bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation between ESBL-Producing Bacteria Infection with Sepsis Severity of Patient in Medical Ward of Internal Medicine Department Dr. Soetomo General Hospital in 2016
Authors: Pratiwi Asri Dhea , Rusli Musofa , Utomo Budi
Published: September 2019

Introduction: Sepsis is life-threatening condition that begins with infections that trigger pro-inflammation overresponse. Delaying antibiotic treatment in sepsis can cause serious condition. In ESBL-producing bacteria, the antibiotic resistance is common and it might cause harm to sepsis patient. This research aims to analyze the correlation between infections of ESBL-producing bacteria with sepsis severity. Methods: This study was observational analytic on sepsis patient in Internal Medicine Ward of Dr. Soetomo General Hospital. The data were taken from medical records of the patient. The severity of sepsis was based on Surviving Sepsis Campaign 2012. Results: A total 72 sepsis patients were included in this study, which consist of 40 patients with non-producing ESBL GNB and 32 patients with ESBL-producing bacteria. The most common bacteria in ESBL infection is Escherichia coli ESBL+ (75%) and non ESBL infection is Acinetobacter baumanii (27.5%). Septic shock is more common in patient with ESBL-producing bacteria (53.1% vs 22.5%). The correlation between ESBL infection and sepsis severity is significant and the power of correlation is low (p = 0.048; r = 0.234). Conclusion: There is a correlation between ESBL-producing bacteria infection with sepsis severity and the power of correlation is low (p = 0.048, r = 0.234).
Nerve, Muscle and Synaptogenesis
Authors: Swenarchuk Lauren
Published: September 2019

The vertebrate skeletal neuromuscular junction (NMJ) has long served as a model system for studying synapse structure, function and development. Over the last several decades a neuron-specific isoform of agrin, a heparan sulfate proteoglycan, has been identified as playing a central role in synapse formation at all vertebrate skeletal neuromuscular synapses. While agrin was initially postulated to be the inductive molecule that initiates synaptogenesis, this model has been modified in response to work showing that postsynaptic differentiation can develop in the absence of innervation, and that synapses can form in transgenic mice in which the agrin gene is ablated. In place of a unitary mechanism for neuromuscular synapse formation, studies in both mice and zebrafish have led to the proposal that two mechanisms mediate synaptogenesis, with some synapses being induced by nerve contact while others involve the incorporation of prepatterned postsynaptic structures. Moreover, the current model also proposes that agrin can serve two functions, to induce synaptogenesis and to stabilize new synapses, once these are formed. This review examines the evidence for these propositions, and concludes that it remains possible that a single molecular mechanism mediates synaptogenesis at all NMJs, and that agrin acts as a stabilizer, while its role as inducer is open to question. Moreover, if agrin does not act to initiate synaptogenesis, it follows that as yet uncharacterized molecular interactions are required to play this essential inductive role. Several alternatives to agrin for this function are suggested, including focal pericellular proteolysis and integrin signaling, but all require experimental validation.
Emphasis Learning (EL), Feature Repetition in Width Instead of Length, to Obtain Better Classification Performance; Case Study: Alzheimer’s Disease Diagnosis
Authors: Akramifard Hamid , Balafar MohammadAli , Razavi SeyedNaser , Ramli Abd Rahman
Published: September 2019

A method for classification is introduced in this article, and it is tested on ADNI database to diagnose alzheimer’s disease (AD). It is obvious that tunning the performance of a classification to get better results is a complicated problem, and when we want model’s accuracy or other peformance measurments higher than 90%, the problem will be more complicated. In this study, we tried and succeeded to discover a method to solve this problem. The final feature set can be used clustering too, because outgrowth feature set of the proposed method is invigorated. In the recent years, a lot of activities is done to develop computer aided systems (CAD) for alzheimer’s disease diagnosis. Most of these recently developed systems concenterated on extracting and combining features from MRI, PET, CSF, and …; in this article, we made attempt to do so and utilized one more technique to increase classification performance. Finding and producing the best features to solve three binary classiﬁcation problems of AD vs. Normal Control (NC), Mild Cognitive Impairment (MCI) vs. NC, and MCI vs. AD are the purposes of this article. Experiments indicate performance and effectiveness rates of the proposed method, which are accuracies of 98.81%, 81.61%, and 81.40% for AD vs. NC, MCI vs. NC, and AD vs. MCI classification problems, respectively. As can be seen, using this method increased the performance of the three binary problems incredibly.
Novel Mutations Evading Avian Immunity around the Receptor Binding Site of the Clade 2.3.2.1c Hemagglutinin Gene Reduce Viral Thermostability and Mammalian Pathogenicity
Authors: An Se-Hee , Lee Chung-Young , Hong Seung-Min , Song Chang-Seon , Kim Jae-Hong , Kwon Hyuk-Joon
Published: September 2019

Since 2007, highly pathogenic clade 2.3.2 H5N1 avian influenza A [A(H5N1)] viruses have evolved to clade 2.3.2.1a, b and c, and currently only 2.3.2.1c A(H5N1) viruses circulate in wild birds and poultry. During antigenic evolution, clade 2.3.2.1a and c A(H5N1) viruses acquired both S144N and V223I mutations around the receptor binding site of hemagglutinin (HA), with S144N generating an N-glycosylation sequon. We introduced single or combined reverse mutations, N144S and/or I223V, into the HA gene of clade 2.3.2.1c A(H5N1) virus and generated PR8-derived, 2 + 6 recombinant A(H5N1) viruses. When we compared replication efficiency in embryonated chicken eggs, mammalian cells and mice, the recombinant virus containing both N144S and I223V mutations showed increased replication efficiency in avian and mammalian hosts and pathogenicity in mice. The N144S mutation significantly decreased avian receptor affinity and egg white inhibition, but not all mutations increased mammalian receptor affinity. Interestingly, the combined reverse mutations dramatically increased the thermostability of HA. Therefore, the adaptive mutations possibly acquired to evade avian immunity may decrease viral thermostability as well as mammalian pathogenicity.
Recent Advances in Anomaly Detection Methods applied to Aviation
Authors: Basora Luis , Olive Xavier , Dubot Thomas
Published: September 2019

Anomaly detection is an active area of research with numerous methods and applications. This survey reviews the state-of-the-art of data-driven anomaly detection techniques and their application to the the aviation domain. After a brief introduction to the main traditional data-driven methods for anomaly detection, we review the recent advances in the area of neural networks, deep learning and temporal-logic based learning. We cover especially unsupervised techniques applicable to time series data because of their relevance to the aviation domain, where the lack of labeled data is the most usual case, and the nature of flight trajectories and sensor data is sequential, or temporal. The advantages and disadvantages of each method are presented in terms of computational efficiency and detection efficacy. The second part of the survey explores the application of anomaly detection techniques to aviation and their contributions to the improvement of the safety and performance of flight operations and aviation systems. As far as we know, some of the presented methods have not yet found an application in the aviation domain. We review applications ranging from the identification of significant operational events in air traffic operations to the prediction of potential aviation system failures for predictive maintenance.
The Uterine-Chemokine-Brain Axis: Menstrual Cycle-Associated Symptoms (MCAS) are in Part Mediated by CCL2, CCL5, CCL11, CXCL8 and CXCL10
Authors: Roomruangwong Chutima , Sirivichayakul Sunee , Carvalho Andre F. , Maes Michael
Published: September 2019

Objective: To examine associations between chemokines and menstrual cycle associated symptoms (MCAS). Methods: Forty-one women completed the Daily Record of Severity of Problems (DRSP) rating scale during 28 consecutive days of the menstrual cycle. MCAS is diagnosed when the total daily DRSP score during the menstrual cycle is > 0.666 percentile. We assayed plasma CCL2, CCL5, CCL11, CXCL8, CXCL10, EGF, IGF-1, and PAI-1 at days 7, 14, 21 and 28 of the menstrual cycle. Results: CCL2, CCL5, CCL11 and EGF are significantly higher in women with MCAS than in those without. Increased CCL2, CXCL10, CXCL8, CCL11 and CCL5 levels are significantly associated with DRSP scores while CCL2 is the most significant predictor explaining 39.6% of the variance. The sum of the neurotoxic chemokines CCL2, CCL11 and CCL5 is significantly associated with the DRSP score and depression, physiosomatic, breast-craving and anxiety symptoms. The impact of chemokines on MCAS symptoms may differ between consecutive weeks of the menstrual cycle with CCL2 being the most important predictor of increased DRSP levels during the first two weeks, and CXCL10 or a combination of CCL2, CCL11 and CCL5 being the best predictors during week 3 and 4, respectively. Discussion: The novel case definition “MCAS” is externally validated by increased levels of uterus-associated chemokines and EGF. Those chemokines are involved in MCAS and are regulated by sex hormones and modulate endometrium functions and brain neuro-immune responses, which may underpin MCAS symptoms. As such, uterine-related chemokines may link the uterus with brain functions via a putative uterine-chemokine-brain axis.
Synthesis Polymer Styrene Butadiene Hybrid Latex with Laponite Organoclay as Filler via Emulsion Polymerization Technique for Application in Paper Coating
Authors: Soegijono Bambang , Chanra Johannes , Zheng Zhongwu , Mi Puke
Published: September 2019

Synthesis of styrene butadiene hybrid latex was performed via emulsion polymerization technique using various amount of laponite clay as filler. Laponite clay was modified with cationic surfactant methyl triphenylphosphonium bromide (MTPB) with ion exchange technique prior to polymerization process. The main objective of the modification is to render the surface of the clay layers to more organophilic. Emulsion polymerization was performed under semi batch process using 2 L laboratory stainless steel reactor with temperature 85°C to 90°C for 8 hours. Polymer hybrid styrene butadiene latex was characterized for its physical and chemical properties with standard ASTM Methods. Characterization of its binding and printing properties were carried out with standard testing method (TAPPI Methods) using single coating formulation on 80 gsm woodfree paper. Polymer hybrid latex based on styrene and butadiene monomers with laponite clay enhanced binding and printing properties of coated paper, addition of laponite clay to 6.0 wt % increased the binding resistance of the coated paper two times higher than pure latex. Reducing binder level become possible for cost saving.
Prevalence of Carnitine Deficiency and Decreased Carnitine Levels in Patients on Peritoneal Dialysis
Authors: Shimizu Satoshi , Takashima Hiroyuki , Tei Ritsukou , Furukawa Tetsuya , Okamura Makiyo , Kitai Maki , Nagura Chinami , Maruyama Takashi , Higuchi Terumi , Abe Masanori
Published: September 2019

Background: Carnitine deficiency is common in patients on dialysis. Serum free carnitine concentration is significantly lower in patients on hemodialysis (HD) than in healthy individuals. However, there are few reports on serum free carnitine concentration in patients on peritoneal dialysis (PD). Methods: We examined serum concentrations of total, free, and acylcarnitine and the acylcarnitine/free carnitine ratio in 34 PD and 34 age-, sex-, and dialysis duration-matched HD patients. We investigated the prevalence of carnitine deficiency and clinical factors associated with carnitine deficiency in the PD group. Results: Prevalence of carnitine deficiency was 8.8% in the PD group and 14.7% in the HD group (P = 0.45). High risk of carnitine deficiency was found in 79.4% of the PD group and 85.3% of the HD group (P = 0.52). Carnitine insufficiency was found in 82.3% of the PD group and 88.2% of HD group (P = 0.49). Multivariate analysis revealed that duration of dialysis and age were independent predictors of serum free carnitine level in the PD group. Conclusions: The prevalence of carnitine deficiency, high risk of carnitine deficiency, and carnitine insufficiency in PD patients was 8.8%, 79.4%, and 82.3%, respectively. These rates were comparable to those in patients on HD.
BIODIESEL SYNTHESIS OF COTTON SEEDS OIL (CEIBAPENTANDRA) BY CHEMICALLY TRANSESTERIFICATION PROCESS AND ION FRAGMENTATION OF METHYL ESTER
Authors: Gunawan Erin Ryantin , Wulandari Siska Ayu , Yuanita Emmy , Suhendra Dedy
Published: September 2019

Fossil  fuel  is  commercial  energy  sources  in  many  communities  where  their abundance  progressively  reduced  and  the  resulting  environmental  pollution.  Biodiesel  is one alternative fuel made  from vegetable  which oils are suitable to replace the function of fossil fuels and environmentally friendly. Synthesis of biodiesel from  cotton  seeds oil  was carried  out  by  chemically  ransesterification  process.  Composition  of  methyl  esters  in biodiesel  thatwas  analyzed  by  GC-MS  are  methyl palmitate  (16.71%),  methyl  8,11-octadecadienoic (46.45 %) and  methyl linoleate (4.21  %).The highest amount of  biodiesel conversion  isat  ratio of oil and  methanol (1:1)  with  the catalyst 1% (weight  of oil).  The produced biodiesel was 93.7  %.  Chemical properties of  the produced  biodiesel meets the standard SNI 04-7182-2006 i.e.  saponification value of  120.167    mg KOH / g, acid value of 0.28 mg KOH / g and iod value 55.84g iod/100g of sample.
The Temperature Effect on Ultrasonic-assisted of Synthesis Methyl Ferulate and Its Antiplatelet Assay
Authors: Ekowati Juni , Pratama Rian Putra , Nofianti Kholis Amalia , Diyah Nuzul Wahyuning
Published: September 2019

Ferulic acid (FA) has been reported to have antiplatelet activity through indirectly inhibiting P2Y12 receptor. In order to increase the activity of FA, by improving its lipophilicity, so that it is easier to enter the cell, synthesis methyl ferulate was conducted through Fisher esterification. Ultrasonic waves were utilized as source of energy emitted through water as the medium at two various of temperature, i.e., 55 °C and 65 °C. The purposes of this study are to produce methyl ferulate and to determine the reaction constant rate (k) and its energy activation (Ea), at temperature of 55 °C and 65 °C. Moreover, the biological activity as antiplatelet was investigated at dose 20 mg/kg BW. The antiplatelet assay was conducted by clotting time and bleeding time methods. The results were analyzed by one way ANOVA program (P<0.05). The yield of methyl ferulate are 50.3% and 67.1% at 55 °C and 65 °C, respectively. The k value at 55°C is 4x10-5 cons-1min-1, while that of at 65 °C is 9x10-5 cons-1min-1. The clotting time and bleeding time of methyl ferulate obtained were 265 sec and 175 sec, respectively. The antiplatelet activity of methyl ferulate is better than ferulic acid.
Decision Support System for Determining Mini Sugar Mill Location in Madura
Authors: Rum Mokh. , Darwanto Dwidjono Hadi , Hartono Slamet , Masyhuri Masyhuri
Published: September 2019

Madura has widely potential farming business of sugarcane and has enough raw material to build a mini sugar mill. Sugarcane is cultivated in Madura, particularly in four regencies, namely Bangkalan, Sampang, Pamekasan and Sumenep. To decide the location of mini sugar mill in one of the regencies requires decision support system (DSS). This study aimed to determine the priority of mini sugar mill location in Madura. This research used primary and secondary data. The primary data were collected using questionnaires. Then, the results of evaluation from the experts, on the items of questions, were analyzed with analytical hierarchy process (AHP). This was accomplished using Expert Choice 2000 software. Analysis of the selection of mini sugar mill location considered six criteria, namely the land suitability level, existing infrastructure, the potential of raw materials, the availability of labor, social capital and institutions. The selected criteria were further classified into sub-criteria to clarify the definitions of operational criteria and facilitate assessment for respondents. The results show that social capital had the greatest influence on decision making, followed by the land suitability level and the potential of raw materials. The finding in this research is that the mini sugar mill location is given priority in Bangkalan Regency, Madura. The conclusion of this research is that AHP analysis can be used as a method to take accurate decision in determining the location of sugarcane factory in certain area of sugarcane farming business development.
Estimation Variability, Heritability and Genetic Advance of Mutant Black Rice (M6)
Authors: Sofian Ahmad , Nandariyah Nandariyah , Djoar Djati Waluyo , Sutarno Sutarno
Published: September 2019

A better understanding of variability in plant populations is crucial for crop improvement which plant breeders can use through selection. This study aimed to determine selection criteria for the sixth generation of black rice through genetic variability, heritability value and genetic advance. This research was conducted from March to July 2018 at Pakahan Village, Jogonalan Sub-district, Klaten Regency, Central Java, using a Randomized Complete Block Design (RCBD). The variables observed were plant height, total number of tillers and productive tillers, panicle length, number of seeds per panicle, panicle intensity index, weight per panicle, 1,000 seed weight, seed weight per plant, flowering age, harvest age, plot yield, yield per hectare, rice color and total anthocyanin content. Variance analysis showed that there was a very significant difference (p <0.01) among the genotypes tested for all observed characters indicating variability. In this study, the phenotypic coefficient of variance (PCV) values was relatively higher than the genotypic coefficient of variance (GCV) for all traits. However, GCV values were close to PCV values in some characters such as plant height, flowering age, harvest age, rice color and anthocyanin content which showed a high contribution of genotypic effects to the phenotypic expression of these characters. The high heritability and high average value of genetic advance were indicated in the parameters of plant height, flowering age, harvest age, rice color and anthocyanin content. The characters of plant height, flowering age, harvest age, rice color and anthocyanin content can be used as sixth-generation black rice selection criteria.
Similarity and Phylogenetic Analysis of Herbicide-Resistant Goosegrass (Eleusine indica) Biotypes
Authors: Tampubolon Koko , Sihombing Fransisca Natalia , Siburian Elseria , Sulastri Yustina Sri , Purba Zavandri , Samosir Sony Tri Septian , Karim Syahibal
Published: September 2019

Molecular approach as a herbicide-resistant agent detector is an initial solution before controlling of Eleusine indica weed. This review article is aimed to obtain the basic data of similarity and phylogenetic values among herbicide-resistant E. indica biotypes. This research used a descriptive analytical method. The analysis involved 14 nucleotide sequences of herbicide-resistant E.indica biotypes obtained from the National Center for Biotechnology Information. The nucleotide alignment of herbicide-resistant E. indica biotypes was conducted with ClustaLW using the Molecular Evolutionary Genetics Analysis (MEGA) v. 5.05 software based on a method of neighbor-joining tree construct/test. The results showed that two nucleotides of 7,921 herbicide-resistant E. indica biotypes were homologous (sequence 1,231 and sequence 1,408). The similarity values among herbicide-resistant E. indica biotypes ranged from 0.00 to 1.19. The information of phylogenetic pattern is needed in the selection of the herbicides mode of action rotation in order to control herbicide-resistant E. indica biotypes.
Physiological Response of Upland Rice Varieties to Furrow with Organic Matter on Agroforestry System with Kayu Putih (Melaleuca leucadendra L.)
Authors: Tarigan Puji Lestari , Tohari Tohari , Suryanto Priyono
Published: September 2019

Drought is one of the major limitations in dry land cultivation. Drought affects plant physiology processes such as photosynthesis, respiration, mineral and water transportation, and transpiraton, briefly called drought stress. Drought stress can be avoided by managing environment. Furrow containing organic matter for rain fed rice has been the subject of many studies, with special emphasis on soil moisture. This research is aimed to know the effects of the furrow containing organic matter on physiological responses of several upland rice varieties on agroforestry system based on kayu putih (cajuput). The experimental design applied the strip plot design. The vertical factor is the furrow system of treatment consisting of 2 levels i.e. without furrow + without organic matter and furrow + organic matters. The horizontal factors are the upland rice varieties consisting of 3 varieties i.e. Situ Patenggang, Situ Bagendit and Ciherang. The collected data were analyzed by Analysis of Variance (ANOVA) applying a level of significance α = 5%. Whenever significant differences among treatments were found, further analysis was carried out by applying the Tukey's HSD (Honestly Significant Difference) test α = 5% levels. The result shows that drought affects plant physiology and can be avoided by using furrow containing organic matters. Situ Patenggang with furrow containing organic matters has the higher physiology capability, it had photosynthesis 387.18 µmol CO2 per clump s-1, transpiration 3038.50 mg per clump per secondand CO2 721.11 mol CO2 clump per mol. There different plant requirements for Cu between varieties.
GGE-Biplot Analysis for Soybean Varieties Suitability in an Agroforestry System based on Kayu Putih Stands
Authors: Alam Taufan , Suryanto Priyono , Nurmalasari Aprilia Ike , Kurniasih Budiastuti
Published: September 2019

The existence of genotype and environment (G x E) interaction causes difficulty in selecting suitable varieties of soybean in an agroforestry system based on kayu putih stands. This study aimed to determine the suitability of adaptive, stable and high yield soybean varieties in an agroforestry system based on kayu putih stands by using GGE-Biplot analysis. The experiment was conducted from May to August 2018 at Menggoran Forest Resort, Playen District, Gunung Kidul Regency, Special Region of Yogyakarta, Indonesia. The experiment was conducted using a randomized complete block design (RCBD) with five block as replications. The first factor was soil type in Menggoran Forest Resort, consisting of Lithic Haplusterts, Vertic Haplustalfs and Ustic Endoaquerts. The second factor was soybean varieties, consisting of Anjasmoro, Argomulyo, Burangrang, Dering I, Devon I, Gema and Grobogan. The observation was carried out on seed dry weight of soybean per hectare. The data were analyzed using Combined Analysis of Variance (ANOVA) with α = 5% and GGE-Biplot. Dering I was the most suitable varieties in an agroforestry system based on kayu putih stands and showed the mean of highest yield of 1.22 tons ha-1.
Constituent Mineral and Water-Soluble Components of Volcanic Ash from the 2018 Eruption of Mt. Motoshirane of Kusatsu-Shirane Volcano, Japan
Authors: Yaguchi Muga , Ohba Takeshi , Numanami Nozomi , Kawaguchi Ryohei ,   Volcanology Research Department, Meteorological Research Institute, Japan Meteorological Agency 1-1 Nagamine, Tsukuba, Ibaraki 305-0052, Japan,   Department of Chemistry, School of Science, Tokai University, Kanagawa, Japan
Published: September 2019

Constituent minerals and water-soluble components of the volcanic ash discharged from the eruption of Mt. Motoshirane on January 23, 2018, were analyzed to investigate the source environment of this eruption. The ash sample included quartz, plagioclase, cristobalite, pyrite, alunite, kaolinite, and pyrophyllite; its mineral assemblage suggests that a high-temperature acid alteration zone had been formed in the volcanic edifice of Mt. Motoshirane. The presence of pyrophyllite in the ash sample indicates that the explosion of this eruption took place at a depth reaching the basement rocks of Mt. Motoshirane. Further, the adhesion amount of water-soluble components detected from the ash sample is smaller than that in the ashes from the 1982 eruption of Mt. Shirane, indicating that the ash discharge of the 2018 eruption of Mt. Motoshirane took place in a condition in which the degree of involvement of the liquid phase was relatively small.
A Standard for Rotatory Power Measurement
Authors: Brüge Andreas , Pfeiffer Harald
Published: September 2019

In Germany, the realisation and dissemination of the unit of rotatory power is a legal task of the national metrology institute aimed at ensuring the safe operation of ergometers for patients. At the Physikalisch-Technische Bundesanstalt, this task is carried out by means of a standard that can be operated both as a regulated brake and as a regulated drive, so that the effective torque and the revolution speed can be measured traceably. In this article, technical details and uncertainty calculations about this standard are given.
Introductory notes for the Acta IMEKO Special Section on the Asia-Pacific Symposium on Measurement of Mass, Force and Torque (APMF 2017)
Authors: Wongpithayadisai Rugkanawan , Pitakarnnop Jeerasak
Published: September 2019

This special issue of Acta IMEKO is the second issue, which presents the research highlights of the biannual Asia-Pacific Symposium on Measurement of Mass, Force and Torque (APMF). The purpose of the symposium is to offer researchers and scientists the opportunities of exchanging the latest scientific information and mise en pratique in the field of Mass, Force and Torque.

The recent APMF was organized by National Institute of Metrology (Thailand) in November 2017 in Krabi, Thailand, around the theme “Metrology Moving Towards Foundation”. The fields of the discussions and presentations were extended to cover the area of mass, force, torque, density, hardness, pressure, vacuum and gravimetry. The International Program Committee of APMF 2017 considered and selected 10 potential papers to be published as the enhanced versions in Acta IMEKO journal. With the journal’s standards of the review process by the expert referees, 6 articles were accepted for this special issue. The state of the art and recent research works developed to improve the accuracy and quality of the measurements in the aforesaid fields are presented in this issue.
Determinants of First Line Antiretroviral Treatment Failure among Patients on Highly Active Antiretroviral Therapy in selected Public Hospitals Jimma, Southwest Ethiopia a Case Control Study
Authors: Asfaw Amrachu Bekele , Tekelehaimanot Aderajew Nigusie , Shewanew Tamirat , Gudina Esayas Kebede , Getnet Masrie , Amdisa Demuma , Lemma Tefera Belachew , Dadi Lelisa Sena
Published: September 2019

Background: Highly Active Antiretroviral Therapy (HAART) has substantially declined morbidity and mortality related to Human immunodeficiency virus/Acquired immunodeficiency syndrome (HIV/AIDS). Despite this fact, first-line ART failure has emerged as a growing concern. However, factors associated with first-line ART failure are not well empathized and studied. Hence, we aimed to identify the determinants of first-line ART failure among patients attending ART in Public Hospitals Jimma, Southwest Ethiopia.
Methods: A case-control study was conducted in March 2018 on a sample of 384(288 controls and 96 cases) adult people living with HIV/AIDS (PLWHA). Cases were HIV patients aged 15 years or older who were on first-line ART regimens with documented therapeutic failure. Controls were HIV patients aged 15 years or older who were on first-line ART regimen but without evidence of therapeutic failure. Data were extracted from electronic databases and supplemented by data collected through interviewer-administered questionnaires. Bivariate and multivariate logistic regression analyses were used. Adjusted odds ratios and 95% confidence intervals were used to report independently associated factors at P-value<0.05.
Results: In this study, higher odds of first-line ART failure was experinced among urban residents (AOR:2.2;95%CI: 1.1, 3.6), smokers (AOR:5.9; 95%CI:3.2, 10.8), Khat users (AOR:2.2; 95%CI:1.3,3.7), poor treatment adherents (AOR:2.2; 95%CI: 1.1,4.5), tuberculosis coinfection (AOR:3.9; 95%CI:2.2, 6.8), prior exposure to ART (AOR:3.8; 95%CI:1.7, 8.1), zidovudine based regimen (AOR:4.8; 95%CI: 2.5,9.0) and longer duration on ART more than 73 months (AOR:1.9; 95%CI:1.2, 3.3).
Conclusions: This study evidenced that being an urban resident, TB co-infection, poor treatment adherence, and zidovudine-based regiment were positively and independently associated with first-line ART failure. Thus, enhanced adherence counseling should be provided for those urban residents as well as substance users to improve adherence to ART; early screening and management of tuberculosis is highly recommended. Moreover, close follow up of adverse effects of ARVs must be strengthened.
Keywords : determinants, first-line ART failure, HIV/AIDS, Jimma Zone, Public hospitals
WITHDRAWN: De novo assembly and comparative transcriptome analysis reveal genes potentially involved in changes of terpenoids in wheat germplasm resource, that defend against the wheat aphid Sitobion avenae (Fabricius)
Authors: Zhao Lei , Liu Zhen , Zhan Yidi , Liu Yong
Published: September 2019

Background Terpenoid volatiles play an important role in direct and indirect plant defense responses against herbivores, including in gramineous crops such as transgenic rice and corn. The conventional varieties of wheat, an important gramineous cereal crop, lack aphid-resistant genes. It is therefore, necessary to seek aphid-resistant genes by screening for potential terpenoid synthase genes in wheat germplasm resources. Results The result showed that aphid-damaged Octoploid Tirtitrigia emitted a higher amount of S-linalool, ent-kaurene, (+)-delta-cadinene, (3S,6E)- nerolidol compared to intact plant. In addition, (E)-β-caryophyllene, β‐Myrcene, (E)-4,8-dimethyl-1,3,7-nonatriene (DMNT) were new volatile terpenoids emitted by the damaged plant. Further olfactory responses tests showed that S-linalool significantly repelled Sitobion avenae (Fabricius). Using the Illumina sequencing platform, approximately 203.09 million high quality paired-end reads were obtained. After de novo assembly and quantitative assessment, a total of 182,348(74.8%) unigenes were annotated by alignment with public protein databases. Of these unigenes, 2,389 differentially expressed genes were identified between intact and damaged ears of Octoploid Trititrigia. The expression profile of 10 randomly selected TPSs was confirmed with RT-qPCR. Candidate genes involved in terpenes biosynthesis were identified showing significant transcript changes between intact and damaged plant ears of Octoploid Trititrigia. Also transcript abundances of terpenes biosynthetic pathway-related genes were positively correlated with the production of volatile terpenoids in ears. The unigenes of S-linalool synthase gene was mapped to the cloned cDNA WT008_M07 (AK333728) and WT013_P07 (AK335856) of the Chinese spring wheat cultivar. The predicted protein complete ORF sequence (TaLIS1/2) when compared with the S-linalool synthase gene of other species, contained an aspartate-rich region DDxxD motif. Its function was characterized as coordinating the divalent metal ions involved in substrate binding. Furthermore, phylogenetic tree results showed that the TaLIS1 and TuNES1 are highly homologous. Conclusions This assembled transcriptome of S. avenae-damaged Octoploid Trititrigia and intact ears can provide more molecular resources for future functional characterization analysis of genomics in volatile terpenoids involved in direct or indirect defenses. Our study describes the metabolic regulation mechanism of volatile terpenoids in gramineous crops, which provides support for both breeding and genetic modification of wheat varieties resistant to wheat aphids.
Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars
Authors: Ding Haisheng , Liu Min , Zhou Changfan , You Xiangbin , Su Tao , Yang Youbing , Xu Dequan
Published: September 2019

Background: MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results: In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-165 mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 ( PLCβ1) gene was verified to be a target of ssc-mir-423-5p . Conclusions: This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.
Integrated Analysis of lncRNA, miRNA and mRNA Reveals Novel Insights into the Fertility Regulation of Large White Sows
Authors: Hu Huiyan , Jia Qing , Xi Jianzhong , Zhou Bo , Li Zhiqiang
Published: September 2019

Background: Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular phases (F) of the estrous cycle in Large White pigs with high (H) and low fecundity (L), and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics. Results: In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log2 (fold change)| ≥ 1to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data.Conclusions: These results provide further insights into the fertility of pigs and can contribute to further experimental investigation of the functions of these genes.
“Little things do not get to me anymore”: a qualitative study of older adults’ perspectives on initiating exercise and mindfulness practice
Authors: Parra Diana C. , Wetherell Julie Loebach , Zandt Alexandria Van , Brownson Ross , Abhishek Janardan , Lenze Eric
Published: September 2019

Background: Mindfulness practice and exercise are ways by which older adults can improve and maintain their physical, emotional and cognitive health. Methods: This single-site qualitative study gathered insights of older adults’ perceptions about initiating and maintaining mindfulness and exercise practices. We carried out focus groups with 41 adults aged 65-85 who had recently initiated Mindfulness Based Stress Reduction (MBSR), structured exercise, or their combination as part of participation in a clinical trial. We used a semi-structured interview to ask them open-ended questions regarding the benefits, barriers and facilitators of participating in mindfulness and/or exercise interventions. The interview also included questions regarding translation of these practices into community settings as well as the long-term maintenance potential of these practices. Results : Older adults indicated that the mindfulness training increased their awareness and self-reflection and fostered a more self-accepting attitude. Furthermore, they improved their self-care habits and reported having better familial and social relationships. The main barrier for both the exercise and mindfulness group was time management. The social benefits and sense of community were some of the primary motivators for older adults in the exercise and/or MBSR interventions. However, the research on how to motivate older adults to initiate healthy behavioral changes also needs to be answered. The benefits of exercise and MBSR are a motivation in and of themselves, as indicated by some of the participants. Conclusions: This study indicates that mindfulness training and exercise can serve as tools to cultivate important health lifestyle qualities among older adults, who are in the midst of mental, social, emotional and physical change. If it were not for the purpose of the research or the incentives provided by the research team, these older adults may have never started the healthy behavioral changes. From the responses, this may indicate that older adults may need more incentives to begin and maintain behavioral changes other than for their own health benefit.
The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers.
Authors: Orjuela Stephany , Menigatti Mirco , Schraml Peter , Kambakamba Patryk , Robinson Mark D. , Marra Giancarlo
Published: September 2019

Identifying molecular differences between primary and metastatic colorectal cancers—now possible with the aid of omics technologies—can improve our understanding of the biological mechanisms of cancer progression and facilitate the discovery of novel treatments for late-stage cancer. We compared the DNA methylomes of primary colorectal cancers (CRCs) and CRC metastases to the liver. Laser microdissection was used to obtain epithelial tissue (10 to 25 x 10 6 µm 2 ) from sections of fresh-frozen samples of primary CRCs (n=6), CRC liver metastases (n=12), and normal colon mucosa (n=3). DNA extracted from tissues was enriched for methylated sequences with a methylCpG binding domain (MBD) polypeptide-based protocol and subjected to deep sequencing. The performance of this protocol was compared with that of targeted enrichment for bisulfite sequencing used in a previous study of ours. MBD enrichment captured a total of 322,551 genomic regions (249.5 Mb of the genome) that included over seven million CpG sites. A few of these regions were differentially methylated at an expected false discovery rate (FDR) of 5% in neoplastic tissues (primaries: 0.67%, i.e., 2155 regions containing 279,441 CpG sites; liver metastases: 1%, i.e., 3223 regions containing 312,723 CpG sites) as compared with normal mucosa samples. Most of the differentially methylated regions (DMRs; 94% in primaries; 70% in metastases) were hyper methylated, and almost 80% of these (1882 of 2396) were present in both lesion types. At 5% FDR, no DMRs were detected in liver metastases vs. primary CRC. However, short regions of low-magnitude hypo methylation were frequent in metastases but rare in primaries. Hypermethylated DMRs were far more abundant in sequences classified as intragenic, gene-regulatory, or CpG shelves-shores-island segments, whereas hypomethylated DMRs were equally represented in extragenic (mainly, open-sea) and intragenic (mainly, gene bodies) sequences of the genome. Compared with targeted enrichment, MBD capture provided a better picture of the extension of CRC-associated DNA hypermethylation but was less powerful for identifying hypomethylation. Our findings demonstrate that the hypermethylation phenotype in CRC liver metastases remains similar to that of the primary tumor, whereas CRC-associated DNA hypomethylation probably undergoes further progression after the cancer cells have migrated to the liver.
The effect of periodontal bacteria infection on incidence and prognosis of cancer: a systematic review and meta-analysis
Authors: Xiao Li , Zhang Qianyu , Peng Yanshuang , Wang Daqing , Liu Ying
Published: September 2019

Background Periodontal bacteria is the major pathogens in the oral cavity and the main cause of adult chronic periodontitis, but their association with incidence and prognosis in cancer is controversial. The aim of this study was to evaluate the effect of periodontal bacteria infection on incidence and prognosis of cancer.Methods A systematic literature search of PubMed, Embase, Web of Science and Cochrane Library databases was performed to obtain 39 studies comprising 7184 participants. The incidence of cancer was evaluated as odd ratios (OR) with a 95% confidence interval (95% CI) using Review Manager 5.2 software. Overall survival (OS), cancer-specific survival (CSS) and disease-free survival (DFS), which were measured as hazard ratios (HR) with a 95% confidence interval (95% CI) using Review Manager 5.2 software.Results Our results indicated that periodontal bacteria infection increased the incidence of cancer (OR=1.25; 95%CI: 1.03–1.52) and was associated with poor OS (HR = 1.75; 95% CI: 1.40–2.20), DFS (HR=2.18; 95%CI: 1.24–3.84) and CSS (HR=1.85, 95%CI: 1.44–2.39). Subgroup analysis indicted that the risk of cancer was associated with Porphyromonas gingivalis (Pg) infection (OR=2.16; 95%CI: 1.34–3.47) and Prevotella intermedia (Pi) infection (OR=1.28; 95%CI: 1.01–1.63) but not Tannerella forsythia (Tf) (OR=1.06; 95%CI: 0.8–1.41), Treponema denticola (Td) (OR=1.30; 95%CI: 0.99–1.72), Aggregatibacter actinomycetemcomitans (Aa) (OR=1.00; 95%CI: 0.48–2.08) and Fusobacterium nucleatum (Fn) (OR=0.61; 95%CI: 0.32–1.16).Conclusion This meta-analysis revealed periodontal bacteria infection increased the incidence of cancer and predicted poor prognosis of cancer.
Lower 2D:4D digit ratio is associated with reduced impulse control in women
Authors: Rodríguez-Ramos Ángel , Moriana Juan Antonio , García-Torres Francisco , Ruiz-Rubio Manuel
Published: September 2019

Sex hormones induce sexual differentiation of the brain which might result in sex-specific behaviors. 2D:4D digit ratio is commonly used as a marker of the balance between prenatal testosterone and estrogen. In this study we analyzed if there was an association between 2D:4D and personality in women. We found that 2D:4D might be related with emotional stability, and specifically with its subdimension impulse control; while no associations were found with the dimensions energy, friendliness, conscientiousness and openness.
Temporal expression patterns of Pasteuria spp. sporulation genes
Authors: Dyrdahl-Young Ruhiyyih , Hu Weiming , DiGennaro Peter
Published: September 2019

Endospore-forming bacterium in the genus Pasteuria spp. infect multiple agriculturally significant plant parasitic nematodes and has potential as a potent biological control. Success as a biological control requires not only spore attachment to the cuticle, but sporulation and reproduction within the nematode host. Tracking and identifying Pasteuria spp. development is then critical to demonstrating efficacy as a biocontrol. Microscopic observations suggest Pasteuria spp. follows the model bacterium, Bacillus subtilis, sporulation. Here, we identified B. subtilis homologs of sporulation regulators in Pasteuria spp. and characterized the temporal expression of these genes throughout the bacterium’s ∼30-d lifecycle in Meloidogyne arenaria as a means of tracking sporulation development. Detectable levels of transcripts of Spo0F were present as early as 5 d after the nematodes were exposes to Pasteuria spp. and were relatively constant throughout the 30-d lifecycle. Transcripts to Sigma-F were significantly higher in the middle of the lifecycle, while the transcripts of Sigma-G were detectable between 15 and 25 d, nearing the end of the lifecycle. These three markers can be used to track the process of sporulation in the nematode and augment microscopic observations. Tracking sporulation of Pasteuria spp. is important to fully realize its potential as a biological control method as it can more readily identify successful parasitism, define host ranges, and inform in vitro growth progress.
Maternal Stress Reduces the Susceptibility of Root-Knot Nematodes to Pasteuria Penetrans
Authors: Liu Chang , Ji Pingsheng , Timper Patricia
Published: September 2019

Pasteuria penetrans is an obligate parasite of root-knot nematodes (Meloidogyne spp.). Endospores of P. penetrans attach to the cuticle of second-stage juveniles (J2) and complete their life cycle within the nematode female body. Infected females will be filled with spores and will be sterilized. Studies with Daphnia magna and its parasite Pasteuria ramosa showed that a poor maternal environment can lead to offspring resistant to P. ramosa. Therefore, we hypothesized that Meloidogyne arenaria females raised under a stressed environment would produce offspring that were more resistant to P. penetrans. Females were exposed to a stressed environment created by crowding and low-food supply, or a non-stressed environment and their offspring evaluated for endospore attachment and infection by P. penetrans. No difference in spore attachment was observed between the two treatments. However, infection rate of P. penetrans in the stressed treatment was significantly lower than that in the non-stressed treatment (8 vs 18%). Mothers raised under stressed conditions appeared to produce more resistant offspring than did mothers raised under favorable conditions. Under stressful conditions, M. arenaria mothers may provide their progeny with enhanced survival traits. In the field, when nematode populations are not managed, they often reach the carrying capacity of their host plant by the end of the season. This study suggests that the next generation of inoculum may be more resistant to infection by P. penetrans.