bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of ultimate bearing capacity based on empirical method, interpretation of loading pile test and finite element
Authors: Lastiasih Y , Sari P T K
Published: November 2020

Civil Engineers in designing the ultimate brearing capacity of the pile usually uses several empirical methods. Then usually the loading pile test will be conducted to confirm the ultimate carrying capcity in the field. Based on conditions that often occurs in the field, an empirical method of research is carried out to find out which method is closest to results of the field test. So that in designing the ultimate bearing capacity of the deep foundation will be closer to the field conditions. The empirical methods used in this case are the method of Bazara and Luciano Decourt, while the interpretation pf filed results uses the methods of Chin, Mazurkiewiz and Lastiasih. Based on the results of empirical methods and interpretation of the ultimate bearing capacity of the field test, the results of the pile loading test will be analysed using finite element. The result of this research shows Finite Elemet method, Luciono Decourt and Lastiasih are the closest produce produce ultimate bearing capacity with loading pile test until failure.
The stabilization of soft soil using admixture of palm oil boiler ash and MATOS
Authors: Ma’ruf M. A. , Rusliansyah  , Ritonga F. I. D. , Azizah B.
Published: November 2020

Banjarmasin has an alluvial area with soft soil thickness of 28-42.4m. Therefore, the land is not structurally feasible for construction due to the low California Bearing Ratio (CBR). One of the solutions used to overcome this problem is soil stabilization. This study aims to examine the effect of adding palm oil boiler ash and MATOS in accordance with CBR value to stabilize soil conditions. The laboratory CBR method was used to determine the original and stabilized conditions of the soil. The initial and stabilized soils used an admixture of 2% MATOS as an additive and palm oil boiler ash with percentage variations of 6%, 9%, and 12% of the dry weight soil. This was further kept for 7 days curing before being tested. The result showed that the highest CBR value is obtained at the variation of 6% palm oil boiler ash + 2% MATOS with an increase in CBR value of 7.542% from the original soil condition.
Analytical modeling of 3D-printed reinforced concrete beams
Authors: Chandra J , Pudjisuryadi P , Antoni A , Wibowo H
Published: November 2020

Three-dimensional (3D) printing for cementitious materials such as concrete has become increasingly popular. Numerous research efforts have been undertaken to fabricate structural elements, such as beams, using 3D-printed concrete. Because the behavior of 3D-printed reinforced concrete (RC) beams is not well understood, research in this area is still ongoing to investigate the behavior and compare it with conventional RC beams. In this paper, the results of an analytical study using finite element software on 3D-printed RC beams are presented. The main challenge was to determine a constitutive material model of the 3D-printed concrete for nonlinear analysis that was quite different from normal concrete. The developed model was validated using the results from several past experimental tests on 3D-printed RC beams. The results showed that the analytical model can accurately predict the maximum flexural strengths of the 3D-printed RC beams. However, the analytical model overestimated the initial stiffness of the beams. Furthermore, several local failures, such as shear failure of nodal points and bond failure between rebars and concrete, could not be well simulated by the analytical model. Thus, future research is needed to correctly define the constitutive material model for 3D-printed RC beams.
Effect of reinforced concrete beam confinement under cyclic loading on ultimate drift ratio
Authors: Wibowo L S B , Cahyono M S D
Published: November 2020

The purpose of this paper is to evaluate the effect confinement on ultimate drift ratio of reinforced concrete beam specimens using normal concrete. All beam specimens were tested under cyclic loading. The measured compressive strength of the concrete is in the range of 25 – 41.8 MPa, longitudinal reinforcement yield strength is in the range 350 – 570 MPa and transverse reinforcement yield strength is in the range 275 –570 MPa. Test parameters include s/db
ratio, ρt
, and Vs,a/Mn
ratio. The results showed that Vs,a/Mn
ratio have a significant effect on the ultimate drift ratio. Increase the nominal shear strength by confinement leads to an increase of ultimate drift ratio. In other hands, spacing of transverse reinforcement not exceeding 8db
can achieve minimum 3.00% ultimate drift ratio.
Determination of LRFD environmental load factor in the java sea for unbraced monopod structures using reliability analysis
Authors: Paramashanti  , Larasati D A
Published: November 2020

Case studies were carried out for unbraced monopod structures located in the Java Sea by reviewing the value of the reliability index. This sea has a depth of 33 meters and a 100-yr wave height of 6.29 meters. The structures are designed optimally with a unity check ratio of 1.00 using API RP 2A WSD and API RP 2A LRFD standards under storm condition, assumed to be unmanned. For LRFD criteria, the value of the environmental load factor is varied, namely 1.35, 1.20, 1.10, and 1.00. Collapse analysis using static pushover analysis of the model produces a minimum RSR value meeting the minimum criteria for un-manned structures of 1.6. The reliability analysis process uses the First Order Reliability Method II (FORM II). The structural reliability index value has met the minimum criteria issued by DNV of 3.71 for the structure that is designed using the environmental load factor of 1.35. It can be concluded for unbraced monopod structures designed in the Java Sea, the environmental load factor value of 1.35 is following the minimum reliability index value proposed by DNV.
The effect of Street canyon width towards wind flow in between high-rise buildings
Authors: Sanjaya Y , Priambodo D , Sarli P W , Setio H D
Published: November 2020

Wind load is often defined as a static uniform distributed load in the design code, especially on small structures such as billboard, pedestrian cross bridge, etc. However, as a fluid, wind can deform from a laminar flow to a turbulence flow or it can also be amplified if enough disturbance around the object exists. If these small structures are not designed for a dynamic load or the corrected amplified load, it will collapse. This study aims to investigate the effect of street canyon width towards wind flow by observing a simplified model of 4 symmetrical high-rise buildings with changing street canyon width. The numerical model uses CFD with RANS in OpenFOAM v1912 which is validated with experimental results using a low wind speed wind tunnel and Particle Image Velocimetry (PIV). An Experiment has been performed in BBTA3 using a model with 1:420 scale, there are 2 models with different street canyon width. The result showed there is an increment of the mean wind speed about 5.92-20.20%.
Rapid visual assessment of building vulnerability due to earthquake potential hazard in Surabaya
Authors: Irawan D , Suswanto B , Amalia A R , Iranata D
Published: November 2020

This article studies about Rapid Visual Assessment using android application RViSITS. The Institut Teknologi Sepuluh Nopember team has developed this application, and the purpose is to conduct a more accessible assessment survey in the digital version instead of using the standard form, applying the same standard called FEMA 154. This building vulnerability research was carried out using the application, due to data requirement for mitigation action needed by Surabaya government, due to two newly discovered faults passing the city, namely Surabaya and Waru faults. These two new faults concealed by the National Earthquake Research Centre (PuSGeN) lead to higher earthquake potential hazards in Surabaya, as stated in the SNI 1726. In this research, a two-phase survey was conducted to a total of 366 buildings. From the development of the result mapping of the application, it is discovered that the buildings built after SNI 1726 regulation issued have a higher level of resistance toward earthquake loads, especially the buildings in Surabaya, where gradual seismic risks keep increasing. Therefore, it is necessary to develop mitigation strategies due to the earthquake potential hazard in Surabaya.
Connection system of precast beam and column with wet joint for short span bridge
Authors: Karjanto A , Nindyawati  , Susanto P B
Published: November 2020

The objective of this study is to see whether or not there is a difference in the flexure behavior between three-supported continued segmental precast concrete beam joined with a cast in place. The formation of the bond is 90° vertical combined with 45° against the horizontal reinforcement, making use of the beam as the formwork. The monotonic pressure was applied constantly at one stage until the beams reached the ultimate. The result of the experiment showed that the flexure behavior of the three-supported continued pre-cast beams joined with the cast in place at the condition before cracks (elastic) had the same trend as that of monolith beam at the base area, as well as at the supporting points. However, before passing the yielding condition (the pulling reinforcer yielded), the precast beam had broken into pieces at the supported area, while the monolith beam had a trend in elastic condition, yielding condition, and ultimate condition. The ductility value of the pre-cast beam was 1.33 (at the base area) and 1,5 (at the supported area). The ductility value of the pre-cast beam was 1.0 at the base as well as at the supported area. This means pre-cast beams reach ultimate before the iron reinforcer yield (the ultimate structure is collapse). The cracking patterns showed that at the joined area the bonding failed to happen between the pre-cast beam and the bonding agent.
A simplified method to estimate the fundamental frequency of simple span bridges supported on lead rubber bearing
Authors: Sugihardjo H , Habieb A B
Published: November 2020

The impulsive load method applied on the mid-span of a girder is often used to measure the fundamental frequency of the bridge. This method commonly involves a truck that is dropped from a certain height to generate an impulsive load. In high seismicity zones, bridge structures often involve base isolators such as lead rubber bearing (LRB) to reduce the seismic force demand. However, the application of LRBs on the bridge girders may reduce its vertical fundamental frequency. This fundamental frequency may decrease further if the girder is supported on the frames or cantilever beams on high columns. In this study, the fundamental frequency of several bridge spans is computed through a simplified analytical study based on a single degree of freedom assumption. The results show that the application of LRBs does not significantly affect the fundamental frequency of the girder when compared to the identical girder supported on hinge-roller supports, due to the high vertical stiffness of the LRBs. In average, the values of fundamental frequency obtained through the simplified method and the FE modeling are lower than which obtained from the dynamic loading test. It indicates that the stiffness of the existing bridge is higher than the analyses.
Analysis study of extended end plate connection due to cyclic load using finite element method
Authors: Yoganata Y S , Suswanto B , Iranata D , Irawan D
Published: November 2020

In steel frame structures, the connection is very important element to design, especially for earthquake resistant structures. How to choose the material and and dimension are very important things in steel connection to receive the load. Nowadays, the application of joints using extended end-plate has become popular because of it easy fabrication, the erection, and precise seismic performance. This connection is used to connect beam to column or connect the two beams. As a study material, we’ll make the detail of steel connection due to cyclic load using Abaqus 2017. In this research, we will remodel the connection from previous research with a end-plate modification using finite element method. The dimension of beam is I - 360 × 170 × 12 × 8 and the column is I - 213 × 222 × 10 × 7 with the thickness of end plate is 15 mm and using Grade 8.8 bolts. There are 3 types variation model, one for verification of previous research, and the other two were modified connections. The result of the study is Extended End-Plate can affect the value of the displacement. Connection using Extended End-Plate has smaller displacements, so its better to receive the loads that can cause the collapse. Extended End-Plate also affects the value of lateral load that can be borne. Connection using Extended End-Plate can receive the greater lateral loads, so its more stable and stronger to holding the loads. From the three specimens analyzed, the first model has the best performance where there are extended end plates on both sides.
Experimental investigations on the durability performance of normal concrete and engineered cementitious composite
Authors: Komara I , Suprobo P , Iranata D , Tambusay A , Sutrisno W
Published: November 2020

This paper presents the experimental investigations in studying the durability performance of normal concrete and engineered cementitious composite (ECC) under varying key influencing factors. To this end, direct measurements on sorptivity, water absorption and rapid chloride penetration were undertaken for both normal concrete and ECC; each of which was tested using 67-mm thick sliced cylinder specimens with a diameter of 100 mm. The results from this studies highlight that the inherent low permeability properties in ECC are shown to provide excellent durability performance, in particular to the improvement of sorptivity rate and water absorption which is twice higher than that of normal concrete, indicating the very dense capillary pores microstructure. It is also found that chloride concentration on the surface of ECC is twice lesser than normal concrete, owing to the fact marginal manifestation of the electrical conductance.
Railway capacity analysis using Indonesian method and UIC code 405 method
Authors: Widyastuti H , Budhi W S
Published: November 2020

The government has been constructing double track at Surabaya-Madiun segment to improve railway operations performance. Accordingly, after the double track has been constructed in this segment, it is necessary to analyze existing railway capacity to determine the effect of development as a cost-effective solution. Nowadays, Indonesia is using the Indonesian method as a capacity analysis method and only provides railway capacity analysis using fixed block. On the other hand, another method such as the UIC method has different variables. Therefore in this study, the railway capacity analysis uses two analytic methods that are Indonesian and UIC code 405. The analysis result of both methods shows an improvement in railway capacity because of the double-track construction. These two methods have different results due to each variable. Moreover, one of the UIC variables is additional time due to maintenance differentiated based on its utilization. Utilization in the UIC method is differenced based on its operational conditions by peak and non-peak hours or normal conditions that may also affect the capacity. It also happens in MRT Jakarta operating systems in which the headway is divided into peak and non-peak hours. Accordingly, this study could be a preliminary study for policymakers to analyze capacity in the next near future condition.
Intercity train dwell time estimation by using robust regression method: a study case on Surabaya-Yogyakarta line
Authors: Dewi P , Widyastuti H
Published: November 2020

Dwell time is important an issue to optimise not only for train operation efficiency but also punctuality. This paper proposes a model based on a field survey of intercity trains along the Surabaya-Yogyakarta line by using a robust regression analysis of 138 observations from 13 trainsets operating on the line. Assuming no differences in door or platform width, a model has been formulated to include the number of people who are alighting and boarding, the type of platform and the number of train doors on one side. There were three robust estimators applied to the model. With a 2.037% mean absolute percentage error, the robust regression using the M estimator formed the dwell time model for this study. The results show that, between the dummy variable for platform type using a binary number (0 or 1), dummy variables for high-level platforms and mid-level platforms have opposing tendencies. High-level platform use reduces dwell time by 2.014 sec based on continuous variables; in contrast, dwell time increases by 9.353 sec based on continuous variables by using mid-level platforms. Furthermore, people who are alighting need less time than those boarding. Dwell time will increase by 1.222 sec per alighting passenger and 1.314 per boarding passenger, while it will decrease by 2.727 sec per door on a one-sided trainset. Moreover, dwell time estimates with the model have reduced trainset travel time.
Analysis the use of steel slag as a replacement of natural aggregate in the asphalt concrete binder course (AC-BC) mixture
Authors: Kasaf M , Prastyanto C A
Published: November 2020

Aggregates are the largest component of the flexible pavement structure. The quality of the road is largely determined by the nature and type of aggregates used. Currently, the development of road infrastructure in Indonesia continues to experience increasing amount of natural aggregate use, so this will cause the availability of natural aggregate raw materials to continue to thin out. For that reason, an effort should be made to find alternatives to the use of natural aggregates, one of which is the utilization of steel slag. In this study, it will be examined the characteristics of the steel slag aggregates by referring to the 2018 Bina Marga specifications and the Marshall characteristic test method. This study used steel slag addition with variations of 0%, 50%, 80% and 100%. The results obtained in this study are that the value characteristics of the slag aggregate meet the standard specifications. The use of steel slag at 80% variation in coarse aggregate produces the best stability value which is equal to 2320,19 Kg. Overall, the use of steel slag can be an alternative to the use of natural aggregates. Moreover, steel slag can also be an alternative to an effort to reduce waste.
Diversion canal to decrease flooding at Kemuning river, Sampang district
Authors: Idfi G , Rahayuningsih T , Suryoputro N
Published: November 2020

Flooding occurs when rain runoff water cannot be accommodated by a river, due to the flow of water that exceeds its drainage capacity. Flooding can occur anywhere, one of which occurs in the Kemuning river, Sampang Regency. The existing ag factor of the river profile that is experiencing siltation is also a cause of flooding, especially in the rainy season. This study aims to reduce flood discharge in the Kemuning river by planning a diversion channel as a solution using HEC HMS and HEC RAS modeling. Diversion channel is a divider discharge channel or shortcut to reduce flood discharge in rivers that flow directly into the sea. In this study three alternative solutions are planned, alternative 1 is planned to use a rectangular cross-section, alternative 2 is planned to use a trapezoidal cross-section and alternative 3 is planned to use a trapezoidal cross-section and adding and raising existing river embankments. The results of the analysis and planning showed that the flood discharge plan for the 25 year return period in the HEC HMS modeling was 781.9 m3/sec. The results of the HEC RAS modeling with flood hydrograph input during the 25-year return period, Kemuning river conditions overtopping at all stations as high as 1-4 m. From the trial and error results in the HEC RAS modeling, the maximum capacity of the Kemuning river is 90 m3 / second. Based on the maximum capacity of the Kemuning river, alternative diversion channels 1 and alternative 2 are planned to accommodate flood discharge of 681.9 m3 / sec. An alternative diversion channel 3 is planned to only discharge flood discharges of 300 m3 / sec by adding and raising embankments on the Kemuning river. All alternative diversion channel planning can reduce flood discharge by a percentage of 88.5% for alternatives 1 and 2, 38.4% for alternative 3. Based on the maximum capacity of the Kemuning river, alternative diversion channels 1 and alternative 2 are planned to accommodate flood discharge of 681.9 m3 / sec. An alternative diversion channel 3 is planned to only discharge flood discharges of 300 m3 / sec by adding and raising embankments on the Kemuning river. All alternative diversion channel planning can reduce flood discharge by a percentage of 88.5% for alternatives 1 and 2, 38.4% for alternative 3. Based on the maximum capacity of the Kemuning river, alternative diversion channels 1 and alternative 2 are planned to accommodate flood discharge of 681.9 m3 / sec. An alternative diversion channel 3 is planned to only discharge flood discharges of 300 m3 / sec by adding and raising embankments on the Kemuning river. All alternative diversion channel planning can reduce flood discharge by a percentage of 88.5% for alternatives 1 and 2, 38.4% for alternative 3.
Hydrological analysis of moveable weir planning for tidal flood handling in Cilacap, Central Java
Authors: Taufiq M , Adi H P , Wahyudi S I
Published: November 2020

Global warming resulting in climate change has become a new disaster in the world. One of the changes in climate is the rise of sea water to land surface, which causes tidal flooding. One area that experienced tidal flooding was Kawunganten District, Cilacap, Central Java Province. The area is traversed by the Parit River with the river estuary located in Ujungmanik Village. The problem of tidal flooding in Kawunganten District can be overcome by constructing a moveable weir in the estuary of the Parit River. In planning on the moveable weir, a hydrological analysis is needed to determine the flood discharge plan. Rainfall data used as a basis for calculation of flood discharge at the study site is rainfall data from 3 observation stations namely Cilacap Station, Majenang Station and Ujungbarang Station with the recording period from 2009 to 2018. Calculation of rainfall plan is done using the Pearson Log Method III with a value of T100 = 165.463 mm. The results of the calculation of the flood discharge plan with the haspers method Q100 = 280.989 m3/sec, while the weduwen method Q100 = 132.804 m3/sec and the HSS Nakayasu method Q100 = 102.444. Furthermore, an analysis of tides on the coast of Cilacap Regency with the results of MWL (Mean Water Level) = 110 cm, LWL (Low Water Level) = 20 cm, HWL (High Water Level) = 220 cm.
The flood prediction model using Artificial Neural Network (ANN) and weather Application Programming Interface (API) as an alternative effort to flood mitigation in the Jenelata Sub-watershed
Authors: Gessang O M , Lasminto U
Published: November 2020

Jenelata is a sub of the Jeneberang watershed in South Sulawesi which has rainfall intensity from 2,800 mm to 4,000 mm per year on the upstream area, some of the rainfall occurs in a short period with high intensity, resulting significant rise to river water level. It potentially to cause floods downstream. Topography of the upstream area is mountainous with an average slope of ± 0.024 along the river, with flow length of 38,314 km it has a large velocity flow. Purpose of this research is to providing alternative for flood mitigation using rainfall predictions and runoff calculations, hypoteticaly it can reduce the impact of possible flood. This research was conducted using Artificial Neural Network (ANN) as rainfall predictor and input variable for runoff calculation using SCS method. ANN input variable will use weather prediction data from the global weather API, while SCS method will calculate maximum runoff in the catchment for the next 24 hours. Results of the rainfall prediction model get deviation of 28.81 mm and accuracy of 58% compared to the observations. Meanwhile, runoff model discharge acquires deviation of 1181.7 m3 and water level ± 0.19 m at the designated location of water level gauge.
Directed self-assembly of spheroids into modular vascular beds for engineering large tissue constructs
Authors: Carvalho Daniel T O , Feijão Tália , Neves Mariana I , da Silva Ricardo M P , Barrias Cristina C
Published: November 2020

Spheroids can be used as building-blocks for bottom-up generation of artificial vascular beds, but current biofabrication strategies are often time-consuming and complex. Also, pre-optimization of single spheroid properties is often neglected. Here, we report a simple setup for rapid biomanufacturing of spheroid-based patch-like vascular beds. Prior to patch assembly, spheroids combining mesenchymal stem/stromal cells (MSCs) and outgrowth endothelial cells (OECs) at different ratios (10:1; 5:1; 1:1; 1:5) were formed in non-adhesive microwells and monitored along 7 d. Optimal OEC retention and organization was observed at 1:1 MSC/OEC ratio. Dynamic remodelling of spheroids led to changes in both cellular and extracellular matrix components (ECMs) over time. Some OEC formed internal clusters, while others organized into a peripheral monolayer, stabilized by ECM and pericyte-like cells, with concomitant increase in surface stiffness. Along spheroid culture, OEC switched from an active to a quiescent state, and their endothelial sprouting potential was significantly abrogated, suggesting that immature spheroids may be more therapeutically relevant. Non-adhesive moulds were subsequently used for triggering rapid, one-step, spheroid formation/fusion into square-shaped patches, with spheroids uniformly interspaced via a thin cell layer. The high surface area, endothelial sprouting potential, and scalability of the developed spheroid-based patches make them stand out as artificial vascular beds for modular engineering of large tissue constructs.
PTP-3 phosphatase promotes intramolecular folding of SYD-2 to inactivate kinesin-3 UNC-104 in neurons
Authors: Muniesh Muthaiyan Shanmugam , Barmaver Syed Nooruzuha , Huang Hsin-Yi , Bayansan Odvogmed , Wagner Oliver Ingvar
Published: November 2020

Kinesin-3 UNC-104 is the major transporter of synaptic vesicles and is activated by SYD-2. However, how SYD-2 binding to UNC-104 is controlled remains unknown. Here, we show that PTP-3 phosphatase is upstream of SYD-2 to regulate its intramolecular folding. Open conformation of SYD-2 scaffolds more UNC-104 along axons and boosts transport speeds.
Guanine nucleotide binding protein like-1 (GNL1) promotes cancer cell proliferation and survival through AKT/p21 CIP1 signaling cascade
Authors: Krishnan Rehna , Murugiah Mariappan , Lakshmi, Naga Padma , Mahalingam Sundarasamy
Published: November 2020

GNL1 inhibits cell apoptosis and promotes cell growth by inducing cytoplasmic retention and stabilization of p21 through AKT-mediated phosphorylation. Our data elucidate a novel GNL1/AKT/p21 signaling cascade to provide a growth benefit to cancer cells and this may be an ideal target for cancer therapeutic intervention.
R-loops at centromeric chromatin contribute to defects in kinetochore integrity and chromosomal instability in budding yeast
Authors: Mishra Prashant K. , Chakraborty Arijita , Yeh Elaine , Feng Wenyi , Bloom Kerry S. , Basrai Munira A.
Published: November 2020

This study from budding yeast provides mechanistic insights into how accumulation of R-loops at centromeric chromatin perturbs kinetochore integrity and contributes to chromosome instability.
CGPE: an integrated online server for Cancer Gene and Pathway Exploration
Authors: Liu Jiannan , Dong Chuanpeng , Liu Yunlong , Wu Huanmei
Published: November 2020

Cancer Gene and Pathway Explorer (CGPE) is developed to guide biological and clinical researchers, especially those with limited informatics and programming skills, performing preliminary cancer-related biomedical research using transcriptional data and publications. CGPE enables three user-friendly online analytical and visualization modules without requiring any local deployment. The GenePub HotIndex applies natural language processing, statistics and association discovery to provide analytical results on gene-specific PubMed publications, including gene-specific research trends, cancer types correlations, top-related genes and the WordCloud of publication profiles. The OnlineGSEA enables Gene Set Enrichment Analysis (GSEA) and results visualizations through an easy-to-follow interface for public or in-house transcriptional datasets, integrating the GSEA algorithm and preprocessed public TCGA and GEO datasets. The preprocessed datasets ensure gene sets analysis with appropriate pathway alternation and gene signatures. The CellLine Search presents evidence-based guidance for cell line selections with combined information on cell line dependency, gene expressions and pathway activity maps, which are valuable knowledge to have before conducting gene-related experiments. In a nutshell, the CGPE webserver provides a user-friendly, visual, intuitive and informative bioinformatics tool that allows biomedical researchers to perform efficient analyses and preliminary studies on in-house and publicly available bioinformatics data.

Availability and implementation

The webserver is freely available online at https://cgpe.soic.iupui.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.
Metabolite-Investigator: an integrated user-friendly workflow for metabolomics multi-study analysis
Authors: Beuchel Carl , Kirsten Holger , Ceglarek Uta , Scholz Markus
Published: November 2020

Motivation

Many diseases have a metabolic background, which is increasingly investigated due to improved measurement techniques allowing high-throughput assessment of metabolic features in several body fluids. Integrating data from multiple cohorts is of high importance to obtain robust and reproducible results. However, considerable variability across studies due to differences in sampling, measurement techniques and study populations needs to be accounted for.

Results

We present Metabolite-Investigator, a scalable analysis workflow for quantitative metabolomics data from multiple studies. Our tool supports all aspects of data pre-processing including data integration, cleaning, transformation, batch analysis as well as multiple analysis methods including uni- and multivariable factor-metabolite associations, network analysis and factor prioritization in one or more cohorts. Moreover, it allows identifying critical interactions between cohorts and factors affecting metabolite levels and inferring a common covariate model, all via a graphical user interface.

Availability and implementation

We constructed Metabolite-Investigator as a free and open web-tool and stand-alone Shiny-app. It is hosted at https://apps.health-atlas.de/metabolite-investigator/, the source code is freely available at https://github.com/cfbeuchel/Metabolite-Investigator.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Effect of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Mitigation Strategies on Seasonal Respiratory Viruses: A Tale of 2 Large Metropolitan Centers in the United States
Authors: Sherman Amy C , Babiker Ahmed , Sieben Andrew J , Pyden Alexander , Steinberg James , Kraft Colleen S , Koelle Katia , Kanjilal Sanjat
Published: November 2020

To assess the impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic on seasonal respiratory viruses, absolute case counts and viral reproductive rates from 2019–2020 were compared against previous seasons. Our findings suggest that the public health measures implemented to reduce SARS-CoV-2 transmission significantly reduced the transmission of other respiratory viruses.
Do we need new phosphate binders in dialysis?
Authors: Cozzolino Mario , Galassi Andrea , Ciceri Paola
Published: November 2020

Patients affected by chronic kidney disease (CKD) have a greater risk of mortality than the general population. Fatal cardiovascular events are the most frequent cause of death in CKD patients, especially in the late stages of disease. Derangement of mineral metabolism and hyperphosphataemia are currently accepted as pivotal triggers of these vascular complications. Phosphate binders represent the common strategy to counteract hyperphosphataemia in dialysis patients. Several studies have reported a reduction in mortality risk in dialysis patients receiving phosphate binders compared with untreated patients, independent of the class of binder prescribed.
Optimizing the Use of High-Sensitivity Troponin Assays for the Early Rule-out of Myocardial Infarction in Patients Presenting with Chest Pain: A Systematic Review
Authors: Westwood Marie E , Armstrong Nigel , Worthy Gill , Fayter Debra , Ramaekers Bram L T , Grimm Sabine , Buksnys Titas , Ross Janine , Mills Nicholas L , Body Richard , Collinson Paul O , Timmis Adam , Kleijnen Jos
Published: November 2020

Background

We assessed the accuracy and clinical effectiveness of high-sensitivity cardiac troponin (hs-cTn) assays for early rule-out of non-ST-segment elevation myocardial infarction (NSTEMI) in adults presenting with acute chest pain.

Methods

Sixteen databases were searched to September 2019. Review methods followed published guidelines. The bivariate model was used to estimate summary sensitivity and specificity with 95% confidence intervals for meta-analyses involving 4 or more studies, otherwise random-effects logistic regression was used.

Results

Thirty-seven studies (124 publications) were included in the review. The hs-cTn test strategies evaluated in the included studies were defined by the combination of 4 factors (assay, number of tests, timing of tests, and threshold concentration or change in concentration between tests). Clinical opinion indicated a minimum acceptable sensitivity of 97%. A single test at presentation using a threshold at or near the assay limit of detection could reliably rule-out NSTEMI for a range of hs-cTn assays. Serial testing strategies, which include an immediate rule-out step, increased the proportion ruled out without loss of sensitivity. Finally, serial testing strategies without an immediate rule-out step had excellent sensitivity and specificity, but at the expense of the option for immediate patient discharge.

Conclusion

Test strategies that comprise an initial rule-out step, based on low hs-cTn concentrations at presentation and a minimum symptom duration, and a second step for those not ruled-out that incorporates a small absolute change in hs-cTn at 1, 2, or 3 hours, produce the highest rule-out rates with a very low risk of missed NSTEMI.

PROSPERO registration

CRD42019154716
Ciclosporin or Infliximab as Rescue Therapy in Acute Glucorticosteroid-Refractory Ulcerative Colitis: Systematic Review and Network Meta-Analysis
Authors: Barberio Brigida , Black Christopher J , Savarino Edoardo V , Ford Alexander C
Published: November 2020

Background

Despite randomized controlled trials [RCTs] and trial-based meta-analyses, the optimal rescue therapy for patients with acute glucorticosteroid-refractory ulcerative colitis [UC], to avoid colectomy and improve long-term outcomes, remains unclear. We conducted a network meta-analysis examining this issue.

Methods

We searched MEDLINE, EMBASE, EMBASE Classic and the Cochrane central register up to June 2020. We included RCTs comparing ciclosporin and infliximab, either with each other or with placebo, in patients with glucorticosteroid-refractory UC.

Results

We identified seven RCTs containing 534 patients [415 in head-to-head trials of ciclosporin vs infliximab]. Risk of colectomy at ≤ 1 month was reduced significantly with both treatments, compared with placebo (relative risk [RR] of colectomy with infliximab vs placebo = 0.37; 95% confidence interval [CI] 0.21–0.65, RR with ciclosporin vs placebo = 0.40; 95% CI 0.21–0.77). In terms of colectomy between > 1 month and < 1 year, both drugs ranked equally [P-score 0.75]. Neither treatment was more effective than placebo in reducing the risk of colectomy at ≥ 1 year. Both ciclosporin and infliximab were significantly more efficacious than placebo in achieving a response. Neither treatment was more effective than placebo in inducing remission, nor more likely to cause serious adverse events than placebo.

Conclusions

Both ciclosporin and infliximab were superior to placebo in terms of response to therapy and avoiding colectomy up to 1 year, with no significant differences in efficacy or safety between the two. Ciclosporin remains a valid option to treat refractory UC patients, especially those who do not respond to previous treatment with infliximab, or as a bridge to other biological therapies.
Cardiac arrest, chronic total occlusion, and occluded stent in a 16-year-old boy with Kawasaki disease: a case report
Authors: Connolly Michelle J , Khan Sarosh , Li Kam Wa Matthew E , Faircloth Matthew E , Clapp Brian
Published: November 2020

Background

Kawasaki disease is the leading cause of premature coronary artery disease in developed countries. As such, patients may require revascularisation as children. However, there are no randomized data guiding treatment so this must be individualized. This case report describes the decision-making in a young patient requiring revascularization who had already suffered stent occlusion.

Case summary

Our patient, a 16-year-old boy with Kawasaki disease, presented with cardiac arrest during exercise. Coronary angiography showed that a proximal left anterior descending artery stent implanted at the age of 8 years had occluded some time ago and his right coronary artery was also chronically occluded. He has discussed in several Heart Team meetings and with international colleagues and a consensus reached to revascularize him surgically.

Discussion

It is vital that young patients with complex coronary disease are discussed in an extensive multidisciplinary setting to determine the most suitable means of treatment. The previously occluded stent was crucial in the individualized decision-making in this patient.
Multi-Task Agents and Incentives: The Case of Teaching and Research for University Professors
Authors: De Philippis Marta
Published: November 2020

This paper exploits a natural experiment to study the effects of providing stronger research incentives to faculty members on universities’ average teaching and research performance. The results indicate that professors are induced to reallocate effort from teaching towards research. Moreover, tighter research requirements affect the faculty composition, as they lead lower-research-ability professors to leave. Given the estimated positive correlation between teaching and research ability, those who leave are also characterized by lower teaching ability. The average effect on teaching for the university is therefore ambiguous, as positive composition effects countervail effort substitution.
The Evolving Overdose Epidemic: Synthetic Opioids and Rising Stimulant-Related Harms
Authors: Jones Christopher M , Bekheet Faraah , Park Ju Nyeong , Alexander G Caleb
Published: November 2020

The opioid overdose epidemic is typically described as having occurred in 3 waves, with morbidity and mortality accruing over time principally from prescription opioids (1999–2010), heroin (2011–2013), and illicit fentanyl and other synthetic opioids (2014–present). However, the increasing presence of synthetic opioids mixed into the illicit drug supply, including with stimulants such as cocaine and methamphetamine, as well as rising stimulant-related deaths, reflects the rapidly evolving nature of the overdose epidemic, posing urgent and novel public health challenges. We synthesize the evidence underlying these trends, consider key questions such as where and how concomitant exposure to fentanyl and stimulants is occurring, and identify actions for key stakeholders regarding how these emerging threats, and continued evolution of the overdose epidemic, can best be addressed.
'We Shall Become French': Reconsidering Algerian Jews' Citizenship, c. 1860–1900
Authors: Ofrath Avner
Published: November 2020

This article reconsiders a key episode at the intersection of French, Algerian and Jewish history: the naturalization of Algerian Jews in 1870, commonly known as the Crémieux Decree. Whilst historiography largely portrays this as a unilateral French endeavour, this article draws on new Judeo-Arabic sources to trace an Algerian–Jewish campaign for citizenship in the 1860s. Exploring the use of the Judeo-Arabic dialect and religious terminology in this campaign, the article uncovers a complex and much overlooked dimension of Jewish citizenship in colonial Algeria. Beyond the vertical connection between the metropole and the colony, this is a story of the afterlife of pre-colonial practices, as well as of reformist influences from Tunisia, Morocco and Istanbul. Yet as the article demonstrates, soliciting citizenship in a language other than French disrupted the French orthodoxy of assimilation as a precondition for citizenship. The backlash from settlers, politicians and administrators was fierce and long-lasting.
Contrasting Competitor and Predator Responses to a Short-Lived Southern Pine Beetle Outbreak: A Case Study
Authors: Clarke Stephen R , Hartshorn Jessica
Published: November 2020

The southern pine beetle (SPB) Dendroctonus frontalis Zimmermann, is the most important insect pest of pines in the southeastern United States, with outbreaks often resulting in thousands of hectares of pine mortality. Natural enemies and competitors have been cited as significant regulators of SPB populations and, therefore, outbreaks. A recent outbreak on the Homochitto National Forest (NF) in Mississippi provided an opportunity to undertake a case study comparing population fluctuations of SPB, its major predator Thanasimus dubius, and its competitors, Ips bark beetles. Trap catches of all three were tracked through the course of the outbreak on the Homochitto NF as well as in two other forests with low or no SPB activity. The number of predators collected initially increased on the Homochitto NF in response to the SPB outbreak, but their impact on reducing infestation numbers was unclear. Numbers of Ips trapped were similar across all three forests, indicating that other factors were regulating SPB populations. The outbreak only lasted a single year, and its brevity likely limited the availability of host resources for natural enemy and competitor populations. Additional studies are warranted to explore the mechanisms affecting the extent and duration of SPB outbreaks, such as active forest management.
A New Stage of the Caregiving Career: Informal Caregiving After Long-term Institutionalization
Authors: Robison Julie T , Shugrue Noreen A , Fortinsky Richard H , Fabius Chanee D , Baker Kristin , Porter Martha , Grady James J
Published: November 2020

Background and Objectives

The “unexpected career” of caregiving has previously been conceptualized in stages: community care through institutional placement/residence, ending with death of the care recipient. Transition programs such as Money Follows the Person (MFP) created a new stage of the caregiving career, caring for someone post–long-term institutionalization, about which little is known. Using Pearlin’s Caregiver Stress Process Model, this study explores effects on caregivers from the return of their loved ones to the community after a long-term institutional stay.

Research Design and Methods

Cross-sectional surveys of 656 caregivers of persons transitioned through Connecticut’s MFP program 2014–2018, completed 6 months posttransition.

Results

Regardless of the age/disability of the care recipient, and despite experiencing high caregiving intensity, caregivers experienced less burden, anxiety, and depression, and higher benefits of caregiving than demonstrated in literature for the general caregiving population. Most felt less stressed than before and during the participant’s institutional stay. Factors associated with worse outcomes included worry about safety, strained finances, missing work, and desiring additional services. Black and Hispanic caregivers experienced lower burden and anxiety and higher benefits of caregiving than White caregivers.

Discussion and Implications

By providing community supports to participants, transition programs can have broad ancillary benefits for caregivers and improve outcomes in the Pearlin model, lessening potentially deleterious effects of an unexpected return to intensive caregiving duties after institutional placement. Positive results for Black and Hispanic caregivers may reflect cultural expectations in caring for family that buffer the adverse effects of caregiving.
Modeling Ecological Dynamics of a Major Agricultural Pest Insect (Melanoplus sanguinipes; Orthoptera: Acrididae): A Cohort-Based Approach Incorporating the Effects of Weather on Grasshopper Development and Abundance
Authors: Olfert Owen , Weiss Ross M , Giffen David , Vankosky Meghan A
Published: November 2020

Grasshoppers have been a chronic problem for agriculture on the Canadian prairies, the northern limits of the Northern Great Plains, since settlement of the region in the mid-1800s. Grasshopper pest management tools include biological control, cultural control, and insecticides. This article describes a mechanistic, or process-based, modeling approach used to assess the development and abundance of the migratory grasshopper, Melanoplus sanguinipes (Fabricius), based on a complex of environmental drivers. The purpose of the study was to develop and validate a model (using extensive field data) to quantify the effects of interannual weather variation on M. sanguinipes development and abundance in Saskatchewan, Canada. Overall, the accuracy of model predictions improved for later instars and adults such that predictions regarding adult populations were highly similar to field-collected data. The model provides greater understanding of how M. sanguinipes oviposition is related not only to adult densities, but also to the first appearance of adults and to weather conditions during the oviposition period. The model output can be used to provide accurate within-season updates of the status of grasshopper populations in western Canada to optimize pest management.
Generation of Synthetic Data with Conditional Generative Adversarial Networks
Authors: Vega-Márquez Belén , Rubio-Escudero Cristina , Nepomuceno-Chamorro Isabel
Published: November 2020

The generation of synthetic data is becoming a fundamental task in the daily life of any organization due to the new protection data laws that are emerging. Because of the rise in the use of Artificial Intelligence, one of the most recent proposals to address this problem is the use of Generative Adversarial Networks (GANs). These types of networks have demonstrated a great capacity to create synthetic data with very good performance. The goal of synthetic data generation is to create data that will perform similarly to the original dataset for many analysis tasks, such as classification. The problem of GANs is that in a classification problem, GANs do not take class labels into account when generating new data, it is treated as any other attribute. This research work has focused on the creation of new synthetic data from datasets with different characteristics with a Conditional Generative Adversarial Network (CGAN). CGANs are an extension of GANs where the class label is taken into account when the new data is generated. The performance of our results has been measured in two different ways: firstly, by comparing the results obtained with classification algorithms, both in the original datasets and in the data generated; secondly, by checking that the correlation between the original data and those generated is minimal.