bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular adaptation in the world's deepest‐living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas
Authors: Lan Yi , Sun Jin , Tian Renmao , Bartlett Douglas H. , Li Runsheng , Wong Yue Him , Zhang Weipeng , Qiu Jian‐Wen , Xu Ting , He Li‐Sheng , Tabata Harry G. , Qian Pei‐Yuan 
Published: April 2017

AbstractThe Challenger Deep in the Mariana Trench is the deepest point in the oceans of our planet. Understanding how animals adapt to this harsh environment characterized by high hydrostatic pressure, food limitation, dark and cold is of great scientific interest. Of the animals dwelling in the Challenger Deep, amphipods have been captured using baited traps. In this study, we sequenced the transcriptome of the amphipod Hirondellea gigas collected at a depth of 10,929 m from the East Pond of the Challenger Deep. Assembly of these sequences resulted in 133,041 contigs and 22,046 translated proteins. Functional annotation of these contigs was made using the go and kegg databases. Comparison of these translated proteins with those of four shallow‐water amphipods revealed 10,731 gene families, of which 5659 were single‐copy orthologs. Base substitution analysis on these single‐copy orthologs showed that 62 genes are positively selected in H. gigas, including genes related to β‐alanine biosynthesis, energy metabolism and genetic information processing. For multiple‐copy orthologous genes, gene family expansion analysis revealed that cold‐inducible proteins (i.e., transcription factors II A and transcription elongation factor 1) as well as zinc finger domains are expanded in H. gigas. Overall, our results indicate that genetic adaptation to the hadal environment by H. gigas may be mediated by both gene family expansion and amino acid substitutions of specific proteins.
Quantitative depth‐resolved microcirculation imaging with optical coherence tomography angiography (Part Ι): Blood flow velocity imaging
Authors: Gao Wanrong 
Published: April 2017

AbstractThe research goal of the microvascular network imaging withOCTangiography is to achieve depth‐resolved blood flow and vessel imaging in vivo in the clinical management of patents. In this review, we review the main phenomena that have been explored inOCTto image the blood flow velocity vector and the vessels of the microcirculation within living tissues. Parameters that limit the accurate measurements of blood flow velocity are then considered. Finally, initial clinical diagnosis applications and future developments of OCT flow images are discussed.
Assembly and activation of the Escherichia coli divisome
Authors: Du Shishen , Lutkenhaus Joe 
Published: April 2017

SummaryCell division in Escherichia coli is mediated by a large protein complex called the divisome. Most of the divisome proteins have been identified, but how they assemble onto the Z ring scaffold to form the divisome and work together to synthesize the septum is not well understood. In this review, we summarize the latest findings on divisome assembly and activation as well as provide our perspective on how these two processes might be regulated.
To CURe or not to CURe? Differential effects of the chaperone sorting factor Cur1 on yeast prions are mediated by the chaperone Sis1
Authors: Barbitoff Yury A. , Matveenko Andrew G. , Moskalenko Svetlana E. , Zemlyanko Olga M. , Newnam Gary P. , Patel Ayesha , Chernova Tatiana A. , Chernoff Yury O. , Zhouravleva Galina A. 
Published: April 2017

SummaryYeast self‐perpetuating protein aggregates (prions) provide a convenient model for studying various components of the cellular protein quality control system. Molecular chaperones and chaperone‐sorting factors, such as yeast Cur1 protein, play key role in proteostasis via tight control of partitioning and recycling of misfolded proteins. In this study, we show that, despite the previously described ability of Cur1 to antagonize the yeast prion [URE3], it enhances propagation and phenotypic manifestation of another prion, [PSI+]. We demonstrate that both curing of [URE3] and enhancement of [PSI+] in the presence of excess Cur1 are counteracted by the cochaperone Hsp40‐Sis1 in a dosage‐dependent manner, and show that the effect of Cur1 on prions parallels effects of the attachment of nuclear localization signal to Sis1, indicating that Cur1 acts on prions via its previously reported ability to relocalize Sis1 from the cytoplasm to nucleus. This shows that the direction in which Cur1 influences a prion depends on how this specific prion responds to relocalization of Sis1.
Globotriaosylsphingosine induces oxidative DNA damage in cultured kidney cells
Authors: Biancini Giovana Brondani , Morás Ana Moira , Reinhardt Luiza Steffens , Busatto Franciele Faccio , de Moura Sperotto Nathalia Denise , Saffi Jenifer , Moura Dinara Jaqueline , Giugliani Roberto , Vargas Carmen Regla 
Published: April 2017

AbstractFabry disease (FD) is a lysosomal disorder caused by mutations leading to a deficient activity α‐galactosidase A with progressive and systemic accumulation of its substrates. Substrates deposition is related to tissue damage in FD, but the underlying molecular mechanisms remain not completely understood. DNA damage has been associated with disease progression in chronic diseases and was recently described in high levels in Fabry patients. Once renal complications are major morbidity causes in FD, we investigated the effects of the latest biomarker for FD – globotriaosylsphingosine (lyso‐Gb3) in a cultured renal lineage – human embryonic kidney cells (HEK‐293 T) – on DNA damage. In concentrations found in Fabry patients, lyso‐Gb3 induced DNA damage (by alkaline comet assay) with oxidative origin in purines and pyrimidines (by comet assay with endonucleases). These data provide new information about a deleterious effect of lyso‐Gb3 and could be useful to studies looking for new therapeutic strategies to FD.
Parathyroid hormone targets in chronic kidney disease and managing severe hyperparathyroidism
Authors: Hawley Carmel M , Holt Stephen G 
Published: April 2017

AbstractAppropriate targets for parathyroid hormone (PTH) in patients with chronic kidney disease (CKD) stages 3–5D are controversial, as are the means by which these targets might be achieved. Secondary hyperparathyroidism is linked to symptoms like bone pain and itch, in addition to less clinically overt issues like bone fragility as well as vascular and soft tissue calcification which may lead to adverse hard endpoints, particularly fracture and death. Recognized therapies for managing a rising PTH include vitamin D analogues, with or without calcimimetic (where available), in addition to management of serum mineral concentrations with diet, binders and dialysis. Despite these interventions, many patients eventually develop refractory metabolic abnormalities of severe hyperparathyroidism (HPT). Treatment decisions in severe HPT in Australia previously centred around whether to perform parathyroidectomy or use calcimimetics in combination with calcitriol (or its analogues) with goals of symptom relief, fracture reduction and reducing vascular risk. The decision to remove Pharmaceutical Benefits Scheme reimbursement for the calcimimetic cinacalcet during 2015, means that parathyroidectomy has now become the only treatment likely to benefit most patients with severe HPT who are medically fit for operative intervention. Although improvements in care are apparent for patients with CKD, there remains an urgent need for basic science and large international trials to inform better ways to manage HPT.
The emerging role of maxillofacial radiology in the diagnosis and management of patients with complex periodontitis
Authors: Scarfe William C. , Azevedo Bruno , Pinheiro Lucas R. , Priaminiarti Menik , Sales Marcelo A. O. 
Published: April 2017

AbstractContemporary periodontal therapy has evolved to become more interdisciplinary and increasingly involves more complex treatments, including bone and soft‐tissue regenerative procedures. Therapeutic options require an imaging modality or combination of techniques that are capable of providing a diagnostic osseous baseline and facilitating quantification of smaller increments of bony change, both loss and additive, which are comparable over time. Intra‐oral and panoramic radiography are the modalities most commonly used to identify the location, quantify the amount and the pattern of alveolar bone loss and determine response to therapy. Cone‐beam computed tomography imaging offers specific advantages for periodontal diagnosis in that three‐dimensional images of dental and alveolar bone structures can be rendered with accuracy. Cone‐beam computed tomography has been shown to be clinically efficacious in demonstrating localized defects, such as furcation involvement and intrabony vertical and buccal/lingual defects, and in assessing the effects of regenerative therapy. In these situations, limited‐field‐of‐view, high‐resolution protocols are indicated.
Management of periodontal health in children: pediatric dentistry and periodontology interface
Authors: Drummond Bernadette K. , Brosnan Michael G. , Leichter Jonathan W. 
Published: April 2017

AbstractThe oral health of children and adolescents mirrors their general health. Because oral health care is often delivered in isolation from general health care, oral signs and symptoms do not always alert practitioners to their significance beyond the mouth. An important example of this is the association of a higher risk of dental caries and periodontal disease in children and adolescents with overweight, obesity and prediabetic conditions. Oral‐health practitioners need to consider the health conditions that their patients may have. This will aid in diagnosis and alert the practitioner to oral conditions that may not resolve without general health‐care intervention also. This paper reviews the more common oral conditions involving periodontal health in children and adolescents, and discusses the diagnosis of these conditions, potential associated health problems and the roles of pediatric dentistry and periodontology in the management of these conditions with the goal of children entering adulthood with healthy dentitions.
The nexus between periodontics and oral pathology
Authors: Rich Alison M. , Seo Benedict , Parachuru Venkata , Hussaini Haizal M. 
Published: April 2017

AbstractA wide variety of lesions may arise from the oral mucosa, fibrous connective tissue, bone and cementum of the periodontium. The commonest pathology occurs as a result of bacterial infection and is very well known to dentists and periodontists, but rarer conditions present as gingival pathology. The pathogenesis of these conditions ranges from genetic to traumatic to immunological to neoplastic, and includes benign, malignant and metastatic lesions. This paper outlines some of these conditions and describes how the periodontist and oral pathologist can work together using a framework, and how with careful consideration of the clinical features and the use of appropriate special tests, including obtaining an adequate tissue specimen, a timely and accurate diagnosis can be obtained.
Endotoxin testing of a wound debridement device containing medicinal Lucilia sericata larvae
Authors: Pickles Samantha F. , Pritchard David I. 
Published: April 2017

AbstractAlimentary products of medicinal Lucilia sericata larvae are studied to determine their mechanisms of action, particularly in the contexts of wound debridement and disinfection. Furthermore, the larvae can be applied to patients in contained medical devices (such as the BioBag; BioMonde). Here, we tested the materials and larval content of the most commonly used debridement device (the “BB‐50”) to explore the possibility that endotoxins may be contributing to the bio‐activity of the product, given that endotoxins are potent stimulants of cellular activation. Using standardised protocols to collect larval alimentary products (LAP), we proceeded to determine residual endotoxin levels in LAP derived from the device, before and after the neutralisation of interfering enzymatic activity. The debridement device and its associated larval content was not a significant source of lipopolysaccharide (LPS) activity. However, it is clear from these experiments that a failure to remove the confounding serine proteinase activity would have resulted in spuriously high and erroneous results. The residual LPS levels detected are unlikely to be active in wound healing assays, following cross‐referencing to publications where LPS at much higher levels has been shown to have positive and negative effects on processes associated with wound repair and tissue regeneration.
Genome Sequence of
Microbacterium
sp. Strain TPU 3598, a Lumichrome Producer
Authors: Yamamoto Kazunori , Asano Yasuhisa 
Published: April 2017

ABSTRACT

We report here the genome sequence of
Microbacterium
sp. strain TPU 3598, previously described as a producer of lumichrome. The sequenced genome size is 3,787,270 bp, the average G+C content is 68.39%, and 3,674 protein-coding sequences are predicted.
Genome Sequence of Canine Adenovirus Type 1 Isolated from a Wolf (
Canis lupus
) in Southern Italy
Authors: Pizzurro Federica , Marcacci Maurilia , Zaccaria Guendalina , Orsini Massimiliano , Cito Francesca , Rosamilia Alfonso , Di Renzo Ludovica , Malatesta Daniela , Di Sabatino Daria , Lorusso Alessio 
Published: April 2017

ABSTRACT

Canine adenovirus type 1 (CAdV-1), a DNA virus of the family
Adenoviridae
, causes infectious canine hepatitis, a highly contagious disease primarily affecting canids. In this report, we describe the isolation and whole-genome sequence of a CAdV-1 isolate from the liver of a free-ranging wolf (
Canis lupus
).
Draft Genome Sequence of a Chromium-Reducing Strain, Pseudomonas fluorescens S613, Isolated from a Chromium-Contaminated Aquifer in Los Alamos, New Mexico
Authors: Wang Dongping , Boukhalfa Hakim , Ware Doug S. , Daligault Hajnalka E. 
Published: April 2017

ABSTRACT

In this report, a chromium-reducing bacterium,
Pseudomonas fluorescens
strain S613, was isolated from a Cr(VI)-contaminated aquifer at Los Alamos, NM, and sequenced. The size of the draft genome sequence is approximately 6.7 Mb.
Complete Genome Sequence of the Original Escherichia coli Isolate, Strain NCTC86
Authors: Khetrapal Varnica , Mehershahi Kurosh S. , Chen Swaine L. 
Published: April 2017

ABSTRACT

Escherichia coli
is the most well-studied bacterium and a common colonizer of the lower mammalian gastrointestinal tract. We report here the complete genome sequence of the original
Escherichia coli
isolate, strain NCTC86, which was described by Theodor Escherich, for whom the genus is named.
Robot Software Platform for IoT-Based Context-Awareness
Authors: Cho Yongseong , Choi Jongsun , Choi Jaeyoung , Ryoo Young-Jae 
Published: April 2017

As Internet of Things (IoT)-based sensors have emerged recently, new technologies are being developed for users to provide suitable services by recognizing the surrounding situations. In the service robot sector, many researches are being carried out in order to exploit the collected data from IoT-based sensors. In addition, researches on robot middleware using context information are actively performed. In this paper, we propose a robot SW platform, which provides IoT-based context-aware services. This robot software platform consists of Ontology Agent, Robot Service Execution Engine, and Context Handler. The Ontology Agent is a module that searches information, such as sensor location, value type, etc., of the IoT devices stored in Ontology Repository and provides them to the Context Handler. The Context Handler reads IoT devices’ data and checks whether service transition conditions are met. If the conditions are satisfied, the data is delivered to the Robot Service Execution Engine, which is in charge of executing services. In experiments, we show a procedure executing the context-aware robot services through definition of robot services, a robot service execution engine, and a context handler, etc.
Statistical Algorithms and a Lower Bound for Detecting Planted Cliques
Authors: Feldman Vitaly , Grigorescu Elena , Reyzin Lev , Vempala Santosh S. , Xiao Ying 
Published: April 2017

We introduce a framework for proving lower bounds on computational problems over distributions against algorithms that can be implemented using access to astatistical queryoracle. For such algorithms, access to the input distribution is limited to obtaining an estimate of the expectation of any given function on a sample drawn randomly from the input distribution rather than directly accessing samples. Most natural algorithms of interest in theory and in practice, for example, moments-based methods, local search, standard iterative methods for convex optimization, MCMC, and simulated annealing, can be implemented in this framework. Our framework is based on, and generalizes, the statistical query model in learning theory [Kearns 1998].Our main application is a nearly optimal lower bound on the complexity ofanystatistical query algorithm for detecting planted bipartite clique distributions (or planted dense subgraph distributions) when the planted clique has sizeO(n1/2 − δ) for any constant δ > 0. The assumed hardness of variants of these problems has been used to prove hardness of several other problems and as a guarantee for security in cryptographic applications. Our lower bounds provide concrete evidence of hardness, thus supporting these assumptions.
Epithelial-to-Mesenchymal Transition Contributes to Immunosuppression in Breast Carcinomas
Authors: Dongre Anushka , Rashidian Mohammad , Reinhardt Ferenc , Bagnato Aaron , Keckesova Zuzana , Ploegh Hidde L. , Weinberg Robert A. 
Published: April 2017

AbstractThe epithelial-to-mesenchymal transition (EMT) is a cell biological program that confers mesenchymal traits on carcinoma cells and drives their metastatic dissemination. It is unclear, however, whether the activation of EMT in carcinoma cells can change their susceptibility to immune attack. We demonstrate here that mammary tumor cells arising from more epithelial carcinoma cell lines expressed high levels of MHC-I, low levels of PD-L1, and contained within their stroma CD8+ T cells and M1 (antitumor) macrophages. In contrast, tumors arising from more mesenchymal carcinoma cell lines exhibiting EMT markers expressed low levels of MHC-I, high levels of PD-L1, and contained within their stroma regulatory T cells, M2 (protumor) macrophages, and exhausted CD8+ T cells. Moreover, the more mesenchymal carcinoma cells within a tumor retained the ability to protect their more epithelial counterparts from immune attack. Finally, epithelial tumors were more susceptible to elimination by immunotherapy than corresponding mesenchymal tumors. Our results identify immune cells and immunomodulatory markers that can be potentially targeted to enhance the susceptibility of immunosuppressive tumors to various therapeutic regimens. Cancer Res; 77(15); 3982–9. ©2017 AACR.
Combination of Ibrutinib and ABT-199 in Diffuse Large B-Cell Lymphoma and Follicular Lymphoma
Authors: Kuo Hsu-Ping , Ezell Scott A. , Schweighofer Karl J. , Cheung Leo W.K. , Hsieh Sidney , Apatira Mutiah , Sirisawad Mint , Eckert Karl , Hsu Ssucheng J. , Chen Chun-Te , Beaupre Darrin M. , Versele Matthias , Chang Betty Y. 
Published: April 2017

Abstract
Diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma are the most prevalent B-lymphocyte neoplasms in which abnormal activation of the Bruton tyrosine kinase (BTK)–mediated B-cell receptor signaling pathway contributes to pathogenesis. Ibrutinib is an oral covalent BTK inhibitor that has shown some efficacy in both indications. To improve ibrutinib efficacy through combination therapy, we first investigated differential gene expression in parental and ibrutinib-resistant cell lines to better understand the mechanisms of resistance. Ibrutinib-resistant TMD8 cells had higher BCL2 gene expression and increased sensitivity to ABT-199, a BCL-2 inhibitor. Consistently, clinical samples from ABC-DLBCL patients who experienced poorer response to ibrutinib had higher BCL2 gene expression. We further demonstrated synergistic growth suppression by ibrutinib and ABT-199 in multiple ABC-DLBCL, GCB-DLBCL, and follicular lymphoma cell lines. The combination of both drugs also reduced colony formation, increased apoptosis, and inhibited tumor growth in a TMD8 xenograft model. A synergistic combination effect was also found in ibrutinib-resistant cells generated by either genetic mutation or drug treatment. Together, these findings suggest a potential clinical benefit from ibrutinib and ABT-199 combination therapy. Mol Cancer Ther; 16(7); 1246–56. ©2017 AACR.
A dádiva organizacional: dádiva à distância e circuitos de troca
Authors: Steiner Philippe 
Published: April 2017

Este artigo apresenta as características da dádiva organizacional: uma forma particular de doação na qual uma ou mais organizações colocam-se entre o doador e o donatário. Após uma caracterização dessa doação em comparação com a dádiva maussiana, o artigo examina três características da dádiva organizacional: o papel desempenhado pela organização que separa ao mesmo tempo que conecta; os “circuitos de comércio” pelos quais passam as dádivas organizacionais e, por fim, aquestão levantada pela dificuldade de reciprocar a dádiva na ausência de um contato direto entre doador e donatário. Por fim, o artigo sublinha a importância dessa dádiva para compreender a formação de uma solidariedade à distância entre os seres humanos.
Control without Controllers: Toward a Distributed Neuroscience of Executive Control
Authors: Eisenreich Benjamin R. , Akaishi Rei , Hayden Benjamin Y. 
Published: April 2017

AbstractExecutive control refers to the regulation of cognition and behavior by mental processes and is a hallmark of higher cognition. Most approaches to understanding its mechanisms begin with the assumption that our brains have anatomically segregated and functionally specialized control modules. The modular approach is intuitive: Control is conceptually distinct from basic mental processing, so an organization that reifies that distinction makes sense. An alternative approach sees executive control as self-organizing principles of a distributed organization. In distributed systems, control and controlled processes are colocalized within large numbers of dispersed computational agents. Control then is often an emergent consequence of simple rules governing the interaction between agents. Because these systems are unfamiliar and unintuitive, here we review several well-understood examples of distributed control systems, group living insects and social animals, and emphasize their parallels with neural systems. We then reexamine the cognitive neuroscience literature on executive control for evidence that its neural control systems may be distributed.