bluuebunny/crossref_metadata_2025_split huggingface dataset:
Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry
Authors: Garcia Natalie K. , Deperalta Galahad , Wecksler Aaron T. 
Published: November 2018

Background:
Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing
class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability
are linked to the proper three-dimensional organization of the primary sequence into
Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods
that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant
protein-protein interactions and assessing properly folded structures. Irreversible covalent protein
footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl
radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility
influenced by tertiary and quaternary structure. Here we discuss the methodology, examples
of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting
MS in biotherapeutic research and development.

Conclusion:
Bottom-up mass spectrometry using irreversible labeling techniques provide valuable
information for characterizing solution-phase protein structure. Examples range from epitope mapping
and protein-ligand interactions, to probing challenging structures of membrane proteins. By
paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase
structural data such as crystallography or electron microscopy, a comprehensive understanding of
protein structure can be obtained.
Using X-ray Footprinting and Mass Spectrometry to Study the Structure and Function of Membrane Proteins
Authors: Gupta Sayan 
Published: November 2018

Background:
Membrane proteins are crucial for cellular sensory cascades and metabolite
transport, and hence are key pharmacological targets. Structural studies by traditional highresolution
techniques are limited by the requirements for high purity and stability when handled in
high concentration and nonnative buffers. Hence, there is a growing requirement for the use of alternate
methods in a complementary but orthogonal approach to study the dynamic and functional
aspects of membrane proteins in physiologically relevant conditions. In recent years, significant
progress has been made in the field of X-ray radiolytic labeling in combination with mass spectroscopy,
commonly known as X-ray Footprinting and Mass Spectrometry (XFMS), which provide
residue-specific information on the solvent accessibility of proteins. In combination with both lowresolution
biophysical methods and high-resolution structural data, XFMS is capable of providing
valuable insights into structure and dynamics of membrane proteins, which have been difficult to
obtain by standalone high-resolution structural techniques. The XFMS method has also demonstrated
a unique capability for identification of structural waters and their dynamics in protein cavities
at both a high degree of spatial and temporal resolution, and thus capable of identifying conformational
hot-spots in transmembrane proteins.

Conclusion:
We provide a perspective on the place of XFMS amongst other structural biology
methods and showcase some of the latest developments in its usage for studying conformational
changes in membrane proteins.
Identification, Prediction and Data Analysis of Noncoding RNAs: A Review
Authors: Emamjomeh Abbasali , Zahiri Javad , Asadian Mehrdad , Behmanesh Mehrdad , Fakheri Barat A. , Mahdevar Ghasem 
Published: November 2018

Background:Noncoding RNAs (ncRNAs) which play an important role in various cellular processes are important in medicine as well as in drug design strategies. Different studies have shown that ncRNAs are dis-regulated in cancer cells and play an important role in human tumorigenesis. Therefore, it is important to identify and predict such molecules by experimental and computational methods, respectively. However, to avoid expensive experimental methods, computational algorithms have been developed for accurately and fast prediction of ncRNAs.Objective:The aim of this review was to introduce the experimental and computational methods to identify and predict ncRNAs structure. Also, we explained the ncRNA’s roles in cellular processes and drugs design, briefly.Method:In this survey, we will introduce ncRNAs and their roles in biological and medicinal processes. Then, some important laboratory techniques will be studied to identify ncRNAs. Finally, the state-of-the-art models and algorithms will be introduced along with important tools and databases.Results:The results showed that the integration of experimental and computational approaches improves to identify ncRNAs. Moreover, the high accurate databases, algorithms and tools were compared to predict the ncRNAs.Conclusion:ncRNAs prediction is an exciting research field, but there are different difficulties. It requires accurate and reliable algorithms and tools. Also, it should be mentioned that computational costs of such algorithm including running time and usage memory are very important. Finally, some suggestions were presented to improve computational methods of ncRNAs gene and structural prediction.
Ephedrine Analysis in Real Urine Sample via Solvent Bar Microextraction Technique Coupled with HPLC-UV and Chemometrics
Authors: Behbahani Persia , Qomi Mahnaz , Ghasemi Nahid , Tahvildari Kambiz 
Published: November 2018

Background:
Ephedrine, an alpha/beta-adrenergic agonist, is one of the most common doping
agents not only among athletes but also the ordinary people, therefore its detection at low trace levels
with a sensitive and cost effective method has become a priority to investigate many analytical
methods.

Objective:
In this work, solvent bar microextraction followed by high-performance liquid chromatography
(HPLC-UV) was used for extraction and determination of ephedrine at low trace levels from urine
samples at optimum condition.

Methods:
In this study, a designed experiment was carried out using solvent bar microextraction technique,
which has been proved to be a green method. This method requires three phases consisting of a
donor phase with an alkaline pH, an acceptor phase with an acidic pH, and organic solvent to impregnate
the pores of the hollow fiber. The obtained results were used for estimating the optimum ranges for
each parameter, analyzing the effect of different parameters, simultaneously.

Results:

Under optimized circumstances, the preconcentration factor was 129. The calibration curves
represented good linearity for urine sample with coefficient estimations higher than 0.9991. The limit of
detection and quantitation for ephedrine were 16.7 µg L-1 and 50 µg L-1, respectively. The relative standard
deviations of analysis were 3.5% within a day (n=3) and 4.1% between days (n=9).

Conclusion:
According to the results and previous studies, it can be concluded that the preconcentration
factor for ephedrine was the best result ever reported considering selectivity and cost-effectiveness.
Simultaneous Determination of Kirenol, Rosmarinic Acid and Caffeic Acid in Rat Plasma and Pharmacokinetic Study After Oral Administration of the Extract of Manxingshizhen Preparation by UPLC-MS/MS
Authors: Sun Shuo , Zhang Xue , Luo Linda , Wang Ping , Bai Mengxuan , Yu Jia , Guo Xingjie 
Published: November 2018

Introduction:
A rapid, sensitive and convenient ultra-performance liquid chromatography
with tandem mass spectrometric detection (UPLC-MS/MS) method has been validated and applied to
the simultaneous determination of kirenol, rosmarinic acid and caffeic acid after oral administration of
the extract of Manxingshizhen preparation in rat plasma.

Materials and Methods:
Puerarin was selected as the internal standard (IS). The plasma sample preparation
was pretreated by liquid-liquid extraction of the mixture with ethyl acetate. All analytes were
simultaneously detected in multiple reaction monitoring (MRM) mode via both the positive electrospray
ionization (ESI+) and negative electrospray ionization (ESI). In the experiment, all calibration curves
revealed good linearity (r > 0.999). The LLOQ were between 0.80-2.00 ng/mL, respectively.

Besides, the intra-day and inter-day precision ranged from 6.4 to 13.8%, respectively. Moreover, the
accuracy was within - 11.4% and 12.8% for all the QC levels of all analytes. The extraction recoveries
of the analytes and IS in plasma at three concentration levels ranged from 88.5 to 103.2%, moreover,
the matrix effects of all the analytes and the IS were found to be satisfied with the acceptable range of
89.8%-101.7%. Meanwhile, the RSD values of stability met the requirement of not more than 15%.
Furthermore, the pharmacokinetic parameters of three compounds were analyzed using concentrationtime
profiles.

Conclusion and Results:
Plasma concentrations of the three compounds were determined up to 24 h
after oral administration, and their pharmacokinetic parameters were in agreement with previous studies.
The validated method was successfully applied in a pharmacokinetic study in rat plasma after oral
administration of Manxingshizhen preparation.
Characterization of Biocompatible Gold Nanoparticles Synthesized by using Curcuma xanthorrhiza and their Catalytic Activity
Authors: Lubis Khairiza , Chudapongse Nuannoi , Doan Hau Van , Weeranantanapan Oratai 
Published: November 2018

Background:
Based on various distinguished physical and chemical properties of gold
nanoparticles, they have far wide applications in several areas of industry and medicine, such as catalysis,
bio-sensor and drug delivery. Compared to a chemical method, biological synthesis is an
economical and less toxic process, thus it is a better alternative for nanoparticle synthesis. In this
study, an environmentally friendly method was chosen to produce AuNPs using Curcuma
xanthorrhiza.

Methods:
Alkaline aqueous extract of C. xanthorrhiza rhizomes, which acts as a reducing and stabilizing
agent was used to produce AuNPs by bio-reduction of HAuCl4. The formation of AuNPs was
periodically monitored by UV-visible spectroscopy. The obtained AuNPs were characterized by Xray
diffraction, energy dispersive spectroscopy, scanning electron microscopy, transmission electron
microscopy, and Fourier transform infrared (FTIR) spectroscopy. Catalytic activity and toxicity of
the AuNPs were evaluated.

Results:
The AuNPs obtained from this study mostly were spherical in shape with approximately 15
nm in size. The presence of functional groups derived from C. xanthorrhiza rhizome extract involved
in the gold bio-reduction process was confirmed by the spectrum of FTIR spectroscopy. The biosynthesized
AuNPs at the concentration of 0.5 μg/ml had catalytic activity in dye degradation of Congo
red. The results showed that this biogenic AuNPs did not cause any toxicity to zebrafish embryos and
all tested cell lines.

Conclusion:
The biocompatible AuNPs with catalytic activity were successfully fabricated with C.
xanthorrhiza rhizome extract by simple eco-friendly and inexpensive method. This catalytic activity
of the obtained AuNPs is potentially useful for industrial applications as well as nanoscience and
nanotechnology.
Effect of Plasma of Argon Treated Implants on Bone Density: A Randomized, Controlled, Histomorphometric Study in Dogs
Authors: Tanaka Kazushige , Silva Erick Ricardo , Kawakami Shunsuke , Canullo Luigi , Botticelli Daniele , Xavier Samuel P. 
Published: November 2018

Background:Altering surface characteristics by increasing its energy and hydrophilicity will accelerate the interaction between cells and implant surface. Energy and hydrophilicity tend to disappear over a short time. The implant surface may be reactivated by the use of argon plasmaObjective:To assess bone density at cleaned and activated titanium implants using argon plasma.Methods:Mandibular premolars and first molars were extracted bilaterally in eight Beagle dogs. After three months, four implants, two treated with argon plasma (test; plasma) and two left without treatment (control), were randomly installed in one side of the mandible. Abutments were applied on the implants and a non-submerged healing was allowed. After one month, the same surgical procedures were adopted on the opposite side of the mandible. The animals were euthanized after one month and ground sections representing the healing after 1 and 2 months were obtained for histological examination.Results:No statistically significant differences were found between test and control sites (p< 0.05). After 1 month of healing, new bone was 32.5 ± 12.2% and 33.8 ± 8.8% at the plasma and control sites, respectively. After 2 months, the respective values were 50.8 ± 21.5% and 47.6 ± 15.6%.Conclusion:The treatment of the implant surface with argon plasma did not have a significant effect on bone density around implants.
Machine Learning Based Support System for Students to Select Stream (Subject)
Authors: Sethi Kapil , Jaiswal Varun , Ansari Mohammad Dilshad 
Published: November 2018

Background:In most of the countries, students have to select a subject/stream in the secondary education phase. Selection of subject/stream is crucial for students because further their career proceeds according to their selection. Mostly subject/stream selection cannot be changed in the further career. Inappropriate selection of subjects due to parental pressure, lack of information etc. can lead to limited success in the selected stream. Guidance for subject/stream selection based on information of successful scholars of their stream and information of students such as interest, family background, previous education and other associated can enhance the success in career.Methods:Data mining and machine learning based methods were developed on the above information. Data from the different institutions and students of two different streams were used for training and testing purposes. Different machine learning algorithms were used and methods with high accuracy (86.72) were developed.Result:Developed methods can be extended and used for different subject/stream selection.
An Implementation of Three-level Multi-objective ABC Algorithm for RNA Multiple Structural Alignment
Authors: Lalwani Soniya , Sharma Harish , Deep Kusum 
Published: November 2018

Background:
Structural alignment of ribose nucleic acid (RNA) is one of the most challenging
multi-objective real world problems from the field of bioinformatics.

Objective:
RNA molecules are less stable; hence they require inclusion of most stable secondary
structure during their alignment. Therefore, the structural alignment requires the consideration of
similarity score and structure score, as two objectives. Trade-off between these two objectives exists
since obtaining optimum similarity score at concurrent optimum structure score is not possible. This
paper presents artificial bee colony algorithm based three level multi-objective approach for performing
structural alignment of RNA sequences, namely MO-3LABC.

Methods:
Algorithm firstly builds the secondary structure of all sequences at minimum free energy
(MFE). Then sequence alignment is performed in level one at average percent sequence identity
(APSI) score based gap length, optimized by ABC algorithm. Level two now builds the secondary
structure of these aligned sequences based on base-pair probability and co-variation. Now the scores
of level one and level two move towards level three for multi-objective optimization at Pareto optimality
criteria with few additional strategies.

Results:
The results of MO-3LABC are compared with an already established efficient strategy
MO-TLPSO; multi-objective two level strategy based on particle swarm optimization. The outputs
are compared for pairwise and multiple sequence alignment datasets at prediction accuracy and solution
quality criteria.

Conclusion:
MO-3LABC is found significantly better than MO-TLPSO at all the four evaluation
criteria for both the datasets.
Catechize Global Optimization through Leading Edge Firefly Based Zone Routing Protocol
Authors: Sharma Neha , Zafar Sherin , Batra Usha 
Published: November 2018

Background:
Zone Routing Protocol is evolving as an efficient hybrid routing protocol
with an extremely high potentiality owing to the integration of two radically different schemes,
proactive and reactive in such a way that a balance between control overhead and latency is
achieved. Its performance is impacted by various network conditions such as zone radius, network
size, mobility, etc.

Objective:
The research work described in this paper focuses on improving the performance of zone
routing protocol by reducing the amount of reactive traffic which is primarily responsible for
degraded network performance in case of large networks. The usage of route aggregation approach
helps in reducing the routing overhead and also help achieve performance optimization.

Methods:
The performance of proposed protocol is assessed under varying node size and mobility.
Further applied is the firefly algorithm which aims to achieve global optimization that is quite difficult
to achieve due to non-linearity of functions and multimodality of algorithms. For performance
evaluation a set of benchmark functions are being adopted like, packet delivery ratio and end-to-end
delay to validate the proposed approach.

Results:
Simulation results depict better performance of leading edge firefly algorithm when compared
to zone routing protocol and route aggregation based zone routing protocol. The proposed
leading edge FRA-ZRP approach shows major improvement between ZRP and FRA-ZRP in Packet
Delivery Ratio. FRA-ZRP outperforms traditional ZRP and RA-ZRP even in terms of End to End
Delay by reducing the delay and gaining a substantial QOS improvement.

Conclusion:
The achievement of proposed approach can be credited to the formation on zone head
and attainment of route from the head hence reduced queuing of data packets due to control packets,
by adopting FRA-ZRP approach. The routing optimized zone routing protocol using Route aggregation
approach and FRA augments the QoS, which is the most crucial parameter for routing performance
enhancement of MANET.
Influências Europeias no Cinema Gaúcho Urbano
Authors: Gerbase Carlos 
Published: November 2018

Este texto investiga se o cinema urbano em super- 8, surgido em Porto Alegre no final da década de 70 - e que acabou influenciando decisivamente a estética das filmes gaúchos das décadas seguintes - recebeu algum tipo de influência europeia. Para tanto, foram ouvidos os dois diretores do filme "Deu pra ti, anos 70", Nelson Nadotti e Giba Assis Brasil, e seus depoimentos foram analisados em relação às
noções de "autoria" e "influência".
Biografia: do estado da arte à prática da escrita da vida em Jornalismo
Authors: Martinez Monica 
Published: November 2018

O artigo discute, a partir da etimologia, os conceitos de biografia em áreas distintas
do conhecimento, como Ciências Sociais e Literatura, enfocando as narrativas biográficas
na perspectiva do Jornalismo. Neste âmbito, descreve as concepções jornalísticas atuais
de perfil, memória, biografia, ensaio pessoal e narrativa de viagem, exemplificando-as. Em
seguida, aborda a necessidade de aprofundamento da compreensão humana na construção
biográfica, resgatando a noção de missão da cultura antiga grega e sua contraparte atual por
meio da teoria do fruto do carvalho. Delineia também as visões psiquiátricas freudiana e
junguiana, complementando-as com a questão da memória do ponto de vista da Mitologia,
Neurologia e da Psicologia Social. As discussões são propostas no âmbito do tempo escalonado
da Nova História. Para finalizar, dada a complexidade da reconstrução das narrativas
biográficas, propõe-se o conhecimento de novas metodologias, como Jornada Humana,
Biografia Humana e Teoria do Caos e dos Fractais.
Os meios de comunicação e o suicídio: uma breve genealogia da narrativa da própria morte
Authors: Tucherman Ieda , Clair Ericson Saint 
Published: November 2018

O objetivo deste trabalho é abordar, em perspectiva genealógica, a questão do
suicídio em relação com os meios de comunicação. O recente caso do jovem brasileiro que
narrou o próprio suicídio na Internet é ponto de partida para investigarmos de que forma o
ciberespaço interfere na criação de si, sendo a narrativa da própria morte um caso extremo
de produção biográfica. Para redimensionar o problema, tecemos uma breve genealogia da
vinculação entre suicídio e meios de comunicação cm dois outros casos: a publicação, no
século XIX, de "Os sofrimentos do jovem Werther", de Goethe - e a profusão de suicídios
decorrentes dela - e a morte do roqueiro Kurt Cobain, em um século XX profundamente
mediado pela cultura de massas. Sugerimos que o suicídio é, fundamentalmente, uma questão
de biopolítica, em um contexto em que a mídia tem importante papel na produção de
diversos quadros culturais em nossa atualidade de medicina salvacionista.
Transmidiação e cultura participativa: pensando as práticas textuais de agenciamento dos fãs de telenovelas brasileiras
Authors: Fechine Yvana 
Published: November 2018

A digitalização e a convergência de meios
inseriram a televisão na era da transmidiação,
que é entendida como um modelo de produção
orientado pela distribuição em distintas mídias
e plataformas tecnológicas de conteúdos
associados entre si e cuja articulação está
ancorada em estratégias e práticas interacionais
propiciadas pela cultura participativa. Em uma
etapa anterior de pesquisa, foram identificadas
e categorizadas as estratégias transmídias
adotadas pela televisão brasileira na produção
de telenovelas. Como elas convocam algum tipo
de participação dos fãs telespectadores, resta
ainda o desafio de inventariar e analisar o modo
como eles se relacionam com os conteúdos
transmídias disponibilizados pelos produtores.
Neste artigo, foram problematizadas noções
que parecem interligadas e preliminares ao
processo de observação empírica dessas
relações: cultura participativa, fãs e práticas
textuais do agenciamento de conteúdos.
Por um modo de existência do lúdico
Authors: Lemos André 
Published: November 2018

O objetivo deste artigo é discutir a teoria
ator-rede a parti r dos “modos de existência”,
sugerindo a inclusão de mais um modo para
pensar a modernidade. Discute-se uma questão
que a leitura do últi mo livro do sociólogo francês
Bruno Latour, Enquête sur les modes d’Existence
(2012), deixa em aberto: a ausência de um
“modo de existência” do lúdico. Parece faltar
esta que é uma das importantes dimensões da
produção da subjeti vidade moderna. O arti go
apresenta os modos de existência, propõe mais
um modo (lúdico), apontando para a existência
de “seres do jogo”, e estabelece correlações
deste com outros modos, como o da técnica,
o da metamorfose e o da fi cção. O objeti vo é
contribuir para a discussão sobre a teoria atorrede,
os estudos sobre os games e ao campo
da comunicação como um todo.