bluuebunny/crossref_metadata_2025 huggingface dataset:
Groundwater and resilience to drought in the Ethiopian highlands
Authors: MacDonald A M , Bell R A , Kebede S , Azagegn T , Yehualaeshet T , Pichon F , Young M , McKenzie A A , Lapworth D J , Black E , Calow R C
Published: June 2019

During drought, groundwater is often relied on to provide secure drinking water, particularly in rural Africa where other options are limited. However, the technology chosen to access groundwater significantly affects local water security. Here we examine the performance of springs, hand-dug-wells and boreholes in northern Ethiopia through direct high frequency monitoring of water-levels (n = 19) and water quality (n = 48) over an 18 month period and gathering information on community impacts of declining water access during the El Niño 2015/2016 drought. We found that shallow boreholes equipped with handpumps were the most reliable water supply, recovering within hours to daily abstraction throughout all conditions. Recovery and performance of most hand-dug-wells and springs declined significantly throughout the extended dry season, although in specific aquifer conditions they were reliable. All sources types had negligible measured contamination from Thermo-tolerant Coliforms through the extended dry season, but were contaminated during the rains marking drought cessation. Boreholes were least affected, median 10 cfu/100 ml, compared to 190 and 59 cfu/100 ml for hand-dug-wells and springs respectively. Many communities who relied solely on springs, wells or rivers experienced severe water shortage in the El Niño drought with mean daily collection times up to 12 h and volumes collected reducing to 3–5 litre per-capita-per-day. This led to reports of violent conflict, missed meals, reduction in school attendance and farm activity and increased health impacts. From this study there is a clear case for improving resilience to drought by installing boreholes equipped with handpumps where feasible even if collection times are >30 min.
Effect of Clove Essential Oil Addition on Characteristics of Cassava Starch Bioplastic Film Incorporated Zinc Oxide-organoclay as Reinforcement
Authors: Harunsyah  , Yunus M. , Fauzan Reza
Published: June 2019

The main objective of this study is to improve mechanical properties of bioplastic film and resistant to bacteria by the addition of percent ratio Zinc Oxide/Organoclay (ZnO/Clay) nanoparticles as enforcement and clove essential oil. All bioplastic film was formed by casting method. The addition of clay nanoparticles in the plastic films was varied from 1:9%, 2:8%, 3:7%, 4:6%, and 5:5% (w/w) by weight of starch. Structural characterization was done by Fourier Transform Infrared Spectroscopy (FTIR). Surface morphologies of the plastic film were examined by scanning electron microscope (SEM). The result showed that the Tensile strength (TS) was improved significantly with the addition of ZnO/Clay nanoparticles. The optimum tensile strength obtained was 20.87 M.Pa on the additional of ZnO/Clay nanoparticles by 0.3:0.7% and plasticizer by 25%. Based on data of FTIR, the produced film plastic does not change the group function and it can be concluded that the interaction in biodegradable plastic produced was only a physical interaction. The biodegradable plastic based on cassava starch-ZnO/Clay nanoparticles and plasticizer glycerin showed that interesting mechanical properties being transparent and clear.
Overview of Hysteresis Current Controller Application in Renewable Energy Based Power Systems
Authors: Yunus A. M. Shiddiq , Swasti Sri , Purwito
Published: June 2019

This paper presents an overview of the Hysteresis Current Controller (HCC) application in Renewable Energy Based Power System. The beginning concept of HCC is considered to be formally introduced by Thomas M. Freederiksen and Ronald W. Russel in 1971 that was registered in US Patent No. US3725673. The fundamental principle of HCC is based on the comparison of the instantaneous load current to the instantaneous sine wave reference where the difference between the two is maintained within the defined upper and lower band. There are some advantages of using HCC including simple, insensitivity to load parameters variations, fast dynamic response and inherent maximum current limiting characteristics. Therefore, based on its robustness, HCC has currently applied also in renewable energy based power plants such as PV converter system, Power Electronics System of Wind Energy, and in SMES control system for Wind Energy Application. However, the drawback of HCC system was also discussed in some papers compared with other control systems, for instant HCC is giving high chattering in torque in IM drive test. Therefore the combination of HCC with other controllers also becomes a new trend to improve the applied system that involving HCC as the main controller.
Monitoring System for Organic Fertilizer Plant Controller Using Solar Energy
Authors: Mardiyanto Arief , Syamsul  , Azhar
Published: June 2019

In this applied research, a solar energy powered process control monitoring system of inorganic fertilizer plant with capacity of 300 liters has been developed. The process control system consists of PLC with solar energy panel as its power source and a monitoring process system. The monitoring process system includes a Raspberry Pi minicomputer, an LCD touchscreen, level shifter converters, Arduino Nano, RS485 modules, four analog sensors, and one digital sensor. This system works by collecting temperature, humidity, and gas concentrations data and controlling the heater, exhaust fan, and aerator to maintain desired processing conditions.DHT-22 digital sensor measures temperature and humidity, pH probe analog sensor measures pH values, MQ-4, MQ-7 and MiCS-2714 measures methane, carbon monoxide, and nitrogen dioxide gases respectively. Analog output sensor is read by PLC’s analog to digital converter while digital output sensor is read by 1-wire bus by Arduino. The collected data is send over RS485 to Raspberry Pi. The plant temperature is set constant at 40°C. The heater is turned on at temperature of ≤ 38°C, when temperature reach ≤ 42°C the aerator, exhaust fan, and mixer will be on and will be switched off all together at 40°C. The temperature, humidity and PH are set as the reference of the control process.
Reactive Black-5 Removal by Ozonation as Post Treatment
Authors: Wantoputri NI , Notodarmojo S , Helmy Q
Published: June 2019

The textile industry is one of industries that growing rapidly in Bandung, Indonesia. It discharges enormous quantity of highly colored wastewater due to the use of water in large quantity and the use of dyes in the production process. One of the problems in processing textile wastewater with conventional biological treatment method is the ineffectiveness of color removal. A further treatment as post treatment is needed for treated wastewater discharge to remove the color. One of the method that known has high efficiency for textile color removal is by using ozonation method. In this ongoing study, the decolorization of artificial textile wastewater containing azo dye reactive-black 5 (RB5) from secondary treatment was investigated in a continuous system. Artificial treated textile wastewater from secondary biological treatment is made using 5 mg/L azo dye RB5 in 16 L volume batch reactor. The experiments show that the efficiency of color removal achieved is 100% within 10 minutes of reaction time with 24.66 mg/minutes of ozone dosage. In continuous system operation, ozonation process also conducted in 16 L volume reactor with up flow and down flow of influent feeding and HRT 10 minutes, 30 minutes and 50 minutes. The experiments show that the color removal was fluctuate Andromeda oscillation in certain interval contact time for each HRT, but higher color removal efficiency achieved in HRT 50 minutes.
Enhancing removal efficiency of heavy metals and ammonia in bioretention system using quartz sand and zeolite as filter media
Authors: Sari A Y , Suwartha N , Hartono D M , Gusniani I
Published: June 2019

Bioretention is one of the stormwater runoff managements to reduce pollutant concentration such as heavy metals and ammonia. However, removal efficiency of bioretention was affected by variation of filter media. So, the aims of this study are to enhance removal efficiency of bioretention system. Three bioretention system were applied on pilot scale sized 30 × 30 × 80 cm3 combined with Iris pseudacorus. Variation of filter media composition of quartz sand and zeolite was used with ratio 1:3, 1:1, 3:1, on reactor 1, 2 and 3, respectively. Synthetic runoff water with different concentration were simulated. The results shown that variations in influent concentrations has small effect on the removal efficiency (20-40%). The average removal efficiency of bioretention 1, 2 and 3 for Pb was 91%, 78%, 83%, respectively, followed 88%, 95%, 94% for Zn and 97%, 98%, 96% for NH3. The combination of quartz sand and zeolite as filter media significantly enhance removal efficiency by 11,5% for NH3, 18% Pb and 20% Zn compared to previous similar research.
Development of Poly Lactic Acid/Kitosan Elastomer with Essential Oil Addition to Improved Performance Antibacterial Materials
Authors: Suryani  , Agusnar Harry , Wirjosentono Basuki , Rihayat Teuku , Fitria  , Nurhanifa
Published: June 2019

Consumer demand for high quality food without chemical preservatives is a challenge for the food industry. Therefore, food packaging is needed which can extend the shelf life of food products by protecting from external factors such as microorganisms, moisture, and ultraviolet light. In this study, we synthesize Poly Lactic Acid (PLA) derived from environmentally friendly materials and the addition of chitosan to produce a material that are resistant to the development of microorganisms in food packaging applications which is a new concept innovation of biodegradable active packaging, where packaging is developed this has an ability to reduce or inhibit the growth of microorganisms on the food surface. The results obtained in this study are as follows: the addition of turmeric as essential oil and chitosan have been shown to increase antibacterial activity. Elastomer biofilms produced are able to fight S.aureus and E. coli bacteria on exposure for 72 hours in an open room. They are more effective against gram-positive bacteria when compared to gram-negative. Maximum biofilm tensile strength in 4-gram chitosan variation, 0.3 mL TEO and 0.5 mL / biofilm glycerol with tensile strength of 40.01 MPa. The maximum decomposition temperature of the biofilm is obtained at 315.74°C with 4 grams chitosan variation, TEO 0.3 mL and 0.5 mL glycerol. The addition of TEO into the chitosan biofilm is also able to bind molecules of chitosan and evenly distributed molecules on the surface.
Design and Development of Real-Time Plant Process Control Monitoring System in Organic Fertilizer Production
Authors: Mardiyanto Arief
Published: June 2019

In this applied research, a plant controller with capacity of 300 litres has been developed. The system provides graphical user interface (graphics and tables) using Visual Basic program to show and monitor the fermentation process. Communication between the software and hardware is established through microcontroller’s interface. The microcontroller acts as the main controller which controls the humidity, temperature, pH, aerator, heater, exhaust fan, and the speed of the motor. Temperature and humidity sensor (DHT-22), Methane Gas sensor (CH), Carbon Gas sensor (MQ7), and Nitrogen Gas sensor (MiCS-2714) are used in this system. The domestic waste raw materials such as vegetables and sugar cane waste are thinly sliced while the fruits are grinded. Temperature, humidity, and pH readings are collected as reference parameters prior to the process starts. During the anaerobic digestion process, temperature is kept at 40°C ±1 while plant’s tube is maintained at 40°C. When the temperature falls to 39°C, the heater is switched on, when the temperature reach 40°C the heater is switched off. This research is carried on using two kind of mixture models which are: mixture model X (mixture of vegetables, fruits and sugar cane waste) and mixture model Y (same as X with additional rice husk). The mixture model X and Y C/N’s ratio is in compliance with SNI-7030-2004 standard. The real-time plant controller system proposed in this research is successfully.
Properties of Composite Boards from Coconut Coir, Plastic Waste and Urea Formaldehyde Adhesives
Authors: Milawarni  , Yassir
Published: June 2019

The objective of this research was to evaluate the characteristic of composite boards made from coir, plastic waste, and urea formaldehyde (UF). The board samples were manufactured at a target density of 0.7 gr/cm3. The weight ratio of waste plastic and coir was 50: 50. The UF adhesive added at 0%, 4%, 8%, 12% and 16% of the total weight of the composite board. The result shows that the characteristic of composite boards improves with UF adhesive added, however, no significant difference was found statistically.
Comparison of methods of heating soybean to yield and the characteristics of tofu with a mixture of acetic acid and Ie Kuloh Sira
Authors: Salmyah
Published: June 2019

Tofu is one of the vegetable proteins made from clumping of soy milk which is accompanied by heating soybean porridge and adding clumps from either acid, organic salt or a mixture of both. For heating soybean porridge can be done without filtering or heating directly with the pulp. This research was carried out by comparing the two methods and the addition of a mixture of acid and organic salts namely acetic acid and Ie Kuloh Sira in the amount of 100 ml in (0; 5; 10; 15; 20) ml, clotting time (10; 15; 20; 25; 30 ) men and soybean immersion time (5; 5.5; 6; 6.5; 7) hours. The results showed that the optimization process was in the addition of Ie Kuloh Sira 10 ml clumping time 20 minutes and soybean immersion time 6 hours. Process optimization was in the addition of Ie Kuloh Sira 10 ml clumping time 20 minutes and soybean immersion time 6 hours. The highest yield was 14.5% with the pulp heating method and no pulp heating, but the protein content test (Lowry method) differed slightly from the method without pulp residue, 24.3381% and 24.941%. Texture Test with higher Texture Analyzer with 480 gr pulp heating/mm2.
Separation of the Mature Level of Papaya Callina Fruit Automatically Based on Color (RGB) uses Digital Image Processing
Authors: Simbolon Z K , Syakry S A , Mulyadi  , Syahroni M
Published: June 2019

The process of sorting papaya fruit based on quality is one of the processes that greatly determines the quality of papaya fruit that will be sold to consumers. The process of identifying the quality of fruits using the human eye has the disadvantages of requiring more energy to sort, the level of human perception in terms of different fruit sorting, the level of human consistency in assessing fruit quality is also unstable because humans can experience fatigue. Research on fruit using image processing is the current trend, especially for fruit conditions, both qualities weight and size because this system processes faster and avoids or reduces failures that occur as a result of human nature. The process of selecting the level of fruit maturity in the process of recognition and determination and classification of post-harvest agricultural products on papaya fruit, depends on how the system is built. This study aims to build a quality recognition system for papaya fruits using Digital Image Processing technology, to analyze the level of color values (RGB), to determine the maturity level of papaya-callina fruit, so that later can be used as a reference in determining the maturity level of papaya fruit. First, the image of papaya is taken, or the acquisition uses a camera to be used as a database based on the condition of its maturity level. Second, the separation of the fruit image with the background based on the pixels, calculating the pixel value looking for the mean value, min, the max that is used later in the reference in determining the fruit maturity condition: young ripe, the half mature, mature. The results of this study provide information about pixel data in which young ripe papaya, red value does not dominate that is 7.785495, the green value becomes the highest value of 10.23922, papaya the half mature, it can be seen that the red and green composition of the pixel value is almost the same, namely 12.56288 and 12.12431, while the fully mature condition of the papaya, average red pixel value becomes more dominant when compared to green, which is 24,111901 for red and 13,70812 for green.
The Implementation of Graphene Composites for Automotive: An Industrial Perspective
Authors: Izzaty N. , Sastra H.Y. , Ilyas
Published: June 2019

Graphene with its exceptional properties in particular the mechanical ones: strength and flexibility, has been found potentially applicable to improve performance of composite materials. Graphene composites is expected to be lighter yet provide more strength, much stronger than steel. This meets the growing demand in the automotive sector which requires lightweight as well as energy efficient and safe vehicles (EESVs) in order to reduce CO2 emission and achieve more fuel economy of the vehicles. Hence, it is suggested to be applied in structural applications for automobiles. However, its scalability for massive production scale is still under investigation. It encounters challenges such as high manufacturing cost, feasible fabrication techniques, as well as safety issues. This study elaborates further the industrial perspectives on the implementation of graphene composites in automotive industry. The analysis in this study emphasises on three different aspects of innovation management: business ecosystem, PESTEL analysis, and scenario planning. The results of this study reveal key partners as well as potential competitors from the insights of business ecosystem, and two major concerns from PESTEL analysis and scenario planning: sustainable supply chains and quality of the graphene composites.
Hardware Based Data Aggregation Routing Protocol for Forest Preventive Fire System
Authors: Yasri Indra , Meirizal Novri
Published: June 2019

A hardware based Data Aggregation (DA) routing protocol to achieve energy efficiency in Wireless Sensor Network (WSN) is presented in this paper. There are 4 stages of scenarios involved in this hardware operational design i.e. the user node broadcast the interest messages, the coordinator node performs storing and transmitting the gradient information, the user node perform storing the gradient information in the interest cache and the target node to respond the interest message through the gradient flow. The hardware design testing shows the operational of Directed Diffusion is successfully implemented for all of 4 stages. Each of nodes is connected through their individual address.
Contour to Centroid Distance Graph as Feature in Hand Gesture Recognition
Authors: Fachri Yanuar Rudi F , Yuniarno Eko Mulyanto
Published: June 2019

Hand gesture is often used as a way of communication that is intuitive and convenient in everyday human life. Kinect camera gives cheaper and easier way to research about the hand gesture than data glove. This research combines previous research Finger-Earth Mover’s Distance (FEMD) base and Fuzzy to recognize hand gestures captured by Kinect camera. The results are graphic of each gesture obtained from a distance of centroids to hand contour. This research will be followed by next research applying fuzzy of classifying each graph of hand gesture.
Preliminary Study of Digital Laminography Parameters on Carbon Steel Plate
Authors: Hamidi Shahfuan Hanif A. , Salleh Khairul Anuar M. , Hamzah Ab Razak , Wahab Mahamad Noor , Azaman Noorhazleena , Ahmad Anis Salwa
Published: June 2019

Laminography is a technique used to determine the depth of a defect in Radiographic Testing (RT). It enables RT operators to accurately locate the defect from the object’s surface especially for welded components. The technique will ensure the quality of weld components meets the standard requirement for reliability and safety purposes. This paper intends to study the exposure parameters of laminography technique on carbon steel plate by using Radiographic Testing – Digital. (RT-D). The important exposure parameters that are considered in this preliminary study are voltage, current, and frame time. The radiography images with achievable level of contrast sensitivity and image quality are analyzed according to the ISO 17636-2. Discussion on correlation between the normalized Signal to Noise ratio (SNRN) and the exposure parameters are done based on the plotting graphs. The results show the exposure parameters has significantly influenced the value of SNRN. Further experimental works are performed using triangulation technique on welded sample. The deviation between the calculated depth of defects and actual results is less than 1.0mm.
Shearography Technique on Inspection of Advanced Aircraft Composite Material
Authors: Yusof Mohd Yusnisyam , Loganathan Tamil Moli , Burhan Ibrahim , Abdullah Wan Saffiey Wan , Mohamed Mohd Noorul Ikhsan , Abidin Ilham Mukriz Zainal , Zakaria Norhayati
Published: June 2019

The A320 aft fixed fairing is an advanced composite structure fabricated from laminate carbon woven and combines with honeycomb core which is externally mounted on the flap track fairing as a wing part of Airbus aircraft. These flaps are movable control surfaces to widen up the surface of the wing in order to increase the lifting. This paper discussed on the inspection of A320 aft fixed fairing by using shearography NDT technique. Shearography technique reveals the stress-affected zone due to additional loading that can be realized by the laser speckle correlation on the inspected composite panel. This A320 aft fixed fairing is identified as a scrap composite panel which having different sizes and orientations of defect. The results showed that the changes of shearing direction in laser shearography technique are an effective means to reveal the defects propagation in the composite component. The shearing at Y-axes direction is able to detect the cracks at horizontal orientation while shearing at X-axis has successfully detects the cracks at vertical orientation. Therefore, shearography could be utilized as an alternative inspection for other NDT method for inspection of composite material.
Ultrasonic Evaluation at the Interface of Aluminum/Steel Obtained by TIG Welding
Authors: Ahsan Qumrul , Kato Hiroshi
Published: June 2019

Aluminum filler (Al-5%Si) is bonded on steel substrate by gas tungsten arc welding process under different current setting conditions. After welding a thorough metallographic analyses using optical and scanning electron microscopy were carried out to observe Al-Steel interface. Ultrasonic measurements by immersion and scanning acoustic microscopy were made to characterise the bond at Al-Steel interface. The ultrasonic wave reflected from the Al-Steel interface clearly indicated the more debonded area when the welding current is changed from direct current straight polarity (DCSP) mode to alternate current high frequency (ACHF) or the welding current in case of current for DCSP mode is reduced. This may be attributed either adequate amount of oxides along with intermediate phase make the bond interface rough and uneven due to introduction of ACHF mode or debonded areas are higher due to lower heat input when the current reduced to 125 amps from 150 amps in DCSP mode. Whereas smooth and even bond interface due to uniform heat input resulted stable Al-Steel interface and the mapping of bonded area by ultrasonic measurement showed spectrum of minimum peak for using current of 150 amps in DC mode. Thus the non-destructive assessments of interface between dissimilar materials through ultrasonic measurements could be important tools for evaluating the state of the bond.
Food deprivation affects egg laying and maternal care but not offspring performance in a beetle
Authors: Richardson Jon , Ross Jennifer , Smiseth Per T
Published: June 2019

Individuals vary with respect to their nutritional state and such variation is an important determinant of the amount of resources individuals allocate toward reproductive functions. Currently, we have a relatively poor understanding of the downstream consequences of food deprivation on different traits associated with reproduction. Here, we address this gap by investigating how food deprivation affected different traits across the breeding cycle in the burying beetle, Nicrophorus vespilloides; a species that breeds on carcasses of small vertebrates serving as food for both parents and offspring. We found that food-deprived females took longer to start egg laying than control females, which may allow them more time to feed from the carcass. There was no difference between food-deprived and control females in the number, size, laying pattern, or hatching success of eggs, suggesting that this delay allowed females to compensate for their poor initial state. However, food-deprived females spent less time providing care, suggesting that this compensation was incomplete. Finally, we found no evidence for negative effects of food deprivation on the offspring’s growth or survival, which is surprising given that food-deprived females took longer to initiate egg laying and provided less care to their offspring. Our results highlight that food deprivation can have complex effects on parental and offspring traits, and suggest that females face a trade-off between the benefits of mitigating downstream consequences of nutritional stress and the costs associated with delaying the start of reproduction.
Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: update of the Clonality R package
Authors: Mauguen Audrey , Seshan Venkatraman E , Begg Colin B , Ostrovnaya Irina
Published: June 2019

The Clonality R package is a practical tool to assess the clonal relatedness of two tumors from the same patient. We have previously presented its functionality for testing tumors using loss of heterozygosity data or copy number arrays. Since then somatic mutation data have been more widely available through next generation sequencing and we have developed new methodology for comparing the tumors’ mutational profiles. We thus extended the package to include these two new methods for comparing tumors as well as the mutational frequency estimation from external data required for their implementation. The first method is a likelihood ratio test that is readily available on a patient by patient basis. The second method employs a random-effects model to estimate both the population and individual probabilities of clonal relatedness from a group of patients with pairs of tumors. The package is available on Bioconductor.

Availability and implementation

Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html).

Supplementary information

Supplementary data are available at Bioinformatics online.
Gestation alters the gut microbiota of an oviparous lizard
Authors: Trevelline Brian K , MacLeod Kirsty J , Langkilde Tracy , Kohl Kevin D
Published: June 2019

Mammalian pregnancy can alter the diversity, membership and structure of the maternal gut microbiota, but it is unclear whether this phenomenon occurs in vertebrates with different reproductive strategies. We conducted 16S rRNA bacterial inventories to investigate whether oviparous lizards exhibit shifts in gut microbiota similar to those observed in mammals. Using wild-caught eastern fence lizards from Alabama, USA, we collected and extracted fecal DNA from gravid and non-gravid individuals over 54 days in captivity. We predicted that, like mammals, the alpha diversity of lizard gut microbiota would decrease over gestation, and that inter-individual variation in community composition would increase. Indeed, we found that individuals in late-gestation harbored lower gut bacterial richness compared to non-gravid females. Lizard gut microbial communities of late-gestational females exhibited higher pairwise distances for both community membership and community structure compared to earlier gestation stages, indicating a higher degree of inter-individual variation as gestation progressed. Additionally, we found that the relative abundance and prevalence of the candidate phylum Melainabacteria tended to decrease over the course of gestation. While the consequences of these specific alterations are unknown, our results suggest that a general restructuring of gut microbial communities over gestation may be widespread across vertebrate reproductive strategies.
A multidimensional perspective on microbial interactions
Authors: Pacheco Alan R , Segrè Daniel
Published: June 2019

Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts.
Effects of even-aged and uneven-aged management on carbon dynamics and timber yield in boreal Norway spruce stands: a forest ecosystem model approach
Authors: Kellomäki S , Strandman H , Peltola H
Published: June 2019

We used a gap-type forest ecosystem model to study how even- and uneven-aged management affected the carbon dynamics and timber production in boreal Norway spruce stands. In business-as-usual management, the intensity of thinnings (from below) and single-tree selective cuttings followed those recommended for even-aged (BT) and uneven-aged management (BSC) in practical forestry in Finland. Moreover, higher or lower basal area thresholds, and shorter or longer production cycles, were used in simulations. We found that, the mean annual carbon uptake, volume growth, and carbon stock in trees and harvested timber, were nearly the same under even-aged (BT) and uneven-aged (BSC) management, when assuming full seed crop in latter one. However, the carbon stock in the soil and ecosystem and the mean annual net ecosystem exchange were slightly smaller under BT. The carbon retention time was longer under BSC. The net present value (NPV with interest rate of 3 per cent) of timber production was clearly lower under BT, when the calculation was initiated at planting on clear-cutting area, in opposite to when initiating calculation a few years before the second thinning. Higher basal area thresholds and longer production cycles increased carbon stocks, carbon retention and timber yield, regardless of management system. On the other hand, the results of uneven-aged management (BSC) were very sensitive to the success of natural regeneration and ingrowth of seedlings, as a reduction of the seed crop by 25–75 per cent from the full seed crop decreases the volume growth by 44–74 per cent and timber yield up to 46 per cent.
Estimating Biological Age in the Singapore Longitudinal Aging Study
Authors: Zhong Xin , Lu Yanxia , Gao Qi , Nyunt Ma Shwe Zin , Fulop Tamas , Monterola Christopher Pineda , Tong Joo Chuan , Larbi Anis , Ng Tze Pin
Published: June 2019

Background

Biological age (BA) is a more accurate measure of the rate of human aging than chronological age (CA). However, there is limited consensus regarding measures of BA in life span and healthspan.

Methods

This study investigated measurement sets of 68 physiological biomarkers using data from 2,844 Chinese Singaporeans in two age subgroups (55–70 and 71–94 years) in the Singapore Longitudinal Aging Study (SLAS-2) with 8-year follow-up frailty and mortality data. We computed BA estimate using three commonly used algorithms: Principal Component Analysis (PCA), Multiple Linear Regression (MLR), and Klemera and Doubal (KD) method, and additionally, explored the use of machine learning methods for prediction of mortality and frailty. The most optimal algorithmic estimate of BA compared to CA was evaluated for their associations with risk factors and health outcome.

Results

Stepwise selection procedures resulted in the final selection of 8 biomarkers in males and 10 biomarkers in females. The highest-ranking biomarkers were estimated glomerular filtration rate for both genders, and the forced expiratory volume in 1 second in males and females. The BA estimates robustly predicted frailty and mortality and outperformed CA. The best performing KD measure of BA was notably predictive in the younger group (aged 55–70 years). BA estimates obtained using a machine learning train-test method were not more accurate than conventional BA estimates in predicting mortality and frailty in most situations. Biologically older people with the same CA as biologically younger individuals had higher prevalence of frailty and 8-year mortality, and worse health, behavioral, and functional characteristics.

Conclusions

BA is better than CA for measuring life span (mortality) and healthspan (frailty). This measurement set of physiological markers of biological aging among Chinese robustly differentiate biologically old from younger individuals with the same CA.
Variability in synthetic earthquake ground motions caused by source variability and errors in wave propagation models
Authors: Spudich Paul , Cirella Antonella , Scognamiglio Laura , Tinti Elisa
Published: June 2019

Numerical simulations of earthquake ground motions are used both to anticipate the effects of hypothetical earthquakes by forward simulation and to infer the behaviour of the real earthquake source ruptures by the inversion of recorded ground motions. In either application it is necessary to assume some Earth structure that is necessarily inaccurate and to use a computational method that is also inaccurate for simulating the wavefield Green's functions. We refer to these two sources of error as ‘propagation inaccuracies’, which might be considered to be epistemic. We show that the variance of the Fourier spectrum of the synthetic earthquake seismograms caused by propagation inaccuracies is related to the spatial covariance on the rupture surface of errors in the computed Green's functions, which we estimate for the case of the 2009 L'Aquila, Italy, earthquake by comparing erroneous computed Green's functions with observed L'Aquila aftershock seismograms (empirical Green's functions). We further show that the variance of the synthetic seismograms caused by the rupture variability (aleatory uncertainty) is related to the spatial covariance on the rupture surface of aleatory variations in the rupture model, and we investigate the effect of correlated variations in Green's function errors and variations in rupture models. Thus, we completely characterize the variability of synthetic earthquake seismograms induced by errors in propagation and variability in the rupture behaviour. We calculate the spectra of the variance of the ground motions of the L'Aquila main shock caused by propagation inaccuracies for two specific broad-band stations, the AQU and the FIAM stations. These variances are distressingly large, being comparable or in some cases exceeding the data amplitudes, suggesting that the best-fitting L'Aquila rupture model significantly overfits the data and might be seriously in error. If these computed variances are typical, the accuracy of many other rupture models for past earthquakes may need to be reconsidered. The results of this work might be useful in seismic hazard estimation because the variability of the computed ground motion, caused both by propagation inaccuracies and variations in the rupture model, can be computed directly, not requiring laborious consideration of multiple Earth structures.
Integration and the Developmental Genetics of Allometry
Authors: Hallgrímsson Benedikt , Katz David C , Aponte Jose D , Larson Jacinda R , Devine Jay , Gonzalez Paula N , Young Nathan M , Roseman Charles C , Marcucio Ralph S
Published: June 2019

Allometry refers to the ways in which organismal shape is associated with size. It is a special case of integration, or the tendency for traits to covary, in that variation in size is ubiquitous and evolutionarily important. Allometric variation is so commonly observed that it is routinely removed from morphometric analyses or invoked as an explanation for evolutionary change. In this case, familiarity is mistaken for understanding because rarely do we know the mechanisms by which shape correlates with size or understand their significance. As with other forms of integration, allometric variation is generated by variation in developmental processes that affect multiple traits, resulting in patterns of covariation. Given this perspective, we can dissect the genetic and developmental determinants of allometric variation. Our work on the developmental and genetic basis for allometric variation in craniofacial shape in mice and humans has revealed that allometric variation is highly polygenic. Different measures of size are associated with distinct but overlapping patterns of allometric variation. These patterns converge in part on a common genetic basis. Finally, environmental modulation of size often generates variation along allometric trajectories, but the timing of genetic and environmental perturbations can produce deviations from allometric patterns when traits are differentially sensitive over developmental time. These results question the validity of viewing allometry as a singular phenomenon distinct from morphological integration more generally.
Andrographolide Exerts Significant Antidepressant-Like Effects Involving the Hippocampal BDNF System in Mice
Authors: Zhang Jing-Jing , Gao Ting-Ting , Wang Yuan , Wang Jin-Liang , Guan Wei , Wang Ying-Jie , Wang Cheng-Niu , Liu Jian-Feng , Jiang Bo
Published: June 2019

Background

Major depressive disorder is a worldwide neuropsychiatric disorder associated with various symptoms, but current antidepressants used in clinical practice have various side effects and high failure rates. Andrographolide is the main bioactive ingredient of Andrographis paniculata and exhibits numerous pharmacological actions. This study aimed to evaluate the antidepressant-like effects of andrographolide in male C57BL/6J mice.

Methods

The antidepressant-like effects of andrographolide in mice were explored in a forced swim test, tail suspension test, and chronic unpredictable mild stress model of depression. Western blotting and immunofluorescence were further performed to assess the effects of chronic unpredictable mild stress and andrographolide on the brain-derived neurotrophic factor signalling cascade and hippocampal neurogenesis. Moreover, a pharmacological inhibitor (K252a) and a lentiviral-short hairpin RNA (LV-TrkB-shRNA) were used to clarify the antidepressant-like mechanism of andrographolide.

Results

Andrographolide exhibited antidepressant-like potential in the forced swim test and tail suspension test without influencing the locomotor activity of mice. Repeated andrographolide treatment not only produced significant antidepressant-like effects in the chronic unpredictable mild stress model but also prevented the decreasing effects of chronic unpredictable mild stress on hippocampal brain-derived neurotrophic factor signalling and neurogenesis in mice. Importantly, blockade of the hippocampal brain-derived neurotrophic factor system by K252a and TrkB-shRNA fully abolished the antidepressant-like effects of andrographolide in mice.

Conclusions

Andrographolide exerts antidepressant-like effects in mice via promoting the hippocampal brain-derived neurotrophic factor signalling cascade.
Guidance for Studies Evaluating the Accuracy of Tuberculosis Triage Tests
Authors: Nathavitharana Ruvandhi R , Yoon Christina , Macpherson Peter , Dowdy David W , Cattamanchi Adithya , Somoskovi Akos , Broger Tobias , Ottenhoff Tom H M , Arinaminpathy Nimalan , Lonnroth Knut , Reither Klaus , Cobelens Frank , Gilpin Christopher , Denkinger Claudia M , Schumacher Samuel G
Published: June 2019

Approximately 3.6 million cases of active tuberculosis (TB) go potentially undiagnosed annually, partly due to limited access to confirmatory diagnostic tests, such as molecular assays or mycobacterial culture, in community and primary healthcare settings. This article provides guidance for TB triage test evaluations. A TB triage test is designed for use in people with TB symptoms and/or significant risk factors for TB. Triage tests are simple and low-cost tests aiming to improve ease of access and implementation (compared with confirmatory tests) and decrease the proportion of patients requiring more expensive confirmatory testing. Evaluation of triage tests should occur in settings of intended use, such as community and primary healthcare centers. Important considerations for triage test evaluation include study design, population, sample type, test throughput, use of thresholds, reference standard (ideally culture), and specimen flow. The impact of a triage test will depend heavily on issues beyond accuracy, primarily centered on implementation.
Invasive Meningococcal Disease in Africa’s Meningitis Belt: More Than Just Meningitis?
Authors: Reese Heather E , Ronveaux Olivier , Mwenda Jason M , Bita Andre , Cohen Adam L , Novak Ryan T , Fox LeAnne M , Soeters Heidi M
Published: June 2019

Since the progressive introduction of the meningococcal serogroup A conjugate vaccine within Africa’s meningitis belt beginning in 2010, the burden of meningitis due to Neisseria meningitidis serogroup A (NmA) has substantially decreased. Non-A serogroups C/W/X are now the most prevalent. Surveillance within the belt has historically focused on the clinical syndrome of meningitis, the classic presentation for NmA, and may not adequately capture other presentations of invasive meningococcal disease (IMD). The clinical presentation of infection due to serogroups C/W/X includes nonmeningeal IMD, and there is a higher case-fatality ratio associated with these non-A serogroups; however, data on the nonmeningeal IMD burden within the belt are scarce. Expanding surveillance to capture all cases of IMD, in accordance with the World Health Organization’s updated vaccine-preventable disease surveillance standards and in preparation for the anticipated introduction of a multivalent meningococcal conjugate vaccine within Africa’s meningitis belt, will enhance meningococcal disease prevention across the belt.
Transfer dynamics of Tn6648, a composite integrative conjugative element generated by tandem accretion of Tn5801 and Tn6647 in Enterococcus faecalis
Authors: León-Sampedro Ricardo , Fernández-de-Bobadilla Miguel D , San Millán Álvaro , Baquero Fernando , Coque Teresa M
Published: June 2019

Background

Tn5801 [tet(M)], a Tn916-like element with site-specific affinity for the 3′ end of the housekeeping gene guaA, may integrate at different chromosomal sites.

Objectives

To characterize the genetic context of Tn5801 to define its transfer dynamics and impact on the evolution of Enterococcus faecalis (Efs).

Methods

WGS (Illumina HiSeq 2500) was performed on the Efs clinical strain Ef1 and primary and secondary transconjugants of Efs strains JH2-2 [which naturally contains Tn5801.B23, an unusual variant that lacks tet(M)], OG1RF and OG1SS carrying different copies of Tn5801-like elements. The transposon structures were analysed using a range of bioinformatics tools allowing us to identify the context of Tn5801-like elements. Growth rates at different tetracycline concentrations (0.5–20 mg/L) were estimated using a Synergy HTX plate reader.

Results

Tn5801.B15 [tet(M), 20.3 kb] exists and can be transferred either singly or within Tn6648 (53.2 kb), a composite element that comprises Tn5801.B15 and Tn6647, a newly identified 32.8 kb transposon that contains the prgABCT operon of pheromone-responsive plasmids. These transposons are able to integrate at specific 11 nt sequences at the 3′ end of guaA and at other chromosomal sites in Efs genomes, thus being able to generate tandem accretions. These events may increase the number of tet(M) copies, enhancing tetracycline resistance in the recipient strain.

Conclusions

This study describes Tn6647 and Tn6648 (comprising Tn6647 and Tn5801.B15) and highlights the diversity of mechanisms for conjugative mobilization and chromosomal insertion of these elements, which can result in tandem accretion. This strategy would facilitate the adaptation of Efs clones to environmental challenges.
Antibiotics with activity against intestinal anaerobes and the hazard of acquired colonization with ceftriaxone-resistant Gram-negative pathogens in ICU patients: a propensity score-based analysis
Authors: Boutrot Maxime , Azougagh Khalid , Guinard Jérôme , Boulain Thierry , Barbier François
Published: June 2019

Background

Intestinal colonization resistance is mainly exerted by commensal anaerobes.

Objectives

To assess whether exposure to non-carbapenem antibiotics with activity against intestinal anaerobes (namely, piperacillin/tazobactam, amoxicillin/clavulanate and metronidazole) may promote the acquisition of gut colonization with ceftriaxone-resistant Gram-negative bacteria (CFR-GNB) in ICU patients.

Patients and methods

All patients with a first stay >3 days in a single surgical ICU over a 30 month period were retrospectively included. Rectal carriage of CFR-GNB (i.e. ESBL-producing Enterobacteriaceae, AmpC-hyperproducing Enterobacteriaceae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia and CFR Acinetobacter baumannii) was routinely screened for at admission then weekly. The impact of anti-anaerobe antibiotics was investigated in propensity score (PS)-matched cohorts of patients exposed and not exposed to these drugs and through PS-based inverse probability of treatment weighting on the whole study cohort, treating in-ICU death or discharge as competing risks for CFR-GNB acquisition.

Results

Among the 352 included patients [median ICU stay 16 (9–30) days, in-ICU mortality 12.2%], 120 (34.1%) acquired one or more CFR-GNB, mostly AmpC-hyperproducing Enterobacteriaceae (17.6%) and P. aeruginosa (14.8%). Exposure to anti-anaerobe antibiotics was the main predictor of CFR-GNB acquisition in both the PS-matched cohorts [adjusted HR (aHR) 3.92, 95% CI 1.12–13.7, P = 0.03] and the whole study cohort (aHR 4.30, 95% CI 1.46–12.63, P = 0.01). Exposure to other antimicrobials—especially ceftriaxone and imipenem/meropenem—exerted no independent impact on the likelihood of CFR-GNB acquisition.

Conclusions

Exposure to non-carbapenem antibiotics with activity against intestinal anaerobes may predispose to CFR-GNB acquisition in ICU patients. Restricting the use of these drugs appears to be an antibiotic stewardship opportunity.