bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harnessing Citizenry Awareness and Technology to Improve Fisheries Information: The Power of Data
Authors: Gutierrez Nicolas L. 
Published: December 2017

Abstract
Fisheries sustainability is imperative if we aim to feed an ever-growing population and sustain the livelihoods that depend on them. Despite substantial progress in the science behind fisheries management, more than 90% of the world's fisheries remain unassessed due mostly to data deficiencies. Here, I illustrate the importance of data collection and accessibility in driving fisheries sustainability and propose some innovative solutions to address data deficiencies needed to provide informed management decisions and policy making.
From collective representations to social imaginaries: How society represents itself to itself
Authors: Gilleard Chris 
Published: December 2017

ABSTRACT
This paper aims to reconsider the relevance of Cornelius Castoriadis’ concept of the social imaginary as a way of re-invigorating the study of ‘collective representations’ within the social sciences. The paper begins with a review of how social thought has been understood, from Durkheim's writing on collective representations onwards. A case is made for the utility of Castoriadis’ concept of social imaginary significations in restoring their centrality within the social sciences. In contrast to viewing social thought as ‘super-structural’ ideology, or as a constellation of social attitudes and opinions commonly shared, Castoriadis’ view of social imaginary significations articulates a view of social representations as under-determined by, though never articulated without reference to, social morphology. However the imaginative capacity of individuals and society to generate this surplus of signifiers is understood, Castoriadis’ thinking allies the study of social imaginary significations with the study of social morphology without reducing either to mere representations of the other. What is needed now is a methodology suited to the empirical exploration of the network of significations that constitute the ‘imaginary institution of society’.
Bupivacaine Indirectly Potentiates Glutamate-induced Intracellular Calcium Signaling in Rat Hippocampal Neurons by Impairing Mitochondrial Function in Cocultured Astrocytes
Authors: Xing Yuan , Zhang Nan , Zhang Wei , Ren Lei-Ming 
Published: December 2017

Abstract

Background
Bupivacaine induces central neurotoxicity at lower blood concentrations than cardiovascular toxicity. However, central sensitivity to bupivacaine is poorly understood. The toxicity mechanism might be related to glutamate-induced excitotoxicity in hippocampal cells.

Methods
The intracellular free Ca2+ concentration ([Ca2+]i), mitochondrial membrane potential, and reactive oxygen species generation were measured by fluorescence and two-photon laser scanning microscopy in fetal rat hippocampal neurons and astrocytes.

Results
In astrocyte/neuron cocultures, 300 μM bupivacaine inhibited glutamate-induced increases in [Ca2+]i in astrocytes by 40% (P < 0.0001; n = 20) but significantly potentiated glutamate-induced increases in [Ca2+]i in neurons by 102% (P = 0.0007; n = 10). Ropivacaine produced concentration-dependent effects similar to bupivacaine (0.3 to 300 μM). Tetrodotoxin did not mimic bupivacaine’s effects. In pure cell cultures, bupivacaine did not affect glutamate-induced increases in [Ca2+]i in neurons but did inhibit increased [Ca2+]i in astrocytes. Moreover, bupivacaine produced a 61% decrease in the mitochondrial membrane potential (n = 20) and a 130% increase in reactive oxygen species generation (n = 15) in astrocytes. Cyclosporin A treatment suppressed bupivacaine’s effects on [Ca2+]i, mitochondrial membrane potential, and reactive oxygen species generation. When astrocyte/neuron cocultures were incubated with 500 μM dihydrokainic acid (a specific glutamate transporter–1 inhibitor), bupivacaine did not potentiate glutamate-induced increases in [Ca2+]i in neurons but still inhibited glutamate-induced increases in [Ca2+]i in astrocytes.

Conclusions
In primary rat hippocampal astrocyte and neuron cocultures, clinically relevant concentrations of bupivacaine selectively impair astrocytic mitochondrial function, thereby suppressing glutamate uptake, which indirectly potentiates glutamate-induced increases in [Ca2+]i in neurons.
Sebaceous Neoplasms With Rippled, Labyrinthine/Sinusoidal, Petaloid, and Carcinoid-Like Patterns: A Study of 57 Cases Validating Their Occurrence as a Morphological Spectrum and Showing No Significant Association With Muir–Torre Syndrome or DNA Mismatch Repair Protein Deficiency
Authors: Wiedemeyer Katharina , Kyrpychova Liubov , Işikci Özlem Tanas , Spagnolo Dominic V. , Kutzner Heinz , Rütten Arno , Fernandez-Figueras Maria T. , Denisjuk Natalja , Suster Saul , Pavlovsky Michal , Petersson Fredrik , Michal Michal , Lee Joyce , Kerl Katrin , Kazakov Dmitry V. 
Published: December 2017

Abstract:
Sebaceous neoplasms with an organoid pattern (rippled, labyrinthine/sinusoidal, carcinoid-like, and petaloid) are rare. Previous studies suggested that the above patterns likely represent variations along a morphological continuum. The objectives of this study were to (1) validate this proposition by studying a large number of cases, (2) determine whether there are specific associations with clinical features, (3) establish their frequency, and (4) determine whether they have any association with Muir–Torre syndrome. Fifty-seven sebaceous neoplasms (54 sebaceomas and 3 sebaceous carcinomas) with organoid growth patterns were studied. These occurred in 36 men and 18 women (sex unknown in 3), with ages at diagnosis ranging from 22 to 89 years (mean, 63 years). All patients presented with a solitary nodule (mean size, 11 mm) on the head and neck area. Of the 57 tumors, 24 manifested a single growth pattern, 23 had a combination of 2 patterns, and 10 a combination of 3 patterns, indicating that these patterns are part of a morphological continuum of changes. The carcinoid-like pattern was the most frequent in the “monopatterned” neoplasms (13 cases), whereas the labyrinthine/sinusoidal pattern comprised most of the “polypatterned” lesions, in which various combinations occurred. Immunohistochemically, mismatch repair protein deficiency was detected in 3 of the 22 cases studied, whereas 5 of the 33 patients with available follow-up had an internal malignancy/premalignancy. In conclusion, sebaceous neoplasms with organoid growth patterns are predominantly sebaceomas having a predilection for the scalp, occurring as solitary lesions in elderly patients (male to female ratio of 2:1). Such patterns are expected to be found in a quarter of sebaceomas. In most cases, more than one of the organoid patterns is present. These lesions do not appear to be associated with internal malignancy or mismatch repair deficiency in most cases. However, confirmation of the absence of any significant association with Muir–Torre syndrome syndrome will require genetic studies.
Intraoperative Near-Infrared Fluorescence Imaging of Multiple Pancreatic Neuroendocrine Tumors
Authors: Handgraaf Henricus J.M. , Boogerd Leonora S.F. , Shahbazi Feshtali Shirin , Fariña Sarasqueta Arantza , Snel Marieke , Swijnenburg Rutger-Jan , Vahrmeijer Alexander L. , Bonsing Bert A. , Mieog J. Sven D. 
Published: December 2017

Abstract
Multiple endocrine neoplasia type 1 syndrome can feature pancreatic neuroendocrine lesions that have the potential to degenerate into malignancies (pancreatic neuroendocrine tumors [PNETs]). Resection is required in selected cases and aims to cure patients and to prevent metastasis. Preoperative imaging is important to assess the number, size, and location of PNETs. However, sensitivity of preoperative imaging modalities to detect small lesions can be rather disappointing. This makes intraoperative reassessment of the pancreas crucial. Methylene blue (MB) accumulates in neuroendocrine lesions after intravenous administration. Methylene blue emits fluorescence of approximately 700 nm and can be visualized using a dedicated near-infrared (NIR) fluorescence imaging system. We present a 58-year-old male patient with multiple endocrine neoplasia type 1 syndrome and 2 lesions suspected as PNETs identified during regular follow-up. Intraoperative administration of MB allowed successful NIR fluorescence imaging of multiple lesions missed by preoperative imaging. After confirmation by intraoperative ultrasound, this new finding led to a major change in treatment: from enucleations to total pancreatectomy. Histopathologic examination confirmed that the fluorescent lesions were indeed neuroendocrine lesions ranging from microadenomas to PNETs. This case demonstrates that intraoperative assessment of neuroendocrine lesions can be improved by intraoperative NIR fluorescence imaging using MB, a safe and relatively easy technique.
Concomitant Anterior Repair, Preoperative Prolapse Severity, and Anatomic Prolapse Outcomes After Vaginal Apical Procedures
Authors: Nager Charles W. , Grimes Cara L. , Nolen Tracy L. , Wai Clifford Y. , Brubaker Linda , Jeppson Peter C. , Wilson Tracey S. , Visco Anthony G. , Barber Matthew D. , Sutkin Gary , Norton Peggy , Rardin Charles R. , Arya Lily , Wallace Dennis , Meikle Susan F. 
Published: December 2017

Objective
The aim of the study was to compare anterior and overall prolapse prevalence at 1 year in surgical participants with or without concomitant anterior repair (AR) at the time of sacrospinous ligament fixation (SSLF) or uterosacral ligament suspension (ULS).

Methods
This is a secondary analysis of two surgical trials; concomitant AR was performed at surgeon's discretion. Anterior anatomic success was defined as pelvic organ prolapse quantification of prolapse point Ba ≤0 and overall success was defined as pelvic organ prolapse quantification points Ba, Bp, and C ≤0 at 12 months.

Results
Sixty-three percent (441/701) of the participants underwent concomitant AR and were older, more often postmenopausal, had previous hysterectomy, and had higher-stage anterior, but not apical prolapse. Anterior anatomic success was marginally but statistically better in the combined group (SSLF and ULS) with concomitant AR (82% vs 80%, P = 0.03). In subanalyses, the improvement in anatomic support with AR was observed only in the SSLF subgroup (81% vs 73%, P = 0.02) and mostly in the SSLF subgroup with higher preoperative stage (74% vs 57%, P = 0.02). Anterior repair did not improve success rates in participants with lower-stage prolapse or undergoing ULS. Overall success rates were similar to anterior anatomic success rates. Participants with higher-stage preoperative anterior prolapse had significantly lower success rates.

Conclusions
In the absence of clinical trial data, this analysis suggests an AR should be considered for women with higher-stage prolapse undergoing an SSLF. Preoperative prolapse severity is a strong predictor of poor anatomic outcomes with native tissue vaginal apical surgeries.
Factors Associated With Lack of Vision Improvement in Children With Cortical Visual Impairment
Authors: Handa Swati , Saffari Seyed E. , Borchert Mark 
Published: December 2017

Background:
Improvement in vision has been noted in children with cortical visual impairment (CVI), resulting from disparate types of brain injury. The purpose of our study was to determine the risk factors associated with poor recovery of vision in this group of patients.

Methods:
Case records of children who were born before 2010 with at least 4 follow-up visits for CVI were reviewed for underlying etiologies of CVI, visual acuity (VA), and associated neurological and ophthalmological disorders. VA was assessed in 6 qualitative grades. Changes in VA were recorded as the difference between the grades of VA at presentation and the last follow-up visit. The outcome was calculated as a ratio of actual improvement to potential improvement in grades of qualitative VA. Multiple linear regression determined factors associated with lack of vision improvement in all children and based on etiology.

Results:
Fifty-three children with CVI were identified. The median age at presentation was 13.6 months (range: 2.9–76.4 months) and the median follow-up was 5.8 years (1.1–16.3 years). CVI resulted from central nervous system (CNS) malformation (9.4%), hypoxic/inflammatory injury (15.1%), seizures (24.5%), and combined causes (51.0%). Vision improvement was noted in 83% of children. Lack of VA improvement was associated with older age at presentation in all children with CVI and within each etiological group except CNS malformation. None of the other investigated variables were associated with poor recovery of VA.

Conclusions:
Most of the children with CVI showed improvement in vision. Older age at presentation, but not etiology of CVI, was associated with poor improvement in VA.
Solitary interfacial hydroelastic waves
Authors: Părău Emilian I. 
Published: December 2017

Solitary waves travelling along an elastic plate present between two fluids with different densities are computed in this paper. Different two-dimensional configurations are considered: the upper fluid can be of infinite extent, bounded by a rigid wall or under a second elastic plate. The dispersion relation is obtained for each case and numerical codes based on integro-differential formulations for the full nonlinear problem are derived.
This article is part of the theme issue ‘Nonlinear water waves’.
New exact relations for steady irrotational two-dimensional gravity and capillary surface waves
Authors: Clamond Didier 
Published: December 2017

Steady two-dimensional surface capillary–gravity waves in irrotational motion are considered on constant depth. By exploiting the holomorphic properties in the physical plane and introducing some transformations of the boundary conditions at the free surface, new exact relations and equations for the free surface only are derived. In particular, a physical plane counterpart of the Babenko equation is obtained.This article is part of the theme issue ‘Nonlinear water waves’.
TORC1 inhibition as an immunotherapy to reduce infections in the elderly
Authors: Mannick Joan B. , Morris Melody , Hockey Hans-Ulrich P. , Roma Guglielmo , Beibel Martin , Kulmatycki Kenneth , Watkins Mollie , Shavlakadze Tea , Zhou Weihua , Quinn Dean , Glass David J. , Klickstein Lloyd B. 
Published: December 2017

AbstractmTOR inhibition extends lifespan and ameliorates aging-related pathologies including declining immune function in model organisms. The objective of this Phase 2a clinical trial was to determine if low dose mTOR inhibitor therapy enhanced immune function and thereby decreased infection rates in elderly subjects. The results indicate that 6 weeks of treatment with a low dose combination of a catalytic (BEZ235) plus an allosteric (RAD001) mTOR inhibitor (that selectively inhibits TORC1 downstream of mTOR) was safe, significantly decreased the rate of infections reported by elderly subjects for a year following study drug initiation, upregulated antiviral gene expression, and significantly improved influenza vaccination response. Thus selective TORC1 inhibition with a combination of BEZ235 and RAD001 may be efficacious as immunotherapy to reduce infections, a leading cause of death in the elderly.One Sentence SummaryTreatment of elderly subjects with a low dose mTOR inhibitor regimen that selectively inhibits TORC1 significantly decreased infection rates
Understanding Research Development Needs in Capacity Building for NCD Research: The Case of Thailand
Authors: Singha-Dong N , Bigelow A , Furspan P , Rajataramya B , Villarruel A , Barton D , Potempa K 
Published: December 2017

AbstractChronic non-communicable diseases (NCD) are the most significant causes of death globally. In Thailand, NCDs have increased 10.4% and 11%, respectively, since 2002. Thus, there is a compelling need in Thailand to enhance the capacity for research aimed at improving both NCD prevention and care. A survey was conducted of current multi-disciplinary doctorally prepared faculty (n=115) to determine perceived NCD research training needs. The results of this survey showed that the greatest exposure to NCD was in clinical practice, followed by teaching NCD content, and then research. Few researchers published their findings in journals. All responders reported needing significant support in research design, methods and statistical analysis procedures. These results were used to guide the development of a post-doctoral training program for NCD research in Thailand. After three years of the training program, we found that trainee applicants’ preferences and choices were aligned with the original survey-based planning.
Predicting Response to Platin Chemotherapy Agents with Biochemically-inspired Machine Learning
Authors: Mucaki Eliseos J. , Zhao Jonathan Z.L. , Lizotte Dan , Rogan Peter K. 
Published: December 2017

ABSTRACTSelection of effective genes that accurately predict chemotherapy response could improve cancer outcomes. We compare optimized gene signatures for cisplatin, carboplatin, and oxaliplatin response in the same cell lines, and respectively validate each with cancer patient data. Supervised support vector machine learning was used to derive gene sets whose expression was related to cell line GI50values by backwards feature selection with cross-validation. Specific genes and functional pathways distinguishing sensitive from resistant cell lines are identified by contrasting signatures obtained at extreme vs. median GI50thresholds. Ensembles of gene signatures at different thresholds are combined to reduce dependence on specific GI50values for predicting drug response. The most accurate models for each platin are: cisplatin:BARD1,BCL2,BCL2L1,CDKN2C,FAAP24,FEN1,MAP3K1,MAPK13,MAPK3,NFKB1,NFKB2,SLC22A5,SLC31A2,TLR4,TWIST1; carboplatin:AKT1,EIF3K,ERCC1,GNGT1,GSR,MTHFR,NEDD4L,NLRP1,NRAS,RAF1,SGK1,TIGD1,TP53,VEGFB,VEGFC;oxaliplatin:BRAF,FCGR2A,IGF1,MSH2,NAGK,NFE2L2,NQO1,PANK3,SLC47A1,SLCO1B1,UGT1A1. TCGA bladder, ovarian and colorectal cancer patients were used to test cisplatin, carboplatin and oxaliplatin signatures (respectively), resulting in 71.0%, 60.2% and 54.5% accuracy in predicting disease recurrence and 59%, 61% and 72% accuracy in predicting remission. One cisplatin signature predicted 100% of recurrence in non-smoking bladder cancer patients (57% disease-free; N=19), and 79% recurrence in smokers (62% disease-free; N=35). This approach should be adaptable to other studies of chemotherapy response, independent of drug or cancer types.
Are Nonsense Alleles of Drosophila melanogaster Genes under Any Selection?
Authors: Potapova Nadezhda A. , Andrianova Maria A. , Bazykin Georgii A. , Kondrashov Alexey S. 
Published: December 2017

AbstractA gene which carries a bona fide loss-of-function mutation effectively becomes a functionless pseudogene, free from selective constraint. However, there is a number of molecular mechanisms that may lead to at least a partial preservation of the function of genes carrying even drastic alleles. We performed a direct measurement of the strength of negative selection acting on nonsense alleles of protein-coding genes in the Zambian population of Drosophila melanogaster. Within those exons that carry nonsense mutations, negative selection, assayed by the ratio of missense over synonymous nucleotide diversity levels, appears to be absent, consistent with total loss of function. In other exons of nonsense alleles, negative selection was deeply relaxed but likely not completely absent, and the per site number of missense alleles declined significantly with the distance from the premature stop codon. This pattern may be due to alternative splicing which preserves function of some isoforms of nonsense alleles of genes.
Large-scale structural variation detection in subterranean clover subtypes using optical mapping validated at nucleotide level
Authors: Yuan Yuxuan , Milec Zbyněk , Bayer Philipp E. , Vrána Jan , Doležel Jaroslav , Edwards David , Erskine William , Kaur Parwinder 
Published: December 2017

AbstractWhole genome sequencing has been widely used to detect structural variations (SVs). However, the limited single molecule size makes it difficult to characterize large-scale SVs in a genome because they cannot fully cover such vast and complex regions. Recently, optical mapping in nanochannels has provided novel resolution to detect large-scale SVs by comparing the physical location of the nickase recognition sequence in genomes. Other than in humans, SVs discovered in plants by optical mapping have not been validated. To assess the accuracy of SV calling in plants by optical mapping, we selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs. Daliak and Yarloop. The SVs discovered by BioNano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions containing deletions and 19 containing insertions in Yarloop. The 12 large-scale regions contained 71 small deletions when validated by Illumina short reads. The results suggest that BOM could detect the total size of deletions and insertions, but it could not precisely report the location and actual quantity of SVs in the genome. Nucleotide-level validation is crucial to confirm and characterize SVs reported by optical mapping. The accuracy of SV detection by BOM is highly dependent on the quality of reference genomes and the density of selected nickases.
Results of follow-up experiments to “Odorant cues linked to social immunity induce lateralized antennal stimulation in honey bees (Apis mellifera L.)”
Authors: McAfee Alison , Collins Troy F. , Foster Leonard J. 
Published: December 2017

AbstractIn 2017, we published the paper “Odorant cues linked to social immunity induce lateralized antennal stimulation in honey bees (Apis mellifera L.)” in Scientific Reports. Since then, we have performed three follow-up experiments which have either negative or contradictory results. Previously, we used electrophysiology to show that hygienic bees displayed significantly higher sensitivity to β-ocimene when stimulated via their left antennae compared to their right. We repeated this assay using worker honey bees from a single hygienic colony and found, to our surprise, that the right antennae elicited higher sensitivity. We also previously attempted to identify a molecular basis for lateralization by using mass spectrometry-based proteomics to compare left and right antennal proteomes. Of the 1,845 proteins, none were differentially expressed. Here, we repeated this experiment but employed orthogonal peptide fractionation to increase proteome coverage to 3,114 proteins; however, still none were differentially expressed. Finally, we attempted to manipulate gene expression of a key antennal odorant binding protein linked to hygienic behaviour (OBP18) using RNA interference via antenna microinjection. We were not able to achieve long-lasting OBP18 knock-down, but comparing the proteomes of untreated, mock dsRNA-treated and OBP18 dsRNA-treated worker antennae revealed numerous off-target effects of the act of injecting alone. By openly reporting this data, we hope to set an example for information transparency.