bluuebunny/crossref_metadata_2025_split huggingface dataset:
An assemblages of fungal endophytes isolated from medicinal plants collected from Toba and Samosir, North Sumatra
Authors: Ilyas M , Praptiwi  , Wulansari D , Fathoni A , Agusta A 
Published: September 2019

Abstract
Endophytic fungi are a group of microorganisms that grow in plant tissue without causing symptoms of disease in host plants. Fungal endophytes have a great diversity and potential as an agent of bioactive compound and metabolites that are important in the pharmaceutical industry, agriculture, and environment. In this study isolation and identification of fungal endophytes inhabiting an assemblages of medicinal plants collected from Toba and Samosir Regency, North Sumatra, Indonesia were carried out. Fungal endophytes were isolated using surface sterilization methods with slightly modification and totally 88 selected endophytic fungal strains were isolated from roots, stems, barks, leaves, and fruits of 12 species of medicinal plants. The fungal strains identification through morphological observation showed that selected fungal endophytes were associated with host plant belonging to the taxa Colletotrichum, Fusarium, Lasiodiplodia, Neopestalotiopsis, Phoma, Phomopsis, Phyllosticta, Schizophyllum, Trichoderma, and Xylaria. In this study endophytic Phomopsis dominating the obtained strains where 30% (27/88) strains of them were isolated from 8 species of medicinal host plants. Preliminary exploration of fungal endophytes through isolation and identification was the first step in order to discover the potential strains were able to produce promising metabolites and bioactive materials. The results of the study are expected to be initial microbial resources and information for screening and utilization of endophytic fungi through bioprospecting.
Phytoplankton characteristics in Lake Matano, Indonesia
Authors: Sulawesty F 
Published: September 2019

Abstract
Lake Matano is one of the oligotrophic lake in Indonesia that has unique phytoplankton characteristic. This study was aimed to find out the composition and abundance of phytoplankton at Lake Matano. Observations were conducted in 2015 (April and August) and 2016 (May and August). A total 10-20 L of water samples were collected from eight locations in the Lake Matano. Temperature, pH, dissolved oxygen, conductivity and turbidity were measured to determine the water quality. Phytoplankton abundance was calculated using the Sedgewick Rafter method. Phytoplankton community structure was analysed by Diversity Index (H’), Evenness Index (E) and Simpson Dominance Index (D). A total five phyla and 80 species of phytoplankton were found in Lake Matano, comprised of Chlorophyta (26 species), Dinophyta (2 species), Bacillariophyta (43 species), Chrysophyta (1 species) and Cyanophyta (8 species). The abundance of phytoplankton ranged between 0.36 × 102 – 1.281 × 104 individual/L. Peridinium inconspicuum and P.cinctum (Dinophyta) was found highest in abundance in April and August 2015 (96.38% of the abundance). Low to moderate community (H’=0.122 to 3.454) and low uniformity (E = 0.065 to 0.556) among species in phytoplankton community was found in Lake Matano. Dominance species (D = 0.216 to 0.967) occurred in several locations at Lake Matano. CCA ordination shows that the presence of all phytoplankton groups is strongly influenced by turbidity of which the lower turbidity value causes the higher phytoplankton abundance.
Population Structure, Growth and Production of Corbicula moltkiana and Their Relation to Cage Aquaculture Activity in Lake Maninjau, West Sumatra Indonesia
Authors: Lukman L , Setyobudiandi I , Muchsin I , Hariyadi S 
Published: September 2019

Abstract
Cage aquaculture that has been growing enormously in Lake Maninjau, West Sumatera, Indonesia, is supposed to have an impact on benthic fauna including Corbicula moltkiana, the species of bivalves. The objective of this study addresses the population structure, growth and production of C. moltkiana that describing the impact potential of cage aquaculture activity. The result show that annual 2013-2014 production [P] of C. moltkiana were 465-1559 g AFDM m−2 y−1 and the annual biomass [B] was 183-453 g AFDM m−2, resulting in P/B ratio of 2.54-3.44 y−1. Even though the P/B ratio was not consistent with the cage density level, as consequently of different L∞ in determined zones. The increased cage aquaculture activity that marked by adding number of cage from <225 cages km−1 to > 675 cages km−1 impact to decrease of biomass [B] and production [P] of C. molktiana.
Variation of Ammonium Persulfate Concentration Determines Particle Morphology and Electrical Conductivity in HCl Doped Polyaniline
Authors: Reza Muhammad , Srikandi Nona , Amalina Auliya Nur , Benu Didi Prasetyo , Steky Fry Voni , Rochliadi Achmad , Suendo Veinardi 
Published: September 2019

Abstract
Polyaniline (PANI) is one of conducting polymers which is widely used in various applications especially energy field, like solar cells and batteries. PANI emeraldine salt (PANI ES) is the only type of conducting PANI which can be easily synthesized using a direct mixing method in an oxidizing solution. Ammonium persulfate (APS) is one example of a strong oxidizing agent which is often used in PANI synthesis. The APS concentrations used in this study ranged from 0.1 to 1 M. Infrared and Raman spectroscopy shows that the addition of APS concentrations above 0.5 M produces the non-conducting fully oxidized PANI and phenazine species. Scanning electron microscope (SEM) showed morphological changes of PANI ES from nanofiber (diameter 80 - 110 nm) to granules (diameter 20 - 70 nm) as APS concentration increases. Based on Electrochemical impedance spectroscopy (EIS), conductivity of PANI increases as APS concentration increases with maximum conductivity of 0.36 S cm−1 at 0.5 M.
Tin-Empty Palm Bunch Ash Impregnated Zeolite as Suitable Catalyst for Simultaneous Transesterification-Esterification Reaction of Palm Oil
Authors: Usman Thamrin , Rudiyansyah  , Wahyuni Nelly , Astar Ismail , Yustira Yudi , Alimuddin Andi Hairil , Rahmalia Winda 
Published: September 2019

Abstract
A single-step method was developed for methyl ester production from palm oil using tin-empty palm bunch ash impregnated zeolite (Sn-PBA-Zeolite) as heterogeneous catalyst. The weight ratios between Sn solution and zeolite 1:4, while the weight of the PBA was varied from 5, 10, 15, 20, 25, and 30 g in 60 mL of distilled water. Effects of reaction time, molar ratio of reactants, and catalyst concentration on the yield of methyl ester were studied. Characteristics of methyl ester produced were also investigated. The optimal conditions for transesterification reaction carried out by using a Sn-PBA-Zeolite of 1:4:25 weight ratio were a palm oil/methanol molar ratio 1:6, catalyst concentration (3% wt/wt), and 3 hours reaction time, whereas the maximum yield of methyl ester reached 76.21% wt/wt. The optimal conditions for esterification reaction carried out by using a Sn-PBA-Zeolite of 1:4:5 weight ratio were a palm oil/methanol molar ratio 1:12, catalyst concentration (3% wt/wt), and 3 hours reaction time, and the maximum yield of methyl ester reached 94.76% wt/wt. The methyl ester resulted has a density of 0.89 g/mL, viscosity of 7.82 cSt, and dominated by a methyl oleate, methyl palmitate, and methyl stearate.
What’s the target: understanding two decades of in silico microRNA-target prediction
Authors: Kern Fabian , Backes Christina , Hirsch Pascal , Fehlmann Tobias , Hart Martin , Meese Eckart , Keller Andreas 
Published: September 2019

Abstract

Motivation
Since the initial discovery of microRNAs as post-transcriptional, regulatory key players in the 1990s, a total number of $2656$ mature microRNAs have been publicly described for Homo sapiens. As discovery of new miRNAs is still on-going, target identification remains to be an essential and challenging step preceding functional annotation analysis. One key challenge for researchers seems to be the selection of the most appropriate tool out of the larger multiverse of published solutions for a given research study set-up.

Results
In this review we collectively describe the field of in silico target prediction in the course of time and point out long withstanding principles as well as recent developments. By compiling a catalog of characteristics about the 98 prediction methods and identifying common and exclusive traits, we signpost a simplified mechanism to address the problem of application selection. Going further we devised interpretation strategies for common types of output as generated by frequently used computational methods. To this end, our work specifically aims to make prospective users aware of common mistakes and practical questions that arise during the application of target prediction tools.

Availability
An interactive implementation of our recommendations including materials shown in the manuscript is freely available at https://www.ccb.uni-saarland.de/mtguide.
Sequentially additive nonignorable missing data modelling using auxiliary marginal information
Authors: Sadinle Mauricio , Reiter Jerome P 
Published: September 2019

Summary
We study a class of missingness mechanisms, referred to as sequentially additive nonignorable, for modelling multivariate data with item nonresponse. These mechanisms explicitly allow the probability of nonresponse for each variable to depend on the value of that variable, thereby representing nonignorable missingness mechanisms. These missing data models are identified by making use of auxiliary information on marginal distributions, such as marginal probabilities for multivariate categorical variables or moments for numeric variables. We prove identification results and illustrate the use of these mechanisms in an application.
Determination of 12 Carbamate Insecticides in Typical Vegetables and Fruits by Rapid Multi-Plug Filtration Cleanup and Ultra-Performance Liquid Chromatography/Tandem Mass Spectrometry Detection
Authors: Ma Lili , Zhao Liuwei , Wang Jiaqi , Pan Canping , Liu Cong , Wang Yu , Ding Qi , Feng Yuechao , Zhou Huijuan , Jia Li 
Published: September 2019

AbstractA multiresidue method for determining 12 carbamate pesticides in purple cabbage, orange, watermelon, cucumber, cowpea and Lactuca sativa L. employing multi-plug filtration cleanup (m-PFC) and ultra-performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) was developed. M-PFC was carried out by cleanup at dispersive solid phase extraction (d-SPE), one m-PFC tip-filtration, two m-PFC tip-filtration and other methods (1–3 m-PFC cleanups). Results demonstrated that filtration simplified the cleanup method compared with d-SPE and other m-PFC methods (1–3 m-PFC cleanups). The method validation results showed that the method was linear, selective and accurate. The limits of quantification (LOQs) were 0.05–5.0 μg/kg, and the recoveries were in the range of 70.1–119.9% in different matrices. Although matrix effects were observed, they were successfully compensated using matrix-matched calibration. Finally, the developed method was successfully applied to detect pesticides in real samples.
A Multicenter Cost-of-Illness and Long-term Socioeconomic Follow-up Study in the Severe Typhoid Fever in Africa Program: Study Protocol
Authors: Ramani Enusa , Park Seeun , Toy Trevor , Panzner Ursula , Mogeni Ondari D , Im Justin , Cruz Espinoza Ligia Maria , Jeon Hyon Jin , Pak Gi Deok , Seo Hyeongwon , Chon Yun , Rakotozandrindrainy Raphaël , Owusu-Dabo Ellis , Osei Isaac , Soura Abdramane Bassiahi , Teferi Mekonnen , Marks Florian , Mogasale Vittal 
Published: September 2019

AbstractBackgroundThere are limited data on typhoid fever cost of illness (COI) and economic impact from Africa. Health economic data are essential for measuring the cost-effectiveness of vaccination or other disease control interventions. Here, we describe the protocol and methods for conducting the health economic studies under the Severe Typhoid Fever in Africa (SETA) program.MethodsThe SETA health economic studies will rely on the platform for SETA typhoid surveillance in 4 African countries—Burkina Faso, Ethiopia, Ghana, and Madagascar. A COI and long-term socioeconomic study (LT-SES) will be its components. The COI will be assessed among blood culture–positive typhoid fever cases, blood culture–negative clinically suspected cases (clinical cases), and typhoid fever cases with pathognomonic gastrointestinal perforations (special cases). Repeated surveys using pretested questionnaires will be used to measure out-of-pocket expenses, quality of life, and the long-term socioeconomic impact. The cost of resources consumed for diagnosis and treatment will be collected at health facilities.ResultsResults from these studies will be published in peer-reviewed journals and presented at scientific conferences to make the data available to the wider health economics and public health research communities.ConclusionsThe health economic data will be analyzed to estimate the average cost per case, the quality of life at different stages of illness, financial stress due to illness, and the burden on the family due to caregiving during illness. The data generated are expected to be used in economic analysis and policy making on typhoid control interventions in sub-Saharan Africa.
Acute Febrile Illness Among Children in Butajira, South–Central Ethiopia During the Typhoid Fever Surveillance in Africa Program
Authors: Teferi Mekonnen , Desta Mulualem , Yeshitela Biruk , Beyene Tigist , Cruz Espinoza Ligia Maria , Im Justin , Jeon Hyon Jin , Kim Jong-Hoon , Konings Frank , Kwon Soo Young , Pak Gi Deok , Park Jin Kyung , Park Se Eun , Yedenekachew Melaku , Kim Jerome , Baker Stephen , Sir Won Seok , Marks Florian , Aseffa Abraham , Panzner Ursula 
Published: September 2019

Abstract

Background
Clearly differentiating causes of fever is challenging where diagnostic capacities are limited, resulting in poor patient management. We investigated acute febrile illness in children aged ≤15 years enrolled at healthcare facilities in Butajira, Ethiopia, during January 2012 to January 2014 for the Typhoid Fever Surveillance in Africa Program.

Methods
Blood culture, malaria microscopy, and blood analyses followed by microbiological, biochemical, and antimicrobial susceptibility testing of isolates were performed. We applied a retrospectively developed scheme to classify children as malaria or acute respiratory, gastrointestinal or urinary tract infection, or other febrile infections and syndromes. Incidence rates per 100 000 population derived from the classification scheme and multivariate logistic regression to determine fever predictors were performed.

Results
We rarely observed stunting (4/513, 0.8%), underweight (1/513, 0.2%), wasting (1/513, 0.2%), and hospitalization (21/513, 4.1%) among 513 children with mild transient fever and a mean disease severity score of 12 (95% confidence interval [CI], 11–13). Blood cultures yielded 1.6% (8/513) growth of pathogenic agents; microscopy detected 13.5% (69/513) malaria with 20 611/µL blood (95% CI, 15 352–25 870) mean parasite density. Incidences were generally higher in children aged ≤5 years than >5 to ≤15 years; annual incidences in young children were 301.3 (95% CI, 269.2–337.2) for malaria and 1860.1 (95% CI, 1778.0–1946.0) for acute respiratory and 379.9 (95% CI, 343.6–420.0) for gastrointestinal tract infections.

Conclusions
We could not detect the etiological agents in all febrile children. Our findings may prompt further investigations and the reconsideration of policies and frameworks for the management of acute febrile illness.
Spatial and Temporal Patterns of Typhoid and Paratyphoid Fever Outbreaks: A Worldwide Review, 1990–2018
Authors: Kim Samuel , Lee Kang Sung , Pak Gi Deok , Excler Jean-Louis , Sahastrabuddhe Sushant , Marks Florian , Kim Jerome H , Mogasale Vittal 
Published: September 2019

AbstractBackgroundAnalyses of the global spatial and temporal distribution of enteric fever outbreaks worldwide are important factors to consider in estimating the disease burden of enteric fever disease burden.MethodsWe conducted a global literature review of enteric fever outbreak data by systematically using multiple databases from 1 January 1990 to 31 December 2018 and classified them by time, place, diagnostic methods, and drug susceptibility, to illustrate outbreak characteristics including spatial and temporal patterns.ResultsThere were 180 940 cases in 303 identified outbreaks caused by infection with Salmonella enterica serovar Typhi (S. Typhi) and Salmonella enterica serovar Paratyphi A or B (S. Paratyphi). The size of outbreak ranged from 1 to 42 564. Fifty-one percent of outbreaks occurred in Asia, 15% in Africa, 14% in Oceania, and the rest in other regions. Forty-six percent of outbreaks specified confirmation by blood culture, and 82 outbreaks reported drug susceptibility, of which 54% had multidrug-resistant pathogens. Paratyphoid outbreaks were less common compared to typhoid (22 vs 281) and more prevalent in Asia than Africa. Risk factors were multifactorial, with contaminated water being the main factor.ConclusionsEnteric fever outbreak burden remains high in endemic low- and middle-income countries and, despite its limitations, outbreak data provide valuable contemporary evidence in prioritizing resources, public health policies, and actions. This review highlights geographical locations where urgent attention is needed for enteric fever control and calls for global action to prevent and contain outbreaks.
Pharmacokinetics and Pharmacodynamics of Depot Medroxyprogesterone Acetate in African Women Receiving Treatment for Human Immunodeficiency Virus and Tuberculosis: Potential Concern for Standard Dosing Frequency
Authors: Mngqibisa Rosie , Kendall Michelle A , Dooley Kelly , Wu Xingye (Shirley) , Firnhaber Cynthia , Mcilleron Helen , Robinson Jennifer , Cramer Yoninah , Rosenkranz Susan L , Roa Jhoanna , Coughlin Kristine , Mawlana Sajeeda , Badal-Faesen Sharlaa , Schnabel David , Omoz-Oarhe Ayotunde , Samaneka Wadzanai , Godfrey Catherine , Cohn Susan E ,   for the A5338 Study Team
Published: September 2019

Abstract

Background
Effective contraception is critical to young women with HIV-associated tuberculosis (TB), as unintended pregnancy is associated with increased perinatal morbidity and mortality. The effects of co-administration of efavirenz and rifampicin on the pharmacokinetics of depot medroxyprogesterone acetate (DMPA) are unknown. We hypothesized that clearance of medroxyprogesterone acetate (MPA) would increase when given with rifampicin and efavirenz, thus increasing risk of ovulation.

Methods
This pharmacokinetics (PK) study assessed DMPA among HIV/TB coinfected women on an efavirenz-based antiretroviral treatment and rifampicin-based TB treatment. Plasma MPA concentrations and progesterone were measured predose (MPA only) and 2, 4, 6, 8, 10, and 12 weeks after a single DMPA 150 mg intramuscular injection. The primary outcome measure, MPA concentration (&lt;0.1 ng/mL) at week 12, was assessed using exact 95% Clopper-Pearson confidence intervals. MPA PK parameters were calculated using noncompartmental analysis.

Results
Among 42 PK-evaluable women from 5 African countries, median age was 32 years and median CD4 was 414 cells/mm3. Five women (11.9%; 95% CI, 4.0–25.6%) had MPA &lt;0.1 ng/mL at week 12; of these, one had MPA &lt;0.1 ng/mL at week 10. The median clearance of MPA was 19 681 L/week compared with 12 118 L/week for historical controls. There were no adverse events related to DMPA, and progesterone concentrations were &lt;1 ng/mL for all women for the study duration.

Conclusions
DMPA, when given with rifampicin and efavirenz, was safe. MPA clearance was higher than in women with HIV not on ART, leading to subtherapeutic concentrations of MPA in 12% of women, suggesting that more frequent dosing might be needed.

Clinical Trials Registration
NCT02412436.
Prospective International Study of Incidence and Predictors of Immune Reconstitution Inflammatory Syndrome and Death in People Living With Human Immunodeficiency Virus and Severe Lymphopenia
Authors: Sereti Irini , Sheikh Virginia , Shaffer Douglas , Phanuphak Nittaya , Gabriel Erin , Wang Jing , Nason Martha C , Roby Gregg , Ngeno Hellen , Kirui Fredrick , Pau Alice , Mican Joann M , Rupert Adam , Bishop Rachel , Agan Brian , Chomchey Nitiya , Teeratakulpisarn Nipat , Tansuphaswadikul Somsit , Langat Deborah , Kosgei Josphat , French Martyn , Ananworanich Jintanat , Sawe Fredrick 
Published: September 2019

Abstract

Background
Patients living with human immunodeficiency virus (PLWH) with low CD4 counts are at high risk for immune reconstitution inflammatory syndrome (IRIS) and death at antiretroviral therapy (ART) initiation.

Methods
We investigated the clinical impact of IRIS in PLWH and CD4 counts &lt;100 cells/μL starting ART in an international, prospective study in the United States, Thailand, and Kenya. An independent review committee adjudicated IRIS events. We assessed associations between baseline biomarkers, IRIS, immune recovery at week 48, and death by week 48 with Cox models.

Results
We enrolled 506 participants (39.3% were women). Median age was 37 years, and CD4 count was 29 cells/μL. Within 6 months of ART, 97 (19.2%) participants developed IRIS and 31 (6.5%) died. Participants with lower hemoglobin at baseline were at higher IRIS risk (hazard ratio [HR], 1.2; P = .004). IRIS was independently associated with increased risk of death after adjustment for known risk factors (HR, 3.2; P = .031). Being female (P = .004) and having a lower body mass index (BMI; P = .003), higher white blood cell count (P = .005), and higher D-dimer levels (P = .044) were also significantly associated with increased risk of death. Decision-tree analysis identified hemoglobin &lt;8.5 g/dL as predictive of IRIS and C-reactive protein (CRP) &gt;106 μg/mL and BMI &lt;15.6 kg/m2 as predictive of death.

Conclusions
For PLWH with severe immunosuppression initiating ART, baseline low BMI and hemoglobin and high CRP and D-dimer levels may be clinically useful predictors of IRIS and death risk.
The Construction of a Majority-Voting Ensemble Based on the Interrelation and Amount of Information of Features
Authors: Aydın Fatih , Aslan Zafer 
Published: September 2019

AbstractIn this paper, we introduced a new ensemble learning algorithm called VIBES, which is better in terms of performance when compared to 85 machine learning algorithms in WEKA tool. This new algorithm is based on three major processes: (i) making an assumption regarding whether features are dependent on or independent of each other, (ii) computing the amount of information of features when it is assumed that they are dependent on each other and then sorting them in a descending manner based on the amount of information, (iii) speeding up the algorithm by optimizing the forward search algorithm that is used in the construction of the final hypothesis from base learner hypotheses. As a result of these processes, it has been seen in the experiments that choosing the relevant assumption can boost learning performance if features are independent of each other; considering features according to the amount of information provides high accuracy and diversity of base learner models. According to experiment results, the algorithm that has been developed has the highest average classification accuracy rate across the 33 datasets. The highest and the lowest average classification accuracy rates have been found to be 89.80 and 78.03%, respectively.