bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of key sugarcane harvester features using the Analytic Hierarchy Process
Authors: Gonzaga J A , Dela Cruz E , Lopez N S
Published: March 2021

The Philippine sugarcane industry is worth roughly 88 billion pesos and employs around 700,000 Filipinos. However, the competitiveness of the local industry ($0.17 per lb sugar) is currently under threat from international producers ($0.14 per lb sugar) because of the upcoming ASEAN 2015 integration. One of the major blockages to cost effectiveness is the low productivity of the local industry. This may be addressed with the use of a semi-automated mechanical harvester. As a preliminary study, the present work captures the expert preferences of various stakeholders in the selection of a semi-automated mechanical harvester. This is done using the Analytic Hierarchy Process (AHP) surveying tool. The study assumes the following important factors: a) Ease of use, b) Productivity, c) Adaptability to different terrains, d) with Lifter, and e) with Topper. Using a survey with a series of pairwise comparison questions, it is able to quantify even qualitative factors affecting decision making. The priorities of the surveyed stakeholders are averaged and discussed in the results section. Widely used in policy making and planning, the paper introduces the use of the AHP tool to commercial machinery design. The model may be expanded and improved to consider other key factors.
Influence of outlet/inlet area ratio on performance of a vertical solar chimney for natural ventilation of buildings
Authors: Nguyen Y Q , Huynh T N
Published: March 2021

In this study, effects of the contractions of the inlet and outlet areas of a vertical solar chimney were examined with a Computational Fluid Dynamics. The results show that the flow rate decreased with both the inlet and outlet areas. The outlet area influenced more than the inlet area did. The flow rate decreased linearly with the outlet area, however, was affected significantly only when the inlet area was below half of the air gap.
Visual effects creation to improve user performance in fully immersive virtual environment of automobile engine assembly
Authors: Win L L , Faieza A A , Hairuddin A A , Abdullah L N , Yap H J , Saito H , Hisham S
Published: March 2021

Virtual reality (VR) technologies and computer-generated technologies are very useful for many industries, such as medical, education, gaming, mining, engineering, and other sectors. In engineering sector specifically for assembly department, the major problem they are facing was that traditional components of automotive engine are complex and very difficult to assemble using current method which use paper manual. The goal of this project is to create an interactive VR application such that users can quickly integrate and perform the work easily. In this work, the authors designed and developed an immersive VR application with several stages, such as 3D model creation, visual effects creation and gaming scene building. The application was built using Unreal and HTC vive headset. As this is an on-going project work, further functionality will be added to render the application immensely for users and assist the sense of pedagogy in terms of the digital method of learning.
Comparative analysis of Ormat and Kalina Cycle for the geothermal resource in Mabini, Batangas using thermoeconomic analysis
Authors: Dela Cruz III G E E , Manuel PhD M C E
Published: March 2021

The Philippines is amongst the countries located in the ring of fire, thus makes it rich in geothermal energy. The Department of Energy is considering the low-temperature resource for power generation to address the continuous increase in electricity demand. The binary plants designed by Ormat technologies are currently in use for power production for the Philippine low-temperature heat source. Another technology used for the low-temperature heat source is the Kalina power cycle. In this paper, both cycles are evaluated using the parameters from the Mabini, Batangas geothermal resource, and principles of thermoeconomics are applied to determine the performance of the two cycles under Philippine conditions.
Energy and exergy evaluation of an onshore solar dryer for seaweeds
Authors: Culaba A , Atienza A H , Ubando A , Mayol A , Cuello J
Published: March 2021

The possible sources of the energy losses in the drying systems can occur in the drying chamber and solar collector. The energy from these parts were not properly utilized so it is evident to further search for improvements. Energy and exergy analyses were being used to identify the possible source of inefficiencies quantitatively and qualitatively in the drying system and aid in recommendation for its improvement. This study aimed to evaluate the performance of an onshore drying system for seaweeds by conducting energy and exergy analyses. It has shown that the dryer efficiency was 33.58% and its solar collector efficiency was 68%. The exergy efficiency was obtained as 41.38% relates to an exergy improvement potential of 256.30 W. It is recommended to perform partial to full exhaust air recirculation and provide thermal storage may boost the exergy efficiency hence minimizing energy losses in the drying system.
Multi-sector decomposition analysis of Philippine CO2 emissions
Authors: Ng E A S , Lopez N S A
Published: March 2021

Global CO2 emissions are rising due to the rising energy demand and the extent to which this is fed by fossil fuels. The LMDI method of IDA is a valuable tool for determining the contributing driving forces behind emissions in a particular time frame, region, or economy. This study applies the techniques of spatial LMDI across the industry sectors of the 2017 Philippine economy to understand the effects of value share, energy intensity, energy structure, and fuel types on carbon emissions per sector. A combination of IEA, PSA, and IPCC data are used in order to ascertain these effects based on the Kaya identity. Results and tabulated and visualized in Cartesian scatter plots. Trends identified include the negative relationship between value share and energy intensity effects and between oil use and natural gas use effects. Outliers to these trends and in the Figures were also highlighted and elucidated. The study recommended increased use of natural gas due to its lower emission factor vs oil and coal, government assistance to low-value sectors in procurement of more efficient equipment, and bespoke solutions per sector based on the given data herein.
Seaweed drying characterization via serial statistical criteria analysis
Authors: Culaba A , Atienza A H , Ubando A , Mayol A , Cuello J
Published: March 2021

In drying seaweeds, it is important to describe its drying behavior using semi-theoretical models. Predicting the best drying model for the seaweed was commonly done by testing the goodness of the curve for seaweed drying models by calculating the coefficient of determination R2, the reduced chi square X
2, root means square error (RMSE) and mean bias error (MBE). However, it is essential to rank the drying models before selection by assessing its performance index Φ and mean relative deviation (MRD). It is also necessary to test the normality by evaluating the skewness and kurtosis statistics using the D’ Agostino Pearson test which is the best test for goodness of fit. The simple sample run test statistics and confidence interval must also be satisfied These are the conditions that should be met under the serial statistical criteria analysis. This study utilized it to choose the best drying model for seaweeds. Employing this statistical analysis for testing commonly used drying models, Modified Page model emerged as the best model that depicts the drying behavior of the seaweeds with accuracy of 99.98% and highest performance index of 452.1967.
Evaluation of filtering facepiece respirators using chemical decontamination methods
Authors: Osman Baderin , Mahmud Haalah , Mamat Hussin
Published: March 2021

Disposable filtering facepiece respirators (FFRs) are often recommended for use by healthcare workers and the general public for infection control. During pandemic, shortage in supply of FFRs is reported due to excessive demand. Hence, suitable decontamination methods of used FFRs are required to be identified. Various chemical decontamination methods (isopropyl alcohol (IPA), vaporized hydrogen peroxide (VHP) and detergent) have been explored in the present study. The performance of the FFRs after exposed to three types of chemical decontamination methods was evaluated based on average aerosol penetration and average filter resistance values. Face mask type N95 and KN95 with four different models were used in the study. Based on the normalized data for filter aerosol penetration of the three decontamination methods, VHP is recommended to be used for decontamination methods for FFRs. Model 3 FFRs showed good performance where less deviation in the normalized filter aerosol penetration and normalized filter air flow resistance for the three decontamination methods was observed.
Prediction of flow field in a solar chimney using ANFIS technique
Authors: Huynh Minh-Thu T , Truong Tri Q , Doan Thinh N , Huynh Trieu N , Nguyen Tung V , Nguyen Viet T , Nguyen Y Q
Published: March 2021

Solar chimneys have been intensively studied as an effective method for natural ventilation of buildings. Though numerical methods, such as Computational Fluid Dynamics (CFD), have been widely utilized in such studies, they usually require extensive computational resources. Moreover, experimental study is quite complicated and costly. In recent years, machine learning has started to be used as a tool in the thermal-fluid field. In this study, in order to save time and cost, Adaptive Neuro-Fuzzy Inference System (ANFIS) technique, a class of adaptive networks that incorporate both neural networks and fuzzy logic principles, is combined with CFD. A simulation model was first validated by experiment from another study in the field. The result was documented as a dataset using CFD code ANSYS Fluent (Academic version 2020 R2). Then, they are used to train and validate the ANFIS model. In particular, the study is to predict the fluid flow field in a 2-dimensional typical solar chimney when heat flux changes in the range of 400 to 1000 W/m2. Inputs of the ANFIS model are position and heat flux, while outputs are temperature and velocity at that location. As a result, the 2 ANFIS models could achieve R2 values of 0.997, 0.97 (training set) and 0.994, 0.9715 (testing set); RMSE are 1.009, 0.00224 (training set) and 1.074, 0.0204 (testing set) for outputs of temperature and velocity, respectively. Those results are acceptable. By using the ANFIS model, large amounts of flow fields with different scenarios can be estimated simultaneously. Therefore, it is expected that engineers and architects can have a quick tool in the process of design.
Finite element simulations of stresses in bone implants made by three-dimensional printing
Authors: Mikushev V M , Samarkin A I , Khomutova A S
Published: March 2021

The article is devoted to the analysis of the strength properties of a compact bone tissue in order to produce subsequently the equivalent in strength individual implant. An example of a fragment of a skeleton bone shows the fundamental possibility of solving the problem using a 3d modelling finite element analysis software package.
Research on the dissociation of yucca to the organic solubility of wastewater
Authors: Lu Sun , Wu Xin-Da , Qiu Ze-Sheng , Zheng Tong-Huai , Wen Yu-Hong , Zhu Min
Published: March 2021

With the development of society, the pollution of wastewater has become extremely serious, and the amount of wastewater is also gradually increasing. The water quality discharge does not meet the standards, which has a serious impact on the water quality of our country, it also has a very important impact on people’s daily water use. Yucca has a wide variety of plants, and the main components of its extract are steroidal saponins, free radical saponins and carbohydrate complexes. It has a special physiological structure, macromolecules and sequence molecules are directly adsorbed, and it has a strong adsorption capacity for harmful gases, which can improve the odours and is widely used, But it is less used in wastewater treatment, this project uses yucca extract to conduct preliminary analysis and exploration on the dissociation of organic solubility in wastewater, to improve the solubility and treatment of free ions and organic dissolved matter in water, preliminary results found that adding 200ppm-20% and 500ppm-10% concentration of yucca is the most suitable range for water quality treatment. It will be a bigger breakthrough when used in wastewater treatment, and my country’s water pollution will be in great improvement.
The Effect of Long Term Hygrothermal Aging by Immersion on Carbon/Epoxy Composites Exposed to the Heat Sources for Naval and Marine Applications
Authors: Hong Soon Kook
Published: March 2021

Fiber-Reinforced Polymer (FRP) composites have many advantages over conventional materials in terms of high strength-to-weight and stiffness-to-weight ratios, design flexibility and enhanced service life. Due to these advantages, FRP composites are used in many different fields such as Construction, Electric/power generation, Marine, Corrosion/infrastructure, transportation and so on. Most researches of FRP composites were focused on the applications used in ground field. However, in Navy, marine composite materials are increasingly being used in diverse applications: Submarine, Autonomous Underwater vehicle, Unmanned Surface vehicle and Payloads in Naval vessel. It is known that polymer composites are very sensitive and are friendly to water or moisture in any forms. Moisture in polymer composites often causes degradation by swelling and hydrolysis. Especially, if polymer composites will be immersed in water and seawater, faster degradation can be caused by water uptake than any other moisture environments. While general investigations regarding water uptake are concentrated on the composite materials cured in ambient temperature, the immersion effects of polymer composites exposed to elevated temperatures were studied because underwater applications of composite materials can be exposed to the various heat sources. For example, fires on naval vessels and underwater vehicles can be started by any number of causes such as electrical faults and ignition of flammable gases or liquids. Accordingly, immersion effects must be studied on marine composite materials exposed to various temperatures in order to evaluate service life in an underwater environment. This study investigated the water uptake, diffusion coefficient, and Short beam shear (SBS) for Interlaminar Shear Strength(ILSS), delamination between fiber and resin using test specimens exposed to the elevated temperatures. The specimens were immersed for a definite period of time (~one and a half years) in seawater and deionized water (DI water) to compare both degradation mechanisms.
An Empirical Study on Smart Steel Stockyard Management System through Character Recognition on Steel Materials using CNN
Authors: Cho Gi Yeong , Yoo Nam Hyun
Published: March 2021

In shipyards wherein large ships and plants are constructed, the timely supply of steel is a critical factor that can decrease the production costs and shorten the construction period. However, the standard size of the steel materials utilized in shipyards exceeds at least 10m, and the weight of the steel is heavy; therefore, it is difficult to readjust the steel once it is deployed. Moreover, if any part of the production plan is changed, the steel that has been deployed according to the existing plan must be relocated. However, when cumbersome, heavy steel is vertically stacked in several layers, it is difficult for a shipyard worker to directly identify the desired steel’s location. Therefore, it is not easy to spot the location of the steel to be found. In cases such as this, one attempts to recognize characters on the steel’s surface using OCR, but it is difficult to apply this to an actual system as the recognition rate is only about 50 to 70% on average. Therefore, through this study, we intend to develop a model that recognizes characters printed on the steel’s surface using CNN and to check whether it can be employed in a smart steel stockyard management system.
Determination of rock fracture parameters in directional percussion drilling with drillhole path adjustability
Authors: Chernienkov E M
Published: March 2021

The paper reviews the existing technologies and equipment for drilling in rocks and soil with adjustable path of drillholes. The author describes a new method of percussion drilling and its application prospects. A lab-scale testing installation for physical simulation of rock fracture in drilling by the new method is presented. The force and impact characteristics required for the method implementation are updated.
Ion-Plasma Treated Parts Quality Improvement Analysis Based on the Reliability Theory Criteria
Authors: Bogdanovich V I , Giorbelidze M G
Published: March 2021

The procedure of using reliability theory indices to evaluate parts vacuum ion-plasma treatment efficiency has been considered. Efficiency coefficient of technological procedures improving life and reliability of engineering parts taking into account alteration of average index value, its dispersion, and probability level of faultless operation has been suggested.
Effect of Glow Discharge Treatment on the Depth and Degree of Structural Phase Modification of Tool Steel Products
Authors: Shemenkov V M , Rabyko M A
Published: March 2021

The structure and phase composition of 1.1625, 1.2080 and 1.3343 tool steels (DIN) were studied and the research results are presented. The glow discharge treatment is shown to lead to dissolution and redistribution of the carbide phase, a change in the degree of crystal lattice distortion of the matrix phase, and a decrease in the residual austenite in the surface layer to a depth of 80 μm, which results in a 15% to 30% increase in the microhardness of the surface layers of materials.
Study of the magnetic property of supermagnetic fluid
Authors: Kuvandikov O K , Kuvandikov Sh J , Salakhitdinova M K , Kayumov Kh A
Published: March 2021

In this work, the magnetic fluids based on Fe3O4 have been obtained by the chemical co-precipitation method. Analysis of the size and morphology of the synthesized iron oxide nanoparticles of the magnetic fluid using transmission electron microscopy revealed that nanoparticles are of 25-38 nm in size and spherical in shape. The elemental composition of magnetite nanoparticles of the fluid was examined in energy-dispersive X-ray analysis and determined to contain only Iron and Oxygen. The magnetic property of the magnetic fluid was measured using vibrating sample magnetometer. The results showed that the magnetic fluid has a superparamagnetic character which of specific saturation magnetization of 3.4 emu/g
Efficient Technologies for Producing Cast Iron Billets and Products with Specified Properties and Microstructure
Authors: Lubyanoi D A , Markidonov A V , Pudov E Yu , Shakhmanov V N , Kuzin E G , Semenova O S
Published: March 2021

The article discusses the use of resonant-pulsating refining technology in order to improve the quality of cast iron products. This technology is used in the cast iron production and cast iron mold induction. It is relatively simple and easily fits into existing production. The effectiveness of this technology is at the world’s best indicator level. The chemical composition and smelting modes of cast iron influences significantly on the microstructure of gray cast iron. The determining factors are the content of silicon in cast iron, carbon, manganese, titanium and vanadium. The carbon content affects significantly taking into account its content above 3.8%, since this content increases the content of large, ripe forms of graphite in cast iron. Titanium and vanadium also influence significantly on the microstructure of cast iron. These two elements, even in small amounts, affect the size and shape of graphite greatly. It also affects the amount of ferrite, perlite and cementite in the structure of cast iron. Vanadium also affects greatly the service life of cast iron products.
Developing the calculation methods of effective values of current and voltage for nonsinusoidal transient modes in electric power systems based wavelet transform
Authors: Arkhipova O V , Dolgikh N N , Kovalev V Z , Osipov D S , Paramzin A O , Tkachenko V A
Published: March 2021

The necessity to develop analysis and calculation methods of nonsinusoidal modes in electric power networks is conditioned by the increasing number of electrical receivers parental to non-linear distortions (variable-frequency electric drive, LED-based lightning and so on). Higher harmonic components increase power and efficiency loss in current carrying parts, result in overheating of conductors and intense insulation deterioration, can cause resonance overvoltage and automation equipment malfunctions. Due to digitalization of the electric power industry it is necessary to develop methods of receiving, processing and digital communication on system state variables (currents, voltage, power), including nonsinusoidal modes. Wavelet transform is wider applied to analyze complex harmonic processes in electric power industry in conditions of transient modes. The paper introduces calculation methods of integrated indexes of electric power system modes – currents, voltage and power in the presence of electrical receivers with non-linear current-voltage characteristics. The method is based on Parseval equality and allows calculating via wavelet coefficients received by transformation of the initial stream of transient values of currents and voltages. Herewith the issue of data compressing is solved when transmitting digital information. The method allows determining the variables of every frequency component, interpreting the data in the three-dimensional scale (peak values, frequency and time) which will be used in choosing activities for higher harmonics filtration to reduce the loss in current carring parts.
Influence of some parameters of magnetization and cutting modes on the tool life when machining construction materials
Authors: Khasanov S M , Yakubov A A
Published: March 2021

The article examines the study of the influence of the magnetic field on the wear resistance of tool materials. The issues of optimal modes of magnetization and cutting modes, as well as the influence of the rake angle are considered.
Non-universal scaling of thermoelectric efficiency in 3D and 2D thermoelectric semiconductors
Authors: Octavian Kevin , Hasdeo Eddwi H
Published: March 2021

We performed the first-principles calculation on common thermoelectric semiconductors Bi2Te3, Bi2Se3, SiGe, and PbTe in bulk three-dimension (3D) and two-dimension (2D). We found that miniaturisation of materials does not generally increase the thermoelectric figure of merit (ZT) according to the Hicks and Dresselhaus (HD) theory. For example, ZT values of 2D PbTe (0.32) and 2D SiGe (0.04) are smaller than their 3D counterparts (0.49 and 0.09, respectively). Meanwhile, the ZT values of 2D Bi2Te3 (0.57) and 2D Bi2Se3 (0.43) are larger than the bulks (0.54 and 0.18, respectively), which agrees with HD theory. The HD theory breakdown occurs because the band gap and band flatness of the materials change upon dimensional reduction. We found that flat bands give a larger electrical conductivity (σ) and electronic thermal conductivity (κ
el) in 3D materials, and smaller values in 2D materials. In all cases, maximum ZT values increase proportionally with the band gap and saturate for the band gap above 10 k
B
T. The 2D Bi2Te3 and Bi2Se3 obtain a higher ZT due to the flat corrugated bands and narrow peaks in their DOS. Meanwhile, the 2D PbTe violates HD theory due to the flatter bands it exhibits, while 2D SiGe possesses a small gap Dirac-cone band.
A note on finiteness properties of graphs of groups
Authors: Haglund Frédéric , Wise Daniel
Published: March 2021

We show that if

G
G

is of type

F

n

\mathcal {F}_n

, and

G
G

splits as a finite graph of groups, then the vertex groups are of type

F

n

\mathcal {F}_n

if the edge groups are of type

F

n

\mathcal {F}_n

.
Invited Commentary: The Society for Epidemiologic Research—Striving for Equity in Our Own Backyard
Authors: Marchbanks Polly A
Published: March 2021

Using a bibliometric approach, Nobles et al. (Am J Epidemiol. 2021;190(9):1710-1720) conducted a study to explore dimensions of participation at the annual meetings of the Society for Epidemiologic Research (SER). Their findings suggested differences in representation by gender and affiliation in key presentation formats, which raises concerns about possible equity issues within the organization. In this commentary, I discuss the context, limitations, and strengths of the study, as well as reflections on interpretation and implications of the findings. Suggested next steps include: continuing the conversation; evaluating SER processes and making needed adjustments with equity in mind; and conducting ongoing surveillance and further research. Nobles et al. have provided a baseline for monitoring trends, as well as a starting point for future research efforts that should aim to refine methodologic aspects of the current study to obtain a more complete range of information. Although firm conclusions about possible determinants cannot be made at this time, the work of Nobles et al. can be expected to raise awareness of equity issues among SER members and the broader epidemiology community.
Preliminary Prospective and Randomized Study of Highly Purified Polynucleotide vs Placebo in Treatment of Moderate to Severe Acne Scars
Authors: Araco Antonino , Araco Francesco
Published: March 2021

Background

Managing acne scars is a challenge and therapies are divided into nonsurgical and surgical. Highly Purified Technology Polynucleotides (PN-HPT) is a compound that contains a mixture of DNA polymers of different lengths. Numerous studies have shown that PN-HPT also serves as an energy source, thus influencing cellular growth and cell vitality.

Objectives

The authors aimed to assess the improvement in dermal quality and acne scars after PN-HPT vs placebo according to Antera 3D and the patient responses to the patient satisfaction questionnaire after a comparison of pretreatment and posttreatment photographs at 1 and 3 months.

Methods

Included were women aged 30 to 50 years with grade 3 to 4 moderate-to-severe atrophic scars according to the Goodman classification; nonsmokers; and had not had active acne during the past 5 years. Ten patients (PN-HPT group) were treated with 4.0 mL of PN-HPT, and 10 patients (control) were treated with 4.0 mL of normal saline. All medical treatments were performed in a double-blinded manner; neither the injection doctor nor the patient knew if the PN-HPT or the placebo was being administered.

Results

Twenty women who fit the inclusion criteria were enrolled in this study. Only patients in the PN-HPT group improved significantly at 1 and 3 months after treatment compared with baseline.

Conclusions

This prospective and randomized study showed that PN-HPT in monotherapy was safe and effective treatment for atrophic scar acne compared with placebo. Prospective and randomized studies will be necessary to investigate the clinical effectiveness in a larger cohort of patients and for a longer follow-up.

Level of Evidence: 2
The Aging Surgeon: Evidence and Experience
Authors: Asserson Derek B , Janis Jeffrey E
Published: March 2021

Background

With doctors in short supply and a strong demand for surgeon services in all areas of the United States, urban and rural, there are pressures to remain in active practice for longer. Even with an older workforce, there are currently no requirements for when a surgeon must retire in the United States.

Objectives

The aim of this article was to highlight the importance of the aging surgeon to the medical community and to provide an evidence-based overview of age-related cognitive and physical issues that develop during the later stages of a surgeon’s career.

Methods

A search of the PubMed/MEDLINE database was performed for the phrase “aging surgeon.” Inclusion criteria were applied to include only those articles related to surgeon age or retirement. Additional reports were handpicked from citations to substantiate claims with statistical evidence.

Results

The aging surgeon contributes extensive experience to patient care, but is also prone to age-related changes in cognition, vision, movement, and stress as it relates to new techniques, surgical performance, and safety measures. Studies show that although surgeons are capable of operating well into their senior years, there is the potential of decline. Nevertheless, there are proven recommendations on how to prepare an older surgeon for retirement.

Conclusions

Age-related trends in cognitive and physical decline must be counterbalanced with wisdom gained through decades of surgical experience.
DNA methylation and histone modifications are essential for regulation of stem cell formation and differentiation in zebrafish development
Authors: Marchione Alissa D , Thompson Zanshé , Kathrein Katie L
Published: March 2021

The complex processes necessary for embryogenesis require a gene regulatory network that is complex and systematic. Gene expression regulates development and organogenesis, but this process is altered and fine-tuned by epigenetic regulators that facilitate changes in the chromatin landscape. Epigenetic regulation of embryogenesis adjusts the chromatin structure by modifying both DNA through methylation and nucleosomes through posttranslational modifications of histone tails. The zebrafish is a well-characterized model organism that is a quintessential tool for studying developmental biology. With external fertilization, low cost and high fecundity, the zebrafish are an efficient tool for studying early developmental stages. Genetic manipulation can be performed in vivo resulting in quick identification of gene function. Large-scale genome analyses including RNA sequencing, chromatin immunoprecipitation and chromatin structure all are feasible in the zebrafish. In this review, we highlight the key events in zebrafish development where epigenetic regulation plays a critical role from the early stem cell stages through differentiation and organogenesis.
TAD boundary and strength prediction by integrating sequence and epigenetic profile information
Authors: Wang Yunlong , Liu Yaqi , Xu Qian , Xu Yao , Cao Kai , Deng Nan , Wang Ruimin , Zhang Xueying , Zheng Ruiqin , Li Guoliang , Fang Yaping
Published: March 2021

Topologically associated domains (TADs) are one of the important higher order chromatin structures with various sizes in the eukaryotic genomes. TAD boundaries, as the flanking regions between adjacent domains, can restrict the interactions of regulatory elements, including enhancers and promoters, and are generally dynamic and variable in different cells. However, the influence of sequence and epigenetic profile-based features in the identification of TAD boundaries is largely unknown. In this work, we proposed a method called pTADS (prediction of TAD boundary and strength), to predict TAD boundaries and boundary strength across multiple cell lines with DNA sequence and epigenetic profile information.

The performance was assessed in seven cell lines and three TAD calling methods. The results demonstrate that the TAD boundary can be well predicted by the selected shared features across multiple cell lines. Especially, the model can be transferable to predict the TAD boundary from one cell line to other cell lines. The boundary strength can be characterized by boundary score with good performance. The predicted TAD boundary and TAD boundary strength are further confirmed by three Hi-C contact matrix-based methods across multiple cell lines.

The codes and datasets are available at https://github.com/chrom3DEpi/pTADS.
miR-71 mediates age-dependent opposing contributions of the stress-activated kinase KGB-1 in Caenorhabditis elegans
Authors: Ruediger Cyrus , Karimzadegan Siavash , Lin Sonya , Shapira Michael
Published: March 2021

Studying the evolutionary processes that shaped aging offers a path for understanding the causes of aging. The antagonistic pleiotropy theory for the evolution of aging proposes that the inverse correlation between age and natural selection strength allows positive selection of gene variants with early-life beneficial contributions to fitness despite detrimental late-life consequences. However, mechanistic understanding of how this principle manifests in aging is still lacking. We previously identified antagonistic pleiotropy in the function of the Caenorhabditis elegans JNK homolog KGB-1, which provided stress protection in developing larvae, but sensitized adults to stress and shortened their lifespan. To a large extent, KGB-1’s contributions depended on age-dependent and opposing regulation of the stress-protective transcription factor DAF-16, but the underlying mechanisms remained unknown. Here, we describe a role for the microRNA miR-71 in mediating effects of KGB-1 on DAF-16 and downstream phenotypes. Fluorescent imaging along with genetic and survival analyses revealed age-dependent regulation of mir-71 expression by KGB-1—upregulation in larvae, but downregulation in adults—and showed that mir-71 was required both for late-life effects of KGB-1 (infection sensitivity and shortened lifespan), as well as for early life resistance to cadmium. While mir-71 disruption did not compromise development under protein-folding stress (known to depend on KGB-1), disruption of the argonaute gene alg-1, a central component of the microRNA machinery, did. These results suggest that microRNAs play a role in mediating age-dependent antagonistic contributions of KGB-1 to survival, with mir-71 playing a central role and additional microRNAs potentially contributing redundantly.
Conversion of a colorectal cancer guideline into clinical decision trees with assessment of validity
Authors: Keikes Lotte , Kos Milan , Verbeek Xander A A M , Van Vegchel Thijs , Nagtegaal Iris D , Lahaye Max J , Méndez Romero Alejandra , De Bruijn Sandra , Verheul Henk M W , Rütten Heidi , Punt Cornelis J A , Tanis Pieter J , Van Oijen Martijn G H
Published: March 2021

Objective

The interpretation and clinical application of guidelines can be challenging and time-consuming, which may result in noncompliance to guidelines. The aim of this study was to convert the Dutch guideline for colorectal cancer (CRC) into decision trees and subsequently implement decision trees in an online decision support environment to facilitate guideline application.

Methods

The recommendations of the Dutch CRC guidelines (published in 2014) were translated into decision trees consisting of decision nodes, branches and leaves that represent data items, data item values and recommendations, respectively. Decision trees were discussed with experts in the field and published as interactive open access decision support software (available at www.oncoguide.nl). Decision tree validation and a concordance analysis were performed using consecutive reports (January 2016–January 2017) from CRC multidisciplinary tumour boards (MTBs) at Amsterdam University Medical Centers, location AMC.

Results

In total, we developed 34 decision trees driven by 101 decision nodes based on the guideline recommendations. Decision trees represented recommendations for diagnostics (n = 1), staging (n = 10), primary treatment (colon: n = 1, rectum: n = 5, colorectal: n = 9), pathology (n = 4) and follow-up (n = 3) and included one overview decision tree for optimal navigation. We identified several guideline information gaps and areas of inconclusive evidence. A total of 158 patients’ MTB reports were eligible for decision tree validation and resulted in treatment recommendations in 80% of cases. The concordance rate between decision tree treatment recommendations and MTB advices was 81%. Decision trees reported in 22 out of 24 non-concordant cases (92%) that no guideline recommendation was available.

Conclusions

We successfully converted the Dutch CRC guideline into decision trees and identified several information gaps and areas of inconclusive evidence, the latter being the main cause of the observed disagreement between decision tree recommendations and MTB advices. Decision trees may contribute to future strategies to optimize quality of care for CRC patients.
Benefits and risks of non-slip socks in hospitals: a rapid review
Authors: Jazayeri Dana , Heng Hazel , Slade Susan C , Seymour Brent , Lui Rosalie , Volpe Daniele , Jones Cathy , Morris Meg E
Published: March 2021

Background

Non-slip socks are sometimes used in an attempt to prevent falls in hospitals despite limited evidence of benefit. We critique the current literature on their risks, benefits and effects.

Methods

A rapid review was conducted following the Cochrane Rapid Review Methods Group Guidelines. To be included, studies needed to have data on single or multifactorial interventions that used non-slip socks in hospitals or their safety, risks or effects in a laboratory setting. Six electronic databases were searched: Medline, Embase, Cinahl, Cochrane, Allied and Medical Health Database (AMED) and Proquest Central.

Results

Fourteen articles met the inclusion criteria. Nine used non-slip socks as an intervention in hospitals. Three assessed their effects in laboratory settings. Two reported risks in relation to bacterial transfer. Most studies that used non-slip socks to prevent hospital falls had negative or equivocal results and were of comparatively low method quality, with a high risk of bias. Two of the laboratory tests reported traction socks to be no safer than walking barefoot and to have similar slip resistance. The laboratory studies had a low risk of bias and showed that bacteria can sometimes be acquired from socks.

Conclusion

Non-slip socks have the potential to carry an infection control risk that requires careful management. There was no strong or conclusive evidence that they prevent hospital falls.
Replacing dietary antibiotics with 0.20% l-glutamine in swine nursery diets: impact on intestinal physiology and the microbiome following weaning and transport
Authors: Duttlinger Alan W , Centeno Martinez Ruth E , McConn Betty R , Kpodo Kouassi R , Lay Donald C , Richert Brian T , Johnson Timothy A , Johnson Jay S
Published: March 2021

Previous research demonstrates that supplementing 0.20% l-glutamine (GLN) in the diets of newly weaned and transported pigs improves growth rate to a similar extent as providing dietary antibiotics (AB). However, research comparing the effects of GLN vs. AB on intestinal physiology and the microbiome is limited. Therefore, the study objective was to compare the effects of supplementing nursery diets with GLN, AB, or no dietary antibiotics (NA) on intestinal physiology and the microbiome of pigs in a production environment following weaning and transport. Mixed-sex piglets (N = 480; 5.62 ± 0.06 kg body weight [BW]) were weaned (18.4 ± 0.2 d of age) and transported for 12 h in central Indiana, for two replicates, during the summer of 2016 and the spring of 2017. Pens were blocked by BW and allotted to one of the three dietary treatments (n = 10 pens/dietary treatment/replicate [8 pigs/pen]): AB (chlortetracycline [441 ppm] + tiamulin [38.6 ppm]), GLN (0.20% as-fed), or NA fed for 14 d. From day 14 to 34, pigs were fed common AB-free diets in two phases. On day 33, villus height:crypt depth tended to be increased (P = 0.07; 7.0%) in GLN and AB pigs vs. NA pigs. On day 33, glucagon-like peptide 2 (GLP-2) mRNA abundance was decreased (P = 0.01; 50.3%) in GLN and NA pigs vs. AB pigs. Crypt depth was increased overall on day 33 (P = 0.01; 16.2%) during the spring replicate compared with the summer replicate. Villus height:crypt depth was reduced (P = 0.01; 9.6%) during the spring replicate compared with the summer replicate on day 33. On day 13, tumor necrosis factor-alpha and occludin mRNA abundance was increased (P ≤ 0.04; 45.9% and 106.5%, respectively) and zonula occludens-1 mRNA abundance tended to be greater (P = 0.10; 19.2%) in the spring replicate compared with the summer replicate. In addition, AB pigs had increased (P = 0.01; 101.3%) GLP-2 mRNA abundance compared with GLN and NA pigs. Microbiome analysis indicated that on day 13, dietary treatment altered the microbiota community structure (P = 0.03). Specifically, the AB pigs tended to be distinct from both the NA and GLN pigs (P = 0.08), and Lactobacillus was increased nearly 2-fold in AB compared with NA pigs (q = 0.04) and GLN pigs (q = 0.22). In conclusion, GLN supplementation tended to improve some morphological markers of intestinal health similarly to AB pigs, while the microbiome composition in GLN pigs was more similar to NA pigs than AB pigs.
Cholesterol metabolic enzyme Ggpps regulates epicardium development and ventricular wall architecture integrity in mice
Authors: Zheng Feng , Chen Zhong , Tang Qiao-Li , Wang Xin-Ying , Chong Dan-Yang , Zhang Tong-Yu , Gu Ya-Yun , Hu Zhi-Bin , Li Chao-Jun
Published: March 2021

During embryonic heart development, the progenitor cells in the epicardium would migrate and differentiate into noncardiomyocytes in myocardium and affect the integrity of ventricular wall, but the underlying mechanism has not been well studied. We have found that myocardium geranylgeranyl diphosphate synthase (Ggpps), a metabolic enzyme for cholesterol biosynthesis, is critical for cardiac cytoarchitecture remodelling during heart development. Here, we further reveal that epicardial Ggpps could also regulate ventricular wall architecture integrity. Epicardium-specific deletion of Ggpps before embryonic day 10.5 (E10.5) is embryonic lethal, whereas after E13.5 is survival but with defects in the epicardium and ventricular wall structure. Ggpps deficiency in the epicardium enhances the proliferation of epicardial cells and disrupts cell‒cell contact, which makes epicardial cells easier to invade into ventricular wall. Thus, the fibroblast proliferation and coronary formation in myocardium were found enhanced that might disturb the coronary vasculature remodelling and ventricular wall integrity. These processes might be associated with the activation of YAP signalling, whose nuclear distribution is blocked by Ggpps deletion. In conclusion, our findings reveal a potential link between the cholesterol metabolism and heart epicardium and myocardium development in mammals, which might provide a new view of the cause for congenital heart diseases and potential therapeutic target in pathological cardiac conditions.
Two-stage Cox-nnet: biologically interpretable neural-network model for prognosis prediction and its application in liver cancer survival using histopathology and transcriptomic data
Authors: Zhan Zhucheng , Jing Zheng , He Bing , Hosseini Noshad , Westerhoff Maria , Choi Eun-Young , Garmire Lana X
Published: March 2021

Pathological images are easily accessible data with the potential of prognostic biomarkers. Moreover, integration of heterogeneous data types from multi-modality, such as pathological image and gene expression data, is invaluable to help predicting cancer patient survival. However, the analytical challenges are significant. Here, we take the hepatocellular carcinoma (HCC) pathological image features extracted by CellProfiler, and apply them as the input for Cox-nnet, a neural network-based prognosis prediction model. We compare this model with the conventional Cox proportional hazards (Cox-PH) model, CoxBoost, Random Survival Forests and DeepSurv, using C-index and log-rank P-values. The results show that Cox-nnet is significantly more accurate than Cox-PH and Random Survival Forests models and comparable with CoxBoost and DeepSurv models, on pathological image features. Further, to integrate pathological image and gene expression data of the same patients, we innovatively construct a two-stage Cox-nnet model, and compare it with another complex neural-network model called PAGE-Net. The two-stage Cox-nnet complex model combining histopathology image and transcriptomic RNA-seq data achieves much better prognosis prediction, with a median C-index of 0.75 and log-rank P-value of 6e−7 in the testing datasets, compared to PAGE-Net (median C-index of 0.68 and log-rank P-value of 0.03). Imaging features present additional predictive information to gene expression features, as the combined model is more accurate than the model with gene expression alone (median C-index 0.70). Pathological image features are correlated with gene expression, as genes correlated to top imaging features present known associations with HCC patient survival and morphogenesis of liver tissue. This work proposes two-stage Cox-nnet, a new class of biologically relevant and interpretable models, to integrate multiple types of heterogenous data for survival prediction.
Posterior Polyethylene Tethers Reduce Occurrence of Proximal Junctional Kyphosis After Multilevel Spinal Instrumentation for Adult Spinal Deformity: A Retrospective Analysis
Authors: Rabinovich Emily P , Snyder M Harrison , McClure Jesse J , Buell Thomas J , Smith Justin S , Shaffrey Christopher I , Buchholz Avery L
Published: March 2021

BACKGROUND

Proximal junctional kyphosis (PJK) is a common postoperative complication after adult spinal deformity (ASD) surgery and may manifest with neurological decline, worsening spinal deformity, and spinal instability, which warrant reoperation. Rates of PJK may be as high as 69.4% after ASD surgery.

OBJECTIVE

To evaluate the efficacy of junctional tethers for PJK prophylaxis after multilevel instrumented surgery for ASD with minimum 2-yr follow-up.

METHODS

Single-center retrospective analysis of adult patients (age ≥18 yr) who underwent ASD surgery with index operations performed between November 2010 and June 2016 and achieved minimum 2-yr follow-up. Patients with ASD were subdivided into 3 treatment cohorts based on institutional protocol: no tether (NT), polyethylene tether-only (TO), and tether with crosslink (TC). PJK was defined as a proximal junctional angle (PJA) >10° and 10° greater than the corresponding preoperative measurement. Patient demographics, operative details, standard radiographic scoliosis measurements (including PJA and assessment of PJK), and complications were analyzed.

RESULTS

Of 184 patients, 146 (79.3%) achieved minimum 2-yr follow-up (mean = 45 mo; mean age = 67 yr; 67.8% women). PJK rates reported for the NT, TO, and TC cohorts were 60.7% (37/61), 35.7% (15/42), and 23.3% (10/43), respectively. PJK rates among TC patients were significantly lower than NT (P = .01601).

CONCLUSION

Junctional tethers with crosslink significantly reduced the incidence of PJK and revisions for PJK among ASD patients treated with long-segment posterior instrumented fusions who achieved minimum 2-yr follow-up.