bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of different drug classes on transient sciatic nerve injury–depressed marble burying in mice
Authors: Wilkerson Jenny L. , Curry Zachary A. , Kinlow Pamela D. , Mason Brittany L. , Hsu Ku-Lung , van der Stelt Mario , Cravatt Benjamin F. , Lichtman Aron H. 
Published: March 2018

Abstract
A great need exists for the identification of new effective analgesics to treat sustained pain. However, most preclinical nociceptive assays measure behavioral responses evoked by noxious stimuli (ie, pain-stimulated behavior), which presents a challenge to distinguish between motor impairing and antinociceptive effects of drugs. Here, we demonstrate that chronic constriction injury (CCI) of the sciatic nerve elicits common pain-stimulated responses (ie, mechanical allodynia and thermal hyperalgesia) as well as reduces marble burying/digging behaviors that occur during the early stages of the neuropathy and resolve within 1 week. Although drugs representing distinct classes of analgesics (ie, morphine, valdecoxib, and gabapentin) reversed both CCI-induced and CCI-depressed nociceptive measures, diazepam lacked antinociceptive effects in all assays and the kappa-opioid receptor agonist U69593 reversed pain-stimulated, but not pain-depressed behaviors. In addition, we tested drugs targeting distinct components of the endocannabinoid system, including agonists at cannabinoid receptors type 1 (CB1) and type 2 (CB2), as well as inhibitors of the endocannabinoid-regulating enzymes fatty acid amide hydrolase and monoacylglycerol lipase. Each of these drugs reversed all CCI-induced nociceptive measures, with the exception of the fatty acid amide hydrolase inhibitor that reversed pain-stimulated behaviors, only. These findings support the use of the mouse marble-burying assay as a model of pain-depressed behavior within the first week of sciatic nerve injury to examine candidate analgesics. These data also support existing preclinical research that cannabinoid receptor agonists and inhibitors of endocannabinoid-regulating enzymes merit consideration for the treatment of pain.
The Dutch Pancreas Biobank Within the Parelsnoer Institute
Authors: Strijker Marin , Gerritsen Arja , van Hilst Jony , Bijlsma Maarten F. , Bonsing Bert A. , Brosens Lodewijk A. , Bruno Marco J. , van Dam Ronald M. , Dijk Frederike , van Eijck Casper H. , Farina Sarasqueta Arantza , Fockens Paul , Gerhards Michael F. , Groot Koerkamp Bas , van der Harst Erwin , de Hingh Ignace H. , van Hooft Jeanin E. , Huysentruyt Clément J. , Kazemier Geert , Klaase Joost M. , van Laarhoven Cornelis J. , van Laarhoven Hanneke W. , Liem Mike S. , de Meijer Vincent E. , van Rijssen L. Bengt , van Santvoort Hjalmar C. , Suker Mustafa , Verhagen Judith H. , Verheij Joanne , Verspaget Hein W. , Wennink Roos A. , Wilmink Johanna W. , Molenaar I. Quintus , Boermeester Marja A. , Busch Olivier R. , Besselink Marc G. 
Published: March 2018

Objectives
Large biobanks with uniform collection of biomaterials and associated clinical data are essential for translational research. The Netherlands has traditionally been well organized in multicenter clinical research on pancreatic diseases, including the nationwide multidisciplinary Dutch Pancreatic Cancer Group and Dutch Pancreatitis Study Group. To enable high-quality translational research on pancreatic and periampullary diseases, these groups established the Dutch Pancreas Biobank.

Methods
The Dutch Pancreas Biobank is part of the Parelsnoer Institute and involves all 8 Dutch university medical centers and 5 nonacademic hospitals. Adult patients undergoing pancreatic surgery (all indications) are eligible for inclusion. Preoperative blood samples, tumor tissue from resected specimens, pancreatic cyst fluid, and follow-up blood samples are collected. Clinical parameters are collected in conjunction with the mandatory Dutch Pancreatic Cancer Audit.

Results
Between January 2015 and May 2017, 488 patients were included in the first 5 participating centers: 4 university medical centers and 1 nonacademic hospital. Over 2500 samples were collected: 1308 preoperative blood samples, 864 tissue samples, and 366 follow-up blood samples.

Conclusions
Prospective collection of biomaterials and associated clinical data has started in the Dutch Pancreas Biobank. Subsequent translational research will aim to improve treatment decisions based on disease characteristics.
Enhancing Placebo Effects in Somatic Symptoms Through Oxytocin
Authors: Skvortsova Aleksandrina , Veldhuijzen Dieuwke S. , Van Middendorp Henriët , Van den Bergh Omer , Evers Andrea W.M. 
Published: March 2018

ABSTRACT

Objective
Placebo effects relieve various somatic symptoms, but it is unclear how they can be enhanced to maximize positive treatment outcomes. Oxytocin administration may potentially enhance placebo effects, but few studies have been performed, and they have had conflicting findings. The study aim was to investigate the influence of positive verbal suggestions and oxytocin on treatment expectations and placebo effects for pain and itch.

Methods
One hundred eight female participants were allocated to one of the following four groups: (1) oxytocin with positive verbal suggestions, (2) placebo with positive verbal suggestions, (3) oxytocin without suggestions, and (4) placebo without suggestions. The administration of 24 IU oxytocin or a placebo spray was preceded by positive verbal suggestions regarding the pain- and itch-relieving properties of the spray or no suggestions, depending on group allocation. Pain was assessed with a cold pressor test, and itch was assessed with histamine iontophoresis.

Results
Positive verbal suggestions induced expectations of lower pain (F = 4.77, p = .031) and itch (F = 5.38, p = .022). Moreover, positive verbal suggestions elicited placebo analgesia (F = 5.48, p = .021) but did not decrease itch. No effect of oxytocin on the placebo effect or on expectations was found.

Conclusions
Positive suggestions induced placebo analgesia but oxytocin did not enhance the placebo effect. Study limitations are that we only included a female sample and a failure to induce placebo effect for itch. Future studies should focus on how oxytocin might influence placebo effects, taken into account the role of sex, dose-dependent effects, and various expectation manipulations.

Trial registration: The study was registered as a clinical trial on www.trialregister.nl (number 6376).
Polymethyl Methacrylate Custom-Made Prosthesis: A Novel Three-Dimension Printing-Aided Fabrication Technique for Cranial and/or Orbital Reconstruction
Authors: Martinez-Seijas Pedro , Díaz-Galvis Luis A. , Hernando Josué , Leizaola-Cardesa Ignacio O. , Aguilar-Salvatierra Antonio , Gómez-Moreno Gerardo 
Published: March 2018

Background:
Over the years, many materials have been used in orbital reconstruction and cranioplasty. Among the materials in current use, polymethyl methacrylate (PMMA) offers a high degree of compatibility with human tissue.

Objective:
This work describes a new, custom-made, 3D printing-aided, prosthetic fabrication process for orbital and/or cranial reconstruction using PMMA.

Methods:
On the basis of information obtained from computerized tomography scanning processed in Digital Imaging and Communication in Medicine format and exported to treatment planning software, a 3D prosthesis master model was designed and digitally printed. This was then used to create an injection mold from which the prosthesis was cast in PMMA and implanted in the patient. Five patients with cranial and/or orbital defects of tumoral or traumatic etiology were treated by this method. After 5 to 7 years follow-up, no complications occurred to cause the removal of the prostheses.

Conclusion:
This novel method makes it possible to produce customized PMMA prostheses to treat orbital and/or cranial defects that are cost-effective and individualized to each case.
When and How to Perform Cultures on Chronic Wounds?
Authors: Stallard Yvonne 
Published: March 2018

PURPOSE:
The purpose of this Evidence-Based Report Card was to examine current best evidence related to when and how to perform cultures on chronic wounds to guide clinicians in determining the appropriate treatment.

QUESTION:
(1) When should cultures be performed on chronic wounds? and (2) What is the best method or technique to perform a culture on a chronic wound?

SEARCH STRATEGY:
A search of the literature was performed, resulting in 45 publications relevant to the topic. Following a review of titles and abstracts, 7 studies were identified that met inclusion criteria. Key search terms used were “chronic wound,” “chronic infected wound,” “wound culture,” “specimen collection,” and “wound swab.” Strength of the evidence was rated based on the methodology from Essential Evidence Plus: Levels of Evidence and Oxford Center for Evidence-Based Medicine, adapted by Gray and colleagues.

FINDINGS:
Seven studies were identified as pertinent to the topic on wound culture and meeting inclusion criteria. The study designs included 1 randomized controlled trial, 1 quasi-experimental comparative study, 1 systematic review, 1 scoping literature review, 1 integrative literature review, and 2 professional organization expert panel reviews (consensus statement and position statement). Of the 7 studies, 3 studies suggest that classic signs of infection may not always be present but culturing may be indicated when additional signs such as pain, necrotic tissue, prolonged or delayed healing, and wound bed deterioration occur. Four studies report that a quantitative culture of wound tissue is the gold standard to obtain a wound culture, but the swab method is an acceptable alternative option. Two articles demonstrate the Levine technique is more reliable than the Z-technique to determine microbial load in the wound bed. The strength of the evidence was identified as 2 level A studies, 1 level B study, and 4 level C studies. Using Johns Hopkins methodology, the quality of the studies was deemed either high quality or good quality.

CONCLUSION/RECOMMENDATION:
Evidence indicates that identification of potential chronic wound infection should be considered early using clinical signs such as pain, necrotic tissue, delayed healing, and wound deterioration (in addition to classic signs of infection) to determine the need for collecting a culture (Strength of Recommendation Taxonomy [SORT] level 2); and when a culture is deemed necessary, swab culture using the Levine method is a clinically practical alternative if performed correctly (SORT level 1).
Experimentally Induced Metamorphosis in Axolotl (Ambystoma mexicanum) Under Constant Diet Restructures Microbiota Accompanied by Reduced Limb Regenerative Capacity
Authors: Demircan Turan , Ovezmyradov Guvanch , Yıldırım Berna , Keskin İlknur , İlhan Ayse Elif , Fesçioğlu Ece Cana , Öztürk Gürkan , Yıldırım Süleyman 
Published: March 2018

AbstractAxolotl (Ambystoma mexicanum) is a critically endangered salamander species and a model organism for regenerative and developmental biology. Despite life-long neoteny in nature and in captive-bred colonies, metamorphosis of these animals can be experimentally induced by administering Thyroid hormones (THs). However, biological consequences of this experimental procedure, such as host microbiota response and implications for regenerative capacity, remain largely unknown. Here, we systematically compared host bacterial microbiota associated with skin, stomach, gut tissues and fecal samples based on 16S rRNA gene sequences, along with limb regenerative capacity, between neotenic and metamorphic Axolotls. Our results show that distinct bacterial communities inhabit individual organs of Axolotl and undergo substantial restructuring through metamorphosis. Drastic restructuring was observed for skin microbiota, highlighted by a major transition from Firmicutes-enriched to Proteobacteria-enriched relative abundance and precipitously decreased diversity. Remarkably, shifts in microbiota was accompanied by a steep reduction in limb regenerative capacity. Fecal microbiota of neotenic and metamorphic Axolotl shared relatively higher similarity, suggesting that diet continues to shape microbiota despite fundamental transformations in the host digestive organs. The results provide novel insights into microbiological and regenerative aspects of Axolotl metamorphosis and will establish a baseline for future in-depth studies.
The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis
Authors: Melamed Anat , Yaguchi Hiroko , Miura Michi , Witkover Aviva , Fitzgerald Tomas W , Birney Ewan , Bangham Charles R M 
Published: March 2018

AbstractChromatin looping controls gene expression by regulating promoter-enhancer contacts, the spread of epigenetic modifications, and the segregation of the genome into transcriptionally active and inactive compartments. We studied the impact on the structure and expression of host chromatin by the human retrovirus HTLV-1. We show that HTLV-1 disrupts host chromatin structure by forming loops between the provirus and the host genome; certain loops depend on the critical chromatin architectural protein CTCF, which we recently showed binds to the HTLV-1 provirus. Finally, we show that the provirus causes two distinct patterns of abnormal transcription of the host genome in cis: bidirectional transcription in the host genome immediately flanking the provirus, and clone-specific transcription in cis at non-contiguous loci up to >300 kb from the integration site. We conclude that HTLV-1 causes insertional mutagenesis up to the megabase range in the host genome in >104 persistently-maintained HTLV-1+ T-cell clones in vivo.
Integrin β1 optimizes diabetogenic T cell migration and function in the pancreas
Authors: Espinosa-Carrasco Gabriel , Saout Cécile Le , Fontanaud Pierre , Michau Aurélien , Mollard Patrice , Hernandez Javier , Schaeffer Marie 
Published: March 2018

AbstractT cell search behavior is dictated by their need to encounter their specific antigen to eliminate target cells. However, mechanisms controlling effector T cell motility are highly tissue-dependent. Specifically, how diabetogenic T cells encounter their target beta cells in dispersed islets throughout the pancreas during autoimmune diabetes remains unclear. Using intra-vital 2-photon microscopy in a mouse model of diabetes, we found that CXCR3 chemokine downregulated CD8+ T cell motility specifically within islets, promoting effector cell confinement to their target sites. In contrast, T cell velocity and directionality in the exocrine tissue were enhanced along blood vessels and extra-cellular matrix fibers. This guided migration implicated integrin-dependent interactions, since integrin blockade impaired exocrine T cell motility. In addition, integrin β1 blockade decreased CD4+ T cell effector phenotype specifically in the pancreas. Thus, we unveil an important role for integrins in the pancreas during autoimmune diabetes that may have important implications for the design of new therapies.
American Gut: an Open Platform for Citizen-Science Microbiome Research
Authors: McDonalda Daniel , Hyde Embriette , Debelius Justine W. , Morton James T. , Gonzalez Antonio , Ackermann Gail , Aksenov Alexander A. , Behsaz Bahar , Brennan Caitriona , Chen Yingfeng , Goldasich Lindsay DeRight , Dorrestein Pieter C. , Dunn Robert R. , Fahimipour Ashkaan K. , Gaffney James , Gilbert Jack A , Gogul Grant , Green Jessica L. , Hugenholtz Philip , Humphrey Greg , Huttenhower Curtis , Jackson Matthew A. , Janssen Stefan , Jeste Dilip V. , Jiang Lingjing , Kelley Scott T. , Knights Dan , Kosciolek Tomasz , Ladau Joshua , Leach Jeff , Marotz Clarisse , Meleshko Dmitry , Melnik Alexey V. , Metcalf Jessica L. , Mohimani Hosein , Montassier Emmanuel , Navas-Molina Jose , Nguyen Tanya T. , Peddada Shyamal , Pevzner Pavel , Pollard Katherine S. , Rahnavard Gholamali , Robbins-Pianka Adam , Sangwan Naseer , Shorenstein Joshua , Smarr Larry , Song Se Jin , Spector Timothy , Swafford Austin D. , Thackray Varykina G. , Thompson Luke R. , Tripathi Anupriya , Vazquez-Baeza Yoshiki , Vrbanac Alison , Wischmeyer Paul , Wolfe Elaine , Zhu Qiyun ,   The American Gut Consortium, Knight Rob 
Published: March 2018

AbstractAlthough much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the USA, UK, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes as compared to environmental samples, demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations, uncover new molecules and kinds of molecular communities in the human stool metabolome, and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness, and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education.ImportanceWe show that a citizen-science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n=1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet which we confirm with untargeted metabolomics on hundreds of samples.
EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution
Authors: del Campo Javier , Kolisko Martin , Boscaro Vittorio , Santoferrara Luciana F. , Massana Ramon , Guillou Laure , Simpson Alastair , Berney Cedric , de Vargas Colomban , Brown Matt , Keeling Patrick , Parfrey Laura Wegener 
Published: March 2018

AbstractEnvironmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors, and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is a community driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the complete eukaryotic tree of life and microbial ecologists that actively use environmental sequencing data for the purpose of developing reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so.
Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula
Authors: Lehmann Robert , Lightfoot Damien J. , Schunter Celia , Michell Craig T. , Ohyanagi Hajime , Mineta Katsuhiko , Foret Sylvain , Berumen Michael L. , Miller David J. , Aranda Manuel , Gojobori Takashi , Munday Philip L. , Ravasi Timothy 
Published: March 2018

AbstractThe iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that anti-predator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.
Trends in female lifespan in South Korea, 1987–2016
Authors: Weon Byung Mook 
Published: March 2018

AbstractSouth Korea shows a remarkable rapid increase in lifespan in recent decades. Employing a mathematical model that is appropriate for human survival curves, we evaluate current trends in female lifespan for South Korea over three recent decades, 1987–2016, and predict coming trends in female lifespan until 2030. From comparative analyses with industrialized countries such as Japan, France, Australia, Switzerland, UK, Sweden, and USA, we confirm that South Korea has the highest increase rate of female lifespan in recent decades, and estimate that maximum lifespan would reach 125 years and characteristic life would surpass 95 years for South Korean female by 2030. South Korea would deserve much attention in study on human health and longevity as the longest-lived country in coming decades.
Genome-wide Methylation Patterns Under Caloric Restriction inDaphnia magna
Authors: Hearn Jack , Pearson Marianne , Blaxter Mark , Wilson Philip , Little Tom J. 
Published: March 2018

AbstractThe degradation of epigenetic control with age is associated with progressive diseases of ageing, including cancers, immunodeficiency and diabetes. Reduced caloric intake slows the effects of aging and age-related diseases, a process likely to be mediated by the impact of caloric restriction on epigenetic factors such as DNA methylation. We used whole genome bisulphite sequencing to study how DNA methylation patterns change with diet in a small invertebrate, the crustaceanDaphnia magna.Daphniashow the classic response of longer life under CR, and they reproduce clonally, which permits the study of epigenetic changes in the absence of genetic variation. Global CpG methylation was 0.7-0.9%, and there was no difference in overall methylation levels between normal and calorie restricted replicates. However, 453 regions were differentially methylated (DMRs) between the normally fed and calorie restricted (CR) replicates. Of these 61% were hypomethylated in the CR group, and 39% were hypermethylated in the CR group. Gene Ontogeny (GO) term enrichment of hyper and hypo-methylated genes showed significant over- and under-representation in three molecular function terms and four biological process GO terms. Notable among these were kinase and phosphorylation activity, which have a well-known functional link to cancers.