bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Madura Head”—A Rare Case of Craniocerebral Maduromycosis
Authors: Behera Bikash , Mishra Sanjib , Dhir Manmath , Panda Rabi , Samantaray Sagarika 
Published: May 2017

AbstractAs maduromycosis is mostly confined to lower extremities. It was rightly named as “Madura foot” by John Gill in 1842, after the name of Madurai district, in Tamil Nadu state of India. Mycetoma is a chronic granulomatous infection mostly caused by a true fungus, Madurella mycetomatis (Eumycotic mycetoma). Craniocerebral involvement by eumycotic mycetoma is rare in world literature and confined to few case reports only. Here we present an interesting case of craniocerebral maduromycosis presenting with focal seizure, hemiparesis, and multiple discharging sinuses all over the scalp. The patient was diagnosed by histopathologic biopsy and managed conservatively with antifungal medications in view of widespread involvement of the scalp, not amenable to surgery.
Listeria monocytogenes Brain Abscess within a Metastatic Intracerebellar Space-Occupying Lesion in a Patient with Carcinoma Lung: First Case Report from India
Authors: Oommen Arun , Johny Molly , Pratap Thara , Paul Renu , Chinnan Jily , Jalal Muhammed 
Published: May 2017

Abstract
Listeria monocytogenes infections are rare. Neonates and geriatric population, pregnant women, and diabetic and immunocompromised patients are at higher risk for invasive listeriosis. Early recognition of Listeria brain abscess remains a major challenge. Here, we describe a case of intratumoral abscess with L. monocytogenes in a patient with intracerebellar metastasis from poorly differentiated adenocarcinoma lung. Right cerebellar tumor with a thick-walled purulent cavity was resected. Histopathologic examination revealed acute inflammation consistent with abscess and showed metastatic poorly differentiated adenocarcinoma. Cultures of the abscess fluid grew L. monocytogenes. She responded well to ampicillin-gentamycin therapy and the surveillance imaging done on the seventh postoperative day showed clearance of the abscess. The patient is further being planned for radiotherapy in regard to metastasis. Listeria abscess within a metastatic tumor is very rare and only one case is reported as of our knowledge. Listeria abscess being reported within an intracerebellar metastatic space-occupying lesion is for the first time.
Parathyroid Hormone Levels Predict Long-Term Outcome After Operative Management of Parathyroid Cancer
Authors: Machens Andreas , Lorenz Kerstin , Dralle Henning 
Published: May 2017

AbstractThe role of parathyroid hormone (PTH) serum levels for prediction of outcome is ill defined for parathyroid cancer, which is a very rare disease. This investigation of 17 consecutive patients with parathyroid cancer, (re-)operated on at a tertiary referral center between 1994 and July 2016, with a mean follow-up of 179.6 months (15 years) aimed to clarify the suitability of PTH serum levels for prediction of clinical outcome after comprehensive operative management of parathyroid cancer. Cancer-specific mortality occurred significantly more often with the performance of sternotomy before or at first operation at this institution (80 vs. 0%; p=0.002); mean PTH serum levels before first operation (1 105 vs. 357 pg/ml; p=0.008; r=0.77) and at most recent follow-up (3 167 vs. 101 pg/ml; p=0.019; r=0.60); and normalization of PTH serum levels at most recent follow-up (0 vs. 64%; p=0.034). For cancer-specific survival, receiver-operating characteristics analysis identified as optimum cut-off point an initial PTH serum level of 700 pg/ml. For local recurrence, no significant associations were found. Kaplan-Meier analysis confirmed that the patients with initial PTH serum levels >700 pg/ml (plog-rank=0.011) and sternotomy (plog-rank<0.001), but not node or lung metastases, had worse cancer-specific survival. Parathyroid cancer is much more an endocrine disease with oncological features than an oncological disease with endocrine features. Operative intervention(s) should be comprehensive and directed at clearing all metabolically active parathyroid tumor deposits early. If surgical cure cannot be reached, it is pivotal to achieve metabolic control, obviating the need for, or facilitating, medical therapy of hypercalcemia, and preserve renal function.
The agenda-setting function of mass media1
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Authors: McCombs Maxwell E. , Shaw Donald L. 
Published: May 2017

Abstract
In choosing and displaying news, editors, newsroom staff, and broadcasters play an important part in shaping political reality. Readers learn not only about a given issue, but also how much importance to attach to that issue from the amount of information in a news story and its position. In reflecting what candidates are saying during a campaign, the mass media may well determine the important issues – that is, the media may set the "agenda" of the campaign.
Online agenda-setting research
Authors: Ariel Yaron , Elishar-Malka Vered , Weimann-Saks Dana , Avidar Ruth 
Published: May 2017

AbstractAgenda-setting research has been performed for more than four decades, both in traditional and online media, and the tools employed for this task have been very much accepted by media researchers around the world. Nevertheless, analysis of the public agenda in new media, particularly across social networks, requires re-thinking these same tools, which creates a series of methodological and theoretical challenges. The present paper seeks to illuminate these challenges and propose possible solutions for some of them.
Do english-language newspapers make universities prestigious?
Authors: Tanikawa Miki , Lu Shuning 
Published: May 2017

AbstractThis study investigated whether English-language news media, which increased coverage of two large, well known private universities in Japan, increased their salience in the minds of international residents in Japan. Based on the agenda-setting theory of media influence, the authors made use of university enrollment trends as an indicator of public salience and found that the English-language media contributed to the growing prestige of the universities among the non-Japanese population. Academic reality in Japan underwent little change during that period with the top ranking government-funded universities, whose coverage in the English-language media did not increase, remained more prestigious within the local context, as is evident from local university rankings. This study also demonstrates that the media can exert an agenda-setting influence on institutions of higher learning, a domain that has not been traditionally investigated. The study also addresses the influences of the international, English-language press in the context of a non-English speaking country, Japan, and how the, “need for orientation” (NFO), might have been a factor.
News sources and the same sex marriage issue
Authors: Chen Victoria , Pain Paromita 
Published: May 2017

AbstractUsing agenda-setting theory, this study explores the effects of news sources on public opinion on the issue of the same-sex marriage over 10 years. It examines immediate substantive salience, immediate affective salience, cumulative substantive salience and cumulative affective salience of the news sources cited in news articles from The New York Times from 2003 to 2013 and compares the coverage to public opinion polls. Four findings merit notice. First, news sources with a clear standpoint had counter effects on public opinion. Second, the salience of news sources is as influential as the affective attribute salience of news sources on public opinion. Official sources had the power to influence public opinion the most. Thirdly, the influence of the media is stronger than the influence of news sources on influencing public opinion. Fourth, LGBTQ sources were the least used sources in the same-sex marriage coverage.
Intra-Annual Variability of Silver Carp Populations in the Des Moines River, USA
Authors: Sullivan Christopher J. , Camacho Carlos A. , Weber Michael J. , Pierce Clay L. 
Published: May 2017

Abstract
Since their introduction in the 1970s, Silver Carp Hypophthalmichthys molitrix have spread throughout the Mississippi River basin. Management of any species relies on an accurate understanding of population characteristics and dynamics. However, Silver Carp seasonal sampling variation is unknown. Sampling during periods of peak catch rates would facilitate Silver Carp assessment and management, improving monitoring and removal techniques. The objective of this study was to evaluate adult Silver Carp seasonal sampling variation with boat electroshocking and trammel nets. Silver Carp were collected monthly (April–October) during 2014 and 2015 from four locations in the Des Moines River, Iowa. Trammel nets rarely captured Silver Carp (mean ± SE = 4.9 ± 1.6 fish/net; 60% of fish were captured in 6.3% of net sets) and therefore were not included in analyses. Electroshocking catch rates (CPUEs) exhibited a bimodal distribution, with peak CPUEs generally occurring in May, June, and September and lower catch rates observed during July and August. Catch rates were positively related to river discharge at upstream sites but not at downstream sites. Silver Carp size structure was similar among months and sites except at Cliffland, where fish were smaller during August and October compared to earlier in the year. Finally, Silver Carp condition peaked during April and May and decreased throughout the year except at Keokuk, where peaks were observed during both May and August. Although spatiotemporal variability was substantial, these results suggest that sampling of Silver Carp via electroshocking in May–June and September–October generally produces higher catch rates compared to July–August sampling and generates a more representative size structure. Using site-specific knowledge, monitoring and surveillance programs could more effectively sample during these periods of high vulnerability and densities in order to manage the spread and impacts of Silver Carp at statewide and regionwide scales.
Received December 7, 2016; accepted May 11, 2017Published online June 30, 2017
Data sharing in low-resourced research environments
Authors: Rappert Brian , Bezuidenhout Louise 
Published: May 2017

Abstract
‘Open data’ has recently emerged as a label for renewed attempts to promote scientific exchange. As part of such efforts, the posting of data online is often portrayed as commonly beneficial: individual scientists accrue greater prominence while at the same time fostering communal knowledge. Yet, how scientists in non-Western research settings assess such calls for openness has been the subject of little empirical study. Based on extended fieldwork with biochemistry laboratories in sub-Sahara Africa, this paper examines a variety of reasons why scientists opt for closure over openness with regard to their own data. We argue that the heterogeneity of research environments calls into question many of the presumptions made as part of open data. Inequalities in research environments can mean that moves towards sharing create binds and dilemmas. These observations suggest that those promoting openness must critically examine current research governance and funding systems that continue to perpetuate disparities. The paper proposes an innovative approach to facilitating openness: coupling the sharing of data with enabling scientists to redress their day-to-day research environment demands. Such a starting basis provides an alternative but vital link between the aspirations for science aired today as part of international discussions and the daily challenges of undertaking research in low-resourced environments.
Chemoenzymatic synthesis and characterization of N-glycolylneuraminic acid-carrying sialoglycopolypeptides as effective inhibitors against equine influenza virus hemagglutination
Authors: Ogata Makoto , Koizumi Ami , Otsubo Tadamune , Ikeda Kiyoshi , Sakamoto Mao , Aita Rena , Kato Tatsuya , Park Enoch Y , Yamanaka Takashi , Hidari Kazuya I P J 
Published: May 2017

Abstract
A series of novel sialoglycopolypeptides carrying N-glycolylneuraminic acid (Neu5Gc)-containing trisaccharides having α(2 → 3)- and α(2 → 6)-linkages in the side chains of γ-polyglutamic acid (γ-PGA) were designed as competitive inhibitors against equine influenza viruses (EIV), which critically recognize the Neu5Gc residue for receptor binding. Using horse red blood cells (HRBC) we successfully evaluated the binding activity of the multivalent Neu5Gc ligands to both equine and canine influenza viruses in the hemagglutination inhibition (HI) assay. Our findings show the multivalent α2,3-linked Neu5Gc-ligands (3a–c and 7) selectively inhibit hemagglutination mediated by both influenza viruses and display a strong inhibitory activity. Our results indicate that the multivalent Neu5Gc-ligands can be used as novel probes to elucidate the mechanism of infection/adhesion of Neu5Gc-binding influenza viruses.
The receptor-like cytoplasmic kinase BSR1 mediates chitin-induced defense signaling in rice cells
Authors: Kanda Yasukazu , Yokotani Naoki , Maeda Satoru , Nishizawa Yoko , Kamakura Takashi , Mori Masaki 
Published: May 2017

Abstract
Broad-Spectrum Resistance 1 (BSR1) encodes a rice receptor-like cytoplasmic kinase, and enhances disease resistance when overexpressed. Rice plants overexpressing BSR1 are highly resistant to diverse pathogens, including rice blast fungus. However, the mechanism responsible for this resistance has not been fully characterized. To analyze the BSR1 function, BSR1-knockout (BSR1-KO) plants were generated using a clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system. Experiments using suspension-cultured cells revealed that defense responses including H2O2 production (i.e. oxidative burst) and expression of defense-related genes induced by autoclaved conidia of the rice blast fungus significantly decreased in BSR1-KO cells. Furthermore, a treatment with chitin oligomers which function as microbe-associated molecular patterns (MAMPs) of the rice blast fungus resulted in considerably suppressed defense responses in BSR1-KO cells. These results suggest that BSR1 is important for the rice innate immunity triggered by the perception of chitin.
Recommendations on the Use of Ecosystem Modeling for Informing Ecosystem-Based Fisheries Management and Restoration Outcomes in the Gulf of Mexico
Authors: Grüss Arnaud , Rose Kenneth A. , Simons James , Ainsworth Cameron H. , Babcock Elizabeth A. , Chagaris David D. , De Mutsert Kim , Froeschke John , Himchak Peter , Kaplan Isaac C. , O’Farrell Halie , Zetina Rejon Manuel J. 
Published: May 2017

Abstract
Ecosystem-based fisheries management (EBFM) and ecosystem restoration are gaining momentum worldwide, including in U.S. waters of the Gulf of Mexico (GOM). Ecosystem models are valuable tools for informing EBFM and restoration activities. In this paper, we provide guidance and a roadmap for ecosystem modeling in the GOM region, with an emphasis on model development and use of model products to inform EBFM and the increasing investments in restoration. We propose eight “best practices” for ecosystem modeling efforts, including (1) identification of priority management questions, (2) scenarios as simulation experiments, (3) calibration and validation needs, (4) sensitivity and uncertainty analyses, (5) ensuring transparency, (6) improving communication between ecosystem modelers and the various stakeholders, (7) documentation of modeling efforts, and (8) maintaining the ecosystem models and codes. Fisheries management in the USA adheres to a prescriptive set of calculations. Therefore, the use of ecosystem modeling in EBFM for the GOM will likely be incremental, starting with the incorporation of environmental variables into single-species assessments, the provision of background (stage-setting) information on environmental and food web effects (e.g., the impacts of lionfish Pterois spp. invasion), and strategic advice through management strategy evaluation. Management questions related to restoration in the GOM (e.g., the impacts of freshwater and sediment diversions as part of coastal restoration, habitat preservation, and rehabilitation; and measures to mitigate nutrient loading and hypoxia) have more flexibility in how they are addressed and thus are primed for immediate use of ecosystem modeling. The questions related to restoration are appropriate for ecosystem modeling, and data collection at the restoration project level can provide critical information for modeling to then scale up to regional responses. Ecosystem modeling efforts need to be initiated and advanced now in order for the tools to be ready in the near future. Addressing resource management issues and questions will benefit greatly from the proper use of ecosystem modeling.
Diabatic models with transferrable parameters for generalized chemical reactions
Authors: Reimers Jeffrey R , McKemmish Laura K , McKenzie Ross H , Hush Noel S 
Published: May 2017

Abstract
Diabatic models applied to adiabatic electron-transfer theory yield many equations involving just a few parameters that connect ground-state geometries and vibration frequencies to excited-state transition energies and vibration frequencies to the rate constants for electron-transfer reactions, utilizing properties of the conical-intersection seam linking the ground and excited states through the Pseudo Jahn-Teller effect. We review how such simplicity in basic understanding can also be obtained for general chemical reactions. The key feature that must be recognized is that electron-transfer (or hole transfer) processes typically involve one electron (hole) moving between two orbitals, whereas general reactions typically involve two electrons or even four electrons for processes in aromatic molecules. Each additional moving electron leads to new high-energy but interrelated conical-intersection seams that distort the shape of the critical lowest-energy seam. Recognizing this feature shows how conical-intersection descriptors can be transferred between systems, and how general chemical reactions can be compared using the same set of simple parameters. Mathematical relationships are presented depicting how different conical-intersection seams relate to each other, showing that complex problems can be reduced into an effective interaction between the ground-state and a critical excited state to provide the first semi-quantitative implementation of Shaik’s “twin state” concept. Applications are made (i) demonstrating why the chemistry of the first-row elements is qualitatively so different to that of the second and later rows, (ii) deducing the bond-length alternation in hypothetical cyclohexatriene from the observed UV spectroscopy of benzene, (iii) demonstrating that commonly used procedures for modelling surface hopping based on inclusion of only the first-derivative correction to the Born-Oppenheimer approximation are valid in no region of the chemical parameter space, and (iv), demonstrating the types of chemical reactions that may be suitable for exploitation as a chemical qubit in some quantum information processor.
Predicting accurate contacts in thousands of Pfam domain families using PconsC3
Authors: Michel Mirco , Skwark Marcin J , Menéndez Hurtado David , Ekeberg Magnus , Elofsson Arne 
Published: May 2017

Abstract

Motivation
A few years ago it was shown that by using a maximum entropy approach to describe couplings between columns in a multiple sequence alignment it is possible to significantly increase the accuracy of residue contact predictions. For very large protein families with more than 1000 effective sequences the accuracy is sufficient to produce accurate models of proteins as well as complexes. Today, for about half of all Pfam domain families no structure is known, but unfortunately most of these families have at most a few hundred members, i.e. are too small for such contact prediction methods.

Results
To extend accurate contact predictions to the thousands of smaller protein families we present PconsC3, a fast and improved method for protein contact predictions that can be used for families with even 100 effective sequence members. PconsC3 outperforms direct coupling analysis (DCA) methods significantly independent on family size, secondary structure content, contact range, or the number of selected contacts.

Availability and implementation
PconsC3 is available as a web server and downloadable version at http://c3.pcons.net. The downloadable version is free for all to use and licensed under the GNU General Public License, version 2. At this site contact predictions for most Pfam families are also available. We do estimate that more than 4000 contact maps for Pfam families of unknown structure have more than 50% of the top-ranked contacts predicted correctly.

Supplementary information
Supplementary data are available at Bioinformatics online.
Predictable spatiotemporal dynamics of a dense cuttlefish spawning aggregation increases its vulnerability to exploitation
Authors: Hall Karina C , Fowler Anthony J , Geddes Michael C , Taylor Julian D 
Published: May 2017

Abstract
The giant Australian cuttlefish, Sepia apama, forms a dense spawning aggregation at a single known location across its wide southern Australian distribution. After a rapid increase in fishing pressure on the aggregation in the late 1990s, a series of fishing closures were introduced before any biological information could be collected. We surveyed the habitats, timing, and spatial distribution of the spawning aggregation over 4 years, using underwater visual transects and passive tagging, to assess the suitability of the closures. We found that the annual aggregation was both temporally (April–August) and spatially (over 8 km of coastline) localized and predictable, with a consistent peak in abundances in late May–early June. Cuttlefish densities were generally highest over the shallow, broken bedrock habitat, which was more extensive in several sites left open to fishing. Although the original closure covered about 43% of the hard substrate, it accounted for only 23–37% of the total cuttlefish abundance. The extremely high densities recorded during this study verified that this is a massive spawning aggregation for cuttlefish species worldwide, and that it could be highly vulnerable to overexploitation in the absence of adequate protection, because it is so spatiotemporally predictable and localized.