bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of factors underlying the metabolic shifts in developing kernels of colored maize
Authors: Hu Chaoyang , Li Quanlin , Shen Xuefang , Quan Sheng , Lin Hong , Duan Lei , Wang Yifa , Luo Qian , Qu Guorun , Han Qing , Lu Yuan , Zhang Dabing , Yuan Zheng , Shi Jianxin 
Published: October 2016

AbstractElucidation of the metabolic pathways determining pigmentation and their underlying regulatory mechanisms in maize kernels is of high importance in attempts to improve the nutritional composition of our food. In this study, we compared dynamics in the transcriptome and metabolome between colored SW93 and white SW48 by integrating RNA-Seq and non-targeted metabolomics. Our data revealed that expression of enzyme coding genes and levels of primary metabolites decreased gradually from 11 to 21 DAP, corresponding well with the physiological change of developing maize kernels from differentiation through reserve accumulation to maturation, which was cultivar independent. A remarkable up-regulation of anthocyanin and phlobaphene pathway distinguished SW93 from SW48, in which anthocyanin regulating transcriptional factors (R1 and C1), enzyme encoding genes involved in both pathways and corresponding metabolic intermediates were up-regulated concurrently in SW93 but not in SW48. The shift from the shikimate pathway of primary metabolism to the flavonoid pathway of secondary metabolism, however, appears to be under posttranscriptional regulation. This study revealed the link between primary metabolism and kernel coloration, which facilitate further study to explore fundamental questions regarding the evolution of seed metabolic capabilities as well as their potential applications in maize improvement regarding both staple and functional foods.
Differential Predictors of Adult versus Juvenile Distributions of Two Coastal Pelagic, Surf Zone Fishes along the Northern Gulf of Mexico
Authors: Schrandt Meagan N. , Gregalis Kevan C. , Powers Sean P. 
Published: October 2016

AbstractAs coastal human populations increase and offshore fishery regulations become more stringent in the northern Gulf of Mexico, nearshore fisheries may be subjected to increased exploitation. Spanish Mackerel Scomberomorus maculatus and Florida Pompano Trachinotus carolinus are two nearshore, coastal migratory pelagic species vulnerable to undergoing changes in fishing pressure; however, information is incomplete in regards to understanding their current distributions and movement patterns, both of which are important for effective fishery management. We used a 2‐year (2011–2012) gill‐net and seine survey to assess surf zone distributions of Spanish Mackerel and Florida Pompano in the northern Gulf of Mexico (Horn Island, Mississippi, to Pensacola, Florida). Unbiased catch‐per‐unit‐effort estimates (by the delta method) were greatest in Alabama and during spring months. Lowest catches occurred during the warm summer months. Overall, subadult–adult Spanish Mackerel presence could be predicted (using a delta‐lognormal general linear model) by geographic area, beach habitat, and depth. Florida Pompano presence could be predicted by month and beach habitat. For both species, the abundance could not be predicted by any of the examined variables. Juvenile Florida Pompano presence, contrastingly, could be predicted by month and salinity, and abundance by month and water temperature. Both species had spatiotemporal variability in distribution and catch rates, but beach habitat appeared to be a better predictor for subadults and adults of both species, whereas month and salinity were better predictors for juvenile Florida Pompano catches. Greater catches generally corresponded with proposed migration patterns but also suggest that individuals, at least temporarily, leave the surf zone during the day in the warm summer months. Furthermore, although legal‐sized individuals of both species can co‐occur in the surf zone in the northern Gulf of Mexico, the increase in Spanish Mackerel presence with depth suggests that Spanish Mackerel fisheries could potentially move further offshore to avoid user conflict with Florida Pompano fisheries.Received March 16, 2016; accepted August 1, 2016 Published online October 14, 2016
Multiple Passages of Grunt Fin Cells Persistently Infected with Red Seabream Iridovirus (RSIV) at 15ºC or 30ºC to Yield Uninfected Cells
Authors: Oh So-Young , Nishizawa Toyohiko 
Published: October 2016

Abstract
Red seabream iridovirus (RSIV), a member within genus Megalocytivirus (Iridoviridae), causes serious economic losses to marine fish aquaculture industry in East Asia. In this study, we established a Blue Striped Grunt Haemulon sciurus fin (grunt fin; GF) cell line persistently infected with RSIV (PI-GFRSIV) by subculturing GF cells that survived RSIV inoculation. PI-GFRSIV cells were morphologically indistinguishable from naive GF cells. They could stably produce RSIV at approximately 104.9 ± 0.5 genomes per microliter after 24 passages over 18 months. The optimum temperature to produce RSIV in PI-GFRSIV cells was 25°C. These cells also produced RSIV at 15, 20, and 30°C with multiple subcultures. The amount of RSIV yielded from PI-GFRSIV cells decreased gradually by multiple subculturing at 15°C or 30°C. Red seabream iridovirus was no longer detected from PI-GFRSIV cells after subcultures at these temperatures. These PI-GFRSIV cells freed from RSIV infection exhibited a level of RSIV productivity similar to those of naive GF cells after inoculation with RSIV. Therefore, we consider that these PI-GFRSIV cells were no longer infected with RSIV after multiple subculturing at 15°C or 30°C.
Received October 15, 2015; accepted June 27, 2016Published online October 13, 2016
Laboratory-scale production of (S)-reticuline, an important intermediate of benzylisoquinoline alkaloids, using a bacterial-based method
Authors: Matsumura Eitaro , Nakagawa Akira , Tomabechi Yusuke , Koyanagi Takashi , Kumagai Hidehiko , Yamamoto Kenji , Katayama Takane , Sato Fumihiko , Minami Hiromichi 
Published: October 2016

Abstract
Benzylisoquinoline alkaloids (BIAs) are a group of plant secondary metabolites that have been identified as targets for drug discovery because of their diverse pharmaceutical activities. Well-known BIAs are relatively abundant in plants and have therefore been extensively studied. However, although unknown BIAs are also thought to have valuable activities, they are difficult to obtain because the raw materials are present at low abundance in nature. We have previously reported the fermentative production of an important intermediate (S)-reticuline from dopamine using Escherichia coli. However, the yield is typically limited. Here, we improved production efficiency by combining in vivo tetrahydropapaveroline production in E. coli with in vitro enzymatic synthesis of (S)-reticuline. Finally, 593 mg of pure (S)-reticuline was obtained from 1 L of the reaction mixture. Because this bacterial-based method is simple, it could be widely used for production of (S)-reticuline and related BIAs, thereby facilitating studies of BIAs for drug discovery.
Diagnostic Test Accuracy in Childhood Pulmonary Tuberculosis: A Bayesian Latent Class Analysis
Authors: Schumacher Samuel G. , van Smeden Maarten , Dendukuri Nandini , Joseph Lawrence , Nicol Mark P. , Pai Madhukar , Zar Heather J. 
Published: October 2016

AbstractEvaluation of tests for the diagnosis of childhood pulmonary tuberculosis (CPTB) is complicated by the absence of an accurate reference test. We present a Bayesian latent class analysis in which we evaluated the accuracy of 5 diagnostic tests for CPTB. We used data from a study of 749 hospitalized South African children suspected to have CPTB from 2009 to 2014. The following tests were used: mycobacterial culture, smear microscopy, Xpert MTB/RIF (Cepheid Inc.), tuberculin skin test (TST), and chest radiography. We estimated the prevalence of CPTB to be 27% (95% credible interval (CrI): 21, 35). The sensitivities of culture, Xpert, and smear microscopy were estimated to be 60% (95% CrI: 46, 76), 49% (95% CrI: 38, 62), and 22% (95% CrI: 16, 30), respectively; specificities of these tests were estimated in accordance with prior information and were close to 100%. Chest radiography was estimated to have a sensitivity of 64% (95% CrI: 55, 73) and a specificity of 78% (95% CrI: 73, 83). Sensitivity of the TST was estimated to be 75% (95% CrI: 61, 84), and it decreased substantially among children who were malnourished and infected with human immunodeficiency virus (56%). The specificity of the TST was 69% (95% CrI: 63%, 76%). Furthermore, it was estimated that 46% (95% CrI: 42, 49) of CPTB-negative cases and 93% (95% CrI: 82; 98) of CPTB-positive cases received antituberculosis treatment, which indicates substantial overtreatment and limited undertreatment.
Ultra-Processed Food Consumption and the Incidence of Hypertension in a Mediterranean Cohort: The Seguimiento Universidad de Navarra Project
Authors: Mendonça Raquel de Deus , Lopes Aline Cristine Souza , Pimenta Adriano Marçal , Gea Alfredo , Martinez-Gonzalez Miguel Angel , Bes-Rastrollo Maira 
Published: October 2016

Abstract

BACKGROUND
Some available evidence suggests that high consumption of ultra-processed foods (UPFs) is associated with a higher risk of obesity. Collectively, this association and the nutritional characteristics of UPFs suggest that UPFs might also be associated with hypertension.

METHODS
We prospectively evaluated the relationship between UPF consumption and the risk of hypertension in a prospective Spanish cohort, the Seguimiento Universidad de Navarra project. We included 14,790 Spanish adult university graduates who were initially free of hypertension at baseline who were followed for a mean of 9.1 years (SD, 3.9 years; total person-years: 134,784). UPF (industrial formulations of chemical compounds which, beyond substances of common culinary use such as salt, sugar, oils, and fats, include substances also derived from foods but not used in culinary preparations) consumption was assessed using a validated semi-quantitative 136-item food-frequency questionnaire. Cox proportional hazards models were used to estimate adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for hypertension incidence.

RESULTS
During follow-up, 1,702 incident cases of hypertension were identified. Participants in the highest tertile of UPF consumption had a higher risk of developing hypertension (adjusted HR, 1.21; 95% CI, 1.06, 1.37; P for trend = 0.004) than those in the lowest tertile after adjusting for potential confounders.

CONCLUSIONS
In this large prospective cohort of Spanish middle-aged adult university graduates, a positive association between UPF consumption and hypertension risk was observed. Additional longitudinal studies are needed to confirm our results.
Localized structural frustration for evaluating the impact of sequence variants
Authors: Kumar Sushant , Clarke Declan , Gerstein Mark 
Published: October 2016

Abstract
Population-scale sequencing is increasingly uncovering large numbers of rare single-nucleotide variants (SNVs) in coding regions of the genome. The rarity of these variants makes it challenging to evaluate their deleteriousness with conventional phenotype–genotype associations. Protein structures provide a way of addressing this challenge. Previous efforts have focused on globally quantifying the impact of SNVs on protein stability. However, local perturbations may severely impact protein functionality without strongly disrupting global stability (e.g. in relation to catalysis or allostery). Here, we describe a workflow in which localized frustration, quantifying unfavorable local interactions, is employed as a metric to investigate such effects. Using this workflow on the Protein Databank, we find that frustration produces many immediately intuitive results: for instance, disease-related SNVs create stronger changes in localized frustration than non-disease related variants, and rare SNVs tend to disrupt local interactions to a larger extent than common variants. Less obviously, we observe that somatic SNVs associated with oncogenes and tumor suppressor genes (TSGs) induce very different changes in frustration. In particular, those associated with TSGs change the frustration more in the core than the surface (by introducing loss-of-function events), whereas those associated with oncogenes manifest the opposite pattern, creating gain-of-function events.
Finding Agency in Adversity: Applying the Refugee Convention in the Context of Disasters and Climate Change
Authors: Scott Matthew 
Published: October 2016

This article argues that, as individuals are already applying for refugee status in the context of disasters and climate change, a robust understanding of why disasters happen and how different groups are affected, combined with a principled methodology for determining such claims, are critical aspects of the anxious scrutiny that each claim should receive. The limitations of the “hazards” paradigm, which is shown to be dominant in international refugee law, are highlighted. Adopting the “social” paradigm developed within the field of disaster risk reduction, the argument is advanced that an understanding of disasters as social phenomena within which existing patterns of discrimination contribute to differential impacts, provides a sharper lens with which to consider eligibility for refugee status.
The article argues that recent case-law from the New Zealand Immigration and Protection Tribunal reflects an awareness of the social paradigm, and the methodology for determining such claims is described and largely endorsed. It concludes by identifying sources of country of origin information that can help to address some of the evidentiary challenges claimants may face, and argues that the risk assessment under refugee law is more generous than the “immediacy” requirement identified by the New Zealand Immigration and Protection Tribunal in relation to complementary protection claims.
Anticytokine autoantibodies in infection and inflammation: an update
Authors: Barcenas-Morales Gabriela , Jandus Peter , Döffinger Rainer 
Published: October 2016

Purpose of review
Concise overview of the field of anticytokine autoantibodies with a focus on recent developments.

Recent findings
Advances in particular in the analysis of autoantibodies to IFNγ, granulocyte-macrophage colony-stimulating factor (GM-CSF) and type I IFN are presented. The target epitope for anti-IFNγ autoantibodies has been found to have high homology to a protein from Aspergillus suggesting molecular mimicry as a mechanism of breaking self-tolerance. A treatment strategy using a recombinant, epitope-depleted version of IFNγ is suggested. Autoantibodies to GM-CSF are associated with disseminated Crytococcus and Nocardia infections thus expanding the spectrum of associated diseases beyond pulmonary alveolar proteinosis. Detailed analysis of anti-GM-CSF autoantibody clones derived from pulmonary alveolar proteinosis patients show evidence of high somatic mutation suggesting T cell-dependent affinity maturation; full GM-CSF neutralization is achieved by synergistic binding of antibodies targeting various distinct noncross-reactive epitopes and leading to antigen sequestration and Fc-mediated clearance. Single mAbs in contrast may lead to higher GM-CSF bioavailability. Anti type I IFN-specific autoantibodies derived from autoimmune polyglandular syndrome type I patients are of extreme high affinity and negatively correlate with the incidence of type I diabetes and may be thus considered to be protective. Hypomorphic severe combined immune deficiency may be associated with complex anticytokine patterns and the emergence of anti type I IFN autoantibodies correlates with severe viral infection histories.

Summary
Anticytokine autoantibodies may cause susceptibility to infections. In autoimmune/autoinflammatory conditions, anticytokine autoantibodies may be protective or promote disease.
No! When the immunologist becomes a virologist: Norovirus – an emerging infection in immune deficiency diseases
Authors: Hartono Stella , Bhagia Amrita , Joshi Avni Y. 
Published: October 2016

Purpose of review
Norovirus infection is an emerging chronic infection in immunocompromised hosts. The aim of this review is to discuss the pathophysiology of Norovirus infection and explore mechanistic models for chronic infection/shedder state, especially in patients with immune deficiency diseases.

Recent findings
Chronic Norovirus infection is increasingly associated with enteropathy associated with both primary and secondary immune deficiency diseases. There is an ongoing debate in the immune deficiency community whether it is truly a causative agent for the enteropathy or it is an innocent bystander.
We describe the historic aspects of Norovirus infection, its immunology and viral structure and the basis for preventive and vaccination strategies.
We also postulate in this review a disease model in immune deficiency subjects which creates a milieu for it to become a chronic and explore newer frontiers for disease modification and prevention.

Summary
Norovirus is the most common cause of acute gastroenteritis in general population but the factors that lead to its persistence in patients with immune deficiency need further holistic studies. This should include host assessment, microbiome signatures, and viral pathogenic factors assessment.
Performance-Intensity Function and Aided Improvement in Individuals With Late-Onset Auditory Neuropathy Spectrum Disorder
Authors: Mathai Jijo Pottackal , Yathiraj Asha 
Published: October 2016

Objectives:
The purpose of the study was to explore the effect of intensity on speech perception in individuals with late-onset auditory neuropathy spectrum disorder (ANSD) by obtaining their performance-intensity (PI) function. Additionally, the study investigated the effect of PI function on aided speech perception. It was hypothesized that speech perception abilities of individuals with ANSD vary with intensity and may provide information regarding their aided performance.

Design:
A factorial research design was used to obtain the PI function and aided performance. Thirty individuals with late-onset ANSD in the age range of 14 to 42 years were evaluated. All the participants had bilateral mild to moderately-severe symmetrical hearing loss and were naive hearing aid users. A PI function was obtained for each participant for phonemically-balanced words. Further, aided performance was evaluated for binaural digital hearing aids fitted using the National Acoustic Laboratories-Non-linear 1 method.

Results:
It was found that the sensation level at which maximum word recognition scores were obtained varied across the participants. However, the majority of the participants had maximum scores below 30 dB SL. A large number of participants had a rollover PI function where the word recognition scores deteriorated with increase in presentation level. However, a few individuals demonstrated improvement in word recognition scores with increase in presentation level. Rollover index calculated from the PI function clearly demarcated those who had improved speech perception with hearing aids from those who did not. It was found that those with a rising pattern had aided speech identification scores that were significantly higher than their unaided scores. No such difference was found in those with a rollover. Further, aided benefit calculated by obtaining the difference between the aided and unaided scores was significantly higher in those with a rising PI function than those with a rollover function.

Conclusions:
The word recognition scores of individuals with ANSD varied with sensation level. This implies that obtaining the word recognition scores at a single presentation level may not accurately represent the speech perception abilities of those with ANSD. Further, a PI function helps differentiate those individuals with ANSD who benefit from hearing aids from those who do not.
Vasculitis in the autoinflammatory diseases
Authors: Peleg Hagit , Ben-Chetrit Eldad 
Published: October 2016

Purpose of review
This article addresses the prevalence and relationship between autoinflammatory diseases and vasculitis.

Recent findings
Autoimmune diseases (AIDs) are a group of syndromes characterized by episodes of unprovoked inflammation due to dysregulation of the innate immune system. Despite the common occurrence of rashes and other skin lesions in these diseases, vasculitis is reported in only a few. On the other hand, neutrophilic dermatoses are more prevalent. Large vessel vasculitis is reported in patients with Behcet's and Blau's syndromes. Small and medium size vasculitides are reported in familial Mediterranean fever mainly as Henoch-Schonlein purpura and polyarteritis nodosa, respectively. It is rarely described in hyper IgD with periodic fever syndrome, cryopyrin associated periodic syndromes, TNF receptor-associated periodic syndrome, deficiency of interleukin-1 receptor antagonist and pyoderma gangrenosum and acne syndrome. In most AID where bones and skin are mainly involved (CRMO, Majeed syndrome, Cherubism and DITRA) – vasculitis has not been described at all. In AID small vessel vasculitis affects mainly the skin with no involvement of internal organs.

Summary
In AID, neutrophilic dermatoses are more common and prominent than vasculitis. This may reflect a minor role for interleukin-1 in the pathogenesis of vasculitis. The rarity of vasculitis in AID suggests that in most reported cases its occurrence has been probably coincidental rather than being an integral feature of the disease.
Anticitrullinated protein antibodies: origin and role in the pathogenesis of rheumatoid arthritis
Authors: England Bryant R. , Thiele Geoffrey M. , Mikuls Ted R. 
Published: October 2016

Purpose of review
This article reviews recent literature on the origin and pathogenic role of anticitrullinated protein antibodies (ACPAs) in rheumatoid arthritis (RA).

Recent findings
ACPAs and ACPA-immune complexes interact with immune cells to facilitate articular inflammation. Findings from recent in vitro and in vivo studies are congruent with epidemiologic observations in RA supporting a pathogenic role of ACPAs.

Summary
ACPAs target proteins/peptides with citrullinated epitopes and serve as informative RA biomarkers. ACPAs are generated within synovium and possibly at extra-articular sites prior to disease onset. Proximate to RA onset, critical qualitative and quantitative changes to ACPAs occur that drive proinflammatory responses. Unable to induce arthritis alone, the administration of ACPAs enhances the development and severity of inflammation in mice when a mild synovitis is already present. In vitro studies have elucidated several possible mechanisms linking ACPA to disease progression including: first, activation of inflammatory cells by ACPA-immune complexes; second, ACPA-mediated neutrophil cell death producing neutrophil extracellular traps, which drives inflammation and autoimmunity by releasing citrullinated autoantigen; and finally, direct binding of ACPAs to osteoclasts and resulting osteoclastogenesis. Together, these recent investigations have begun to elucidate the different mechanisms by which ACPAs may be directly pathogenic in RA.