bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatocellular carcinomas with intracellular hyaline bodies have a poor prognosis
Authors: Aigelsreiter Ariane , Neumann Jens , Pichler Martin , Halasz Judith , Zatloukal Kurt , Berghold Andrea , Douschan Philipp , Rainer Florian , Stauber Rudolf , Haybaeck Johannes , Denk Helmut , Lackner Carolin 
Published: November 2016

AbstractBackground & AimsMallory‐Denk bodies (MDBs) and intracellular hyaline bodies (IHBs) are cytoplasmic inclusions found in a subset of hepatocellular carcinoma (HCC). MDBs are mainly composed of the intermediate filament proteins keratin (K) 8 and K18, the cellular stress‐ and adapter‐protein sequestosome 1/p62 (p62) and ubiquitin, whereas IHBs consist of p62 and/or ubiquitin. Of note, cytoplasmic inclusions containing p62 can serve as markers of suppressed autophagy, which in turn has been associated with poor prognosis. The aim of this study was to evaluate the prognostic significance of p62‐containing MDB and IHB in patients with HCC.MethodsNinety resected HCCs were assessed by H&E histology for MDB or IHB, and their presence was confirmed by immunohistochemistry using K8/18, p62 and ubiquitin antibodies. The prognostic impact of inclusions was assessed using Kaplan‐Meier and multivariate Cox proportional model.ResultsMallory‐Denk bodies and/or IHB were found in about 50% of HCC. Both types of inclusions were seen in 21%, MDB only in 19% and IHB only in 10% of cases. The presence of MDB in tumours was associated with the steatohepatitic variant of HCC, which also showed fatty change, ballooning of tumour cells, MDBs, inflammation and pericellular fibrosis (P<.001). In contrast, IHBs were not associated with steatohepatitic morphology but were associated with significantly shorter overall survival (P=.006). Multivariate analysis revealed macroscopic vascular invasion (P=.045) and presence of IHB in HCC cells (P=.005) as independently associated with overall survival.ConclusionsIntracellular hyaline bodies and macroscopic vascular invasion identify a subset of HCC patients with poor prognosis.
Evolution, genomics and epidemiology of Pseudomonas syringae
Authors: Baltrus David A. , McCann Honour C. , Guttman David S. 
Published: November 2016

SummaryA remarkable shift in our understanding of plant‐pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant–microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant–microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens.
Onychophoran‐like myoanatomy of the Cambrian gilled lobopodian Pambdelurion whittingtoni
Authors: Young Fletcher J. , Vinther Jakob 
Published: November 2016

AbstractArthropods are characterized by a rigid, articulating, exoskeleton operated by a lever‐like system of segmentally arranged, antagonistic muscles. This skeletomuscular system evolved from an unsegmented body wall musculature acting on a hydrostatic skeleton, similar to that of the arthropods’ close relatives, the soft‐bodied onychophorans. Unfortunately, fossil evidence documenting this transition is scarce. Exceptionally‐preserved panarthropods from the Cambrian Lagerstätte of Sirius Passet, Greenland, including the soft‐bodied stem‐arthropod Pambdelurion whittingtoni and the hard‐bodied arthropods Kiisortoqia soperi and Campanamuta mantonae, are unique in preserving extensive musculature. Here we show that Pambdelurion's myoanatomy conforms closely to that of extant onychophorans, with unsegmented dorsal, ventral and longitudinal muscle groups in the trunk, and extrinsic and intrinsic muscles controlling the legs. Pambdelurion also possesses oblique musculature, which has previously been interpreted as an arthropodan characteristic. However, this oblique musculature appears to be confined to the cephalic region and first few body segments, and does not represent a shift towards arthropodan myoanatomy. The Sirius Passet arthropods, Kiisortoqia and Campanamuta, also possess large longitudinal muscles in the trunk, although, unlike Pambdelurion, they are segmentally divided at the tergal boundaries. Thus, the transition towards an arthropodan myoanatomy from a lobopodian ancestor probably involved the division of the peripheral longitudinal muscle into segmented units.
5‐ALA‐mediated photodynamic therapy reduces the parasite load in mice infected with Leishmania braziliensis
Authors: Souza D. M. , Alves P. M. , Silva M. L. F. , Paulino T. P. , Coraspe H. O. , Mendonça M. M. S. , Ribeiro B. M. , da Silva M. V. , Rodrigues Júnior V. , Rodrigues D. B. R. 
Published: November 2016

SummaryPhotodynamic therapy (PDT) has proven to be an effective alternative for the treatment of cutaneous leishmaniasis. Skin lesions consist of ulcers with well‐defined raised edges, and granular floor. Th1 immune response is the protective profile in patients infected with Leishmania. In this study, the photodynamic therapy with 5‐aminolevulinic acid, the parasitic load, and the modulation of the immune response was evaluated in mice infected with Leishmania braziliensis. Balb/c mice were infected with L. braziliensis and subsequently treated with three sections of PDT. The parasite load and mRNA expression of cytokines (IFN‐γ, IL‐4, IL‐17, IL‐22, IL‐27, IL‐10) and transcription factors (GATA‐3, Foxp3 and T‐bet) were analysed by quantitative PCR. The parasite load in the treated group was significantly lower than in the untreated group (P<.0001); in PDT treated animals, we observed an increase in IFN‐γ and T‐bet mRNA (P=.012 and P=.0071). There was a significant reduction in mRNA expression of IL‐22 associated with an increased expression of IL‐27 mRNA in the animals treated with light only (P=.0001). 5‐ALA associated with photodynamic therapy promotes a reduction in parasite load and an increased expression of IFN‐γ and T‐bet mRNA.
Identification of lactoferrin and glutamate receptor‐interacting protein 1 in bovine cervical mucus: A putative marker for oestrous detection
Authors: Lee WY , Park MH , Kim KW , Song H , Kim KB , Lee CS , Kim NK , Park JK , Yang BC , Oh KB , Im GS , Chung HJ 
Published: November 2016

ContentsAccurate detection of oestrus is important for artificial insemination. The aim of this study was to identify oestrous‐specific bovine cervical mucus proteins that could be used to determine the optimal time for artificial insemination. Non‐oestrous and controlled internal drug release (CIDR)‐induced oestrous‐stage mucus proteins were purified and subjected to surface‐enhanced laser desorption/ionization time‐of‐flight mass spectrometry, sodium dodecyl sulphate polyacrylamide gel electrophoresis and MALDI‐TOF/TOF. Among differentially expressed proteins, lactoferrin (LF) and glutamate receptor‐interacting protein 1 (GRIP1) showed a twofold increase during the CIDR‐induced oestrous stage compared to the levels in non‐oestrous stage in bovine cervical mucus. The RT‐PCR, Western blotting and immunohistochemistry results showed that LF and GRIP1 expression was significantly increased during the oestrous stage in the uterus. This study demonstrated that bovine LF and GRIP1 exist during the oestrous stage, but not during the non‐oestrous stage, suggesting that cervical mucus LF and GRIP1 are useful oestrous detection markers in cattle.
Pathophysiology of dyspnoea in acute pulmonary embolism: A cross‐sectional evaluation
Authors: Sanchez Olivier , Caumont‐Prim Aurore , Riant Elisabeth , Plantier Laurent , Dres Martin , Louis Bruno , Collignon Marie‐Anne , Diebold Benoit , Meyer Guy , Peiffer Claudine , Delclaux Christophe 
Published: November 2016

ABSTRACT
Background and objectiveDyspnoea in pulmonary embolism (PE) remains poorly characterized. Little is known about how to measure intensity or about the underlying mechanisms that may be related to ventilatory abnormalities, alveolar dead space ventilation or modulating factors such as psychological modulate. We hypothesized that dyspnoea would mainly be associated with pulmonary vascular obstruction and its pathophysiological consequences, while the sensory‐affective domain of dyspnoea would be influenced by other factors.MethodsWe undertook a prospective study of 90 consecutive non‐obese patients (mean ± SD age: 49 ± 16 years, 41 women) without cardiorespiratory disease. All patients were hospitalized with symptoms for <15 days and a confirmed PE (multi‐detector computed tomography (MDCT) scan, n = 87 and high‐probability ventilation/perfusion scan, n = 3). Patients underwent assessment of dyspnoea using the Borg score, modified Medical Research Council (mMRC) scale, assessment of psychological trait, state of anxiety and depression and chest pain via the Visual Analogical Scale at the time of maximum dyspnoea. Functional evaluations such as the quantitative ventilation–perfusion lung scan, echocardiography, alveolar dead space fraction and tidal ventilation measurements were completed within 48 h of admission.ResultsMultivariate analyses demonstrated that dyspnoea was mainly linked to pulmonary vascular obstruction and/or its consequences such as raised pulmonary arterial pressure and chest pain. The sensory‐affective domain of dyspnoea showed additional determinants such as age, depression and breathing variability.ConclusionDyspnoea is mainly related to vascular consequences of PE such as increased pulmonary arterial pressure or chest pain. The sensory‐affective domain of dyspnoea also correlates with age, depression and breathing variability.
A new tool to quantify the geometrical characteristics of facial skin pores. Changes with age and a making‐up procedure in Caucasian women
Authors: Shaiek A. , Flament F. , François G. , Lefebvre‐Descamps V. , Barla C. , Vicic M. , Giron F. , Bazin R. 
Published: November 2016

BackgroundFacial skin pores (FSP) are common and benign signs that generate frequent esthetic concerns or complaints. Despite their worldwide prevalence, related literature remains scarce. Hence, a new device has been developed and applied to validating studies, aiming at best describing FSP as they are self‐perceived, i.e. their anatomic features, their possible alterations with age and their appearance after application of a make‐up product.MethodsDermascore+® is an imaging device dedicated to a direct observation and acquisition of various characteristics of the skin surface. Images are captured under a high magnification and under different lighting configurations, to highlight the skin relief, based upon parallel polarized images. Dedicated software allows FSP to being detected and their morphological parameters to being extracted and computed. By measuring each detected FSP in a given region of interest, a statistically significant impact of both age and an applied cosmetic product upon their morphological features can be observed and quantified.ResultsAlthough the size and density of FSP are not affected by aging, their shape becomes elongated. A few tested make up products show variable effects that closely correlate with visual assessments made by trained estheticians.ConclusionThe shape of FSP present on cheeks shows age‐related changes, toward a more elongated aspect, likely linked to a progressively altered (more isotropic) skin surface micro‐relief. The new tool Dermascore+® allows foundations to being rapidly differentiated and screened according to their variable effects upon the visual appearance through instrumental, objective depiction of FSP.
Enhancing pedotransfer functions with environmental data for estimating bulk density and effective cation exchange capacity in a data‐sparse situation
Authors: Akpa S. I. C. , Ugbaje S. U. , Bishop T. F. A. , Odeh I. O. A. 
Published: November 2016

AbstractSoil bulk density (BD) and effective cation exchange capacity (ECEC) are among the most important soil properties required for crop growth and environmental management. This study aimed to explore the combination of soil and environmental data in developing pedotransfer functions (PTFs) for BD and ECEC. Multiple linear regression (MLR) and random forest model (RFM) were employed in developing PTFs using three different data sets: soil data (PTF‐1), environmental data (PTF‐2) and the combination of soil and environmental data (PTF‐3). In developing the PTFs, three depth increments were also considered: all depth, topsoil (<0.40 m) and subsoil (>0.40 m). Results showed that PTF‐3 (R2; 0.29–0.69) outperformed both PTF‐1 (R2; 0.11–0.18) and PTF‐2 (R2; 0.22–0.59) in BD estimation. However, for ECEC estimation, PTF‐3 (R2; 0.61–0.86) performed comparably as PTF‐1 (R2; 0.58–0.76) with both PTFs out‐performing PTF‐2 (R2; 0.30–0.71). Also, grouping of data into different soil depth increments improves the estimation of BD with PTFs (especially PTF‐2 and PTF‐3) performing better at subsoils than topsoils. Generally, the most important predictors of BD are sand, silt, elevation, rainfall, temperature for estimation at topsoil while EVI, elevation, temperature and clay are the most important BD predictors in the subsoil. Also, clay, sand, pH, rainfall and SOC are the most important predictors of ECEC in the topsoil while pH, sand, clay, temperature and rainfall are the most important predictors of ECEC in the subsoil. Findings are important for overcoming the challenges of building national soil databases for large‐scale modelling in most data‐sparse countries, especially in the sub‐Saharan Africa (SSA).
Comprehending 3D Diagrams: Sketching to Support Spatial Reasoning
Authors: Gagnier Kristin M. , Atit Kinnari , Ormand Carol J. , Shipley Thomas F. 
Published: November 2016

AbstractScience, technology, engineering, and mathematics (STEM) disciplines commonly illustrate 3D relationships in diagrams, yet these are often challenging for students. Failing to understand diagrams can hinder success in STEM because scientific practice requires understanding and creating diagrammatic representations. We explore a new approach to improving student understanding of diagrams that convey 3D relations that is based on students generating their own predictive diagrams. Participants’ comprehension of 3D spatial diagrams was measured in a pre‐ and post‐design where students selected the correct 2D slice through 3D geologic block diagrams. Generating sketches that predicated the internal structure of a model led to greater improvement in diagram understanding than visualizing the interior of the model without sketching, or sketching the model without attempting to predict unseen spatial relations. In addition, we found a positive correlation between sketched diagram accuracy and improvement on the diagram comprehension measure. Results suggest that generating a predictive diagram facilitates students’ abilities to make inferences about spatial relationships in diagrams. Implications for use of sketching in supporting STEM learning are discussed.
Analysis of Germination Capacity and Germinant Receptor (Sub)clusters of Genome-Sequenced Bacillus cereus Environmental Isolates and Model Strains
Authors: Warda Alicja K. , Xiao Yinghua , Boekhorst Jos , Wells-Bennik Marjon H. J. , Nierop Groot Masja N. , Abee Tjakko 
Published: November 2016

ABSTRACT

Spore germination of 17
Bacillus cereus
food isolates and reference strains was evaluated using flow cytometry analysis in combination with fluorescent staining at a single-spore level. This approach allowed for rapid collection of germination data under more than 20 conditions, including heat activation of spores, germination in complex media (brain heart infusion [BHI] and tryptone soy broth [TSB]), and exposure to saturating concentrations of single amino acids and the combination of alanine and inosine. Whole-genome sequence comparison revealed a total of 11 clusters of operons encoding germinant receptors (GRs): GerK, GerI, and GerL were present in all strains, whereas GerR, GerS, GerG, GerQ, GerX, GerF, GerW, and GerZ (sub)clusters showed a more diverse presence/absence in different strains. The spores of tested strains displayed high diversity with regard to their sensitivity and responsiveness to selected germinants and heat activation. The two laboratory strains,
B. cereus
ATCC 14579 and ATCC 10987, and 11 food isolates showed a good germination response under a range of conditions, whereas four other strains (
B. cereus
B4085, B4086, B4116, and B4153) belonging to phylogenetic group IIIA showed a very weak germination response even in BHI and TSB media. Germination responses could not be linked to specific (combinations of) GRs, but it was noted that the four group IIIA strains contained pseudogenes or variants of subunit C in their
gerL
cluster. Additionally, two of those strains (B4086 and B4153) carried pseudogenes in the
gerK
and
gerR
I
(sub)clusters that possibly affected the functionality of these GRs.

IMPORTANCE
Germination of bacterial spores is a critical step before vegetative growth can resume. Food products may contain nutrient germinants that trigger germination and outgrowth of
Bacillus
species spores, possibly leading to food spoilage or foodborne illness. Prediction of spore germination behavior is, however, very challenging, especially for spores of natural isolates that tend to show more diverse germination responses than laboratory strains. The approach used has provided information on the genetic diversity in GRs and corresponding subclusters encoded by
B. cereus
strains, as well as their germination behavior and possible associations with GRs, and it provides a basis for further extension of knowledge on the role of GRs in
B. cereus
(group member) ecology and transmission to the host.
First Report on the Draft Genome Sequences of Corynebacterium diphtheriae Isolates from India
Authors: Veeraraghavan Balaji , Anandan Shalini , Rajamani Sekar Suresh Kumar , Gopi Radha , Devanga Ragupathi Naveen Kumar , Ramesh Srilekha , Verghese Valsan Philip , Korulla Sophy , Mathai Sarah , Sangal Lucky , Joshi Sudhir 
Published: November 2016

ABSTRACT

We report here the draft genome sequences of five
Corynebacterium diphtheriae
isolates of Indian origin. The
C. diphtheriae
isolates TH1141, TH510, TH1526, TH1337, and TH2031 belong to sequence type ST-50, ST-295, ST-377, ST-405, and ST-405, with an average genome size of 2.5 Mbp.
Alternative Polyadenylation of Human Bocavirus at Its 3′ End Is Regulated by Multiple Elements and Affects Capsid Expression
Authors: Hao Sujuan , Zhang Junmei , Chen Zhen , Xu Huanzhou , Wang Hanzhong , Guan Wuxiang 
Published: November 2016

ABSTRACT

Alternative processing of human bocavirus (HBoV) P5 promoter-transcribed RNA is critical for generating the structural and nonstructural protein-encoding mRNA transcripts. The regulatory mechanism by which HBoV RNA transcripts are polyadenylated at proximal [(pA)p] or distal [(pA)d] polyadenylation sites is still unclear. We constructed a recombinant HBoV infectious clone to study the alternative polyadenylation regulation of HBoV. Surprisingly, in addition to the reported distal polyadenylation site, (pA)d, a novel distal polyadenylation site, (pA)d2, which is located in the right-end hairpin (REH), was identified during infectious clone transfection or recombinant virus infection. (pA)d2 does not contain typical hexanucleotide polyadenylation signal, upstream elements (USE), or downstream elements (DSE) according to sequence analysis. Further study showed that HBoV nonstructural protein NS1, REH, and
cis
elements of (pA)d were necessary and sufficient for efficient polyadenylation at (pA)d2. The distance and sequences between (pA)d and (pA)d2 also played a key role in the regulation of polyadenylation at (pA)d2. Finally, we demonstrated that efficient polyadenylation at (pA)d2 resulted in increased HBoV capsid mRNA transcripts and protein translation. Thus, our study revealed that all the bocaviruses have distal poly(A) signals on the right-end palindromic terminus, and alternative polyadenylation at the HBoV 3′ end regulates its capsid expression.

IMPORTANCE
The distal polyadenylation site, (pA)d, of HBoV is located about 400 nucleotides (nt) from the right-end palindromic terminus, which is different from those of bovine parvovirus (BPV) and canine minute virus (MVC) in the same genus whose distal polyadenylation is located in the right-end stem-loop structure. A novel polyadenylation site, (pA)d2, was identified in the right-end hairpin of HBoV during infectious clone transfection or recombinant virus infection. Sequence analysis showed that (pA)d2 does not contain typical polyadenylation signals, and the last 42 nt form a stem-loop structure which is almost identical to that of MVC. Further study showed that NS1, REH, and
cis
elements of (pA)d are required for efficient polyadenylation at (pA)d2. Polyadenylation at (pA)d2 enhances capsid expression. Our study demonstrates alternative polyadenylation at the 3′ end of HBoV and suggests an additional mechanism by which capsid expression is regulated.
Associations of occupational standing with musculoskeletal symptoms: a systematic review with meta-analysis
Authors: Coenen Pieter , Willenberg Lisa , Parry Sharon , Shi Joyce W , Romero Lorena , Blackwood Diana M , Maher Christopher G , Healy Genevieve N , Dunstan David W , Straker Leon M 
Published: November 2016

ObjectiveGiven the high exposure to occupational standing in specific occupations, and recent initiatives to encourage intermittent standing among white-collar workers, a better understanding of the potential health consequences of occupational standing is required. We aimed to review and quantify the epidemiological evidence on associations of occupational standing with musculoskeletal symptoms.DesignA systematic review was performed. Data from included articles were extracted and described, and meta-analyses conducted when data were sufficiently homogeneous.Data sourcesElectronic databases were systematically searched.Eligibility criteriaPeer-reviewed articles on occupational standing and musculoskeletal symptoms from epidemiological studies were identified.ResultsOf the 11 750 articles screened, 50 articles reporting 49 studies were included (45 cross-sectional and 5 longitudinal; n=88 158 participants) describing the associations of occupational standing with musculoskeletal symptoms, including low-back (39 articles), lower extremity (14 articles) and upper extremity (18 articles) symptoms. In the meta-analysis, ‘substantial’ (>4 hours/workday) occupational standing was associated with the occurrence of low-back symptoms (pooled OR (95% CI) 1.31 (1.10 to 1.56)). Evidence on lower and upper extremity symptoms was too heterogeneous for meta-analyses. The majority of included studies reported statistically significant detrimental associations of occupational standing with lower extremity, but not with upper extremity symptoms.ConclusionsThe evidence suggests that substantial occupational standing is associated with the occurrence of low-back and (inconclusively) lower extremity symptoms, but there may not be such an association with upper extremity symptoms. However, these conclusions are tentative as only limited evidence was found from high-quality, longitudinal studies with fully adjusted models using objective measures of standing.