bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of forage introduction on cattle grazing practices and crop–livestock systems: a case study in an upland village in northern Laos
Authors: Phouyyavong Khamphou , Tomita Shinsuke , Yokoyama Satoshi
Published: August 2019

Lao smallholders are experiencing livestock grazing land constraints due to resettlement, increasing cattle numbers and commercial cash crop plantations. In this paper we describe changes in cattle grazing systems in an upland village in northern Laos, including the role of forage crops and their effects on cattle productivity. We interviewed 92 Hmong and Khmu households about their migration history, cattle grazing practices, cattle productivity and other livelihood activities. In addition, we measured the heart girths of 231 cattle. We found that the traditional free-range cattle grazing has diverged into three distinct systems incorporating fields fenced to different degrees. Although none of the three systems increased cattle body size, the forage pasture and swidden-farming system successfully increased the grazing capacity compared with other systems. Thus, this method appeared to be the most suitable for Hmong smallholders to manage crop and cattle production in the context of land constraints. Efforts should be made to examine how the newly implemented systems could attenuate villager livelihood and pre-emptively address the problems associated with degrading fallow land.
Decline in body condition and high drought mortality limit the spread of wild chital deer in north-east Queensland, Australia
Authors: Watter Kurt , Baxter Greg , Brennan Michael , Pople Anthony , Murray Peter
Published: August 2019

Chital deer (Axis axis) were introduced to the Burdekin district of northern Queensland, Australia in 1886. Compared with most successful ungulate introductions they have been slow to expand their distribution and increase in abundance (Moriarty 2004). In this study we consider the possibility that forage shortages caused by periodic droughts have caused sufficient mortalities to limit the increase and spread of chital in the region. The Burdekin district experiences fluctuations in forage according to seasonal rainfall as well as multi-year droughts. This study recorded the decline in body condition, measured as kidney fat index (KFI) and bone marrow fat (BMF), over the wet and dry seasons of two successive years in two chital deer populations during a period when annual rainfall was ~40% below average. We relate the falls in mean KFI from ~45–15%, and mean BMF from ~80–50% to the surveyed decline in chital populations of ~80%. The extent of the decline implies increased mortalities in all age classes as well as reduced reproductive output. We propose that it is likely that chital populations have experienced several such drought mortality events since the 1890s which have contributed to their limited spread.
Mitochondrial transcription factor A promotes DNA strand cleavage at abasic sites
Authors: Xu Wenyan , Boyd Riley M. , Tree Maya O. , Samkari Faris , Zhao Linlin
Published: August 2019

Significance

Failure to maintain mitochondrial DNA (mtDNA) has been implicated in a variety of mitochondrial disorders and human diseases. mtDNA degradation is an important process for mtDNA maintenance and stress response; nevertheless, the mechanism by which mtDNA is degraded remains partially understood. We demonstrate that mitochondrial transcription factor A (TFAM) facilitates damaged DNA degradation by accelerating strand cleavage at abasic sites, reducing the half-life of abasic DNA by 2 to 3 orders of magnitude relative to free DNA. The TFAM-catalyzed AP-lesion destabilization occurs with nonspecific DNA or mitochondrial light-strand promoter sequence, facilitated by lysine residues of TFAM to form Schiff base intermediates. The catalytic effect of TFAM on abasic DNA suggests a novel role of TFAM in mtDNA metabolism.
Molecule counts in complex oligomers with single-molecule localization microscopy
Authors: Baldering Tim N , Bullerjahn Jakob T , Hummer Gerhard , Heilemann Mike , Malkusch Sebastian
Published: August 2019

Single-molecule localization microscopy resolves nano-scale protein clusters in cells, and in addition can extract protein copy numbers from within these clusters. A powerful approach for such molecular counting is the analysis of fluorophore blinking using stochastic model functions. Here, we develop a theoretical model for quantitative analysis of PALM data that accounts for the detection efficiency. By this, we are able to extract populations of different oligomers reliably and in complex mixtures. We demonstrate this approach analyzing simulated PALM data of a photoactivatable fluorescent protein. We generate simulations of blinking data of oligomers and of mixtures of oligomers, and show robust oligomer identification. In addition, we demonstrate this approach for experimental PALM data.
Monte Carlo calculation of beam quality correction factors in proton beams using PENH
Authors: Gomà Carles , Sterpin Edmond
Published: August 2019

This work calculates beam quality correction factors (

) in both modulated and unmodulated proton beams using the Monte Carlo (MC) code

. The latest ICRU 90 recommendations on key data for ionizing-radiation dosimetry were adopted to calculate the electronic stopping powers and to select the mean energy to create an ion pair in dry air (

). For modulated proton beams,

factors were calculated in the middle of a spread-out Bragg peak, while for monoenergetic proton beams they were calculated at the entrance region. Fifteen ionization chambers were simulated. The

factors calculated in this work were found to agree within 0.8% or better with the experimental data reported in the literature. For some ionization chambers, the simulation of proton nuclear interactions were found to have an effect on the

factors of up to 1%; while for some others, perturbation factors were found to differ from unity by more than 1%. In addition, the combined standard uncertainty in the MC calculated

factors in proton beams was estimated to be of the order of 1%. Thus, the results of this work seem to indicate that: (i) the simulation of proton nuclear interactions should be included in the MC calculation of

factors in proton beams, (ii) perturbation factors in proton beams should not be neglected, and (iii) the detailed MC simulation of ionization chambers allows for an accurate and precise calculation of

factors in clinical proton beams.
Litter production and decomposition of mangrove in the Northern Coast of Aceh Besar district, Aceh province
Authors: Dewiyanti I , Nurfadillah N , Setiawati T , Yanti F , Elrahimi S A
Published: August 2019

Mangrove vegetation plays an important role and supplier of organic matter derived from litter fall and litter decomposition The purposes of this research was to obtain the productivity of mangrove vegetation by analyzing the litter fall, decomposition coefficient, and percentage of litter decomposed in the northern coast of Aceh Besar District. The research used purpossive sampling method to determine the 6 stations devided into 2 substations (landward and seaward). This research was conducted in July to September 2016. Each substation was put one of the litter trap. The litter trap method was used to know the mangrove litter production. Litter decomposition focused on R. mucronata leaves were studied by using litterbag technique. The litter bags were made of synthetic nylon which had size 20cm x 30cm and mesh size was 1 x 1.25 mm2. There were 3 types of mangrove found, litter production of Rhizophora mucronata as much as 79.21 g/m2/day, Avicennia marina as much as 0.70 g/m2/day and Sonneratia alba was 17.46 g/m2/day. Based on the substation influenced by tidal, mangrove litters found in the seaward higher than in the landward, the average litter fall was 52.05 g/m2/day and 43.32 g/m2/day. Result of mangrove decomposition showed that the percentage of decomposition for the 49th day in the seaward substation was 48.58% and the landward was 41.53%. Mangrove litter decomposition increased during the time at both substation. Decomposition rate of litter for Rhizopora mucronata species classified very quickly where the substation on the seaward was 0.012 (d−1) and landward was 0.010 (d−1). The half-time took in the leaf litter of mangroves for the landward was 69 days and seaward was 57 days, R. mucronata leaves litter decomposited in seaward substation was faster than landward.
Optimization of impeller design for stirred tank using computational fluid dynamics
Authors: Priyadi K , Lu Chin-Tu , Sutanto H
Published: August 2019

Stirred tanks are widely used for mixing to pseudo-plastic fluids in chemical, food and many processing industries. Impeller stirred tanks play a very important role throughout process industries. Design of such systems and the effective control of the relevant processes require an understanding and prediction of the flow characteristics. One technique to develop high efficiency of this fluid production such as bioethanol is to reduce the stagnant or dead zones formation phenomena inside the stirred tank using computational fluid dynamics. The results have shown that the new impeller design as dependent variables were able to eliminate the dead zone formation related with the independent variables such as power number P0
, pumping number N

q
, wall shear stress τ, mixing time τ, and average effective viscosity μ.
Heuristic approach for solving capacitated location-routing problems
Authors: Ahmad H N , Bakhtiar T , Supriyo P T
Published: August 2019

This paper deals with the standard capacitated location-routing problem (CLRP), where two types of interdependent decisions must be made: which facilities among a number of potential ones should be operated and which vehicle routes should be built to fulfil the demand of customers from the operated facilities using a given fleet. We propose a heuristic mechanism to address the problem. The algorithm consists of four stages, namely optimally clustering customers by k-means and assessed by Dunn index, selecting the nearest depot to be opened based on Euclidean distance calculation, customers-to-depot matching and searching the optimal distribution route. This heuristic algorithm is then implemented to a dataset comprises of 20 customers and 5 potential depot facility locations.
Determination of optimal insurance company reimbursement by using exponential utility functions
Authors: Sukono  , Lesmana E. , Hasbullah E.S. , Rosario V. , Hidayat Y. , Subiyanto
Published: August 2019

In an insurance company, it is very possible that there is an imbalance between the amount of the premium and the amount of claims submitted by the insured. In managing the risk of such an imbalance, the insurance company must be able to make a decision to determine the appropriate amount of premium based on a number of claims by the insured. To make these decisions, insurance companies can do so by using certain utility functions. This paper examines the use of exponential utility functions in transferring risk between insurance companies, optimal Pareto exchanges, equilibrium, Bowley solutions, and optimal reinsurance purchases. Furthermore, using the exponential utility function is calculated the optimal amount of reimbursement that will be carried out by the insurer. The results of the discussion obtained the factors that influence the calculation and the optimal amount of reimbursement value, from a property policy or group policy that needs to be carried out by the insurer. So that based on the results of the optimal reimbursement calculation, it can be used to determine the balance between the amount of the premium and the amount of claims that may be submitted by the insured.
Mixed integer formulation for multiproduct maritime inventory routing problem
Authors: Maulana S , Hanum F , Bakhtiar T
Published: August 2019

Companies that want to market their products to the outer islands need a large-capacity transportation mode that can distribute the product to every place. Other important consideration is the cost of the company must be efficient. The most commonly used by transportation logistics company is the mode of sea transportation. This paper presents an optimization model for determining vessel travel routes by meeting demand and paying attention to inventory levels at each ports so that the company’s costs are minimum. The problem is known as the maritime inventory routing problem (MIRP) and the delivered product can be just one type (single product) or it can be multiproduct. MIRP models are formulated using integer linear programming and numerically solved by the aid of MiniZinc IDE 2.1.5.
A comparative analysis of machining of parts from 38H2MYuA by cutting tool of different materials
Authors: Astashchenko V I , Gilazov I N
Published: August 2019

The variant of mechanical treatment of gear parts made of steel 38H2MYuA is described Tool life of different materials - from R6M5K5 and ASP2052 is analyzed. It was found that for treatment of gear-wheels of steel 38H2MYUA by method of skiving, the most preferred variant is the use of tool made of powder steel than of high-speed steel.
Control of the process of pulsed laser thermal hardening based on emerging potential
Authors: Bashmakov D A
Published: August 2019

The article studies the relationship between the time power distribution of pulsed laser radiation and the emerging electric potential in metals. It is shown that the emerging potential characterizes the shape of the laser pulse during processing and characterizes the penetration depth of the thermal influence zone. It is revealed if the energy of laser action pulse does not exceed 12 J and duration is less than 1 μs the form of the emerging potential is the same for all types of time distribution of laser action power.
Research of the impact of low-frequency pulse force of lorentz on the process of motion of conducting liquid
Authors: Ilyin V K , Koppen D A , Khaibullina A I , Ilyin O V , Sabitov L S
Published: August 2019

The aim of the work was a numerical and experimental study of the influence of the low-frequency pulsed strength of the electromagnetic (EM) field (Lorentz force) on the melt motion GaInSn.
Simulation as a tool for supporting assembly systems
Authors: Iskandarov M , Khisamutdinov R
Published: August 2019

This article considers the first comprehensive introduction to simulation modeling of assembly systems, and considers the assumption that simulation is a reliable method for testing production and assembly systems. Simulation is an important software tool with which you can perform a large number of experiments with various system parameters. Simulation modeling allows to describe the structure of the system and its processes in a natural form, without resorting to use of complex formulas, equations, and strict mathematical dependencies. Modeling allows to detect and eliminate problems that manifest themselves in the early stages of commissioning the assembly system, which implies significant savings in costs and time [1]. This article provides a part of the theoretical base of the topic and a practical example of using modeling. For practical research software was used Tecnomatix Plant Simulation from the company SIEMENS.
The state of the technical level of domestic agricultural machinery
Authors: Kashapov N F , Nafikov M M , Nigmatzyanov A R , Gajnutdinov I G
Published: August 2019

Comparative tests of domestic and foreign equipment designed for carrying out soil tillage and sowing, plant protection techniques and the application of organic and mineral fertilizers under the conditions of compliant regulatory documentation, carried out in recent years, have shown that by basic technical and economic and agrotechnical indicators domestic technology is not inferior to foreign counterparts and may well replace them in a crisis relationship.

It has been shown that it has been carried out in recent years under the conditions of the regulatory documentation, It was shown that technical indicators of domestic equipment were not affected by the equipment.
Current issues of resource and energy savings in the domestic oil and gas complex
Authors: Kiyamov I K , Sabitov L S , Kabirova G I , Akhtyamova L Sh , Iskhakova L Sh
Published: August 2019

The paper deals with the effective implementation of resource and energy saving policy in the oil and gas complex of the Russian Federation (RF). modern regulatory and legal framework is analyzed. The key features of the new “Energy Strategy until 2035” are identified. The development of the modern oil and gas complex of the Russian Federation is analyzed. Justified the problems of direct and indirect effects of the efficiency of resource and energy saving in the oil and gas industry of the Russian Federation, focusing on the problem of metrological provision of domestic oil and gas industry. Promising technologies in the field of geological exploration, as well as in the field of oil and gas production, aimed at improving the efficiency of the resource and energy saving process in the oil and gas complex are proposed.
To a question from About modern state and prospects of development ah Russian oil and gas complex
Authors: Kiyamov I K , Sabitov L S , Kabirova G I , Akhtyamova L Sh , Iskhakova L Sh
Published: August 2019

The work explains the reasons for the high level of energy intensity of the Russian economy. The analysis of the current state of the domestic oil and gas complex is presented. Its key’s problems are identified. Further promising directions for the effective development of the Russian oil and gas complex are proposed. As one of the most promising mechanisms to improve the competitiveness of domestic companies’ oil and gas complex, organization is invited to consider the effective process and resource and energy efficiency of these companies.
Management of elastic displacements of a milling technological system based on the study of the main deformation axes
Authors: Sabirov A R , Khusainov R M
Published: August 2019

The article describes some issues of optimization of technological system parameters and processing parameters to ensure compliance of cutting forces and main deformation axes. As a result there appears a decrease in elastic displacements and an increase in dynamic stability.
Assessment of the impact of technological parameters of hot stamping on the cost of the product
Authors: Shibakov V G , Pankratov D L , Nizamov R S , Nizamova L M
Published: August 2019

The main parameters of the technological process that have the greatest impact on the cost of forgings obtained by hot stamping are established
Predicting the time of corrosion damage to a plate with a deep double-sided external undercut under stretching
Authors: Talibly L H , Imranov F B , Jafarova A M
Published: August 2019

The statement is formulated and the solution of the problem of determining the time of corrosion destruction of an elastic homogeneous plate with a deep bilateral external recess is given. A plate of corrosive material is subjected to bilateral stretching in a corrosive environment in a direction perpendicular to the axis of the recesses. The well-known solution of the problem of the stress state of this plate, obtained by H. Neuber, is used. The following cases are considered: a) the effect of stress, which occurs in the plate when it is stretched, on the corrosion process is negligible; b) the effect of plate voltage on the corrosion process is significant. In both cases, the dependences of the change in the area of the narrowest cross-section of the plate on time are found. The time of complete corrosion wear and the time of corrosion cracking of the plate before its complete wear are also determined.
Technological complexes of laser welding and hardening tool
Authors: Zvezdin V V , Hisamutdinov R M , Saubanov R R , Rakhimov R R , Sirkin S S
Published: August 2019

The control system of the automated laser technological complex for the technology of surfacing and hardening the cutting edge of the teeth of the mill with the positioning of the focus of laser radiation on the tooth is considered. Automating the process of laser hardening and surfacing of parts in mechanical engineering makes it possible to increase the efficiency of the technological process of tool restoration, with its specified quality indicators.
A Conflict Index to Assess Traffic Safety at Intersections
Authors: Abdul Majeed Raghad Zeki , Ewadh Hussein A.
Published: August 2019

In this paper, a conflicts-based technique, using an index measure is introduced to assess traffic safety at intersections. The technique helps in identifying sites most probable to profit from safety improvement as an alternative to crashes-based analyses. As a case study, the analysis and measure of safety for 11 four-leg signalized intersections at different sites in Baghdad city, have been done independently using direct methods based on crash rate and indirect methods based on the level of conflict risk measures. A comparison is achieved between the two methods and their outputs. The study results imply that a developed method of conflicts index of signalized intersections (CISI) (based on traffic conflict frequency and severity) could serve as a viable way of measuring the safety performance of signalized intersection at urban area. CISI can be established for existing conditions at intersections as well as in evaluating different design alternatives to more accurate safety comparison and better decision-making. Application of direct and indirect method results in identifying the same sites to profit from safety improvement. In addition, the research demonstrates a promising application of CISI in; relative comparison of conflict risk at various intersections and estimating conflict risk after potential countermeasures for before-after assessment of traffic safety at intersections.
Bearing capacity and settlement of shallow footings on liquefiable soil subjected to seismic loading
Authors: Al-Salakh Ahmed M. Sadeq , Albusoda Bushra Suhale
Published: August 2019

In liquefying soils, Shallow foundations may experience a reduction in bearing capacity and increase in settlement and tilt due to seismic loading. Therefore, the buildings on shallow footings may settle and tilt excessively. In this paper, the bearing capacity and settlement of shallow foundation on liquefiable deposits has studied. The study includes a shaking table test, reviewing of theoretical equations (available in literature), which estimating settlement of shallow footings due to seismic loading, calibration, and verification of these equations with data from the shaking table test for improved soil by grouting and unimproved soil. It is important to note that the grouting materials used in this study are the CKD and Bentonite slurries. A modification to the seismic bearing capacity and settlement equations had been done to account for the liquefaction state. Good convergence has been gotten between predicted and measured settlement.
Seismic Behavior of Composite Simply Supported Bridge Decks supported on Elastomeric Bearings
Authors: Rubaee Sara k AL , Rahman Ammar A Abdul
Published: August 2019

This paper studies the behavior of bridges’ superstructure under seismic action. The bridge under investigation is one of the typical bridges usually used in overpasses in Iraq, which is made of simply supported steel built up girders and reinforced concrete deck slab isolated from the substructure by elastomeric bearing pads. A three-dimensional finite element model was developed using CSI Bridge Software. Time history analysis was carried out using true-recorded earthquake took place in Iraq near the city of Halabja in 2017. The results of the analysis show that the displacements of the elastomeric bearing pads under transverse seismic loading are much higher than the permissible displacements’ limit which will produce failure of these bearings and potential failure of the bridge superstructure.
Experimental study for strengthening octagonal castellated steel beams using circular and octagonal ring stiffeners
Authors: Al-Thabhawee H W , Mohammed A
Published: August 2019

Castellated beams made by cutting web of hot rolled steel I-section in particular zigzag pattern and recollecting the two parts by welding, to form a castellated beam with hexagonal openings, or more increasing of section depth by placing expansion plates between these parts to fabricate castellated beam with octagonal openings. The main advantage of fabrication this type of beam is increasing section depth, which leads to improve its behavior compared with original beam. So as to use the castellated beams with expansion plates into its best advantages, the failure modes due to web opening need to be avoided. This paper aims to provide added strength of castellated beams with expansion plates by using two types of stiffeners (circular and octagonal ring) around octagonal web opening. This strengthening technique was suggested to reinforce web portion and avoid failure due to web-post buckling. Standard (IPE140) were chosen as a parent section for fabricating four specimens as well as original beam. The important observation through this study is that using ring stiffener leads to have significant effect on ultimate strength. In case of using circular ring stiffeners, the ultimate strength was increased up to (188%) compare with original beam. Whereas the increment in ultimate load at using octagonal ring stiffeners was reach to about (77.6%). Consequent, using circular ring stiffeners to reinforced this type of beams was more efficient than using octagonal ring stiffeners. It is worthwhile to mention that it can be used (37%) as additional steel material (Expansion plates and ring stiffeners) for increasing the load capacity of castellated beams up to (288%) relative to original beam.
Underground ventilated wall based on TRC blocks
Authors: Pazderka J , Nývlt M , Žáková H
Published: August 2019

Ventilated wall is an air-insulating method, which principle is to create a ventilated cavity along the surface of remediated underground wall (usually masonry). The paper describes an innovative solution of this remediation method based on the precast blocks made form textile-reinforced concrete - TRC. The main advantages of the solution (compared to traditional constructions - masonry, hollow bricks filled by cement mortar, monolithic concrete) are low labour difficulty, fast montage and high durability. Since the blocks are not structurally connected or anchored to remediated structure, it is a non-invasive method, which is also suitable for installation in historically valuable buildings. The technical solution is protected by patent CZ307501(B6).
Fire temperature influence on the textile reinforced concrete with non-woven polypropylene fabric
Authors: Žák J , Štemberk P
Published: August 2019

Textile reinforced concrete with non-woven polypropylene fabric has variable utilization for non-load bearing structures. One of the possible uses is production of facade panels or protective layers in the interior of buildings. For that reason it is important to determine fire resistance of this material. There was examined behaviour of specimens exposed to temperature in range 100 – 650°C for times from 5 to 60 minutes. Weight loss of the specimens caused by heating was also measured. Regardless to the relatively high moisture of material, the effect of spalling didn’t occur.
Near-field effects on partially coherent light scattered by an aperture
Authors: Hyde Milo W , Havrilla Michael J
Published: August 2019

We investigate how the near field affects partially coherent light scattered from an aperture in an opaque screen. Prior work on this subject has focused on the role of surface plasmons, and how they affect spatial coherence is well documented. Here, we consider other near-field effects that might impact spatial coherence. We do this by examining the statistics of the near-zone field scattered from an aperture in a perfect electric conductor plane—a structure that does not support surface plasmons. We derive the near-field statistics (in particular, cross-spectral density functions) by applying electromagnetic equivalence theorems and the Method of Moments. We find, even in the absence of surface plasmons, that near-field physics can affect the coherence of the scattered field. The analysis and findings presented herein complement the existing coherence-related surface plasmons literature, and could find use in the design of photonic devices built to engineer spatial coherence.
Optimized uni-traveling carrier photodiode and mushroom-mesa structure for high-power and sub-terahertz bandwidth under zero- and low-bias operation
Authors: Liu Tao , Huang Yongqing , Wei Qi , Liu Kai , Duan Xiaofeng , Ren Xiaomin
Published: August 2019

In this paper, physically-based simulations are carried out to investigate and design uni-traveling carrier photodiode (UTC-PD) for high-power sub-terahertz wave generation at zero- and low-bias operation. The reliability of the physically-based simulation is demonstrated by comparing with our experimental result. Both the bandwidth and RF output power of the proposed UTC-PD is significantly improved by careful design the built-in electric field distribution under high-power input. For the optimized UTC-PD with the mesa diameter of 5 μm, its 3dB bandwidth large than 100 GHz even if the photocurrent reaches 6 mA under zero-bias operation. The device can reach a high bandwidth of 92.4 GHz, 105 GHz, and 119.5 GHz under the reverse bias of 0.5 V, 1 V, and 2 V, respectively, even the input photocurrent as high as 18.2 mA. The peak output-power of the device has enhanced at least 7 dB even at 170 GHz and zero- or low-bias operation. Besides, a novel design of mushroom-mesa UTC-PD (MM-UTC-PD) is proposed which with 4.3% improved high-speed performance. The MM-UTC-PD can trade-off between the external quantum-efficiency and bandwidth when miniaturized junction size is required.
Machine Learning Models Improve the Diagnostic Yield of Peripheral Blood Flow Cytometry
Authors: Zhang M Lisa , Guo Alan X , Kadauke Stephan , Dighe Anand S , Baron Jason M , Sohani Aliyah R
Published: August 2019

Objectives

Peripheral blood flow cytometry (PBFC) is useful for evaluating circulating hematologic malignancies (HM) but has limited diagnostic value for screening. We used machine learning to evaluate whether clinical history and CBC/differential parameters could improve PBFC utilization.

Methods

PBFC cases with concurrent/recent CBC/differential were split into training (n = 626) and test (n = 159) cohorts. We classified PBFC results with abnormal blast/lymphoid populations as positive and used two models to predict results.

Results

Positive PBFC results were seen in 58% and 21% of training cases with and without prior HM (P < .001). % neutrophils, absolute lymphocyte count, and % blasts/other cells differed significantly between positive and negative PBFC groups (areas under the curve [AUC] > 0.7). Among test cases, a decision tree model achieved 98% sensitivity and 65% specificity (AUC = 0.906). A logistic regression model achieved 100% sensitivity and 54% specificity (AUC = 0.919).

Conclusions

We outline machine learning-based triaging strategies to decrease unnecessary utilization of PBFC by 35% to 40%.
Do Deviations From Historical Precipitation Trends Influence Child Nutrition? An Analysis From Uganda
Authors: Epstein Adrienne , Torres Jacqueline M , Glymour M Maria , López-Carr David , Weiser Sheri D
Published: August 2019

Changes in precipitation patterns might have deleterious effects on population health. We used data from the Uganda National Panel Survey from 2009 to 2012 (n = 3,223 children contributing 5,013 assessments) to evaluate the link between rainfall and undernutrition in children under age 5 years. We considered 3 outcomes (underweight, wasting, and stunting) and measured precipitation using household-reported drought and deviations from long-term precipitation trends measured by satellite. We specified multilevel logistic regression models with random effects for the community, village, and individual. Underweight (13%), wasting (4%), and stunting (33%) were common. Reported drought was associated with underweight (marginal risk ratio (RR) = 1.18, 95% confidence interval (CI): 1.04, 1.35) in adjusted analyses. Positive annual deviations (greater rainfall) from long-term precipitation trends were protective against underweight (marginal RR per 50-mm increase = 0.94, 95% CI: 0.92, 0.97) and wasting (marginal RR per 50-mm increase = 0.93, 95% CI: 0.87, 0.98) but not stunting (marginal RR per 50-mm increase = 1.00, 95% CI: 0.98, 1.01). Precipitation was associated with measures of acute but not chronic malnutrition using both objective and subjective measures of exposure. Sudden reductions in rainfall are likely to have acute adverse effects on child nutritional status.
CrossICC: iterative consensus clustering of cross-platform gene expression data without adjusting batch effect
Authors: Zhao Qi , Sun Yu , Liu Zekun , Zhang Hongwan , Li Xingyang , Zhu Kaiyu , Liu Ze-Xian , Ren Jian , Zuo Zhixiang
Published: August 2019

Unsupervised clustering of high-throughput gene expression data is widely adopted for cancer subtyping. However, cancer subtypes derived from a single dataset are usually not applicable across multiple datasets from different platforms. Merging different datasets is necessary to determine accurate and applicable cancer subtypes but is still embarrassing due to the batch effect. CrossICC is an R package designed for the unsupervised clustering of gene expression data from multiple datasets/platforms without the requirement of batch effect adjustment. CrossICC utilizes an iterative strategy to derive the optimal gene signature and cluster numbers from a consensus similarity matrix generated by consensus clustering. This package also provides abundant functions to visualize the identified subtypes and evaluate subtyping performance. We expected that CrossICC could be used to discover the robust cancer subtypes with significant translational implications in personalized care for cancer patients.

Availability and Implementation

The package is implemented in R and available at GitHub (https://github.com/bioinformatist/CrossICC) and Bioconductor (http://bioconductor.org/packages/release/bioc/html/CrossICC.html) under the GPL v3 License.
EPIP: a novel approach for condition-specific enhancer–promoter interaction prediction
Authors: Talukder Amlan , Saadat Samaneh , Li Xiaoman , Hu Haiyan
Published: August 2019

Motivation

The identification of enhancer–promoter interactions (EPIs), especially condition-specific ones, is important for the study of gene transcriptional regulation. Existing experimental approaches for EPI identification are still expensive, and available computational methods either do not consider or have low performance in predicting condition-specific EPIs.

Results

We developed a novel computational method called EPIP to reliably predict EPIs, especially condition-specific ones. EPIP is capable of predicting interactions in samples with limited data as well as in samples with abundant data. Tested on more than eight cell lines, EPIP reliably identifies EPIs, with an average area under the receiver operating characteristic curve of 0.95 and an average area under the precision–recall curve of 0.73. Tested on condition-specific EPIPs, EPIP correctly identified 99.26% of them. Compared with two recently developed methods, EPIP outperforms them with a better accuracy.

Availability and implementation

The EPIP tool is freely available at http://www.cs.ucf.edu/˜xiaoman/EPIP/.

Supplementary information

Supplementary data are available at Bioinformatics online.
StrainHub: a phylogenetic tool to construct pathogen transmission networks
Authors: de Bernardi Schneider Adriano , Ford Colby T , Hostager Reilly , Williams John , Cioce Michael , Çatalyürek Ümit V , Wertheim Joel O , Janies Daniel
Published: August 2019

In exploring the epidemiology of infectious diseases, networks have been used to reconstruct contacts among individuals and/or populations. Summarizing networks using pathogen metadata (e.g. host species and place of isolation) and a phylogenetic tree is a nascent, alternative approach. In this paper, we introduce a tool for reconstructing transmission networks in arbitrary space from phylogenetic information and metadata. Our goals are to provide a means of deriving new insights and infection control strategies based on the dynamics of the pathogen lineages derived from networks and centrality metrics. We created a web-based application, called StrainHub, in which a user can input a phylogenetic tree based on genetic or other data along with characters derived from metadata using their preferred tree search method. StrainHub generates a transmission network based on character state changes in metadata, such as place or source of isolation, mapped on the phylogenetic tree. The user has the option to calculate centrality metrics on the nodes including betweenness, closeness, degree and a new metric, the source/hub ratio. The outputs include the network with values for metrics on its nodes and the tree with characters reconstructed. All of these results can be exported for further analysis.

Availability and implementation

strainhub.io and https://github.com/abschneider/StrainHub.
NACHO: an R package for quality control of NanoString nCounter data
Authors: Canouil Mickaël , Bouland Gerard A , Bonnefond Amélie , Froguel Philippe , ’t Hart Leen M , Slieker Roderick C
Published: August 2019

The NanoStringTM nCounter® is a platform for the targeted quantification of expression data in biofluids and tissues. While software by the manufacturer is available in addition to third parties packages, they do not provide a complete quality control (QC) pipeline. Here, we present NACHO (‘NAnostring quality Control dasHbOard’), a comprehensive QC R-package. The package consists of three subsequent steps: summarize, visualize and normalize. The summarize function collects all the relevant data and stores it in a tidy format, the visualize function initiates a dashboard with plots of the relevant QC outcomes. It contains QC metrics that are measured by default by the manufacturer, but also calculates other insightful measures, including the scaling factors that are needed in the normalization step. In this normalization step, different normalization methods can be chosen to optimally preprocess data. Together, NACHO is a comprehensive method that optimizes insight and preprocessing of nCounter® data.

Availability and implementation

NACHO is available as an R-package on CRAN and the development version on GitHub https://github.com/mcanouil/NACHO.

Supplementary information

Supplementary data are available at Bioinformatics online.
Synaptic clustering differences due to different GABRB3 mutations cause variable epilepsy syndromes
Authors: Shi Yi-Wu , Zhang Qi , Cai Kefu , Poliquin Sarah , Shen Wangzhen , Winters Nathan , Yi Yong-Hong , Wang Jie , Hu Ningning , Macdonald Robert L , Liao Wei-Ping , Kang Jing-Qiong
Published: August 2019

Mutations in GABRB3, which encodes the β3 subunit of GABAA receptors, cause variable epilepsy syndromes with autism and intellectual disability. Shi et al. report that mutant β3 subunits reduce expression of wildtype γ2 subunits, which are critical for receptor synaptic clustering. However, they do so to different degrees, contributing to disease heterogeneity.
Sex Differences in Functional Brain Networks for Language
Authors: Xu Min , Liang Xiuling , Ou Jian , Li Hong , Luo Yue-jia , Tan Li Hai
Published: August 2019

Men and women process language differently, but how the brain functions to support this difference is poorly understood. A few studies reported sex influences on brain activation for language, whereas others failed to detect the difference at the functional level. Recent advances of brain network analysis have shown great promise in picking up brain connectivity differences between sexes, leading us to hypothesize that the functional connections among distinct brain regions for language may differ in males and females. To test this hypothesis, we scanned 58 participants’ brain activities (28 males and 30 females) in a semantic decision task using functional magnetic resonance imaging. We found marked sex differences in dynamic interactions among language regions, as well as in functional segregation and integration of brain networks during language processing. The brain network differences were further supported by a machine learning analysis that accurately discriminated males from females using the multivariate patterns of functional connectivity. The sex-specific functional brain connectivity may constitute an essential neural basis for the long-held notion that men and women process language in different ways. Our finding also provides important implications for sex differences in the prevalence of language disorders, such as dyslexia and stuttering.
An Orthogonal Approach for Determination of Acetamide Content in Pharmaceutical Drug Substance and Base-Contaminated Acetonitrile by GC and GC-MS External Method
Authors: Rajana Nagaraju , Yarbagi Kaviaraj M , Balakumaran K , Madhubabu M V , Mosesbabu J , Basavaiah K , Rama Devi Dharamasoth
Published: August 2019

Acetamide is a potential genotoxic impurity; it should control in drug substance based on daily dosage level. It forms from base-contaminated acetonitrile and by-product of some drug substances. The available methods for acetamide in drug substance and water samples were determined by GC-MS using internal standard with critical procedures. These developed and validated methods can assist in evaluating the reaction between acetonitrile and different bases and also determine trace level acetamide in drug substances. The method development was initiated with DB-624, 30 m, 0.32 width and 1.0-μm column. The column was used to validate at the 600 ppm TTC value. Similarly, the CP-SIL 5CB, 60 m, 0.32 width, the 5-μm column was used for the remaining TTC values. The validation study was performed for all TTC limits. The % RSD for precision at 600, 60, 20, 10 and 2.5 ppm was <15%. The % recovery at all TTC level was in between the 70 and 130%. Solution stability study was performed up to the 24 h. At 2.5 ppm, the results were <15% variation from the initial value. The linearities from the 50 to 150% concerning TTC values were more than limit of 0.98 correlation coefficient. The limit of detection and limit of quantitation values were 0.4 to the 1.3 ppm, respectively, for 2.5 ppm TTC limit method.
Effect of Monthly High-Dose Vitamin D Supplementation on Acute Respiratory Infections in Older Adults: A Randomized Controlled Trial
Authors: Camargo Carlos A , Sluyter John , Stewart Alistair W , Khaw Kay-Tee , Lawes Carlene M M , Toop Les , Waayer Debbie , Scragg Robert
Published: August 2019

Background

Although adults with low vitamin D status are at increased risk of acute respiratory infection (ARI), randomized controlled trials of vitamin D supplementation have provided inconsistent results.

Methods

We performed a randomized, double-blinded, placebo-controlled trial of 5110 adults aged 50–84 years. In 2011–2012, participants were randomized to an initial oral dose of 200 000 IU vitamin D3 followed by 100 000 IU monthly (n = 2558) or placebo (n = 2552) until late 2013 (median follow-up, 1.6 years). Participants reported upper and lower ARIs on monthly questionnaires. Cox models analyzed time to first ARI (upper or lower) by treatment group.

Results

Participants’ mean age was 66 years and 58% were male; 83% were of European/other ethnicity, with the rest Maori, Polynesian, or South Asian. Mean (SD) baseline blood 25-hydroxyvitamin D [25(OH)D] level was 63 (24) nmol/L; 25% were <50 nmol/L. In a random sample (n = 441), vitamin D supplementation increased mean 25(OH)D to 135 nmol/L at 3 years, while those on placebo remained at 63 nmol/L. During follow-up, 3737 participants reported ≥1 ARI: 74.1% in the vitamin D group versus 73.7% in the placebo group. The hazard ratio for vitamin D compared with placebo was 1.01 (95% CI, 0.94, 1.07). Similar results were seen in most subgroups, including those with baseline 25(OH)D <50 nmol/L and in analyses of the upper/lower components of the ARI outcome.

Conclusions

Monthly high-dose vitamin D supplementation does not prevent ARI in older adults with a low prevalence of profound vitamin D deficiency at baseline. Whether effects of daily or weekly dosing differ requires further study.

Clinical Trials Registration

Australian New Zealand Clinical Trials Registry, identifier ACTRN12611000402943.
Getting to the Bottom of It: Sexual Positioning and Stage of Syphilis at Diagnosis, and Implications for Syphilis Screening
Authors: Cornelisse Vincent J , Chow Eric P F , Latimer Rosie L , Towns Janet , Chen Marcus , Bradshaw Catriona S , Fairley Christopher K
Published: August 2019

Background

Syphilis control among men who have sex with men (MSM) would be improved if we could increase the proportion of cases who present for treatment at the primary stage rather than at a later stage, as this would reduce their duration of infectivity. We hypothesized that MSM who practiced receptive anal intercourse were more likely to present with secondary syphilis, compared to MSM who did not practice receptive anal intercourse.

Methods

In this retrospective analysis of MSM diagnosed with primary or secondary syphilis at Melbourne Sexual Health Centre between 2008 and 2017, we analyzed associations between the stage of syphilis (primary vs secondary) and behavioral data collected by computer-assisted self-interviews.

Results

There were 559 MSM diagnosed with primary (n = 338) or secondary (n = 221) syphilis. Of these, 134 (24%) men reported not practicing receptive anal sex. In multivariable logistic regression analysis, MSM were more likely to present with secondary rather than primary syphilis if they reported practicing receptive anal intercourse (adjusted odds ratio 3.90; P < .001) after adjusting for age, human immunodeficiency virus status, and condom use. MSM with primary syphilis who did not practice receptive anal intercourse almost always (92%) had their primary syphilis lesion on their penis.

Conclusions

The finding that MSM who practiced receptive anal intercourse more commonly presented with secondary syphilis—and hence, had undetected syphilis during the primary stage—implies that anorectal syphilis chancres are less noticeable than penile chancres. These men may need additional strategies to improve early detection of anorectal chancres, to reduce their duration of infectivity and, hence, reduce onward transmission.

Men who practiced receptive anal intercourse (AI) were more likely to present with secondary syphilis, compared to men who exclusively practiced insertive AI. Hence, men who practice receptive AI may need additional strategies to detect anal chancres, to reduce transmission.
Human needs, consumerism and welfare
Authors: Fellner Wolfgang J , Goehmann Benedikt
Published: August 2019

Adam Smith considered consumption the sole end and purpose of all production. This presupposes a sound connection between consumption and welfare. The consumerist conceptualisation of this connection suggests that the amount of consumption equals welfare and the level of production can consequently be an indicator for welfare. The limits and problems of production measures are widely accepted. Yet, indicators like GDP remain the focus of mainstream economic theory and policy. We trace the origin of this lock-in back to the axiom of authentic and stable preferences. The suggested alternative stems from literature about human needs in heterodox economics and psychology. This literature incorporates the relevance of social aspects and cultural change for welfare. It turns out that consumerism can be a threat to well-being and welfare, rather than a requirement for it.