bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute Treatment of Open Foot and Ankle Fractures Using a Bioartificial Dermal Regeneration Template and Split-Thickness Skin Grafting
Authors: McMillan Logan J. , Parikh Harsh R. , Cunningham Brian P. 
Published: May 2019

Case:
Two patients with open foot and ankle fractures were treated with aggressive irrigation and debridement and acute placement of a dermal regeneration template (DRT) followed by split-thickness skin grafting. Patient 1 was an 82-year-old female with a type IIIB open ankle fracture complexed with 2 significant regions of soft tissue loss. Patient 2 was a 54-year-old male with type IIIB open metatarsal fractures. Both patients healed without complication.

Conclusions:
Complex open fractures in lower extremities can be managed with acute DRT application. This may be a more cost-effective solution compared to free flaps.
Upscaling the Steam-Assisted-Gravity-Drainage Model for Heterogeneous Reservoirs
Authors: Takbiri-Borujeni Ali , Mohammadnia Vahid , Mansouri-Boroujeni Mahdi , Nourozieh Hossein , Ghahfarokhi Payam Kavousi 
Published: May 2019

Summary
The effects of heterogeneities in the rock and fluid properties on the governing equations in modeling the steam-assisted-gravity-drainage (SAGD) process are investigated using a spectrum-based upscaling approach. In this approach, heterogeneity is included by assigning random perturbation fields to permeability and thermal diffusivity that hold the assumption of first and second orders of stationarity. Heat and mass-transport parameters and dependent variables (e.g., temperature and viscosity) that are affected by heterogeneity are represented by their mean and perturbations around the mean values. Substituting the perturbed variables and coefficients into the basic governing equations (heat-diffusion and Darcy equations) results in new sets of stochastic partial-differential equations that include mean and perturbation. Mean equations are essentially upscaled new governing equations that include the autocorrelations and cross correlations between different perturbed quantities. The cross correlations are derived by applying the Fourier-Stieltjes transform. Verification and validation of the developed results for the heat-diffusion equation are performed using numerical simulations with synthetic heterogeneities.
The upscaled equations embrace the heterogeneity in permeability and thermal diffusivity and can predict the flow rate and shape of the steam chamber. The upscaled model is compared with the homogeneous model, developed by Butler (1991), to quantify the effects of heterogeneities in permeability and thermal diffusivity on the SAGD efficiency. A case is studied by assigning harmonic distribution to the perturbations of thermal diffusivity and permeability. Different cases with different relationships between permeability and thermal-diffusivity fields are considered to investigate their effects on the oil flow rate. The results show that local perturbations decrease the oil flow rate. Furthermore, steam-chamber growth is retarded in a reservoir with local perturbations compared with homogeneous reservoirs.
The developed model can be used in the initial stages of SAGD development projects for long-range planning as a guide to find the upper and lower limits of production in reservoirs with heterogeneities.
Genome-wide identification of MAPKKK genes and their response to phytoplasma stress in Chinese jujube (Ziziphus jujuba Mill.)
Authors: Liu ZhiGuo , Wang Lixin , Xue Chaoling , Chu Yuetong , Gao Weilin , Zhao Yitong , Zhao Jin , Liu Mengjun 
Published: May 2019

Abstract
Backgrounds

Mitogen activated protein kinase (MAPK) cascades play vital roles in signal transduction in response to various biotic and abiotic stresses. In the previous study we have identified 10 ZjMAPKs and 5 ZjMAPKKs in Chinese jujube genome and found some crucial members of ZjMAPKs and ZjMAPKKs might function importantly in the process of phytoplasma infection. But how these ZjMAPKKs were modulated by ZjMAPKKKs during this process is still elusive and little information is known about the MAPKKKs in Chinese jujube.

Results

In the current study, 56 ZjMAPKKKs were identified in the jujube genome and all of them contain the key S-TKc (serine/threonine protein kinase) domain which distributed in all 12 chromosomes. Phylogenetic analysis showed that these ZjMAPKKKs could be classified into two subfamilies, of which 41 belonged to Raf, and 15 to MEKK subfamily. In addition, the ZjMAPKKKs in each subfamily share the same conserved motifs and gene structures, one pair of ZjMAPKKKs (15/16) was the only tandem duplication event on Chromosome 5. Furthermore, the expression profiles of these MAPKKKs in response to phytoplasma disease were investigated by qPCR. In the three main infected tissues (witches’ broom leaves, phyllody leaves, apparent normal leaves), the ZjMAPKKK26 and 45 were significantly up regulated and the ZjMAPKKK3, 43 and 50 were down regulated. While the ZjMAPKKK4, 10, 25 and 44 were significant highly induced in the sterile cultivated tissues infected by phytoplasma, and the ZjMAPKKK7, 30, 35, 37, 40, 41, 43 and 46 were significantly down regulated.

Conclusions

The identification and classification analysis of ZjMAPKKKs was firstly reported and some key individual ZjMAPKKKs genes might play essential roles in response to phytoplasma infection. This could provide initial understanding for the mechanism that how the ZjMAPKKKs were involved in jujube - phytoplasma infection.
The effects of a globin blocker on the resolution of 3’mRNA sequencing data in porcine blood
Authors: Lim Kyu-Sang , Dong Qian , Moll Pamela Renate , Vitkovska Jana , Wiktorin Gregor , Bannister Stephanie , Daujotyte Dalia , Tuggle Christopher K. , Lunney Joan K. , Plastow Graham S. , Dekkers Jack C. M. 
Published: May 2019

Abstract
Background

Gene expression profiling in blood is a potential source of biomarkers to evaluate or predict phenotypic differences between pigs but is expensive and inefficient because of the high abundance of hemoglobin (HB) mRNA in porcine blood. These limitations can be overcome by the use of QuantSeq 3’mRNA sequencing (QuantSeq) combined with a method to deplete or block the processing of HB mRNA prior to or during library construction. Here, we validated the effectiveness of QuantSeq using a novel specific globin blocker (GB) that is included in the library preparation step of QuantSeq.

Results

In data set 1, four concentrations of the GB were applied to RNA samples from two pigs. The GB significantly reduced the proportion of HB reads compared to non-GB (NGB) samples (P = 0.005) and increased the number of detectable non-HB genes. The second highest concentration C2, which showed very similar globin depletion rates (from 56.4 to 12%) as C1 but a better correlation of the expression of non-HB genes between NGB and GB (r = 0.98), allowed the expression of an additional 1,295 non-HB genes to be detected, although 40 genes that were detected in the NGB sample (at a low level) were not present in the GB library. Concentration C2 was applied in the rest of the study. In data set 2, the distribution of the percentage of HB reads for NGB (n=184) and GB (n=189) samples clearly showed the effects of the GB on reducing HB reads. Data set 3 (n=84) revealed that the proportion of HB reads that remained in GB samples was significantly and positively correlated with the reticulocyte count in the original blood sample (P < 0.001).

Conclusions

The effect of the GB on reducing the proportion of HB reads in porcine blood QuantSeq was demonstrated in three data sets. In addition to increasing the efficiency of sequencing non-HB mRNA, the GB for QuantSeq has as advantage that it does not require an additional step prior to or during library creation. Therefore, the GB is a useful tool in the quantification of whole gene expression profiles in porcine blood.
An insight into the sialome, mialome and virome of the horn fly, Haematobia irritans
Authors: Ribeiro Jose M. , Debat Humberto Julio , Boiani M. , Ures X. , Rocha S , Breijo Martin 
Published: May 2019

Abstract
Background

The horn fly (Haematobia irritans) is an obligate blood feeder that causes considerable economic losses in livestock industries worldwide. The control of this cattle pest is mainly based on insecticides; unfortunately in many regions, horn flies have developed resistance. Vaccines or biological control have been proposed as alternative control methods, but the available information about the biology or physiology of this parasite is rather scarce.

Results

We present a comprehensive description of the salivary and midgut transcriptomes of the horn fly (Haematobia irritans), using deep sequencing achieved by the Illumina protocol, as well as exploring the virome of this fly. Comparison of the two transcriptomes allow for identification of uniquely salivary or uniquely midgut transcripts, as identified by statistically differential transcript expression at a level of 16 x or more. In addition, we provide genomic highlights and phylogenetic insights of Haematobia irritans Nora virus and present evidence of a novel densovirus, both associated to midgut libraries of H. irritans.

Conclusions

We provide a catalog of protein sequences associated with the salivary glands and midgut of the horn fly that will be useful for vaccine design. Additionally, we discover two midgut-associated viruses that infect these flies in nature. Future studies should address the prevalence, biological effects and life cycles of these viruses, which could eventually lead to translational work oriented to the control of this economically important cattle pest.
Multiple-Omics analysis revealed the high fiber diets promote the gluconeogenesis and inhibit the glycolysis process in muscle
Authors: Wu Jianghong , Yang Ding , Gong Husile , Qi Yunxia , Sun Hailian , Liu Yongbin , Liu Yahong , Qiu Xiao 
Published: May 2019

Abstract
Background

In a previous study, we found that the human essential fatty acid is significantly increased in the mutton fed with the Ceratoides pellets comparing with the alfalfa pellets, which is not consistent with common sense.

Results

In this study, to investigate the influence mechanisms of meat quality of twins sheep with two kinds of feed high fiber low protein (HFLP) forage (Ceratoides) and low fiber high protein (LFHP) forage (alfalfa), multi-omics techniques were utilized for integration analysis based on the feed nutrition, microbiome, transcriptome, metabolome and fatty acids profile. The results showed that the production performance and the muscle components of lambs were significantly affected by feeds. The lamb muscles fed HFLP have increased the content of essential fatty acid (linoleic acid and arachidonic acid). The diversity of rumen microbes in lamb with HFLP has increased than those of LFHP. The ratio of the Bacteroidetes and the Firmicutes in the rumen of the sheep fed the LFHP was 2.6 times higher than that of the HFLP. The transcriptome analysis of muscle revealed that those genes related with the glucose metabolic process and fat acids biosynthesis were significantly differentially expressed in the muscle of the lamb with two feeds.

Conclusion

The feed system could affect the epigenetic regulation of those genes that are involved in glucose metabolic pathway. HFLP feeds could induce the gluconeogenesis to maintain the glucose level in blood, which resulted in the fat content of muscle decreasing. The multiple-Omics analysis showed that the microbiota structure is significantly correlated with the metabolome and the gene expression in muscle. This study laid a theoretical foundation for controlling the nutrient intake of sheep, modifying its fatty acid spectrum, and removing the material which was detrimental to the quality of mutton, which could guide the directive sheep feeding for functional mutton.
How Computational Epitope Mapping Identifies the Interactions between Nanoparticles Derived from Papaya Mosaic Virus Capsid Proteins and Immune System
Authors: Zamani-Babgohari Mahbobeh , Hefferon Kathleen L. , Huang Tsu , AbouHaidar Mounir G. 
Published: May 2019

Background:Nanoparticles derived from plant viruses possess fascinating structures, versatile functions and safe properties, rendering them valuable for a variety of applications. Papaya mosaic Virus-Like Particles (VLPs) are nanoparticles that contain a repetitive number of virus capsid proteins (PMV-CP) and are considered to be promising platforms for vaccine design. Previous studies have reported the antigenicity of PMV nanoparticles in mammalian systems.Materials and Methods:As experiments that concern vaccine development require careful design and can be time consuming, computational experiments are of particular importance. Therefore, prior to expressing PMV-CP in E. coli and producing nanoparticles, we performed an in silico analysis of the virus particles using software programs based on a series of sophisticated algorithms and modeling networks as useful tools for vaccine design. A computational study of PMV-CP in the context of the immune system reaction allowed us to clarify particle structure and other unknown features prior to their introduction in vitro.Results:The results illustrated that the produced nanoparticles can trigger an immune response in the absence of fusion with any foreign antigen.Conclusion:Based on the in silico analyses, the empty capsid protein was determined to be recognised by different B and T cells, as well as cells which carry MHC epitopes.
A Truncated Snail1 Transcription Factor Alters the Expression of Essential EMT Markers and Suppresses Tumor Cell Migration in a Human Lung Cancer Cell Line
Authors: Gholami Mohammad Davoodzadeh , Falak Reza , Heidari Sahel , Khoshmirsafa Majid , Kazemi Mohammad H. , Zarnani Amir-Hassan , Safari Elaheh , Tajik Nader , Kardar Gholam A. 
Published: May 2019

Background:
Epithelial-to-Mesenchymal Transition (EMT) is necessary for metastasis.
Zinc- finger domain-containing transcription factors, especially Snail1, bind to E-box motifs and play a
crucial role in the induction and regulation of EMT.

Objective:
We hypothesized if C-terminal region of Snail1 (CSnail1) may competitively bind to E-box
and block cancer metastasis.

Methods:
The CSnail1 gene coding sequence was inserted into the pIRES2-EGFP vector. Following
transfection of A549 cells with the designed construct, EMT was induced with TGF-β1 and the expression
of essential EMT markers was evaluated by real-time PCR and immunoblotting. We also monitored
cell migration.

Results:
CSnail1 inhibited TGF-β1-induced N-cadherin and vimentin mRNA expression and increased
β-catenin expression in transfected TGF-β1-treated A549 cells. A similar finding was obtained in western
blotting. CSnail1 also blocked the migration of transfected cells in the scratch test.

Conclusions:
Transfection of A549 cells with CSnail1 alters the expression of essential EMT markers
and consequently suppresses tumor cell migration. These findings confirm the capability of CSnail1 in
EMT blocking and in parallel to current patents could be applied as a novel strategy in the prevention
of metastasis.
Association of CYP2C19 and HSP70 Genes Polymorphism with Aspirin- Exacerbated Respiratory Disease in a Kurd Population
Authors: Kooti Wesam , Abdi Mohammad , Malik Yashpal S. , Nouri Bijan , Jalili Ali , Rezaee Mohammad A. , Rahmani Mohammad R. , Kalmarzi Rasoul N. 
Published: May 2019

Background:
CYP2C19 a metabolizing enzyme and Heat Shock Proteins (HSP) are induced
in stress conditions, such as hypoxia and ischemia. Recently, polymorphism in the CYP2C19 and HSP
genes has been established in Aspirin-Exacerbated Respiratory Disease (AERD).

Objective:
We investigated the polymorphism of these two genes in Kurdish patients with AERD.

Methods:
This study involved 306 subjects, referred to the Be’sat hospital in Kurdistan Province,
which were divided into three groups, (i) Aspirin Induced Asthma (AIA), (ii) Aspirin Tolerant Asthma
(ATA), and (iii) healthy subjects as control. The subjects as control and ATA\AIA groups were verified
by the physician. The demographic data of each subject with respect to age, sex, parental
education, and residence was collected. Spirometry was performed on subjects and blood samples were
collected for serum Immunoglobulin E (IgE) estimation and molecular tests. Genotyping was done for
CYP2C19 681G>A، CYP2C19 636G>A, and HSPA1B1267A>G by using PCR- Restriction Fragment
Length Polymorphism (RFLP) and for HSPA1B-179C>T by High Resolution Melting (HRM).

Results:
Demographic statistics were not significantly different between the three groups (p>0.05).
Further, genotypes were also not observed to be significantly different in the genes of CYP2C19
681G>A, CYP2C19 636G>A and HSPA1B1267A>G (p>0.05). However, the heterozygote genotype
in HSPA1B-179 C>T in AIA group was higher than the control group (p<0.05). Notably, 92.8 % of the
subjects showed heterozygote genotype in HSPA1B1267 A>G. In clinical tests, FEV-1, FVC, and
asthma severity in the AIA group were higher than control and additionally IgE levels were lower in
this group (p<0.05).

Conclusion:
The results confirm the association of polymorphism in the HSPA1B-179C>T and
HSPA1B1267A>G with AERD in the Kurdish population.
CFD Investigation of Air Flow Patterns and Thermal Comfort in a Room with Diverse Heating Systems
Authors: Sobhi Mohammed , Khalil Essam E. 
Published: May 2019

Objective:
The main focus in the current work is to investigate how diverse
heating systems and their locations influence the indoor thermal environment in an exhaust-
ventilated room.

Methods:
Four systems for heating the room were used in the current study, in which,
heat was transferred by convection and radiation. The four systems were: wall and floor
heating at low temperatures, Medium Temperature Radiator (M.T. radiator) heating and
High Temperature Radiator (H.T. radiator). Computational Fluid Dynamics (CFD) simulation
was used to investigate indoor temperature, vertical air temperature gradient and
thermal comfort for each case. The ventilation rate was set to be 6 air changes per hour
(ACH) entering the room through a vent over the window.

Results:
The findings from the current work were that the low temperature heating systems
had better temperature distributions with lower vertical Air Temperature Differences
compared to high and medium temperature radiator systems.

Conclusion:
The Predicted Mean Vote (PMV) and the predicted percentage of dissatisfied
(PPD) based on Fanger’s model were calculated for all cases, and were found to be
in the recommended ranges.
Teachers and Students' Illocutionary Act in Bahasa Indonesia Subject
Authors: Wahyuni Neneng 
Published: May 2019

<p><em>This research describes the students' and teachers' illocutionary act in learning Indonesian at state senior high school number 1 of Payakumbuh. The object of the research was the students and teachers at SMAN 1 of Payakumbuh for Bahasa Indonesia subject. The research applied qualitative descriptive method in collecting and analyzing the data. The research shows that the illocutionary acts of students' of 11<sup>th</sup> grade and teacher's for Bahasa Indonesia subject acquired 61 speech acts, which are (1) 18 assertive, (2) 2 explanatory assertive, (3) 2 reporting assertive speech, (4) 21 directive utterance commanded which is consisted of 17 teacher’s utterances and 4 student’s utterances, (5) 4 directive requests begging, (6) 3 directive of advice, (7)) 2 directive reminding, (8 ) 2 directive asked for something (9) 6 accused expressive. (10) 4 expressive complained, and (11) 1 commissive promissing. In conclusion, most of illocutionary acts used towards teacher and the students at 11<sup>th</sup> grade for Bahasa Indonesia subject in SMAN 1 Payakumbuh was directive speech act. The rarely used speech act was commissive.</em><em></em></p>
Antioxidant Activities of Muntingia calabura, Syzygium cumini, Ocimum basilicum, and Eleutherine bulbosa using DPPH Method
Authors: Haerani Ani , Chaerunisa Anis Yohana , Subarnas Anas 
Published: May 2019

Antioxidants are substances that can provide endogenous protection and exogenous oxidative stress by capturing free radicals. Many plants are efficacious as antioxidants, namely plants that contain polyphenols, especially flavonoids, so many are formulated as natural antioxidants. Plants such as Muntingia calabura, Syzygium cumini, Ocimum basilicum, and Eleutherine bulbosa contain polyphenol compounds, especially flavonoids which are efficacious as natural antioxidants. This research aimed to study antioxidant activity derived from some potential plants using the DPPH method by calculating the IC50 value of each plant extract. This research method starts from the determination process to prove the validity of the plants used, the extraction process using the maceration method with 70% ethanol solvent, then the antioxidant activity of extracts from each plant was carried out using the DPPH method. This research starts from the determination process to ensure the correctness of the plants used, then the extraction process is carried out using the maceration method with 70% ethanol solvent. After that the antioxidant activity was determined from the four plants using the DPPH method to see the strongest IC50 value among the four plants. IC50 is the concentration of the sample to inhibit 50% of free radicals. The results of IC50 values from ethanol extract of M. calabura leaves, Syzygium cumini leaves, Ocimum basilicum leaves and Eleutherine bulbosa bulbs, were 18.72; 63,84; 141.59 and 173.15 ppm. Ethanol extract of M. Calabura has a smaller IC50 value of 18.72 ppm which has a very strong and most powerful antioxidant from the ethanol extract of Syzygium cumini, Ocimum basilicum and Eleutherine bulbosa. Keywords : Antioxidant, Muntingia calabura, Syzygium cumini, Ocimum basilicum, Eleutherine bulbosa, DPPH Method
Implementasi antara Legislatif dan Eksekutif dalam Pembentukan Peraturan Daerah yang Partisipatif
Authors: Mustafa Adriana 
Published: May 2019

Peraturan Daerah ditetapkan oleh Kepala Daerah dengan persetujuan Dewan Perwakilan Rakyat Daerah. Disamping kewenangan yang ada pada Kepala Daerah dan Dewan Perwakilan Rakyat Daerah mengandung pengertian bahwa pembentukan Peraturan Daerah dilakukan bersama-sama. Pembentukan Peraturan Daerah melibatkan peran serta masyarakat dalam menyampaikan aspirasi-aspirasinya dalam proses pembentukan peraturan perundang-undangan sehingga menghasilkan Peraturan Daerah yang baik, bermanfaat bagi seluruh lapisan masyarakat, menciptakan kehidupan yang lebih teratur (taat hukum) dan sesuai dengan tujuan dan asas-asas pembentukan Peraturan Daerah. Implementasi dari ketentuan ini diatur lebih lanjut melalui Peraturan Tata Tertib DPRD. DPRD dapat meminta laporan keterangan pertanggungjawaban Gubernur, Bupati dan Walikota. Dengan klausul ini maka kedudukan DPRD dalam menjalankan tugasnya menjadi sangat kuat. Pemerintahan daerah hendaknya dapat mengatur dan mengurus sendiri urusan pemerintahan menurut asas otonomi dan tugas pembantuan. Local Regulations are formed by the local leaders or mayor with the approval of the House of Representatives. In addition, the authority of the Regional Head and the house of Representative means that the formation of Regional Regulations is carried out both parties. The establishment of Regional Regulations involves the participation of the community in conveying their aspirations in the process of establishing legislation in order to produce proper Regional Regulations, to be beneficial to all levels of society, to create a more orderly (law-abiding) life and in accordance with the objectives and principles of formation Local regulation. The implementation of this provision is further regulated through the DPRD Rules of Procedure. The DPRD could ask a statement of responsibility for the Governor, Regent, and Mayor. With this clause, the position of the DPRD in carrying out its duties becomes very strong. Regional governments should be able to organize and manage their own government affairs according to the principle of autonomy and co-administration..