bluuebunny/crossref_metadata_2025_split huggingface dataset:
LMAP: Lightweight Multigene Analyses in PAML
Authors: Maldonado Emanuel , Almeida Daniela , Escalona Tibisay , Khan Imran , Vasconcelos Vitor , Antunes Agostinho 
Published: September 2016

Abstract
Background
Uncovering how phenotypic diversity arises and is maintained in nature has long been a major interest of evolutionary biologists. Recent advances in genome sequencing technologies have remarkably increased the efficiency to pinpoint genes involved in the adaptive evolution of phenotypes. Reliability of such findings is most often examined with statistical and computational methods using Maximum Likelihood codon-based models (i.e., site, branch, branch-site and clade models), such as those available in codeml from the Phylogenetic Analysis by Maximum Likelihood (PAML) package. While these models represent a well-defined workflow for documenting adaptive evolution, in practice they can be challenging for researchers having a vast amount of data, as multiple types of relevant codon-based datasets are generated, making the overall process hard and tedious to handle, error-prone and time-consuming.

Results
We introduce LMAP (Lightweight Multigene Analyses in PAML), a user-friendly command-line and interactive package, designed to handle the codeml workflow, namely: directory organization, execution, results gathering and organization for Likelihood Ratio Test estimations with minimal manual user intervention. LMAP was developed for the workstation multi-core environment and provides a unique advantage for processing one, or more, if not all codeml codon-based models for multiple datasets at a time. Our software, proved efficiency throughout the codeml workflow, including, but not limited, to simultaneously handling more than 20 datasets.

Conclusions
We have developed a simple and versatile LMAP package, with outstanding performance, enabling researchers to analyze multiple different codon-based datasets in a high-throughput fashion. At minimum, two file types are required within a single input directory: one for the multiple sequence alignment and another for the phylogenetic tree. To our knowledge, no other software combines all codeml codon substitution models of adaptive evolution. LMAP has been developed as an open-source package, allowing its integration into more complex open-source bioinformatics pipelines. LMAP package is released under GPLv3 license and is freely available at http://lmapaml.sourceforge.net/.
RETRACTED ARTICLE: HOXA7 plays a critical role in metastasis of liver cancer associated with activation of Snail
Authors: Tang Bo , Qi Guangying , Sun Xiaoyu , Tang Fang , Yuan Shengguang , Wang Zhenran , Liang Xingsi , Li Bo , Yu Shuiping , Liu Jie , Huang Qi , Wei Yangchao , Zhai Run , Lei Biao , Guo Xinjin , He Songqing 
Published: September 2016

Abstract
Background
Liver cancer is one of the main causes of cancer-related death in human. HOXA7 has been proved to be related with several cancers.

Method
The expression levels of HOXA7 were examined by Western blot, qRT-PCR or ICH. MTT was used to detect the proliferative rate of liver cancer cells. The invasive abilities were examined by matrigel and transwell assay. The metastatic abilities of liver cancer cells were revealed in BALB/c nude mice.

Results
In this report, we revealed that HOXA7 promoted metastasis of HCC patients. First, increased levels of HOXA7 were examined in liver cancer especially in metastatic liver cancer. Moreover, higher expression level of HOXA7 was associated with poorer prognosis of liver cancer patients. Overexpression of HOXA7 significantly enhanced proliferation, migration, invasion in vitro and tumor growth and metastasis in vivo meanwhile silencing HOXA7 significantly inhibited the aboves abilities of liver cancer cells. In this research, we identified that HOXA7 performed its oncogenic characteristics through activating Snail.

Conclusion
Collectively, we identify the critical role and possible mechanism of HOXA7 in metastasis of liver cancer which suggest that HOXA7 may be a potential therapeutic target of liver cancer patients.
M-Constants, Dominguez-Benavides coefficient, and weak fixed point property in Orlicz sequence spaces equipped with the p-Amemiya norm
Authors: Cui Yunan , Hudzik Henryk , Wisła Marek 
Published: September 2016

AbstractIn this paper, a formula for the M-constants $\mu_{n}(l_{\Phi,p})$

μ
n

(

l

Φ
,
p

)
of Orlicz sequence spaces $l_{\Phi,p}$

l

Φ
,
p

equipped with the p-Amemiya norm as well as for the equalities $\mu_{n}(l_{\Phi,p})=n$

μ
n

(

l

Φ
,
p

)
=
n
for any $n\in \mathcal{N}$
n
∈
N
are given. Moreover, the Fatou property, weak orthogonality, and the weak fixed point property of these spaces are discussed. Finally a direct formula for the Dominguez-Benavides coefficient of the spaces $l_{\Phi,p}$

l

Φ
,
p

is given in terms of the Orlicz function generating these spaces. Both, M-constants and Dominguez-Benavides coefficient, are strongly related to the fixed point theory.
The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales
Authors: Li Yang , Leahy Sinead C. , Jeyanathan Jeyamalar , Henderson Gemma , Cox Faith , Altermann Eric , Kelly William J. , Lambie Suzanne C. , Janssen Peter H. , Rakonjac Jasna , Attwood Graeme T. 
Published: September 2016

AbstractMethane emissions from agriculture represent around 9 % of global anthropogenic greenhouse emissions. The single largest source of this methane is animal enteric fermentation, predominantly from ruminant livestock where it is produced mainly in their fermentative forestomach (or reticulo-rumen) by a group of archaea known as methanogens. In order to reduce methane emissions from ruminants, it is necessary to understand the role of methanogenic archaea in the rumen, and to identify their distinguishing characteristics that can be used to develop methane mitigation technologies. To gain insights into the role of methylotrophic methanogens in the rumen environment, the genome of a methanogenic archaeon has been sequenced. This isolate, strain ISO4-H5, was isolated from the ovine rumen and belongs to the order Methanomassiliicoccales. Genomic analysis suggests ISO4-H5 is an obligate hydrogen-dependent methylotrophic methanogen, able to use methanol and methylamines as substrates for methanogenesis. Like other organisms within this order, ISO4-H5 does not possess genes required for the first six steps of hydrogenotrophic methanogenesis. Comparison between the genomes of different members of the order Methanomassiliicoccales revealed strong conservation in energy metabolism, particularly in genes of the methylotrophic methanogenesis pathway, as well as in the biosynthesis and use of pyrrolysine. Unlike members of Methanomassiliicoccales from human sources, ISO4-H5 does not contain the genes required for production of coenzyme M, and so likely requires external coenzyme M to survive.
Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57
Authors: Schofield Benjamin J. , Skarshewski Adam , Lachner Nancy , Ouwerkerk Diane , Klieve Athol V. , Dart Peter , Hugenholtz Philip 
Published: September 2016

AbstractBacillus amyloliquefaciens H57 is a bacterium isolated from lucerne for its ability to prevent feed spoilage. Further interest developed when ruminants fed with H57-inoculated hay showed increased weight gain and nitrogen retention relative to controls, suggesting a probiotic effect. The near complete genome of H57 is ~3.96 Mb comprising 16 contigs. Within the genome there are 3,836 protein coding genes, an estimated sixteen rRNA genes and 69 tRNA genes. H57 has the potential to synthesise four different lipopeptides and four polyketide compounds, which are known antimicrobials. This antimicrobial capacity may facilitate the observed probiotic effect.
A comparative study of enzyme initiators for crosslinking phenol-functionalized hydrogels for cell encapsulation
Authors: Roberts Justine J. , Naudiyal Pratibha , Lim Khoon S. , Poole-Warren Laura A. , Martens Penny J. 
Published: September 2016

Abstract

Background
Dityrosine crosslinking in proteins is a bioinspired method of forming hydrogels. This study compares oxidative enzyme initiators for their relative crosslinking efficiency and cytocompatibility using the same phenol group and the same material platform. Four common enzyme and enzyme-like oxidative initiators were probed for resulting material properties and cell viability post-encapsulation.

Results
All four initiators can be used to form phenol-crosslinked hydrogels, however gelation rates are dependent on enzyme type, concentration, and the oxidant. Horseradish peroxidase (HRP) or hematin with hydrogen peroxide led to a more rapid poly (vinyl alcohol)-tyramine (PVA-Tyr) polymerization (10–60 min) because a high oxidant concentration was dissolved within the macromer solution at the onset of crosslinking, whereas laccase and tyrosinase require oxygen diffusion to crosslink phenol residues and therefore took longer to gel (2.5+ hours). The use of hydrogen peroxide as an oxidant reduced cell viability immediately post-encapsulation. Laccase- and tyrosinase-mediated encapsulation of cells resulted in higher cell viability immediately post-encapsulation and significantly higher cell proliferation after one week of culture.

Conclusions

Overall this study demonstrates that HRP/H
2
O
2
, hematin/H
2
O
2
, laccase, and tyrosinase can create injectable,
in situ
phenol-crosslinked hydrogels, however oxidant type and concentration are critical parameters to assess when phenol crosslinking hydrogels for cell-based applications.
Monopoly Pricing in the Presence of Social Learning
Authors: Crapis Davide , Ifrach Bar , Maglaras Costis , Scarsini Marco 
Published: September 2016

A monopolist offers a product to a market of consumers with heterogeneous quality preferences. Although initially uninformed about the product quality, they learn by observing past purchase decisions and reviews of other consumers. Our goal is to analyze the social learning mechanism and its effect on the seller’s pricing decision. Consumers follow an intuitive, non-Bayesian decision rule. Under conditions that we identify, we show that consumers eventually learn the product’s quality. We show how the learning trajectory can be approximated in settings with high demand intensity via a mean-field approximation that highlights the dynamics of this learning process, its dependence on the price, and the market heterogeneity with respect to quality preferences. Two pricing policies are studied: a static price and one with a single price change. Finally, numerical experiments suggest that pricing policies that account for social learning may increase revenues considerably relative to policies that do not. This paper was accepted by Yossi Aviv, operations management.
Continuing Professional Development: Understanding paramedic treatment and management of pulmonary embolism
Authors: Parry Andy , Higginson Ray 
Published: September 2016

Overview Pulmonary embolism (PE) is one of the most common preventable deaths in the UK. Causing occlusion of the pulmonary arteries, a PE is most often the result of the formation of a deep vein thrombosis (DVT) which ‘breaks free’ and travels to the lungs where it alters the normal ventilation/perfusion (V/Q) relationship, resulting in hypoxia, increased dead space and intrapulmonary shunting. This Continuing Professional Development (CPD) module will explore the pathophysiology, assessment and management of PE by paramedics, and explore the condition's main causes and treatment from the paramedic's perspective.
A survey of the eutrophication state of an urbanized tropical estuary, the case of the Great Vitória Estuarine System, Brazil.
Authors: Grilo Caroline F. , Dos Santos Carina C. , Boina Catarina D. , Pinto Taciana K.O. , Barroso Gilberto F. , Neto Renato R. , Ribeiro de Castro Eustáquio Vinicius , De Araújo Vicente Maristela 
Published: September 2016

Although, estuarine ecosystems have an ecological and economical importance as they have a high biological productivity and occur within a unique and dynamic environment, they have been subjected to anthropogenic alterations. The Great Vitória Estuarine System (GVES), Espírito Santo State, Brazil, is not an exception, as urbanization is growing around it with a high quantity of sewage been added to the system. In order to evaluate the eutrophication state as well as the meiofauna response to it, several parameters in both sediments and in the water column were assessed. Orthophosphate, nitrite, nitrate, ammonia, chla and Fecal Coliform counts (FC) ranged from 0.2 to 3.2 μM, 0.25 to 1.14 μM, 1.83 to 0.19μM, 4.19 to 49.23 μM, 0.61 to 6.72 μg/L and 14 to 5.0x104 MPN/100 mL of water, respectively. These results showed that the GVES is under an eutrophication process and that the Passagem Channel experienced the largest impacts. Sewage plays an important role in this eutrophication process as indicated by PCA and correlations tests. The density of meiofauna showed similar values to those found in environments with similar levels of anthropogenic stress. This multi-approach evaluation revealed several aspects of the impacted estuary and could be used as an important tool to manage better the estuary.
Medical Genetics and the First Studies of the Genetics of Populations in Mexico
Authors: Barahona Ana 
Published: September 2016

AbstractFollowing World War II (WWII), there was a new emphasis within genetics on studying the genetic composition of populations. This probably had a dual source in the growing strength of evolutionary biology and the new international interest in understanding the effects of radiation on human populations, following the atomic bombings in Japan. These global concerns were shared by Mexican physicians. Indeed, Mexico was one of the leading centers of this trend in human genetics. Three leading players in this story were Mario Salazar Mallén, Adolfo Karl, and Rubén Lisker. Their trajectories and the international networks in human genetics that were established after WWII, paved the way for the establishment of medical and population genetics in Mexico. Salazar Mallén’s studies on the distribution and characterization of ABO blood groups in indigenous populations were the starting point while Karl’s studies on the distribution of abnormal hemoglobin in Mexican indigenous populations showed the relationships observed in other laboratories at the time. It was Lisker’s studies, however, that were instrumental in the development of population genetics in the context of national public policies for extending health care services to the Mexican population. In particular, he conducted studies on Mexican indigenous groups contributing to the knowledge of the biological diversity of human populations according to international trends that focused on the variability of human populations in terms of genetic frequencies. From the start, however, Lisker was as committed to the reconstruction of shared languages and practices as he was to building networks of collaboration in order to guarantee the necessary groundwork for establishing the study of the genetics of human populations in Mexico. This study also allows us to place Mexican science within a global context in which connected narratives describe the interplay between global trends and national contexts.
Recommendations for Prevention and Control of Influenza in Children, 2016–2017
Authors:   COMMITTEE ON INFECTIOUS DISEASES, Byington Carrie L. , Maldonado Yvonne A. , Barnett Elizabeth D. , Campbell James D. , Davies H. Dele , Edwards Kathryn M. , Lynfield Ruth , Munoz Flor M. , Nolt Dawn L. , Nyquist Ann-Christine , O’Leary Sean T. , Rathore Mobeen H. , Sawyer Mark H. , Steinbach William J. , Tan Tina Q. , Zaoutis Theoklis E. 
Published: September 2016

The purpose of this statement is to update recommendations for the routine use of seasonal influenza vaccine and antiviral medications for the prevention and treatment of influenza in children. The AAP recommends annual seasonal influenza immunization for everyone 6 months and older, including children and adolescents. Highlights for the upcoming 2016–2017 season include the following:
1. Annual universal influenza immunization is indicated with either a trivalent or quadrivalent (no preference) inactivated vaccine.
2. The 2016–2017 influenza A (H3N2) vaccine strain differs from that contained in the 2015–2016 seasonal vaccines. The 2016–2017 influenza B vaccine strain (Victoria lineage) included in the trivalent vaccine differs from that contained in the 2015–2016 seasonal trivalent vaccines (Yamagata lineage).
a. Trivalent vaccine contains an A/California/7/2009 (H1N1)pdm09–like virus, an A/Hong Kong/4801/2014 (H3N2)–like virus, and a B/Brisbane/60/2008-like virus (B/Victoria lineage).
b. Quadrivalent vaccine contains an additional B virus (B/Phuket/3073/2013-like virus [B/Yamagata lineage]).
3. Quadrivalent live attenuated influenza vaccine (LAIV4) should not be used in any setting during the 2016–2017 influenza season in light of the evidence for poor effectiveness of LAIV4 in recent seasons, particularly against influenza A (H1N1)pdm09 viruses.
4. All children with egg allergy can receive influenza vaccine with no additional precautions from those of routine vaccinations.
5. All HCP should receive an annual influenza vaccine, a crucial step in preventing influenza and reducing health care–associated influenza infections. Because HCP may care for or live with people at high risk of influenza-related complications, it is especially important for them to get vaccinated annually.
6. Pediatricians should attempt to promptly identify children suspected of having influenza for rapid antiviral treatment, when indicated, to reduce morbidity and mortality.
МЕТОДИКА РАСЧЕТА ВОДНОГО БАЛАНСА ДЛЯ СУХОЙ СТЕПИ ЮГА ЗАПАДНОЙ СИБИРИ ПО ДАННЫМ МЕЖДУНАРОДНОЙ МОНИТОРИНГОВОЙ СЕТИ
Authors: Meissner R. , Bondarovich A. A. , Scherbinin V. V. , Ponkina E. V. , Matsyura A. V. , Puzanov A. V. , Rupp H. , Schmidt G. , Stephan E. , Illiger P. , Fruhauf M. , Harlamova N. F. , Galahov V. P. , Balykin D. V. , Rudev N. V. 
Published: September 2016

<p>The study of the water balance is not only of great practical importance, but also of interest from the standpoint of basic science for the researchers of the steppe zone, which has traditionally attracted people for its climate and soil resources. The article presents the results obtained from a network of automatic stations deployed in the framework of the Russian-German scientific cooperation in the field of climate, soil, and hydrological monitoring for 2012-2015. The instrumental data were obtained and the method of soil water balance calculation was performed on the basis of data of automatic weather station observations and lysimetric stations of new generation in the conditions of Western Siberia.</p><p> </p>
Functionalized Regioregular Polyalkylthiophenes for Biosensing Applications
Authors: Higgins Simon J. , Mouffouk Fouzi , Brown Stewart J. , Sedghi Naser , Eccleston Bill , Reeman Stuart 
Published: September 2016

AbstractA regioregular copolymer of 3–hexylthiophene and 3–(6–hydroxyhexan–1yl)thiophene has been functionalised with biotin hydrazide; binding of avidin to the biotin moieties causes drastic changes to the absorption spectrum of the polymer in solution, and to the electrochemistry and conductivity of the polymer in thin films.
13.56 MHz Organic Transistor Based Rectifier Circuits for RFID Tags
Authors: Rotzoll Robert , Mohapatra Siddharth , Olariu Viorel , Wenz Robert , Grigas Michelle , Shchekin Oleg , Dimmler Klaus , Dodabalapur Ananth 
Published: September 2016

AbstractOne of the potential application areas for organic and polymers transistors is in radiofrequency identification (RFID) tags. One of the key components of an RFID tag is the front-end rectifier that must rectify a 13.56 MHz AC signal received from a resonant tuned antenna. The rectifier supplies operating power to the tag. Organic transistor circuits have hitherto not operated at this high frequency. We show that by operating pentacene transistors in the non-quasi-static (NQS) regime such operating speeds can be achieved in rectifier circuits. The circuits were fabricated on flexible plastic substrates and employed a solution-cast dielectric. The pentacene mobilities are in the range 0.1-1.5 cm2/V-s. The channel lengths of the transistors are in the range 2-4 μm. Full-wave NQS mode rectifiers were measured to have voltage rectification efficiency in excess of 28% at 14 MHz, demonstrating that such circuits can be used in RFID tags. These circuits operated successfully at speeds up to 20 MHz.
Organic Thin Film Transistors with Contacts Printed from Metal Nanoparticles
Authors: Wu Yiliang , Li Yuning , Gardner Sandra , Ong Beng S. 
Published: September 2016

AbstractMetal nanoparticles were studied as solution printable precursors to highly conductive elements for electronic device applications. Dispersions of gold and silver nanoparticles stabilized respectively with butanethiol and hexadecylamine in organic solvents were used to prepare electrode features for organic thin film transistors (OTFTs) via stencil printing. The printed features, annealed at a relatively low temperature of 140-160°C, yielded metal electrodes with conductivities resembling those of vacuum-evaporated pure metals. The OTFTs with the source and drain electrodes of this nature exhibited field effect transistor performance identical to those of devices having vacuum-evaporated metal electrodes.
Highly Efficient Multifunctional Phosphorescent Dendrimers Consisting of an Iridium-Complex Core and Charge-Transporting Dendrons for Organic Light-Emitting Devices
Authors: Tsuzuki Toshimitsu , Shirasawa Nobuhiko , Suzuki Toshiyasu , Tokito Shizuo 
Published: September 2016

AbstractWe report a novel class of emitting materials for use in the organic light-emitting devices (OLEDs): multifunctional phosphorescent dendrimers that have a phosphorescent core and have charge transporting dendrons. We have synthesized first-generation and second-generation dendrimers consisting of a fac-tris(2-phenylpyridine)iridium [Ir(ppy)3] core and hole transporting phenylcarbazole-based dendrons. Smooth amorphous films of these dendrimers were formed by spin-coating them from solutions. The OLEDs using the dendrimer exhibited bright green or yellowish-green emission from the Ir(ppy)3 core. The external quantum efficiency of the OLED using the mixture film of the first-generation dendrimer and an electron-transporting material was as high as 7.6%.
Control of Thin Film Transistor Operations with Polar Self-Assembled Monolayers
Authors: Iwasa Y. , Nishikawa T. , Kobayashi S. , Takenobu T. , Shimoda T. , Mitani T. , Kubozono K. 
Published: September 2016

AbstractFrom the view point of materials sciences, one of the central issues in organic thin film transistors (TFTs) is the interface between different materials inherent in the device structure. For example, the interface between organic semiconductors and electrodes controls the carrier injection, while the interface between organic semiconductors and gate insulators governs the trap and carrier densities. Here, we show that interface modification with self-assembeld monolayers (SAMs) using polar organosilane molecules offers novel functions in organic TFTs. SAMs on SiO2 gate dielectrics was found to the carrier density at the conduction channel, while the adsorbed SAMs molecules on metal electrodes causes an ambipolar operation in fullerene TFTs. These interface modification techniques, since they are low temperature processes, provide novel opportunities for improving device manufacturing processes.