bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)
Authors: Fernandes Júnior Gerardo Alves , de Oliveira Henrique Nunes , Carvalheiro Roberto , Cardoso Diercles Francisco , Fonseca Larissa Fernanda Simielli , Ventura Ricardo Vieira , de Albuquerque Lucia Galvão 
Published: June 2020

AbstractMost of the knowledge about genetic variants at the sequence level in cattle is for Bos primigenius taurus populations. Here, we presented a complete genomic characterization of 52 Nellore (Bos primigenius indicus) bulls, revealing specific zebu DNA variants with putative impact in tropical adaptation and productive traits. Single nucleotide polymorphisms (SNPs) and insertion/deletion (INDELs) mutations were identified using the newest bovine reference genome ARS_UCD1.2, and variant functional consequences were predicted using the Ensembl VEP software. A total of 35,753,707 SNPs and 4,492,636 INDELs were detected and annotated to their functional effects. We identified 400 genes that comprised both, a SNP and an INDEL, of high functional impact on proteins (i.e. variants that cause protein truncation, loss of function or triggering nonsense-mediated decay). Among these, we highlight the following genes: BoLA, associated with cattle immune response to infections and reproduction aspects; HSPA8, DNAJC27, and DNAJC28, involved with thermoregulatory protective mechanisms in mammals; and many olfactory signaling pathway related genes that are important genetic factors in the evolution of mammalian species. All these functional aspects are directly related to cattle adaptability to tropical environments.
Characterization of different alginate lyases for dissolving Pseudomonas aeruginosa biofilms
Authors: Blanco-Cabra Núria , Paetzold Bernhard , Ferrar Tony , Mazzolini Rocco , Torrents Eduard , Serrano Luis , LLuch-Senar Maria 
Published: June 2020

AbstractAggregates of Pseudomonas aeruginosa form a protective barrier against antibiotics and the immune system. These barriers, known as biofilms, are associated with several infectious diseases. One of the main components of these biofilms is alginate, a homo- and hetero-polysaccharide that consists of β-D-mannuronate (M) and α-L-guluronate (G) units. Alginate lyases degrade this sugar and have been proposed as biotherapeutic agents to dissolve P. aeruginosa biofilms. However, there are contradictory reports in the literature regarding the efficacy of alginate lyases against biofilms and their synergistic effect with antibiotics. We found that most positive reports used a commercial crude extract from Flavobacterium multivorum as the alginate lyase source. By using anion exchange chromatography coupled to nano LC MS/MS, we identified two distinct enzymes in this extract, one has both polyM and polyG (polyM/G) degradation activities and it is similar in sequence to a broad-spectrum alginate lyase from Flavobacterium sp. S20 (Alg2A). The other enzyme has only polyG activity and it is similar in sequence to AlyA1 from Zobellia galactanivorans. By characterizing both of these enzymes together with three recombinant alginate lyases (a polyM, a polyG and a polyM/G), we showed that only enzymes with polyM/G activity such as Alg2A and A1-II’ (alginate lyase from Sphingomonas sp.) are effective in dissolving biofilms. Furthermore, both activities are required to have a synergistic effect with antibiotics.
Reference Genes for Expression Studies in Human CD8+ Naïve and Effector Memory T Cells under Resting and Activating Conditions
Authors: Geigges Marco , Gubser Patrick M. , Unterstab Gunhild , Lecoultre Yannic , Paro Renato , Hess Christoph 
Published: June 2020

AbstractReverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) is widely used for mRNA quantification. To accurately measure changing gene transcript levels under different experimental conditions, the use of appropriate reference gene transcripts is instrumental. In T cell immunology, suitable reference genes have been reported for bulk CD4+ and CD8+ T cells. However, many CD4+ and CD8+ T cell subsets have been described in the past. Although they respond differently to given activation stimuli, proper validation of suitable reference genes in these subsets is lacking. In this study, we evaluated twelve commonly used reference gene products in human naïve (NV) and effector memory (EM) CD8+ T cells under non-activated and activated (2 h, 10 h and 20 h) conditions. We used five different statistical approaches for data analysis. Our results show that a number of widely used reference transcripts become differentially expressed under activating conditions. Using them as references markedly alters results as exemplified with IFNG mRNA expression. The only candidate reference gene products that remained stable during the activation process were 18S rRNA and SDHA mRNA, encouraging their usage as reference gene products for RT-qPCR experiments, when quantifying mRNA levels in human NV and EM CD8+ T cells.
Clinical Validation of Targeted and Untargeted Metabolomics Testing for Genetic Disorders: A 3 Year Comparative Study
Authors: Almontashiri Naif A. M. , Zha Li , Young Kim , Law Terence , Kellogg Mark D. , Bodamer Olaf A. , Peake Roy W. A. 
Published: June 2020

AbstractGlobal untargeted metabolomics (GUM) has entered clinical diagnostics for genetic disorders. We compared the clinical utility of GUM with traditional targeted metabolomics (TM) as a screening tool in patients with established genetic disorders and determined the scope of GUM as a discovery tool in patients with no diagnosis under investigation. We compared TM and GUM data in 226 patients. The first cohort (n = 87) included patients with confirmed inborn errors of metabolism (IEM) and genetic syndromes; the second cohort (n = 139) included patients without diagnosis who were undergoing evaluation for a genetic disorder. In patients with known disorders (n = 87), GUM performed with a sensitivity of 86% (95% CI: 78–91) compared with TM for the detection of 51 diagnostic metabolites. The diagnostic yield of GUM in patients under evaluation with no established diagnosis (n = 139) was 0.7%. GUM successfully detected the majority of diagnostic compounds associated with known IEMs. The diagnostic yield of both targeted and untargeted metabolomics studies is low when assessing patients with non-specific, neurological phenotypes. GUM shows promise as a validation tool for variants of unknown significance in candidate genes in patients with non-specific phenotypes.
Nano-engineering the material structure of preferentially oriented nano-graphitic carbon for making high-performance electrochemical micro-sensors
Authors: Cuniberto Edoardo , Alharbi Abdullah , Wu Ting , Huang Zhujun , Sardashti Kasra , You Kae-Dyi , Kisslinger Kim , Taniguchi Takashi , Watanabe Kenji , Kiani Roozbeh , Shahrjerdi Davood 
Published: June 2020

AbstractDirect synthesis of thin-film carbon nanomaterials on oxide-coated silicon substrates provides a viable pathway for building a dense array of miniaturized (micron-scale) electrochemical sensors with high performance. However, material synthesis generally involves many parameters, making material engineering based on trial and error highly inefficient. Here, we report a two-pronged strategy for producing engineered thin-film carbon nanomaterials that have a nano-graphitic structure. First, we introduce a variant of the metal-induced graphitization technique that generates micron-scale islands of nano-graphitic carbon materials directly on oxide-coated silicon substrates. A novel feature of our material synthesis is that, through substrate engineering, the orientation of graphitic planes within the film aligns preferentially with the silicon substrate. This feature allows us to use the Raman spectroscopy for quantifying structural properties of the sensor surface, where the electrochemical processes occur. Second, we find phenomenological models for predicting the amplitudes of the redox current and the sensor capacitance from the material structure, quantified by Raman. Our results indicate that the key to achieving high-performance micro-sensors from nano-graphitic carbon is to increase both the density of point defects and the size of the graphitic crystallites. Our study offers a viable strategy for building planar electrochemical micro-sensors with high-performance.
Activation of GPR35 protects against cerebral ischemia by recruiting monocyte-derived macrophages
Authors: Sharmin Ozayra , Abir Ariful Haque , Potol Abdullah , Alam Mahabub , Banik Jewel , Rahman A.F.M. Towheedur , Tarannum Nuzhat , Wadud Rasiqh , Habib Zaki Farhad , Rahman Mahbubur 
Published: June 2020

AbstractPamoic acid is a potent ligand for G protein Coupled Receptor 35 (GPR35) and exhibits antinociceptive property. GPR35 activation leads to increased energy utilization and the expression of anti-inflammatory genes. However, its role in brain disorders, especially in stroke, remains unexplored. Here we show in a mouse model of stroke that GPR35 activation by pamoic acid is neuroprotective. Pharmacological inhibition of GPR35 reveals that pamoic acid reduces infarcts size in a GPR35 dependent manner. The flowcytometric analysis shows the expression of GPR35 on the infiltrating monocytes/macrophages and neutrophils in the ischemic brain. Pamoic acid treatment results in a preferential increment of noninflammatory Ly-6CLo monocytes/macrophages in the ischemic brain along with the reduced neutrophil counts. The neuroprotective effect of GPR35 activation depends on protein kinase B (Akt) and p38 MAPK. Together we conclude that GPR35 activation by pamoic acid reprograms Ly-6CLo monocytes/macrophages to relay a neuroprotective signal into the ischemic brain.
Involvement of GLWamide neuropeptides in polyp contraction of the adult stony coral Euphyllia ancora
Authors: Shikina Shinya , Chiu Yi-Ling , Zhang Yan , Yi-ChenYao  , Liu Tai-Yu , Tsai Pin-Hsuan , Zatylny-Gaudin Céline , Chang Ching-Fong 
Published: June 2020

AbstractThe existence and function of neurons remain largely unexplored in scleractinian corals. To gain a better understanding of neuronal functions in coral physiology, this study focused on Glycine-Leucine-Tryptophan-amide family neuropeptides (GLWamides), which have been shown to induce muscle contraction and larval metamorphosis in other cnidarians. Molecular identification and functional characterization of GLWamides in the adult stony coral Euphyllia ancora were performed. We successfully elucidated the full-length cDNA of GLWamide preprohormone in E. ancora (named EaGLW preprohormone). The deduced amino acid sequence was predicted to contain six potential GLWamide peptides. Tissue distribution analysis demonstrated that transcripts of EaGLW preprohormone were mainly expressed in the mouth (including the pharynx) and tentacles of the polyps. Immunodetection with an anti-GLWamide monoclonal antibody revealed that GLWamide neurons were mainly distributed in the epidermis of the mouth region and tentacle, in agreement with the distribution patterns of the transcripts. Treatment of the isolated mouth and tentacles with synthetic GLWamide peptides induced the contraction of these isolated tissues. Treatment of polyps with synthetic GLWamide peptides induced the contraction of polyps. These results suggest that GLWamides are involved in polyp contraction (myoactivity) in adult scleractinians. Our data provide new information on the physiological function of neuropeptides in scleractinians.
Predictive Factors for Outcomes of Selective Laser Trabeculoplasty
Authors: Hirabayashi Matthew , Ponnusamy Vikram , An Jella 
Published: June 2020

Abstract We sought to determine predictive factors for selective laser trabeculoplasty (SLT) outcome. 252 eyes from 198 adult patients with open-angle glaucoma who underwent SLT between July 2016 and February 2018 with a minimum 6 month follow up were reviewed. We defined success as ≥20% IOP reduction or ≥1 medication reduction without an IOP lowering procedure. We also evaluated the relationship of these factors to postoperative IOP elevation >5 mmHg (IOP spikes). Our primary outcome measure was association between age, type and severity of glaucoma, pigmentation of the trabecular meshwork (PTM), total energy delivered, and baseline intraocular pressure (IOP) with success. At 2 and 6 months, 33.6% (76/226) and 38.5% (97/252) of eyes met success criteria respectively. Baseline IOP > 18 mmHg was significantly associated with success both at 2 and 6 months, reducing IOP by 5.4 ± 5.3 mmHg (23.7% reduction), whereas those with lower baseline remained at −0.7 ± 4.6 mmHg (4.9% increase) at 6 months (P < 0.001). No other baseline characteristics significantly predicted success or IOP spikes. Patients with higher baseline IOPs had greater success rates and mean IOP reduction at both 2 and 6 months following SLT. Age, type and severity of glaucoma, PTM, or total energy delivery had no association with procedural success or IOP spikes. Patients with higher baseline IOP may experience greater lowering of IOP after SLT. However, SLT may be equally successful for patients with a variety of other characteristics.
Verbesserungspotenziale durch neue Resektions- und Bildgebungstechniken bei der TUR-B
Authors: Hennig Martin J. P. , Kramer Mario W. 
Published: June 2020

ZusammenfassungDie transurethrale Resektion von Harnblasentumoren (TURB) ist ein Grundpfeiler in der urologischen Versorgung von Harnblasenkarzinompatienten. Seit der initialen Einführung von Resektoskopen vor knapp 100 Jahren hat sich an der grundlegenden Resektionstechnik wenig geändert. Erst mit der Verbreitung der sog. En-Bloc-Resektion (ERBT), welche im Gegensatz zur fragmentierten Abtragung die Tumorintegrität erhält, findet eine zögerliche Neujustierung der Technik statt. Vorteile, die der ERBT zugeschrieben werden, sind die bessere histopathologische Beurteilbarkeit und die höhere Detrusormuskulaturrate. Zudem sind Tendenzen für eine geringere Rate an sog. „in-field“ Rezidiven sowie eine verminderte Komplikationsrate beschrieben worden. Randomisierte, kontrollierte Studien mit geeigneter Fallzahl und Methodik stehen allerdings aus. Nur wenige Neuerungen hinsichtlich verbesserter endoskopischer Tumordiagnostik sind in den letzten Jahren hinzugekommen. Erwähnenswert ist die multiparametrische Magnetresonanztomografie der Blase, welche die Genauigkeit der lokalen Tumorausbreitung im Vergleich zur alleinigen konventionellen Bildgebung verbessern soll, sowie Verfahren aus dem Bereich der künstlichen Intelligenz. Die Intention dieses Artikels ist es einen aktuellen Stand über die ERBT sowie die lokale Diagnostik bei Harnblasentumoren zu geben.
Bioactive Properties of the Aqueous Extracts of Endophytic Fungi Associated with Scots Pine (Pinus sylvestris) Roots
Authors: Tienaho Jenni , Karonen Maarit , Muilu-Mäkelä Riina , Kaseva Janne , de Pedro Nuria , Vicente Francisca , Genilloud Olga , Aapola Ulla , Uusitalo Hannu , Vuolteenaho Katriina , Franzén Robert , Wähälä Kristiina , Karp Matti , Santala Ville , Sarjala Tytti 
Published: June 2020

AbstractDespite the continuing interest in various plant and natural products, only a small portion of the biologically active compounds from nature has been discovered and exploited. In this study, antioxidant and antibacterial properties of aqueous fractions of three endophytic fungi isolated from the roots of 8-year-old Scots pines (Pinus sylvestris) growing on a drained peatland were investigated. The endophytic fungi species were Acephala applanata, Phialocephala fortinii, and Humicolopsis cephalosporioides/Coniochaeta mutabilis. The bioactivities were examined using hydrogen peroxide scavenging and oxygen radical absorbance capacity tests as well as sensitive Escherichia coli-based biosensors, which produce a luminescent signal in the presence of substances with oxidative or genotoxic properties. In addition, cell models for Parkinsonʼs disease, age-related macular degeneration, and osteoarthritis were used to evaluate the potential for
pharmaceutical applications. The aqueous extracts of fungi and 19 out of 42 fractions were found to be active in one or more of the tests used. However, no activity was found in the age-related macular degeneration and osteoarthritis cell model tests. Additionally, bioactivity data was connected with metabolites putatively annotated, and out of 330 metabolites, 177 were interesting in view of the bioactivities investigated. A majority of these were peptides and all three fungal species shared a highly similar metabolome. We propose that Scots pine endophytic fungi are a rich source of interesting metabolites, and synergistic effects may cause the bioactivities, as they were found to vary after the fractionation process.
Resultado funcional dos pacientes submetidos a artrodese de joelho após artroplastia total infectada
Authors: Vivacqua Thiago , Moraes Rui , Barretto João , Cavanelas Naasson , Albuquerque Rodrigo , Mozella Alan 
Published: June 2020

Resumo
Objetivo Avaliar de modo retrospectivo o resultado funcional dos pacientes submetidos a artrodese após falha séptica da artroplastia total de joelho.
Métodos Foram avaliados 18 pacientes com tempo médio de 3,7 anos de seguimento. A cirurgia de artrodese foi realizada com placa do tipo dynamic compression plate (DCP) estreita, anterior e medial, ou fixador externo em dois planos da articulação (Orthofix Bone Growth Therapy, Lewisville, TS, EUA), a critério do cirurgião.
Resultados O patógeno mais frequentemente encontrado foi o Staphylococcus aureus sensível a meticilina (38,9%). A discrepância de membros inferiores média foi de 3,63 cm. O da knee society score (KSS) médio foi de 68 pontos. Segundo a escala analógica visual de dor, 44% dos pacientes apresentaram pontuação zero no momento da avaliação, e 22,2% estavam muito insatisfeitos a despeito da consolidação óssea obtida. Os pacientes foram avaliados quanto à capacidade de deambular com ou sem auxílio de apoio.
Conclusão A cirurgia de artrodese do joelho se mostrou eficiente quanto ao controle do processo infeccioso e diminuição das queixas álgicas, porém a satisfação com o procedimento é baixa.
Factors Associated with the Need for Ventriculoperitoneal Shunting in Patients with Spontaneous Intracerebral Hemorrhage Requiring Emergency Cerebrospinal Fluid Diversion
Authors: Alimohammadi Ehsan , Bagheri Seyed Reza , Hadidi Homa , Habibi Shabnam , Amiri Akram , Moradi Sahar , Abdi Alireza 
Published: June 2020

Abstract
Introduction Intracerebral hemorrhage (ICH) is a serious medical condition that is frequently complicated by acute hydrocephalus, necessitating emergency cerebrospinal fluid (CSF) diversion in a subset of patients, ultimately requiring long-term treatment via placement of permanent ventricular shunts. The present study aimed to determine factors associated with the need for permanent ventricular shunt placement in these patients.
Methods A total of 309 consecutive patients who underwent emergent CSF diversion with external ventricular drain (EVD) as a treatment for ICH between July 2009 and July 2018 were studied retrospectively to assess the factors that might be correlated with shunt-dependent chronic hydrocephalus. A binary logistic regression model was designed to identify independent related factors of shunt-dependent hydrocephalus after ICH.
Results Of 309 patients included in this study, 102 (33.00%) required permanent ventricular CSF shunting before discharge. In univariate analysis, age,ventriculitis, ICP elevation >30 mm Hg, ICH evacuation, the Graeb score, days of EVD in place, and CSF protein levels were significantly associated with the requirement for permanent CSF diversion (p < 0.05). The age and ICH evacuation were protective variables and the ventriculoperitoneal (VP) shunt possibility was reduced by 22.6 and 63.5%, respectively.
Conclusion Our results showed that higher Graeb score, ICP elevation >30 mm Hg, more days of EVD in place, and higher CSF protein levels were associated with permanent CSF diversion in these patients. Advanced age and ICH evacuation decreased the possibility of VP shunting in our study.These factors may help in predicting which patients will need permanent CSF diversion and could ultimately lead to improvements in the management of these patients.
Pattern of Pulmonary Dysfunctions in Craniovertebral Junction Anomaly and Its Persistence after Rigid Occipitocervical Fixation
Authors: Bodeliwala Shaam , Nagar Vikas , Singh Hukum , Singh Daljit , Jagetia Anita , Pandey Sharad , Ruttala Rajesh , Kumar Pankaj 
Published: June 2020

Abstract
Introduction Despite a significant advancement in operative techniques of occipitocervical fixation, there is a poor postoperative patient outcome. This can be attributed to restrictive lung pattern in craniovertebral junction anomalies (CVJAs) patients resulting from repeated trauma to cervicomedullary junction by the pincer action of the bony anomalies and compression of the brainstem. We evaluate the changes in pulmonary function tests (PFTs) following rigid occipitocervical fixation in CVJA.
Methods PFTs of 20 CVJA patients were measured pre and postoperatively using spirometry. Measurements included forced vital capacity (FVC), forced expiratory volume in one second (FEV1), maximum forced mid-expiratory flow rate (FEF25–75%), and ratio of FEV1 and FVC (FEV1%). The parameters were compared with the predicted normal values based on their age and sex. PFTs were repeated on the seventh postoperative day. McCormick grading was used to assess neurological function.
Results  The values of PFTs in the preoperative period were significantly lower than predicted normal values. The mean values of FVC, FEV1, FEF25–75% were 72, 68, and 71% of their mean predicted values, with FEV1% in the range of 70 to 95% with a mean of 81.4%. Postoperatively there was further significant reduction in the mean values of FVC, FEV1, FEF25–75%, and FEV1% compared with the preoperative values. There was neurological improvement in McCormick grades of patients postoperatively (from grade III and IV to grade II).
Conclusion A significant restrictive lung disease is present in patients of CVJA, even though not clinically apparent, and it persists in the early postoperative period. However, a long-term follow-up is required to assess whether pulmonary function parameters improve subsequently.