bluuebunny/crossref_metadata_2025 huggingface dataset:
Information seeking behaviour of residents towards the work of the architect
Authors: Wijaksono Sigit , Sasmoko  , Indrianti Yasinta
Published: March 2020

Indonesia is included in the area of the ring of fire so that various regions in Indonesia are vulnerable to disasters, including areas around the capital Jakarta. Unpredictable disasters can occur at any time so the community must equip themselves with knowledge of disasters, especially related to shelter. This study aims to look at the information seeking behaviour of the community in relation to their place of residence and in the context of the work of architects. Is the architect’s work in community dwellings considered safe enough in the face of disasters? The research method used is the Neuroresearch method, mixed method research. The study population is residents of housing complexes in the Greater Jakarta area. The sampling technique used is cluster random sampling. The number of samples was 743 people. Data collection techniques using a questionnaire scale Likert 1 to 5. The results showed a difference in the ability of the community in information seeking behaviour viewed from the area of residence and educational background.
Disaster awareness scale
Authors: Sasmoko  , Wijaksono Sigit , Indrianti Yasinta
Published: March 2020

Disaster awareness is a concept that must be understood by everyone, especially residents of housing in disaster prone areas. However, is disaster awareness also owned by the architects who do housing designs? This study tries to explore the views of housing residents on the work of architects who have awareness of disasters by looking at various categories of housing residents’ backgrounds. Research using the Neuroresearch method. The number of samples taken was 743 respondents with a sampling technique using cluster random sampling. Data collection techniques were carried out using a questionnaire and a Likert scale of 1 to 5. The results of the study showed the diversity of the occupants’ background which showed that the work of housing architects was considered to have a bit of disaster awareness and disaster awareness but not yet maximal. Therefore, it is very important for architects to be given an understanding and education about disaster awareness in order to produce work in the form of housing designs that can accommodate a sense of security for residents, especially in the face of disasters.
The universal design approach on sport center in Jakarta to create livable public facilities
Authors: Nurdiani N , Katarina W , Grestio I
Published: March 2020

The DKI Jakarta Government is actively implementing a sports center rehabilitation program for sports and arts activities for the community. One problem that has not been considered in the design of sports centers in Jakarta is the provision of facilities for persons with disabilities, in order to that they have the same opportunities as other normal people in using sports centers. From the results of a study using descriptive methods through observation of existing sports centers, the results are obtained that to realize a livable public facilities requires the design of a sports center that applies the principles of Universal Design, namely Equitable Use, Flexibility in Use, Perceptible Information, Simple & Intuitive, Tolerance for Error, Low Physical Effort, Size and Space for Approach Use.
The study of physical condition of settlement in Penjaringan – Jakarta to build liveable human settlement
Authors: Aror S M , Nurdiani N , Katarina W
Published: March 2020

High population growth due to urbanization has led to the emergence of many densely populated and uninhabitable settlements in Jakarta. Jakarta has 445 RWs which are categorized as unfit for habitation, one of which is the Penjaringan sub-district, and the government will organize it. The purpose of this study is to determine the physical condition of the settlement environment in Penjaringan and the design solutions needed. The method used in this study is descriptive-qualitative method. The results of the study show that the Penjaringan area requires redevelopment in a portion of the planning area using 8 design criteria, namely land use, architectural character, landscaping, circulation and parking, property maintenance, signage, site furnishings, and lighting and utilities.
Kansei engineering, MANOVA and quality function deployment to design bottle packaging and seasoning quality
Authors: Ariyanti Fransisca Dini , Chan Senny
Published: March 2020

Customers at recent time, want practical consumer goods, eye catching designs, with low price, so smart producers should realize all customer desires in the appropriate products and packaging. One of “ready to eat seasoning” producer, PT Kiantaka Rasa, KR, has planning to be more popular among the “end user” customer, by launch their ready to eat seasoning series. Their goal of new packaging is expected to attract public’s interest for buying KR’s products. In this research, we use Kansei Engineering, Quality Function Deployment, QFD, and Multivariate Analysis of Variance (MANOVA) in purpose ergonomic, simple and attractive packaging and products. Nine prototype packaging design was offer into focused discussion group respondent, using Kansai word then Manova, the result, Design 2 is the best design. So as to fit the “end client” desire for the surface of fine flavors, fiery taste, reusable and solid bundling, we utilized QFD technique. The result, the seasoning particle size is less than 250 microns, increase composition of spicy material, bottle design is slim shape with a thickness of 0.05 cm, the bottle cap has many small holes for sprinkle option.
3D Printed 6-Axis Collaborative Arm Robot Using Force Limiting Feature for Service Robot
Authors: Saerang Raymond , Wiliem David , Tinggogoy Feraldy , Carles Deddi , Dani M. , Suwandi Agri , Oey Endra , Tan Sofyan
Published: March 2020

Collaborative arm robot is a robot that can work alongside humans. By using force limiting (FL) feature, where the force of the arm robot is limited and controlled, the robot can sense collision and stop its movement when it occurs. The idea is to apply the mentioned concept for service purposes. In this research a 6-axis arm robot with collision detection is developed. The design of the arm robot adopted the design of Universal Robot’s UR3 with each joint capable of 360° rotation. The design approach is chosen for its flexibility to work in tight space with a maximum reach of half meter, as it is intended to work closely with human. This initial version robot is not intended to carry heavy load or move at high precision. With a maximum load of one Kg, this arm robot targets numerous applications that help human to do complex repetitive tasks, extend the reach of human operators, and help humans on many daily chores that usually does not involve heavy loads. The whole frame, which also serve as the cover of the robot, was made by 3D printing with multiple materials that fit to the strength and temperature requirement at each part of the robot. In order to detect collision, the arm robot employed smart servos at each joint with the ability to detect overcurrent and overvoltage, which allow the implementation of force limiting (FL) feature that will stop the robot in case of collision. The resulting arm robot managed to lift1 kg load and able stop its movement in the event of collision. Future research to improve the movement precision of the arm robot by adaptive methods is promising.
Advanced PID Simulation for DC Motor using Scilab
Authors: Linggarjati Jimmy
Published: March 2020

DC motor is simulated in this paper, in which Scilab simulator is used. The most advantage of using Scilab, as a simulation tool is that it is an open source software. Thereby it is very suitable for our laboratory condition, where budgets are very tied and our students would certainly could not afford a proprietary simulation software such as Matlab, i.e. already well-known in academia and industry. In this paper, a full feature PID Model, namely advanced PID Model is described and simulated, to introduce the importance of PID control in industrial. By understanding these advances in PID control, students are aware of their usage as a prime mover in industrial world. This paper starts with anti-windup, command weightings, derivative term replacement, and autotuning relay-feedback using descriptive function, that finally form a full feature advanced PID model. By using this advanced PID model, it will promote green technology for industrial applications, by consuming fewer energy due to highly efficient design.
AI-Based Ripeness Grading for Oil Palm Fresh Fruit Bunch in Smart Crane Grabber
Authors: Harsawardana  , Rahutomo Reza , Mahesworo Bharuno , Cenggoro Tjeng Wawan , Budiarto Arif , Suparyanto Teddy , Surya Atmaja Don Bosco , Samoedro Bayu , Pardamean Bens
Published: March 2020

Indonesia is one of the biggest palm oil exporters in the world. For Indonesia to stay competitive in thepalm oil industry, the harvesting and evacuating process in its oil palm plantation need to be optimized. This research introduces machinerycalled as Smart Crane Grabber. This machinery can be used for automatic harvesting and evacuation process of oil palm fresh fruit bunch. To enable automation, Smart Crane Grabber is equipped with an Artificial Intelligencesystem for automatic ripeness sorting. TheArtificial Intelligence system developed for Smart Crane Grabber achieves 71.34% accuracy by using only 400 images as preliminary training data.
Maintaining the Quality and Aroma of Coffee with Fuzzy Logic Coffee Roasting Machine
Authors: Harsawardana  , Samodro Bayu , Mahesworo Bharuno , Suparyanto Teddy , Surya Atmaja Don Bosco , Pardamean Bens
Published: March 2020

With the increasing global demands of coffee, Indonesia need to increase their coffee beans supply and improve the quality to maintain its position in the international coffee industry. One of the most important coffeepre-processing, coffee bean roasting, is under developed in Indonesia. Indonesia coffee farmers prefer to use the traditional cauldron to roast their coffee beans. Roasting coffee beans using traditional cauldron is inefficient and resulting unequal roasted level for the coffee beans. In this study, we proposed atemperature control system based on fuzzy logic for coffee roaster machine. The system controls the temperature in accordance with the demanded roasting level. A thermal camera is attached inside the roasting chamber to monitor the heaton the roasted coffee beans. The thermal camera is integrated with a stirring mechanism to equalise the heat among the beans.
Green productivity methodology for furniture industry
Authors: Christian Yosua , Sahroni Taufik Roni
Published: March 2020

This project presents the implementation of green productivity methodology for furniture industry. The main issue in furniture industry is reducing environment pollution and industry waste. The objective of this study is ti apply and implement the green productivity methodology in furniture industry to carry out the environment and waste problems. The green productivity utilizes three tools, specifically material balance, eco-mapping and plant layout. Through the analysis results of material balance, the majority of production wastes were sawdust and a small piece of woods that cannot be exploited again. Instead of being burned, it will be preferable to be accumulated and sold it at the market. With eco-mapping analysis, it can be recognized about which area that produced the most substantial amount of wasted pieces. Hence, the remaining of sawdust will also be collected to be sold. After that, the proposal of the plant layout has been established with the consideration of production scheme and also the distance between all stations will be closer than before. The plant layout chosen is the first of proposed plant layout because it has the shortest production flow distance, which is 49,5m, which can intensify the efficiency of 160% from the original layout. Besides of the reduction industrial waste of this workshop, the company productivity is increased and obtained the additional income as a consequence of invaluable waste at first, to be processed to gain value-added.
Re-layout facility to minimize defects and production cost in PT. Sendanis Jaya Makmur
Authors: Permatasari A A , Pramandha F N , Karima M I , Santoso E
Published: March 2020

This research conducted at PT Sendanis Jaya Makmur’s facility. There are some problems regarding lack of equipment, product defects and distances between facilities that impact for delayed. The Operation Process Chart (OPC), Multi Product Process Chart (MPPC), and Routing sheet utilized to map the main problem in the facility. Activity Relationship Chart (ARC) method, Dimensionless Block Diagram, Activity Relationship Diagram (ARD), and aisle method applied in design new layout facility to improve its effectiveness. The proposed layout efficiency level is 55.7% compared to the current layout. This research is expected to solve the problem which become one of the main focus point at PT Sendanis Jaya Makmur.
Android-based member card “DigiCard” storage application
Authors: Agusrianto K , Chandra T , Wijono A T , Sari A C
Published: March 2020

The purpose of this research is to develop mobile application that can store cards to digital form base on Android, that being used by user which have member card as a media to getting rid from the card being damaged or stolen. In the making of this application, literature review and questionaire are being used as data colletion methodology and extreme programming is being used as research methodology. The goals in making this application is the application can store a physical card into digital form, scan barcode from member card, show realtime promo, online registration, and showing nearest retail location using Android Studio with Java programming language. The conclusion of this research is, this application can help the user as media to avoid careless user in using the card in physical form.
The Principle of Some In vitro Antioxidant Activity Methods: Review
Authors: Romulo Andreas
Published: March 2020

The antioxidant is defined as any substance that could delay or prevent oxidative damage by free radicals. The antioxidant inhibits the oxidative damage by free radicals through several mechanisms. The sources of the antioxidant are abundantly available in nature and can be found in the daily diet such as fruit, vegetables, seeds, nuts, leaves, roots, and barks. Several major compounds identified as antioxidants such as polyphenols, vitamins, and carotenoids. This article provides ageneral summary of the most common in vitromethods for determining antioxidant activity. It emphasizes the working principle, methodology, advantages, and disadvantages of different methods. The determination of antioxidant activity could not only follow one single approach due to the diversity of antioxidant mode of actions. Therefore, the choices of the appropriate method of analysis need to be considered to achieve the purpose of the research.
Half-life Estimation of Encapsulated Enterococcus faecium IS-27526 by Accelerated Shelf Life Testing (ASLT)
Authors: Horison Ronald , Surono I S
Published: March 2020

Probiotics are live microbes with beneficial effect to the host when administrated in adequate quantities. Ensuring the functionality of probiotics can be a challenge for manufacturers due to harsh environment conditions during processing, handling and storage.Enterococcus faeciumIS-27526 is one of novel probiotic strain isolated from dadih, traditional fermented buffalo milk of West Sumatra. The purpose of this study was to determine the effect of microencapsulation, moisture absorber, and storage temperature on the half-life of probiotic powder estimated by Accelerated Shelf Life Testing (ASLT). There were two treatment groups, namely free cell (FC), and microencapsulated cell (EC), with additional treatment in each group, with addition of moisture absorber (MA) and without moisture absorber, stored at various temperatures (5°C, 27°C and 37°C) for 21 days and viable counts was assessed every 7 days. Storage temperature significantly affects the half-life of probiotic powder (p<0.05). At 5°C, EC significantly showed longer half-life than EC-MA, 140.14 ± 5.701 and 113.45 ± 3.242 days, respectively, at 27°C, EC significantly shorter half-life than EC-MA, 38.64 ± 6.831 and 42.35 ± 0.973 days, respectively. Microencapsulation and moisture absorber didn’t show significant effect on half-life (p>0.05) at various temperature storage.
Effect of Cocoyam Modified Starch (Xanthosoma sagittifolium), Beetroot Juice, Cocoyam Modified Starch Adsorbing Beetroot on Plasma Selenium and Glutathione Peroxidase of Pre-Diabetic Rat
Authors: Hibaturrahman Said Naufal , Koyama Hiroshi , Kameo Satomi , Waspodo Priyo , Wardana Ata Aditya , Surono Ingrid Suryanti
Published: March 2020

This research was aimed to identify effect of cocoyam (Xanthosoma sagittifilum) and beetroot on plasma Glutathione Peroxidase (GPx) and selenium of pre-diabetic rats. The pre-diabetic rats were fed with cocoyam modified starch, beetroot juice and cocoyam modified starch adsorbing beetroot for 3 weeks. The plasma selenium and GPx were analyzed. The blood were withdrawn once in a week during 3 weeks. Selenium levels in pre-diabetic rats consumed each of feeding treatment were not significantly diffrent as compared to control feeding (AIN). Plasma GPx activity in pre-diabetic rats consumed cocoyam modified starch and cocoyam modified starch adsobing beetroot tended to have higher values than control in every week. Plasma GPx activity of pre-diabetic rats consumed beetroot juice tended to have higher values than control at the first and the second week.
Predicting incident delirium diagnoses using data from primary-care electronic health records
Authors: Bowman Kirsty , Jones Lindsay , Masoli Jane , Mujica-Mota Ruben , Strain David , Butchart Joe , Valderas José M , Fortinsky Richard H , Melzer David , Delgado João
Published: March 2020

Importance

risk factors for delirium in hospital inpatients are well established, but less is known about whether delirium occurring in the community or during an emergency admission to hospital care might be predicted from routine primary-care records.

Objectives

identify risk factors in primary-care electronic health records (PC-EHR) predictive of delirium occurring in the community or recorded in the initial episode in emergency hospitalisation. Test predictive performance against the cumulative frailty index.

Design

Stage 1: case-control; Stages 2 and 3: retrospective cohort.

Setting

clinical practice research datalink: PC-EHR linked to hospital discharge data from England.

Subjects

Stage 1: 17,286 patients with delirium aged ≥60 years plus 85,607 controls. Stages 2 and 3: patients ≥ 60 years (n = 429,548 in 2015), split into calibration and validation groups.

Methods

Stage 1: logistic regression to identify associations of 110 candidate risk measures with delirium. Stage 2: calibrating risk factor weights. Stage 3: validation in independent sample using area under the curve (AUC) receiver operating characteristic.

Results

fifty-five risk factors were predictive, in domains including: cognitive impairment or mental illness, psychoactive drugs, frailty, infection, hyponatraemia and anticholinergic drugs. The derived model predicted 1-year incident delirium (AUC = 0.867, 0.852:0.881) and mortality (AUC = 0.846, 0.842:0.853), outperforming the frailty index (AUC = 0.761, 0.740:0.782). Individuals with the highest 10% of predicted delirium risk accounted for 55% of incident delirium over 1 year.

Conclusions

a risk factor model for delirium using data in PC-EHR performed well, identifying individuals at risk of new onsets of delirium. This model has potential for supporting preventive interventions.
First explorations: ontogeny of central place foraging directions in two tropical seabirds
Authors: Collet Julien , Prudor Aurélien , Corbeau Alexandre , Mendez Loriane , Weimerskirch Henri
Published: March 2020

A widespread hypothesis for the ontogeny of behavior and decision-making is the early-exploration-later-canalization hypothesis. It postulates that juveniles are more exploratory and adults more consistent in their behavior. In addition, it is often assumed that naïve juveniles could overcome the costs of individual experience building by copying more the decisions of others than adults (early-conformism-later-self-defining hypothesis). Here, we compare the central place foraging movements of adults and postfledging juveniles in their first flights around the colony before dispersal and migration in two sympatric species of tropical seabirds: red-footed boobies and great frigatebirds. Using GPS records of individual movements, we analyzed the foraging directions of seabirds from the colony across successive trips. Juveniles of both species showed significant within-individual consistency in foraging direction but at lower levels than adults. Juveniles leaving the colony within the same time window showed significant but low between-individual resemblance in foraging direction at levels similar to adults. In both species, homing efficiency was lower in juveniles than in adults. Juvenile foraging directions were initially influenced by wind conditions, particularly in low wing loading frigatebirds. Wind conditions progressively lost influence on juvenile foraging directions during their first weeks of flights. In contrast, within-individual consistency, between-individual resemblance, and homing efficiency did not show signs of progression in juveniles. Our results support the early-exploration-later-canalization hypothesis but not the early-conformism-later-self-defining hypothesis. Relaxed constraints on self-feeding efficiency could favor high variability in postfledging tropical seabirds. Our simple approach could be applied to further test these hypotheses by comparing strategies across a wide range of central place foragers.
Heritability and correlations among learning and inhibitory control traits
Authors: Langley Ellis J G , Adams Gracie , Beardsworth Christine E , Dawson Deborah A , Laker Philippa R , van Horik Jayden O , Whiteside Mark A , Wilson Alastair J , Madden Joah R
Published: March 2020

To understand the evolution of cognitive abilities, we need to understand both how selection acts upon them and their genetic (co)variance structure. Recent work suggests that there are fitness consequences for free-living individuals with particular cognitive abilities. However, our current understanding of the heritability of these abilities is restricted to domesticated species subjected to artificial selection. We investigated genetic variance for, and genetic correlations among four cognitive abilities: inhibitory control, visual and spatial discrimination, and spatial ability, measured on >450 pheasants, Phasianus colchicus, over four generations. Pheasants were reared in captivity but bred from adults that lived in the wild and hence, were subject to selection on survival. Pheasant chicks are precocial and were reared without parents, enabling us to standardize environmental and parental care effects. We constructed a pedigree based on 15 microsatellite loci and implemented animal models to estimate heritability. We found moderate heritabilities for discrimination learning and inhibitory control (h2 = 0.17–0.23) but heritability for spatial ability was low (h2 = 0.09). Genetic correlations among-traits were largely positive but characterized by high uncertainty and were not statistically significant. Principle component analysis of the genetic correlation matrix estimate revealed a leading component that explained 69% of the variation, broadly in line with expectations under a general intelligence model of cognition. However, this pattern was not apparent in the phenotypic correlation structure which was more consistent with a modular view of animal cognition. Our findings highlight that the expression of cognitive traits is influenced by environmental factors which masks the underlying genetic structure.
CeRNASeek: an R package for identification and analysis of ceRNA regulation
Authors: Zhang Mengying , Jin Xiyun , Li Junyi , Tian Yi , Wang Qi , Li Xinhui , Xu Juan , Li Yongsheng , Li Xia
Published: March 2020

Competitive endogenous RNA (ceRNA) represents a novel layer of gene regulation that controls both physiological and pathological processes. However, there is still lack of computational tools for quickly identifying ceRNA regulation. To address this problem, we presented an R-package, CeRNASeek, which allows identifying and analyzing ceRNA–ceRNA interactions by integration of multiple-omics data. CeRNASeek integrates six widely used computational methods to identify ceRNA–ceRNA interactions, including two global and four context-specific ceRNA regulation prediction methods. In addition, it provides several downstream analyses for predicted ceRNA–ceRNA pairs, including regulatory network analysis, functional annotation and survival analysis. With examples of cancer-related ceRNA prioritization and cancer subtyping, we demonstrate that CeRNASeek is a valuable tool for investigating the function of ceRNAs in complex diseases. In summary, CeRNASeek provides a comprehensive and efficient tool for identifying and analysis of ceRNA regulation. The package is available on the Comprehensive R Archive Network (CRAN) at https://CRAN.R-project.org/package=CeRNASeek.
A blind and independent benchmark study for detecting differentially methylated regions in plants
Authors: Kreutz Clemens , Can Nilay S , Bruening Ralf Schulze , Meyberg Rabea , Mérai Zsuzsanna , Fernandez-Pozo Noe , Rensing Stefan A
Published: March 2020

Motivation

Bisulfite sequencing (BS-seq) is a state-of-the-art technique for investigating methylation of the DNA to gain insights into the epigenetic regulation. Several algorithms have been published for identification of differentially methylated regions (DMRs). However, the performances of the individual methods remain unclear and it is difficult to optimally select an algorithm in application settings.

Results

We analyzed BS-seq data from four plants covering three taxonomic groups. We first characterized the data using multiple summary statistics describing methylation levels, coverage, noise, as well as frequencies, magnitudes and lengths of methylated regions. Then, simulated datasets with most similar characteristics to real experimental data were created. Seven different algorithms (metilene, methylKit, MOABS, DMRcate, Defiant, BSmooth, MethylSig) for DMR identification were applied and their performances were assessed. A blind and independent study design was chosen to reduce bias and to derive practical method selection guidelines. Overall, metilene had superior performance in most settings. Data attributes, such as coverage and spread of the DMR lengths, were found to be useful for selecting the best method for DMR detection. A decision tree to select the optimal approach based on these data attributes is provided. The presented procedure might serve as a general strategy for deriving algorithm selection rules tailored to demands in specific application settings.

Availability and implementation

Scripts that were used for the analyses and that can be used for prediction of the optimal algorithm are provided at https://github.com/kreutz-lab/DMR-DecisionTree. Simulated and experimental data are available at https://doi.org/10.6084/m9.figshare.11619045.

Contact

ckreutz@imbi.uni-freiburg.de

Supplementary information

Supplementary data are available at Bioinformatics online.
Juvenile-juvenile social signalling: a case for precocial sexual selection in the collared lizard,Crotaphytus collaris(Squamata: Crotaphytidae)?
Authors: Fox Stanley F , Rodríguez-Romero Felipe De Jesús , Crosby Andrea Acevedo
Published: March 2020

Sexual selection is widespread in animals, but quite naturally studied in adults. Juvenile males in most animals are not differentiated from females and coloration is usually drab. However, there is no reason to suspect that sexual differences cannot develop before puberty, influence social interactions, and then have fitness pay-offs later in life. Juvenile collared lizards (Crotaphytus collaris (Say, 1822)) show marked dichromatism: males develop bright dorsolateral orange bars whereas females do not. These juvenile orange bars (JOB) disappear at sexual maturity, when males develop different colour traits maintained by sexual selection. We conducted field experiments with juvenile males on their developing territories in which we utilized staged intruders of juvenile males (with JOB) and juvenile females (lacking JOB) and also juvenile male intruders whose JOB were manipulated. Residents reacted significantly more aggressively toward males vs. females, and also toward males whose JOB were emphasized with paint than those whose JOB were masked by paint. These JOB are used in signalling among juveniles and we suggest the social relations established then are retained until sexual maturation the next spring (after the JOB are lost) to benefit males that previously displayed strong JOB by increased matings in the spring as sexually mature yearlings as per a phenomenon we call precocial sexual selection.
Macrophage-induced reactive oxygen species promote myometrial contraction and labor-associated mechanisms†
Authors: Wendremaire Maeva , Hadi Tarik , Pezze Maria , Barrichon Marina , Lopez Tatiana , Neiers Fabrice , Sagot Paul , Garrido Carmen , Lirussi Frédéric
Published: March 2020

At labor, the myometrium is infiltrated by a massive influx of macrophages that secrete high levels of pro-inflammatory cytokines inducing the expression of specific labor-associated markers. However, the interactions between myocytes and macrophages and the role of macrophages in the myometrium at labor remain to be elucidated. In this work, we studied the role of myometrium-infiltrated macrophages and their interaction with myocytes in lipopolysaccharide-induced preterm labor. A co-culture model of human primary myometrial cells and macrophages was developed and validated. Collagen lattices were used to evaluate myocyte contraction. Differentiation steps were assessed by (i) phalloidin and vinculin staining for cytoskeleton reorganization, (ii) gap junction protein alpha 1 expression and scrape loading/dye transfer with Lucifer Yellow for gap junction intercellular communication, and (iii) calcium imaging for cell excitability. We demonstrated that macrophages favored lipopolysaccharide-induced contraction and early differentiation of myometrial cells. Transwell assays showed that previous activation of macrophages by lipopolysaccharide was essential for this differentiation and that macrophage/myocyte interactions involved macrophage release of reactive oxygen species (ROS). The effects of macrophage-released ROS in myometrial cell transactivation were mimicked by H2O2, suggesting that superoxide anion is a major intermediate messenger in macrophage/myocyte crosstalk during labor. These novel findings provide the foundation for innovative approaches to managing preterm labor, specifically the use of antioxidants to inhibit the initial stages of labor before the contractile phenotype has been acquired. In addition, the co-culture model developed by our team could be used in future research to decipher pathophysiological signaling pathways or screen/develop new tocolytics.
Neurofilaments: neurobiological foundations for biomarker applications
Authors: Gafson Arie R , Barthélemy Nicolas R , Bomont Pascale , Carare Roxana O , Durham Heather D , Julien Jean-Pierre , Kuhle Jens , Leppert David , Nixon Ralph A , Weller Roy O , Zetterberg Henrik , Matthews Paul M
Published: March 2020

Interest in neurofilaments has risen sharply in recent years with recognition of their potential as biomarkers of brain injury or neurodegeneration in CSF and blood. This is in the context of a growing appreciation for the complexity of the neurobiology of neurofilaments, new recognition of specialized roles for neurofilaments in synapses and a developing understanding of mechanisms responsible for their turnover. Here we will review the neurobiology of neurofilament proteins, describing current understanding of their structure and function, including recently discovered evidence for their roles in synapses. We will explore emerging understanding of the mechanisms of neurofilament degradation and clearance and review new methods for future elucidation of the kinetics of their turnover in humans. Primary roles of neurofilaments in the pathogenesis of human diseases will be described. With this background, we then will review critically evidence supporting use of neurofilament concentration measures as biomarkers of neuronal injury or degeneration. Finally, we will reflect on major challenges for studies of the neurobiology of intermediate filaments with specific attention to identifying what needs to be learned for more precise use and confident interpretation of neurofilament measures as biomarkers of neurodegeneration.
Identification and Comparison of Tannins in Gall of Rhus chinensis Mill. and Gall of Quercus infectoria Oliv. by High-Performance Liquid Chromatography–Electrospray Mass Spectrometry
Authors: Ma Shangzhi , Qin Huiyu , Jiang Min , Wang Junqi , Wang Wei , Guo Gang , Zhou Liangxue , Chen Wen , Han Bo
Published: March 2020

Gall of Rhus chinensis Mill. (Chinese galls) and gall of Quercus infectoria Oliv. (Turkish galls) have similar applications and chemical compositions, and their extracts have been widely used for industrial production and for medicinal applications. In this study, high-performance liquid chromatography–electrospray mass spectrometry (HPLC-ESI-MS/MS) methods were established for profiling the components of Chinese galls and Turkish galls. Compounds representing 96.56 and 99.15% of the total peak area of Chinese galls and Turkish galls were identified. The results identified that the ellagic acid, galloyl-HHDP-glucose and pedunculagin act as the identifying markers for the comparison of Chinese galls and Turkish galls in HPLC-ESI-MS/MS. The peak area of tetragalloyl-glucoside, heptagalloyl-glucoside and pentagalloyl-glucoside can be used to distinguish these two phytomedicines. This work provides a reference for the study of the chemical composition of Chinese galls and Turkish galls, which not only introduce a simple and reliable method to prevent the adulteration or misuse of Chinese galls and Turkish galls but also lay the foundations for clarifying the material basis of their similar pharmacological action.
Longitudinal Care Cascade Outcomes Among People Eligible for Antiretroviral Therapy Who Are Newly Linking to Care in Zambia: A Multistate Analysis
Authors: Mody Aaloke , Glidden David V , Eshun-Wilson Ingrid , Sikombe Kombatende , Simbeza Sandra , Mukamba Njekwa , Somwe Paul , Beres Laura K , Pry Jake , Bolton-Moore Carolyn , Padian Nancy , Holmes Charles B , Sikazwe Izukanji , Geng Elvin H
Published: March 2020

Background

Retention in human immunodeficiency virus (HIV) care is dynamic, with patients frequently transitioning in and out of care. Analytical approaches (eg, survival analyses) commonly used to assess HIV care cascade outcomes fail to capture such transitions and therefore incompletely represent care outcomes over time.

Methods

We analyzed antiretroviral therapy (ART)-eligible adults newly linking to care at 64 clinics in Zambia between 1 April 2014 and 31 July 2015. We used electronic medical record data and supplemented these with updated care outcomes ascertained by tracing a multistage random sample of patients lost to follow-up (LTFU, >90 days late for last appointment). We performed multistate analyses, incorporating weights from sampling, to estimate the prevalence of 9 care states over time since linkage with respect to ART initiation, retention in care, transfers, and mortality.

Results

In sum, 23 227 patients (58% female; median age 34 years [interquartile range 28–41]) were ART-eligible at enrollment. At 1 year, 75.2% had initiated ART and were in care: 61.8% were continuously retained, 6.1% had reengaged after LTFU, and 7.3% had transferred. Also, 10.1% were LTFU within 7 days of enrollment, and 15.2% were LTFU at 1 year (6.7% prior to ART). One year after LTFU, 51.6% of those LTFU prior to ART remained out of care compared to 30.2% of those LTFU after initiating ART. Overall, 6.9% of patients had died by 1 year with 3.0% dying prior to ART.

Conclusion

Multistate analyses provide more complete assessments of longitudinal HIV cascade outcomes and reveal treatment gaps at distinct timepoints in care that will still need to be addressed even with universal treatment.
Human Immunodeficiency Virus–2 (HIV-2): A Summary of the Present Standard of Care and Treatment Options for Individuals Living with HIV-2 in Western Europe
Authors: Berzow Dirk , Descamps Diane , Obermeier Martin , Charpentier Charlotte , Kaiser Rolf , Guertler Lutz , Eberle Josef , Wensing Annemarie , Sierra Saleta , Ruelle Jean , Gomes Perpetua , Mansinho Kamal , Taylor Ninon , Jensen Björn , Döring Matthias , Stürmer Martin , Rockstroh Jürgen , Camacho Ricardo
Published: March 2020

Human immunodeficiency virus–2 (HIV-2) is endemic in some countries in West Africa. Due to the lower prevalence in industrialized countries, there is limited experience and knowledge on the management of individuals living with HIV-2 in Europe. Compared to HIV-1, there are differential characteristics of HIV-2 regarding diagnostic procedures, the clinical course, and, most importantly, antiretroviral therapy.

We integrated the published literature on HIV-2 (studies and reports on epidemiology, diagnostics, the clinical course, and treatment), as well as expert experience in diagnosing and clinical care, to provide recommendations for a present standard of medical care of those living with HIV-2 in Western European countries, including an overview of strategies for diagnosis, monitoring, and treatment, with suggestions for effective drug combinations for first- and second-line treatments, post-exposure prophylaxis, and the prevention of mother-to-child transmission, as well as listings of mutations related to HIV-2 drug resistance and C-C motif chemokine receptor type 5 and C-X-C motif chemokine receptor type 4 coreceptor tropism.
Applying conservation social science to study the human dimensions of Neotropical bird conservation
Authors: Dayer Ashley A , Silva-Rodríguez Eduardo A , Albert Steven , Chapman Mollie , Zukowski Benjamin , Ibarra J Tomás , Gifford Gemara , Echeverri Alejandra , Martínez-Salinas Alejandra , Sepúlveda-Luque Claudia
Published: March 2020

As the global human population increases, and many bird populations in the Neotropics and the rest of the world continue to decline, the study of the intersection of humans, birds, and conservation has become more relevant than ever. The field of conservation social science is an interdisciplinary field that applies the social sciences and humanities to examine research questions that have implications for biodiversity conservation, and encompasses disciplines as diverse as psychology, economics, and political ecology. An understanding of the human dimensions of biodiversity conservation issues can be an essential element in the success or failure of a conservation initiative, policy, or practice. The purpose of this article is to provide an understanding of the growing body of conservation social science relevant to Neotropical bird conservation research and to demonstrate its importance. We discuss how this research can contribute to addressing 5 major threats to bird conservation in the Neotropics, including future research needs, and we provide 3 case studies of bird conservation social science projects, demonstrating the insights that can be gained. We close with a discussion of how conservation biologists and ornithologists can most effectively work with conservation social scientists.
Outcomes for the superior cavopulmonary connection in children with hypoplastic left heart syndrome: a 30-year experience
Authors: Hunt Mallory L , Ittenbach Richard F , Kaplinski Michelle , Ravishankar Chitra , Rychik Jack , Steven James M , Fuller Stephanie M , Nicolson Susan C , Spray Thomas L , Gaynor J William , Mascio Christopher E
Published: March 2020

OBJECTIVES

The objective of this study was to estimate hospital mortality and length of stay (LOS) for children with hypoplastic left heart syndrome undergoing superior cavopulmonary connection (SCPC).

METHODS

All hypoplastic left heart syndrome interstage survivors who underwent SCPC between 1 January 1988 and 31 December 2017 were included. The study period was divided into 4 eras based on changes in operative or medical management. Mortality rates were estimated using standard binomial proportions. Adjusted and unadjusted logistic regression models were used to identify risk factors for mortality and LOS.

RESULTS

The most common procedures for the cohort (n = 958) were Hemi-Fontan (57.3%) or Bidrectional Glenn shunt (35.7%). The mortality was 4.1% overall and decreased in all 3 later eras compared to era 1. Factors associated with mortality in a multiple covariate model included longer total support time, earlier gestational age, longer LOS at the Norwood Procedure and need for additional procedures. Overall, the median LOS was 7.0 days with a decrease from eras 1 to 2 and plateaued in eras 3 and 4. Predictors of longer LOS included genetic anomaly, longer Norwood LOS, additional procedures, lower weight at surgery and longer total support time. The type of SCPC was not associated with mortality or LOS.

CONCLUSIONS

In this large cohort of patients with hypoplastic left heart syndrome undergoing SCPC, hospital mortality has decreased significantly. LOS initially declined but plateaued in recent eras. The risk factors for mortality and longer LOS are related to patient and procedural complexity, especially the need for additional procedures at the time of SCPC.
Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha)
Authors: Ruiz César , Villegas-Plazas Marcela , Thomas Olivier P , Junca Howard , Pérez Thierry
Published: March 2020

The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.
Complex Evolutionary History of the Y Chromosome in Flies of the Drosophila obscura Species Group
Authors: Bracewell Ryan , Bachtrog Doris
Published: March 2020

The Drosophila obscura species group shows dramatic variation in karyotype, including transitions among sex chromosomes. Members of the affinis and pseudoobscura subgroups contain a neo-X chromosome (a fusion of the X with an autosome), and ancestral Y genes have become autosomal in species harboring the neo-X. Detailed analysis of species in the pseudoobscura subgroup revealed that ancestral Y genes became autosomal through a translocation to the small dot chromosome. Here, we show that the Y-dot translocation is restricted to the pseudoobscura subgroup, and translocation of ancestral Y genes in the affinis subgroup likely followed a different route. We find that most ancestral Y genes have translocated to unique autosomal or X-linked locations in different taxa of the affinis subgroup, and we propose a dynamic model of sex chromosome formation and turnover in the obscura species group. Our results suggest that Y genes can find unique paths to escape unfavorable genomic environments that form after sex chromosome–autosome fusions.
A statistical representation and frequency-domain window-rejection algorithm for single-station HVSR measurements
Authors: Cox Brady R , Cheng Tianjian , Vantassel Joseph P , Manuel Lance
Published: March 2020

The horizontal-to-vertical spectral ratio (HVSR) of ambient noise measurement is commonly used to estimate a site's resonance frequency (${f_0}$). For sites with a strong impedance contrast, the HVSR peak frequency (${f_{0,\mathrm{ HVSR}}}$) has been shown to be a good estimate of ${f_0}$. However, the random nature of ambient noise (both in time and space), in conjunction with variable environmental conditions and sensor coupling issues, can lead to uncertainty in ${f_{0,\mathrm{ HVSR}}}$ estimates. Hence, it is important to report ${f_{0,\mathrm{ HVSR}}}$ in a statistical manner (e.g. as a mean or median value with standard deviation). In this paper, we first discuss widely accepted procedures to process HVSR data and estimate the variance in ${f_{0,\mathrm{ HVSR}}}$. Then, we propose modifications to improve these procedures in two specific ways. First, we propose using a lognormal distribution to describe ${f_{0,\mathrm{ HVSR}}}$ rather than the more commonly used normal distribution. The use of a lognormal distribution for ${f_{0,\mathrm{ HVSR}}}$ has several advantages, including consistency with earthquake ground motion processing and allowing for a seamless transition between HVSR statistics in terms of both frequency and its reciprocal, period. Second, we introduce a new frequency-domain window-rejection algorithm to decrease variance and enhance data quality. Finally, we use examples of 114 high-variance HVSR measurements and 77 low-variance HVSR measurements collected at two case study sites to demonstrate the effectiveness of the new rejection algorithm and the proposed statistical approach. To encourage their adoption, and promote standardization, the rejection algorithm and lognormal statistics presented in this paper have been incorporated into hvsrpy, an open-source Python package for HVSR processing.
An inverse semi-oriented radial data envelopment analysis measure for dealing with negative data
Authors: Ghiyasi Mojtaba , Zhu Ning
Published: March 2020

The conventional inverse data envelopment analysis (DEA) model is only applicable to positive data, while negative data are commonly present in most real-world applications. This paper proposes a novel inverse DEA model that can handle negative data. The conventional inverse DEA model is a special case of our model as our model is more general in terms of returns-to-scale properties. The proposed model is used to evaluate the efficiency of the Chinese commercial banks after the global financial crisis, where negative outputs existed. We show that our model is feasible in the presence of negative data and generates empirical findings that are consistent with reality.