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https://www.readbyqxmd.com/read/29043112/tumor-infiltrating-cd8-lymphocytes-predict-different-clinical-outcomes-in-organ-and-non-organ-confined-urothelial-carcinoma-of-the-bladder-following-radical-cystectomy
#1
Shiqiang Zhang, Jun Wang, Xinyu Zhang, Fangjian Zhou
Tumor-infiltrating lymphocytes (TILs) are associated with better clinical outcomes in many tumors. TILs represent a cell-mediated immune response against the carcinoma. CD8+ TILs are a crucial component of cell-mediated immunity. The significance of CD8+ TILs has not been reported respectively in organ- and non-organ-confined urothelial carcinoma (UC) of the bladder. We explored the prognostic value of CD8+ TILs in the two groups. The presence of CD8+ TILs was assessed by immunohistochemical staining of whole tissue sections from 75 organ and 51 non-organ-confined disease patients with long-term follow-up, and its correlation with clinicopathological features and overall survival (OS) was determined...
2017: PeerJ
https://www.readbyqxmd.com/read/29043111/a-retrospective-study-does-upper-airway-morphology-differ-between-non-positional-and-positional-obstructive-sleep-apnea
#2
Xiao Jiao, Jianyin Zou, Suru Liu, Jian Guan, Hongliang Yi, Shankai Yin
OBJECTIVE: The objective of this study was to explore the differences in upper airway morphology between positional (POSA) and non-positional (NPOSA) obstructive sleep apnea. METHODS: This retrospective study enrolled 75 patients (45 NPOSA and 30 POSA) who underwent polysomnography (PSG) and computed tomography (CT). The differences in, and relationships of, the PSG values and CT data between POSA and NPOSA were analyzed. RESULTS: Significant (p < 0...
2017: PeerJ
https://www.readbyqxmd.com/read/29043110/neurodynamic-mobilization-and-foam-rolling-improved-delayed-onset-muscle-soreness-in-a-healthy-adult-population-a-randomized-controlled-clinical-trial
#3
Blanca Romero-Moraleda, Roy La Touche, Sergio Lerma-Lara, Raúl Ferrer-Peña, Víctor Paredes, Ana Belén Peinado, Daniel Muñoz-García
OBJECTIVES: Compare the immediate effects of a Neurodynamic Mobilization (NM) treatment or foam roller (FR) treatment after DOMS. DESIGN: Double blind randomised clinical trial. SETTING: The participants performed 100 drop jumps (5 sets of 20 repetitions, separated by 2 min rests) from a 0.5-m high box in a University biomechanics laboratory to induce muscle soreness. The participants were randomly assigned in a counter-balanced fashion to either a FR or NM treatment group...
2017: PeerJ
https://www.readbyqxmd.com/read/29043109/multigene-phylogeny-of-the-scyphozoan-jellyfish-family-pelagiidae-reveals-that-the-common-u-s-atlantic-sea-nettle-comprises-two-distinct-species-chrysaora-quinquecirrha-and-c-chesapeakei
#4
Keith M Bayha, Allen G Collins, Patrick M Gaffney
BACKGROUND: Species of the scyphozoan family Pelagiidae (e.g., Pelagia noctiluca, Chrysaora quinquecirrha) are well-known for impacting fisheries, aquaculture, and tourism, especially for the painful sting they can inflict on swimmers. However, historical taxonomic uncertainty at the genus (e.g., new genus Mawia) and species levels hinders progress in studying their biology and evolutionary adaptations that make them nuisance species, as well as ability to understand and/or mitigate their ecological and economic impacts...
2017: PeerJ
https://www.readbyqxmd.com/read/29043108/mysterious-inhibitory-cell-regulator-investigated-and-found-likely-to-be-secretogranin-ii-related
#5
John E Hart, Iain J Clarke, Gail P Risbridger, Ben Ferneyhough, Mónica Vega-Hernández
In the context of a hunt for a postulated hormone that is tissue-mass inhibiting and reproductively associated, there is described probable relatedness to a granin protein. A 7-8 kDa polypeptide candidate (gels/MS) appeared in a bioassay-guided fractionation campaign involving sheep plasma. An N-terminal sequence of 14 amino acids was obtained for the polypeptide by Edman degradation. Bioinformatics and molecular biology failed to illuminate any ovine or non-ovine protein which might relate to this sequence...
2017: PeerJ
https://www.readbyqxmd.com/read/29043107/the-intervals-method-a-new-approach-to-analyse-finite-element-outputs-using-multivariate-statistics
#6
Jordi Marcé-Nogué, Soledad De Esteban-Trivigno, Thomas A Püschel, Josep Fortuny
BACKGROUND: In this paper, we propose a new method, named the intervals' method, to analyse data from finite element models in a comparative multivariate framework. As a case study, several armadillo mandibles are analysed, showing that the proposed method is useful to distinguish and characterise biomechanical differences related to diet/ecomorphology. METHODS: The intervals' method consists of generating a set of variables, each one defined by an interval of stress values...
2017: PeerJ
https://www.readbyqxmd.com/read/29043106/sediment-microbial-taxonomic-and-functional-diversity-in-a-natural-salinity-gradient-challenge-remane-s-species-minimum-concept
#7
Christina Pavloudi, Jon B Kristoffersen, Anastasis Oulas, Marleen De Troch, Christos Arvanitidis
Several models have been developed for the description of diversity in estuaries and other brackish habitats, with the most recognized being Remane's Artenminimum ("species minimum") concept. It was developed for the Baltic Sea, one of the world's largest semi-enclosed brackish water body with a unique permanent salinity gradient, and it argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum (5 to 8 psu). The aim of the present study was to investigate the relationship between salinity and sediment microbial diversity at a freshwater-marine transect in Amvrakikos Gulf (Ionian Sea, Western Greece) and assess whether species composition and community function follow a generalized concept such as Remane's...
2017: PeerJ
https://www.readbyqxmd.com/read/29038767/evaluation-of-plasma-cytokines-in-patients-with-cocaine-use-disorders-in-abstinence-identifies-transforming-growth-factor-alpha-tgf%C3%AE-as-a-potential-biomarker-of-consumption-and-dual-diagnosis
#8
Rosa Maza-Quiroga, Nuria García-Marchena, Pablo Romero-Sanchiz, Vicente Barrios, María Pedraz, Antonia Serrano, Raquel Nogueira-Arjona, Juan Jesus Ruiz, Maribel Soria, Rafael Campos, Julie Ann Chowen, Jesus Argente, Marta Torrens, Meritxell López-Gallardo, Eva María Marco, Fernando Rodríguez de Fonseca, Francisco Javier Pavón, Pedro Araos
BACKGROUND: Cocaine use disorder (CUD) is a complex health condition, especially when it is accompanied by comorbid psychiatric disorders (dual diagnosis). Dual diagnosis is associated with difficulties in the stratification and treatment of patients. One of the major challenges in clinical practice of addiction psychiatry is the lack of objective biological markers that indicate the degree of consumption, severity of addiction, level of toxicity and response to treatment in patients with CUD...
2017: PeerJ
https://www.readbyqxmd.com/read/29038766/external-validation-of-cut-off-points-for-foveal-thickness-taking-into-account-the-intraretinal-fluid-using-optical-coherence-tomography-to-diagnose-diabetic-macular-oedema
#9
Carmen Hernández-Martínez, Antonio Palazón-Bru, Cesar Azrak, Aída Navarro-Navarro, Manuel Vicente Baeza-Díaz, José Juan Martínez-Toldos, Vicente Francisco Gil-Guillén
BACKGROUND: In late 2015, cut-off points were published for foveal thickness to diagnose diabetic macular oedema taking into account the presence of intraretinal fluid using optical coherence tomography (OCT) in primary care patients (90 µm in the presence of intraretinal fluid and 310 µm otherwise). METHODS: This cross-sectional observational study was carried out on 134 eyes of diabetic patients treated in specialised ophthalmology services in a Spanish region in 2012-2013, to externally validate the aforementioned cut-off points...
2017: PeerJ
https://www.readbyqxmd.com/read/29038765/the-complete-chloroplast-genome-sequence-of-strawberry-fragaria-%C3%A2-%C3%A3-%C3%A2-ananassa-duch-and-comparison-with-related-species-of-rosaceae
#10
Hui Cheng, Jinfeng Li, Hong Zhang, Binhua Cai, Zhihong Gao, Yushan Qiao, Lin Mi
Compared with other members of the family Rosaceae, the chloroplast genomes of Fragaria species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of Fragaria species is needed. In this study, we sequenced the complete chloroplast genome of F. × ananassa 'Benihoppe' using the Illumina HiSeq 2500-PE150 platform and then performed a combination of de novo assembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences...
2017: PeerJ
https://www.readbyqxmd.com/read/29038764/pulmonary-transcriptomic-responses-indicate-a-dual-role-of-inflammation-in-pneumonia-development-and-viral-clearance-during-2009-pandemic-influenza-infection
#11
Raquel Almansa, Pamela Martínez-Orellana, Lucía Rico, Verónica Iglesias, Alicia Ortega, Beatriz Vidaña, Jorge Martínez, Ana Expósito, María Montoya, Jesús F Bermejo-Martin
BACKGROUND: The interaction between influenza virus and the host response to infection clearly plays an important role in determining the outcome of infection. While much is known on the participation of inflammation on the pathogenesis of severe A (H1N1) pandemic 09-influenza virus, its role in the course of non-fatal pneumonia has not been fully addressed. METHODS: A systems biology approach was used to define gene expression profiles, histology and viral dynamics in the lungs of healthy immune-competent mice with pneumonia caused by a human influenza A (H1N1) pdm09 virus, which successfully resolved the infection...
2017: PeerJ
https://www.readbyqxmd.com/read/29038763/mouse-spermatozoa-with-higher-fertilization-rates-have-thinner-nuclei
#12
Daisuke Mashiko, Masahito Ikawa, Koichi Fujimoto
BACKGROUND: Although spermatozoa with normal morphology are assumed to have uniform fertilization ability, recent data show that even normal spermatozoa have considerable variation in their head shape which is associated with differences in fertilization ability. Appropriate quantitative indicators for good sperm morphology, however, remain unidentified. METHODS: Therefore, in an effort to identify such an indicator, we compared the nuclear contour of normal mouse spermatozoa by quantitative multivariate analysis using elliptic Fourier descriptors combined with principal component analysis...
2017: PeerJ
https://www.readbyqxmd.com/read/29038762/clinical-outcomes-of-residual%C3%A2-or%C3%A2-recurrent-nasopharyngeal-carcinoma-treated-with-endoscopic-nasopharyngectomy-plus-chemoradiotherapy-or-with-chemoradiotherapy-alone-a-retrospective-study
#13
Jingjin Weng, Jiazhang Wei, Jinyuan Si, Yangda Qin, Min Li, Fei Liu, Yongfeng Si, Jiping Su
BACKGROUND: Local residual and recurrent nasopharyngeal carcinoma (NPC) generally shows treatment failure after standard radiotherapy with or without concurrent chemotherapy. Whether endoscopic nasopharyngectomy might provide an additional therapeutic advantage remains controversial. Therefore, we retrospectively compared the clinical prognoses of patients with residual or recurrent NPC treated with endoscopic nasopharyngectomy combined with chemoradiotherapy (CRT) with those of patients treated with CRT alone...
2017: PeerJ
https://www.readbyqxmd.com/read/29038761/comparison-of-human-papillomavirus-hpv-detection-in-urine-and-cervical-swab-samples-using-the-hpv-genoarray-diagnostic-assay
#14
Pornjarim Nilyanimit, Jira Chansaenroj, Anant Karalak, Piyawat Laowahutanont, Pairoj Junyangdikul, Yong Poovorawan
Human papillomavirus (HPV) is the leading cause of cervical cancer. Urine-based HPV testing offers a simple and non-invasive method because of its increasing acceptance. A total of 164 pairs of cervical swab and urine samples from Thai women who underwent cervical cancer screening were used for HPV testing with HPV GenoArray Diagnostic Kits. The overall concordance percentage for HPV detection in the cervical swab and urine samples was 65.2%. The HPV genotypes most commonly detected were HPV16 and HPV18. An analysis of the urine samples and a second analysis of the cervical swab samples showed that the differences in the overall HPV detection rate between women with normal and abnormal cytology were not significant (p > 0...
2017: PeerJ
https://www.readbyqxmd.com/read/29038760/cellobiohydrolase-b-of-aspergillus-niger-over-expressed-in-pichia-pastoris-stimulates-hydrolysis-of-oil-palm-empty-fruit-bunches
#15
James Sy-Keen Woon, Mukram M Mackeen, Rosli M Illias, Nor M Mahadi, William J Broughton, Abdul Munir Abdul Murad, Farah Diba Abu Bakar
BACKGROUND: Aspergillus niger, along with many other lignocellulolytic fungi, has been widely used as a commercial workhorse for cellulase production. A fungal cellulase system generally includes three major classes of enzymes i.e., β-glucosidases, endoglucanases and cellobiohydrolases. Cellobiohydrolases (CBH) are vital to the degradation of crystalline cellulose present in lignocellulosic biomass. However, A. niger naturally secretes low levels of CBH. Hence, recombinant production of A...
2017: PeerJ
https://www.readbyqxmd.com/read/29038759/nests-of-red-wood-ants-formica-rufa-group-are-positively-associated-with-tectonic-faults-a-double-blind-test
#16
Israel Del Toro, Gabriele M Berberich, Relena R Ribbons, Martin B Berberich, Nathan J Sanders, Aaron M Ellison
Ecological studies often are subjected to unintentional biases, suggesting that improved research designs for hypothesis testing should be used. Double-blind ecological studies are rare but necessary to minimize sampling biases and omission errors, and improve the reliability of research. We used a double-blind design to evaluate associations between nests of red wood ants (Formica rufa, RWA) and the distribution of tectonic faults. We randomly sampled two regions in western Denmark to map the spatial distribution of RWA nests...
2017: PeerJ
https://www.readbyqxmd.com/read/29038758/illegal-use-of-natural-resources-in-federal-protected-areas-of-the-brazilian-amazon
#17
Érico E Kauano, Jose M C Silva, Fernanda Michalski
BACKGROUND: The Brazilian Amazon is the world's largest rainforest regions and plays a key role in biodiversity conservation as well as climate adaptation and mitigation. The government has created a network of protected areas (PAs) to ensure long-term conservation of the region. However, despite the importance of and positive advances in the establishment of PAs, natural resource depletion in the Brazilian Amazon is pervasive. METHODS: We evaluated a total of 4,243 official law enforcement records generated between 2010 and 2015 to understand the geographical distribution of the illegal use of resources in federal PAs in the Brazilian Amazon...
2017: PeerJ
https://www.readbyqxmd.com/read/29038757/complete-mitochondrial-genome-sequences-of-the-northern-spotted-owl-strix-occidentalis-caurina-and-the-barred-owl-strix-varia-aves-strigiformes-strigidae-confirm-the-presence-of-a-duplicated-control-region
#18
Zachary R Hanna, James B Henderson, Anna B Sellas, Jérôme Fuchs, Rauri C K Bowie, John P Dumbacher
We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100-375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S...
2017: PeerJ
https://www.readbyqxmd.com/read/29038756/the-effects-of-familiarity-on-escape-responses-in-the-trinidadian-guppy-poecilia-reticulata
#19
Hayley L Wolcott, Alfredo F Ojanguren, Miguel Barbosa
Predation is the main cause of mortality during early life stages. The ability to avoid and evade potential threats is, therefore, favoured to evolve during the early stages of life. It is also during these early stages that the process of familiarization occurs. It has long been recognized that associating with familiar individuals confers antipredator benefits. Yet gaps in our knowledge remain about how predator evasion is affected by social experience during early stages. In this study, we test the hypothesis that familiarization acquired during early life stages improves escape responses...
2017: PeerJ
https://www.readbyqxmd.com/read/29038755/evidence-for-continual-hybridization-rather-than-hybrid-speciation-between-ligularia-duciformis-and-l-%C3%A2-paradoxa-asteraceae
#20
Rong Zhang, Xun Gong, Ryan Folk
BACKGROUND: Hybrids possess phenotypic traits that are often intermediate between their parental taxa, which commonly serves as evidence of hybridization in morphological analyses. Natural hybridization has been shown to occur frequently in Ligularia (Asteraceae). In a previous study, Ligularia ×maoniushanensis was demonstrated as a natural hybrid species between L. duciformis and L. paradoxa based on morphological and reproductive traits. METHODS: We used three chloroplast (cpDNA) fragments (psbA-trnH, trnL-rpl32 and trnQ-5'rps16), the nuclear ribosomal internal transcribed spacer (nrITS), and co-dominant SSR and dominant ISSR markers to study natural hybridization between L...
2017: PeerJ
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