bluuebunny/crossref_metadata_2025 huggingface dataset:
Study of Generation, Composition, Characteristics, and Recycling Potential of Industrial Food Waste in Padang City
Authors: Dewilda Y , Warnares S A , Zulkarnaini
Published: September 2020

The purpose of research to measure and analyze the generation, composition, characteristics, and potential recycling industrial food waste in Padang City. The sampling and determination of samples based on SNI 19-3964-1994, which was carried out for eight consecutive days with sampling from 35 food industry consist of large industrial, medium industries, and small industries. The average quantities of food waste generated from the large, medium, and small industries in Padang City were 0.005 kg/d, 0.083 kg/d, and 0.262 kg/d, respectively. The composition of food waste consists of 94.01% organic waste, 5.97% plastic waste, 0.01% paper waste, and 0.01% other waste. The potential for recycling of industrial food waste was 75.20% plastic, 100% nonferrous metal, and 97.38% organic waste. The characteristics of the waste based on parameters average density, water content, volatile content, ash content, fixed carbon, C/N ratio, calorific value, and biodegradability fraction were 13.32 kg/l, 13.77%, 26.75%, 45.39%, 14.09%, 13.77, 1,798 kJ/kg, 38.87%, respectively. The generation, composition, characteristics, and potential recycling industrial food waste is very important for proper waste management.
Determination of Construction Design to Reduce the Amount of Marine Litter at Seawater Intake Using Particle Tracking Module of Numerical Method by Mike 21 (Case Study: Tanjung Awar - Awar, Tuban, East Java)
Authors: Khoirunnisa H , Wibowo M , Hendriyono W
Published: September 2020

This research aims to analyze and estimate the amount of marine litter which get into seawater intake of PT Trans-Pacific Petrochemical Indonesia (TPPI) Tuban in existing conditions during west monsoon and east monsoon. Ten designs will be simulated to reduce and trap the marine debris entering the seawater intake (SWI). These designs will be tested for their effectiveness in reducing the number of debris entering the SWI using the particle tracking module of MIKE 21 numerical modelling package. The required data in this simulation are wind (speed and direction), wave (significant height, direction and period), the bathymetry of and coastline. Besides, this simulation is conducted based on primary data provided by TPPI Tuban management as the validation data. Based on the simulation results, the amount of marine litter entering SWI in the west monsoon is greater than the east monsoon, which is 349.14 kg/year for west monsoon and 100.84 kg/year for east monsoon. Based on the simulation results using the particle tracking module, it was found that design 5 is the most effective design, with the effectiveness of 73.97%. The biggest accumulation of marine litter using construction design 5 occurred in November, which was 355.36 kg.
Wave Model for the Design of Sustainable Coastal Infrastructures at an Industrial Site in Tuban, East Java
Authors: Hendriyono W , Wibowo M , Subarkah A , Aziz H
Published: September 2020

This study focuses on the use of computational model in the design of a breakwater structure, which aims to determine the propagation pattern of the long-term ocean waves, in order to understand their propagation from the deep waters, and to determine the distribution of their energy around a proposed breakwater construction site. The method used is computational simulation of the wave model using the 2D Boussinesq Wave (BW) Module of MIKE21 software. The simulation used an incoming wave of 4.6 m high, which corresponds to the 100 years return-period value. The results show that the existing breakwater layout can protect the harbour by reducing the incoming waveheight by up to 75%. At the proposed design condition, the propagation pattern of the incoming wave slightly differs from the existing condition. The presence of the slopes on both sides of the channel changes the wave direction outwards due to shoaling effects, and consequently, larger concentration of wave energy occurs at some parts of the proposed breakwater design. Results from the model are useful for the design of the new breakwater structures, which is designed according to the predicted wave energy distribution.
Mangrove Damage Evaluation using Two Species of Acanthus as a Biomonitoring Agent, Case Study: Segara Anakan Cilacap, Indonesia
Authors: Ardli E R , Yani E
Published: September 2020

Mangrove area continues to be decreased and lost in Indonesia due to human activities as well as natural disturbances. Segara Anakan is the largest mangrove ecosystem left in Java Island, where also in critical condition that mainly due to sedimentation and people use. This mangrove degradation can be evaluated by using mangrove understorey as a bioindicator. Acanthus genera are one of mangrove vegetation that can overgrow after mangrove degraded and canopy been opened. There are two species, which are Acanthus ilicifolius and Acanthus ebracteatus in Segara Anakan mangrove ecosystems. The survey method with purposive sampling was used in this study in 2010 and 2018. Ecological data were analyzed using PRIMER-E, mapping, and spatial analysis using Surfer and ArcView 3.2. The study shows two species of Acanthus were distributed aggregate, especially in the damaged mangrove that found a low density of mangrove in the sapling and tree category. The density of Acanthus has increased during one decade as well as its distribution than one decade before. Therefore, Acanthus can be used for biomonitoring agent of mangrove damage because of its specific characteristics and distribution.
Translocation Factor of Zinc (Zn) in Water and Sediment by Root and Stem of Rhizophora sp. at Blanakan Riparian, West Java
Authors: Purwaningdyah A R , Takarina N D
Published: September 2020

Mangroves are plants that can transport, absorb, and store heavy metals in the surrounding environment. This study aims to measure the capacity of Rhizophora sp. root and stem in transporting, absorbing, and storing Zn from water and sediment of Blanakan Riparian, West Java. Rhizophora sp. root, stem, water, and sediment samples were collected from 3 stations located on the Blanakan Riparian, West Java. Atomic Absorption Spectrophotometer was used to analyze the Zn contents from the samples. Likewise, Bioconcentration Factor (BCF) and Translocation Factor (TF) were used to calculate the Zn contents from water and sediment stored in root and stem. The results showed that the range of BCF of Zn in water and sediment in root were 108.214-284.204 and 0.254-0.271, respectively. Meanwhile, the range of BCF of Zn in water and sediment in the stem were 112.193-189.611 and 0.233-0.297. Furthermore, the range of TF of Zn in water and sediment were 0.667-1.036 and 0.917-1.095. To conclude, the root and stem of Rhizophora sp. can be used to translocate Zn contents from water and sediment at Blanakan Riparian, West Java.
Macrozoobenthos Diversity as a Bioindicator of Heavy Metal Pollution in Segara Anakan Lagoon, Cilacap District, Indonesia
Authors: Lestari S , Rahmanto T A
Published: September 2020

Various methods are available for monitoring pollution levels in surface water and sediments, including using organisms as bioindicators. Segara Anakan Lagoon is an estuarine ecosystem that could be affected by contaminants transported by rivers. Pollution sources include pesticides and fertilizers from upstream agricultural areas, domestic waste, and shipping traffic. Macrozoobenthos are among the organisms commonly used as bioindicators of environmental pollution. Macrozoobenthos live at the bottom of the water column, and as deposit feeders, they lend themselves to use as bioindicators. The structure of the macrozoobenthos community in Segara Anakan has changed, as evidenced by the diversity and abundance of benthic species. Furthermore, environmental pollution parameters, such as heavy metal concentrations in water and sediments, are relatively high in the lagoon. Concentrations of Hg, Pb, Cd, and Cr varied among collection sites, with average concentrations of 0.04, 4.4, 1.2, and 1.4 ppm, respectively. In general, the abundance of macrozoobenthos was low at collection stations with high heavy metal concentrations, demonstrating that heavy metal pollution has occurred in Segara Anakan. Correlation tests between macrozoobenthos and heavy metal concentrations in water and sediments yielded r-values of > 0.8225 and 0.7473, respectively.
Enzymatic Activities of Streptomyces spp. Isolated from Natural Habitat of Nipah Worm in Sungai Kakap District, West Kalimantan
Authors: Yanti A H , Setyawati T R , Kurniatuhadi R
Published: September 2020

Streptomyces involves in the degradation process of organic compounds on the soils, including mangrove forests. In this process, Streptomyces secretes several enzymes to convert the substrates into other substances, which will readily be available for detritus feeders, including nipah worms (Namalycastis rhodochorde). This study investigated the enzyme activities of six Streptomyces spp. that has been isolated from mangrove soil in Sungai Kakap District, West Kalimantan. Enzymatic activities were detected on four different media: CMC-congo red agar, skim milk agar, gelatine nutritive agar, starch casein agar. Catalase activity was detected using 3% of H2O2 solution. The results showed that six Streptomyces spp. had proteolytic, cellulolytic, amylolytic, gelatin liquefaction, and catalase activities. Streptomyces NrASA1 has the highest proteolytic activity index values, namely 0.57. Streptomyces NrASA3 and Streptomyces NrASA4 have the highest amylolytic and cellulolytic activity index values, respectively 0.76 and 1.15. The enzymatic activity profile of indigenous Streptomyces spp. can be utilized for the development of feed formula for nipah worm cultivation.
Rhizospheric Soil Fungi from Several Food Crops in Purwokerto
Authors: Purwati E S , Dwiputranto U , Ekowati N , Ratnaningtyas N I
Published: September 2020

There are several interaction patterns of fungus that live in the rhizosphere of plants, i.e. mutualism, commensalism, saprophytism, and parasitism. The objective of this study was to determine the genera of microscopic fungus collected from the rhizosphere of groundnut, mays plant, and rice field. In addition, the diversity of soil fungi of those three plants was considered. Research method applied was survey with purposive sampling. The rhizospheric soil sample was obtained from research locations of groundnut, mays plants, and rice field in Purwokerto area. The soil samples were taken from 1-10 cm deep. Next they were isolated, and then they were purified. Furthermore, the obtained data of fungus collection were then analysed descriptively, and also described based on their macro and micro morphology. Then, the collected fungus were identified by using identification manual for fungus. The result showed that fifteen (15) isolates were found in three different rhizosphere of ground nut, mays plants, and rice field. The description is as follow: Aspergillus-1, Aspergillus-2, Penicillium-1, Penicillium-2, Mycophyta, Aureobasidia, Cylindrocarpon, Mucor-1, Mucor-2, Chaetomium, Gliocladium, Trichoderma-1, Trichoderma-2, Pleurophragmium, and Gonytrichum. Finally, the diversity Index (H’) noted from rhizosphere of groundnut plants was 0.312; mays was 0.195; and (H’) of rice field was 0.124.
The Plankton Composition from the Lagoon to the Marine Entrance at the West Part of Segara Anakan Mangrove Ecosystem in Cilacap
Authors: Sastranegara M H , Widyartini D S , Fitriana I , Rani K M
Published: September 2020

There was a unique brackish water ecosystem and affected a chance in the plankton composition at lagoon and riverside in Segara Anakan Cilacap. This study aimed to map phytoplankton and zooplankton composition consisting of freshwater and marine plankton from the lagoon to the marine entrance in the west part of Segara Anakan Cilacap. The survey method was taken with purposive random sampling in fourteen stations and four replicates with new and full moon conditions from March to April 2018 in a wet season. The result showed 52 species of plankton. All species belonged to phylum Cyanophyta (9 species), Chlorophyta (13 species), Chrysophyta (19 species), Euglenozoa (2 species), Rotifera (2 species) and Arthropoda (7 species). Of the 52 species collected in all stations and replicates, phytoplankton has a greater species richness (41 species) than zooplankton (11 species). And also, freshwater plankton (47 species) has a higher species richness than marine plankton (5 species) due to the wet season condition causing freshwater enters brackish water. The largest freshwater of River Citanduy enters the brackish water of Segara Anakan mangrove ecosystem in Cilacap and causing the freshwater phytoplankton abundance, especially Staurastrum sp. in inland waters of Segara Anakan Cilacap.
Effect of Temperature and Zinc (Zn) Temporal Variation in Water on Size Distribution of River Catfish (Mystus sp.) at Blanakan River, West Java
Authors: Sekarini D A , Takarina N D
Published: September 2020

River catfish (Mystus sp.) is a species commonly found in the Blanakan river. The community also consumes this species lived around Blanakan. This study aimed to investigate the effect of temporal variation of temperature and metal Zn on the Mystus sp. size distribution. The fish samples and water were collected from the river in the early and end of June to represent temporal variation. Simultaneously, the water temperatures were also recorded. The fish samples’ length and weight were measured. The AAS (Atomic Absorption Spectroscopy) was used to analyze Zn in water samples. The results showed that there was a temperature decrease from 32.9 0C to 30.8 0C. The Zn was also decreased from 1.12 mg/l to 0.14 mg/l. The length of Mystus sp. was increased from 13.27 cm to 14.00 cm. In contrast, the weight was reduced from 36.29 g to 32.88 g. To conclude, the temperature and Zn temporal variation affected the increasing length and reducing weight.
The Potential of Nereis sp. (Polychaete) as Prawn Feed at the Coastal Farming of Jeruklegi, Cilacap
Authors: Wibowo E S , Puspitasari I G A R , Palupi E S , Atang
Published: September 2020

Nereis sp. (Polychaete) belongs to the Nereidae family that lives as benthic organisms in estuarine. The high level of amino acid and unsaturated fatty acid in Nereis sp. is potentially used as a nutrient in prawn feed. These compositions increase the quality of prawn gametes and larvae. However, there is still less information about the nutrient composition of Nereis sp. in the Jeruklegi area. Therefore, a study about nutrient composition (chemical composition) of Nereis sp. in this area was conducted to provide necessary information for the Nereis sp. culture in the future. This study used a survey method, and sampling was conducted in four stations with three replications at each three-sampling point in each station. The result showed no significant differences in protein and fat composition of Nereis sp. among stations. The protein contents ranging from 42.06 to 51.68%, and fat content range from 12.93 to 22%. The high content of both protein and lipid are reliable to fulfill the requirements in prawn farming. Therefore, Nereis sp. from Jeruklegi has a high potential to be utilized as a new food resource on prawn farming.
Light management using CsPbBr3 colloidal quantum dots for luminescent solar concentrators
Authors: Singh Akhilesh Kumar
Published: September 2020

CsPbBr3 colloidal quantum dots have been synthesized by hot-injection method showing spherical shape with an average diameter of ∼10.5 nm. UV–vis absorption of CsPbBr3 colloidal quantum dots shows a broad spectrum with an optical bandgap of ∼2.3682 eV. The steady-state photoluminescence measurement reveals a narrow emission peak at 2.352 eV with full-width at half maximum of 0.113 eV. Absolute photoluminescence quantum yield of colloidal quantum dots dispersed in poly(methyl methacrylate) was found to be 60 ± 1%. The time-resolved photoluminescence data recorded at 266 nm excitation were well fitted using a mono-exponential curve with a decay time of 25.36 (5) ns. A luminescent solar concentrator was fabricated using colloidal quantum dots in transparent poly(methyl methacrylate) polymer uniformly coated over glass substrate that shows an external optical conversion efficiency of ∼5.4% under one sun illumination. The experimental results presented in this manuscript reveals that luminescent solar concentrator prepared using colloidal CsPbBr3 quantum dots shows absorption in wide spectral range, high absorption coefficient, high photoluminescence quantum yield, high external optical conversion efficiency, and good photostability, thermal stability and long-term stability under ambient conditions and therefore are in many ways superior to the other luminescent materials explored for LSC devices.
The three-cavity microstructures and mechanical properties of honeybee stingers
Authors: Miao Bo-Jun , Yang Qing-Sheng , Liu Li-Ya , Li Shuai-Wei
Published: September 2020

To investigate the microstructure-property relations of honeybee stingers, the cross-section microstructures were analyzed by scanning electron microscope (SEM) and the mechanical properties of honeybee stingers were tested by nanoindentation experiment in vivo in this paper. The Young’s modulus and hardness in the cross section of different segments of honeybee stingers were obtained. It is found that the honeybee stinger is of a hierarchical structure in cross section, which varies from the root to the tip and leads to quite different mechanical properties of the stingers. The natural optimized microstructure and excellent mechanical properties of the stingers effectively contribute to the biological function and self-protection performance of honeybees.
Design of a hybrid plasmonic waveguide device using a trench structure
Authors: Okamoto Hiroyuki , Kamada Shun , Haraguchi Masanobu , Okamoto Toshihiro
Published: September 2020

A hybrid plasmonic waveguide device was designed using a trench structure. This waveguide device was designed to improve the affinity of plasmonic devices with optical circuits by connecting them with traditional waveguide structures. The waveguide device consists of three structural segments, comprising two traditional waveguide sections for input and transmission and a hybrid plasmonic waveguide. The designed waveguide structure was evaluated using numerical analysis techniques such as the finite-difference time-domain method. The device's transmission property affects the interference between the guided light and the surface plasmon polaritons. Controlling the length of the hybrid waveguide device, which is composed of a traditional waveguide coated with a gold layer, allows the transmission intensity of the device to be controlled. The device's transmission characteristic can be controlled based on the relationship between the wavelength of the incident light and the length of the hybrid waveguide device. The device will transmit only specific incident light wavelengths because the length of the hybrid plasmonic waveguide remains constant. The characteristics of this device indicate potential for applications to nanoscale devices, optical integrated circuits and plasmonic sensors.
Yeast Rgd3 is a phospho-regulated F-BAR–containing RhoGAP involved in the regulation of Rho3 distribution and cell morphology
Authors: Gingras Robert M. , Lwin Kyaw Myo , Miller Abigail M. , Bretscher Anthony
Published: September 2020

RGD3 ( YHR182w) is a novel RhoGAP in budding yeast whose overexpression suppresses the temperature sensitivity of myo2 smy1 mutants defective in secretory vesicle transport. We show that Rgd3 localizes to polarized vesicles distinct from constitutive secretory vesicles and contributes to cell polarity through its GAP activity on Rho3.
Personal Jurisdiction in Comparative Context
Authors: Dodson Scott
Published: September 2020

This Article places the recent evolution of U.S. personal jurisdiction in comparative context. Comparativism helps illuminate and explain both the modest convergences and the more pervasive divergences. On the convergences side, the Supreme Court’s acknowledgment of transnational litigation and express invocation of European approaches to personal jurisdiction have helped move general jurisdiction away from the exorbitant “doing business” jurisdiction that seemed previously to be settled U.S. law. But persistent divergences tell the more interesting story. The Court’s refusal to deviate from its commitment to transient jurisdiction, its recent narrowing of specific jurisdiction since 2011, its implicit rejection of pendent-party personal jurisdiction, and its adherence to a strong form of consent-based personal jurisdiction all reveal a stark contrast with other countries’ approaches to personal jurisdiction. That contrast is founded on deep and stubborn ties to American history, political structure, and litigation norms, all of which make broader convergence difficult, if not implausible. For these reasons, U.S. personal-jurisdiction doctrine is more likely to continue to develop on an independent track rather than hew to global trends. Some areas of parallelism might still occur, but substantial convergence is likely to remain elusive.
Preanalytical Sample Handling Conditions and Their Effects on the Human Serum Metabolome in Epidemiologic Studies
Authors: McClain Kathleen M , Moore Steven C , Sampson Joshua N , Henderson Theresa R , Gebauer Sarah K , Newman John W , Ross Sharon , Pedersen Theresa L , Baer David J , Zanetti Krista A
Published: September 2020

Many epidemiologic studies use metabolomics for discovery-based research. The degree to which sample handling may influence findings, however, is poorly understood. In 2016, serum samples from 13 volunteers from the US Department of Agriculture’s Beltsville Human Nutrition Research Center were subjected to different clotting (30 minutes/120 minutes) and refrigeration (0 minutes/24 hours) conditions, as well as different numbers (0/1/4) and temperatures (ice/refrigerator/room temperature) of thaws. The median absolute percent difference (APD) between metabolite levels and correlations between levels across conditions were estimated for 628 metabolites. The potential for handling artifacts to induce false-positive associations was estimated using variable hypothetical scenarios in which 1%–100% of case samples had different handling than control samples. All handling conditions influenced metabolite levels. Across metabolites, the median APD when extending clotting time was 9.08%. When increasing the number of thaws from 0 to 4, the median APD was 10.05% for ice and 5.54% for room temperature. Metabolite levels were correlated highly across conditions (all r’s ≥ 0.84), indicating that relative ranks were preserved. However, if handling varied even modestly by case status, our hypotheticals showed that results can be biased and can result in false-positive findings. Sample handling affects levels of metabolites, and special care should be taken to minimize effects. Shorter room-temperature thaws should be preferred over longer ice thaws, and handling should be meticulously matched by case status.
Laterality in foraging phalaropes promotes phenotypically assorted groups
Authors: Gutiérrez Jorge S , Soriano-Redondo Andrea
Published: September 2020

Asymmetry of the brain and behavior (lateralization) is widespread in the animal kingdom and could be particularly advantageous for gregarious organisms. Here, we investigate the possibility that lateralized behaviors affect the structure of foraging flocks. Phalaropes (Scolopacidae: Phalaropus) are highly aquatic shorebirds and the only vertebrates that spin on the water to feed, often in large flocks. There is anecdotal evidence that individuals spin in a single direction and that those spinning counter the majority are usually found at the periphery of a flock. Although such phenotypic segregation may reduce interference among socially foraging birds, its extent and underlying mechanism remain unexplored. Using over 900 spinning bouts from freely available video repositories, we find support for individual, but not population, lateralization of spinning in the three phalarope species. Although spinning direction was not determined by the position occupied within a flock (periphery vs. core), nearest neighbors were more likely to spin in the same direction; moreover, they were three times less likely to interfere with each other when aligning spinning direction. Our results indicate that a simple rule (keep foraging with similarly lateralized individuals) can generate self-organized interactions among flockmates, resulting in groups phenotypically assorted.
PyMod 3: a complete suite for structural bioinformatics in PyMOL
Authors: Janson Giacomo , Paiardini Alessandro
Published: September 2020

The PyMod project is designed to act as a fully integrated interface between the popular molecular graphics viewer PyMOL, and some of the most frequently used tools for structural bioinformatics, e.g. BLAST, HMMER, Clustal, MUSCLE, PSIPRED, DOPE and MODELLER. Here we report its latest release, PyMod 3, which has been completely renewed with a graphical interface written in PyQt, to make it compatible with the most recent PyMOL versions, and has been extended with a large set of new functionalities compared to its predecessor, i.e. PyMod 2. Starting from the amino acid sequence of a target protein, users can take advantage of PyMod 3 to carry out all the steps of the homology modeling process (i.e. template searching, target–template sequence alignment, model building and quality assessment). Additionally, the integrated tools in PyMod 3 may also be used alone, in order to extend PyMOL with a wide range of capabilities. Sequence similarity searches, multiple sequence/structure alignment building, phylogenetic trees and evolutionary conservation analyses, domain parsing, single/multiple chains and loop modeling can be performed in the PyMod 3/PyMOL environment.

Availability and implementation

A cross-platform PyMod 3 installer package for Windows, Linux and Mac OS X and a complete user guide with tutorials, are available at https://github.com/pymodproject/pymod

Supplementary information

Supplementary data are available at Bioinformatics online.
Can Existing Improvements of Water, Sanitation, and Hygiene (WASH) in Urban Slums Reduce the Burden of Typhoid Fever in These Settings?
Authors: Im Justin , Islam Md Taufiqul , Ahmmed Faisal , Kim Deok Ryun , Islam Khan Ashraful , Zaman Khalequ , Ali Mohammad , Marks Florian , Qadri Firdausi , Kim Jerome , Clemens John D
Published: September 2020

Background

Sustained investments in water, sanitation, and hygiene (WASH) have lagged in resource-poor settings; incremental WASH improvements may, nonetheless, prevent diseases such as typhoid in disease-endemic populations.

Methods

Using prospective data from a large cohort in urban Kolkata, India, we evaluated whether baseline WASH variables predicted typhoid risk in a training subpopulation (n = 28 470). We applied a machine learning algorithm to the training subset to create a composite, dichotomous (good, not good) WASH variable based on 4 variables, and evaluated sensitivity and specificity of this variable in a validation subset (n = 28 470). We evaluated in Cox regression models whether residents of “good” WASH households experienced a lower typhoid risk after controlling for potential confounders. We constructed virtual clusters (radius 50 m) surrounding each household to evaluate whether a prevalence of good WASH practices modified the typhoid risk in central household members.

Results

Good WASH practices were associated with protection in analyses of all households (hazard ratio [HR] = 0.57; 95% confidence interval [CI], .37–.90; P = .015). This protection was evident in persons ≥5 years old at baseline (HR = 0.47; 95% CI, .34–.93; P = .005) and was suggestive, though not statistically significant, in younger age groups (HR = 0.61; 95% CI, .27–1.38; P = .235). The level of surrounding household good WASH coverage was also associated with protection (HR = 0.988; 95% CI, .979–.996; P = .004, for each percent coverage increase). However, collinearity between household WASH and WASH coverage prevented an assessment of their independent predictive contributions.

Conclusions

In this typhoid-endemic setting, natural variation in household WASH was associated with typhoid risk. If replicated elsewhere, these findings suggest that WASH improvements may enhance typhoid control, short of major infrastructural investments.
Differences in biomarkers and molecular pathways according to age for patients with HFrEF
Authors: Ferreira João Pedro , Ouwerkerk Wouter , Santema Bernadet T , van Veldhuisen Dirk J , Lang Chim C , Ng Leong L , Anker Stefan D , Dickstein Kenneth , Metra Marco , Cleland John G F , Nilesh Samani J , Filippatos Gerasimos , Aboumsallem Joseph-Pierre , de Boer Rudolf A , Figarska Sylwia , Sama Iziah E , Voors Adriaan A , Zannad Faiez
Published: September 2020

Aims 

Elderly patients with heart failure with reduced ejection fraction (HFrEF) have worse prognosis and less often receive guideline-recommended therapies. We aim to better understand the underlying pathophysiological processes associated with ageing in HFrEF potentially leading to targeted therapies in this vulnerable population.

Methods and results 

From a panel of 363 cardiovascular biomarkers available in 1611 patients with HFrEF in the BIOSTAT-CHF index cohort and cross-validated in 823 patients in the BIOSTAT-CHF validation cohort, we tested which biomarkers were dysregulated in patients aged >75 vs. <65 years. Second, pathway overrepresentation analyses were performed to identify biological pathways linked to higher plasma concentrations of biomarkers in elderly vs. younger patients. After adjustment, multiple test correction [false discovery rate (FDR) 1%], and cross-validation, 27/363 biomarkers were associated with older age, 22 positively and 5 negatively. The biomarkers that were positively associated with older age were associated with tumour cell regulation, extra-cellular matrix organization, and inflammatory processes, whereas biomarkers negatively associated with older age were associated with pathways that may point to cell proliferation and tumourigenesis. Among the 27 biomarkers, WFDC2 (WAP four-disulphide core domain protein 2)—that broadly functions as a protease inhibitor—was associated with older age and had the strongest association with all outcomes. No protein-by-sex interaction was observed.

Conclusions 

In elderly HFrEF patients, pathways associated with extra-cellular matrix organization, inflammatory processes, and tumour cell regulation were activated, while pathways associated with tumour proliferation functions were down-regulated. These findings may help in a better understanding of the ageing processes in HFrEF and identify potential therapeutic targets.
Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events
Authors: Ballouz Sara , Mangala Melissa M , Perry Matthew D , Heitmann Stewart , Gillis Jesse A , Hill Adam P , Vandenberg Jamie I
Published: September 2020

Aims

Cardiac electrical activity is extraordinarily robust. However, when it goes wrong it can have fatal consequences. Electrical activity in the heart is controlled by the carefully orchestrated activity of more than a dozen different ion conductances. While there is considerable variability in cardiac ion channel expression levels between individuals, studies in rodents have indicated that there are modules of ion channels whose expression co-vary. The aim of this study was to investigate whether meta-analytic co-expression analysis of large-scale gene expression datasets could identify modules of co-expressed cardiac ion channel genes in human hearts that are of functional importance.

Methods and results

Meta-analysis of 3653 public human RNA-seq datasets identified a strong correlation between expression of CACNA1C (L-type calcium current, ICaL) and KCNH2 (rapid delayed rectifier K+ current, IKr), which was also observed in human adult heart tissue samples. In silico modelling suggested that co-expression of CACNA1C and KCNH2 would limit the variability in action potential duration seen with variations in expression of ion channel genes and reduce susceptibility to early afterdepolarizations, a surrogate marker for proarrhythmia. We also found that levels of KCNH2 and CACNA1C expression are correlated in human-induced pluripotent stem cell-derived cardiac myocytes and the levels of CACNA1C and KCNH2 expression were inversely correlated with the magnitude of changes in repolarization duration following inhibition of IKr.

Conclusion

Meta-analytic approaches of multiple independent human gene expression datasets can be used to identify gene modules that are important for regulating heart function. Specifically, we have verified that there is co-expression of CACNA1C and KCNH2 ion channel genes in human heart tissue, and in silico analyses suggest that CACNA1C–KCNH2 co-expression increases the robustness of cardiac electrical activity.
Crohn’s Disease: Is the Cold Chain Hypothesis Still Hot?
Authors: Hugot Jean-Pierre , Dumay Anne , Barreau Frédérick , Meinzer Ulrich
Published: September 2020

Crohn’s disease [CD] is an inflammatory bowel disease of unknown aetiology. During recent decades, significant technological advances led to development of -omic datasets allowing a detailed description of the disease. Unfortunately these have not, to date, resolved the question of the aetiology of CD. Thus, it may be necessary to [re]consider hypothesis-driven approaches to resolve the aetiology of CD. According to the cold chain hypothesis, the development of industrial and domestic refrigeration has led to frequent exposure of human populations to bacteria capable of growing in the cold. These bacteria, at low levels of exposure, particularly those of the genus Yersinia, are believed to be capable of inducing exacerbated inflammation of the intestine in genetically predisposed subjects. We discuss the consistency of this working hypothesis in light of recent data from epidemiological, clinical, pathological, microbiological, and molecular studies.
Trajectories of Late-Life Disability Vary by the Condition Leading to Death
Authors: Stolz Erwin , Gill Thomas M , Mayerl Hannes , Rásky Éva , Freidl Wolfgang
Published: September 2020

Background

Previous research suggested that there might be distinct patterns of functional decline in the last years of life depending on the condition leading to death, but the validity of these results and hence the explanatory value of the condition leading to death for late-life disability are uncertain.

Methods

A total of 636 decedents from a cohort of 754 community-living persons, 70+ years of age (Yale PEP Study) provided 33 700 monthly observations of self-/proxy-reported disability during the last 5 years of life. Nonlinear trajectories and short-term fluctuations of late-life disability by condition leading to death (cancer, organ failure, frailty, severe dementia, sudden death, other) were estimated with flexible mixed spline regression models.

Results

Disability trajectories at the end of life varied distinctively by the condition leading to death. Estimated disability trajectories among cancer deaths increased gradually up until about 6 months before death, after which a steep terminal decline set in. Among those with organ failure, frailty, and dementia, in contrast, disability was higher, increased more gradually, and there was no clear-cut terminal phase. Adding the condition leading to death to other known risk factors increased the amount of explained between-person variation in late-life disability from R2 = 0.35 to 0.49. Short-term fluctuations in disability were not specific for decedents with organ failure.

Conclusions

The condition leading to death is an important determinant of trajectories of late-life disability. These trajectories follow distinct patterns partially resembling a previously outlined theoretical typology.
Association Between the Multidimensional Prognostic Index and Mortality During 15 Years of Follow-up in the InCHIANTI Study
Authors: Pilotto Alberto , Veronese Nicola , Siri Giacomo , Bandinelli Stefania , Tanaka Toshiko , Cella Alberto , Ferrucci Luigi
Published: September 2020

Background

Multidimensional Prognostic Index (MPI) is recognized as a prognostic tool in hospitalized patients, but data on the value of MPI in community-dwelling older persons are limited. Using data from a representative cohort of community-dwelling persons, we tested the hypothesis that MPI explains mortality during 15 years of follow-up.

Methods

A standardized comprehensive geriatric assessment was used to calculate the MPI and to categorize participants in low-, moderate-, and high-risk classes. The results were reported as hazard ratios (HRs) and the accuracy was evaluated with the area under the curve (AUC), with 95% confidence intervals (CIs) and the C-index. We also reported the median survival time by standard age groups.

Results

All 1453 participants (mean age 68.9 years, women = 55.8%) enrolled in the InCHIANTI study at baseline were included. Compared to low-risk group, participants in moderate (HR = 2.10; 95% CI: 1.73–2.55) and high-risk MPI group (HR = 4.94; 95% CI: 3.91–6.24) had significantly higher mortality risk. The C-index of the model containing age, sex, and MPI was 82.1, indicating a very good accuracy of this model in explaining mortality. Additionally, the time-dependent AUC indicated that the accuracy of the model incorporating MPI to age and sex was excellent (>85.0) during the whole follow-up period. Compared to participants in the low-risk MPI group across different age groups, those in moderate- and high-risk groups survived 2.9–7.0 years less and 4.3–8.9 years less, respectively.

Conclusions

In community-dwelling individuals, higher MPI values are associated with higher risk of all-cause mortality with a dose–response effect.
Upper-mantle discontinuities beneath Australia from transdimensional Bayesian inversions using multimode surface waves and receiver functions
Authors: Taira Toru , Yoshizawa Kazunori
Published: September 2020

Radially anisotropic S-wave structures under the permanent seismic stations in Australia are reconstructed using multimode surface waves (SWs) and receiver functions (RFs) in a framework of the Bayesian inference. We have developed a fully nonlinear method of joint inversions incorporating P-RFs and multimode Rayleigh and Love waves, based on the transdimensional Hierarchical Bayesian formulation. The method allows us to estimate a probabilistic Earth model taking account of the complexity and uncertainty of Earth structure, by treating the model parameters and data errors as unknowns. The Parallel Tempering algorithm is employed for the effective parameter search based on the reversible-jump Markov Chain Monte Carlo method. The use of higher modes enables us to enhance the sensitivity to the depth below the continental asthenosphere. Synthetic experiments indicate the importance of higher mode SWs for the better recovery of radial anisotropy in the whole depth range of the upper mantle. The method is applied to five Global Seismographic Network stations in Australia. While the S-wave models in eastern Australia show shallow lithosphere–asthenosphere boundary (LAB) above 100 km depth, those in central and Western Australia exhibit both mid-lithosphere discontinuities (MLDs) and LAB. Also, seismic velocity jumps equivalent to the Lehmann discontinuity (L-D) are found in all seismic stations. The L-D under the Australian continents is found at around 200–300 km depth, depending on locations. Radial anisotropy in the depth range between LAB and L-D tends to show faster SH anomalies, which may indicate the effects of horizontal shear underneath the fast-moving Australian plate.
Monocyte-Independent and -Dependent Regulation of Regulatory T-Cell Development in Mycoplasma Infection
Authors: Takahashi Ryo , Shiohara Tetsuo , Mizukawa Yoshiko
Published: September 2020

Background

Although Mycoplasma pneumoniae (MP) infection has been implicated in the pathogenesis of allergic diseases, the mechanism of this trigger remains unknown. We explored the mechanism for how MP infection could tilt the balance between regulatory T cells (Tregs) and Th17 cells.

Methods

We analyzed the frequency, phenotype, and function of Tregs in patients at the different stages of MP and various virus infections over a period of more than 1 year. We examined the effect of monocytes to elucidate signals that can regulate the balance between Treg and Th17 cells.

Results

The functional activity of Tregs was profoundly impaired during the acute stage of MP as well as viral infections. Upon resolution, however, the Treg function remained impaired even 1 year after MP infection. In the resolution stage, the impaired Treg function was associated with an increase in interleukin (IL) 17A+ Tregs and Th17 cells. Development of Th17 cells was dependent on the “aberrant” proinflammatory monocytes (pMOs), characterized by potent ability to produce IL-6 in a Toll-like receptor 2–dependent manner.

Conclusions

Depending on the prevalence of the pMOs, Tregs and Th17 cells could mutually regulate the number and function of the other. The pMOs/IL-6 could be crucial therapeutic targets against MP-induced allergic diseases.
Mycobacterium tuberculosis Infection Drives Mitochondria-Biased Dysregulation of Host Transfer RNA–Derived Fragments
Authors: Looney Monika M , Lu Yin , Karakousis Petros C , Halushka Marc K
Published: September 2020

Background

Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis, causes 10 million infections and 1.5 million deaths per year worldwide. The success of Mtb as a human pathogen is directly related to its ability to suppress host responses, which are critical for clearing intracellular pathogens. Emerging evidence suggests that key response pathways may be regulated by a novel class of small noncoding RNA, called transfer RNA (tRNA)–derived fragments (tRFs). tRFs can complex with Argonaute proteins to target and degrade messenger RNA targets, similarly to micro RNAs, but have thus far been overlooked in the context of bacterial infections.

Methods

We generated a novel miRge2.0-based tRF-analysis tool, tRFcluster, and used it to analyze independently generated and publicly available RNA-sequencing datasets to assess tRF dysregulation in host cells following infection with Mtb and other intracellular bacterial pathogens.

Results

We found that Mtb and Listeria monocytogenes drive dramatic tRF dysregulation, whereas other bacterial pathogens do not. Interestingly, Mtb infection uniquely increased the expression of mitochondria-derived tRFs rather than genomic-derived tRFs, suggesting an association with mitochondrial damage in Mtb infection.

Conclusions

tRFs are dysregulated in some, but not all, bacterial infections. Biased dysregulation of mitochondria-derived tRFs in Mtb infection suggests a link between mitochondrial distress and tRF production.
AMR-Intervene: a social–ecological framework to capture the diversity of actions to tackle antimicrobial resistance from a One Health perspective
Authors: Léger Anaïs , Lambraki Irene , Graells Tiscar , Cousins Melanie , Henriksson Patrik J G , Harbarth Stephan , Carson Carolee , Majowicz Shannon , Troell Max , Parmley E Jane , Jørgensen Peter S , Wernli Didier
Published: September 2020

The global threat of antimicrobial resistance (AMR) requires coordinated actions by and across different sectors. Increasing attention at the global and national levels has led to different strategies to tackle the challenge. The diversity of possible actions to address AMR is currently not well understood from a One Health perspective. AMR-Intervene, an interdisciplinary social–ecological framework, describes interventions to tackle AMR in terms of six components: (i) core information about the publication; (ii) social system; (iii) bio-ecological system; (iv) triggers and goals; (v) implementation and governance; and (vi) assessment. AMR-Intervene provides a broadly applicable framework, which can inform the design, implementation, assessment and reporting of interventions to tackle AMR and, in turn, enable faster uptake of successful interventions to build societal resilience to AMR.
Resistance/fitness trade-off is a barrier to the evolution of MarR inactivation mutants in Escherichia coli
Authors: Praski Alzrigat Lisa , Huseby Douglas L , Brandis Gerrit , Hughes Diarmaid
Published: September 2020

Background

Mutations that inactivate MarR reduce susceptibility to ciprofloxacin and competitive growth fitness in Escherichia coli. Both phenotypes are caused by overexpression of the MarA regulon, which includes the AcrAB-TolC drug efflux pump.

Objectives

We asked whether compensatory evolution could reduce the fitness cost of MarR-inactivating mutations without affecting resistance to ciprofloxacin.

Methods

The cost of overexpressing the AcrAB-TolC efflux pump was measured independently of MarA overexpression. Experimental evolution of MarR-inactive strains was used to select mutants with increased fitness. The acquired mutations were identified and their effects on drug susceptibility were measured.

Results

Overexpression of the AcrAB-TolC efflux pump was found not to contribute to the fitness cost of MarA regulon overexpression. Fitness-compensatory mutations were selected in marA and lon. The mutations reduced the level of MarA protein thus reducing expression of the MarA regulon. They restored growth fitness but also reduced resistance to ciprofloxacin.

Conclusions

The fitness cost caused by overexpression of the MarA regulon has multiple contributing factors. Experimental evolution did not identify any single pump-independent cost factor. Instead, efficient fitness compensation occurred only by mechanisms that reduce MarA concentration, which simultaneously reduce the drug resistance phenotype. This resistance/fitness trade-off is a barrier to the successful spread of MarR inactivation mutations in clinical isolates where growth fitness is essential.
Laboratory Perspective on Racial Disparities in Sexually Transmitted Infections
Authors: Lieberman Joshua A , Cannon Chase A , Bourassa Lori A
Published: September 2020

Background

Rates of sexually transmitted infections (STI) have risen steadily in recent years, and racial and ethnic minorities have borne the disproportionate burden of STI increases in the United States. Historical inequities and social determinants of health are significant contributors to observed disparities and affect access to diagnostic testing for STI.

Content

Public health systems rely heavily on laboratory medicine professionals for diagnosis and reporting of STI. Therefore, it is imperative that clinicians and laboratory professionals be familiar with issues underlying disparities in STI incidence and barriers to reliable diagnostic testing. In this mini-review, we will summarize contributors to racial/ethnic disparity in STI, highlight current epidemiologic trends for gonorrhea, chlamydia, and syphilis, discuss policy issues that affect laboratory and public health funding, and identify specific analytic challenges for diagnostic laboratories.

Racial and ethnic disparities in STI in the US are striking and are due to complex interactions of myriad social determinants of health. Budgetary cuts for laboratory and public health services and competition for resources during the COVID-19 pandemic are major challenges. Laboratory professionals must be aware of these underlying issues and work to maximize efforts to ensure equitable access to diagnostic STI testing for all persons, particularly those most disproportionately burdened by STI.