatment. In patients with GRA ≥ 2, the success rates at 1 month and at 3 months after the 4th PRP injection were 70.6% and 76.7%, respectively. The VAS pain score, frequency, and nocturia showed a significant decrease (all p < 0.05). Urinary levels of nerve growth factor, matrix metalloproteinase-13, and vascular endothelial growth factor significantly decreased post-treatment (p = 0.043, p = 0.02, and p = 0.000, respectively); platelet-derived growth factor-AB showed a significant increase (p = 0.004) at the 4th PRP treatment compared with baseline. In this study, repeated intravesical PRP injections provided significant symptom improvement in IC/BPS patients with concomitant changes in the related biomarker levels.Trial registration: ClinicalTrial.gov: NCT03104361; IRB: TCGH 105-48-A.